From 536c9bffc9ffb375dfd4ae886f65667eb30497c9 Mon Sep 17 00:00:00 2001
From: lukemartinlogan <lukemartinlogan@users.noreply.github.com>
Date: Fri, 9 Feb 2024 16:33:34 +0000
Subject: [PATCH] deploy: c45c273d8f51c9ecab4fa8b8a4c6e793fe36e6eb

---
 404.html                                      |   4 +-
 about/index.html                              |   4 +-
 assets/js/0df86f4d.af9faf83.js                |   1 +
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 143 files changed, 422 insertions(+), 402 deletions(-)
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 rename assets/js/{3d9099ed.785c61b8.js => 219da0fd.53e7a999.js} (96%)
 create mode 100644 assets/js/2638f36e.72f61884.js
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 create mode 100644 assets/js/57efaafb.0488aa50.js
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 delete mode 100644 assets/js/main.75710903.js
 delete mode 100644 assets/js/runtime~main.b14c14cf.js
 create mode 100644 assets/js/runtime~main.dc8b3105.js
 rename docs/hermes/{quick-start => containers}/index.html (69%)
 delete mode 100644 docs/hermes/debugging/index.html
 create mode 100644 docs/hermes/developer-guide/index.html

diff --git a/404.html b/404.html
index 4f05fe0b..106a104a 100644
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+++ b/404.html
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aria-hidden="true"><path stroke="currentColor" stroke-linecap="round" stroke-miterlimit="10" stroke-width="2" d="M4 7h22M4 15h22M4 23h22"></path></svg></button><a class="navbar__brand" href="/"><div class="navbar__logo"><img src="/img/logo.png" alt="Gnosis Research Center" class="themedComponent_mlkZ themedComponent--light_NVdE"><img src="/img/logo.png" alt="Gnosis Research Center" class="themedComponent_mlkZ themedComponent--dark_xIcU"></div><b class="navbar__title text--truncate">Gnosis Research Center</b></a><div class="navbar__item dropdown dropdown--hoverable"><a href="#" aria-haspopup="true" aria-expanded="false" role="button" class="navbar__link">Gnosis</a><ul class="dropdown__menu"><li><a class="dropdown__link" href="/about">About</a></li><li><a class="dropdown__link" href="/members">Members</a></li><li><a class="dropdown__link" href="/network">Network</a></li><li><a class="dropdown__link" href="/contact">Contact</a></li></ul></div><div class="navbar__item dropdown 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diff --git a/about/index.html b/about/index.html
index 9ad4ed54..edc9ae60 100644
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diff --git a/assets/js/0df86f4d.af9faf83.js b/assets/js/0df86f4d.af9faf83.js
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+"use strict";(self.webpackChunkgrc=self.webpackChunkgrc||[]).push([[339],{7987:(e,t,n)=>{n.r(t),n.d(t,{assets:()=>a,contentTitle:()=>o,default:()=>h,frontMatter:()=>s,metadata:()=>c,toc:()=>l});var i=n(5893),r=n(1151);const s={},o="Programming",c={id:"hermes/programming",title:"Programming",description:"In this section, we will discuss the general steps of building a program",source:"@site/docs/03-hermes/07-programming.md",sourceDirName:"03-hermes",slug:"/hermes/programming",permalink:"/docs/hermes/programming",draft:!1,unlisted:!1,tags:[],version:"current",sidebarPosition:7,frontMatter:{},sidebar:"tutorialSidebar",previous:{title:"Adapters",permalink:"/docs/hermes/adapters"},next:{title:"Buffer Organizer",permalink:"/docs/hermes/components/buffer-organizer"}},a={},l=[{value:"Basic API Example",id:"basic-api-example",level:2}];function d(e){const t={a:"a",code:"code",h1:"h1",h2:"h2",li:"li",p:"p",pre:"pre",ul:"ul",...(0,r.a)(),...e.components};return(0,i.jsxs)(i.Fragment,{children:[(0,i.jsx)(t.h1,{id:"programming",children:"Programming"}),"\n",(0,i.jsx)(t.p,{children:"In this section, we will discuss the general steps of building a program\non top of the Hermes native API. We will focus on the core data structures\nprovided by Hermes -- Buckets and Blobs."}),"\n",(0,i.jsxs)(t.p,{children:["To see demonstrations of the API, check out our ",(0,i.jsx)(t.a,{href:"https://github.com/HDFGroup/hermes/blob/master/test/unit/hermes/test_bucket.cc",children:"API tests"})]}),"\n",(0,i.jsx)(t.h2,{id:"basic-api-example",children:"Basic API Example"}),"\n",(0,i.jsx)(t.p,{children:"This example will place a blob into the DMSH and then retrieve that blob."}),"\n",(0,i.jsx)(t.pre,{children:(0,i.jsx)(t.code,{className:"language-cpp",children:'#include <hermes.h>\n#include <bucket.h>\n\nint main() {\n  TRANSPARENT_HERMES();\n  Bucket bkt = HERMES->GetBucket("hello");\n  size_t blob_size = KILOBYTES(4);\n  Context ctx;\n\n  std::vector<int> data_put(1024, i);\n  bkt.Put<std::vector<int>>("0", data_put, ctx);\n\n  std::vector<int> data_get(1024, i);\n  bkt.Get<std::vector<int>>("0", data_get, ctx);\n\n  REQUIRE(data_put == data_get);\n}\n'})}),"\n",(0,i.jsxs)(t.ul,{children:["\n",(0,i.jsxs)(t.li,{children:[(0,i.jsx)(t.code,{children:"TRANSPARENT_HERMES()"})," will initialize your connection to Hermes"]}),"\n",(0,i.jsxs)(t.li,{children:[(0,i.jsx)(t.code,{children:"HERMES"})," is a singleton macro provided in hermes.h."]}),"\n",(0,i.jsxs)(t.li,{children:[(0,i.jsx)(t.code,{children:"GetBucket"})," will either create a bucket or get the bucket if it exists.\nThis operation is concurrency-safe. I.e., it is guaranteed only one\nthread or process calling this function will create the bucket if it\nDNE."]}),"\n",(0,i.jsxs)(t.li,{children:[(0,i.jsx)(t.code,{children:"Context"})," is optional. It contains the ability to override\ndefaults defined in the server and client configuration files. For\nexample, you can set a custom DPE to use for a blob Put."]}),"\n",(0,i.jsxs)(t.li,{children:[(0,i.jsx)(t.code,{children:"hermes::Blob analagous to and std::vector<char>"}),". It's not quite the\nsame thing, but we won't go into detail here."]}),"\n",(0,i.jsxs)(t.li,{children:[(0,i.jsx)(t.code,{children:"bkt.Put"})," will put a blob into the bucket. Put replaces all content\nif the blob previously existed."]}),"\n",(0,i.jsxs)(t.li,{children:[(0,i.jsx)(t.code,{children:"bkt.Get"})," will get the contents of an entire blob."]}),"\n"]})]})}function h(e={}){const{wrapper:t}={...(0,r.a)(),...e.components};return t?(0,i.jsx)(t,{...e,children:(0,i.jsx)(d,{...e})}):d(e)}},1151:(e,t,n)=>{n.d(t,{Z:()=>c,a:()=>o});var i=n(7294);const r={},s=i.createContext(r);function o(e){const t=i.useContext(s);return i.useMemo((function(){return"function"==typeof e?e(t):{...t,...e}}),[t,e])}function c(e){let t;return t=e.disableParentContext?"function"==typeof e.components?e.components(r):e.components||r:o(e.components),i.createElement(s.Provider,{value:t},e.children)}}}]);
\ No newline at end of file
diff --git a/assets/js/14268422.cff0bb89.js b/assets/js/14268422.cff0bb89.js
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@@ -0,0 +1 @@
+"use strict";(self.webpackChunkgrc=self.webpackChunkgrc||[]).push([[8893],{9121:(e,n,i)=>{i.r(n),i.d(n,{assets:()=>o,contentTitle:()=>l,default:()=>d,frontMatter:()=>a,metadata:()=>t,toc:()=>c});var s=i(5893),r=i(1151);const a={},l="Deploying Hermes",t={id:"hermes/deploying-hermes",title:"Deploying Hermes",description:"Configuring + Deploying Hermes",source:"@site/docs/03-hermes/03-deploying-hermes.md",sourceDirName:"03-hermes",slug:"/hermes/deploying-hermes",permalink:"/docs/hermes/deploying-hermes",draft:!1,unlisted:!1,tags:[],version:"current",sidebarPosition:3,frontMatter:{},sidebar:"tutorialSidebar",previous:{title:"Building Hermes",permalink:"/docs/hermes/building-hermes"},next:{title:"Configuration",permalink:"/docs/hermes/configuration"}},o={},c=[{value:"Configuring + Deploying Hermes",id:"configuring--deploying-hermes",level:2},{value:"Install Jarvis",id:"install-jarvis",level:3},{value:"Initialize Jarvis",id:"initialize-jarvis",level:3},{value:"Build a Resource Graph",id:"build-a-resource-graph",level:3},{value:"Bootstrapping from an existing machine",id:"bootstrapping-from-an-existing-machine",level:4},{value:"Building a new resource graph",id:"building-a-new-resource-graph",level:4},{value:"Building an Environment",id:"building-an-environment",level:3},{value:"Set the active Hostfile",id:"set-the-active-hostfile",level:3},{value:"Create an empty pipeline",id:"create-an-empty-pipeline",level:4},{value:"Copy the environment cache",id:"copy-the-environment-cache",level:4},{value:"Add Hermes runtime",id:"add-hermes-runtime",level:4},{value:"Starting + Stopping Hermes",id:"starting--stopping-hermes",level:3},{value:"Stopping and Killing Hermes",id:"stopping-and-killing-hermes",level:3},{value:"Cleanup",id:"cleanup",level:3},{value:"Configuring + Deploying Hermes with an Application",id:"configuring--deploying-hermes-with-an-application",level:2},{value:"Build an Environment",id:"build-an-environment",level:3},{value:"Create an empty pipeline",id:"create-an-empty-pipeline-1",level:3},{value:"Copy the environment cache",id:"copy-the-environment-cache-1",level:3},{value:"Set the active hostfile",id:"set-the-active-hostfile-1",level:3},{value:"Add Hermes runtime",id:"add-hermes-runtime-1",level:3},{value:"Add Hermes MPI-IO interceptor",id:"add-hermes-mpi-io-interceptor",level:3},{value:"Add IOR",id:"add-ior",level:3},{value:"Run the Pipeline",id:"run-the-pipeline",level:3},{value:"Cleanup",id:"cleanup-1",level:3},{value:"Why is my application hanging?",id:"why-is-my-application-hanging",level:2},{value:"Resource Graph Misconfiguration",id:"resource-graph-misconfiguration",level:3},{value:"Dependency Problems",id:"dependency-problems",level:3},{value:"Machine Misconfiguration",id:"machine-misconfiguration",level:3},{value:"Permissions Problems",id:"permissions-problems",level:3}];function h(e){const n={a:"a",code:"code",em:"em",h1:"h1",h2:"h2",h3:"h3",h4:"h4",li:"li",p:"p",pre:"pre",strong:"strong",ul:"ul",...(0,r.a)(),...e.components};return(0,s.jsxs)(s.Fragment,{children:[(0,s.jsx)(n.h1,{id:"deploying-hermes",children:"Deploying Hermes"}),"\n",(0,s.jsx)(n.h2,{id:"configuring--deploying-hermes",children:"Configuring + Deploying Hermes"}),"\n",(0,s.jsxs)(n.p,{children:["The Hermes daemon is responsible for tracking various metadata, and it is\nrequired to be launched before your application. There should only be\none Hermes daemon per node. We recommend\n",(0,s.jsx)(n.a,{href:"https://github.com/grc-iit/jarvis-cd.git",children:"Jarvis"})," for deploying Hermes.\nJarvis is a framework that configures and deploys complex applications and\nservices. Jarvis will automatically set various environment variables\nthat Hermes expects in order for applications to be deployed. We have\nalso integrated several applications into Jarvis that can be seamlessly\ndeployed with Hermes."]}),"\n",(0,s.jsx)(n.h3,{id:"install-jarvis",children:"Install Jarvis"}),"\n",(0,s.jsx)(n.p,{children:"To install jarvis, do the following:"}),"\n",(0,s.jsx)(n.pre,{children:(0,s.jsx)(n.code,{className:"language-bash",children:"export JARVIS_PATH=${PWD}/jarvis-cd\ngit clone https://github.com/grc-iit/jarvis-cd.git ${JARVIS_PATH}\ncd ${JARVIS_PATH}\npip install -e .\n"})}),"\n",(0,s.jsx)(n.h3,{id:"initialize-jarvis",children:"Initialize Jarvis"}),"\n",(0,s.jsxs)(n.p,{children:["After installing, Jarvis MUST be configured for your specific system. The first\nstep is to define places for storing Jarvis configuration data. Note that large data\nobjects are ",(0,s.jsx)(n.strong,{children:"never"})," intended to be stored in these directories."]}),"\n",(0,s.jsx)(n.p,{children:"There are three places where configuration data is stored:"}),"\n",(0,s.jsxs)(n.ul,{children:["\n",(0,s.jsxs)(n.li,{children:[(0,s.jsx)(n.strong,{children:"CONFIG_DIR:"})," A directory where jarvis metadata for pkgs and pipelines are stored. This\ndirectory can be anywhere that the current user can access. ",(0,s.jsx)(n.code,{children:"${HOME}/jarvis_config"})," would be an example."]}),"\n",(0,s.jsxs)(n.li,{children:[(0,s.jsx)(n.strong,{children:"PRIVATE_DIR:"})," A directory which is common across all machines, but stores data locally to the\nmachine. Some jarvis pkgs require certain data to be stored per-machine. ",(0,s.jsx)(n.code,{children:"/tmp/jarvis_priv"})," would be an example."]}),"\n",(0,s.jsxs)(n.li,{children:[(0,s.jsx)(n.strong,{children:"SHARED_DIR:"})," A directory which is common across all machines, where each machine has the same\nview of data in the directory. In a supercomputing site, this would typically be\nin your home directory. For example ",(0,s.jsx)(n.code,{children:"${HOME}/jarvis_shared"})]}),"\n"]}),"\n",(0,s.jsx)(n.p,{children:"Make sure that all these paths are absolute paths. Environment variables can be used to make absolute paths less cumbersome. This command will automatically create the directories if they don't exist."}),"\n",(0,s.jsx)(n.pre,{children:(0,s.jsx)(n.code,{className:"language-bash",children:"jarvis init [CONFIG_DIR] [PRIVATE_DIR] [SHARED_DIR]\n"})}),"\n",(0,s.jsx)(n.p,{children:"This above command produces the jarvis configuration and store it here:"}),"\n",(0,s.jsx)(n.pre,{children:(0,s.jsx)(n.code,{className:"language-bash",children:"${JARVIS_PATH}/config/jarvis_config.yaml\n"})}),"\n",(0,s.jsx)(n.h3,{id:"build-a-resource-graph",children:"Build a Resource Graph"}),"\n",(0,s.jsx)(n.p,{children:"A resource graph contains the storage and networking configuration\nof the machines you intend to deploy Hermes on."}),"\n",(0,s.jsx)(n.h4,{id:"bootstrapping-from-an-existing-machine",children:"Bootstrapping from an existing machine"}),"\n",(0,s.jsxs)(n.p,{children:["We have several resource graphs for different machines, located under\n",(0,s.jsx)(n.code,{children:"${JARVIS_PATH}/builtin/resource_graph"}),". There are resource graphs\nfor different machines spanning IIT, PNNL, and Argonne. To view the\nset of preconfigured machines, run:"]}),"\n",(0,s.jsx)(n.pre,{children:(0,s.jsx)(n.code,{className:"language-bash",children:"ls ${JARVIS_PATH}/builtin/resource_graph\n"})}),"\n",(0,s.jsx)(n.p,{children:"If one of your machines is there, then do:"}),"\n",(0,s.jsx)(n.pre,{children:(0,s.jsx)(n.code,{className:"language-bash",children:"jarvis bootstrap from [MY_MACHINE]\n"})}),"\n",(0,s.jsx)(n.p,{children:"For example, ares is one of the machines:"}),"\n",(0,s.jsx)(n.pre,{children:(0,s.jsx)(n.code,{className:"language-bash",children:"jarvis bootstrap from ares\n"})}),"\n",(0,s.jsx)(n.h4,{id:"building-a-new-resource-graph",children:"Building a new resource graph"}),"\n",(0,s.jsx)(n.p,{children:"If a resource graph for your machine is not available, you will have to\ndefine one manually."}),"\n",(0,s.jsxs)(n.p,{children:["The resource graph ",(0,s.jsx)(n.strong,{children:"must"})," be created at exactly the following path:"]}),"\n",(0,s.jsx)(n.pre,{children:(0,s.jsx)(n.code,{className:"language-bash",children:"${JARVIS_PATH}/config/resource_graph.yaml\n"})}),"\n",(0,s.jsx)(n.p,{children:"For storage devices, the required parameters are as follows:"}),"\n",(0,s.jsx)(n.pre,{children:(0,s.jsx)(n.code,{className:"language-yaml",children:"fs:\n  - avail: 500G # Available capacity of the device (Suffix: K,G,T,P)\n    dev_type: ssd # Type of storage hardware (hdd, ssd, nvme, pmem)\n    mount: /mnt/ssd/${USER} # Where to place data on the device\n    shared: false # Is this shared across nodes (e.g., a PFS?)\n"})}),"\n",(0,s.jsx)(n.p,{children:"For networks, the parameters are as follows:"}),"\n",(0,s.jsx)(n.pre,{children:(0,s.jsx)(n.code,{className:"language-yaml",children:"net:\n  - domain: lo # Domain of network. Can be null.\n    fabric: 127.0.0.1/32\n    provider: tcp;ofi_rxm\n    shared: false # Is this network shared across nodes. E.g., localhost is not\n    speed: 40G\n"})}),"\n",(0,s.jsxs)(n.p,{children:["This information can be discovered using tools such as ",(0,s.jsx)(n.code,{children:"fi_info"})," provided by libfabric. The fi_info tool is extremely verbose and requires some expertise to understand. fi_info outputs several networks -- most of which are irrelevant. Many networks printed may only function in single-node cases -- or not at all."]}),"\n",(0,s.jsxs)(n.ul,{children:["\n",(0,s.jsx)(n.li,{children:"The most important information to determine a relevant network is domain, fabric, and provider."}),"\n",(0,s.jsxs)(n.li,{children:["Networks with the ",(0,s.jsx)(n.strong,{children:"lo"})," domain or with fabrics equivalent to 127.0.0.1 will only function in single-node cases."]}),"\n",(0,s.jsxs)(n.li,{children:["Fabrics ending with the format *.0.0.0 will ",(0,s.jsx)(n.strong,{children:"NOT"})," work. These are ",(0,s.jsx)(n.em,{children:"network"})," addresses, not ",(0,s.jsx)(n.em,{children:"host"})," addreses. For example, 127.0.0.0 comes up sometimes in the fi_info output."]}),"\n",(0,s.jsx)(n.li,{children:"Networks where the fabric is not a number are generally irrelevant and will not function when used. For example:"}),"\n"]}),"\n",(0,s.jsx)(n.pre,{children:(0,s.jsx)(n.code,{className:"language-yaml",children:"# This provider is not relevant\nprovider: UDP\nfabric: UDP-IP\ndomain: udp\nversion: 1.1\ntype: FI_EP_DGRAM\nprotocol: FI_PROTO_UDP\n"})}),"\n",(0,s.jsxs)(n.ul,{children:["\n",(0,s.jsxs)(n.li,{children:["One way to filter out dysfunctional fi_info outputs is to use ",(0,s.jsx)(n.code,{children:"ip addr show"})," (or ",(0,s.jsx)(n.code,{children:"fi_info | grep fabric"}),") to list available IP addresses. Do this on two separate machines, compare their output, and then look at only the IP addresses that are similar between the machines. If you can ssh between the machines using these IP addresses, then you should focus on only those fabrics matching their pattern in the fi_info output"]}),"\n",(0,s.jsx)(n.li,{children:"Be careful about the providers. It has come up plenty of times where a provider is listed, but doesn't actually work. Verbs, for example, may fail if your Hermes installation was not correctly configured to support RDMA. This is a guess-and-check game. TCP and Sockets are generally a safe bet. It may be of benefit to try just these providers and get a distributed deployment of Hermes functioning before moving on to verbs."}),"\n"]}),"\n",(0,s.jsx)(n.h3,{id:"building-an-environment",children:"Building an Environment"}),"\n",(0,s.jsx)(n.p,{children:"We will now load all necessary environment variables and build a\nJarvis environment named hermes_env:"}),"\n",(0,s.jsx)(n.pre,{children:(0,s.jsx)(n.code,{className:"language-bash",children:"spack load hermes\njarvis env build hermes_env\n"})}),"\n",(0,s.jsx)(n.p,{children:"hermes_env will store all important environment variables, including PATH,\nLD_LIBRARY_PATH, etc. in a YAML file. This will make it so that you do not\nneed to repeatedly run spack load and module load if the machine is broken."}),"\n",(0,s.jsx)(n.h3,{id:"set-the-active-hostfile",children:"Set the active Hostfile"}),"\n",(0,s.jsx)(n.p,{children:"The hostfile contains the set of nodes that the pipeline will run over.\nThis is structured the same way as a traditional MPI hostfile."}),"\n",(0,s.jsx)(n.p,{children:"An example hostfile:"}),"\n",(0,s.jsx)(n.pre,{children:(0,s.jsx)(n.code,{className:"language-txt",children:"ares-comp-20\nares-comp-[21-25]\n"})}),"\n",(0,s.jsx)(n.p,{children:"To set the active hostfile, run:"}),"\n",(0,s.jsx)(n.pre,{children:(0,s.jsx)(n.code,{className:"language-bash",children:"jarvis hostfile set /path/to/hostfile\n"})}),"\n",(0,s.jsx)(n.p,{children:"Note that every time you change the hostfile, you will need to update the\npipeline. Jarvis does not automatically detect changes to this file."}),"\n",(0,s.jsx)(n.pre,{children:(0,s.jsx)(n.code,{className:"language-bash",children:"jarvis pipeline update\n"})}),"\n",(0,s.jsx)(n.h4,{id:"create-an-empty-pipeline",children:"Create an empty pipeline"}),"\n",(0,s.jsx)(n.pre,{children:(0,s.jsx)(n.code,{className:"language-bash",children:"jarvis pipeline create hermes\n"})}),"\n",(0,s.jsx)(n.p,{children:"hermes is the name of the pipeline. It doesn't need to be hermes,\nit can be any name."}),"\n",(0,s.jsx)(n.h4,{id:"copy-the-environment-cache",children:"Copy the environment cache"}),"\n",(0,s.jsx)(n.pre,{children:(0,s.jsx)(n.code,{className:"language-bash",children:"jarvis pipeline env copy hermes_env\n"})}),"\n",(0,s.jsx)(n.p,{children:"This will use the hermes_env environment that was previously created in"}),"\n",(0,s.jsx)(n.h4,{id:"add-hermes-runtime",children:"Add Hermes runtime"}),"\n",(0,s.jsx)(n.pre,{children:(0,s.jsx)(n.code,{className:"language-bash",children:"jarvis pipeline append hermes_run\njarvis pkg configure hermes_run \\\nsleep=5 \\\ninclude=${HOME}/ior_data\n"})}),"\n",(0,s.jsx)(n.p,{children:"Jarvis will automatically produce a Hermes client and server configuration that\ncontains all storage devices and fastest available network defined in the\nresource graph. These configurations will be located in:"}),"\n",(0,s.jsx)(n.pre,{children:(0,s.jsx)(n.code,{className:"language-bash",children:"$(jarvis path +shared)/hermes_run/hermes_server.yaml\n$(jarvis path +shared)/hermes_run/hermes_client.yaml\n"})}),"\n",(0,s.jsx)(n.p,{children:"To view all parameters of the Hermes package, you can run:"}),"\n",(0,s.jsx)(n.pre,{children:(0,s.jsx)(n.code,{className:"language-bash",children:"jarvis pkg help hermes_run\n"})}),"\n",(0,s.jsx)(n.h3,{id:"starting--stopping-hermes",children:"Starting + Stopping Hermes"}),"\n",(0,s.jsx)(n.p,{children:"To start Hermes:"}),"\n",(0,s.jsx)(n.pre,{children:(0,s.jsx)(n.code,{className:"language-bash",children:"jarvis pipeline start\n"})}),"\n",(0,s.jsx)(n.h3,{id:"stopping-and-killing-hermes",children:"Stopping and Killing Hermes"}),"\n",(0,s.jsx)(n.p,{children:"To gracefully stop Hermes and flush data back to the PFS:"}),"\n",(0,s.jsx)(n.pre,{children:(0,s.jsx)(n.code,{className:"language-bash",children:"jarvis pipeline stop\n"})}),"\n",(0,s.jsx)(n.p,{children:"To kill a Hermes deployment that isn't stopping gracefully:"}),"\n",(0,s.jsx)(n.pre,{children:(0,s.jsx)(n.code,{className:"language-bash",children:"jarvis pipeline kill\n"})}),"\n",(0,s.jsx)(n.h3,{id:"cleanup",children:"Cleanup"}),"\n",(0,s.jsx)(n.p,{children:"To erase data produced by the pipeline:"}),"\n",(0,s.jsx)(n.pre,{children:(0,s.jsx)(n.code,{className:"language-bash",children:"jarvis pipeline clean\n"})}),"\n",(0,s.jsx)(n.p,{children:"To destroy the pipeline:"}),"\n",(0,s.jsx)(n.pre,{children:(0,s.jsx)(n.code,{className:"language-bash",children:"jarvis pipeline destroy\n"})}),"\n",(0,s.jsx)(n.h2,{id:"configuring--deploying-hermes-with-an-application",children:"Configuring + Deploying Hermes with an Application"}),"\n",(0,s.jsx)(n.p,{children:"As previously stated, Jarvis can be used to deploy and application\nwith Hermes. This will automatically set environment variables\n(e.g., LD_PRELOAD) that will be necessary for the application to\nrun."}),"\n",(0,s.jsx)(n.h3,{id:"build-an-environment",children:"Build an Environment"}),"\n",(0,s.jsx)(n.p,{children:"We will now load all necessary environment variables and build a\nJarvis environment named hermes_env:"}),"\n",(0,s.jsx)(n.pre,{children:(0,s.jsx)(n.code,{className:"language-bash",children:"spack load hermes\nspack load ior\njarvis env build hermes_ior_env\n"})}),"\n",(0,s.jsx)(n.p,{children:"hermes_ior_env will store all important environment variables, including PATH,\nLD_LIBRARY_PATH, etc. in a YAML file."}),"\n",(0,s.jsx)(n.h3,{id:"create-an-empty-pipeline-1",children:"Create an empty pipeline"}),"\n",(0,s.jsx)(n.pre,{children:(0,s.jsx)(n.code,{className:"language-bash",children:"jarvis pipeline create hermes_ior\n"})}),"\n",(0,s.jsx)(n.h3,{id:"copy-the-environment-cache-1",children:"Copy the environment cache"}),"\n",(0,s.jsx)(n.pre,{children:(0,s.jsx)(n.code,{className:"language-bash",children:"jarvis pipeline env copy hermes_ior_env\n"})}),"\n",(0,s.jsx)(n.h3,{id:"set-the-active-hostfile-1",children:"Set the active hostfile"}),"\n",(0,s.jsx)(n.pre,{children:(0,s.jsx)(n.code,{className:"language-bash",children:"jarvis hostfile set /path/to/hostfile\n"})}),"\n",(0,s.jsx)(n.h3,{id:"add-hermes-runtime-1",children:"Add Hermes runtime"}),"\n",(0,s.jsx)(n.pre,{children:(0,s.jsx)(n.code,{className:"language-bash",children:"jarvis pipeline append hermes_run\njarvis pkg configure hermes_run \\\nsleep=5 \\\ninclude=${HOME}/ior_data\n"})}),"\n",(0,s.jsxs)(n.p,{children:["This will ensure that if a Hermes interceptor is used, it will intercept\nall paths in ",(0,s.jsx)(n.code,{children:"${HOME}/ior_data"}),"."]}),"\n",(0,s.jsx)(n.h3,{id:"add-hermes-mpi-io-interceptor",children:"Add Hermes MPI-IO interceptor"}),"\n",(0,s.jsx)(n.pre,{children:(0,s.jsx)(n.code,{className:"language-bash",children:"jarvis pipeline append hermes_api\njarvis pkg configure hermes_api +mpi\n"})}),"\n",(0,s.jsx)(n.p,{children:"This will automatically locate the interceptor library by\ntraversing various environment variables. This will ensure\nthat MPI-IO is intercepted by Hermes."}),"\n",(0,s.jsx)(n.p,{children:"hermes_api includes other interceptors that can be used: posix, stdio, vfd. To view the set of options:"}),"\n",(0,s.jsx)(n.pre,{children:(0,s.jsx)(n.code,{className:"language-bash",children:"jarvis pkg help hermes_run\n"})}),"\n",(0,s.jsx)(n.h3,{id:"add-ior",children:"Add IOR"}),"\n",(0,s.jsx)(n.pre,{children:(0,s.jsx)(n.code,{className:"language-bash",children:"jarvis pipeline append ior\njarvis pkg configure ior \\\nxfer=1m \\\nblock=1g \\\nnprocs=64 \\\nppn=16 \\\n+write +read \\\nout=${HOME}/ior_data/ior.bin \\\napi=mpiio\n"})}),"\n",(0,s.jsxs)(n.p,{children:["This IOR will perform 1GB of I/O per-process (block) in units of 1m (xfer) and\nproduce a single output file ",(0,s.jsx)(n.code,{children:"${HOME}/ior_data/ior.bin"}),"(out) using MPI-IO\n(api). The total amount of I/O performed will be 64GB spread across 4 nodes."]}),"\n",(0,s.jsx)(n.h3,{id:"run-the-pipeline",children:"Run the Pipeline"}),"\n",(0,s.jsx)(n.p,{children:"To run the pipeline:"}),"\n",(0,s.jsx)(n.pre,{children:(0,s.jsx)(n.code,{className:"language-bash",children:"jarvis pipeline run\n"})}),"\n",(0,s.jsx)(n.p,{children:"This will launch Hermes, execute IOR, and then stop Hermes. It is equivalent\nto:"}),"\n",(0,s.jsx)(n.pre,{children:(0,s.jsx)(n.code,{className:"language-bash",children:"jarvis pipeline start\njarvis pipeline stop\n"})}),"\n",(0,s.jsx)(n.h3,{id:"cleanup-1",children:"Cleanup"}),"\n",(0,s.jsx)(n.p,{children:"The following will delete intermediate data generated by Hermes + IOR:"}),"\n",(0,s.jsx)(n.pre,{children:(0,s.jsx)(n.code,{className:"language-bash",children:"jarvis pipeline clean\n"})}),"\n",(0,s.jsx)(n.h2,{id:"why-is-my-application-hanging",children:"Why is my application hanging?"}),"\n",(0,s.jsx)(n.h3,{id:"resource-graph-misconfiguration",children:"Resource Graph Misconfiguration"}),"\n",(0,s.jsxs)(n.p,{children:["Commonly, the cause is a misconfiguration in the resource graph, specifically\nwith the network section. If the resource graph is misconfigured, Hermes may\ncrash with a ",(0,s.jsx)(n.code,{children:"mercury->fatal"})," error and ultimately cause the program to stall\nforever. Make sure that the domain, provider, and fabric are valid. To view the\nHermes configuration to see which network was selected from your resource graph,\nyou can run:"]}),"\n",(0,s.jsx)(n.pre,{children:(0,s.jsx)(n.code,{className:"language-bash",children:"cat $(jarvis path)/hermes_run/hermes_server.yaml\n"})}),"\n",(0,s.jsx)(n.h3,{id:"dependency-problems",children:"Dependency Problems"}),"\n",(0,s.jsx)(n.p,{children:"If you are using the MPI-IO interceptor, make sure that the MPI that Hermes\ncompiled with is equivalent to the one your application was compiled with.\nYou may have multiple versions of MPI installed and if you didn't specify\nwhich one when installing Hermes and your program -- they may be different."}),"\n",(0,s.jsx)(n.p,{children:"If you are using the VFD, make sure the VFD was compiled with the same HDF5\nas the application."}),"\n",(0,s.jsx)(n.p,{children:"To view the dependencies of your installed Hermes, run:"}),"\n",(0,s.jsx)(n.pre,{children:(0,s.jsx)(n.code,{children:"spack find -c -d hermes\n"})}),"\n",(0,s.jsx)(n.h3,{id:"machine-misconfiguration",children:"Machine Misconfiguration"}),"\n",(0,s.jsx)(n.p,{children:"We have found certain instances where using semantic hostnames in the hostfile\nhas resulted in incorrect behavior. If the machine is misconfigured, it is\npossible that a hostname maps to a different network domain on different nodes.\nTo verify this, you can try using exact IP addresses in your hostfile."}),"\n",(0,s.jsxs)(n.p,{children:["To view your machine's IP addresses, you can run\n",(0,s.jsx)(n.code,{children:"ip addr show"})," or ",(0,s.jsx)(n.code,{children:"fi_info | grep fabric"})]}),"\n",(0,s.jsx)(n.h3,{id:"permissions-problems",children:"Permissions Problems"}),"\n",(0,s.jsx)(n.p,{children:"If you cannot SSH between machines or if your known_hosts file is outdated,\nit is possible that Hermes will fail to launch due to permissions problems\non the network. Make sure that you can SSH between machines without error."})]})}function d(e={}){const{wrapper:n}={...(0,r.a)(),...e.components};return n?(0,s.jsx)(n,{...e,children:(0,s.jsx)(h,{...e})}):h(e)}},1151:(e,n,i)=>{i.d(n,{Z:()=>t,a:()=>l});var s=i(7294);const r={},a=s.createContext(r);function l(e){const n=s.useContext(a);return s.useMemo((function(){return"function"==typeof e?e(n):{...n,...e}}),[n,e])}function t(e){let n;return n=e.disableParentContext?"function"==typeof e.components?e.components(r):e.components||r:l(e.components),s.createElement(a.Provider,{value:n},e.children)}}}]);
\ No newline at end of file
diff --git a/assets/js/14268422.e2bec6f6.js b/assets/js/14268422.e2bec6f6.js
deleted file mode 100644
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--- a/assets/js/14268422.e2bec6f6.js
+++ /dev/null
@@ -1 +0,0 @@
-"use strict";(self.webpackChunkgrc=self.webpackChunkgrc||[]).push([[8893],{9121:(e,n,i)=>{i.r(n),i.d(n,{assets:()=>o,contentTitle:()=>l,default:()=>c,frontMatter:()=>a,metadata:()=>t,toc:()=>h});var r=i(5893),s=i(1151);const a={},l="Deploying Hermes",t={id:"hermes/deploying-hermes",title:"Deploying Hermes",description:"Configuring + Deploying Hermes",source:"@site/docs/03-hermes/03-deploying-hermes.md",sourceDirName:"03-hermes",slug:"/hermes/deploying-hermes",permalink:"/docs/hermes/deploying-hermes",draft:!1,unlisted:!1,tags:[],version:"current",sidebarPosition:3,frontMatter:{},sidebar:"tutorialSidebar",previous:{title:"Building Hermes",permalink:"/docs/hermes/building-hermes"},next:{title:"Configuration",permalink:"/docs/hermes/configuration"}},o={},h=[{value:"Configuring + Deploying Hermes",id:"configuring--deploying-hermes",level:2},{value:"Install Jarvis",id:"install-jarvis",level:3},{value:"Initialize Jarvis",id:"initialize-jarvis",level:3},{value:"Build a Resource Graph",id:"build-a-resource-graph",level:3},{value:"Bootstrapping from an existing machine",id:"bootstrapping-from-an-existing-machine",level:4},{value:"Building a new resource graph",id:"building-a-new-resource-graph",level:4},{value:"Building an Environment",id:"building-an-environment",level:3},{value:"Set the active Hostfile",id:"set-the-active-hostfile",level:3},{value:"Create an empty pipeline",id:"create-an-empty-pipeline",level:4},{value:"Copy the environment cache",id:"copy-the-environment-cache",level:4},{value:"Add Hermes runtime",id:"add-hermes-runtime",level:4},{value:"Starting + Stopping Hermes",id:"starting--stopping-hermes",level:3},{value:"Stopping and Killing Hermes",id:"stopping-and-killing-hermes",level:3},{value:"Cleanup",id:"cleanup",level:3},{value:"Configuring + Deploying Hermes with an Application",id:"configuring--deploying-hermes-with-an-application",level:2},{value:"Build an Environment",id:"build-an-environment",level:3},{value:"Create an empty pipeline",id:"create-an-empty-pipeline-1",level:3},{value:"Copy the environment cache",id:"copy-the-environment-cache-1",level:3},{value:"Set the active hostfile",id:"set-the-active-hostfile-1",level:3},{value:"Add Hermes runtime",id:"add-hermes-runtime-1",level:3},{value:"Add Hermes MPI-IO interceptor",id:"add-hermes-mpi-io-interceptor",level:3},{value:"Add IOR",id:"add-ior",level:3},{value:"Run the Pipeline",id:"run-the-pipeline",level:3},{value:"Cleanup",id:"cleanup-1",level:3},{value:"Why is my application hanging?",id:"why-is-my-application-hanging",level:2},{value:"Resource Graph Misconfiguration",id:"resource-graph-misconfiguration",level:3},{value:"Dependency Problems",id:"dependency-problems",level:3},{value:"Machine Misconfiguration",id:"machine-misconfiguration",level:3},{value:"Permissions Problems",id:"permissions-problems",level:3}];function d(e){const n={a:"a",code:"code",em:"em",h1:"h1",h2:"h2",h3:"h3",h4:"h4",li:"li",p:"p",pre:"pre",strong:"strong",ul:"ul",...(0,s.a)(),...e.components};return(0,r.jsxs)(r.Fragment,{children:[(0,r.jsx)(n.h1,{id:"deploying-hermes",children:"Deploying Hermes"}),"\n",(0,r.jsx)(n.h2,{id:"configuring--deploying-hermes",children:"Configuring + Deploying Hermes"}),"\n",(0,r.jsxs)(n.p,{children:["The Hermes daemon is responsible for tracking various metadata, and it is\nrequired to be launched before your application. There should only be\none Hermes daemon per node. We recommend\n",(0,r.jsx)(n.a,{href:"https://github.com/grc-iit/jarvis-cd.git",children:"Jarvis"})," for deploying Hermes.\nJarvis is a framework that configures and deploys complex applications and\nservices. Jarvis will automatically set various environment variables\nthat Hermes expects in order for applications to be deployed. We have\nalso integrated several applications into Jarvis that can be seamlessly\ndeployed with Hermes."]}),"\n",(0,r.jsx)(n.h3,{id:"install-jarvis",children:"Install Jarvis"}),"\n",(0,r.jsx)(n.p,{children:"To install jarvis, do the following:"}),"\n",(0,r.jsx)(n.pre,{children:(0,r.jsx)(n.code,{className:"language-bash",children:"export JARVIS_PATH=${PWD}/jarvis-cd\ngit clone https://github.com/grc-iit/jarvis-cd.git ${JARVIS_PATH}\ncd ${JARVIS_PATH}\npip install -e .\n"})}),"\n",(0,r.jsx)(n.h3,{id:"initialize-jarvis",children:"Initialize Jarvis"}),"\n",(0,r.jsxs)(n.p,{children:["After installing, Jarvis MUST be configured for your specific system. The first\nstep is to define places for storing Jarvis configuration data. Note that large data\nobjects are ",(0,r.jsx)(n.strong,{children:"never"})," intended to be stored in these directories."]}),"\n",(0,r.jsx)(n.p,{children:"There are three places where configuration data is stored:"}),"\n",(0,r.jsxs)(n.ul,{children:["\n",(0,r.jsx)(n.li,{children:"CONFIG_DIR: A directory where jarvis metadata for pkgs and pipelines are stored. This\ndirectory can be anywhere that the current user can access."}),"\n",(0,r.jsx)(n.li,{children:"PRIVATE_DIR: A directory which is common across all machines, but stores data locally to the\nmachine. Some jarvis pkgs require certain data to be stored per-machine. /tmp\nwould be an example."}),"\n",(0,r.jsx)(n.li,{children:"SHARED_DIR: A directory which is common across all machines, where each machine has the same\nview of data in the directory. In a supercomputing site, this would typically be\nin your home directory."}),"\n"]}),"\n",(0,r.jsx)(n.p,{children:"Make sure that all these paths are absolute paths."}),"\n",(0,r.jsx)(n.pre,{children:(0,r.jsx)(n.code,{className:"language-bash",children:"jarvis init [CONFIG_DIR] [PRIVATE_DIR] [SHARED_DIR]\n"})}),"\n",(0,r.jsx)(n.h3,{id:"build-a-resource-graph",children:"Build a Resource Graph"}),"\n",(0,r.jsx)(n.p,{children:"A resource graph contains the storage and networking configuration\nof the machines you intend to deploy Hermes on."}),"\n",(0,r.jsx)(n.h4,{id:"bootstrapping-from-an-existing-machine",children:"Bootstrapping from an existing machine"}),"\n",(0,r.jsxs)(n.p,{children:["We have several resource graphs for different machines, located under\n",(0,r.jsx)(n.code,{children:"${JARVIS_PATH}/builtin/resource_graph"}),". There are resource graphs\nfor different machines spanning IIT, PNNL, and Argonne. To view the\nset of preconfigured machines, run:"]}),"\n",(0,r.jsx)(n.pre,{children:(0,r.jsx)(n.code,{className:"language-bash",children:"ls ${JARVIS_PATH}/builtin/resource_graph\n"})}),"\n",(0,r.jsx)(n.p,{children:"If one of your machines is there, then do:"}),"\n",(0,r.jsx)(n.pre,{children:(0,r.jsx)(n.code,{className:"language-bash",children:"jarvis bootstrap from [MY_MACHINE]\n"})}),"\n",(0,r.jsx)(n.p,{children:"For example, ares is one of the machines:"}),"\n",(0,r.jsx)(n.pre,{children:(0,r.jsx)(n.code,{className:"language-bash",children:"jarvis bootstrap from ares\n"})}),"\n",(0,r.jsx)(n.h4,{id:"building-a-new-resource-graph",children:"Building a new resource graph"}),"\n",(0,r.jsx)(n.p,{children:"If a resource graph for your machine is not available, you will have to\ndefine one manually."}),"\n",(0,r.jsxs)(n.p,{children:["The resource graph ",(0,r.jsx)(n.strong,{children:"must"})," be created at exactly the following path:"]}),"\n",(0,r.jsx)(n.pre,{children:(0,r.jsx)(n.code,{className:"language-bash",children:"${JARVIS_PATH}/config/resource_graph.yaml\n"})}),"\n",(0,r.jsx)(n.p,{children:"For storage devices, the required parameters are as follows:"}),"\n",(0,r.jsx)(n.pre,{children:(0,r.jsx)(n.code,{className:"language-yaml",children:"fs:\n  - avail: 500G # Available capacity of the device (Suffix: K,G,T,P)\n    dev_type: ssd # Type of storage hardware (hdd, ssd, nvme, pmem)\n    mount: /mnt/ssd/${USER} # Where to place data on the device\n    shared: false # Is this shared across nodes (e.g., a PFS?)\n"})}),"\n",(0,r.jsx)(n.p,{children:"For networks, the parameters are as follows:"}),"\n",(0,r.jsx)(n.pre,{children:(0,r.jsx)(n.code,{className:"language-yaml",children:"net:\n  - domain: lo # Domain of network. Can be null.\n    fabric: 127.0.0.1/32\n    provider: tcp;ofi_rxm\n    shared: false # Is this network shared across nodes. E.g., localhost is not\n    speed: 40G\n"})}),"\n",(0,r.jsxs)(n.p,{children:["This information can be discovered using tools such as ",(0,r.jsx)(n.code,{children:"fi_info"})," provided by libfabric. The fi_info tool is extremely verbose and requires some expertise to understand. fi_info outputs several networks -- most of which are irrelevant. Many networks printed may only function in single-node cases -- or not at all."]}),"\n",(0,r.jsxs)(n.ul,{children:["\n",(0,r.jsx)(n.li,{children:"The most important information to determine a relevant network is domain, fabric, and provider."}),"\n",(0,r.jsxs)(n.li,{children:["Networks with the ",(0,r.jsx)(n.strong,{children:"lo"})," domain or with fabrics equivalent to 127.0.0.1 will only function in single-node cases."]}),"\n",(0,r.jsxs)(n.li,{children:["Fabrics ending with the format *.0.0.0 will ",(0,r.jsx)(n.strong,{children:"NOT"})," work. These are ",(0,r.jsx)(n.em,{children:"network"})," addresses, not ",(0,r.jsx)(n.em,{children:"host"})," addreses. For example, 127.0.0.0 comes up sometimes in the fi_info output."]}),"\n",(0,r.jsx)(n.li,{children:"Networks where the fabric is not a number are generally irrelevant and will not function when used. For example:"}),"\n"]}),"\n",(0,r.jsx)(n.pre,{children:(0,r.jsx)(n.code,{className:"language-yaml",children:"# This provider is not relevant\nprovider: UDP\nfabric: UDP-IP\ndomain: udp\nversion: 1.1\ntype: FI_EP_DGRAM\nprotocol: FI_PROTO_UDP\n"})}),"\n",(0,r.jsxs)(n.ul,{children:["\n",(0,r.jsxs)(n.li,{children:["One way to filter out dysfunctional fi_info outputs is to use ",(0,r.jsx)(n.code,{children:"ip addr show"})," (or ",(0,r.jsx)(n.code,{children:"fi_info | grep fabric"}),") to list available IP addresses. Do this on two separate machines, compare their output, and then look at only the IP addresses that are similar between the machines. If you can ssh between the machines using these IP addresses, then you should focus on only those fabrics matching their pattern in the fi_info output"]}),"\n",(0,r.jsx)(n.li,{children:"Be careful about the providers. It has come up plenty of times where a provider is listed, but doesn't actually work. Verbs, for example, may fail if your Hermes installation was not correctly configured to support RDMA. This is a guess-and-check game. TCP and Sockets are generally a safe bet. It may be of benefit to try just these providers and get a distributed deployment of Hermes functioning before moving on to verbs."}),"\n"]}),"\n",(0,r.jsx)(n.h3,{id:"building-an-environment",children:"Building an Environment"}),"\n",(0,r.jsx)(n.p,{children:"We will now load all necessary environment variables and build a\nJarvis environment named hermes_env:"}),"\n",(0,r.jsx)(n.pre,{children:(0,r.jsx)(n.code,{className:"language-bash",children:"spack load hermes\njarvis env build hermes_env\n"})}),"\n",(0,r.jsx)(n.p,{children:"hermes_env will store all important environment variables, including PATH,\nLD_LIBRARY_PATH, etc. in a YAML file. This will make it so that you do not\nneed to repeatedly run spack load and module load if the machine is broken."}),"\n",(0,r.jsx)(n.h3,{id:"set-the-active-hostfile",children:"Set the active Hostfile"}),"\n",(0,r.jsx)(n.p,{children:"The hostfile contains the set of nodes that the pipeline will run over.\nThis is structured the same way as a traditional MPI hostfile."}),"\n",(0,r.jsx)(n.p,{children:"An example hostfile:"}),"\n",(0,r.jsx)(n.pre,{children:(0,r.jsx)(n.code,{className:"language-txt",children:"ares-comp-20\nares-comp-[21-25]\n"})}),"\n",(0,r.jsx)(n.p,{children:"To set the active hostfile, run:"}),"\n",(0,r.jsx)(n.pre,{children:(0,r.jsx)(n.code,{className:"language-bash",children:"jarvis hostfile set /path/to/hostfile\n"})}),"\n",(0,r.jsx)(n.p,{children:"Note that every time you change the hostfile, you will need to update the\npipeline. Jarvis does not automatically detect changes to this file."}),"\n",(0,r.jsx)(n.pre,{children:(0,r.jsx)(n.code,{className:"language-bash",children:"jarvis pipeline update\n"})}),"\n",(0,r.jsx)(n.h4,{id:"create-an-empty-pipeline",children:"Create an empty pipeline"}),"\n",(0,r.jsx)(n.pre,{children:(0,r.jsx)(n.code,{className:"language-bash",children:"jarvis pipeline create hermes\n"})}),"\n",(0,r.jsx)(n.p,{children:"hermes is the name of the pipeline. It doesn't need to be hermes,\nit can be any name."}),"\n",(0,r.jsx)(n.h4,{id:"copy-the-environment-cache",children:"Copy the environment cache"}),"\n",(0,r.jsx)(n.pre,{children:(0,r.jsx)(n.code,{className:"language-bash",children:"jarvis pipeline env copy hermes_env\n"})}),"\n",(0,r.jsx)(n.p,{children:"This will use the hermes_env environment that was previously created in"}),"\n",(0,r.jsx)(n.h4,{id:"add-hermes-runtime",children:"Add Hermes runtime"}),"\n",(0,r.jsx)(n.pre,{children:(0,r.jsx)(n.code,{className:"language-bash",children:"jarvis pipeline append hermes_run\njarvis pkg configure hermes_run \\\nsleep=5 \\\ninclude=${HOME}/ior_data\n"})}),"\n",(0,r.jsx)(n.p,{children:"Jarvis will automatically produce a Hermes client and server configuration that\ncontains all storage devices and fastest available network defined in the\nresource graph. These configurations will be located in:"}),"\n",(0,r.jsx)(n.pre,{children:(0,r.jsx)(n.code,{children:"$(jarvis path +shared)/hermes_run/hermes_server.yaml\n$(jarvis path +shared)/hermes_run/hermes_client.yaml\n"})}),"\n",(0,r.jsx)(n.h3,{id:"starting--stopping-hermes",children:"Starting + Stopping Hermes"}),"\n",(0,r.jsx)(n.p,{children:"To start Hermes:"}),"\n",(0,r.jsx)(n.pre,{children:(0,r.jsx)(n.code,{className:"language-bash",children:"jarvis pipeline start\n"})}),"\n",(0,r.jsx)(n.h3,{id:"stopping-and-killing-hermes",children:"Stopping and Killing Hermes"}),"\n",(0,r.jsx)(n.p,{children:"To gracefully stop Hermes and flush data back to the PFS:"}),"\n",(0,r.jsx)(n.pre,{children:(0,r.jsx)(n.code,{className:"language-bash",children:"jarvis pipeline stop\n"})}),"\n",(0,r.jsx)(n.p,{children:"To kill a Hermes deployment that isn't stopping gracefully:"}),"\n",(0,r.jsx)(n.pre,{children:(0,r.jsx)(n.code,{className:"language-bash",children:"jarvis pipeline kill\n"})}),"\n",(0,r.jsx)(n.h3,{id:"cleanup",children:"Cleanup"}),"\n",(0,r.jsx)(n.p,{children:"To erase data produced by the pipeline:"}),"\n",(0,r.jsx)(n.pre,{children:(0,r.jsx)(n.code,{className:"language-bash",children:"jarvis pipeline clean\n"})}),"\n",(0,r.jsx)(n.p,{children:"To destroy the pipeline:"}),"\n",(0,r.jsx)(n.pre,{children:(0,r.jsx)(n.code,{className:"language-bash",children:"jarvis pipeline destroy\n"})}),"\n",(0,r.jsx)(n.h2,{id:"configuring--deploying-hermes-with-an-application",children:"Configuring + Deploying Hermes with an Application"}),"\n",(0,r.jsx)(n.p,{children:"As previously stated, Jarvis can be used to deploy and application\nwith Hermes. This will automatically set environment variables\n(e.g., LD_PRELOAD) that will be necessary for the application to\nrun."}),"\n",(0,r.jsx)(n.h3,{id:"build-an-environment",children:"Build an Environment"}),"\n",(0,r.jsx)(n.p,{children:"We will now load all necessary environment variables and build a\nJarvis environment named hermes_env:"}),"\n",(0,r.jsx)(n.pre,{children:(0,r.jsx)(n.code,{className:"language-bash",children:"spack load hermes\nspack load ior\njarvis env build hermes_ior_env\n"})}),"\n",(0,r.jsx)(n.p,{children:"hermes_ior_env will store all important environment variables, including PATH,\nLD_LIBRARY_PATH, etc. in a YAML file."}),"\n",(0,r.jsx)(n.h3,{id:"create-an-empty-pipeline-1",children:"Create an empty pipeline"}),"\n",(0,r.jsx)(n.pre,{children:(0,r.jsx)(n.code,{className:"language-bash",children:"jarvis pipeline create hermes_ior\n"})}),"\n",(0,r.jsx)(n.h3,{id:"copy-the-environment-cache-1",children:"Copy the environment cache"}),"\n",(0,r.jsx)(n.pre,{children:(0,r.jsx)(n.code,{className:"language-bash",children:"jarvis pipeline env copy hermes_ior_env\n"})}),"\n",(0,r.jsx)(n.h3,{id:"set-the-active-hostfile-1",children:"Set the active hostfile"}),"\n",(0,r.jsx)(n.pre,{children:(0,r.jsx)(n.code,{className:"language-bash",children:"jarvis hostfile set /path/to/hostfile\n"})}),"\n",(0,r.jsx)(n.h3,{id:"add-hermes-runtime-1",children:"Add Hermes runtime"}),"\n",(0,r.jsx)(n.pre,{children:(0,r.jsx)(n.code,{className:"language-bash",children:"jarvis pipeline append hermes_run\njarvis pkg configure hermes_run \\\nsleep=5 \\\ninclude=${HOME}/ior_data\n"})}),"\n",(0,r.jsxs)(n.p,{children:["This will ensure that if a Hermes interceptor is used, it will intercept\nall paths in ",(0,r.jsx)(n.code,{children:"${HOME}/ior_data"}),"."]}),"\n",(0,r.jsx)(n.h3,{id:"add-hermes-mpi-io-interceptor",children:"Add Hermes MPI-IO interceptor"}),"\n",(0,r.jsx)(n.pre,{children:(0,r.jsx)(n.code,{className:"language-bash",children:"jarvis pipeline append hermes_api\njarvis pkg configure hermes_api +mpi\n"})}),"\n",(0,r.jsx)(n.p,{children:"This will automatically locate the interceptor library by\ntraversing various environment variables. This will ensure\nthat MPI-IO is intercepted by Hermes."}),"\n",(0,r.jsx)(n.h3,{id:"add-ior",children:"Add IOR"}),"\n",(0,r.jsx)(n.pre,{children:(0,r.jsx)(n.code,{className:"language-bash",children:"jarvis pipeline append ior\njarvis pkg configure ior \\\nxfer=1m \\\nblock=1g \\\nnprocs=64 \\\nppn=16 \\\n+write +read \\\nout=${HOME}/ior_data/ior.bin \\\napi=mpiio\n"})}),"\n",(0,r.jsxs)(n.p,{children:["This IOR will perform 1GB of I/O per-process (block) in units of 1m (xfer) and\nproduce a single output file ",(0,r.jsx)(n.code,{children:"${HOME}/ior_data/ior.bin"}),"(out) using MPI-IO\n(api). The total amount of I/O performed will be 64GB spread across 4 nodes."]}),"\n",(0,r.jsx)(n.h3,{id:"run-the-pipeline",children:"Run the Pipeline"}),"\n",(0,r.jsx)(n.p,{children:"To run the pipeline:"}),"\n",(0,r.jsx)(n.pre,{children:(0,r.jsx)(n.code,{className:"language-bash",children:"jarvis pipeline run\n"})}),"\n",(0,r.jsx)(n.p,{children:"This will launch Hermes, execute IOR, and then stop Hermes. It is equivalent\nto:"}),"\n",(0,r.jsx)(n.pre,{children:(0,r.jsx)(n.code,{className:"language-bash",children:"jarvis pipeline start\njarvis pipeline stop\n"})}),"\n",(0,r.jsx)(n.h3,{id:"cleanup-1",children:"Cleanup"}),"\n",(0,r.jsx)(n.p,{children:"The following will delete intermediate data generated by Hermes + IOR:"}),"\n",(0,r.jsx)(n.pre,{children:(0,r.jsx)(n.code,{className:"language-bash",children:"jarvis pipeline clean\n"})}),"\n",(0,r.jsx)(n.h2,{id:"why-is-my-application-hanging",children:"Why is my application hanging?"}),"\n",(0,r.jsx)(n.h3,{id:"resource-graph-misconfiguration",children:"Resource Graph Misconfiguration"}),"\n",(0,r.jsx)(n.p,{children:"Commonly, the cause is a misconfiguration in the resource graph, specifically\nwith the network section. Make sure that the domain, provider, and fabric\nare valid. To view the Hermes configuration to see which network was selected\nfrom your resource graph, you can run:"}),"\n",(0,r.jsx)(n.pre,{children:(0,r.jsx)(n.code,{className:"language-bash",children:"cat $(jarvis path)/hermes_run/hermes_server.yaml\n"})}),"\n",(0,r.jsx)(n.h3,{id:"dependency-problems",children:"Dependency Problems"}),"\n",(0,r.jsx)(n.p,{children:"If you are using the MPI-IO interceptor, make sure that the MPI that Hermes\ncompiled with is equivalent to the one your application was compiled with.\nYou may have multiple versions of MPI installed and if you didn't specify\nwhich one when installing Hermes and your program -- they may be different."}),"\n",(0,r.jsx)(n.p,{children:"If you are using the VFD, make sure the VFD was compiled with the same HDF5\nas the application."}),"\n",(0,r.jsx)(n.p,{children:"To view the dependencies of your installed Hermes, run:"}),"\n",(0,r.jsx)(n.pre,{children:(0,r.jsx)(n.code,{children:"spack find -c -d hermes\n"})}),"\n",(0,r.jsx)(n.h3,{id:"machine-misconfiguration",children:"Machine Misconfiguration"}),"\n",(0,r.jsx)(n.p,{children:"We have found certain instances where using semantic hostnames in the hostfile\nhas resulted in incorrect behavior. If the machine is misconfigured, it is\npossible that a hostname maps to a different network domain on different nodes.\nTo verify this, you can try using exact IP addresses in your hostfile."}),"\n",(0,r.jsxs)(n.p,{children:["To view your machine's IP addresses, you can run\n",(0,r.jsx)(n.code,{children:"ip addr show"})," or ",(0,r.jsx)(n.code,{children:"fi_info | grep fabric"})]}),"\n",(0,r.jsx)(n.h3,{id:"permissions-problems",children:"Permissions Problems"}),"\n",(0,r.jsx)(n.p,{children:"If you cannot SSH between machines or if your known_hosts file is outdated,\nit is possible that Hermes will fail to launch due to permissions problems\non the network. Make sure that you can SSH between machines without error."})]})}function c(e={}){const{wrapper:n}={...(0,s.a)(),...e.components};return n?(0,r.jsx)(n,{...e,children:(0,r.jsx)(d,{...e})}):d(e)}},1151:(e,n,i)=>{i.d(n,{Z:()=>t,a:()=>l});var r=i(7294);const s={},a=r.createContext(s);function l(e){const n=r.useContext(a);return r.useMemo((function(){return"function"==typeof e?e(n):{...n,...e}}),[n,e])}function t(e){let n;return n=e.disableParentContext?"function"==typeof e.components?e.components(s):e.components||s:l(e.components),r.createElement(a.Provider,{value:n},e.children)}}}]);
\ No newline at end of file
diff --git a/assets/js/1b2dbbfc.bcce8997.js b/assets/js/1b2dbbfc.bcce8997.js
deleted file mode 100644
index 16c79f9d..00000000
--- a/assets/js/1b2dbbfc.bcce8997.js
+++ /dev/null
@@ -1 +0,0 @@
-"use strict";(self.webpackChunkgrc=self.webpackChunkgrc||[]).push([[5378],{4391:(e,t,n)=>{n.r(t),n.d(t,{assets:()=>o,contentTitle:()=>r,default:()=>c,frontMatter:()=>a,metadata:()=>d,toc:()=>l});var s=n(5893),i=n(1151);const a={},r="Distributed Metadata",d={id:"hermes/components/distributed-metadata",title:"Distributed Metadata",description:"Metadata is stored in a distributed hash map. In each Hermes Daemon, we",source:"@site/docs/03-hermes/06-components/08-distributed-metadata.md",sourceDirName:"03-hermes/06-components",slug:"/hermes/components/distributed-metadata",permalink:"/docs/hermes/components/distributed-metadata",draft:!1,unlisted:!1,tags:[],version:"current",sidebarPosition:8,frontMatter:{},sidebar:"tutorialSidebar",previous:{title:"Runtime",permalink:"/docs/hermes/components/runtime"},next:{title:"Prefetcher",permalink:"/docs/hermes/components/prefetcher"}},o={},l=[{value:"User View",id:"user-view",level:2},{value:"System View",id:"system-view",level:2},{value:"UniqueId",id:"uniqueid",level:2},{value:"Storage Method",id:"storage-method",level:2},{value:"Maps and ID Lists",id:"maps-and-id-lists",level:2},{value:"Pros",id:"pros",level:3},{value:"Cons",id:"cons",level:3},{value:"Walkthrough of <code>Bucket.Put()</code>",id:"walkthrough-of-bucketput",level:2},{value:"Walkthrough of <code>Bucket.Get()</code>",id:"walkthrough-of-bucketget",level:2},{value:"Limits",id:"limits",level:2}];function h(e){const t={code:"code",h1:"h1",h2:"h2",h3:"h3",li:"li",p:"p",strong:"strong",ul:"ul",...(0,i.a)(),...e.components};return(0,s.jsxs)(s.Fragment,{children:[(0,s.jsx)(t.h1,{id:"distributed-metadata",children:"Distributed Metadata"}),"\n",(0,s.jsxs)(t.p,{children:["Metadata is stored in a distributed hash map. In each Hermes Daemon, we\ninitialize an ",(0,s.jsx)(t.code,{children:"hipc::unordered_map"}),". The main metadata structures we store\nare as follows: Tag Map (note, Buckets are represented as Tags), Blob Map,\nand Trait Map. These maps typically map an integer ID to an\ninformation structure. For example, the Blob Map maps a ",(0,s.jsx)(t.code,{children:"BlobId"})," (a 96-bit int)\nto a ",(0,s.jsx)(t.code,{children:"BlobInfo"})," struct. In addition, we have separate maps for mapping semantic\nstrings to integer IDs. For example, we have a map from a ",(0,s.jsx)(t.code,{children:"hipc::string"})," to\na ",(0,s.jsx)(t.code,{children:"BlobId"}),"."]}),"\n",(0,s.jsx)(t.p,{children:"At this time, metadata is not replicated on nodes and we assume that metadata\ndoesn't grow so large that it exceeds the bounds of main memory."}),"\n",(0,s.jsx)(t.h2,{id:"user-view",children:"User View"}),"\n",(0,s.jsx)(t.p,{children:"Metadata (e.g., Blobs and Tags) can be given semantic names using hipc::strings\nor std::strings. hipc::string is what is eventually stored in Hermes, since it's\ncompatible with shared memory."}),"\n",(0,s.jsx)(t.h2,{id:"system-view",children:"System View"}),"\n",(0,s.jsx)(t.p,{children:"User primitives are referred to by unsigned 96-bit integers (IDs)."}),"\n",(0,s.jsx)(t.p,{children:"Each ID encodes the data it needs to access its metadata."}),"\n",(0,s.jsx)(t.h2,{id:"uniqueid",children:"UniqueId"}),"\n",(0,s.jsx)(t.p,{children:"TagIds, BlobIds, and TraitIds all are instances of a UniqueId. UniqueIds are\nrepresented as follows:"}),"\n",(0,s.jsxs)(t.ul,{children:["\n",(0,s.jsx)(t.li,{children:"Node ID: The identifier of the node the metadata is on (32-bit)"}),"\n",(0,s.jsx)(t.li,{children:"Unique: The unique number of the metadata object (64-bit)"}),"\n"]}),"\n",(0,s.jsx)(t.p,{children:"The unique field is a 64-bit integer which is atomically incremented every time\nthe program creates a new metadata object. 64-bit is large enough that the\nprogram should never be able to use all 2^64 combos."}),"\n",(0,s.jsx)(t.h2,{id:"storage-method",children:"Storage Method"}),"\n",(0,s.jsx)(t.h2,{id:"maps-and-id-lists",children:"Maps and ID Lists"}),"\n",(0,s.jsx)(t.p,{children:"All metadata is distributed among nodes by first hashing the key to\ndetermine the node, then hashing again to determine the slot."}),"\n",(0,s.jsx)(t.h3,{id:"pros",children:"Pros"}),"\n",(0,s.jsxs)(t.ul,{children:["\n",(0,s.jsx)(t.li,{children:"Better load balancing"}),"\n"]}),"\n",(0,s.jsx)(t.h3,{id:"cons",children:"Cons"}),"\n",(0,s.jsxs)(t.ul,{children:["\n",(0,s.jsxs)(t.li,{children:["May require extra RPC calls. Initial tests show that this\nindirection should be avoided. ",(0,s.jsx)(t.strong,{children:"TODO:"})," We need to revisit this."]}),"\n"]}),"\n",(0,s.jsxs)(t.h2,{id:"walkthrough-of-bucketput",children:["Walkthrough of ",(0,s.jsx)(t.code,{children:"Bucket.Put()"})]}),"\n",(0,s.jsxs)(t.p,{children:["1. Create a new ",(0,s.jsx)(t.code,{children:"BlobID"}),". The ID's node index (top 32 bits) is created\nby hashing the blob name, and the ID's offset to a list of ",(0,s.jsx)(t.code,{children:"BufferID"}),"s\n(bottom 32 bits) is allocated from the MDM shared memory segment on the\ntarget node."]}),"\n",(0,s.jsxs)(t.p,{children:["2. Add the new ",(0,s.jsx)(t.code,{children:"BlobID"})," to the ",(0,s.jsx)(t.strong,{children:"IdMap"}),". This could be local, or an\nRPC."]}),"\n",(0,s.jsxs)(t.p,{children:["3. Add the ",(0,s.jsx)(t.code,{children:"BlobID"})," to the ",(0,s.jsx)(t.code,{children:"Bucket"}),"'s list of blobs."]}),"\n",(0,s.jsxs)(t.h2,{id:"walkthrough-of-bucketget",children:["Walkthrough of ",(0,s.jsx)(t.code,{children:"Bucket.Get()"})]}),"\n",(0,s.jsxs)(t.p,{children:["1. Hash the blob name to get the ",(0,s.jsx)(t.code,{children:"BlobID"}),"."]}),"\n",(0,s.jsxs)(t.p,{children:["2. Get the list of ",(0,s.jsx)(t.code,{children:"BufferID"}),"s from the ",(0,s.jsx)(t.code,{children:"BlobID"}),"."]}),"\n",(0,s.jsxs)(t.p,{children:["3. Read each ",(0,s.jsx)(t.code,{children:"BufferID"}),"'s data into a user buffer."]}),"\n",(0,s.jsx)(t.h2,{id:"limits",children:"Limits"}),"\n",(0,s.jsx)(t.p,{children:"There can be a total of 2^64 unique metadata objects. I.e., there can be\na total of 2^64 Tags, Buckets, and Traits."})]})}function c(e={}){const{wrapper:t}={...(0,i.a)(),...e.components};return t?(0,s.jsx)(t,{...e,children:(0,s.jsx)(h,{...e})}):h(e)}},1151:(e,t,n)=>{n.d(t,{Z:()=>d,a:()=>r});var s=n(7294);const i={},a=s.createContext(i);function r(e){const t=s.useContext(a);return s.useMemo((function(){return"function"==typeof e?e(t):{...t,...e}}),[t,e])}function d(e){let t;return t=e.disableParentContext?"function"==typeof e.components?e.components(i):e.components||i:r(e.components),s.createElement(a.Provider,{value:t},e.children)}}}]);
\ No newline at end of file
diff --git a/assets/js/3d9099ed.785c61b8.js b/assets/js/219da0fd.53e7a999.js
similarity index 96%
rename from assets/js/3d9099ed.785c61b8.js
rename to assets/js/219da0fd.53e7a999.js
index 74f468d0..82d3149b 100644
--- a/assets/js/3d9099ed.785c61b8.js
+++ b/assets/js/219da0fd.53e7a999.js
@@ -1 +1 @@
-"use strict";(self.webpackChunkgrc=self.webpackChunkgrc||[]).push([[5592],{9599:(e,t,r)=>{r.r(t),r.d(t,{assets:()=>c,contentTitle:()=>o,default:()=>d,frontMatter:()=>a,metadata:()=>s,toc:()=>h});var n=r(5893),i=r(1151);const a={},o="Prefetcher",s={id:"hermes/components/prefetcher",title:"Prefetcher",description:"The objective of the Prefetcher is to promote and demote content which is",source:"@site/docs/03-hermes/06-components/09-prefetcher.md",sourceDirName:"03-hermes/06-components",slug:"/hermes/components/prefetcher",permalink:"/docs/hermes/components/prefetcher",draft:!1,unlisted:!1,tags:[],version:"current",sidebarPosition:9,frontMatter:{},sidebar:"tutorialSidebar",previous:{title:"Distributed Metadata",permalink:"/docs/hermes/components/distributed-metadata"},next:{title:"Examples",permalink:"/docs/hermes/components/examples"}},c={},h=[{value:"Usage (Configuration)",id:"usage-configuration",level:2},{value:"Usage (C++)",id:"usage-c",level:2},{value:"Application Tracing",id:"application-tracing",level:2},{value:"Apriori Prefetcher",id:"apriori-prefetcher",level:2},{value:"Future Work",id:"future-work",level:2}];function l(e){const t={code:"code",h1:"h1",h2:"h2",li:"li",ol:"ol",p:"p",pre:"pre",strong:"strong",...(0,i.a)(),...e.components};return(0,n.jsxs)(n.Fragment,{children:[(0,n.jsx)(t.h1,{id:"prefetcher",children:"Prefetcher"}),"\n",(0,n.jsxs)(t.p,{children:["The objective of the ",(0,n.jsx)(t.strong,{children:"Prefetcher"})," is to promote and demote content which is\nexpected to be used in the near future or frequently. The prefetcher only\napplies to data which is already staged within Hermes. In order to activate\nprefetching, a Prefetcher Trait can be attached to a Tag (or Bucket)\nto indicate that prefetching should be enabled and which kind of prefetching\nshould be applied."]}),"\n",(0,n.jsx)(t.h2,{id:"usage-configuration",children:"Usage (Configuration)"}),"\n",(0,n.jsx)(t.p,{children:"To enable prefetching with configuration."}),"\n",(0,n.jsx)(t.h2,{id:"usage-c",children:"Usage (C++)"}),"\n",(0,n.jsx)(t.p,{children:"To enable prefetching, attach the Prefetcher trait to a tag (e.g., Bucket).\nIn this example, we attach the PrefetcherTrait with the kApriori prefetcher\nconstant to the SimulationBucket, which represents the data for\nthe simulation workload."}),"\n",(0,n.jsx)(t.pre,{children:(0,n.jsx)(t.code,{className:"language-cpp",children:'auto bkt = HERMES->GetBucket("SimulationBucket");\nTagId bkt_id = bkt.GetId();\nhermes::TraitId apriori_trait =\n    HERMES->RegisterTrait<hermes::PrefetcherTrait>(\n      "apriori", hermes::PrefetcherType::kApriori);\nTraitId trait_id = HERMES->GetTraitId("apriori");\nbkt.AttachTrait(apriori_trait);\n'})}),"\n",(0,n.jsx)(t.h2,{id:"application-tracing",children:"Application Tracing"}),"\n",(0,n.jsx)(t.p,{children:"In order to support prefetching, we implement a tracing system within Hermes.\nThe tracer is called for every Put and Get operation within Hermes. It stores\nthe information called for the Put or Get internally within a multiple-producer\nsingle-consumer (MPSC) shared-memory queue, which is asynchronously digested\nby the prefetcher."}),"\n",(0,n.jsx)(t.p,{children:"The tracer collects the following information:"}),"\n",(0,n.jsxs)(t.ol,{children:["\n",(0,n.jsx)(t.li,{children:"Operation (Put or Get)"}),"\n",(0,n.jsx)(t.li,{children:"Blob Id"}),"\n",(0,n.jsx)(t.li,{children:"Bucket Id"}),"\n",(0,n.jsx)(t.li,{children:"Blob Size"}),"\n",(0,n.jsx)(t.li,{children:"Timestamp (from program start)"}),"\n",(0,n.jsx)(t.li,{children:"Rank (if MPI)"}),"\n"]}),"\n",(0,n.jsx)(t.p,{children:"In the binary file, we store the following information:"}),"\n",(0,n.jsxs)(t.ol,{children:["\n",(0,n.jsx)(t.li,{children:"Operation (Put or Get)"}),"\n",(0,n.jsx)(t.li,{children:"Blob Name (64-bit Hash)"}),"\n",(0,n.jsx)(t.li,{children:"Bucket Name (64-bit Hash)"}),"\n",(0,n.jsx)(t.li,{children:"Blob Size (64-bit)"}),"\n",(0,n.jsx)(t.li,{children:"Timestamp (from program start)"}),"\n",(0,n.jsx)(t.li,{children:"Rank (if MPI)"}),"\n"]}),"\n",(0,n.jsx)(t.p,{children:"The trace can be analyzed live within the prefetcher or be stored in a\nbinary log (created using Cereal) and analyzed offline."}),"\n",(0,n.jsx)(t.h2,{id:"apriori-prefetcher",children:"Apriori Prefetcher"}),"\n",(0,n.jsx)(t.p,{children:"Currently, we implement the apriori prefetcher. Many applications exhibit\ncompletely deterministic I/O patterns. Deep Learning applications for example\nwill have the same I/O pattern when the randomness seed is fixed and all other\nparamters remain the same. Many HPC workloads are executed repeatedly with the\nsame parameters for reasons such as reproducability. This prefetcher assumes\nthat the user will supply a schema with the exact momements of when to\npromote and demote content."}),"\n",(0,n.jsx)(t.h2,{id:"future-work",children:"Future Work"}),"\n",(0,n.jsxs)(t.ol,{children:["\n",(0,n.jsx)(t.li,{children:"Live Prefetcher: Use some sort of short-term memory models to analyze I/O\nstatistics generated live."}),"\n"]})]})}function d(e={}){const{wrapper:t}={...(0,i.a)(),...e.components};return t?(0,n.jsx)(t,{...e,children:(0,n.jsx)(l,{...e})}):l(e)}},1151:(e,t,r)=>{r.d(t,{Z:()=>s,a:()=>o});var n=r(7294);const i={},a=n.createContext(i);function o(e){const t=n.useContext(a);return n.useMemo((function(){return"function"==typeof e?e(t):{...t,...e}}),[t,e])}function s(e){let t;return t=e.disableParentContext?"function"==typeof e.components?e.components(i):e.components||i:o(e.components),n.createElement(a.Provider,{value:t},e.children)}}}]);
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+"use strict";(self.webpackChunkgrc=self.webpackChunkgrc||[]).push([[8791],{8278:(e,t,r)=>{r.r(t),r.d(t,{assets:()=>c,contentTitle:()=>o,default:()=>d,frontMatter:()=>a,metadata:()=>s,toc:()=>h});var n=r(5893),i=r(1151);const a={},o="Prefetcher",s={id:"hermes/components/prefetcher",title:"Prefetcher",description:"The objective of the Prefetcher is to promote and demote content which is",source:"@site/docs/03-hermes/08-components/09-prefetcher.md",sourceDirName:"03-hermes/08-components",slug:"/hermes/components/prefetcher",permalink:"/docs/hermes/components/prefetcher",draft:!1,unlisted:!1,tags:[],version:"current",sidebarPosition:9,frontMatter:{},sidebar:"tutorialSidebar",previous:{title:"Distributed Metadata",permalink:"/docs/hermes/components/distributed-metadata"},next:{title:"Examples",permalink:"/docs/hermes/components/examples"}},c={},h=[{value:"Usage (Configuration)",id:"usage-configuration",level:2},{value:"Usage (C++)",id:"usage-c",level:2},{value:"Application Tracing",id:"application-tracing",level:2},{value:"Apriori Prefetcher",id:"apriori-prefetcher",level:2},{value:"Future Work",id:"future-work",level:2}];function l(e){const t={code:"code",h1:"h1",h2:"h2",li:"li",ol:"ol",p:"p",pre:"pre",strong:"strong",...(0,i.a)(),...e.components};return(0,n.jsxs)(n.Fragment,{children:[(0,n.jsx)(t.h1,{id:"prefetcher",children:"Prefetcher"}),"\n",(0,n.jsxs)(t.p,{children:["The objective of the ",(0,n.jsx)(t.strong,{children:"Prefetcher"})," is to promote and demote content which is\nexpected to be used in the near future or frequently. The prefetcher only\napplies to data which is already staged within Hermes. In order to activate\nprefetching, a Prefetcher Trait can be attached to a Tag (or Bucket)\nto indicate that prefetching should be enabled and which kind of prefetching\nshould be applied."]}),"\n",(0,n.jsx)(t.h2,{id:"usage-configuration",children:"Usage (Configuration)"}),"\n",(0,n.jsx)(t.p,{children:"To enable prefetching with configuration."}),"\n",(0,n.jsx)(t.h2,{id:"usage-c",children:"Usage (C++)"}),"\n",(0,n.jsx)(t.p,{children:"To enable prefetching, attach the Prefetcher trait to a tag (e.g., Bucket).\nIn this example, we attach the PrefetcherTrait with the kApriori prefetcher\nconstant to the SimulationBucket, which represents the data for\nthe simulation workload."}),"\n",(0,n.jsx)(t.pre,{children:(0,n.jsx)(t.code,{className:"language-cpp",children:'auto bkt = HERMES->GetBucket("SimulationBucket");\nTagId bkt_id = bkt.GetId();\nhermes::TraitId apriori_trait =\n    HERMES->RegisterTrait<hermes::PrefetcherTrait>(\n      "apriori", hermes::PrefetcherType::kApriori);\nTraitId trait_id = HERMES->GetTraitId("apriori");\nbkt.AttachTrait(apriori_trait);\n'})}),"\n",(0,n.jsx)(t.h2,{id:"application-tracing",children:"Application Tracing"}),"\n",(0,n.jsx)(t.p,{children:"In order to support prefetching, we implement a tracing system within Hermes.\nThe tracer is called for every Put and Get operation within Hermes. It stores\nthe information called for the Put or Get internally within a multiple-producer\nsingle-consumer (MPSC) shared-memory queue, which is asynchronously digested\nby the prefetcher."}),"\n",(0,n.jsx)(t.p,{children:"The tracer collects the following information:"}),"\n",(0,n.jsxs)(t.ol,{children:["\n",(0,n.jsx)(t.li,{children:"Operation (Put or Get)"}),"\n",(0,n.jsx)(t.li,{children:"Blob Id"}),"\n",(0,n.jsx)(t.li,{children:"Bucket Id"}),"\n",(0,n.jsx)(t.li,{children:"Blob Size"}),"\n",(0,n.jsx)(t.li,{children:"Timestamp (from program start)"}),"\n",(0,n.jsx)(t.li,{children:"Rank (if MPI)"}),"\n"]}),"\n",(0,n.jsx)(t.p,{children:"In the binary file, we store the following information:"}),"\n",(0,n.jsxs)(t.ol,{children:["\n",(0,n.jsx)(t.li,{children:"Operation (Put or Get)"}),"\n",(0,n.jsx)(t.li,{children:"Blob Name (64-bit Hash)"}),"\n",(0,n.jsx)(t.li,{children:"Bucket Name (64-bit Hash)"}),"\n",(0,n.jsx)(t.li,{children:"Blob Size (64-bit)"}),"\n",(0,n.jsx)(t.li,{children:"Timestamp (from program start)"}),"\n",(0,n.jsx)(t.li,{children:"Rank (if MPI)"}),"\n"]}),"\n",(0,n.jsx)(t.p,{children:"The trace can be analyzed live within the prefetcher or be stored in a\nbinary log (created using Cereal) and analyzed offline."}),"\n",(0,n.jsx)(t.h2,{id:"apriori-prefetcher",children:"Apriori Prefetcher"}),"\n",(0,n.jsx)(t.p,{children:"Currently, we implement the apriori prefetcher. Many applications exhibit\ncompletely deterministic I/O patterns. Deep Learning applications for example\nwill have the same I/O pattern when the randomness seed is fixed and all other\nparamters remain the same. Many HPC workloads are executed repeatedly with the\nsame parameters for reasons such as reproducability. This prefetcher assumes\nthat the user will supply a schema with the exact momements of when to\npromote and demote content."}),"\n",(0,n.jsx)(t.h2,{id:"future-work",children:"Future Work"}),"\n",(0,n.jsxs)(t.ol,{children:["\n",(0,n.jsx)(t.li,{children:"Live Prefetcher: Use some sort of short-term memory models to analyze I/O\nstatistics generated live."}),"\n"]})]})}function d(e={}){const{wrapper:t}={...(0,i.a)(),...e.components};return t?(0,n.jsx)(t,{...e,children:(0,n.jsx)(l,{...e})}):l(e)}},1151:(e,t,r)=>{r.d(t,{Z:()=>s,a:()=>o});var n=r(7294);const i={},a=n.createContext(i);function o(e){const t=n.useContext(a);return n.useMemo((function(){return"function"==typeof e?e(t):{...t,...e}}),[t,e])}function s(e){let t;return t=e.disableParentContext?"function"==typeof e.components?e.components(i):e.components||i:o(e.components),n.createElement(a.Provider,{value:t},e.children)}}}]);
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@@ -0,0 +1 @@
+"use strict";(self.webpackChunkgrc=self.webpackChunkgrc||[]).push([[2777],{1421:(e,n,i)=>{i.r(n),i.d(n,{assets:()=>l,contentTitle:()=>t,default:()=>d,frontMatter:()=>r,metadata:()=>o,toc:()=>c});var s=i(5893),a=i(1151);const r={},t="Configuration",o={id:"hermes/configuration",title:"Configuration",description:"Before deploying an application, you need to configure Hermes. Hermes has two types of configurations: server configuration and client configuration. They",source:"@site/docs/03-hermes/05-configuration.md",sourceDirName:"03-hermes",slug:"/hermes/configuration",permalink:"/docs/hermes/configuration",draft:!1,unlisted:!1,tags:[],version:"current",sidebarPosition:5,frontMatter:{},sidebar:"tutorialSidebar",previous:{title:"Deploying Hermes",permalink:"/docs/hermes/deploying-hermes"},next:{title:"Adapters",permalink:"/docs/hermes/adapters"}},l={},c=[{value:"Server Configuration",id:"server-configuration",level:2},{value:"Defining Storage Targets",id:"defining-storage-targets",level:3},{value:"Device Names",id:"device-names",level:3},{value:"<code>mount_point</code>",id:"mount_point",level:3},{value:"<code>capacity</code>",id:"capacity",level:3},{value:"<code>block_size</code>",id:"block_size",level:3},{value:"<code>slab_sizes</code>",id:"slab_sizes",level:3},{value:"<code>bandwidth</code>, <code>latency</code>",id:"bandwidth-latency",level:3},{value:"<code>is_shared_device</code>",id:"is_shared_device",level:3},{value:"<code>borg_capacity_thresh</code>",id:"borg_capacity_thresh",level:3},{value:"Buffer Organizer (BORG)",id:"buffer-organizer-borg",level:2},{value:"Prefetcher",id:"prefetcher",level:2},{value:"Traits",id:"traits",level:2},{value:"Shared Memory",id:"shared-memory",level:2},{value:"System View State",id:"system-view-state",level:2},{value:"Bounding Memory Utilization",id:"bounding-memory-utilization",level:2},{value:"Using RAM as a buffering device",id:"using-ram-as-a-buffering-device",level:3},{value:"Hashtables for storing blobs + buckets",id:"hashtables-for-storing-blobs--buckets",level:3},{value:"Bounding Non-Buffering Tasks",id:"bounding-non-buffering-tasks",level:3},{value:"Calculating Total Amount of Memory",id:"calculating-total-amount-of-memory",level:3},{value:"Client Configuration",id:"client-configuration",level:2},{value:"Path Inclusion / Exclusion",id:"path-inclusion--exclusion",level:3},{value:"Adapter Mode",id:"adapter-mode",level:3},{value:"File Page Size",id:"file-page-size",level:3},{value:"Flushing Mode",id:"flushing-mode",level:3},{value:"Adapter Config",id:"adapter-config",level:3},{value:"Provided Configurations",id:"provided-configurations",level:2},{value:"How To Avoid Repeating the Default Configurations",id:"how-to-avoid-repeating-the-default-configurations",level:2}];function h(e){const n={a:"a",code:"code",h1:"h1",h2:"h2",h3:"h3",li:"li",ol:"ol",p:"p",pre:"pre",strong:"strong",ul:"ul",...(0,a.a)(),...e.components};return(0,s.jsxs)(s.Fragment,{children:[(0,s.jsx)(n.h1,{id:"configuration",children:"Configuration"}),"\n",(0,s.jsx)(n.p,{children:"Before deploying an application, you need to configure Hermes. Hermes has two types of configurations: server configuration and client configuration. They\nare represented as YAML files. We will describe the contents of these YAML\nfiles here."}),"\n",(0,s.jsx)(n.h2,{id:"server-configuration",children:"Server Configuration"}),"\n",(0,s.jsx)(n.p,{children:"The server configuration is primarily used to initialize the daemon.\nClients also parse the server config to get the basic information needed\nto connect to the Hermes daemons."}),"\n",(0,s.jsx)(n.p,{children:"Technically, the server configuration\nis optional. However, the default configuration is more for just setting\nthings up. You do have to configure things like mount points manually\nat this time."}),"\n",(0,s.jsxs)(n.p,{children:["The default server configuration can be found\n",(0,s.jsx)(n.a,{href:"https://github.com/HDFGroup/hermes/blob/master/config/hermes_server_default.yaml",children:"here"}),"."]}),"\n",(0,s.jsx)(n.h3,{id:"defining-storage-targets",children:"Defining Storage Targets"}),"\n",(0,s.jsx)(n.p,{children:'The most important property in the configuration is defining where Hermes\nbuffers data. This is done under the "devices" entry.\nIn the default configuration, we have the following:'}),"\n",(0,s.jsx)(n.pre,{children:(0,s.jsx)(n.code,{className:"language-yaml",children:'devices:\n  ram:\n    mount_point: ""\n    capacity: 50MB\n    block_size: 4KB\n    slab_sizes: [ 4KB, 16KB, 64KB, 1MB ]\n    bandwidth: 6000MBps\n    latency: 15us\n    is_shared_device: false\n    borg_capacity_thresh: [0.0, 1.0]\n\n  nvme:\n    mount_point: "./"\n    capacity: 100MB\n    block_size: 4KB\n    slab_sizes: [ 4KB, 16KB, 64KB, 1MB ]\n    bandwidth: 1GBps\n    latency: 600us\n    is_shared_device: false\n    borg_capacity_thresh: [ 0.0, 1.0 ]\n\n   ssd:\n     mount_point: "./"\n     capacity: 100MB\n     block_size: 4KB\n     slab_sizes: [ 4KB, 16KB, 64KB, 1MB ]\n     bandwidth: 500MBps\n     latency: 1200us\n     is_shared_device: false\n     borg_capacity_thresh: [ 0.0, 1.0 ]\n\n   pfs:\n     mount_point: "./"\n     capacity: 100MB\n     block_size: 64KB\n     slab_sizes: [ 4KB, 16KB, 64KB, 1MB ]\n     bandwidth: 100MBps\n     latency: 200ms\n     is_shared_device: true\n     borg_capacity_thresh: [ 0.0, 1.0 ]\n'})}),"\n",(0,s.jsx)(n.h3,{id:"device-names",children:"Device Names"}),"\n",(0,s.jsx)(n.p,{children:"In the above configuration, we have four unique devices: ram, nvme, ssd,\nand pfs. These names are for the ease of the user, and have no meaning\nto Hermes. In other words, these names can be anything. The following\nconfiguration would be effectively equivalent to the one above:"}),"\n",(0,s.jsx)(n.pre,{children:(0,s.jsx)(n.code,{className:"language-yaml",children:'devices:\n  dev1:\n    mount_point: ""\n    capacity: 50MB\n    ...\n\n  dev2:\n    mount_point: "./"\n    capacity: 100MB\n    ...\n\n   dev3:\n     mount_point: "./"\n     capacity: 100MB\n     ...\n\n   dev4:\n     mount_point: "./"\n     capacity: 100MB\n     ...\n'})}),"\n",(0,s.jsx)(n.h3,{id:"mount_point",children:(0,s.jsx)(n.code,{children:"mount_point"})}),"\n",(0,s.jsx)(n.p,{children:"The mount point parameter is used to indicate which directory Hermes\nshould place data in, if the device has a filesystem."}),"\n",(0,s.jsx)(n.pre,{children:(0,s.jsx)(n.code,{className:"language-yaml",children:'ram:\n  mount_point: ""\n\nnvme:\n  mount_point: "./"\n'})}),"\n",(0,s.jsx)(n.p,{children:'In the default config, for example, we look at ram and nvme. nvme is mounted\nin the current working directory. Hermes will create a file called\n"./slab_nvme". It will create equivalent files for hdd, ssd, and pfs.'}),"\n",(0,s.jsx)(n.p,{children:'For ram, we set the mount point to "". This indicates that the device\nhas no mount point.'}),"\n",(0,s.jsx)(n.h3,{id:"capacity",children:(0,s.jsx)(n.code,{children:"capacity"})}),"\n",(0,s.jsx)(n.p,{children:'This variable implies the amount of capacity to use for buffering.\nThis parameter is a "size variable", which supports various suffixes:'}),"\n",(0,s.jsx)(n.pre,{children:(0,s.jsx)(n.code,{className:"language-yaml",children:"capacity: 100    # 100 bytes\ncapacity: 100k   # 100 KB\ncapacity: 100kb  # 100 KB\ncapacity: 100KB  # 100 KB\ncapacity: 100m   # 100 MB\ncapacity: 100mb  # 100 MB\ncapacity: 100MB  # 100 MB\ncapacity: 100g   # 100 GB\ncapacity: 100gb  # 100 GB\ncapacity: 100GB  # 100 GB\ncapacity: 100T   # 100 TB\ncapacity: 100tb  # 100 TB\ncapacity: 100TB  # 100 TB\n"})}),"\n",(0,s.jsx)(n.p,{children:"There cannot be spaces between the number and the suffix. For example,"}),"\n",(0,s.jsx)(n.pre,{children:(0,s.jsx)(n.code,{className:"language-yaml",children:"capacity: 100 tb #NOT VALID\n"})}),"\n",(0,s.jsx)(n.h3,{id:"block_size",children:(0,s.jsx)(n.code,{children:"block_size"})}),"\n",(0,s.jsx)(n.pre,{children:(0,s.jsx)(n.code,{className:"language-yaml",children:"block_size: 64KB\n"})}),"\n",(0,s.jsx)(n.p,{children:"This is the amount of I/O that the physical block device supports.\nRAM, for example, generally sees data in units of 4KB because this is\nthe page size of the system. HDDs, NVMes, and SSDs generally have block\nsizes of 4KB as well. Generally, this parameter doesn't need to be changed."}),"\n",(0,s.jsx)(n.h3,{id:"slab_sizes",children:(0,s.jsx)(n.code,{children:"slab_sizes"})}),"\n",(0,s.jsx)(n.pre,{children:(0,s.jsx)(n.code,{className:"language-yaml",children:"slab_sizes: [4KB, 16KB, 64KB, 1MB]\n"})}),"\n",(0,s.jsx)(n.p,{children:"This parameter is important to performance and resource utilization. The slab sizes dictates the I/O patterns produced in Hermes. When Hermes wants to\nwrite a 16MB blob, how does this blob actually get mapped to storage?\nIt gets fragmented into buffers, where the size of a buffer is equivalent\nto the best-fitting slab size."}),"\n",(0,s.jsxs)(n.ul,{children:["\n",(0,s.jsx)(n.li,{children:"A 16MB blob will be placed as 16 1MB buffers."}),"\n",(0,s.jsx)(n.li,{children:"A 6KB blob will be placed as 2 4KB buffers"}),"\n",(0,s.jsx)(n.li,{children:"A 33KB blob will be placed as a single 64KB buffer"}),"\n"]}),"\n",(0,s.jsx)(n.p,{children:"You should decide the buffer sizes based on the characteristics of your\nprogram. If unsure, the default slab sizes generally have worked well\nin the workloads we've tried. However, if you're finding Hermes runs\nout of space, this parameter may be the culprit."}),"\n",(0,s.jsxs)(n.h3,{id:"bandwidth-latency",children:[(0,s.jsx)(n.code,{children:"bandwidth"}),", ",(0,s.jsx)(n.code,{children:"latency"})]}),"\n",(0,s.jsx)(n.pre,{children:(0,s.jsx)(n.code,{className:"language-yaml",children:"bandwidth: 1GBps\nlatency: 600us\n"})}),"\n",(0,s.jsx)(n.p,{children:"These are properties of the storage device which are used by data placement\nalgorithms to decide where to buffer data."}),"\n",(0,s.jsxs)(n.ul,{children:["\n",(0,s.jsx)(n.li,{children:"Acceptable suffixes for bandwidth (case doesn't matter):"}),"\n",(0,s.jsx)(n.li,{children:"Acceptable suffixes for latency (case doesn't matter): s, ms, us, ns."}),"\n"]}),"\n",(0,s.jsx)(n.h3,{id:"is_shared_device",children:(0,s.jsx)(n.code,{children:"is_shared_device"})}),"\n",(0,s.jsx)(n.pre,{children:(0,s.jsx)(n.code,{className:"language-yaml",children:"is_shared_device: true\n"})}),"\n",(0,s.jsx)(n.p,{children:"This indicates whether or not the device provides a shared view of\ndata across nodes. For example, a PFS is a shared device, whereas\na single hard drive is not a shared device. This parameter is not\nreally used at this time, but you do need to define it."}),"\n",(0,s.jsx)(n.h3,{id:"borg_capacity_thresh",children:(0,s.jsx)(n.code,{children:"borg_capacity_thresh"})}),"\n",(0,s.jsx)(n.pre,{children:(0,s.jsx)(n.code,{className:"language-yaml",children:"borg_capacity_thresh: [0.0, 1.0]\n"})}),"\n",(0,s.jsx)(n.p,{children:"This parameter is used to trigger the buffer organizer (BORG). When a\ndevice is either really low on capacity (or high on capacity) BORG\nwill be triggered to shuffle content around."}),"\n",(0,s.jsx)(n.p,{children:"The first entry indicates how much space is too little space. In this\ncase if capacity falls below 0% (i.e., never), BORG will be triggered."}),"\n",(0,s.jsx)(n.p,{children:"The second entry indicates how mcuh space is too much space. In this\ncase if capacity grows beyone 100% (i.e., never), BORG will be triggered."}),"\n",(0,s.jsx)(n.p,{children:"In other words, this example, shows how to disable BORG."}),"\n",(0,s.jsx)(n.h2,{id:"buffer-organizer-borg",children:"Buffer Organizer (BORG)"}),"\n",(0,s.jsx)(n.pre,{children:(0,s.jsx)(n.code,{className:"language-yaml",children:"buffer_organizer:\n  num_threads: 1\n  flush_period: 1024\n  blob_reorg_period: 1024\n  recency_min: 0\n  recency_max: 60\n  freq_max: 15\n  freq_min: 0\n"})}),"\n",(0,s.jsx)(n.p,{children:'The BORG contains threads for reorganizing buffers in Hermes. The number\nof threads is indicated by "num_threads". The amount of time (in ms) to\nre-scan for blobs to reorganize is given by "flush_period".'}),"\n",(0,s.jsx)(n.p,{children:"receny_max is the amount of time (in seconds) when the score of a blob\nbecomes 0. recency_min is the amount of time for the blob to have a score\nof 1."}),"\n",(0,s.jsx)(n.p,{children:"freq_max is the minimum number of times a blob needs to be accessed in the\nflushing period for the score to be equal to one. freq_min is the maximum number of times a blob can be accessed before its score becomes larger than 0."}),"\n",(0,s.jsx)(n.p,{children:"The buffer organizer is only triggered when there are space constraints\nthat need to be met at this time. If you want the BORG extremely active,\nchange the borg_capacity_thresh variable."}),"\n",(0,s.jsx)(n.h2,{id:"prefetcher",children:"Prefetcher"}),"\n",(0,s.jsx)(n.pre,{children:(0,s.jsx)(n.code,{className:"language-yaml",children:'prefetch:\n  enabled: false\n  apriori_schema_path: ""\n  epoch_ms: 50\n  is_mpi: false\n'})}),"\n",(0,s.jsx)(n.p,{children:"These parameters dictate properties of the prefetcher."}),"\n",(0,s.jsxs)(n.ul,{children:["\n",(0,s.jsxs)(n.li,{children:[(0,s.jsx)(n.strong,{children:"enabled"}),": whether to turn prefetcher on"]}),"\n",(0,s.jsxs)(n.li,{children:[(0,s.jsx)(n.strong,{children:"apriori_schema_path"}),": internally used by apriori prefetcher"]}),"\n",(0,s.jsxs)(n.li,{children:[(0,s.jsx)(n.strong,{children:"epoch_ms"}),": how often to call the prefetcher thread"]}),"\n",(0,s.jsxs)(n.li,{children:[(0,s.jsx)(n.strong,{children:"is_mpi"}),": whether the program is an MPI program so that clients\nsend their ranks to the daemon during prefetching."]}),"\n"]}),"\n",(0,s.jsx)(n.p,{children:"For now, prefetching is only available to the native API, not the adapters."}),"\n",(0,s.jsx)(n.h2,{id:"traits",children:"Traits"}),"\n",(0,s.jsx)(n.pre,{children:(0,s.jsx)(n.code,{className:"language-yaml",children:'traits:\n  - "hermes_posix_io_client"\n  - "hermes_stdio_io_client"\n  - "hermes_mpiio_io_client"\n  - "hermes_example_trait"\n  - "hermes_prefetcher_trait"\n'})}),"\n",(0,s.jsx)(n.p,{children:"The traits category lists the set of traits that Hermes searches for\nin the LD_LIBRARY_PATH and HERMES_TRAIT_PATH environment variables.\nIt will search each directory specified in those environment variables\nfor shared objects matching these names. For example, libhermes_posix_io_client.so will be searched for."}),"\n",(0,s.jsx)(n.p,{children:"Unless you are adding custom traits, this can be left as default."}),"\n",(0,s.jsx)(n.h2,{id:"shared-memory",children:"Shared Memory"}),"\n",(0,s.jsx)(n.pre,{children:(0,s.jsx)(n.code,{className:"language-yaml",children:'shmem_name: "/hermes_shm_"\n'})}),"\n",(0,s.jsx)(n.p,{children:"This is the name of the shared memory segment hermes will create. In order\nto make this unique across users (since shared memory can be used to\nshare memory across users), we append the name of the user to this key."}),"\n",(0,s.jsx)(n.p,{children:"This generally can be left as the default value."}),"\n",(0,s.jsx)(n.h2,{id:"system-view-state",children:"System View State"}),"\n",(0,s.jsx)(n.p,{children:"This parameter is unused for now, so no need to set it."}),"\n",(0,s.jsx)(n.h2,{id:"bounding-memory-utilization",children:"Bounding Memory Utilization"}),"\n",(0,s.jsx)(n.p,{children:'When running Hermes in a limited environment, ensuring that Hermes is not over-utilizing memory is necessary. It is possible to receive "Bus Error" messages due to the OS complaining that too many pages have been allocated. We find that this happens in Docker containers frequently since they have more limited memory constraints by default.'}),"\n",(0,s.jsx)(n.p,{children:"There are a few parameters which cause Hermes to utilize memory."}),"\n",(0,s.jsx)(n.h3,{id:"using-ram-as-a-buffering-device",children:"Using RAM as a buffering device"}),"\n",(0,s.jsx)(n.p,{children:"Hermes can be configured to use RAM as a buffering device."}),"\n",(0,s.jsx)(n.pre,{children:(0,s.jsx)(n.code,{className:"language-yaml",children:'devices:\n  ram:\n    mount_point: ""\n    capacity: 1g\n'})}),"\n",(0,s.jsx)(n.p,{children:"In this case, Hermes will reserve up to 1GB of space to use for buffering."}),"\n",(0,s.jsx)(n.h3,{id:"hashtables-for-storing-blobs--buckets",children:"Hashtables for storing blobs + buckets"}),"\n",(0,s.jsx)(n.p,{children:"Hermes will reserve space for hashtables for blobs, buckets, and traits.\nThese parameters can be configured as follows:"}),"\n",(0,s.jsx)(n.pre,{children:(0,s.jsx)(n.code,{className:"language-yaml",children:"mdm:\n  # This represents the number of blobs and buckets before collisions start\n  # to happen in the unordered_map tables.\n  est_blob_count: 100000\n  est_bucket_count: 100000\n  est_num_traits: 256\n"})}),"\n",(0,s.jsx)(n.p,{children:"You can set these to lower values if memory is over-utilized.\nThese values should be set to roughly the number of blobs and buckets the program creates to avoid collisions in the hashtables."}),"\n",(0,s.jsx)(n.h3,{id:"bounding-non-buffering-tasks",children:"Bounding Non-Buffering Tasks"}),"\n",(0,s.jsx)(n.p,{children:"You can set a maximum boundary on the amount of memory to use for non-buffering tasks, such as reserving space for the blob + bucket hashtables."}),"\n",(0,s.jsx)(n.pre,{children:(0,s.jsx)(n.code,{className:"language-yaml",children:"# Define the maximum amount of memory Hermes can use for non-buffering tasks.\n# This includes metadata management and memory allocations.\n# This memory will not be preallocated, so if you don't know, 0 indicates\n# any amount of memory\nmax_memory: 0g\n"})}),"\n",(0,s.jsx)(n.p,{children:"0g indicates infinity. Non-zero values can be set to put a boundary here."}),"\n",(0,s.jsx)(n.h3,{id:"calculating-total-amount-of-memory",children:"Calculating Total Amount of Memory"}),"\n",(0,s.jsx)(n.p,{children:"The total amount of memory Hermes can use before an hshm::Error or Bus Error is thrown can be calculated as follows:"}),"\n",(0,s.jsx)(n.pre,{children:(0,s.jsx)(n.code,{className:"language-bash",children:"RAM used for Buffering (3.1.7.1) + RAM used for Non-Buffering (3.1.7.3)\n"})}),"\n",(0,s.jsx)(n.h2,{id:"client-configuration",children:"Client Configuration"}),"\n",(0,s.jsxs)(n.p,{children:["The default client configuration can be found\n",(0,s.jsx)(n.a,{href:"https://github.com/HDFGroup/hermes/blob/master/config/hermes_client_default.yaml",children:"here"}),"."]}),"\n",(0,s.jsx)(n.p,{children:"The client configuration currently only contains parameters used by\nadapters."}),"\n",(0,s.jsx)(n.pre,{children:(0,s.jsx)(n.code,{className:"language-yaml",children:'stop_daemon: false\npath_inclusions: ["/tmp/test_hermes"]\npath_exclusions: ["/"]\nfile_page_size: 1024KB\nbase_adapter_mode: kDefault\nflushing_mode: kAsync\nfile_adapter_configs:\n  - path: "/"\n    page_size: 1MB\n    mode: kDefault\n'})}),"\n",(0,s.jsxs)(n.ul,{children:["\n",(0,s.jsxs)(n.li,{children:[(0,s.jsx)(n.strong,{children:"stop_daemon"}),": stop the daemon when adapters exit. Generally, leave\nthis false and stop the daemon using finalize_daemon script. Will likely\nbe removed in the near future."]}),"\n",(0,s.jsxs)(n.li,{children:[(0,s.jsx)(n.strong,{children:"file_page_size"}),": The page size used to fragment files into blobs in\nHermes."]}),"\n"]}),"\n",(0,s.jsx)(n.h3,{id:"path-inclusion--exclusion",children:"Path Inclusion / Exclusion"}),"\n",(0,s.jsx)(n.pre,{children:(0,s.jsx)(n.code,{className:"language-yaml",children:'path_inclusions: ["/tmp/test_hermes"]\npath_exclusions: ["/"]\n'})}),"\n",(0,s.jsxs)(n.ul,{children:["\n",(0,s.jsxs)(n.li,{children:[(0,s.jsx)(n.strong,{children:"path_inclusions"}),": Which paths to buffer? In this case, everything which\nis a child of /tmp/test_hermes."]}),"\n",(0,s.jsxs)(n.li,{children:[(0,s.jsx)(n.strong,{children:"path_exclusions"}),": Which paths to ignore? In this case, everything which\nis a child of the root directory. Technically everything on the system."]}),"\n"]}),"\n",(0,s.jsx)(n.p,{children:'We prioritize paths in inclusions and exclusions depending on how\nspecific the path is. In other words, we sort the paths by the length\nof the path. For example, in this case, /tmp/test_hermes will be included\nsince it has a longer path than "/". Everything other than /tmp/test_hermes\nwill be excluded.'}),"\n",(0,s.jsx)(n.h3,{id:"adapter-mode",children:"Adapter Mode"}),"\n",(0,s.jsx)(n.p,{children:"The adapter mode determines how Hermes buffers adapter data by default.\nThere are three adapter modes:"}),"\n",(0,s.jsxs)(n.ol,{children:["\n",(0,s.jsx)(n.li,{children:"kDefault: Hermes will buffer data and then flush to the PFS eventually"}),"\n",(0,s.jsx)(n.li,{children:"kScratch: Hermes will buffer data, but never flush"}),"\n",(0,s.jsx)(n.li,{children:"kBypass: Hermes will never buffer data, and always flush to the PFS"}),"\n"]}),"\n",(0,s.jsx)(n.p,{children:"kDefault is the real use case of Hermes, the other two are for benchmarking\nand testing purposes."}),"\n",(0,s.jsx)(n.p,{children:"This parameter can also be set by an environment variable. The\nenvironment variable is prioritized."}),"\n",(0,s.jsx)(n.pre,{children:(0,s.jsx)(n.code,{className:"language-bash",children:"HERMES_ADAPTER_MODE=kDefault \\\n./myhermesapp\n"})}),"\n",(0,s.jsx)(n.h3,{id:"file-page-size",children:"File Page Size"}),"\n",(0,s.jsx)(n.pre,{children:(0,s.jsx)(n.code,{className:"language-yaml",children:"file_page_size: 1024KB\n"})}),"\n",(0,s.jsx)(n.p,{children:"This parameter dictates how adapters convert files into blobs.\nBy default, files are divided into 1024KB (1MB) blobs. Setting\nthis parameter appropriately can have impacts on\nwrite and read amplification and metadata overhead."}),"\n",(0,s.jsx)(n.p,{children:"For workloads which perform 4KB reads to a large file, each read\nwill be amplified to 1MB unless the page size is reset."}),"\n",(0,s.jsx)(n.p,{children:"For the same workload, setting a file page size equal to 4KB may\nresult in a significant increase in metadata being stored in the\nmetadata manager."}),"\n",(0,s.jsx)(n.p,{children:"In other words, this parameter is worth tuning."}),"\n",(0,s.jsx)(n.p,{children:"This parameter can also be set using an environment variable. The\nenvironment variable is prioritized."}),"\n",(0,s.jsx)(n.pre,{children:(0,s.jsx)(n.code,{className:"language-yaml",children:"HERMES_PAGE_SIZE=1024KB \\\n./myhermesapp\n"})}),"\n",(0,s.jsx)(n.h3,{id:"flushing-mode",children:"Flushing Mode"}),"\n",(0,s.jsx)(n.p,{children:"The flushing mode indicates how Hermes should flush data to the PFS.\nCurrently there are two modes provided:"}),"\n",(0,s.jsxs)(n.ol,{children:["\n",(0,s.jsx)(n.li,{children:"kAsync: Flush data asynchronously in a background thread"}),"\n",(0,s.jsx)(n.li,{children:"kSync: Flush data synchronously"}),"\n"]}),"\n",(0,s.jsx)(n.p,{children:"kAsync is recommended. kSync is used only in unit tests since it has\nlow performance."}),"\n",(0,s.jsx)(n.h3,{id:"adapter-config",children:"Adapter Config"}),"\n",(0,s.jsx)(n.pre,{children:(0,s.jsx)(n.code,{className:"language-yaml",children:'file_adapter_configs:\n  - path: "/"\n    page_size: 1MB\n    mode: kDefault\n'})}),"\n",(0,s.jsx)(n.p,{children:"Contains file-specific overrides to the default adapter variables defined\nabove. You can modify the adapter mode (3.2.2) and file page size for each"}),"\n",(0,s.jsx)(n.h2,{id:"provided-configurations",children:"Provided Configurations"}),"\n",(0,s.jsx)(n.p,{children:"We also provide Hermes configurations we use with a few systems to which you\nmight have access:"}),"\n",(0,s.jsxs)(n.ul,{children:["\n",(0,s.jsx)(n.li,{children:(0,s.jsx)(n.a,{href:"https://github.com/HDFGroup/hermes/blob/master/test/data/ares.yaml",children:"Ares (IIT)"})}),"\n",(0,s.jsxs)(n.li,{children:[(0,s.jsx)(n.a,{href:"https://github.com/HDFGroup/hermes/tree/master/test/data",children:"Frontera (TACC)"})," (Coming soon.)"]}),"\n"]}),"\n",(0,s.jsx)(n.p,{children:"Bear in mind that a suitable Hermes configuration also depends on\napplications' I/O workload and not just the configuration of the\nunderlying machine."}),"\n",(0,s.jsx)(n.h2,{id:"how-to-avoid-repeating-the-default-configurations",children:"How To Avoid Repeating the Default Configurations"}),"\n",(0,s.jsx)(n.p,{children:"Many parameters in Hermes can be left as default. Any parameters which\nyou would like to leave as default can be removed from your configuration\nfile completely. Hermes will fill in missing values based on the values\nin our default configurations."})]})}function d(e={}){const{wrapper:n}={...(0,a.a)(),...e.components};return n?(0,s.jsx)(n,{...e,children:(0,s.jsx)(h,{...e})}):h(e)}},1151:(e,n,i)=>{i.d(n,{Z:()=>o,a:()=>t});var s=i(7294);const a={},r=s.createContext(a);function t(e){const n=s.useContext(r);return s.useMemo((function(){return"function"==typeof e?e(n):{...n,...e}}),[n,e])}function o(e){let n;return n=e.disableParentContext?"function"==typeof e.components?e.components(a):e.components||a:t(e.components),s.createElement(r.Provider,{value:n},e.children)}}}]);
\ No newline at end of file
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@@ -1 +0,0 @@
-"use strict";(self.webpackChunkgrc=self.webpackChunkgrc||[]).push([[2777],{1421:(e,n,i)=>{i.r(n),i.d(n,{assets:()=>l,contentTitle:()=>t,default:()=>d,frontMatter:()=>r,metadata:()=>o,toc:()=>c});var s=i(5893),a=i(1151);const r={},t="Configuration",o={id:"hermes/configuration",title:"Configuration",description:"Before deploying an application, you need to configure Hermes. Hermes has two types of configurations: server configuration and client configuration. They",source:"@site/docs/03-hermes/05-configuration.md",sourceDirName:"03-hermes",slug:"/hermes/configuration",permalink:"/docs/hermes/configuration",draft:!1,unlisted:!1,tags:[],version:"current",sidebarPosition:5,frontMatter:{},sidebar:"tutorialSidebar",previous:{title:"Deploying Hermes",permalink:"/docs/hermes/deploying-hermes"},next:{title:"Buffer Organizer",permalink:"/docs/hermes/components/buffer-organizer"}},l={},c=[{value:"Server Configuration",id:"server-configuration",level:2},{value:"Defining Storage Targets",id:"defining-storage-targets",level:3},{value:"Device Names",id:"device-names",level:3},{value:"<code>mount_point</code>",id:"mount_point",level:3},{value:"<code>capacity</code>",id:"capacity",level:3},{value:"<code>block_size</code>",id:"block_size",level:3},{value:"<code>slab_sizes</code>",id:"slab_sizes",level:3},{value:"<code>bandwidth</code>, <code>latency</code>",id:"bandwidth-latency",level:3},{value:"<code>is_shared_device</code>",id:"is_shared_device",level:3},{value:"<code>borg_capacity_thresh</code>",id:"borg_capacity_thresh",level:3},{value:"Buffer Organizer (BORG)",id:"buffer-organizer-borg",level:2},{value:"Prefetcher",id:"prefetcher",level:2},{value:"Traits",id:"traits",level:2},{value:"Shared Memory",id:"shared-memory",level:2},{value:"System View State",id:"system-view-state",level:2},{value:"Bounding Memory Utilization",id:"bounding-memory-utilization",level:2},{value:"Using RAM as a buffering device",id:"using-ram-as-a-buffering-device",level:3},{value:"Hashtables for storing blobs + buckets",id:"hashtables-for-storing-blobs--buckets",level:3},{value:"Bounding Non-Buffering Tasks",id:"bounding-non-buffering-tasks",level:3},{value:"Calculating Total Amount of Memory",id:"calculating-total-amount-of-memory",level:3},{value:"Client Configuration",id:"client-configuration",level:2},{value:"Path Inclusion / Exclusion",id:"path-inclusion--exclusion",level:3},{value:"Adapter Mode",id:"adapter-mode",level:3},{value:"File Page Size",id:"file-page-size",level:3},{value:"Flushing Mode",id:"flushing-mode",level:3},{value:"Adapter Config",id:"adapter-config",level:3},{value:"Provided Configurations",id:"provided-configurations",level:2},{value:"How To Avoid Repeating the Default Configurations",id:"how-to-avoid-repeating-the-default-configurations",level:2}];function h(e){const n={a:"a",code:"code",h1:"h1",h2:"h2",h3:"h3",li:"li",ol:"ol",p:"p",pre:"pre",strong:"strong",ul:"ul",...(0,a.a)(),...e.components};return(0,s.jsxs)(s.Fragment,{children:[(0,s.jsx)(n.h1,{id:"configuration",children:"Configuration"}),"\n",(0,s.jsx)(n.p,{children:"Before deploying an application, you need to configure Hermes. Hermes has two types of configurations: server configuration and client configuration. They\nare represented as YAML files. We will describe the contents of these YAML\nfiles here."}),"\n",(0,s.jsx)(n.h2,{id:"server-configuration",children:"Server Configuration"}),"\n",(0,s.jsx)(n.p,{children:"The server configuration is primarily used to initialize the daemon.\nClients also parse the server config to get the basic information needed\nto connect to the Hermes daemons."}),"\n",(0,s.jsx)(n.p,{children:"Technically, the server configuration\nis optional. However, the default configuration is more for just setting\nthings up. You do have to configure things like mount points manually\nat this time."}),"\n",(0,s.jsxs)(n.p,{children:["The default server configuration can be found\n",(0,s.jsx)(n.a,{href:"https://github.com/HDFGroup/hermes/blob/master/config/hermes_server_default.yaml",children:"here"}),"."]}),"\n",(0,s.jsx)(n.h3,{id:"defining-storage-targets",children:"Defining Storage Targets"}),"\n",(0,s.jsx)(n.p,{children:'The most important property in the configuration is defining where Hermes\nbuffers data. This is done under the "devices" entry.\nIn the default configuration, we have the following:'}),"\n",(0,s.jsx)(n.pre,{children:(0,s.jsx)(n.code,{className:"language-yaml",children:'devices:\n  ram:\n    mount_point: ""\n    capacity: 50MB\n    block_size: 4KB\n    slab_sizes: [ 4KB, 16KB, 64KB, 1MB ]\n    bandwidth: 6000MBps\n    latency: 15us\n    is_shared_device: false\n    borg_capacity_thresh: [0.0, 1.0]\n\n  nvme:\n    mount_point: "./"\n    capacity: 100MB\n    block_size: 4KB\n    slab_sizes: [ 4KB, 16KB, 64KB, 1MB ]\n    bandwidth: 1GBps\n    latency: 600us\n    is_shared_device: false\n    borg_capacity_thresh: [ 0.0, 1.0 ]\n\n   ssd:\n     mount_point: "./"\n     capacity: 100MB\n     block_size: 4KB\n     slab_sizes: [ 4KB, 16KB, 64KB, 1MB ]\n     bandwidth: 500MBps\n     latency: 1200us\n     is_shared_device: false\n     borg_capacity_thresh: [ 0.0, 1.0 ]\n\n   pfs:\n     mount_point: "./"\n     capacity: 100MB\n     block_size: 64KB\n     slab_sizes: [ 4KB, 16KB, 64KB, 1MB ]\n     bandwidth: 100MBps\n     latency: 200ms\n     is_shared_device: true\n     borg_capacity_thresh: [ 0.0, 1.0 ]\n'})}),"\n",(0,s.jsx)(n.h3,{id:"device-names",children:"Device Names"}),"\n",(0,s.jsx)(n.p,{children:"In the above configuration, we have four unique devices: ram, nvme, ssd,\nand pfs. These names are for the ease of the user, and have no meaning\nto Hermes. In other words, these names can be anything. The following\nconfiguration would be effectively equivalent to the one above:"}),"\n",(0,s.jsx)(n.pre,{children:(0,s.jsx)(n.code,{className:"language-yaml",children:'devices:\n  dev1:\n    mount_point: ""\n    capacity: 50MB\n    ...\n\n  dev2:\n    mount_point: "./"\n    capacity: 100MB\n    ...\n\n   dev3:\n     mount_point: "./"\n     capacity: 100MB\n     ...\n\n   dev4:\n     mount_point: "./"\n     capacity: 100MB\n     ...\n'})}),"\n",(0,s.jsx)(n.h3,{id:"mount_point",children:(0,s.jsx)(n.code,{children:"mount_point"})}),"\n",(0,s.jsx)(n.p,{children:"The mount point parameter is used to indicate which directory Hermes\nshould place data in, if the device has a filesystem."}),"\n",(0,s.jsx)(n.pre,{children:(0,s.jsx)(n.code,{className:"language-yaml",children:'ram:\n  mount_point: ""\n\nnvme:\n  mount_point: "./"\n'})}),"\n",(0,s.jsx)(n.p,{children:'In the default config, for example, we look at ram and nvme. nvme is mounted\nin the current working directory. Hermes will create a file called\n"./slab_nvme". It will create equivalent files for hdd, ssd, and pfs.'}),"\n",(0,s.jsx)(n.p,{children:'For ram, we set the mount point to "". This indicates that the device\nhas no mount point.'}),"\n",(0,s.jsx)(n.h3,{id:"capacity",children:(0,s.jsx)(n.code,{children:"capacity"})}),"\n",(0,s.jsx)(n.p,{children:'This variable implies the amount of capacity to use for buffering.\nThis parameter is a "size variable", which supports various suffixes:'}),"\n",(0,s.jsx)(n.pre,{children:(0,s.jsx)(n.code,{className:"language-yaml",children:"capacity: 100    # 100 bytes\ncapacity: 100k   # 100 KB\ncapacity: 100kb  # 100 KB\ncapacity: 100KB  # 100 KB\ncapacity: 100m   # 100 MB\ncapacity: 100mb  # 100 MB\ncapacity: 100MB  # 100 MB\ncapacity: 100g   # 100 GB\ncapacity: 100gb  # 100 GB\ncapacity: 100GB  # 100 GB\ncapacity: 100T   # 100 TB\ncapacity: 100tb  # 100 TB\ncapacity: 100TB  # 100 TB\n"})}),"\n",(0,s.jsx)(n.p,{children:"There cannot be spaces between the number and the suffix. For example,"}),"\n",(0,s.jsx)(n.pre,{children:(0,s.jsx)(n.code,{className:"language-yaml",children:"capacity: 100 tb #NOT VALID\n"})}),"\n",(0,s.jsx)(n.h3,{id:"block_size",children:(0,s.jsx)(n.code,{children:"block_size"})}),"\n",(0,s.jsx)(n.pre,{children:(0,s.jsx)(n.code,{className:"language-yaml",children:"block_size: 64KB\n"})}),"\n",(0,s.jsx)(n.p,{children:"This is the amount of I/O that the physical block device supports.\nRAM, for example, generally sees data in units of 4KB because this is\nthe page size of the system. HDDs, NVMes, and SSDs generally have block\nsizes of 4KB as well. Generally, this parameter doesn't need to be changed."}),"\n",(0,s.jsx)(n.h3,{id:"slab_sizes",children:(0,s.jsx)(n.code,{children:"slab_sizes"})}),"\n",(0,s.jsx)(n.pre,{children:(0,s.jsx)(n.code,{className:"language-yaml",children:"slab_sizes: [4KB, 16KB, 64KB, 1MB]\n"})}),"\n",(0,s.jsx)(n.p,{children:"This parameter is important to performance and resource utilization. The slab sizes dictates the I/O patterns produced in Hermes. When Hermes wants to\nwrite a 16MB blob, how does this blob actually get mapped to storage?\nIt gets fragmented into buffers, where the size of a buffer is equivalent\nto the best-fitting slab size."}),"\n",(0,s.jsxs)(n.ul,{children:["\n",(0,s.jsx)(n.li,{children:"A 16MB blob will be placed as 16 1MB buffers."}),"\n",(0,s.jsx)(n.li,{children:"A 6KB blob will be placed as 2 4KB buffers"}),"\n",(0,s.jsx)(n.li,{children:"A 33KB blob will be placed as a single 64KB buffer"}),"\n"]}),"\n",(0,s.jsx)(n.p,{children:"You should decide the buffer sizes based on the characteristics of your\nprogram. If unsure, the default slab sizes generally have worked well\nin the workloads we've tried. However, if you're finding Hermes runs\nout of space, this parameter may be the culprit."}),"\n",(0,s.jsxs)(n.h3,{id:"bandwidth-latency",children:[(0,s.jsx)(n.code,{children:"bandwidth"}),", ",(0,s.jsx)(n.code,{children:"latency"})]}),"\n",(0,s.jsx)(n.pre,{children:(0,s.jsx)(n.code,{className:"language-yaml",children:"bandwidth: 1GBps\nlatency: 600us\n"})}),"\n",(0,s.jsx)(n.p,{children:"These are properties of the storage device which are used by data placement\nalgorithms to decide where to buffer data."}),"\n",(0,s.jsxs)(n.ul,{children:["\n",(0,s.jsx)(n.li,{children:"Acceptable suffixes for bandwidth (case doesn't matter):"}),"\n",(0,s.jsx)(n.li,{children:"Acceptable suffixes for latency (case doesn't matter): s, ms, us, ns."}),"\n"]}),"\n",(0,s.jsx)(n.h3,{id:"is_shared_device",children:(0,s.jsx)(n.code,{children:"is_shared_device"})}),"\n",(0,s.jsx)(n.pre,{children:(0,s.jsx)(n.code,{className:"language-yaml",children:"is_shared_device: true\n"})}),"\n",(0,s.jsx)(n.p,{children:"This indicates whether or not the device provides a shared view of\ndata across nodes. For example, a PFS is a shared device, whereas\na single hard drive is not a shared device. This parameter is not\nreally used at this time, but you do need to define it."}),"\n",(0,s.jsx)(n.h3,{id:"borg_capacity_thresh",children:(0,s.jsx)(n.code,{children:"borg_capacity_thresh"})}),"\n",(0,s.jsx)(n.pre,{children:(0,s.jsx)(n.code,{className:"language-yaml",children:"borg_capacity_thresh: [0.0, 1.0]\n"})}),"\n",(0,s.jsx)(n.p,{children:"This parameter is used to trigger the buffer organizer (BORG). When a\ndevice is either really low on capacity (or high on capacity) BORG\nwill be triggered to shuffle content around."}),"\n",(0,s.jsx)(n.p,{children:"The first entry indicates how much space is too little space. In this\ncase if capacity falls below 0% (i.e., never), BORG will be triggered."}),"\n",(0,s.jsx)(n.p,{children:"The second entry indicates how mcuh space is too much space. In this\ncase if capacity grows beyone 100% (i.e., never), BORG will be triggered."}),"\n",(0,s.jsx)(n.p,{children:"In other words, this example, shows how to disable BORG."}),"\n",(0,s.jsx)(n.h2,{id:"buffer-organizer-borg",children:"Buffer Organizer (BORG)"}),"\n",(0,s.jsx)(n.pre,{children:(0,s.jsx)(n.code,{className:"language-yaml",children:"buffer_organizer:\n  num_threads: 1\n  flush_period: 1024\n  blob_reorg_period: 1024\n  recency_min: 0\n  recency_max: 60\n  freq_max: 15\n  freq_min: 0\n"})}),"\n",(0,s.jsx)(n.p,{children:'The BORG contains threads for reorganizing buffers in Hermes. The number\nof threads is indicated by "num_threads". The amount of time (in ms) to\nre-scan for blobs to reorganize is given by "flush_period".'}),"\n",(0,s.jsx)(n.p,{children:"receny_max is the amount of time (in seconds) when the score of a blob\nbecomes 0. recency_min is the amount of time for the blob to have a score\nof 1."}),"\n",(0,s.jsx)(n.p,{children:"freq_max is the minimum number of times a blob needs to be accessed in the\nflushing period for the score to be equal to one. freq_min is the maximum number of times a blob can be accessed before its score becomes larger than 0."}),"\n",(0,s.jsx)(n.p,{children:"The buffer organizer is only triggered when there are space constraints\nthat need to be met at this time. If you want the BORG extremely active,\nchange the borg_capacity_thresh variable."}),"\n",(0,s.jsx)(n.h2,{id:"prefetcher",children:"Prefetcher"}),"\n",(0,s.jsx)(n.pre,{children:(0,s.jsx)(n.code,{className:"language-yaml",children:'prefetch:\n  enabled: false\n  apriori_schema_path: ""\n  epoch_ms: 50\n  is_mpi: false\n'})}),"\n",(0,s.jsx)(n.p,{children:"These parameters dictate properties of the prefetcher."}),"\n",(0,s.jsxs)(n.ul,{children:["\n",(0,s.jsxs)(n.li,{children:[(0,s.jsx)(n.strong,{children:"enabled"}),": whether to turn prefetcher on"]}),"\n",(0,s.jsxs)(n.li,{children:[(0,s.jsx)(n.strong,{children:"apriori_schema_path"}),": internally used by apriori prefetcher"]}),"\n",(0,s.jsxs)(n.li,{children:[(0,s.jsx)(n.strong,{children:"epoch_ms"}),": how often to call the prefetcher thread"]}),"\n",(0,s.jsxs)(n.li,{children:[(0,s.jsx)(n.strong,{children:"is_mpi"}),": whether the program is an MPI program so that clients\nsend their ranks to the daemon during prefetching."]}),"\n"]}),"\n",(0,s.jsx)(n.p,{children:"For now, prefetching is only available to the native API, not the adapters."}),"\n",(0,s.jsx)(n.h2,{id:"traits",children:"Traits"}),"\n",(0,s.jsx)(n.pre,{children:(0,s.jsx)(n.code,{className:"language-yaml",children:'traits:\n  - "hermes_posix_io_client"\n  - "hermes_stdio_io_client"\n  - "hermes_mpiio_io_client"\n  - "hermes_example_trait"\n  - "hermes_prefetcher_trait"\n'})}),"\n",(0,s.jsx)(n.p,{children:"The traits category lists the set of traits that Hermes searches for\nin the LD_LIBRARY_PATH and HERMES_TRAIT_PATH environment variables.\nIt will search each directory specified in those environment variables\nfor shared objects matching these names. For example, libhermes_posix_io_client.so will be searched for."}),"\n",(0,s.jsx)(n.p,{children:"Unless you are adding custom traits, this can be left as default."}),"\n",(0,s.jsx)(n.h2,{id:"shared-memory",children:"Shared Memory"}),"\n",(0,s.jsx)(n.pre,{children:(0,s.jsx)(n.code,{className:"language-yaml",children:'shmem_name: "/hermes_shm_"\n'})}),"\n",(0,s.jsx)(n.p,{children:"This is the name of the shared memory segment hermes will create. In order\nto make this unique across users (since shared memory can be used to\nshare memory across users), we append the name of the user to this key."}),"\n",(0,s.jsx)(n.p,{children:"This generally can be left as the default value."}),"\n",(0,s.jsx)(n.h2,{id:"system-view-state",children:"System View State"}),"\n",(0,s.jsx)(n.p,{children:"This parameter is unused for now, so no need to set it."}),"\n",(0,s.jsx)(n.h2,{id:"bounding-memory-utilization",children:"Bounding Memory Utilization"}),"\n",(0,s.jsx)(n.p,{children:'When running Hermes in a limited environment, ensuring that Hermes is not over-utilizing memory is necessary. It is possible to receive "Bus Error" messages due to the OS complaining that too many pages have been allocated. We find that this happens in Docker containers frequently since they have more limited memory constraints by default.'}),"\n",(0,s.jsx)(n.p,{children:"There are a few parameters which cause Hermes to utilize memory."}),"\n",(0,s.jsx)(n.h3,{id:"using-ram-as-a-buffering-device",children:"Using RAM as a buffering device"}),"\n",(0,s.jsx)(n.p,{children:"Hermes can be configured to use RAM as a buffering device."}),"\n",(0,s.jsx)(n.pre,{children:(0,s.jsx)(n.code,{className:"language-yaml",children:'devices:\n  ram:\n    mount_point: ""\n    capacity: 1g\n'})}),"\n",(0,s.jsx)(n.p,{children:"In this case, Hermes will reserve up to 1GB of space to use for buffering."}),"\n",(0,s.jsx)(n.h3,{id:"hashtables-for-storing-blobs--buckets",children:"Hashtables for storing blobs + buckets"}),"\n",(0,s.jsx)(n.p,{children:"Hermes will reserve space for hashtables for blobs, buckets, and traits.\nThese parameters can be configured as follows:"}),"\n",(0,s.jsx)(n.pre,{children:(0,s.jsx)(n.code,{className:"language-yaml",children:"mdm:\n  # This represents the number of blobs and buckets before collisions start\n  # to happen in the unordered_map tables.\n  est_blob_count: 100000\n  est_bucket_count: 100000\n  est_num_traits: 256\n"})}),"\n",(0,s.jsx)(n.p,{children:"You can set these to lower values if memory is over-utilized.\nThese values should be set to roughly the number of blobs and buckets the program creates to avoid collisions in the hashtables."}),"\n",(0,s.jsx)(n.h3,{id:"bounding-non-buffering-tasks",children:"Bounding Non-Buffering Tasks"}),"\n",(0,s.jsx)(n.p,{children:"You can set a maximum boundary on the amount of memory to use for non-buffering tasks, such as reserving space for the blob + bucket hashtables."}),"\n",(0,s.jsx)(n.pre,{children:(0,s.jsx)(n.code,{className:"language-yaml",children:"# Define the maximum amount of memory Hermes can use for non-buffering tasks.\n# This includes metadata management and memory allocations.\n# This memory will not be preallocated, so if you don't know, 0 indicates\n# any amount of memory\nmax_memory: 0g\n"})}),"\n",(0,s.jsx)(n.p,{children:"0g indicates infinity. Non-zero values can be set to put a boundary here."}),"\n",(0,s.jsx)(n.h3,{id:"calculating-total-amount-of-memory",children:"Calculating Total Amount of Memory"}),"\n",(0,s.jsx)(n.p,{children:"The total amount of memory Hermes can use before an hshm::Error or Bus Error is thrown can be calculated as follows:"}),"\n",(0,s.jsx)(n.pre,{children:(0,s.jsx)(n.code,{className:"language-bash",children:"RAM used for Buffering (3.1.7.1) + RAM used for Non-Buffering (3.1.7.3)\n"})}),"\n",(0,s.jsx)(n.h2,{id:"client-configuration",children:"Client Configuration"}),"\n",(0,s.jsxs)(n.p,{children:["The default client configuration can be found\n",(0,s.jsx)(n.a,{href:"https://github.com/HDFGroup/hermes/blob/master/config/hermes_client_default.yaml",children:"here"}),"."]}),"\n",(0,s.jsx)(n.p,{children:"The client configuration currently only contains parameters used by\nadapters."}),"\n",(0,s.jsx)(n.pre,{children:(0,s.jsx)(n.code,{className:"language-yaml",children:'stop_daemon: false\npath_inclusions: ["/tmp/test_hermes"]\npath_exclusions: ["/"]\nfile_page_size: 1024KB\nbase_adapter_mode: kDefault\nflushing_mode: kAsync\nfile_adapter_configs:\n  - path: "/"\n    page_size: 1MB\n    mode: kDefault\n'})}),"\n",(0,s.jsxs)(n.ul,{children:["\n",(0,s.jsxs)(n.li,{children:[(0,s.jsx)(n.strong,{children:"stop_daemon"}),": stop the daemon when adapters exit. Generally, leave\nthis false and stop the daemon using finalize_daemon script. Will likely\nbe removed in the near future."]}),"\n",(0,s.jsxs)(n.li,{children:[(0,s.jsx)(n.strong,{children:"file_page_size"}),": The page size used to fragment files into blobs in\nHermes."]}),"\n"]}),"\n",(0,s.jsx)(n.h3,{id:"path-inclusion--exclusion",children:"Path Inclusion / Exclusion"}),"\n",(0,s.jsx)(n.pre,{children:(0,s.jsx)(n.code,{className:"language-yaml",children:'path_inclusions: ["/tmp/test_hermes"]\npath_exclusions: ["/"]\n'})}),"\n",(0,s.jsxs)(n.ul,{children:["\n",(0,s.jsxs)(n.li,{children:[(0,s.jsx)(n.strong,{children:"path_inclusions"}),": Which paths to buffer? In this case, everything which\nis a child of /tmp/test_hermes."]}),"\n",(0,s.jsxs)(n.li,{children:[(0,s.jsx)(n.strong,{children:"path_exclusions"}),": Which paths to ignore? In this case, everything which\nis a child of the root directory. Technically everything on the system."]}),"\n"]}),"\n",(0,s.jsx)(n.p,{children:'We prioritize paths in inclusions and exclusions depending on how\nspecific the path is. In other words, we sort the paths by the length\nof the path. For example, in this case, /tmp/test_hermes will be included\nsince it has a longer path than "/". Everything other than /tmp/test_hermes\nwill be excluded.'}),"\n",(0,s.jsx)(n.h3,{id:"adapter-mode",children:"Adapter Mode"}),"\n",(0,s.jsx)(n.p,{children:"The adapter mode determines how Hermes buffers adapter data by default.\nThere are three adapter modes:"}),"\n",(0,s.jsxs)(n.ol,{children:["\n",(0,s.jsx)(n.li,{children:"kDefault: Hermes will buffer data and then flush to the PFS eventually"}),"\n",(0,s.jsx)(n.li,{children:"kScratch: Hermes will buffer data, but never flush"}),"\n",(0,s.jsx)(n.li,{children:"kBypass: Hermes will never buffer data, and always flush to the PFS"}),"\n"]}),"\n",(0,s.jsx)(n.p,{children:"kDefault is the real use case of Hermes, the other two are for benchmarking\nand testing purposes."}),"\n",(0,s.jsx)(n.p,{children:"This parameter can also be set by an environment variable. The\nenvironment variable is prioritized."}),"\n",(0,s.jsx)(n.pre,{children:(0,s.jsx)(n.code,{className:"language-bash",children:"HERMES_ADAPTER_MODE=kDefault \\\n./myhermesapp\n"})}),"\n",(0,s.jsx)(n.h3,{id:"file-page-size",children:"File Page Size"}),"\n",(0,s.jsx)(n.pre,{children:(0,s.jsx)(n.code,{className:"language-yaml",children:"file_page_size: 1024KB\n"})}),"\n",(0,s.jsx)(n.p,{children:"This parameter dictates how adapters convert files into blobs.\nBy default, files are divided into 1024KB (1MB) blobs. Setting\nthis parameter appropriately can have impacts on\nwrite and read amplification and metadata overhead."}),"\n",(0,s.jsx)(n.p,{children:"For workloads which perform 4KB reads to a large file, each read\nwill be amplified to 1MB unless the page size is reset."}),"\n",(0,s.jsx)(n.p,{children:"For the same workload, setting a file page size equal to 4KB may\nresult in a significant increase in metadata being stored in the\nmetadata manager."}),"\n",(0,s.jsx)(n.p,{children:"In other words, this parameter is worth tuning."}),"\n",(0,s.jsx)(n.p,{children:"This parameter can also be set using an environment variable. The\nenvironment variable is prioritized."}),"\n",(0,s.jsx)(n.pre,{children:(0,s.jsx)(n.code,{className:"language-yaml",children:"HERMES_PAGE_SIZE=1024KB \\\n./myhermesapp\n"})}),"\n",(0,s.jsx)(n.h3,{id:"flushing-mode",children:"Flushing Mode"}),"\n",(0,s.jsx)(n.p,{children:"The flushing mode indicates how Hermes should flush data to the PFS.\nCurrently there are two modes provided:"}),"\n",(0,s.jsxs)(n.ol,{children:["\n",(0,s.jsx)(n.li,{children:"kAsync: Flush data asynchronously in a background thread"}),"\n",(0,s.jsx)(n.li,{children:"kSync: Flush data synchronously"}),"\n"]}),"\n",(0,s.jsx)(n.p,{children:"kAsync is recommended. kSync is used only in unit tests since it has\nlow performance."}),"\n",(0,s.jsx)(n.h3,{id:"adapter-config",children:"Adapter Config"}),"\n",(0,s.jsx)(n.pre,{children:(0,s.jsx)(n.code,{className:"language-yaml",children:'file_adapter_configs:\n  - path: "/"\n    page_size: 1MB\n    mode: kDefault\n'})}),"\n",(0,s.jsx)(n.p,{children:"Contains file-specific overrides to the default adapter variables defined\nabove. You can modify the adapter mode (3.2.2) and file page size for each"}),"\n",(0,s.jsx)(n.h2,{id:"provided-configurations",children:"Provided Configurations"}),"\n",(0,s.jsx)(n.p,{children:"We also provide Hermes configurations we use with a few systems to which you\nmight have access:"}),"\n",(0,s.jsxs)(n.ul,{children:["\n",(0,s.jsx)(n.li,{children:(0,s.jsx)(n.a,{href:"https://github.com/HDFGroup/hermes/blob/master/test/data/ares.yaml",children:"Ares (IIT)"})}),"\n",(0,s.jsxs)(n.li,{children:[(0,s.jsx)(n.a,{href:"https://github.com/HDFGroup/hermes/tree/master/test/data",children:"Frontera (TACC)"})," (Coming soon.)"]}),"\n"]}),"\n",(0,s.jsx)(n.p,{children:"Bear in mind that a suitable Hermes configuration also depends on\napplications' I/O workload and not just the configuration of the\nunderlying machine."}),"\n",(0,s.jsx)(n.h2,{id:"how-to-avoid-repeating-the-default-configurations",children:"How To Avoid Repeating the Default Configurations"}),"\n",(0,s.jsx)(n.p,{children:"Many parameters in Hermes can be left as default. Any parameters which\nyou would like to leave as default can be removed from your configuration\nfile completely. Hermes will fill in missing values based on the values\nin our default configurations."})]})}function d(e={}){const{wrapper:n}={...(0,a.a)(),...e.components};return n?(0,s.jsx)(n,{...e,children:(0,s.jsx)(h,{...e})}):h(e)}},1151:(e,n,i)=>{i.d(n,{Z:()=>o,a:()=>t});var s=i(7294);const a={},r=s.createContext(a);function t(e){const n=s.useContext(r);return s.useMemo((function(){return"function"==typeof e?e(n):{...n,...e}}),[n,e])}function o(e){let n;return n=e.disableParentContext?"function"==typeof e.components?e.components(a):e.components||a:t(e.components),s.createElement(r.Provider,{value:n},e.children)}}}]);
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-"use strict";(self.webpackChunkgrc=self.webpackChunkgrc||[]).push([[6687],{3978:(e,n,t)=>{t.r(n),t.d(n,{assets:()=>c,contentTitle:()=>i,default:()=>l,frontMatter:()=>r,metadata:()=>a,toc:()=>d});var o=t(5893),s=t(1151);const r={},i="Doxygen",a={id:"hermes/doxygen",title:"Doxygen",description:"The Doxygen portion of the Hermes documentation can be built as follows:",source:"@site/docs/03-hermes/10-doxygen.md",sourceDirName:"03-hermes",slug:"/hermes/doxygen",permalink:"/docs/hermes/doxygen",draft:!1,unlisted:!1,tags:[],version:"current",sidebarPosition:10,frontMatter:{},sidebar:"tutorialSidebar",previous:{title:"Debugging",permalink:"/docs/hermes/debugging"},next:{title:"Frequently Asked Questions",permalink:"/docs/hermes/faq"}},c={},d=[];function h(e){const n={a:"a",code:"code",h1:"h1",p:"p",pre:"pre",...(0,s.a)(),...e.components};return(0,o.jsxs)(o.Fragment,{children:[(0,o.jsx)(n.h1,{id:"doxygen",children:"Doxygen"}),"\n",(0,o.jsxs)(n.p,{children:["The ",(0,o.jsx)(n.a,{href:"https://www.doxygen.nl/index.html",children:"Doxygen"})," portion of the Hermes documentation can be built as follows:"]}),"\n",(0,o.jsx)(n.pre,{children:(0,o.jsx)(n.code,{className:"language-bash",children:"cmake -D <Other Hermes CMake build options> -DHERMES_ENABLE_DOXYGEN=ON ../\nmake dox\n"})}),"\n",(0,o.jsxs)(n.p,{children:["The HTML version of the documentation will be placed into the ",(0,o.jsx)(n.code,{children:"_build/html"})," subfolder of the build directory."]}),"\n",(0,o.jsxs)(n.p,{children:["An online version for the latest release is available at ",(0,o.jsx)(n.a,{href:"https://hdfgroup.github.io/hermes/html/",children:"https://hdfgroup.github.io/hermes/html/"}),"."]}),"\n",(0,o.jsxs)(n.p,{children:["The official version for the stable release is available at ",(0,o.jsx)(n.a,{href:"https://docs.hdfgroup.org/hermes/",children:"https://docs.hdfgroup.org/hermes/"}),"."]})]})}function l(e={}){const{wrapper:n}={...(0,s.a)(),...e.components};return n?(0,o.jsx)(n,{...e,children:(0,o.jsx)(h,{...e})}):h(e)}},1151:(e,n,t)=>{t.d(n,{Z:()=>a,a:()=>i});var o=t(7294);const s={},r=o.createContext(s);function i(e){const n=o.useContext(r);return o.useMemo((function(){return"function"==typeof e?e(n):{...n,...e}}),[n,e])}function a(e){let n;return n=e.disableParentContext?"function"==typeof e.components?e.components(s):e.components||s:i(e.components),o.createElement(r.Provider,{value:n},e.children)}}}]);
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-"use strict";(self.webpackChunkgrc=self.webpackChunkgrc||[]).push([[6466],{7572:(e,n,r)=>{r.r(n),r.d(n,{assets:()=>c,contentTitle:()=>l,default:()=>h,frontMatter:()=>o,metadata:()=>t,toc:()=>a});var i=r(5893),s=r(1151);const o={},l="Frequently Asked Questions",t={id:"hermes/faq",title:"Frequently Asked Questions",description:"What is the minimum version for GCC?",source:"@site/docs/03-hermes/11-faq.md",sourceDirName:"03-hermes",slug:"/hermes/faq",permalink:"/docs/hermes/faq",draft:!1,unlisted:!1,tags:[],version:"current",sidebarPosition:11,frontMatter:{},sidebar:"tutorialSidebar",previous:{title:"Doxygen",permalink:"/docs/hermes/doxygen"},next:{title:"Introduction",permalink:"/docs/chronolog/index"}},c={},a=[{value:"What is the minimum version for GCC?",id:"what-is-the-minimum-version-for-gcc",level:2},{value:"Can I run Hermes on Mac?",id:"can-i-run-hermes-on-mac",level:2},{value:"Does Hermes run on Linux only?",id:"does-hermes-run-on-linux-only",level:2},{value:"Can I run Hermes on Chameleon JupyterLab Server?",id:"can-i-run-hermes-on-chameleon-jupyterlab-server",level:2},{value:"Why do I get <code>mercury-&gt;fatal</code> error when I use <code>rpc_protocol = &quot;ofi+verbs&quot;;</code> in configuration file?",id:"why-do-i-get-mercury-fatal-error-when-i-use-rpc_protocol--ofiverbs-in-configuration-file",level:2},{value:"Why does MPI Adapter fail to compile?",id:"why-does-mpi-adapter-fail-to-compile",level:2}];function d(e){const n={a:"a",code:"code",h1:"h1",h2:"h2",li:"li",p:"p",pre:"pre",ul:"ul",...(0,s.a)(),...e.components};return(0,i.jsxs)(i.Fragment,{children:[(0,i.jsx)(n.h1,{id:"frequently-asked-questions",children:"Frequently Asked Questions"}),"\n",(0,i.jsx)(n.h2,{id:"what-is-the-minimum-version-for-gcc",children:"What is the minimum version for GCC?"}),"\n",(0,i.jsxs)(n.p,{children:["GCC 11. Hermes requires C++17 features that are only available since GCC 7.3. C++17 support is enabled by default in GCC 11; it can be explicitly selected in earlier versions with the ",(0,i.jsx)(n.code,{children:"-std=c++17"})," command-line flag or ",(0,i.jsx)(n.code,{children:"-std=gnu++17"})," to enable GNU extensions as well. See ",(0,i.jsx)(n.a,{href:"https://gcc.gnu.org/projects/cxx-status.html#cxx17",children:"C++17 Support in GCC"})," for the details. Use ",(0,i.jsx)(n.code,{children:"spack install gcc"})," first if your system has GCC 4. It will install GCC 12.2.0 by default. Then, run ",(0,i.jsx)(n.code,{children:"spack compiler find"})," to use the newly installed gcc."]}),"\n",(0,i.jsx)(n.h2,{id:"can-i-run-hermes-on-mac",children:"Can I run Hermes on Mac?"}),"\n",(0,i.jsx)(n.p,{children:"No. macOS lacks several system calls that Hermes components use:"}),"\n",(0,i.jsxs)(n.ul,{children:["\n",(0,i.jsxs)(n.li,{children:[(0,i.jsx)(n.code,{children:"fopen64"})," / ",(0,i.jsx)(n.code,{children:"fseeko64"})]}),"\n",(0,i.jsxs)(n.li,{children:[(0,i.jsx)(n.code,{children:"O_DIRECT"})," / ",(0,i.jsx)(n.code,{children:"O_TMPFILE"})]}),"\n",(0,i.jsx)(n.li,{children:(0,i.jsx)(n.code,{children:"gethostbyname_r"})}),"\n",(0,i.jsx)(n.li,{children:(0,i.jsx)(n.code,{children:"_STAT_VER"})}),"\n"]}),"\n",(0,i.jsx)(n.h2,{id:"does-hermes-run-on-linux-only",children:"Does Hermes run on Linux only?"}),"\n",(0,i.jsxs)(n.p,{children:["Yes. Hermes uses the fixed ",(0,i.jsx)(n.code,{children:"/proc"})," code:"]}),"\n",(0,i.jsx)(n.pre,{children:(0,i.jsx)(n.code,{className:"language-cpp",children:"inline std::string GetFilenameFromFD(int fd) {\n  char proclnk[kMaxPathLen];\n  char filename[kMaxPathLen];\n  snprintf(proclnk, kMaxPathLen, \"/proc/self/fd/%d\", fd);\n  size_t r = readlink(proclnk, filename, kMaxPathLen);\n  filename[r] = '\\0';\n  return filename;\n}\n"})}),"\n",(0,i.jsx)(n.h2,{id:"can-i-run-hermes-on-chameleon-jupyterlab-server",children:"Can I run Hermes on Chameleon JupyterLab Server?"}),"\n",(0,i.jsx)(n.p,{children:"Maybe. However, installation with Spack will fail due to timeout. For older (< 0.8) Hermes, Google OR-Tools installation will fail."}),"\n",(0,i.jsxs)(n.h2,{id:"why-do-i-get-mercury-fatal-error-when-i-use-rpc_protocol--ofiverbs-in-configuration-file",children:["Why do I get ",(0,i.jsx)(n.code,{children:"mercury->fatal"})," error when I use ",(0,i.jsx)(n.code,{children:'rpc_protocol = "ofi+verbs";'})," in configuration file?"]}),"\n",(0,i.jsxs)(n.p,{children:["Such error occurs when ",(0,i.jsx)(n.code,{children:"libfabric"})," is not compiled with ",(0,i.jsx)(n.code,{children:"verbs"})," support. Try ",(0,i.jsx)(n.code,{children:"spack install hermes ^libfabric fabrics=rxm,sockets,tcp,udp,verbs"}),"."]}),"\n",(0,i.jsx)(n.h2,{id:"why-does-mpi-adapter-fail-to-compile",children:"Why does MPI Adapter fail to compile?"}),"\n",(0,i.jsxs)(n.p,{children:["The MPI-IO adapter only supports MPICH. Use ",(0,i.jsx)(n.code,{children:"spack install mpi ^mpich"})," to install mpi. Load it with ",(0,i.jsx)(n.code,{children:"spack load mpi"}),"."]})]})}function h(e={}){const{wrapper:n}={...(0,s.a)(),...e.components};return n?(0,i.jsx)(n,{...e,children:(0,i.jsx)(d,{...e})}):d(e)}},1151:(e,n,r)=>{r.d(n,{Z:()=>t,a:()=>l});var i=r(7294);const s={},o=i.createContext(s);function l(e){const n=i.useContext(o);return i.useMemo((function(){return"function"==typeof e?e(n):{...n,...e}}),[n,e])}function t(e){let n;return n=e.disableParentContext?"function"==typeof e.components?e.components(s):e.components||s:l(e.components),i.createElement(o.Provider,{value:n},e.children)}}}]);
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+"use strict";(self.webpackChunkgrc=self.webpackChunkgrc||[]).push([[7806],{8988:(e,n,r)=>{r.r(n),r.d(n,{assets:()=>l,contentTitle:()=>o,default:()=>h,frontMatter:()=>i,metadata:()=>a,toc:()=>c});var s=r(5893),t=r(1151);const i={},o="Developer Guide",a={id:"hermes/developer-guide",title:"Developer Guide",description:"Hermes can be complicated to debug due to its distributed and asynchronous",source:"@site/docs/03-hermes/10-developer-guide.md",sourceDirName:"03-hermes",slug:"/hermes/developer-guide",permalink:"/docs/hermes/developer-guide",draft:!1,unlisted:!1,tags:[],version:"current",sidebarPosition:10,frontMatter:{},sidebar:"tutorialSidebar",previous:{title:"Containers",permalink:"/docs/hermes/containers"},next:{title:"Doxygen",permalink:"/docs/hermes/doxygen"}},l={},c=[{value:"Hermes Repo Structure",id:"hermes-repo-structure",level:2},{value:"Preparing Pull Request (PR)",id:"preparing-pull-request-pr",level:2},{value:"PR Check Failure",id:"pr-check-failure",level:2},{value:"Containerized Hermes",id:"containerized-hermes",level:2},{value:"Remote Debugging",id:"remote-debugging",level:2},{value:"Preparing For Release",id:"preparing-for-release",level:2},{value:"Introduction to our Continuous Integration (CI)",id:"introduction-to-our-continuous-integration-ci",level:2},{value:"Adding a New Adapter",id:"adding-a-new-adapter",level:2}];function d(e){const n={a:"a",code:"code",em:"em",h1:"h1",h2:"h2",li:"li",ol:"ol",p:"p",pre:"pre",...(0,t.a)(),...e.components};return(0,s.jsxs)(s.Fragment,{children:[(0,s.jsx)(n.h1,{id:"developer-guide",children:"Developer Guide"}),"\n",(0,s.jsx)(n.p,{children:"Hermes can be complicated to debug due to its distributed and asynchronous\nnature. Faults can happen in the client program, or in the Hermes daemon.\nThe first step when encountering problems is to compile in Debug mode."}),"\n",(0,s.jsx)(n.pre,{children:(0,s.jsx)(n.code,{className:"language-cmake",children:"cmake .. -DCMAKE_BUILD_TYPE=Debug\n"})}),"\n",(0,s.jsx)(n.p,{children:"The Debug mode will increase the number of logging statements the program\nuses to give you a stronger hint as to where the problem occurs. These\nstatements are typically compiled out for performance reasons."}),"\n",(0,s.jsx)(n.p,{children:"Secondly, make sure to use an IDE which supports visual debugging. Debugging\nusing a terminal with gdb can be very cumbersome, especially when multi-process cases come along."}),"\n",(0,s.jsx)(n.h2,{id:"hermes-repo-structure",children:"Hermes Repo Structure"}),"\n",(0,s.jsx)(n.p,{children:"The Hermes repo is organized as follows:"}),"\n",(0,s.jsxs)(n.ol,{children:["\n",(0,s.jsxs)(n.li,{children:[(0,s.jsx)(n.code,{children:"hrun"})," is the Hermes runtime and contains all source files / includes for it. This includes queuing and network code."]}),"\n",(0,s.jsxs)(n.li,{children:[(0,s.jsx)(n.code,{children:"tasks"})," contains the majority of Hermes implementation. These are tasks that execute in the Hermes runtime"]}),"\n",(0,s.jsxs)(n.li,{children:[(0,s.jsx)(n.code,{children:"src"})," contains a single source file that is used to construct the Hermes library object that applications link to. Very little code is here, as most implementation is executed in the runtime."]}),"\n",(0,s.jsxs)(n.li,{children:[(0,s.jsx)(n.code,{children:"codegen"})," contains python code to help with generating and maintaining hrun tasks."]}),"\n",(0,s.jsxs)(n.li,{children:[(0,s.jsx)(n.code,{children:"hermes_adapters"})," includes all code relating to the adapters, such as  POSIX, STDIO, and MPI-IO interception"]}),"\n",(0,s.jsxs)(n.li,{children:[(0,s.jsx)(n.code,{children:"config"})," contains default configurations of Hermes."]}),"\n",(0,s.jsxs)(n.li,{children:[(0,s.jsx)(n.code,{children:"docker"})," contains dockerfiles for building Hermes container."]}),"\n",(0,s.jsxs)(n.li,{children:[(0,s.jsx)(n.code,{children:"wrapper"})," contains all code for binding Hermes to other languages."]}),"\n",(0,s.jsxs)(n.li,{children:[(0,s.jsx)(n.code,{children:"external"})," contains git submodules of repos external to Hermes."]}),"\n",(0,s.jsxs)(n.li,{children:[(0,s.jsx)(n.code,{children:"test"})," includes all unit tests"]}),"\n",(0,s.jsxs)(n.li,{children:[(0,s.jsx)(n.code,{children:"benchmark"})," includes some performance benchmark kernels"]}),"\n",(0,s.jsxs)(n.li,{children:[(0,s.jsx)(n.code,{children:"ci"})," includes all code for continuous integration"]}),"\n"]}),"\n",(0,s.jsx)(n.h2,{id:"preparing-pull-request-pr",children:"Preparing Pull Request (PR)"}),"\n",(0,s.jsx)(n.p,{children:"Please run these two steps and remove all warnings."}),"\n",(0,s.jsx)(n.pre,{children:(0,s.jsx)(n.code,{className:"language-bash",children:"make dox\nmake lint\n"})}),"\n",(0,s.jsx)(n.h2,{id:"pr-check-failure",children:"PR Check Failure"}),"\n",(0,s.jsxs)(n.p,{children:["We use the ",(0,s.jsx)(n.a,{href:"https://github.com/HDFGroup/hermes/blob/master/docker/deps.Dockerfile",children:"deps.Dockerfile"}),"\nto avoid reinstalling packages in the github action. While github has a cache action,\nwe find it somewhat cumbersome. This way, we get the benefit of both a maintained\ndockerfile and a fast github action."]}),"\n",(0,s.jsx)(n.h2,{id:"containerized-hermes",children:"Containerized Hermes"}),"\n",(0,s.jsx)(n.p,{children:"As a developer, it may be beneficial to use Hermes inside of a container to\navoid differences in machines."}),"\n",(0,s.jsx)(n.p,{children:"First, cd into your Hermes directory:"}),"\n",(0,s.jsx)(n.pre,{children:(0,s.jsx)(n.code,{className:"language-bash",children:"cd /path/to/hermes\n"})}),"\n",(0,s.jsx)(n.p,{children:"Then either build the container from scratch or pull (but not both):"}),"\n",(0,s.jsx)(n.p,{children:"From scratch:"}),"\n",(0,s.jsx)(n.pre,{children:(0,s.jsx)(n.code,{className:"language-bash",children:"docker build -t lukemartinlogan/hermes_deps . -f docker/deps.Dockerfile\n"})}),"\n",(0,s.jsx)(n.p,{children:"Pull:"}),"\n",(0,s.jsx)(n.pre,{children:(0,s.jsx)(n.code,{className:"language-bash",children:"docker pull lukemartinlogan/hermes_deps:latest\n"})}),"\n",(0,s.jsx)(n.p,{children:"Then, run the container. This command will mount the Hermes directory\nas /hermes. It will make it so that the container has 4GB of memory and\n4GB of shared memory. By default, containers don't have shared memory, but\nHermes requires it. We then also forward ports 4000 and 4001 to support remote\ndebugging from those ports."}),"\n",(0,s.jsx)(n.pre,{children:(0,s.jsx)(n.code,{className:"language-bash",children:"docker run -it --mount src=${PWD},target=/hermes,type=bind \\\n--name hermes_deps_c \\\n--network host \\\n--memory=8G \\\n--shm-size=8G \\\n-p 4000:4000 \\\n-p 4001:4001 \\\nlukemartinlogan/hermes_deps\n"})}),"\n",(0,s.jsx)(n.p,{children:"To run the github action:"}),"\n",(0,s.jsx)(n.pre,{children:(0,s.jsx)(n.code,{className:"language-bash",children:"bash /hermes/ci/build_hermes.sh\n"})}),"\n",(0,s.jsx)(n.p,{children:"Within the container, build Hermes:"}),"\n",(0,s.jsx)(n.pre,{children:(0,s.jsx)(n.code,{className:"language-bash",children:'# Load spack and other modules\n. /module_load.sh\n. "${SPACK_DIR}/share/spack/setup-env.sh"\n# Load hermes_shm\nspack load hermes_shm\n# Build hermes\ncd /hermes\nmkdir build\ncd build\ncmake ../\nmake -j8\n'})}),"\n",(0,s.jsx)(n.p,{children:"If you make changes to the dependencies container:"}),"\n",(0,s.jsx)(n.pre,{children:(0,s.jsx)(n.code,{className:"language-bash",children:"docker commit hermes_deps_c lukemartinlogan/hermes_deps\ndocker push lukemartinlogan/hermes_deps\ndocker stop /hermes_deps_c\ndocker rm /hermes_deps_c\n"})}),"\n",(0,s.jsx)(n.h2,{id:"remote-debugging",children:"Remote Debugging"}),"\n",(0,s.jsx)(n.p,{children:"At some point, you may have to do a remote debug. The following code will\nforward SSH connections so that you can remotely connect a debugger."}),"\n",(0,s.jsxs)(n.p,{children:["Let's say that you are running Hermes on a machine ",(0,s.jsx)(n.a,{href:"mailto:myusername@myip.org",children:"myusername@myip.org"})," on\nport 4000. You can connect to that by forwarding a local port to that address.\nA debugger would connect to localhost:4000, which will then be routed to\n",(0,s.jsx)(n.a,{href:"mailto:myusername@myip.org",children:"myusername@myip.org"}),":4000."]}),"\n",(0,s.jsx)(n.pre,{children:(0,s.jsx)(n.code,{className:"language-bash",children:"remote_machine_login=myusername@myip.org\n\nlocal_port=4000\nremote_port=4000\nssh -L ${local_port}:localhost:${remote_port} -fN ${ares_node}\n\nlocal_port=4001\nremote_port=4001\nssh -L ${local_port}:localhost:${remote_port} -fN ${ares_node}\n"})}),"\n",(0,s.jsx)(n.p,{children:"To shutdown this forwarding, you kill all routed SSH connections as follows:"}),"\n",(0,s.jsx)(n.pre,{children:(0,s.jsx)(n.code,{className:"language-bash",children:'pkill -f "ssh -L"\n'})}),"\n",(0,s.jsx)(n.p,{children:"If the machine you are running Hermes on has a head/login node, you\nwill have to forward the connection from your head node to the node actually\nrunning the code (the compute nodes). If this is the case, just repeat the\nabove steps on the head node, replacing remote_machine_login with the address\nof the compute node."}),"\n",(0,s.jsx)(n.h2,{id:"preparing-for-release",children:"Preparing For Release"}),"\n",(0,s.jsxs)(n.ol,{children:["\n",(0,s.jsxs)(n.li,{children:["Create a GitHub Project for the ",(0,s.jsx)(n.em,{children:"next"})," release"]}),"\n",(0,s.jsxs)(n.li,{children:["Update the ",(0,s.jsx)(n.code,{children:"HERMES_VERSION_*"})," variables in ",(0,s.jsx)(n.code,{children:"CMakeLists.txt"})]}),"\n",(0,s.jsxs)(n.li,{children:["Update ",(0,s.jsx)(n.code,{children:"PROJECT_NUMBER"})," in ",(0,s.jsx)(n.code,{children:"Doxyfile.in"}),"."]}),"\n",(0,s.jsx)(n.li,{children:"To make release note generation as automated as possible, make sure\nrelevant pull requests that are part of the release have proper labels and and\ntitles, as that information will show up directly in the generated release\nnotes in the next step."}),"\n",(0,s.jsxs)(n.li,{children:["Draft a release on Github. Click ",(0,s.jsx)(n.code,{children:"auto-generate release notes"}),' and edit\nthe result as necessary. Fill in the new tag, and select "Create new tag x.x.x\non publish" so that Github will automatically tag the release when it is\npublished.']}),"\n",(0,s.jsx)(n.li,{children:"The docker containers will be automatically built and pushed to docker hub\nwhenever a new tag is added. Check the CI actions to make sure there were no\nerrors."}),"\n",(0,s.jsx)(n.li,{children:"Copy/move ideas to the project for the next release"}),"\n",(0,s.jsxs)(n.li,{children:["Close and archive the project for the ",(0,s.jsx)(n.em,{children:"current"})," release"]}),"\n",(0,s.jsxs)(n.li,{children:["Merge the latest release branch (if one exists) of the wiki into the ",(0,s.jsx)(n.code,{children:"master"})," branch."]}),"\n",(0,s.jsx)(n.li,{children:"Make an announcement in the Hermes topic of the HDF forum."}),"\n",(0,s.jsx)(n.li,{children:"Send Lori a note for the next HDF5 newsletter."}),"\n"]}),"\n",(0,s.jsx)(n.h2,{id:"introduction-to-our-continuous-integration-ci",children:"Introduction to our Continuous Integration (CI)"}),"\n",(0,s.jsxs)(n.p,{children:["We are primarily using Python for managing for running unit tests. Under\n",(0,s.jsx)(n.a,{href:"https://github.com/HDFGroup/hermes/blob/master/CMakeLists.txt",children:"our root CMakeList"}),", we implement a\nCMake function called jarvis_test, which uses ",(0,s.jsx)(n.a,{href:"https://github.com/grc-iit/jarvis-cd.git",children:"Jarvis"}),"\nand its ",(0,s.jsx)(n.a,{href:"https://github.com/HDFGroup/hermes/tree/master/test/unit/pipelines",children:"pipelines"})," concept."]}),"\n",(0,s.jsx)(n.h2,{id:"adding-a-new-adapter",children:"Adding a New Adapter"}),"\n",(0,s.jsxs)(n.ol,{children:["\n",(0,s.jsxs)(n.li,{children:["Create a new directory under the ",(0,s.jsx)(n.code,{children:"adapter"})," directory."]}),"\n"]})]})}function h(e={}){const{wrapper:n}={...(0,t.a)(),...e.components};return n?(0,s.jsx)(n,{...e,children:(0,s.jsx)(d,{...e})}):d(e)}},1151:(e,n,r)=>{r.d(n,{Z:()=>a,a:()=>o});var s=r(7294);const t={},i=s.createContext(t);function o(e){const n=s.useContext(i);return s.useMemo((function(){return"function"==typeof e?e(n):{...n,...e}}),[n,e])}function a(e){let n;return n=e.disableParentContext?"function"==typeof e.components?e.components(t):e.components||t:o(e.components),s.createElement(i.Provider,{value:n},e.children)}}}]);
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rename to assets/js/495a1267.338761cc.js
index 51e1e351..9c1e6028 100644
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@@ -1 +1 @@
-"use strict";(self.webpackChunkgrc=self.webpackChunkgrc||[]).push([[6238],{7314:(e,s,n)=>{n.r(s),n.d(s,{assets:()=>l,contentTitle:()=>r,default:()=>h,frontMatter:()=>i,metadata:()=>o,toc:()=>c});var t=n(5893),a=n(1151);const i={},r="Runtime",o={id:"hermes/components/runtime",title:"Runtime",description:"Hermes is built as a plugin to the Hermes Runtime, a distributed task processing framework",source:"@site/docs/03-hermes/06-components/07-runtime.md",sourceDirName:"03-hermes/06-components",slug:"/hermes/components/runtime",permalink:"/docs/hermes/components/runtime",draft:!1,unlisted:!1,tags:[],version:"current",sidebarPosition:7,frontMatter:{},sidebar:"tutorialSidebar",previous:{title:"Data Staging",permalink:"/docs/hermes/components/data-staging"},next:{title:"Distributed Metadata",permalink:"/docs/hermes/components/distributed-metadata"}},l={},c=[{value:"Task Repos and Task Libraries",id:"task-repos-and-task-libraries",level:2},{value:"Bootstrapping a Task Library",id:"bootstrapping-a-task-library",level:2},{value:"Overview of Bootstrapped Code",id:"overview-of-bootstrapped-code",level:3},{value:"CreateTask",id:"createtask",level:3},{value:"Task Struct",id:"task-struct",level:4},{value:"Task Client",id:"task-client",level:4},{value:"Task Server",id:"task-server",level:4},{value:"DestructTask",id:"destructtask",level:3},{value:"Overview of Task Submission and Queueing",id:"overview-of-task-submission-and-queueing",level:2},{value:"Creating Custom Tasks",id:"creating-custom-tasks",level:2},{value:"Modify <code>compress_methods.yaml</code>",id:"modify-compress_methodsyaml",level:3},{value:"Modify <code>compress_tasks.h</code>",id:"modify-compress_tasksh",level:3},{value:"The <code>TaskFlags</code> base class",id:"the-taskflags-base-class",level:4},{value:"Task Constructor",id:"task-constructor",level:4},{value:"Modify <code>compress.cc</code>",id:"modify-compresscc",level:3},{value:"Modify <code>compress.h</code>",id:"modify-compressh",level:3},{value:"Task Methods",id:"task-methods",level:3},{value:"Registering a Task Library",id:"registering-a-task-library",level:2},{value:"Task Grouping, Worker Polling, and Deadlock Prevention",id:"task-grouping-worker-polling-and-deadlock-prevention",level:2},{value:"Building a Replicatable Task",id:"building-a-replicatable-task",level:2},{value:"Building a Data-Intensive, RDMA-Capable Task",id:"building-a-data-intensive-rdma-capable-task",level:2}];function d(e){const s={code:"code",em:"em",h1:"h1",h2:"h2",h3:"h3",h4:"h4",li:"li",ol:"ol",p:"p",pre:"pre",strong:"strong",ul:"ul",...(0,a.a)(),...e.components};return(0,t.jsxs)(t.Fragment,{children:[(0,t.jsx)(s.h1,{id:"runtime",children:"Runtime"}),"\n",(0,t.jsx)(s.p,{children:"Hermes is built as a plugin to the Hermes Runtime, a distributed task processing framework\ncapable of scheduling, replicating, distributing, processing, monitoring, and\nload balancing arbitrary tasks. Tasks define various properties which provide\ncontrol over scheduling decisions, memory management, and concurrency.\nThis section will discuss the design of the Hermes Runtime and how to develop\ncustom tasks."}),"\n",(0,t.jsx)(s.h2,{id:"task-repos-and-task-libraries",children:"Task Repos and Task Libraries"}),"\n",(0,t.jsxs)(s.p,{children:["The Hermes Runtime is used for executing arbitrary tasks. Developers can create\nnew tasks and release them using a decentralized package management design,\nsimilar to spack. This is accomplished through ",(0,t.jsx)(s.strong,{children:"task repos"}),"."]}),"\n",(0,t.jsxs)(s.p,{children:["A task repo is a directory which contains a set of ",(0,t.jsx)(s.strong,{children:"task libraries"}),". A\ntask library (or lib) provides the functionality to submit and execute tasks.\nTask libs follow the single responsibility principle. Multiple task libs should\nbe created to separate unrelated or loosely related functionality."]}),"\n",(0,t.jsx)(s.p,{children:'For example, the Hermes Runtime has a task repo named "tasks_required" located under the hrun directory of the Hermes repo.'}),"\n",(0,t.jsx)(s.pre,{children:(0,t.jsx)(s.code,{children:"tasks_required\n\u251c\u2500\u2500 CMakeLists.txt\n\u251c\u2500\u2500 hrun_admin\n\u2502\xa0\xa0 \u251c\u2500\u2500 CMakeLists.txt\n\u2502\xa0\xa0 \u251c\u2500\u2500 include\n\u2502\xa0\xa0 \u2514\u2500\u2500 src\n\u251c\u2500\u2500 proc_queue\n\u2502\xa0\xa0 \u251c\u2500\u2500 CMakeLists.txt\n\u2502\xa0\xa0 \u251c\u2500\u2500 include\n\u2502\xa0\xa0 \u2514\u2500\u2500 src\n\u251c\u2500\u2500 remote_queue\n\u2502\xa0\xa0 \u251c\u2500\u2500 CMakeLists.txt\n\u2502\xa0\xa0 \u251c\u2500\u2500 include\n\u2502\xa0\xa0 \u2514\u2500\u2500 src\n\u251c\u2500\u2500 small_message\n\u2502\xa0\xa0 \u251c\u2500\u2500 CMakeLists.txt\n\u2502\xa0\xa0 \u251c\u2500\u2500 include\n\u2502\xa0\xa0 \u2514\u2500\u2500 src\n\u251c\u2500\u2500 TASK_NAME\n\u2502\xa0\xa0 \u251c\u2500\u2500 CMakeLists.txt\n\u2502\xa0\xa0 \u251c\u2500\u2500 include\n\u2502\xa0\xa0 \u2514\u2500\u2500 src\n\u251c\u2500\u2500 worch_proc_round_robin\n\u2502\xa0\xa0 \u251c\u2500\u2500 CMakeLists.txt\n\u2502\xa0\xa0 \u251c\u2500\u2500 include\n\u2502\xa0\xa0 \u2514\u2500\u2500 src\n\u2514\u2500\u2500 worch_queue_round_robin\n    \u251c\u2500\u2500 CMakeLists.txt\n    \u251c\u2500\u2500 include\n    \u2514\u2500\u2500 src\n"})}),"\n",(0,t.jsx)(s.p,{children:"The tasks_required directory contains tasks which are required for the Hermes Runtime to function. These tasks are non-negotiable and will always be registered automatically by the runtime."}),"\n",(0,t.jsx)(s.h2,{id:"bootstrapping-a-task-library",children:"Bootstrapping a Task Library"}),"\n",(0,t.jsx)(s.p,{children:"A Task Library implements the following concepts:"}),"\n",(0,t.jsxs)(s.ol,{children:["\n",(0,t.jsxs)(s.li,{children:[(0,t.jsx)(s.strong,{children:"Task"}),": A struct containing the parameters to execute"]}),"\n",(0,t.jsxs)(s.li,{children:[(0,t.jsx)(s.strong,{children:"Task Server"}),": A class responsible for executing tasks. This is\nreleased as a shared object."]}),"\n",(0,t.jsxs)(s.li,{children:[(0,t.jsx)(s.strong,{children:"Task Client"}),": A class responsible for submitting tasks to the hermes runtime. This is released as a header file, which is included by the client program."]}),"\n"]}),"\n",(0,t.jsxs)(s.p,{children:['To easily bootstrap a task lib, Hermes provides a python-based code generator called make_task. This script assumes a Linux system at this time (Windows has a different pathing system). Let\'s say you want to create a new task lib named "compress" for creating a factory of compression libraries. The task lib is located in the task repo ',(0,t.jsx)(s.code,{children:"${HOME}/my_task_repo"}),"."]}),"\n",(0,t.jsx)(s.pre,{children:(0,t.jsx)(s.code,{className:"language-bash",children:"codegen/make_task ${HOME}/my_task_repo/compress\n"})}),"\n",(0,t.jsx)(s.p,{children:"This will create a task lib with the following directory structure:"}),"\n",(0,t.jsx)(s.pre,{children:(0,t.jsx)(s.code,{className:"language-bash",children:"compress\n\u251c\u2500\u2500 CMakeLists.txt\n\u251c\u2500\u2500 include\n\u2502\xa0\xa0 \u2514\u2500\u2500 compress\n\u2502\xa0\xa0     \u251c\u2500\u2500 compress.h\n\u2502\xa0\xa0     \u251c\u2500\u2500 compress_lib_exec.h\n\u2502\xa0\xa0     \u251c\u2500\u2500 compress_methods.h\n\u2502\xa0\xa0     \u251c\u2500\u2500 compress_methods.yaml\n\u2502\xa0\xa0     \u2514\u2500\u2500 compress_tasks.h\n\u2514\u2500\u2500 src\n    \u251c\u2500\u2500 CMakeLists.txt\n    \u2514\u2500\u2500 compress.cc\n"})}),"\n",(0,t.jsx)(s.p,{children:"The main files to edit:"}),"\n",(0,t.jsxs)(s.ol,{children:["\n",(0,t.jsxs)(s.li,{children:[(0,t.jsx)(s.code,{children:"include/compress/compress.h"}),":\nThis is the ",(0,t.jsx)(s.strong,{children:"Task Client"}),". User applications (e.g., VPIC, WRF) include this file and use it to submit tasks to the Hermes Runtime."]}),"\n",(0,t.jsxs)(s.li,{children:[(0,t.jsx)(s.code,{children:"include/compress/compress_methods.yaml"}),":\nDefines the name of all methods that will be implemented in the ",(0,t.jsx)(s.strong,{children:"Task Server"}),". This file will be converted into an enumeration."]}),"\n",(0,t.jsxs)(s.li,{children:[(0,t.jsx)(s.code,{children:"include/compress/compress_tasks.h"}),":\nDefines the ",(0,t.jsx)(s.strong,{children:"Tasks"})," that can be constructed. Tasks are implemented as structs that are compatible with shared memory.\nTasks will only implement methods to serialize and copy the task. The actual function of the task is implemented\nin the Task Server."]}),"\n",(0,t.jsxs)(s.li,{children:[(0,t.jsx)(s.code,{children:"src/compress/compress.cc"}),":\nThis is the ",(0,t.jsx)(s.strong,{children:"Task Server"}),". This file will be compiled into a shared object that can be dynamically loaded by the runtime. The task server must include handlers which take as input a task struct and then run a function over it."]}),"\n"]}),"\n",(0,t.jsx)(s.p,{children:"Files that are automatically generated:"}),"\n",(0,t.jsxs)(s.ol,{children:["\n",(0,t.jsxs)(s.li,{children:[(0,t.jsx)(s.code,{children:"include/compress/compress_lib_exec.h"}),":\nThis is included in ",(0,t.jsx)(s.code,{children:"compress.cc"})," automatically.\nThis is an internal file not meant to be included anywhere else.\nThis file produces code to route tasks to functions in compress.cc."]}),"\n",(0,t.jsxs)(s.li,{children:[(0,t.jsx)(s.code,{children:"include/compress/compress_methods.h"}),":\nThis defines an enumeration containing all methods defined\nin compress_methods.yaml. It is included automatically by ",(0,t.jsx)(s.code,{children:"compress_tasks.h"})]}),"\n"]}),"\n",(0,t.jsx)(s.h3,{id:"overview-of-bootstrapped-code",children:"Overview of Bootstrapped Code"}),"\n",(0,t.jsx)(s.p,{children:"The bootstrap method will create a task library with the following methods: Create, Destruct, and Custom. Create and Destruct are required\nby all Task Libraries and should not be removed. Custom is optional and provides an overview of the methods available to you for creating custom tasks. The code generated can be compiled immediately by adding it as a subdirectory to the root CMake of the task repo."}),"\n",(0,t.jsx)(s.h3,{id:"createtask",children:"CreateTask"}),"\n",(0,t.jsx)(s.p,{children:"CreateTask is responsible for initially registering a task state in the Hermes Runtime. This is analgous to class constructors."}),"\n",(0,t.jsx)(s.h4,{id:"task-struct",children:"Task Struct"}),"\n",(0,t.jsxs)(s.p,{children:["In ",(0,t.jsx)(s.code,{children:"include/compress/compress_tasks.h"})]}),"\n",(0,t.jsx)(s.pre,{children:(0,t.jsx)(s.code,{className:"language-cpp",children:'using hrun::Admin::CreateTaskStateTask;\nstruct ConstructTask : public CreateTaskStateTask {\n  /** SHM default constructor */\n  HSHM_ALWAYS_INLINE explicit\n  ConstructTask(hipc::Allocator *alloc)\n  : CreateTaskStateTask(alloc) {}\n\n  /** Emplace constructor */\n  HSHM_ALWAYS_INLINE explicit\n  ConstructTask(hipc::Allocator *alloc,\n                const TaskNode &task_node,\n                const DomainId &domain_id,\n                const std::string &state_name,\n                const TaskStateId &id,\n                const std::vector<PriorityInfo> &queue_info)\n      : CreateTaskStateTask(alloc, task_node, domain_id, state_name,\n                            "compress", id, queue_info) {\n    // Custom params\n  }\n\n  HSHM_ALWAYS_INLINE\n  ~ConstructTask() {\n    // Custom params\n  }\n};\n'})}),"\n",(0,t.jsx)(s.p,{children:"This file defines the task struct that will be communicated between clients and the runtime. This task must always include a minimum of the above parameters. The order of parameters\nshould not be changed. Any additional parameters should be appended after queue_info."}),"\n",(0,t.jsxs)(s.ul,{children:["\n",(0,t.jsxs)(s.li,{children:[(0,t.jsx)(s.code,{children:"alloc"}),": The shared-memory allocator the task was allocated with"]}),"\n",(0,t.jsxs)(s.li,{children:[(0,t.jsx)(s.code,{children:"task_node"}),': Tasks can spawn subtasks. This ability we refer to as Task Graphs. TaskNode stores the root of the Task Graph and the depth of this task in the Task Graph. For "Root" tasks, the TaskNode will be the unique ID of the task with a depth of 0.']}),"\n",(0,t.jsxs)(s.li,{children:[(0,t.jsx)(s.code,{children:"domain_id"}),": Tasks can be scheduled or replicated over a domain of nodes. A domain is analogous to an MPI communicator. However, domains theoretically support dynamic node registration, unlike MPI."]}),"\n",(0,t.jsxs)(s.li,{children:[(0,t.jsx)(s.code,{children:"state_name"}),": This is a semantic, unique, user-defined name to give the state. The state can be queried using this name in the future."]}),"\n",(0,t.jsxs)(s.li,{children:[(0,t.jsx)(s.code,{children:"state_id"}),": This is a unique integer ID to give the state. This is an optional parameter that can be equal to null. When null, the state id is allocated automatically by the runtime and returned as the ",(0,t.jsx)(s.code,{children:"id_"})," parameter in the base class CreateTaskStateTask."]}),"\n",(0,t.jsxs)(s.li,{children:[(0,t.jsx)(s.code,{children:"queue_info"}),": Provides control over the queue to spawn to interact with this state. Each task state"]}),"\n"]}),"\n",(0,t.jsx)(s.h4,{id:"task-client",children:"Task Client"}),"\n",(0,t.jsxs)(s.p,{children:["In ",(0,t.jsx)(s.code,{children:"include/compress/compress.h"}),":"]}),"\n",(0,t.jsx)(s.pre,{children:(0,t.jsx)(s.code,{className:"language-cpp",children:"/** Async create a task state */\nHSHM_ALWAYS_INLINE\nLPointer<ConstructTask> AsyncCreate(const TaskNode &task_node,\n                                    const DomainId &domain_id,\n                                    const std::string &state_name) {\n  id_ = TaskStateId::GetNull();\n  QueueManagerInfo &qm = HRUN_CLIENT->server_config_.queue_manager_;\n  std::vector<PriorityInfo> queue_info = {\n      {1, 1, qm.queue_depth_, 0},\n      {1, 1, qm.queue_depth_, QUEUE_LONG_RUNNING},\n      {qm.max_lanes_, qm.max_lanes_, qm.queue_depth_, QUEUE_LOW_LATENCY}\n  };\n  return HRUN_ADMIN->AsyncCreateTaskState<ConstructTask>(\n      task_node, domain_id, state_name, id_, queue_info);\n}\nHRUN_TASK_NODE_ROOT(AsyncCreate)\ntemplate<typename ...Args>\nHSHM_ALWAYS_INLINE\nvoid CreateRoot(Args&& ...args) {\n  LPointer<ConstructTask> task =\n      AsyncCreateRoot(std::forward<Args>(args)...);\n  task->Wait();\n  id_ = task->id_;\n  queue_id_ = QueueId(id_);\n  HRUN_CLIENT->DelTask(task);\n}\n"})}),"\n",(0,t.jsxs)(s.p,{children:["This code is called in client programs, such as VPIC, HACC, etc. ",(0,t.jsx)(s.code,{children:"CreateRoot"})," calls ",(0,t.jsx)(s.code,{children:"AsyncCreateRoot"}),", which will allocate, construct, and enqueue the CreateTask. ",(0,t.jsx)(s.code,{children:"HRUN_TASK_NODE_ROOT"}),' is a macro that creates the\nAsyncCreateRoot method. The "Root" suffix implies that the method\nis going to spawn a task that represents the root of a Task Graph.\nThis distinction is needed for avoiding potential deadlocks and\nconsistency problems.']}),"\n",(0,t.jsx)(s.h4,{id:"task-server",children:"Task Server"}),"\n",(0,t.jsxs)(s.p,{children:["In ",(0,t.jsx)(s.code,{children:"src/compress.cc"}),":"]}),"\n",(0,t.jsx)(s.pre,{children:(0,t.jsx)(s.code,{className:"language-cpp",children:"void Construct(ConstructTask *task, RunContext &rctx) {\n  task->SetModuleComplete();\n}\n"})}),"\n",(0,t.jsx)(s.p,{children:"This is the method that the ConstructTask will be routed to."}),"\n",(0,t.jsx)(s.h3,{id:"destructtask",children:"DestructTask"}),"\n",(0,t.jsxs)(s.p,{children:["The destruct task is responsible for releasing the Task State when the runtime is shutting down or when the user intentionally frees it. The DestructTask defined in ",(0,t.jsx)(s.code,{children:"compress_tasks.h"})," should never be modified, and is the same across all tasks. It should not take additional parameters since the runtime shutdown process will fail."]}),"\n",(0,t.jsx)(s.h2,{id:"overview-of-task-submission-and-queueing",children:"Overview of Task Submission and Queueing"}),"\n",(0,t.jsx)(s.p,{children:"Communication with the Hermes Runtime is accomplished through queueing.\nThe data structure is termed MultiQueue. The MultiQueue is a shared-memory, lock-free, concurrent priority queue. For each Task State,\nan associated MultiQueue will be created. MultiQueues are defined\nby a vector of PriorityInfo structs."}),"\n",(0,t.jsx)(s.pre,{children:(0,t.jsx)(s.code,{className:"language-cpp",children:"struct PriorityInfo {\n  u32 max_lanes_;       /**< Maximum number of lanes in the queue */\n  u32 num_lanes_;       /**< Current number of lanes in use */\n  u32 depth_;           /**< The maximum depth of individual lanes */\n  bitfield32_t flags_;  /**< Scheduling hints for the queue */\n};\n"})}),"\n",(0,t.jsx)(s.p,{children:"A lane is a multiple-producer, single-consumer lock-free shared memory\nqueue. Each lane is scheduled on workers independently. A lane represents\nthe unit of concurrency in the Hermes Runtime."}),"\n",(0,t.jsxs)(s.p,{children:["In ",(0,t.jsx)(s.code,{children:"include/compress/compress.h"}),":"]}),"\n",(0,t.jsx)(s.pre,{children:(0,t.jsx)(s.code,{className:"language-cpp",children:"/** Async create a task state */\nHSHM_ALWAYS_INLINE\nLPointer<ConstructTask> AsyncCreate(const TaskNode &task_node,\n                                    const DomainId &domain_id,\n                                    const std::string &state_name) {\n  id_ = TaskStateId::GetNull();\n  QueueManagerInfo &qm = HRUN_CLIENT->server_config_.queue_manager_;\n  std::vector<PriorityInfo> queue_info = {\n      {1, 1, qm.queue_depth_, 0},\n      {1, 1, qm.queue_depth_, QUEUE_LONG_RUNNING},\n      {qm.max_lanes_, qm.max_lanes_, qm.queue_depth_, QUEUE_LOW_LATENCY}\n  };\n  return HRUN_ADMIN->AsyncCreateTaskState<ConstructTask>(\n      task_node, domain_id, state_name, id_, queue_info);\n}\n"})}),"\n",(0,t.jsx)(s.p,{children:"This will create a MultiQueue with three priorities. Each element of\nthe vector is a Priority. Priority 0 will contain a single lane with\nthe user-configured default queue depth. Priority 1 will also\nbe a single lane, but with QUEUE_LONG_RUNNING flag. Tasks in these\nlanes will be scheduled on diferent workers for QUEUE_LOW_LATENCY\nlanes for performance reasons."}),"\n",(0,t.jsx)(s.h2,{id:"creating-custom-tasks",children:"Creating Custom Tasks"}),"\n",(0,t.jsx)(s.p,{children:"Now that the task library has been bootstrapped, this section will go over how to add new tasks."}),"\n",(0,t.jsxs)(s.h3,{id:"modify-compress_methodsyaml",children:["Modify ",(0,t.jsx)(s.code,{children:"compress_methods.yaml"})]}),"\n",(0,t.jsx)(s.p,{children:"Initially, the file contains:"}),"\n",(0,t.jsx)(s.pre,{children:(0,t.jsx)(s.code,{className:"language-yaml",children:"kCustom: 0\n"})}),"\n",(0,t.jsx)(s.p,{children:"For compression, let's say we want to have two methods: Compress and\nDecompress. We would modify this file to contain the following:"}),"\n",(0,t.jsx)(s.pre,{children:(0,t.jsx)(s.code,{className:"language-yaml",children:"kCompress: 0\nkDecompress: 1\n"})}),"\n",(0,t.jsx)(s.p,{children:"We then need to refresh the methods in this repo. This will autogenerate\ncode needed by the runtime to route tasks to these functions. This\nis accomplished through the refresh_methods code generator:"}),"\n",(0,t.jsx)(s.pre,{children:(0,t.jsx)(s.code,{className:"language-bash",children:"codegen/refresh_methods ${HOME}/my_task_repo\n"})}),"\n",(0,t.jsx)(s.p,{children:"This will refresh all methods in the my_task_repo. This should be\na very fast operation, so it just does it for all tasks in the\ndirectory to avoid specifying a specific task library."}),"\n",(0,t.jsxs)(s.h3,{id:"modify-compress_tasksh",children:["Modify ",(0,t.jsx)(s.code,{children:"compress_tasks.h"})]}),"\n",(0,t.jsx)(s.p,{children:"Let's add the following task for representing the compression method."}),"\n",(0,t.jsx)(s.pre,{children:(0,t.jsx)(s.code,{className:"language-cpp",children:"struct CompressTask : public Task, TaskFlags<TF_SRL_SYM> {\n  IN int compress_method_;\n  IN hipc::ShmArchive<hipc::string> data_;\n\n  /** SHM default constructor */\n  HSHM_ALWAYS_INLINE explicit\n  CompressTask(hipc::Allocator *alloc) : Task(alloc) {}\n\n  /** Emplace constructor */\n  HSHM_ALWAYS_INLINE explicit\n  CompressTask(hipc::Allocator *alloc,\n             const TaskNode &task_node,\n             const DomainId &domain_id,\n             const TaskStateId &state_id,\n             int compress_method,\n             const std::string &data) : Task(alloc) {\n    // Initialize task\n    task_node_ = task_node;\n    lane_hash_ = 0;\n    prio_ = TaskPrio::kLowLatency;\n    task_state_ = state_id;\n    method_ = Method::kCustom;\n    task_flags_.SetBits(TASK_UNORDERED | TASK_LANE_ANY);\n    domain_id_ = domain_id;\n\n    // Custom params\n    compress_method_ = compress_method;\n    HSHM_MAKE_AR(data_, alloc, data);\n  }\n\n  /** (De)serialize message call */\n  template<typename Ar>\n  void SerializeStart(Ar &ar) {\n    task_serialize<Ar>(ar);\n    ar(compress_method_, data_);\n  }\n\n  /** (De)serialize message return */\n  template<typename Ar>\n  void SerializeEnd(u32 replica, Ar &ar) {\n  }\n\n  /** Create group */\n  HSHM_ALWAYS_INLINE\n  u32 GetGroup(hshm::charbuf &group) {\n    return TASK_UNORDERED;\n  }\n};\n"})}),"\n",(0,t.jsxs)(s.h4,{id:"the-taskflags-base-class",children:["The ",(0,t.jsx)(s.code,{children:"TaskFlags"})," base class"]}),"\n",(0,t.jsx)(s.p,{children:"The CompressTask inherits from TaskFlags, which defines compile-time\nproperties of the task -- particularly the class methods."}),"\n",(0,t.jsx)(s.pre,{children:(0,t.jsx)(s.code,{className:"language-cpp",children:"struct CompressTask : public Task, TaskFlags<TF_SRL_SYM> {\n// };\n"})}),"\n",(0,t.jsx)(s.p,{children:"Here, the TaskFlags has the parameter TF_SRL_SYM. This constant implies\nthe task supports serialization methods. These methods will be called\ninternally when a task gets dispersed to remote nodes."}),"\n",(0,t.jsx)(s.p,{children:"SerializeStart is called when a task is being shipped to a remote\nnode for execution. SerializeEnd is called when returning from\nthe remote node. In this way, the task can store both the input\nand output of the operation performed. This avoids having a separate\ncompletion queue."}),"\n",(0,t.jsx)(s.p,{children:"There are a few kinds of tasks:"}),"\n",(0,t.jsxs)(s.ol,{children:["\n",(0,t.jsx)(s.li,{children:"TF_LOCAL: tasks that execute only on the local node. They cannot\nbe shipped to remote nodes and they cannot be replicated."}),"\n",(0,t.jsx)(s.li,{children:"TF_SRL_SYM: tasks that execute potentially on a remote node. They\ncannot be replicated. Must implement SerializeStart and SerializeEnd."}),"\n",(0,t.jsx)(s.li,{children:"TF_SRL_SYM | TF_REPLICA: tasks that can be shipped to a remote node\nand support replication. Must implement ReplicateStart, ReplicateEnd, Dup, DupEnd."}),"\n",(0,t.jsx)(s.li,{children:"TF_SRL_ASYM_START: task has asymmetric serialization and deserialization methods for input variables (SaveStart, LoadStart instead of SerializeStart)"}),"\n",(0,t.jsx)(s.li,{children:"TF_SRL_ASYM_END: task has asymmetric serialization and deserialization methods for output variables (SaveEnd, LoadEnd instead of SerializeEnd)"}),"\n"]}),"\n",(0,t.jsx)(s.p,{children:"TODO: explain what each candidate method does"}),"\n",(0,t.jsx)(s.h4,{id:"task-constructor",children:"Task Constructor"}),"\n",(0,t.jsx)(s.p,{children:"We will provide a brief overview of an example implementaion of CompressTask. DecompressTask looks similar, so we don't repeat."}),"\n",(0,t.jsx)(s.pre,{children:(0,t.jsx)(s.code,{className:"language-cpp",children:"/** Emplace constructor */\nHSHM_ALWAYS_INLINE explicit\nCompressTask(hipc::Allocator *alloc,\n           const TaskNode &task_node,\n           const DomainId &domain_id,\n           const TaskStateId &state_id,\n           int compress_method,\n           const std::string &data) : Task(alloc) {\n  // Initialize task\n  task_node_ = task_node;\n  lane_hash_ = 0;\n  prio_ = TaskPrio::kLowLatency;\n  task_state_ = state_id;\n  method_ = Method::kCustom;\n  task_flags_.SetBits(TASK_UNORDERED | TASK_LANE_ANY);\n  domain_id_ = domain_id;\n\n  // Custom params\n  compress_method_ = compress_method;\n  HSHM_MAKE_AR(data_, alloc, data);\n}\n"})}),"\n",(0,t.jsxs)(s.ul,{children:["\n",(0,t.jsxs)(s.li,{children:[(0,t.jsx)(s.code,{children:"lane_hash_"}),": The lane of the MultiQueue a request is keyed to if\nTASK_LANE_ANY is not set under the task flags. This gives concurrency control. Tasks in\nthe same lane will be executed sequentially if necessary."]}),"\n",(0,t.jsxs)(s.li,{children:[(0,t.jsx)(s.code,{children:"prio_"}),": The priority of the task. KLowLatency is priority 2."]}),"\n",(0,t.jsxs)(s.li,{children:[(0,t.jsx)(s.code,{children:"method_"}),": The method the task will be routed to by the runtime"]}),"\n",(0,t.jsxs)(s.li,{children:[(0,t.jsx)(s.code,{children:"task_flags_"}),": Various flags that can improve performance"]}),"\n"]}),"\n",(0,t.jsxs)(s.h3,{id:"modify-compresscc",children:["Modify ",(0,t.jsx)(s.code,{children:"compress.cc"})]}),"\n",(0,t.jsx)(s.pre,{children:(0,t.jsx)(s.code,{className:"language-cpp",children:"void Compress(CompressTask *task, RunContext &rctx) {\n  task->SetModuleComplete();\n}\n\nvoid Decompress(DecompressTask *task, RunContext &rctx) {\n  task->SetModuleComplete();\n}\n"})}),"\n",(0,t.jsx)(s.p,{children:"Create the callback functions in the task server.\ntask->SetModuleComplete() indicates that the task is completely finished.\nLong-running tasks should not use this function."}),"\n",(0,t.jsxs)(s.h3,{id:"modify-compressh",children:["Modify ",(0,t.jsx)(s.code,{children:"compress.h"})]}),"\n",(0,t.jsx)(s.pre,{children:(0,t.jsx)(s.code,{className:"language-cpp",children:"HSHM_ALWAYS_INLINE\nvoid AsyncCompressConstruct(CompressTask *task,\n                          const TaskNode &task_node,\n                          const DomainId &domain_id,\n                          int compress_method,\n                          const std::string &data) {\n  HRUN_CLIENT->ConstructTask<CompressTask>>(\n      task, task_node, domain_id, id_, compress_method, data);\n}\nHSHM_ALWAYS_INLINE\nvoid CompressRoot(const DomainId &domain_id,\n                  int compress_method,\n                  const std::string &data) {\n  LPointer<hrunpq::TypedPushTask<CompressTask>> task = AsyncCompressRoot(domain_id);\n  task.ptr_->Wait();\n}\nHRUN_TASK_NODE_PUSH_ROOT(Compress);\n"})}),"\n",(0,t.jsx)(s.p,{children:"CompressRoot will be called by clients directly.\nHRUN_TASK_NODE_PUSH_ROOT will create various helper methods that\neventually call AsyncCompressConstruct. LPointer is a struct that\ncontains a shared-memory pointer to a task and its corresponding\nprivate-memory pointer."}),"\n",(0,t.jsxs)(s.p,{children:["hrunpq::TypedPushTask represents a task that is stored inside of the\n",(0,t.jsx)(s.strong,{children:"process queue"}),". The process queue is a single-priority queue that\nconnects clients to the Hermes runtime. Tasks in this queue are keyed\nto lanes based on standard thread ID. This ensures that all tasks\noriginating from the same thread are in the same lane. This helps\ngive consistency guarantees for I/O operations."]}),"\n",(0,t.jsx)(s.h3,{id:"task-methods",children:"Task Methods"}),"\n",(0,t.jsx)(s.p,{children:"The task methods will be discussed in sections 6, 7, and 8."}),"\n",(0,t.jsx)(s.h2,{id:"registering-a-task-library",children:"Registering a Task Library"}),"\n",(0,t.jsx)(s.p,{children:"After creating a new task library, it must be registered with\nthe Hermes Runtime. This can be done either programmatically or\nthrough configuration."}),"\n",(0,t.jsxs)(s.p,{children:["Through configuration, you must edit the Hermes runtime configuration.\nAn example configuration is stored in ",(0,t.jsx)(s.code,{children:"${HERMES_ROOT}/config/hermes_server_default.yaml"}),"."]}),"\n",(0,t.jsx)(s.pre,{children:(0,t.jsx)(s.code,{className:"language-yaml",children:'task_registry:\n  [\n    "hermes_mdm",\n    "hermes_blob_mdm",\n    "hermes_bucket_mdm",\n    "hermes_data_op",\n    "data_stager",\n    "posix_bdev",\n    "ram_bdev",\n    "compress",\n  ]\n'})}),"\n",(0,t.jsx)(s.p,{children:"This can be passed to the Hermes runtime using the HERMES_CONF environment\nvariable."}),"\n",(0,t.jsx)(s.h2,{id:"task-grouping-worker-polling-and-deadlock-prevention",children:"Task Grouping, Worker Polling, and Deadlock Prevention"}),"\n",(0,t.jsx)(s.p,{children:"This section will provide more insight on how queues are polled\nand processed in the Hermes Runtime to provide fine-grained control\nover scheduling and concurrency."}),"\n",(0,t.jsxs)(s.p,{children:["Tasks must all implement a function called ",(0,t.jsx)(s.code,{children:"GetGroup"}),". Task groups are used to enable look-ahead capabilities with safety. A ",(0,t.jsx)(s.strong,{children:"Task Group"})," represents a collection of tasks that modify the same metadata structure and need to be sequentially executed. For example, the Bucket ID is\nused as the group for calling the bucket methods GetSize and UpdateSize.\nThis ensures that GetSize and UpdateSize will be executed in sequence when\nmade to the same bucket. Certain operations do not require any synchronization (e.g., stateless methods) and can return a group of TASK_UNORDERED."]}),"\n",(0,t.jsxs)(s.p,{children:["A ",(0,t.jsx)(s.strong,{children:"Task Node"})," represents the location of a task in the overall\ntask graph. There is no Task Graph data structure, it's a concept.\nWhen a task spawns a subtask, it can be conceptually be considered\nas a task graph. Tasks apart of the same task graph will be executed\nsimultaneously --regardless of group -- to prevent deadlocks in the\ncase where two tasks from the same graph are keyed to the same queue and lane."]}),"\n",(0,t.jsx)(s.h2,{id:"building-a-replicatable-task",children:"Building a Replicatable Task"}),"\n",(0,t.jsx)(s.p,{children:"To make a task support replication, set the TF_REPLICA flag. This\nwill indicate that a task implements the replication methods."}),"\n",(0,t.jsx)(s.pre,{children:(0,t.jsx)(s.code,{className:"language-cpp",children:"struct CompressTask : public Task, TaskFlags<TF_SRL_SYM | TF_REPLICA> {\n  IN compress_type_;\n  IN hipc::ShmArchive<hipc::string> data_;\n  OUT hipc::ShmArchive<hipc::vector<size_t>> sizes_;\n  OUT size_t final_size_;\n\n  /** (De)serialize message call */\n  template<typename Ar>\n  void SerializeStart(Ar &ar) {\n    task_serialize<Ar>(ar);\n    ar(compress_type_, data_);\n  }\n\n  /** (De)serialize message return */\n  template<typename Ar>\n  void SerializeEnd(u32 replica, Ar &ar) {\n    ar(sizes_, final_size_);\n  }\n\n  /** Duplicate message */\n  void Dup(hipc::Allocator *alloc, CustomTask &other) {\n    task_dup(other);\n    compress_type_ = other.compress_type_;\n    HSHM_MAKE_AR(data_, alloc, other.data_);\n  }\n\n  /** Process duplicate message output */\n  void DupEnd(u32 replica, CustomTask &dup_task) {\n    (*sizes_)[repclica] = other.size_;\n  }\n\n  /** Begin replication */\n  void ReplicateStart(u32 count) {\n    size_->resize(count);\n  }\n\n  /** Finalize replication */\n  void ReplicateEnd() {\n    size_t final_size_ = std::numeric_limits<size_t>::min();\n    for (size_t &size : sizes_) {\n      if (final_size_ > size) {\n        final_size_ = size;\n      }\n    }\n  }\n};\n"})}),"\n",(0,t.jsxs)(s.ul,{children:["\n",(0,t.jsxs)(s.li,{children:[(0,t.jsx)(s.code,{children:"SerializeStart"}),": Will serialize and deserialize the ",(0,t.jsx)(s.em,{children:"input"})," parameters of the task. So anything labeled IN or INOUT."]}),"\n",(0,t.jsxs)(s.li,{children:[(0,t.jsx)(s.code,{children:"SerializeEnd"}),": Will serialize and deserialize the ",(0,t.jsx)(s.em,{children:"output"}),"\nparameters of the task. So anything labeled OUT or INOUT."]}),"\n",(0,t.jsxs)(s.li,{children:[(0,t.jsx)(s.code,{children:"Dup"}),": Analogous to a copy constructor. Will make a local\ncopy of this task (no serialization involved)."]}),"\n",(0,t.jsxs)(s.li,{children:[(0,t.jsx)(s.code,{children:"DupEnd"}),": Will store the output of a replica in the original\ntask the duplicates were spawned from."]}),"\n",(0,t.jsxs)(s.li,{children:[(0,t.jsx)(s.code,{children:"ReplicateStart"}),": Used to allocate data structures in the task\nto account for the replication"]}),"\n",(0,t.jsxs)(s.li,{children:[(0,t.jsx)(s.code,{children:"ReplicateEnd"}),": Called after all replicas have returned. Can\naggregate replica otuput."]}),"\n"]}),"\n",(0,t.jsx)(s.h2,{id:"building-a-data-intensive-rdma-capable-task",children:"Building a Data-Intensive, RDMA-Capable Task"}),"\n",(0,t.jsx)(s.p,{children:"TODO: Make example based on PutBlob and GetBlob."})]})}function h(e={}){const{wrapper:s}={...(0,a.a)(),...e.components};return s?(0,t.jsx)(s,{...e,children:(0,t.jsx)(d,{...e})}):d(e)}},1151:(e,s,n)=>{n.d(s,{Z:()=>o,a:()=>r});var t=n(7294);const a={},i=t.createContext(a);function r(e){const s=t.useContext(i);return t.useMemo((function(){return"function"==typeof e?e(s):{...s,...e}}),[s,e])}function o(e){let s;return s=e.disableParentContext?"function"==typeof e.components?e.components(a):e.components||a:r(e.components),t.createElement(i.Provider,{value:s},e.children)}}}]);
\ No newline at end of file
+"use strict";(self.webpackChunkgrc=self.webpackChunkgrc||[]).push([[3185],{1403:(e,s,n)=>{n.r(s),n.d(s,{assets:()=>l,contentTitle:()=>r,default:()=>h,frontMatter:()=>i,metadata:()=>o,toc:()=>c});var t=n(5893),a=n(1151);const i={},r="Runtime",o={id:"hermes/components/runtime",title:"Runtime",description:"Hermes is built as a plugin to the Hermes Runtime, a distributed task processing framework",source:"@site/docs/03-hermes/08-components/07-runtime.md",sourceDirName:"03-hermes/08-components",slug:"/hermes/components/runtime",permalink:"/docs/hermes/components/runtime",draft:!1,unlisted:!1,tags:[],version:"current",sidebarPosition:7,frontMatter:{},sidebar:"tutorialSidebar",previous:{title:"Data Staging",permalink:"/docs/hermes/components/data-staging"},next:{title:"Distributed Metadata",permalink:"/docs/hermes/components/distributed-metadata"}},l={},c=[{value:"Task Repos and Task Libraries",id:"task-repos-and-task-libraries",level:2},{value:"Bootstrapping a Task Library",id:"bootstrapping-a-task-library",level:2},{value:"Overview of Bootstrapped Code",id:"overview-of-bootstrapped-code",level:3},{value:"CreateTask",id:"createtask",level:3},{value:"Task Struct",id:"task-struct",level:4},{value:"Task Client",id:"task-client",level:4},{value:"Task Server",id:"task-server",level:4},{value:"DestructTask",id:"destructtask",level:3},{value:"Overview of Task Submission and Queueing",id:"overview-of-task-submission-and-queueing",level:2},{value:"Creating Custom Tasks",id:"creating-custom-tasks",level:2},{value:"Modify <code>compress_methods.yaml</code>",id:"modify-compress_methodsyaml",level:3},{value:"Modify <code>compress_tasks.h</code>",id:"modify-compress_tasksh",level:3},{value:"The <code>TaskFlags</code> base class",id:"the-taskflags-base-class",level:4},{value:"Task Constructor",id:"task-constructor",level:4},{value:"Modify <code>compress.cc</code>",id:"modify-compresscc",level:3},{value:"Modify <code>compress.h</code>",id:"modify-compressh",level:3},{value:"Task Methods",id:"task-methods",level:3},{value:"Registering a Task Library",id:"registering-a-task-library",level:2},{value:"Task Grouping, Worker Polling, and Deadlock Prevention",id:"task-grouping-worker-polling-and-deadlock-prevention",level:2},{value:"Building a Replicatable Task",id:"building-a-replicatable-task",level:2},{value:"Building a Data-Intensive, RDMA-Capable Task",id:"building-a-data-intensive-rdma-capable-task",level:2}];function d(e){const s={code:"code",em:"em",h1:"h1",h2:"h2",h3:"h3",h4:"h4",li:"li",ol:"ol",p:"p",pre:"pre",strong:"strong",ul:"ul",...(0,a.a)(),...e.components};return(0,t.jsxs)(t.Fragment,{children:[(0,t.jsx)(s.h1,{id:"runtime",children:"Runtime"}),"\n",(0,t.jsx)(s.p,{children:"Hermes is built as a plugin to the Hermes Runtime, a distributed task processing framework\ncapable of scheduling, replicating, distributing, processing, monitoring, and\nload balancing arbitrary tasks. Tasks define various properties which provide\ncontrol over scheduling decisions, memory management, and concurrency.\nThis section will discuss the design of the Hermes Runtime and how to develop\ncustom tasks."}),"\n",(0,t.jsx)(s.h2,{id:"task-repos-and-task-libraries",children:"Task Repos and Task Libraries"}),"\n",(0,t.jsxs)(s.p,{children:["The Hermes Runtime is used for executing arbitrary tasks. Developers can create\nnew tasks and release them using a decentralized package management design,\nsimilar to spack. This is accomplished through ",(0,t.jsx)(s.strong,{children:"task repos"}),"."]}),"\n",(0,t.jsxs)(s.p,{children:["A task repo is a directory which contains a set of ",(0,t.jsx)(s.strong,{children:"task libraries"}),". A\ntask library (or lib) provides the functionality to submit and execute tasks.\nTask libs follow the single responsibility principle. Multiple task libs should\nbe created to separate unrelated or loosely related functionality."]}),"\n",(0,t.jsx)(s.p,{children:'For example, the Hermes Runtime has a task repo named "tasks_required" located under the hrun directory of the Hermes repo.'}),"\n",(0,t.jsx)(s.pre,{children:(0,t.jsx)(s.code,{children:"tasks_required\n\u251c\u2500\u2500 CMakeLists.txt\n\u251c\u2500\u2500 hrun_admin\n\u2502\xa0\xa0 \u251c\u2500\u2500 CMakeLists.txt\n\u2502\xa0\xa0 \u251c\u2500\u2500 include\n\u2502\xa0\xa0 \u2514\u2500\u2500 src\n\u251c\u2500\u2500 proc_queue\n\u2502\xa0\xa0 \u251c\u2500\u2500 CMakeLists.txt\n\u2502\xa0\xa0 \u251c\u2500\u2500 include\n\u2502\xa0\xa0 \u2514\u2500\u2500 src\n\u251c\u2500\u2500 remote_queue\n\u2502\xa0\xa0 \u251c\u2500\u2500 CMakeLists.txt\n\u2502\xa0\xa0 \u251c\u2500\u2500 include\n\u2502\xa0\xa0 \u2514\u2500\u2500 src\n\u251c\u2500\u2500 small_message\n\u2502\xa0\xa0 \u251c\u2500\u2500 CMakeLists.txt\n\u2502\xa0\xa0 \u251c\u2500\u2500 include\n\u2502\xa0\xa0 \u2514\u2500\u2500 src\n\u251c\u2500\u2500 TASK_NAME\n\u2502\xa0\xa0 \u251c\u2500\u2500 CMakeLists.txt\n\u2502\xa0\xa0 \u251c\u2500\u2500 include\n\u2502\xa0\xa0 \u2514\u2500\u2500 src\n\u251c\u2500\u2500 worch_proc_round_robin\n\u2502\xa0\xa0 \u251c\u2500\u2500 CMakeLists.txt\n\u2502\xa0\xa0 \u251c\u2500\u2500 include\n\u2502\xa0\xa0 \u2514\u2500\u2500 src\n\u2514\u2500\u2500 worch_queue_round_robin\n    \u251c\u2500\u2500 CMakeLists.txt\n    \u251c\u2500\u2500 include\n    \u2514\u2500\u2500 src\n"})}),"\n",(0,t.jsx)(s.p,{children:"The tasks_required directory contains tasks which are required for the Hermes Runtime to function. These tasks are non-negotiable and will always be registered automatically by the runtime."}),"\n",(0,t.jsx)(s.h2,{id:"bootstrapping-a-task-library",children:"Bootstrapping a Task Library"}),"\n",(0,t.jsx)(s.p,{children:"A Task Library implements the following concepts:"}),"\n",(0,t.jsxs)(s.ol,{children:["\n",(0,t.jsxs)(s.li,{children:[(0,t.jsx)(s.strong,{children:"Task"}),": A struct containing the parameters to execute"]}),"\n",(0,t.jsxs)(s.li,{children:[(0,t.jsx)(s.strong,{children:"Task Server"}),": A class responsible for executing tasks. This is\nreleased as a shared object."]}),"\n",(0,t.jsxs)(s.li,{children:[(0,t.jsx)(s.strong,{children:"Task Client"}),": A class responsible for submitting tasks to the hermes runtime. This is released as a header file, which is included by the client program."]}),"\n"]}),"\n",(0,t.jsxs)(s.p,{children:['To easily bootstrap a task lib, Hermes provides a python-based code generator called make_task. This script assumes a Linux system at this time (Windows has a different pathing system). Let\'s say you want to create a new task lib named "compress" for creating a factory of compression libraries. The task lib is located in the task repo ',(0,t.jsx)(s.code,{children:"${HOME}/my_task_repo"}),"."]}),"\n",(0,t.jsx)(s.pre,{children:(0,t.jsx)(s.code,{className:"language-bash",children:"codegen/make_task ${HOME}/my_task_repo/compress\n"})}),"\n",(0,t.jsx)(s.p,{children:"This will create a task lib with the following directory structure:"}),"\n",(0,t.jsx)(s.pre,{children:(0,t.jsx)(s.code,{className:"language-bash",children:"compress\n\u251c\u2500\u2500 CMakeLists.txt\n\u251c\u2500\u2500 include\n\u2502\xa0\xa0 \u2514\u2500\u2500 compress\n\u2502\xa0\xa0     \u251c\u2500\u2500 compress.h\n\u2502\xa0\xa0     \u251c\u2500\u2500 compress_lib_exec.h\n\u2502\xa0\xa0     \u251c\u2500\u2500 compress_methods.h\n\u2502\xa0\xa0     \u251c\u2500\u2500 compress_methods.yaml\n\u2502\xa0\xa0     \u2514\u2500\u2500 compress_tasks.h\n\u2514\u2500\u2500 src\n    \u251c\u2500\u2500 CMakeLists.txt\n    \u2514\u2500\u2500 compress.cc\n"})}),"\n",(0,t.jsx)(s.p,{children:"The main files to edit:"}),"\n",(0,t.jsxs)(s.ol,{children:["\n",(0,t.jsxs)(s.li,{children:[(0,t.jsx)(s.code,{children:"include/compress/compress.h"}),":\nThis is the ",(0,t.jsx)(s.strong,{children:"Task Client"}),". User applications (e.g., VPIC, WRF) include this file and use it to submit tasks to the Hermes Runtime."]}),"\n",(0,t.jsxs)(s.li,{children:[(0,t.jsx)(s.code,{children:"include/compress/compress_methods.yaml"}),":\nDefines the name of all methods that will be implemented in the ",(0,t.jsx)(s.strong,{children:"Task Server"}),". This file will be converted into an enumeration."]}),"\n",(0,t.jsxs)(s.li,{children:[(0,t.jsx)(s.code,{children:"include/compress/compress_tasks.h"}),":\nDefines the ",(0,t.jsx)(s.strong,{children:"Tasks"})," that can be constructed. Tasks are implemented as structs that are compatible with shared memory.\nTasks will only implement methods to serialize and copy the task. The actual function of the task is implemented\nin the Task Server."]}),"\n",(0,t.jsxs)(s.li,{children:[(0,t.jsx)(s.code,{children:"src/compress/compress.cc"}),":\nThis is the ",(0,t.jsx)(s.strong,{children:"Task Server"}),". This file will be compiled into a shared object that can be dynamically loaded by the runtime. The task server must include handlers which take as input a task struct and then run a function over it."]}),"\n"]}),"\n",(0,t.jsx)(s.p,{children:"Files that are automatically generated:"}),"\n",(0,t.jsxs)(s.ol,{children:["\n",(0,t.jsxs)(s.li,{children:[(0,t.jsx)(s.code,{children:"include/compress/compress_lib_exec.h"}),":\nThis is included in ",(0,t.jsx)(s.code,{children:"compress.cc"})," automatically.\nThis is an internal file not meant to be included anywhere else.\nThis file produces code to route tasks to functions in compress.cc."]}),"\n",(0,t.jsxs)(s.li,{children:[(0,t.jsx)(s.code,{children:"include/compress/compress_methods.h"}),":\nThis defines an enumeration containing all methods defined\nin compress_methods.yaml. It is included automatically by ",(0,t.jsx)(s.code,{children:"compress_tasks.h"})]}),"\n"]}),"\n",(0,t.jsx)(s.h3,{id:"overview-of-bootstrapped-code",children:"Overview of Bootstrapped Code"}),"\n",(0,t.jsx)(s.p,{children:"The bootstrap method will create a task library with the following methods: Create, Destruct, and Custom. Create and Destruct are required\nby all Task Libraries and should not be removed. Custom is optional and provides an overview of the methods available to you for creating custom tasks. The code generated can be compiled immediately by adding it as a subdirectory to the root CMake of the task repo."}),"\n",(0,t.jsx)(s.h3,{id:"createtask",children:"CreateTask"}),"\n",(0,t.jsx)(s.p,{children:"CreateTask is responsible for initially registering a task state in the Hermes Runtime. This is analgous to class constructors."}),"\n",(0,t.jsx)(s.h4,{id:"task-struct",children:"Task Struct"}),"\n",(0,t.jsxs)(s.p,{children:["In ",(0,t.jsx)(s.code,{children:"include/compress/compress_tasks.h"})]}),"\n",(0,t.jsx)(s.pre,{children:(0,t.jsx)(s.code,{className:"language-cpp",children:'using hrun::Admin::CreateTaskStateTask;\nstruct ConstructTask : public CreateTaskStateTask {\n  /** SHM default constructor */\n  HSHM_ALWAYS_INLINE explicit\n  ConstructTask(hipc::Allocator *alloc)\n  : CreateTaskStateTask(alloc) {}\n\n  /** Emplace constructor */\n  HSHM_ALWAYS_INLINE explicit\n  ConstructTask(hipc::Allocator *alloc,\n                const TaskNode &task_node,\n                const DomainId &domain_id,\n                const std::string &state_name,\n                const TaskStateId &id,\n                const std::vector<PriorityInfo> &queue_info)\n      : CreateTaskStateTask(alloc, task_node, domain_id, state_name,\n                            "compress", id, queue_info) {\n    // Custom params\n  }\n\n  HSHM_ALWAYS_INLINE\n  ~ConstructTask() {\n    // Custom params\n  }\n};\n'})}),"\n",(0,t.jsx)(s.p,{children:"This file defines the task struct that will be communicated between clients and the runtime. This task must always include a minimum of the above parameters. The order of parameters\nshould not be changed. Any additional parameters should be appended after queue_info."}),"\n",(0,t.jsxs)(s.ul,{children:["\n",(0,t.jsxs)(s.li,{children:[(0,t.jsx)(s.code,{children:"alloc"}),": The shared-memory allocator the task was allocated with"]}),"\n",(0,t.jsxs)(s.li,{children:[(0,t.jsx)(s.code,{children:"task_node"}),': Tasks can spawn subtasks. This ability we refer to as Task Graphs. TaskNode stores the root of the Task Graph and the depth of this task in the Task Graph. For "Root" tasks, the TaskNode will be the unique ID of the task with a depth of 0.']}),"\n",(0,t.jsxs)(s.li,{children:[(0,t.jsx)(s.code,{children:"domain_id"}),": Tasks can be scheduled or replicated over a domain of nodes. A domain is analogous to an MPI communicator. However, domains theoretically support dynamic node registration, unlike MPI."]}),"\n",(0,t.jsxs)(s.li,{children:[(0,t.jsx)(s.code,{children:"state_name"}),": This is a semantic, unique, user-defined name to give the state. The state can be queried using this name in the future."]}),"\n",(0,t.jsxs)(s.li,{children:[(0,t.jsx)(s.code,{children:"state_id"}),": This is a unique integer ID to give the state. This is an optional parameter that can be equal to null. When null, the state id is allocated automatically by the runtime and returned as the ",(0,t.jsx)(s.code,{children:"id_"})," parameter in the base class CreateTaskStateTask."]}),"\n",(0,t.jsxs)(s.li,{children:[(0,t.jsx)(s.code,{children:"queue_info"}),": Provides control over the queue to spawn to interact with this state. Each task state"]}),"\n"]}),"\n",(0,t.jsx)(s.h4,{id:"task-client",children:"Task Client"}),"\n",(0,t.jsxs)(s.p,{children:["In ",(0,t.jsx)(s.code,{children:"include/compress/compress.h"}),":"]}),"\n",(0,t.jsx)(s.pre,{children:(0,t.jsx)(s.code,{className:"language-cpp",children:"/** Async create a task state */\nHSHM_ALWAYS_INLINE\nLPointer<ConstructTask> AsyncCreate(const TaskNode &task_node,\n                                    const DomainId &domain_id,\n                                    const std::string &state_name) {\n  id_ = TaskStateId::GetNull();\n  QueueManagerInfo &qm = HRUN_CLIENT->server_config_.queue_manager_;\n  std::vector<PriorityInfo> queue_info = {\n      {1, 1, qm.queue_depth_, 0},\n      {1, 1, qm.queue_depth_, QUEUE_LONG_RUNNING},\n      {qm.max_lanes_, qm.max_lanes_, qm.queue_depth_, QUEUE_LOW_LATENCY}\n  };\n  return HRUN_ADMIN->AsyncCreateTaskState<ConstructTask>(\n      task_node, domain_id, state_name, id_, queue_info);\n}\nHRUN_TASK_NODE_ROOT(AsyncCreate)\ntemplate<typename ...Args>\nHSHM_ALWAYS_INLINE\nvoid CreateRoot(Args&& ...args) {\n  LPointer<ConstructTask> task =\n      AsyncCreateRoot(std::forward<Args>(args)...);\n  task->Wait();\n  id_ = task->id_;\n  queue_id_ = QueueId(id_);\n  HRUN_CLIENT->DelTask(task);\n}\n"})}),"\n",(0,t.jsxs)(s.p,{children:["This code is called in client programs, such as VPIC, HACC, etc. ",(0,t.jsx)(s.code,{children:"CreateRoot"})," calls ",(0,t.jsx)(s.code,{children:"AsyncCreateRoot"}),", which will allocate, construct, and enqueue the CreateTask. ",(0,t.jsx)(s.code,{children:"HRUN_TASK_NODE_ROOT"}),' is a macro that creates the\nAsyncCreateRoot method. The "Root" suffix implies that the method\nis going to spawn a task that represents the root of a Task Graph.\nThis distinction is needed for avoiding potential deadlocks and\nconsistency problems.']}),"\n",(0,t.jsx)(s.h4,{id:"task-server",children:"Task Server"}),"\n",(0,t.jsxs)(s.p,{children:["In ",(0,t.jsx)(s.code,{children:"src/compress.cc"}),":"]}),"\n",(0,t.jsx)(s.pre,{children:(0,t.jsx)(s.code,{className:"language-cpp",children:"void Construct(ConstructTask *task, RunContext &rctx) {\n  task->SetModuleComplete();\n}\n"})}),"\n",(0,t.jsx)(s.p,{children:"This is the method that the ConstructTask will be routed to."}),"\n",(0,t.jsx)(s.h3,{id:"destructtask",children:"DestructTask"}),"\n",(0,t.jsxs)(s.p,{children:["The destruct task is responsible for releasing the Task State when the runtime is shutting down or when the user intentionally frees it. The DestructTask defined in ",(0,t.jsx)(s.code,{children:"compress_tasks.h"})," should never be modified, and is the same across all tasks. It should not take additional parameters since the runtime shutdown process will fail."]}),"\n",(0,t.jsx)(s.h2,{id:"overview-of-task-submission-and-queueing",children:"Overview of Task Submission and Queueing"}),"\n",(0,t.jsx)(s.p,{children:"Communication with the Hermes Runtime is accomplished through queueing.\nThe data structure is termed MultiQueue. The MultiQueue is a shared-memory, lock-free, concurrent priority queue. For each Task State,\nan associated MultiQueue will be created. MultiQueues are defined\nby a vector of PriorityInfo structs."}),"\n",(0,t.jsx)(s.pre,{children:(0,t.jsx)(s.code,{className:"language-cpp",children:"struct PriorityInfo {\n  u32 max_lanes_;       /**< Maximum number of lanes in the queue */\n  u32 num_lanes_;       /**< Current number of lanes in use */\n  u32 depth_;           /**< The maximum depth of individual lanes */\n  bitfield32_t flags_;  /**< Scheduling hints for the queue */\n};\n"})}),"\n",(0,t.jsx)(s.p,{children:"A lane is a multiple-producer, single-consumer lock-free shared memory\nqueue. Each lane is scheduled on workers independently. A lane represents\nthe unit of concurrency in the Hermes Runtime."}),"\n",(0,t.jsxs)(s.p,{children:["In ",(0,t.jsx)(s.code,{children:"include/compress/compress.h"}),":"]}),"\n",(0,t.jsx)(s.pre,{children:(0,t.jsx)(s.code,{className:"language-cpp",children:"/** Async create a task state */\nHSHM_ALWAYS_INLINE\nLPointer<ConstructTask> AsyncCreate(const TaskNode &task_node,\n                                    const DomainId &domain_id,\n                                    const std::string &state_name) {\n  id_ = TaskStateId::GetNull();\n  QueueManagerInfo &qm = HRUN_CLIENT->server_config_.queue_manager_;\n  std::vector<PriorityInfo> queue_info = {\n      {1, 1, qm.queue_depth_, 0},\n      {1, 1, qm.queue_depth_, QUEUE_LONG_RUNNING},\n      {qm.max_lanes_, qm.max_lanes_, qm.queue_depth_, QUEUE_LOW_LATENCY}\n  };\n  return HRUN_ADMIN->AsyncCreateTaskState<ConstructTask>(\n      task_node, domain_id, state_name, id_, queue_info);\n}\n"})}),"\n",(0,t.jsx)(s.p,{children:"This will create a MultiQueue with three priorities. Each element of\nthe vector is a Priority. Priority 0 will contain a single lane with\nthe user-configured default queue depth. Priority 1 will also\nbe a single lane, but with QUEUE_LONG_RUNNING flag. Tasks in these\nlanes will be scheduled on diferent workers for QUEUE_LOW_LATENCY\nlanes for performance reasons."}),"\n",(0,t.jsx)(s.h2,{id:"creating-custom-tasks",children:"Creating Custom Tasks"}),"\n",(0,t.jsx)(s.p,{children:"Now that the task library has been bootstrapped, this section will go over how to add new tasks."}),"\n",(0,t.jsxs)(s.h3,{id:"modify-compress_methodsyaml",children:["Modify ",(0,t.jsx)(s.code,{children:"compress_methods.yaml"})]}),"\n",(0,t.jsx)(s.p,{children:"Initially, the file contains:"}),"\n",(0,t.jsx)(s.pre,{children:(0,t.jsx)(s.code,{className:"language-yaml",children:"kCustom: 0\n"})}),"\n",(0,t.jsx)(s.p,{children:"For compression, let's say we want to have two methods: Compress and\nDecompress. We would modify this file to contain the following:"}),"\n",(0,t.jsx)(s.pre,{children:(0,t.jsx)(s.code,{className:"language-yaml",children:"kCompress: 0\nkDecompress: 1\n"})}),"\n",(0,t.jsx)(s.p,{children:"We then need to refresh the methods in this repo. This will autogenerate\ncode needed by the runtime to route tasks to these functions. This\nis accomplished through the refresh_methods code generator:"}),"\n",(0,t.jsx)(s.pre,{children:(0,t.jsx)(s.code,{className:"language-bash",children:"codegen/refresh_methods ${HOME}/my_task_repo\n"})}),"\n",(0,t.jsx)(s.p,{children:"This will refresh all methods in the my_task_repo. This should be\na very fast operation, so it just does it for all tasks in the\ndirectory to avoid specifying a specific task library."}),"\n",(0,t.jsxs)(s.h3,{id:"modify-compress_tasksh",children:["Modify ",(0,t.jsx)(s.code,{children:"compress_tasks.h"})]}),"\n",(0,t.jsx)(s.p,{children:"Let's add the following task for representing the compression method."}),"\n",(0,t.jsx)(s.pre,{children:(0,t.jsx)(s.code,{className:"language-cpp",children:"struct CompressTask : public Task, TaskFlags<TF_SRL_SYM> {\n  IN int compress_method_;\n  IN hipc::ShmArchive<hipc::string> data_;\n\n  /** SHM default constructor */\n  HSHM_ALWAYS_INLINE explicit\n  CompressTask(hipc::Allocator *alloc) : Task(alloc) {}\n\n  /** Emplace constructor */\n  HSHM_ALWAYS_INLINE explicit\n  CompressTask(hipc::Allocator *alloc,\n             const TaskNode &task_node,\n             const DomainId &domain_id,\n             const TaskStateId &state_id,\n             int compress_method,\n             const std::string &data) : Task(alloc) {\n    // Initialize task\n    task_node_ = task_node;\n    lane_hash_ = 0;\n    prio_ = TaskPrio::kLowLatency;\n    task_state_ = state_id;\n    method_ = Method::kCustom;\n    task_flags_.SetBits(TASK_UNORDERED | TASK_LANE_ANY);\n    domain_id_ = domain_id;\n\n    // Custom params\n    compress_method_ = compress_method;\n    HSHM_MAKE_AR(data_, alloc, data);\n  }\n\n  /** (De)serialize message call */\n  template<typename Ar>\n  void SerializeStart(Ar &ar) {\n    task_serialize<Ar>(ar);\n    ar(compress_method_, data_);\n  }\n\n  /** (De)serialize message return */\n  template<typename Ar>\n  void SerializeEnd(u32 replica, Ar &ar) {\n  }\n\n  /** Create group */\n  HSHM_ALWAYS_INLINE\n  u32 GetGroup(hshm::charbuf &group) {\n    return TASK_UNORDERED;\n  }\n};\n"})}),"\n",(0,t.jsxs)(s.h4,{id:"the-taskflags-base-class",children:["The ",(0,t.jsx)(s.code,{children:"TaskFlags"})," base class"]}),"\n",(0,t.jsx)(s.p,{children:"The CompressTask inherits from TaskFlags, which defines compile-time\nproperties of the task -- particularly the class methods."}),"\n",(0,t.jsx)(s.pre,{children:(0,t.jsx)(s.code,{className:"language-cpp",children:"struct CompressTask : public Task, TaskFlags<TF_SRL_SYM> {\n// };\n"})}),"\n",(0,t.jsx)(s.p,{children:"Here, the TaskFlags has the parameter TF_SRL_SYM. This constant implies\nthe task supports serialization methods. These methods will be called\ninternally when a task gets dispersed to remote nodes."}),"\n",(0,t.jsx)(s.p,{children:"SerializeStart is called when a task is being shipped to a remote\nnode for execution. SerializeEnd is called when returning from\nthe remote node. In this way, the task can store both the input\nand output of the operation performed. This avoids having a separate\ncompletion queue."}),"\n",(0,t.jsx)(s.p,{children:"There are a few kinds of tasks:"}),"\n",(0,t.jsxs)(s.ol,{children:["\n",(0,t.jsx)(s.li,{children:"TF_LOCAL: tasks that execute only on the local node. They cannot\nbe shipped to remote nodes and they cannot be replicated."}),"\n",(0,t.jsx)(s.li,{children:"TF_SRL_SYM: tasks that execute potentially on a remote node. They\ncannot be replicated. Must implement SerializeStart and SerializeEnd."}),"\n",(0,t.jsx)(s.li,{children:"TF_SRL_SYM | TF_REPLICA: tasks that can be shipped to a remote node\nand support replication. Must implement ReplicateStart, ReplicateEnd, Dup, DupEnd."}),"\n",(0,t.jsx)(s.li,{children:"TF_SRL_ASYM_START: task has asymmetric serialization and deserialization methods for input variables (SaveStart, LoadStart instead of SerializeStart)"}),"\n",(0,t.jsx)(s.li,{children:"TF_SRL_ASYM_END: task has asymmetric serialization and deserialization methods for output variables (SaveEnd, LoadEnd instead of SerializeEnd)"}),"\n"]}),"\n",(0,t.jsx)(s.p,{children:"TODO: explain what each candidate method does"}),"\n",(0,t.jsx)(s.h4,{id:"task-constructor",children:"Task Constructor"}),"\n",(0,t.jsx)(s.p,{children:"We will provide a brief overview of an example implementaion of CompressTask. DecompressTask looks similar, so we don't repeat."}),"\n",(0,t.jsx)(s.pre,{children:(0,t.jsx)(s.code,{className:"language-cpp",children:"/** Emplace constructor */\nHSHM_ALWAYS_INLINE explicit\nCompressTask(hipc::Allocator *alloc,\n           const TaskNode &task_node,\n           const DomainId &domain_id,\n           const TaskStateId &state_id,\n           int compress_method,\n           const std::string &data) : Task(alloc) {\n  // Initialize task\n  task_node_ = task_node;\n  lane_hash_ = 0;\n  prio_ = TaskPrio::kLowLatency;\n  task_state_ = state_id;\n  method_ = Method::kCustom;\n  task_flags_.SetBits(TASK_UNORDERED | TASK_LANE_ANY);\n  domain_id_ = domain_id;\n\n  // Custom params\n  compress_method_ = compress_method;\n  HSHM_MAKE_AR(data_, alloc, data);\n}\n"})}),"\n",(0,t.jsxs)(s.ul,{children:["\n",(0,t.jsxs)(s.li,{children:[(0,t.jsx)(s.code,{children:"lane_hash_"}),": The lane of the MultiQueue a request is keyed to if\nTASK_LANE_ANY is not set under the task flags. This gives concurrency control. Tasks in\nthe same lane will be executed sequentially if necessary."]}),"\n",(0,t.jsxs)(s.li,{children:[(0,t.jsx)(s.code,{children:"prio_"}),": The priority of the task. KLowLatency is priority 2."]}),"\n",(0,t.jsxs)(s.li,{children:[(0,t.jsx)(s.code,{children:"method_"}),": The method the task will be routed to by the runtime"]}),"\n",(0,t.jsxs)(s.li,{children:[(0,t.jsx)(s.code,{children:"task_flags_"}),": Various flags that can improve performance"]}),"\n"]}),"\n",(0,t.jsxs)(s.h3,{id:"modify-compresscc",children:["Modify ",(0,t.jsx)(s.code,{children:"compress.cc"})]}),"\n",(0,t.jsx)(s.pre,{children:(0,t.jsx)(s.code,{className:"language-cpp",children:"void Compress(CompressTask *task, RunContext &rctx) {\n  task->SetModuleComplete();\n}\n\nvoid Decompress(DecompressTask *task, RunContext &rctx) {\n  task->SetModuleComplete();\n}\n"})}),"\n",(0,t.jsx)(s.p,{children:"Create the callback functions in the task server.\ntask->SetModuleComplete() indicates that the task is completely finished.\nLong-running tasks should not use this function."}),"\n",(0,t.jsxs)(s.h3,{id:"modify-compressh",children:["Modify ",(0,t.jsx)(s.code,{children:"compress.h"})]}),"\n",(0,t.jsx)(s.pre,{children:(0,t.jsx)(s.code,{className:"language-cpp",children:"HSHM_ALWAYS_INLINE\nvoid AsyncCompressConstruct(CompressTask *task,\n                          const TaskNode &task_node,\n                          const DomainId &domain_id,\n                          int compress_method,\n                          const std::string &data) {\n  HRUN_CLIENT->ConstructTask<CompressTask>>(\n      task, task_node, domain_id, id_, compress_method, data);\n}\nHSHM_ALWAYS_INLINE\nvoid CompressRoot(const DomainId &domain_id,\n                  int compress_method,\n                  const std::string &data) {\n  LPointer<hrunpq::TypedPushTask<CompressTask>> task = AsyncCompressRoot(domain_id);\n  task.ptr_->Wait();\n}\nHRUN_TASK_NODE_PUSH_ROOT(Compress);\n"})}),"\n",(0,t.jsx)(s.p,{children:"CompressRoot will be called by clients directly.\nHRUN_TASK_NODE_PUSH_ROOT will create various helper methods that\neventually call AsyncCompressConstruct. LPointer is a struct that\ncontains a shared-memory pointer to a task and its corresponding\nprivate-memory pointer."}),"\n",(0,t.jsxs)(s.p,{children:["hrunpq::TypedPushTask represents a task that is stored inside of the\n",(0,t.jsx)(s.strong,{children:"process queue"}),". The process queue is a single-priority queue that\nconnects clients to the Hermes runtime. Tasks in this queue are keyed\nto lanes based on standard thread ID. This ensures that all tasks\noriginating from the same thread are in the same lane. This helps\ngive consistency guarantees for I/O operations."]}),"\n",(0,t.jsx)(s.h3,{id:"task-methods",children:"Task Methods"}),"\n",(0,t.jsx)(s.p,{children:"The task methods will be discussed in sections 6, 7, and 8."}),"\n",(0,t.jsx)(s.h2,{id:"registering-a-task-library",children:"Registering a Task Library"}),"\n",(0,t.jsx)(s.p,{children:"After creating a new task library, it must be registered with\nthe Hermes Runtime. This can be done either programmatically or\nthrough configuration."}),"\n",(0,t.jsxs)(s.p,{children:["Through configuration, you must edit the Hermes runtime configuration.\nAn example configuration is stored in ",(0,t.jsx)(s.code,{children:"${HERMES_ROOT}/config/hermes_server_default.yaml"}),"."]}),"\n",(0,t.jsx)(s.pre,{children:(0,t.jsx)(s.code,{className:"language-yaml",children:'task_registry:\n  [\n    "hermes_mdm",\n    "hermes_blob_mdm",\n    "hermes_bucket_mdm",\n    "hermes_data_op",\n    "data_stager",\n    "posix_bdev",\n    "ram_bdev",\n    "compress",\n  ]\n'})}),"\n",(0,t.jsx)(s.p,{children:"This can be passed to the Hermes runtime using the HERMES_CONF environment\nvariable."}),"\n",(0,t.jsx)(s.h2,{id:"task-grouping-worker-polling-and-deadlock-prevention",children:"Task Grouping, Worker Polling, and Deadlock Prevention"}),"\n",(0,t.jsx)(s.p,{children:"This section will provide more insight on how queues are polled\nand processed in the Hermes Runtime to provide fine-grained control\nover scheduling and concurrency."}),"\n",(0,t.jsxs)(s.p,{children:["Tasks must all implement a function called ",(0,t.jsx)(s.code,{children:"GetGroup"}),". Task groups are used to enable look-ahead capabilities with safety. A ",(0,t.jsx)(s.strong,{children:"Task Group"})," represents a collection of tasks that modify the same metadata structure and need to be sequentially executed. For example, the Bucket ID is\nused as the group for calling the bucket methods GetSize and UpdateSize.\nThis ensures that GetSize and UpdateSize will be executed in sequence when\nmade to the same bucket. Certain operations do not require any synchronization (e.g., stateless methods) and can return a group of TASK_UNORDERED."]}),"\n",(0,t.jsxs)(s.p,{children:["A ",(0,t.jsx)(s.strong,{children:"Task Node"})," represents the location of a task in the overall\ntask graph. There is no Task Graph data structure, it's a concept.\nWhen a task spawns a subtask, it can be conceptually be considered\nas a task graph. Tasks apart of the same task graph will be executed\nsimultaneously --regardless of group -- to prevent deadlocks in the\ncase where two tasks from the same graph are keyed to the same queue and lane."]}),"\n",(0,t.jsx)(s.h2,{id:"building-a-replicatable-task",children:"Building a Replicatable Task"}),"\n",(0,t.jsx)(s.p,{children:"To make a task support replication, set the TF_REPLICA flag. This\nwill indicate that a task implements the replication methods."}),"\n",(0,t.jsx)(s.pre,{children:(0,t.jsx)(s.code,{className:"language-cpp",children:"struct CompressTask : public Task, TaskFlags<TF_SRL_SYM | TF_REPLICA> {\n  IN compress_type_;\n  IN hipc::ShmArchive<hipc::string> data_;\n  OUT hipc::ShmArchive<hipc::vector<size_t>> sizes_;\n  OUT size_t final_size_;\n\n  /** (De)serialize message call */\n  template<typename Ar>\n  void SerializeStart(Ar &ar) {\n    task_serialize<Ar>(ar);\n    ar(compress_type_, data_);\n  }\n\n  /** (De)serialize message return */\n  template<typename Ar>\n  void SerializeEnd(u32 replica, Ar &ar) {\n    ar(sizes_, final_size_);\n  }\n\n  /** Duplicate message */\n  void Dup(hipc::Allocator *alloc, CustomTask &other) {\n    task_dup(other);\n    compress_type_ = other.compress_type_;\n    HSHM_MAKE_AR(data_, alloc, other.data_);\n  }\n\n  /** Process duplicate message output */\n  void DupEnd(u32 replica, CustomTask &dup_task) {\n    (*sizes_)[repclica] = other.size_;\n  }\n\n  /** Begin replication */\n  void ReplicateStart(u32 count) {\n    size_->resize(count);\n  }\n\n  /** Finalize replication */\n  void ReplicateEnd() {\n    size_t final_size_ = std::numeric_limits<size_t>::min();\n    for (size_t &size : sizes_) {\n      if (final_size_ > size) {\n        final_size_ = size;\n      }\n    }\n  }\n};\n"})}),"\n",(0,t.jsxs)(s.ul,{children:["\n",(0,t.jsxs)(s.li,{children:[(0,t.jsx)(s.code,{children:"SerializeStart"}),": Will serialize and deserialize the ",(0,t.jsx)(s.em,{children:"input"})," parameters of the task. So anything labeled IN or INOUT."]}),"\n",(0,t.jsxs)(s.li,{children:[(0,t.jsx)(s.code,{children:"SerializeEnd"}),": Will serialize and deserialize the ",(0,t.jsx)(s.em,{children:"output"}),"\nparameters of the task. So anything labeled OUT or INOUT."]}),"\n",(0,t.jsxs)(s.li,{children:[(0,t.jsx)(s.code,{children:"Dup"}),": Analogous to a copy constructor. Will make a local\ncopy of this task (no serialization involved)."]}),"\n",(0,t.jsxs)(s.li,{children:[(0,t.jsx)(s.code,{children:"DupEnd"}),": Will store the output of a replica in the original\ntask the duplicates were spawned from."]}),"\n",(0,t.jsxs)(s.li,{children:[(0,t.jsx)(s.code,{children:"ReplicateStart"}),": Used to allocate data structures in the task\nto account for the replication"]}),"\n",(0,t.jsxs)(s.li,{children:[(0,t.jsx)(s.code,{children:"ReplicateEnd"}),": Called after all replicas have returned. Can\naggregate replica otuput."]}),"\n"]}),"\n",(0,t.jsx)(s.h2,{id:"building-a-data-intensive-rdma-capable-task",children:"Building a Data-Intensive, RDMA-Capable Task"}),"\n",(0,t.jsx)(s.p,{children:"TODO: Make example based on PutBlob and GetBlob."})]})}function h(e={}){const{wrapper:s}={...(0,a.a)(),...e.components};return s?(0,t.jsx)(s,{...e,children:(0,t.jsx)(d,{...e})}):d(e)}},1151:(e,s,n)=>{n.d(s,{Z:()=>o,a:()=>r});var t=n(7294);const a={},i=t.createContext(a);function r(e){const s=t.useContext(i);return t.useMemo((function(){return"function"==typeof e?e(s):{...s,...e}}),[s,e])}function o(e){let s;return s=e.disableParentContext?"function"==typeof e.components?e.components(a):e.components||a:r(e.components),t.createElement(i.Provider,{value:s},e.children)}}}]);
\ No newline at end of file
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@@ -0,0 +1 @@
+"use strict";(self.webpackChunkgrc=self.webpackChunkgrc||[]).push([[5674],{3628:(e,n,s)=>{s.r(n),s.d(n,{assets:()=>o,contentTitle:()=>l,default:()=>h,frontMatter:()=>r,metadata:()=>t,toc:()=>c});var i=s(5893),a=s(1151);const r={},l="Building Hermes",t={id:"hermes/building-hermes",title:"Building Hermes",description:"Dependencies",source:"@site/docs/03-hermes/02-building-hermes.md",sourceDirName:"03-hermes",slug:"/hermes/building-hermes",permalink:"/docs/hermes/building-hermes",draft:!1,unlisted:!1,tags:[],version:"current",sidebarPosition:2,frontMatter:{},sidebar:"tutorialSidebar",previous:{title:"Main Scenario",permalink:"/docs/hermes/main-scenario"},next:{title:"Deploying Hermes",permalink:"/docs/hermes/deploying-hermes"}},o={},c=[{value:"Dependencies",id:"dependencies",level:2},{value:"Bootstrapping Spack",id:"bootstrapping-spack",level:2},{value:"Installing Hermes on a new machine with Spack",id:"installing-hermes-on-a-new-machine-with-spack",level:2},{value:"Why is my spack installation failing?",id:"why-is-my-spack-installation-failing",level:3},{value:"Environment errors",id:"environment-errors",level:4},{value:"Dependency conflicts",id:"dependency-conflicts",level:4},{value:"Compilation errors",id:"compilation-errors",level:4},{value:"Fetcher errors",id:"fetcher-errors",level:4},{value:"Corruption",id:"corruption",level:4},{value:"Building Hermes with CMake",id:"building-hermes-with-cmake",level:2},{value:"Install Dependencies",id:"install-dependencies",level:3},{value:"Hermes",id:"hermes",level:4},{value:"(Optional) SCSPKG",id:"optional-scspkg",level:4},{value:"Build Hermes",id:"build-hermes",level:3},{value:"Load Hermes dependencies",id:"load-hermes-dependencies",level:4},{value:"(Optional) Create a Hermes SCSPKG repo",id:"optional-create-a-hermes-scspkg-repo",level:4},{value:"Compile and Install",id:"compile-and-install",level:4}];function d(e){const n={a:"a",code:"code",h1:"h1",h2:"h2",h3:"h3",h4:"h4",li:"li",ol:"ol",p:"p",pre:"pre",strong:"strong",ul:"ul",...(0,a.a)(),...e.components};return(0,i.jsxs)(i.Fragment,{children:[(0,i.jsx)(n.h1,{id:"building-hermes",children:"Building Hermes"}),"\n",(0,i.jsx)(n.h2,{id:"dependencies",children:"Dependencies"}),"\n",(0,i.jsxs)(n.ul,{children:["\n",(0,i.jsx)(n.li,{children:"A C++ compiler that supports C++ 17. GCC 9.4 is the minimum version of GCC that Hermes was tested with."}),"\n",(0,i.jsxs)(n.li,{children:[(0,i.jsx)(n.a,{href:"https://mochi.readthedocs.io/en/latest/installing.html",children:"Thallium"})," - RPC library for HPC. Use a version greater than ",(0,i.jsx)(n.code,{children:"0.5"})," for RoCE support."]}),"\n",(0,i.jsxs)(n.li,{children:[(0,i.jsx)(n.a,{href:"https://github.com/jbeder/yaml-cpp",children:"yaml-cpp"})," - YAML file parser"]}),"\n",(0,i.jsxs)(n.li,{children:[(0,i.jsx)(n.a,{href:"https://github.com/lukemartinlogan/hermes_shm",children:"hermes_shm"}),": A library containing shared-memory data structures, configuration parsing, and various helper utilities"]}),"\n",(0,i.jsx)(n.li,{children:"HDF5 1.14.0 if compiling with VFD"}),"\n",(0,i.jsx)(n.li,{children:"MPI-IO adapter only tested with MPICH and OpenMPI."}),"\n"]}),"\n",(0,i.jsx)(n.h2,{id:"bootstrapping-spack",children:"Bootstrapping Spack"}),"\n",(0,i.jsxs)(n.p,{children:[(0,i.jsx)(n.a,{href:"https://spack.io/",children:"Spack"})," is the easiest way to get Hermes and all its dependencies installed."]}),"\n",(0,i.jsx)(n.p,{children:"First, add the Hermes spack repo:"}),"\n",(0,i.jsx)(n.pre,{children:(0,i.jsx)(n.code,{className:"language-bash",children:"git clone https://github.com/HDFGroup/hermes\ncd hermes\ngit submodule update --init --recursive\nspack repo add ci/hermes\n"})}),"\n",(0,i.jsx)(n.p,{children:"Second, introspect your machine to ensure that spack considers software already present on your machine. If there are modulefiles, make sure all relevant modulefiles have been loaded before executing this command.\nYou should ensure that any modules relating to networking (e.g., libfabric or UCX) and MPI are loaded, since they are likely specialized to your machine:"}),"\n",(0,i.jsx)(n.pre,{children:(0,i.jsx)(n.code,{className:"language-bash",children:"spack external find\n"})}),"\n",(0,i.jsx)(n.p,{children:"Third, ensure that a recent compiler is added in spack. Hermes and some of its dependencies use the full C++17 feature set and require a compiler suitable of handling this:"}),"\n",(0,i.jsx)(n.pre,{children:(0,i.jsx)(n.code,{className:"language-bash",children:"spack compiler add\nspack compiler list\n"})}),"\n",(0,i.jsx)("a",{id:"installing-hermes"}),"\n",(0,i.jsx)(n.h2,{id:"installing-hermes-on-a-new-machine-with-spack",children:"Installing Hermes on a new machine with Spack"}),"\n",(0,i.jsx)(n.p,{children:"Before installing, you may want to verify that spack is going to\ninstall Hermes with the correct dependencies."}),"\n",(0,i.jsx)(n.pre,{children:(0,i.jsx)(n.code,{className:"language-bash",children:"spack spec -I hermes@master\n"})}),"\n",(0,i.jsx)(n.p,{children:"Some questions you may want to ask yourself:"}),"\n",(0,i.jsxs)(n.ol,{children:["\n",(0,i.jsx)(n.li,{children:"Is the correct MPI version being used?"}),"\n",(0,i.jsx)(n.li,{children:"Is the correct libfabric being used?"}),"\n"]}),"\n",(0,i.jsx)(n.p,{children:"To install the default Hermes:"}),"\n",(0,i.jsx)(n.pre,{children:(0,i.jsx)(n.code,{className:"language-bash",children:"spack install hermes@master\n"})}),"\n",(0,i.jsx)(n.p,{children:"Hermes additionally has variants for intercepting MPI-IO and HDF5. They\ncan be installed as follows:"}),"\n",(0,i.jsx)(n.pre,{children:(0,i.jsx)(n.code,{className:"language-bash",children:"spack install hermes+vfd+mpiio@master\n"})}),"\n",(0,i.jsx)(n.p,{children:"If you intend to use high-performance networks such as verbs,\nyou will need to have knowledge of your specific system. This step is highly dependent on the machine, and you may need to consult your machine's documentation or sysadmin to determine what kind of network you use. If your machine uses infiniband, libfabric+verbs is probably for you. Libfabric does not come preinstalled with verbs support in spack."}),"\n",(0,i.jsx)(n.pre,{children:(0,i.jsx)(n.code,{children:"spack install hermes@master ^ libfabric fabrics=rxm,sockets,tcp,udp,verbs\n"})}),"\n",(0,i.jsx)(n.h3,{id:"why-is-my-spack-installation-failing",children:"Why is my spack installation failing?"}),"\n",(0,i.jsx)(n.p,{children:"While spack automates the installation of most dependencies, it is under active development and by no means perfect. We have identified several situations that have caused difficulty when installing Hermes across HPC sites. These issues are not necessarily related to Hermes itself, rather spack in general."}),"\n",(0,i.jsx)(n.p,{children:"If Hermes fails to install use debug mode to get more information:"}),"\n",(0,i.jsx)(n.pre,{children:(0,i.jsx)(n.code,{className:"language-bash",children:"spack -d install hermes@master\n"})}),"\n",(0,i.jsx)(n.h4,{id:"environment-errors",children:"Environment errors"}),"\n",(0,i.jsx)(n.p,{children:"Your machine may have specific expectations on certain dependencies.\nBy default, spack installs everything from scratch. However, if your\nmachine has software installed as modulefiles, spack will not see\nthese until explicitly told to."}),"\n",(0,i.jsx)(n.p,{children:"We have found several instances of users installing Hermes before adding relevant modulefiles on their machine to spack. Probably the most important modules are MPI installations and networking libraries (e.g., libfabric, UCX, etc). This is because they are installed and configured specifically by the sysadmin for the particular machine. When installing Hermes, make sure any modulefile that you would typically use to build software is loaded and then run:"}),"\n",(0,i.jsx)(n.pre,{children:(0,i.jsx)(n.code,{className:"language-bash",children:"spack external find\n"})}),"\n",(0,i.jsx)(n.p,{children:"To view the set of external packages discovered, run:"}),"\n",(0,i.jsx)(n.pre,{children:(0,i.jsx)(n.code,{className:"language-bash",children:"cat ~/.spack/packages.yaml\n"})}),"\n",(0,i.jsx)(n.p,{children:"Spack external is not by any means perfect. You may find that some\nmodules you intend to use have not been automatically discovered.\nIn this situation, you can edit the packages.yaml file manually\nto add the packages. The format of the yaml file is straightforward."}),"\n",(0,i.jsx)(n.h4,{id:"dependency-conflicts",children:"Dependency conflicts"}),"\n",(0,i.jsx)(n.p,{children:"There may be multiple versions of the same software installed at the\nsame time. To determine what dependencies Hermes will be using, run:"}),"\n",(0,i.jsx)(n.pre,{children:(0,i.jsx)(n.code,{className:"language-bash",children:"spack spec -I hermes@master\n"})}),"\n",(0,i.jsxs)(n.p,{children:["You may find that some dependencies are not the ones you had intended.\nFor example, maybe you have both MPICH 3.3.2 and 3.4.3 installed.\nYou can choose a specific version of a dependency using ",(0,i.jsx)(n.code,{children:"^"}),". Below\nis an example of installing with mpich@3.3.2"]}),"\n",(0,i.jsx)(n.pre,{children:(0,i.jsx)(n.code,{className:"language-bash",children:"spack install hermes@master ^ mpich@3.3.2\n"})}),"\n",(0,i.jsx)(n.h4,{id:"compilation-errors",children:"Compilation errors"}),"\n",(0,i.jsx)(n.p,{children:"Hermes and some of its dependencies (e.g., thallium) require C++17 support. Not all compilers support this -- even if they say they do.\nGCC 8.5.0, for example, has partial C++17 support, but does not have the full feature set. Many HPC sites have old compilers loaded by default.\nEnsure that a recent C++ compiler is used when compiling Hermes. As a guideline, GCC 9.4 is the earliest GCC version we have tested successfully on Hermes."}),"\n",(0,i.jsx)(n.pre,{children:(0,i.jsx)(n.code,{className:"language-bash",children:"spack compiler add\n"})}),"\n",(0,i.jsxs)(n.p,{children:["In order to ensure that spack uses the correct compiler, you can\nuse the ",(0,i.jsx)(n.code,{children:"%"})," symbol:"]}),"\n",(0,i.jsx)(n.pre,{children:(0,i.jsx)(n.code,{className:"language-bash",children:"spack install hermes@master%gcc@9.4\n"})}),"\n",(0,i.jsx)(n.h4,{id:"fetcher-errors",children:"Fetcher errors"}),"\n",(0,i.jsx)(n.p,{children:"A fetcher error occurs when a package fails to download. There are three reasons this may occur:"}),"\n",(0,i.jsxs)(n.ol,{children:["\n",(0,i.jsx)(n.li,{children:"You lost internet connection when downloading. Ensure you are actually connected to the internet by pinging a well-known website such as google."}),"\n",(0,i.jsx)(n.li,{children:"You are running on a restricted network and your proxy is misconfigured. In this case, you must contact your sysadmins to resolve the issue."}),"\n",(0,i.jsx)(n.li,{children:"The spackage is outdated and contains a broken URL. Either contact the maintainers of the package or visit their documentation to make a custom installation."}),"\n"]}),"\n",(0,i.jsx)(n.h4,{id:"corruption",children:"Corruption"}),"\n",(0,i.jsx)(n.p,{children:"Spack can become corrupted if a package's installation is cutoff prematurely. There's not much that can be done here outside of reinstalling spack and the Hermes dependencies"}),"\n",(0,i.jsx)(n.p,{children:"To effectively uninstall spack:"}),"\n",(0,i.jsx)(n.pre,{children:(0,i.jsx)(n.code,{className:"language-bash",children:"# remove the spack metadata files\nrm -rf ~/.spack\n# remove the cloned spack repo\nrm -rf /path/to/spack\n"})}),"\n",(0,i.jsx)(n.h2,{id:"building-hermes-with-cmake",children:"Building Hermes with CMake"}),"\n",(0,i.jsx)(n.p,{children:"For those developing Hermes, uninstalling and reinstalling from spack\nis extremely cumbersome. As an alternative to spack, Hermes can be\ninstalled manually with a combination of spack and CMake."}),"\n",(0,i.jsx)(n.h3,{id:"install-dependencies",children:"Install Dependencies"}),"\n",(0,i.jsx)(n.h4,{id:"hermes",children:"Hermes"}),"\n",(0,i.jsxs)(n.p,{children:["Install Hermes as you typically would following the instructrions\nin ",(0,i.jsx)(n.a,{href:"#installing-hermes",children:"Section 1"}),". While the Hermes version itself\nis not useful, the installation process will install all dependencies\nwhich will make life much easier for a manual Hermes build. To save\nsome time, you could choose to install ",(0,i.jsx)(n.code,{children:"hermes_shm"})," instead, which contains the same dependencies and variants as Hermes itself."]}),"\n",(0,i.jsx)(n.h4,{id:"optional-scspkg",children:"(Optional) SCSPKG"}),"\n",(0,i.jsxs)(n.p,{children:["To help with managing the organization of manually-built software, we created a tool called ",(0,i.jsx)(n.a,{href:"https://github.com/grc-iit/scspkg",children:"SCSPKG"})," that helps automate the construction of modulefiles."]}),"\n",(0,i.jsx)(n.pre,{children:(0,i.jsx)(n.code,{className:"language-bash",children:'git clone https://github.com/grc-iit/scspkg.git\ncd scspkg\npip install -e . --user\necho "module use $(scspkg module dir)" >> ~/.bashrc\nscspkg init False\n'})}),"\n",(0,i.jsx)(n.h3,{id:"build-hermes",children:"Build Hermes"}),"\n",(0,i.jsx)(n.h4,{id:"load-hermes-dependencies",children:"Load Hermes dependencies"}),"\n",(0,i.jsx)(n.p,{children:"First, load all Hermes dependencies. Hermes_shm is a spackage that\ncontains the same exact dependencies as the full Hermes code:"}),"\n",(0,i.jsx)(n.pre,{children:(0,i.jsx)(n.code,{className:"language-bash",children:"spack load hermes_shm\n"})}),"\n",(0,i.jsx)(n.h4,{id:"optional-create-a-hermes-scspkg-repo",children:"(Optional) Create a Hermes SCSPKG repo"}),"\n",(0,i.jsx)(n.p,{children:"An SCSPKG repo for Hermes can be created as follows:"}),"\n",(0,i.jsx)(n.pre,{children:(0,i.jsx)(n.code,{className:"language-bash",children:"scspkg create hermes_run\n"})}),"\n",(0,i.jsx)(n.p,{children:"This will do three things:"}),"\n",(0,i.jsxs)(n.ol,{children:["\n",(0,i.jsxs)(n.li,{children:["Create the ",(0,i.jsx)(n.strong,{children:"source"})," directory, which is where uncompiled source code is stored. Hermes, for example, could be cloned in this directory -- ",(0,i.jsx)(n.strong,{children:"although this is not required"}),". This directory is created to help developers organize and prevent cluttering their home directory."]}),"\n",(0,i.jsxs)(n.li,{children:["Create the ",(0,i.jsx)(n.strong,{children:"root"})," directory, which is where compiled code is installed to. I.e., this is the directory CMAKE_INSTALL_PREFIX will point to."]}),"\n",(0,i.jsx)(n.li,{children:"Create a modulefile containing most relevant environment variables needed for building HPC software (PATH, LD_LIBRARY_PATH, etc.). The modulefile will contain the root directory."}),"\n"]}),"\n",(0,i.jsx)(n.p,{children:"The path to the source directory is given by the command:"}),"\n",(0,i.jsx)(n.pre,{children:(0,i.jsx)(n.code,{className:"language-bash",children:"scspkg pkg src hermes_run\n"})}),"\n",(0,i.jsx)(n.p,{children:"The path to the root directory is given by the command:"}),"\n",(0,i.jsx)(n.pre,{children:(0,i.jsx)(n.code,{className:"language-bash",children:"scspkg pkg root hermes_run\n"})}),"\n",(0,i.jsx)(n.p,{children:"To view the modulefile, run:"}),"\n",(0,i.jsx)(n.pre,{children:(0,i.jsx)(n.code,{className:"language-bash",children:"module show hermes_run\n"})}),"\n",(0,i.jsx)(n.h4,{id:"compile-and-install",children:"Compile and Install"}),"\n",(0,i.jsx)(n.p,{children:"After this, the local installation can be created as follows:"}),"\n",(0,i.jsx)(n.pre,{children:(0,i.jsx)(n.code,{className:"language-bash",children:"mkdir build\ncd build\ncmake ../ -DCMAKE_INSTALL_PREFIX=$(scspkg pkg root hermes_run)\nmake -j32 install\n"})}),"\n",(0,i.jsx)(n.p,{children:"To compile with MPI-IO and VFD interceptors:"}),"\n",(0,i.jsx)(n.pre,{children:(0,i.jsx)(n.code,{className:"language-bash",children:"cmake ../ \\\n-DHERMES_ENABLE_MPIIO_ADAPTER=ON \\\n-DHERMES_ENABLE_VFD=ON \\\n-DCMAKE_INSTALL_PREFIX=$(scspkg pkg root hermes_run)\n"})}),"\n",(0,i.jsxs)(n.p,{children:["There are several options provided in the root Hermes ",(0,i.jsx)(n.a,{href:"https://github.com/HDFGroup/hermes/blob/master/CMakeLists.txt",children:"CMake"}),". To view these\noptions, one can run run:"]}),"\n",(0,i.jsx)(n.pre,{children:(0,i.jsx)(n.code,{className:"language-bash",children:"ccmake ../\n"})})]})}function h(e={}){const{wrapper:n}={...(0,a.a)(),...e.components};return n?(0,i.jsx)(n,{...e,children:(0,i.jsx)(d,{...e})}):d(e)}},1151:(e,n,s)=>{s.d(n,{Z:()=>t,a:()=>l});var i=s(7294);const a={},r=i.createContext(a);function l(e){const n=i.useContext(r);return i.useMemo((function(){return"function"==typeof e?e(n):{...n,...e}}),[n,e])}function t(e){let n;return n=e.disableParentContext?"function"==typeof e.components?e.components(a):e.components||a:l(e.components),i.createElement(r.Provider,{value:n},e.children)}}}]);
\ No newline at end of file
diff --git a/assets/js/57efaafb.47310bb9.js b/assets/js/57efaafb.47310bb9.js
deleted file mode 100644
index 55a56b1e..00000000
--- a/assets/js/57efaafb.47310bb9.js
+++ /dev/null
@@ -1 +0,0 @@
-"use strict";(self.webpackChunkgrc=self.webpackChunkgrc||[]).push([[5674],{3628:(e,n,s)=>{s.r(n),s.d(n,{assets:()=>o,contentTitle:()=>l,default:()=>h,frontMatter:()=>r,metadata:()=>t,toc:()=>c});var i=s(5893),a=s(1151);const r={},l="Building Hermes",t={id:"hermes/building-hermes",title:"Building Hermes",description:"Dependencies",source:"@site/docs/03-hermes/02-building-hermes.md",sourceDirName:"03-hermes",slug:"/hermes/building-hermes",permalink:"/docs/hermes/building-hermes",draft:!1,unlisted:!1,tags:[],version:"current",sidebarPosition:2,frontMatter:{},sidebar:"tutorialSidebar",previous:{title:"Main Scenario",permalink:"/docs/hermes/main-scenario"},next:{title:"Deploying Hermes",permalink:"/docs/hermes/deploying-hermes"}},o={},c=[{value:"Dependencies",id:"dependencies",level:2},{value:"Bootstrapping Spack",id:"bootstrapping-spack",level:2},{value:"Installing Hermes on a new machine with Spack",id:"installing-hermes-on-a-new-machine-with-spack",level:2},{value:"Why is my spack installation failing?",id:"why-is-my-spack-installation-failing",level:3},{value:"Environment errors",id:"environment-errors",level:4},{value:"Dependency conflicts",id:"dependency-conflicts",level:4},{value:"Compilation errors",id:"compilation-errors",level:4},{value:"Fetcher errors",id:"fetcher-errors",level:4},{value:"Corruption",id:"corruption",level:4},{value:"Building Hermes with CMake",id:"building-hermes-with-cmake",level:2},{value:"Install Dependencies",id:"install-dependencies",level:3},{value:"Hermes",id:"hermes",level:4},{value:"(Optional) SCSPKG",id:"optional-scspkg",level:4},{value:"Build Hermes",id:"build-hermes",level:3},{value:"Load Hermes dependencies",id:"load-hermes-dependencies",level:4},{value:"(Optional) Create a Hermes SCSPKG repo",id:"optional-create-a-hermes-scspkg-repo",level:4},{value:"Compile and Install",id:"compile-and-install",level:4}];function d(e){const n={a:"a",code:"code",h1:"h1",h2:"h2",h3:"h3",h4:"h4",li:"li",ol:"ol",p:"p",pre:"pre",strong:"strong",ul:"ul",...(0,a.a)(),...e.components};return(0,i.jsxs)(i.Fragment,{children:[(0,i.jsx)(n.h1,{id:"building-hermes",children:"Building Hermes"}),"\n",(0,i.jsx)(n.h2,{id:"dependencies",children:"Dependencies"}),"\n",(0,i.jsxs)(n.ul,{children:["\n",(0,i.jsx)(n.li,{children:"A C++ compiler that supports C++ 17. GCC 9.4 is the minimum version of GCC\nthat Hermes was tested with."}),"\n",(0,i.jsxs)(n.li,{children:[(0,i.jsx)(n.a,{href:"https://mochi.readthedocs.io/en/latest/installing.html",children:"Thallium"})," - RPC library for HPC. Use a version greater than ",(0,i.jsx)(n.code,{children:"0.5"})," for RoCE support."]}),"\n",(0,i.jsxs)(n.li,{children:[(0,i.jsx)(n.a,{href:"https://github.com/jbeder/yaml-cpp",children:"yaml-cpp"})," - YAML file parser"]}),"\n",(0,i.jsxs)(n.li,{children:[(0,i.jsx)(n.a,{href:"https://github.com/lukemartinlogan/hermes_shm",children:"hermes_shm"}),": A library containing shared-memory data structures, configuration parsing, and various helper utilities"]}),"\n",(0,i.jsx)(n.li,{children:"HDF5 1.14.0 if compiling with VFD"}),"\n",(0,i.jsx)(n.li,{children:"MPI-IO adapter only tested with MPICH and OpenMPI."}),"\n"]}),"\n",(0,i.jsx)(n.h2,{id:"bootstrapping-spack",children:"Bootstrapping Spack"}),"\n",(0,i.jsxs)(n.p,{children:[(0,i.jsx)(n.a,{href:"https://spack.io/",children:"Spack"})," is the easiest way to get Hermes and all its dependencies installed."]}),"\n",(0,i.jsx)(n.p,{children:"First, add the Hermes spack repo:"}),"\n",(0,i.jsx)(n.pre,{children:(0,i.jsx)(n.code,{className:"language-bash",children:"git clone https://github.com/HDFGroup/hermes\ncd hermes\ngit submodule update --init --recursive\nspack repo add ci/hermes\n"})}),"\n",(0,i.jsx)(n.p,{children:"Second, introspect your machine to ensure that spack considers software already present on your machine. If there are modulefiles, make sure all relevant modulefiles have been loaded before executing this command.\nYou should ensure that any modules relating to networking (e.g., libfabric or UCX) and MPI are loaded, since they are likely specialized to your machine:"}),"\n",(0,i.jsx)(n.pre,{children:(0,i.jsx)(n.code,{className:"language-bash",children:"spack external find\n"})}),"\n",(0,i.jsx)(n.p,{children:"Third, ensure that a recent compiler is added in spack. Hermes and some of its dependencies use the full C++17 feature set and require a compiler suitable of handling this:"}),"\n",(0,i.jsx)(n.pre,{children:(0,i.jsx)(n.code,{className:"language-bash",children:"spack compiler add\nspack compiler list\n"})}),"\n",(0,i.jsx)("a",{id:"installing-hermes"}),"\n",(0,i.jsx)(n.h2,{id:"installing-hermes-on-a-new-machine-with-spack",children:"Installing Hermes on a new machine with Spack"}),"\n",(0,i.jsx)(n.p,{children:"Before installing, you may want to verify that spack is going to\ninstall Hermes with the correct dependencies."}),"\n",(0,i.jsx)(n.pre,{children:(0,i.jsx)(n.code,{className:"language-bash",children:"spack spec -I hermes@master\n"})}),"\n",(0,i.jsx)(n.p,{children:"Some questions you may want to ask yourself:"}),"\n",(0,i.jsxs)(n.ol,{children:["\n",(0,i.jsx)(n.li,{children:"Is the correct MPI version being used?"}),"\n",(0,i.jsx)(n.li,{children:"Is the correct libfabric being used?"}),"\n"]}),"\n",(0,i.jsx)(n.p,{children:"To install the default Hermes:"}),"\n",(0,i.jsx)(n.pre,{children:(0,i.jsx)(n.code,{className:"language-bash",children:"spack install hermes@master\n"})}),"\n",(0,i.jsx)(n.p,{children:"Hermes additionally has variants for intercepting MPI-IO and HDF5. They\ncan be installed as follows:"}),"\n",(0,i.jsx)(n.pre,{children:(0,i.jsx)(n.code,{className:"language-bash",children:"spack install hermes+vfd+mpiio@master\n"})}),"\n",(0,i.jsx)(n.p,{children:"If you intend to use high-performance networks such as verbs,\nyou will need to have knowledge of your specific system. This step is highly dependent on the machine, and you may need to consult your machine's documentation or sysadmin to determine what kind of network you use. If your machine uses infiniband, libfabric+verbs is probably for you. Libfabric does not come preinstalled with verbs support in spack."}),"\n",(0,i.jsx)(n.pre,{children:(0,i.jsx)(n.code,{children:"spack install hermes@master ^ libfabric fabrics=rxm,sockets,tcp,udp,verbs\n"})}),"\n",(0,i.jsx)(n.h3,{id:"why-is-my-spack-installation-failing",children:"Why is my spack installation failing?"}),"\n",(0,i.jsx)(n.p,{children:"While spack automates the installation of most dependencies, it is under active development and by no means perfect. We have identified several situations that have caused difficulty when installing Hermes across HPC sites. These issues are not necessarily related to Hermes itself, rather spack in general."}),"\n",(0,i.jsx)(n.p,{children:"If Hermes fails to install use debug mode to get more information:"}),"\n",(0,i.jsx)(n.pre,{children:(0,i.jsx)(n.code,{className:"language-bash",children:"spack -d install hermes@master\n"})}),"\n",(0,i.jsx)(n.h4,{id:"environment-errors",children:"Environment errors"}),"\n",(0,i.jsx)(n.p,{children:"Your machine may have specific expectations on certain dependencies.\nBy default, spack installs everything from scratch. However, if your\nmachine has software installed as modulefiles, spack will not see\nthese until explicitly told to."}),"\n",(0,i.jsx)(n.p,{children:"We have found several instances of users installing Hermes before adding relevant modulefiles on their machine to spack. Probably the most important modules are MPI installations and networking libraries (e.g., libfabric, UCX, etc). This is because they are installed and configured specifically by the sysadmin for the particular machine. When installing Hermes, make sure any modulefile that you would typically use to build software is loaded and then run:"}),"\n",(0,i.jsx)(n.pre,{children:(0,i.jsx)(n.code,{className:"language-bash",children:"spack external find\n"})}),"\n",(0,i.jsx)(n.p,{children:"To view the set of external packages discovered, run:"}),"\n",(0,i.jsx)(n.pre,{children:(0,i.jsx)(n.code,{className:"language-bash",children:"cat ~/.spack/packages.yaml\n"})}),"\n",(0,i.jsx)(n.p,{children:"Spack external is not by any means perfect. You may find that some\nmodules you intend to use have not been automatically discovered.\nIn this situation, you can edit the packages.yaml file manually\nto add the packages. The format of the yaml file is straightforward."}),"\n",(0,i.jsx)(n.h4,{id:"dependency-conflicts",children:"Dependency conflicts"}),"\n",(0,i.jsx)(n.p,{children:"There may be multiple versions of the same software installed at the\nsame time. To determine what dependencies Hermes will be using, run:"}),"\n",(0,i.jsx)(n.pre,{children:(0,i.jsx)(n.code,{className:"language-bash",children:"spack spec -I hermes@master\n"})}),"\n",(0,i.jsxs)(n.p,{children:["You may find that some dependencies are not the ones you had intended.\nFor example, maybe you have both MPICH 3.3.2 and 3.4.3 installed.\nYou can choose a specific version of a dependency using ",(0,i.jsx)(n.code,{children:"^"}),". Below\nis an example of installing with mpich@3.3.2"]}),"\n",(0,i.jsx)(n.pre,{children:(0,i.jsx)(n.code,{className:"language-bash",children:"spack install hermes@master ^ mpich@3.3.2\n"})}),"\n",(0,i.jsx)(n.h4,{id:"compilation-errors",children:"Compilation errors"}),"\n",(0,i.jsx)(n.p,{children:"Hermes and some of its dependencies (e.g., thallium) require C++17 support. Not all compilers support this -- even if they say they do.\nGCC 8.5.0, for example, has partial C++17 support, but does not have the full feature set. Many HPC sites have old compilers loaded by default.\nEnsure that a recent C++ compiler is used when compiling Hermes. As a guideline, GCC 9.4 is the earliest GCC version we have tested successfully on Hermes."}),"\n",(0,i.jsx)(n.pre,{children:(0,i.jsx)(n.code,{className:"language-bash",children:"spack compiler add\n"})}),"\n",(0,i.jsxs)(n.p,{children:["In order to ensure that spack uses the correct compiler, you can\nuse the ",(0,i.jsx)(n.code,{children:"%"})," symbol:"]}),"\n",(0,i.jsx)(n.pre,{children:(0,i.jsx)(n.code,{className:"language-bash",children:"spack install hermes@master%gcc@9.4\n"})}),"\n",(0,i.jsx)(n.h4,{id:"fetcher-errors",children:"Fetcher errors"}),"\n",(0,i.jsx)(n.p,{children:"A fetcher error occurs when a package fails to download. There are three reasons this may occur:"}),"\n",(0,i.jsxs)(n.ol,{children:["\n",(0,i.jsx)(n.li,{children:"You lost internet connection when downloading. Ensure you are actually connected to the internet by pinging a well-known website such as google."}),"\n",(0,i.jsx)(n.li,{children:"You are running on a restricted network and your proxy is misconfigured. In this case, you must contact your sysadmins to resolve the issue."}),"\n",(0,i.jsx)(n.li,{children:"The spackage is outdated and contains a broken URL. Either contact the maintainers of the package or visit their documentation to make a custom installation."}),"\n"]}),"\n",(0,i.jsx)(n.h4,{id:"corruption",children:"Corruption"}),"\n",(0,i.jsx)(n.p,{children:"Spack can become corrupted if a package's installation is cutoff prematurely. There's not much that can be done here outside of reinstalling spack and the Hermes dependencies"}),"\n",(0,i.jsx)(n.p,{children:"To effectively uninstall spack:"}),"\n",(0,i.jsx)(n.pre,{children:(0,i.jsx)(n.code,{className:"language-bash",children:"# remove the spack metadata files\nrm -rf ~/.spack\n# remove the cloned spack repo\nrm -rf /path/to/spack\n"})}),"\n",(0,i.jsx)(n.h2,{id:"building-hermes-with-cmake",children:"Building Hermes with CMake"}),"\n",(0,i.jsx)(n.p,{children:"For those developing Hermes, uninstalling and reinstalling from spack\nis extremely cumbersome. As an alternative to spack, Hermes can be\ninstalled manually with a combination of spack and CMake."}),"\n",(0,i.jsx)(n.h3,{id:"install-dependencies",children:"Install Dependencies"}),"\n",(0,i.jsx)(n.h4,{id:"hermes",children:"Hermes"}),"\n",(0,i.jsxs)(n.p,{children:["Install Hermes as you typically would following the instructrions\nin ",(0,i.jsx)(n.a,{href:"#installing-hermes",children:"Section 1"}),". While the Hermes version itself\nis not useful, the installation process will install all dependencies\nwhich will make life much easier for a manual Hermes build. To save\nsome time, you could choose to install ",(0,i.jsx)(n.code,{children:"hermes_shm"})," instead, which contains the same dependencies and variants as Hermes itself."]}),"\n",(0,i.jsx)(n.h4,{id:"optional-scspkg",children:"(Optional) SCSPKG"}),"\n",(0,i.jsxs)(n.p,{children:["To help with managing the organization of manually-built software, we created a tool called ",(0,i.jsx)(n.a,{href:"https://github.com/grc-iit/scspkg",children:"SCSPKG"})," that helps automate the construction of modulefiles."]}),"\n",(0,i.jsx)(n.pre,{children:(0,i.jsx)(n.code,{className:"language-bash",children:'git clone https://github.com/grc-iit/scspkg.git\ncd scspkg\npip install -e . --user\necho "module use $(scspkg module dir)" >> ~/.bashrc\nscspkg init False\n'})}),"\n",(0,i.jsx)(n.h3,{id:"build-hermes",children:"Build Hermes"}),"\n",(0,i.jsx)(n.h4,{id:"load-hermes-dependencies",children:"Load Hermes dependencies"}),"\n",(0,i.jsx)(n.p,{children:"First, load all Hermes dependencies. Hermes_shm is a spackage that\ncontains the same exact dependencies as the full Hermes code:"}),"\n",(0,i.jsx)(n.pre,{children:(0,i.jsx)(n.code,{className:"language-bash",children:"spack load hermes_shm\n"})}),"\n",(0,i.jsx)(n.h4,{id:"optional-create-a-hermes-scspkg-repo",children:"(Optional) Create a Hermes SCSPKG repo"}),"\n",(0,i.jsx)(n.p,{children:"An SCSPKG repo for Hermes can be created as follows:"}),"\n",(0,i.jsx)(n.pre,{children:(0,i.jsx)(n.code,{className:"language-bash",children:"scspkg create hermes_run\n"})}),"\n",(0,i.jsx)(n.p,{children:"This will do three things:"}),"\n",(0,i.jsxs)(n.ol,{children:["\n",(0,i.jsxs)(n.li,{children:["Create the ",(0,i.jsx)(n.strong,{children:"source"})," directory, which is where uncompiled source code is stored. Hermes, for example, could be cloned in this directory -- ",(0,i.jsx)(n.strong,{children:"although this is not required"}),". This directory is created to help developers organize and prevent cluttering their home directory."]}),"\n",(0,i.jsxs)(n.li,{children:["Create the ",(0,i.jsx)(n.strong,{children:"root"})," directory, which is where compiled code is installed to. I.e., this is the directory CMAKE_INSTALL_PREFIX will point to."]}),"\n",(0,i.jsx)(n.li,{children:"Create a modulefile containing most relevant environment variables needed for building HPC software (PATH, LD_LIBRARY_PATH, etc.). The modulefile will contain the root directory."}),"\n"]}),"\n",(0,i.jsx)(n.p,{children:"The path to the source directory is given by the command:"}),"\n",(0,i.jsx)(n.pre,{children:(0,i.jsx)(n.code,{className:"language-bash",children:"scspkg pkg src hermes_run\n"})}),"\n",(0,i.jsx)(n.p,{children:"The path to the root directory is given by the command:"}),"\n",(0,i.jsx)(n.pre,{children:(0,i.jsx)(n.code,{className:"language-bash",children:"scspkg pkg root hermes_run\n"})}),"\n",(0,i.jsx)(n.p,{children:"To view the modulefile, run:"}),"\n",(0,i.jsx)(n.pre,{children:(0,i.jsx)(n.code,{className:"language-bash",children:"module show hermes_run\n"})}),"\n",(0,i.jsx)(n.h4,{id:"compile-and-install",children:"Compile and Install"}),"\n",(0,i.jsx)(n.p,{children:"After this, the local installation can be created as follows:"}),"\n",(0,i.jsx)(n.pre,{children:(0,i.jsx)(n.code,{className:"language-bash",children:"mkdir build\ncd build\ncmake ../ -DCMAKE_INSTALL_PREFIX=$(scspkg pkg root hermes_run)\nmake -j32 install\n"})}),"\n",(0,i.jsx)(n.p,{children:"To compile with MPI-IO and VFD interceptors:"}),"\n",(0,i.jsx)(n.pre,{children:(0,i.jsx)(n.code,{className:"language-bash",children:"cmake ../ \\\n-DHERMES_ENABLE_MPIIO_ADAPTER=ON \\\n-DHERMES_ENABLE_VFD=ON \\\n-DCMAKE_INSTALL_PREFIX=$(scspkg pkg root hermes_run)\n"})}),"\n",(0,i.jsxs)(n.p,{children:["There are several options provided in the root Hermes ",(0,i.jsx)(n.a,{href:"https://github.com/HDFGroup/hermes/blob/master/CMakeLists.txt",children:"CMake"}),". To view these\noptions, one can run run:"]}),"\n",(0,i.jsx)(n.pre,{children:(0,i.jsx)(n.code,{className:"language-bash",children:"ccmake ../\n"})})]})}function h(e={}){const{wrapper:n}={...(0,a.a)(),...e.components};return n?(0,i.jsx)(n,{...e,children:(0,i.jsx)(d,{...e})}):d(e)}},1151:(e,n,s)=>{s.d(n,{Z:()=>t,a:()=>l});var i=s(7294);const a={},r=i.createContext(a);function l(e){const n=i.useContext(r);return i.useMemo((function(){return"function"==typeof e?e(n):{...n,...e}}),[n,e])}function t(e){let n;return n=e.disableParentContext?"function"==typeof e.components?e.components(a):e.components||a:l(e.components),i.createElement(r.Provider,{value:n},e.children)}}}]);
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diff --git a/assets/js/5c7d11d5.e5fe4432.js b/assets/js/5c7d11d5.e5fe4432.js
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--- a/assets/js/5c7d11d5.e5fe4432.js
+++ /dev/null
@@ -1 +0,0 @@
-"use strict";(self.webpackChunkgrc=self.webpackChunkgrc||[]).push([[8187],{9963:(e,r,s)=>{s.r(r),s.d(r,{assets:()=>a,contentTitle:()=>i,default:()=>l,frontMatter:()=>o,metadata:()=>c,toc:()=>h});var n=s(5893),t=s(1151);const o={},i="Quick Start Guide",c={id:"hermes/quick-start",title:"Quick Start Guide",description:"CAUTION: The image from DockerHub may throw Illegal Instruction for Spack-installed binaries.",source:"@site/docs/03-hermes/08-quick-start.md",sourceDirName:"03-hermes",slug:"/hermes/quick-start",permalink:"/docs/hermes/quick-start",draft:!1,unlisted:!1,tags:[],version:"current",sidebarPosition:8,frontMatter:{},sidebar:"tutorialSidebar",previous:{title:"Adapters",permalink:"/docs/hermes/adapters"},next:{title:"Debugging",permalink:"/docs/hermes/debugging"}},a={},h=[{value:"Dockerfiles",id:"dockerfiles",level:2},{value:"For Emacs Users",id:"for-emacs-users",level:2}];function d(e){const r={a:"a",code:"code",h1:"h1",h2:"h2",img:"img",li:"li",p:"p",pre:"pre",strong:"strong",ul:"ul",...(0,t.a)(),...e.components};return(0,n.jsxs)(n.Fragment,{children:[(0,n.jsx)(r.h1,{id:"quick-start-guide",children:"Quick Start Guide"}),"\n",(0,n.jsx)(r.pre,{children:(0,n.jsx)(r.code,{className:"language-bash",children:"docker pull hdfgroup/hermes\ndocker run -it hdfgroup/hermes\nhermes@6bcfd7679b0a:~$ stage_in\nUsage: mpirun -n [nprocs] ./stage_in [url] [offset] [size] [dpe]\n"})}),"\n",(0,n.jsxs)(r.p,{children:["CAUTION: The image from DockerHub may throw ",(0,n.jsx)(r.strong,{children:"Illegal Instruction"})," for Spack-installed binaries.\nSee ",(0,n.jsx)(r.a,{href:"https://github.com/HDFGroup/hermes/issues/483",children:"#483"}),"."]}),"\n",(0,n.jsx)(r.h2,{id:"dockerfiles",children:"Dockerfiles"}),"\n",(0,n.jsxs)(r.p,{children:["There are ",(0,n.jsx)(r.a,{href:"https://github.com/HDFGroup/hermes/tree/master/docker",children:"four Dockerfiles"})," at the top level of the Hermes repository.\nThree Docker images built from these Dockerfiles are available on ",(0,n.jsx)(r.a,{href:"https://hub.docker.com/r/hdfgroup/hermes",children:"Docker Hub"}),":"]}),"\n",(0,n.jsxs)(r.ul,{children:["\n",(0,n.jsxs)(r.li,{children:[(0,n.jsx)(r.a,{href:"https://hub.docker.com/repository/docker/hdfgroup/hermes",children:(0,n.jsx)(r.code,{children:"hdfgroup/hermes:latest"})})," - Hermes pre-built & ready to go"]}),"\n",(0,n.jsxs)(r.li,{children:[(0,n.jsx)(r.a,{href:"https://hub.docker.com/repository/docker/hdfgroup/hermes-dev",children:(0,n.jsx)(r.code,{children:"hdfgroup/hermes-dev:latest"})})," - For Hermes developers; it clones Hermes repo."]}),"\n",(0,n.jsxs)(r.li,{children:[(0,n.jsx)(r.a,{href:"https://hub.docker.com/repository/docker/hdfgroup/hermes-deps",children:(0,n.jsx)(r.code,{children:"hdfgroup/hermes-deps:latest"})})," - For testers; this is used by the two images above."]}),"\n"]}),"\n",(0,n.jsxs)(r.p,{children:["Running one of these docker containers usually involves mounting volumes or directories of the host system in the docker container via the ",(0,n.jsx)(r.code,{children:"-v"})," option of the ",(0,n.jsx)(r.code,{children:"docker run"})," command, for example:"]}),"\n",(0,n.jsx)(r.pre,{children:(0,n.jsx)(r.code,{className:"language-bash",children:"docker run --rm -it -v <host mount point1>:<container mount point1> \\\n                    -v <host mount point2>:<container mount point2> \\\n                    ... \\\n           --entrypoint bash <container image ID>\n"})}),"\n",(0,n.jsxs)(r.p,{children:[(0,n.jsx)(r.strong,{children:"Developers:"})," Do a ",(0,n.jsx)(r.code,{children:"git pull"})," and update the Git remotes if you want to keep your changes!"]}),"\n",(0,n.jsx)(r.h2,{id:"for-emacs-users",children:"For Emacs Users"}),"\n",(0,n.jsx)(r.p,{children:(0,n.jsx)(r.img,{src:"https://img.shields.io/badge/Emacs-%237F5AB6.svg?&style=for-the-badge&logo=gnu-emacs&logoColor=white",alt:"Emacs"})}),"\n",(0,n.jsxs)(r.p,{children:["Editing files in a running container in Emacs (running on a host) is rather convenient with ",(0,n.jsx)(r.a,{href:"https://www.emacswiki.org/emacs/TrampAndDocker",children:"Tramp"})," and ",(0,n.jsx)(r.a,{href:"https://github.com/emacs-pe/docker-tramp.el",children:(0,n.jsx)(r.code,{children:"docker-tramp.el"})}),". For example:"]}),"\n",(0,n.jsx)(r.pre,{children:(0,n.jsx)(r.code,{className:"language-bash",children:"C-x C-f /docker:user@container:/path/to/file\n\nwhere\n  user           is the user that you want to use inside the container (optional)\n  container      is the id or name of the container\n"})}),"\n",(0,n.jsx)(r.p,{children:"Multiple hops are supported as well."})]})}function l(e={}){const{wrapper:r}={...(0,t.a)(),...e.components};return r?(0,n.jsx)(r,{...e,children:(0,n.jsx)(d,{...e})}):d(e)}},1151:(e,r,s)=>{s.d(r,{Z:()=>c,a:()=>i});var n=s(7294);const t={},o=n.createContext(t);function i(e){const r=n.useContext(o);return n.useMemo((function(){return"function"==typeof e?e(r):{...r,...e}}),[r,e])}function c(e){let r;return r=e.disableParentContext?"function"==typeof e.components?e.components(t):e.components||t:i(e.components),n.createElement(o.Provider,{value:r},e.children)}}}]);
\ No newline at end of file
diff --git a/assets/js/71933e4b.18ca951b.js b/assets/js/71933e4b.18ca951b.js
deleted file mode 100644
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--- a/assets/js/71933e4b.18ca951b.js
+++ /dev/null
@@ -1 +0,0 @@
-"use strict";(self.webpackChunkgrc=self.webpackChunkgrc||[]).push([[9638],{327:(A,e,t)=>{t.r(e),t.d(e,{assets:()=>i,contentTitle:()=>r,default:()=>f,frontMatter:()=>a,metadata:()=>o,toc:()=>l});var n=t(5893),s=t(1151);const a={},r="Buffer Pool",o={id:"hermes/components/buffer-pool",title:"Buffer Pool",description:"The main idea behind the Buffer Pool is to avoid the runtime",source:"@site/docs/03-hermes/06-components/02-buffer-pool.md",sourceDirName:"03-hermes/06-components",slug:"/hermes/components/buffer-pool",permalink:"/docs/hermes/components/buffer-pool",draft:!1,unlisted:!1,tags:[],version:"current",sidebarPosition:2,frontMatter:{},sidebar:"tutorialSidebar",previous:{title:"Buffer Organizer",permalink:"/docs/hermes/components/buffer-organizer"},next:{title:"Buffering Target",permalink:"/docs/hermes/components/buffering-target"}},i={},l=[{value:"Buffers and BufferIDs",id:"buffers-and-bufferids",level:2},{value:"Buffer Pool Layout",id:"buffer-pool-layout",level:2},{value:"Initialization",id:"initialization",level:3},{value:"API",id:"api",level:2},{value:"Buffer Pool Visualizer",id:"buffer-pool-visualizer",level:2}];function d(A){const e={code:"code",em:"em",h1:"h1",h2:"h2",h3:"h3",img:"img",li:"li",p:"p",pre:"pre",strong:"strong",ul:"ul",...(0,s.a)(),...A.components};return(0,n.jsxs)(n.Fragment,{children:[(0,n.jsx)(e.h1,{id:"buffer-pool",children:"Buffer Pool"}),"\n",(0,n.jsxs)(e.p,{children:["The main idea behind the ",(0,n.jsx)(e.strong,{children:"Buffer Pool"})," is to avoid the runtime\noverhead of memory allocation each time Hermes wishes to buffer data.\nInstead, we pre-allocate a pool of fixed sized (though the size groups\nare configurable) buffers that can be reused throughout an application\nrun. We allocate memory and reserve file system space on startup and\ndivide the available resources into buffers which the system can\nrequest. We deploy one buffer pool per node for a given Hermes instance."]}),"\n",(0,n.jsx)(e.h2,{id:"buffers-and-bufferids",children:"Buffers and BufferIDs"}),"\n",(0,n.jsxs)(e.p,{children:["A ",(0,n.jsx)(e.strong,{children:(0,n.jsx)(e.em,{children:"Buffer"})})," represents a portion of storage that Hermes is aware of\nand is allowed to buffer data in. It can be backed by various storage\ndevices (RAM, NVMe, SSD, burst buffer, parallel file system, object\nstore, etc.). Each ",(0,n.jsx)(e.strong,{children:(0,n.jsx)(e.em,{children:"Buffer"})})," is identified by a globally unique (per\nHermes application instance) ",(0,n.jsx)(e.code,{children:"BufferID"})," which is an unsigned 64 bit\ninteger divided into the following sections:"]}),"\n",(0,n.jsxs)(e.ul,{children:["\n",(0,n.jsx)(e.li,{children:"32 bits for the node ID. Each node is assigned a unique integer\nindex (starting at 1, not 0) during Hermes initialization."}),"\n",(0,n.jsx)(e.li,{children:"32 bits for header index. This is an index into the array of buffer\nheaders on the corresponding node."}),"\n"]}),"\n",(0,n.jsxs)(e.p,{children:["A ",(0,n.jsx)(e.code,{children:"BufferID"})," of 0 (node id = 0 and header index = 0) signifies the NULL\n",(0,n.jsx)(e.code,{children:"BufferID"}),"."]}),"\n",(0,n.jsx)(e.h2,{id:"buffer-pool-layout",children:"Buffer Pool Layout"}),"\n",(0,n.jsxs)(e.ul,{children:["\n",(0,n.jsxs)(e.li,{children:["Terminology\nBlock : A ",(0,n.jsx)(e.strong,{children:"block"})," is the smallest buffering unit available to\nHermes. It defaults to the system's page size (usually 4 KiB on\nLinux) but can be configured to be any value.\nSlab : A ",(0,n.jsx)(e.strong,{children:"slab"})," is the collection of all buffers of the same block\nsize. A typical setup would be a buffer pool with 4 slabs where the\nfirst slab is a collection of buffers that are 1 block each, the\nnext slab consists of buffers of 4 blocks each, then 16-block\nbuffers, and 32-block buffers. The number of slabs and number of\nblocks for each slab is configurable through a Hermes configuration\nfile so that it can be tailored to each application's I/O pattern."]}),"\n"]}),"\n",(0,n.jsx)(e.p,{children:(0,n.jsx)(e.img,{alt:"Buffer Pool Layout",src:t(8241).Z+"",width:"769",height:"469"})}),"\n",(0,n.jsx)(e.h3,{id:"initialization",children:"Initialization"}),"\n",(0,n.jsx)(e.p,{children:"When Hermes initializes, it will read from the Hermes configuration file\nhow much space is available for buffering in each tier. The amount of\nRAM available is allocated as 1 contiguous address space and split into\nslabs and buffer pool metadata. The total amount of metadata is\ncalculated and reserved. The remaining space is split up into slabs,\naccording to the parameters in the configuration file. A free list is\nmaintained for each slab of buffers. Buffers are marked as in use or\nnot. When the system requests buffers, the buffer pool simply returns\nthe first item from the free list, and freeing buffers translates to\npushing them onto the head of the free list."}),"\n",(0,n.jsx)(e.h2,{id:"api",children:"API"}),"\n",(0,n.jsxs)(e.p,{children:["The primary consumer of the buffer pool API is the Hermes API.\n",(0,n.jsx)(e.code,{children:"Bucket::Put"})," is the primary path that will request buffers, and\n",(0,n.jsx)(e.code,{children:"Bucket::Delete"})," will release buffers."]}),"\n",(0,n.jsx)(e.pre,{children:(0,n.jsx)(e.code,{className:"language-cpp",children:"std::vector<hermes::BufferID> GetBuffers(const hermes::PlacementSchema &schema);\nvoid ReleaseBuffers(const std::vector<hermes::BufferID> &buffer_ids);\n"})}),"\n",(0,n.jsxs)(e.p,{children:["Most operations deal with ",(0,n.jsx)(e.code,{children:"BufferID"}),"s, but when the data itself must be\naccessed (e.g., when an I/O client wises to flush buffers to the PFS)\neach ID contains all the information required to get to the actual data."]}),"\n",(0,n.jsxs)(e.ul,{children:["\n",(0,n.jsx)(e.li,{children:"Split and Merge"}),"\n"]}),"\n",(0,n.jsx)(e.p,{children:"In addition, if the system finds that small buffers are underutilized\nwhile large buffers are exhausted, it can merge unused small buffers\ninto larger buffers for better utilization. Conversely, if large buffers\nare underutilized, it can split large buffers into small buffers."}),"\n",(0,n.jsx)(e.h2,{id:"buffer-pool-visualizer",children:"Buffer Pool Visualizer"}),"\n",(0,n.jsx)(e.p,{children:"To facilitate testing and debugging, we've developed a tool to display a\ngraphical view of the state of a buffer pool. The buffer visualization\nupdates in real time by simply reading the buffer pool shared memory, so\nwe can watch how buffers get used and freed as an application executes,\nand it can be attached and detached to/from any running application.\nBelow is a visualization of a buffer pool with 4 slabs. The red slab is\nmade of 1-block (4 KiB in this case) buffers, the yellow of 4-block\nbuffers, the green of 16 block buffers, and the blue of 32-block\nbuffers. Note that the relative sizes are preserved. The space above the\nmagenta line is directly mapped to the RAM buffers in shared memory.\nBelow the magenta line we see the total headers, including those in use\n(green) and unused (grey). In the initial state, we have some unused\nheaders to facilitate splitting buffers."}),"\n",(0,n.jsx)(e.p,{children:(0,n.jsx)(e.img,{alt:"Buffer Pool Visualizer",src:t(7823).Z+"",width:"1200",height:"633"})}),"\n",(0,n.jsx)(e.p,{children:"Here we have merged the yellow 4-block slab into the green 16-block\nslab. We can also see that fewer headers are in use because we now have\nfewer buffers."}),"\n",(0,n.jsx)(e.p,{children:(0,n.jsx)(e.img,{alt:"Buffer Pool Visualizer Merge",src:t(2724).Z+"",width:"1200",height:"516"})}),"\n",(0,n.jsx)(e.p,{children:"Here we have split all slabs into the smallest possible buffers,\nresulting in one slab of 1-block buffers. Here every header is used, and\nthis is the maximum number of buffers the system can support for this\nparticular configuration."}),"\n",(0,n.jsx)(e.p,{children:(0,n.jsx)(e.img,{alt:"Buffer Pool Visualizer Split",src:t(5464).Z+"",width:"1200",height:"508"})}),"\n",(0,n.jsx)(e.p,{children:"Development on the visualizer occurs on an as-needed basis, but should\nthe need arise, it would be great to be able to zoom in and out, and\nhover over buffers to see actual data."})]})}function f(A={}){const{wrapper:e}={...(0,s.a)(),...A.components};return e?(0,n.jsx)(e,{...A,children:(0,n.jsx)(d,{...A})}):d(A)}},8241:(A,e,t)=>{t.d(e,{Z:()=>n});const n=t.p+"assets/images/BufferPoolLayout-6ad491f91329f6452cba250510eeb74f.jpg"},7823:(A,e,t)=>{t.d(e,{Z:()=>n});const n=t.p+"assets/images/buffer_pool_visualizer_default-4f856358bcbb7a8ee79889853c0d1238.png"},2724:(A,e,t)=>{t.d(e,{Z:()=>n});const 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diff --git a/assets/js/74caac71.72eccc7d.js b/assets/js/74caac71.72eccc7d.js
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It attempts to correct sub-optimal DPE\nplacements by moving data among buffers.']}),"\n",(0,r.jsx)(n.h2,{id:"objectives",children:"Objectives"}),"\n",(0,r.jsxs)(n.ul,{children:["\n",(0,r.jsxs)(n.li,{children:["Management of hierarchical buffering space","\n",(0,r.jsxs)(n.ul,{children:["\n",(0,r.jsx)(n.li,{children:"Data flushing"}),"\n",(0,r.jsx)(n.li,{children:"Read acceleration"}),"\n"]}),"\n"]}),"\n",(0,r.jsxs)(n.li,{children:["Manage data life cycle, or journey","\n",(0,r.jsxs)(n.ul,{children:["\n",(0,r.jsx)(n.li,{children:"When is the blob in equilibrium?"}),"\n",(0,r.jsx)(n.li,{children:"How do we eliminate unnecessary data movement?"}),"\n"]}),"\n"]}),"\n"]}),"\n",(0,r.jsx)(n.h2,{id:"blob-scoring",children:"Blob Scoring"}),"\n",(0,r.jsxs)(n.p,{children:["We attempt to meet the above objectives via a ",(0,r.jsx)(n.code,{children:"Blob"})," scoring system. Each ",(0,r.jsx)(n.code,{children:"Blob"})," has two different scores associated with it: the ",(0,r.jsx)(n.strong,{children:"importance score"})," and the ",(0,r.jsx)(n.strong,{children:"access score"}),"."]}),"\n",(0,r.jsx)(n.h3,{id:"importance-score",children:"Importance Score"}),"\n",(0,r.jsxs)(n.p,{children:["The importance score is a real number in the range [0, 1] where 0 represents a ",(0,r.jsx)(n.code,{children:"Blob"})," that is not important to the user (i.e., it will not be accessed) and 1 represents a ",(0,r.jsx)(n.code,{children:"Blob"})," that will be accessed either very frequently, very soon, or both."]}),"\n",(0,r.jsx)(n.h4,{id:"variables-that-might-contribute-to-the-importance-score",children:"Variables that might contribute to the importance score"}),"\n",(0,r.jsxs)(n.ul,{children:["\n",(0,r.jsx)(n.li,{children:"Blob Size"}),"\n",(0,r.jsx)(n.li,{children:"Blob Name"}),"\n",(0,r.jsx)(n.li,{children:"Recency of Blob access"}),"\n",(0,r.jsx)(n.li,{children:"Frequency of Blob access"}),"\n",(0,r.jsx)(n.li,{children:"User-supplied priority (this is only a hint, not a guarantee)."}),"\n"]}),"\n",(0,r.jsx)(n.h3,{id:"access-score",children:"Access Score"}),"\n",(0,r.jsxs)(n.p,{children:["This is a real number in the range [0, 1] where 0 represents a ",(0,r.jsx)(n.code,{children:"Blob"})," with the slowest access time (i.e., all its ",(0,r.jsx)(n.code,{children:"Buffer"}),"s are in the slowest tier) and 1 represents a ",(0,r.jsx)(n.code,{children:"Blob"})," with the quickest access time (all the ",(0,r.jsx)(n.code,{children:"Buffer"}),"s are in the fastest tier)."]}),"\n",(0,r.jsx)(n.h4,{id:"variables-that-contribute-to-the-access-score",children:"Variables that contribute to the access score"}),"\n",(0,r.jsxs)(n.ul,{children:["\n",(0,r.jsxs)(n.li,{children:["Bandwidth of the tiers that contain the ",(0,r.jsx)(n.code,{children:"Blob"}),"'s ",(0,r.jsx)(n.code,{children:"Buffer"}),"s."]}),"\n",(0,r.jsxs)(n.li,{children:["The ",(0,r.jsx)(n.code,{children:"Blob"})," distribution (i.e., is all the data in a single ",(0,r.jsx)(n.code,{children:"Buffer"}),", or is it spread out among multiple ",(0,r.jsx)(n.code,{children:"Buffer"}),"s on multiple nodes?)."]}),"\n"]}),"\n",(0,r.jsx)(n.h3,{id:"how-the-scores-are-used",children:"How the scores are used"}),"\n",(0,r.jsxs)(n.p,{children:["The goal of the ",(0,r.jsx)(n.code,{children:"BufferOrganizer"})," is to ensure that each ",(0,r.jsx)(n.code,{children:"Blob"}),"'s access score is closely aligned to its importance score."]}),"\n",(0,r.jsx)(n.h2,{id:"ideas",children:"Ideas"}),"\n",(0,r.jsxs)(n.ul,{children:["\n",(0,r.jsxs)(n.li,{children:["If a ",(0,r.jsx)(n.code,{children:"Blob"}),"'s ",(0,r.jsx)(n.code,{children:"Bucket"})," has a reference count of 0 (i.e., no process has an open handle to the ",(0,r.jsx)(n.code,{children:"Bucket"}),") then the importance score should be 0. The score is only calculated once at least one process opens the ",(0,r.jsx)(n.code,{children:"Bucket"}),"."]}),"\n"]}),"\n",(0,r.jsx)(n.h2,{id:"operations",children:"Operations"}),"\n",(0,r.jsxs)(n.p,{children:["All ",(0,r.jsx)(n.code,{children:"BufferOrganizer"})," operations are implemented in terms of 3 simple\noperators"]}),"\n",(0,r.jsxs)(n.ul,{children:["\n",(0,r.jsx)(n.li,{children:"MOVE(BufferID, TargetID)"}),"\n",(0,r.jsx)(n.li,{children:"COPY(BufferID, TargetID)"}),"\n",(0,r.jsx)(n.li,{children:"DELETE(BufferID)"}),"\n"]}),"\n",(0,r.jsx)(n.p,{children:"With these operators, we can build more complex tasks:"}),"\n",(0,r.jsx)(n.h3,{id:"transfer",children:"Transfer"}),"\n",(0,r.jsxs)(n.p,{children:["Move a ",(0,r.jsx)(n.code,{children:"BufferID"})," from one set of ",(0,r.jsx)(n.code,{children:"Target"}),"s to another."]}),"\n",(0,r.jsx)(n.h4,{id:"who-can-initiate-transfer-tasks",children:"Who can initiate Transfer tasks?"}),"\n",(0,r.jsxs)(n.ul,{children:["\n",(0,r.jsx)(n.li,{children:"The System (load balancing)"}),"\n",(0,r.jsx)(n.li,{children:"The User (producer/consumer)"}),"\n"]}),"\n",(0,r.jsx)(n.h3,{id:"evictsize_t-bytes-targets",children:"Evict(size_t bytes, Targets[])"}),"\n",(0,r.jsxs)(n.p,{children:["Move a set of ",(0,r.jsx)(n.code,{children:"BufferId"}),"s from one set of ",(0,r.jsx)(n.code,{children:"Target"}),"s to an unspecified\nlocation (could even be swap space)."]}),"\n",(0,r.jsx)(n.h4,{id:"who-can-initiate-eviction-tasks",children:"Who can initiate Eviction tasks?"}),"\n",(0,r.jsxs)(n.ul,{children:["\n",(0,r.jsx)(n.li,{children:"Put (DPE)"}),"\n",(0,r.jsx)(n.li,{children:"Get (Prefetcher)"}),"\n",(0,r.jsxs)(n.li,{children:["Thread that updates the ",(0,r.jsx)(n.code,{children:"SystemViewState"})," (enforces a minimum\ncapacity threshold passed in through the config)."]}),"\n"]}),"\n",(0,r.jsx)(n.h4,{id:"who-translates-an-eviction-into-a-series-of-transfers",children:"Who translates an Eviction into a series of Transfers?"}),"\n",(0,r.jsxs)(n.ul,{children:["\n",(0,r.jsx)(n.li,{children:"DPE?"}),"\n",(0,r.jsx)(n.li,{children:"BO?"}),"\n"]}),"\n",(0,r.jsx)(n.h4,{id:"single-shared-file-pros",children:"Single shared file pros"}),"\n",(0,r.jsxs)(n.ul,{children:["\n",(0,r.jsx)(n.li,{children:"Could theoretically reap performance benefits of collective IO\noperations, although I don't think we'll ever be able to capitalize\non this because each rank must act independently and can't\nsynchronize with the other ranks."}),"\n",(0,r.jsx)(n.li,{children:"Less stress on the PFS metadata server."}),"\n"]}),"\n",(0,r.jsx)(n.h4,{id:"file-per-rank-pros",children:"File per rank pros"}),"\n",(0,r.jsxs)(n.ul,{children:["\n",(0,r.jsx)(n.li,{children:"Don't have to worry about reserving size for each rank."}),"\n",(0,r.jsx)(n.li,{children:"Don't have to worry about locking."}),"\n"]}),"\n",(0,r.jsx)(n.h4,{id:"file-per-node",children:"File per node"}),"\n",(0,r.jsxs)(n.ul,{children:["\n",(0,r.jsx)(n.li,{children:"We'll go with this for the initial implementation."}),"\n",(0,r.jsxs)(n.li,{children:["Don't have to worry about locking or reserving size with respect to\nthe buffer organizer. However, since multiple ranks could\npotentially write to the same swap file, we need to either","\n",(0,r.jsxs)(n.ul,{children:["\n",(0,r.jsx)(n.li,{children:"Filter all swap traffic through the buffer organizer"}),"\n",(0,r.jsx)(n.li,{children:"Synchronize all access to the file"}),"\n"]}),"\n"]}),"\n",(0,r.jsx)(n.li,{children:"Won't overload the metadata servers as bad as file per rank."}),"\n"]}),"\n",(0,r.jsx)(n.h2,{id:"triggers",children:"Triggers"}),"\n",(0,r.jsx)(n.p,{children:"The Buffer Organizer can be triggered in 3 ways:"}),"\n",(0,r.jsx)(n.h3,{id:"periodic",children:"Periodic"}),"\n",(0,r.jsx)(n.p,{children:"The period can be controlled by a configuration variable."}),"\n",(0,r.jsx)(n.h3,{id:"client-triggered",children:"Client-triggered"}),"\n",(0,r.jsxs)(n.ul,{children:["\n",(0,r.jsx)(n.li,{children:"If, for any reason, a client DPE places data to the swap target, it\nwill also trigger the buffer organizer by adding an event to the\nbuffer organizer's queue."}),"\n",(0,r.jsx)(n.li,{children:"We store the blob name, the offset into the swap target (for\nfile-based targets), and the blob size."}),"\n",(0,r.jsx)(n.li,{children:"When the buffer organizer processes an event, it"}),"\n"]}),"\n",(0,r.jsxs)(n.ol,{children:["\n",(0,r.jsx)(n.li,{children:"Reads the blob from the swap target into memory."}),"\n",(0,r.jsxs)(n.li,{children:["Calls ",(0,r.jsx)(n.code,{children:"Put"})," to place the blob into the hierarchy. If the ",(0,r.jsx)(n.code,{children:"Put"}),"\nfails, it tries again, up to ",(0,r.jsx)(n.code,{children:"num_buffer_organizer_retries"}),"\n(configurable) times."]}),"\n"]}),"\n",(0,r.jsx)(n.h3,{id:"system-triggered",children:"System-triggered"}),"\n",(0,r.jsxs)(n.ul,{children:["\n",(0,r.jsx)(n.li,{children:"Nothing is implemented yet."}),"\n",(0,r.jsx)(n.li,{children:"Should the BO constantly monitor the buffering hierarchy and attempt\nto maintain a set of rules (remaining capacity percentage,\nthresholds, etc.)?"}),"\n",(0,r.jsx)(n.li,{children:'Should the BO simply carry out "orders" and not attempt to make its\nown decisions? If so, who gives the orders?'}),"\n",(0,r.jsx)(n.li,{children:"Should the BO be available for other asynchronous tasks?"}),"\n"]}),"\n",(0,r.jsx)(n.h3,{id:"requirements-for-queue-implementation",children:"Requirements for Queue implementation"}),"\n",(0,r.jsxs)(n.ul,{children:["\n",(0,r.jsx)(n.li,{children:"(At least) 2 different priority lanes"}),"\n",(0,r.jsx)(n.li,{children:"Node local and remote queues (but only for neighborhoods, not global\nqueues)."}),"\n",(0,r.jsx)(n.li,{children:"Need ability to restrict queue length"}),"\n"]}),"\n",(0,r.jsx)(n.h2,{id:"design-details",children:"Design Details"}),"\n",(0,r.jsx)(n.h3,{id:"bo-rpc-server",children:"BO RPC Server"}),"\n",(0,r.jsxs)(n.ul,{children:["\n",(0,r.jsxs)(n.li,{children:["RPC is used to route ",(0,r.jsx)(n.code,{children:"BoTask"}),"s to the appropriate Hermes core."]}),"\n"]}),"\n",(0,r.jsxs)(n.ul,{children:["\n",(0,r.jsxs)(n.li,{children:["The ",(0,r.jsx)(n.code,{children:"BO"})," RPC server only has one function:","\n",(0,r.jsx)(n.pre,{children:(0,r.jsx)(n.code,{className:"language-cpp",children:"bool EnqueueBoTask(BoTask task, Priority priority);\n"})}),"\n"]}),"\n"]}),"\n",(0,r.jsx)(n.p,{children:"[[../images/bo_rpc.png]]"}),"\n",(0,r.jsx)(n.h3,{id:"buffer-organizer-1",children:"Buffer Organizer"}),"\n",(0,r.jsx)(n.h4,{id:"work-queues",children:"Work Queues"}),"\n",(0,r.jsxs)(n.ul,{children:["\n",(0,r.jsxs)(n.li,{children:["Argobots ",(0,r.jsx)(n.strong,{children:"pool"}),"s"]}),"\n",(0,r.jsx)(n.li,{children:"High and low priorities"}),"\n",(0,r.jsx)(n.li,{children:"Basic FIFO queue by default"}),"\n",(0,r.jsx)(n.li,{children:"Completely customizable (e.g., could be a priority queue, min-heap,\netc.)"}),"\n"]}),"\n",(0,r.jsx)(n.h4,{id:"schedulers",children:"Schedulers"}),"\n",(0,r.jsxs)(n.ul,{children:["\n",(0,r.jsxs)(n.li,{children:["Argobots ",(0,r.jsx)(n.strong,{children:"scheduler"}),"s"]}),"\n",(0,r.jsx)(n.li,{children:"Takes tasks from the queues and runs them on OS threads as user\nlevel threads (basically coroutines)."}),"\n",(0,r.jsx)(n.li,{children:"Completely customizable."}),"\n",(0,r.jsx)(n.li,{children:"By default, one scheduler is associated with a single execution\nstream (OS thread)."}),"\n",(0,r.jsx)(n.li,{children:"Only take tasks from low priority queue if high priority queue is\nempty?"}),"\n"]}),"\n",(0,r.jsx)(n.h4,{id:"threads",children:"Threads"}),"\n",(0,r.jsxs)(n.ul,{children:["\n",(0,r.jsxs)(n.li,{children:["Argobots ",(0,r.jsx)(n.strong,{children:"execution stream"}),"s"]}),"\n",(0,r.jsxs)(n.li,{children:["Bound to a ",(0,r.jsx)(n.strong,{children:"processing element"})," (CPU core or hyperthread), and\nshouldn't be oversubscribed."]}),"\n"]}),"\n",(0,r.jsx)(n.p,{children:(0,r.jsx)(n.img,{src:i(5181).Z+"",width:"643",height:"495"})}),"\n",(0,r.jsx)(n.h2,{id:"example-flows",children:"Example Flows"}),"\n",(0,r.jsx)(n.h3,{id:"hot-put",children:"Hot Put"}),"\n",(0,r.jsx)(n.p,{children:(0,r.jsx)(n.img,{src:i(8418).Z+"",width:"378",height:"956"})}),"\n",(0,r.jsx)(n.h3,{id:"bo-eviction-flow",children:"BO Eviction Flow"}),"\n",(0,r.jsx)(n.p,{children:(0,r.jsx)(n.img,{src:i(1506).Z+"",width:"553",height:"524"})}),"\n",(0,r.jsx)(n.h2,{id:"ideas-1",children:"Ideas"}),"\n",(0,r.jsxs)(n.ul,{children:["\n",(0,r.jsxs)(n.li,{children:["An importance score of 0 could be the signal to flush a ",(0,r.jsx)(n.code,{children:"Blob"})," to the PFS."]}),"\n",(0,r.jsxs)(n.li,{children:[(0,r.jsx)(n.code,{children:"StageIn"})," and ",(0,r.jsx)(n.code,{children:"StageOut"})," APIs"]}),"\n",(0,r.jsxs)(n.li,{children:['Reverse "gravity" for read heavy workloads. ',(0,r.jsx)(n.code,{children:"Blobs"})," trickle up to higher tiers."]}),"\n",(0,r.jsx)(n.li,{children:"Explicitly maintain Target capacity thresholds."}),"\n",(0,r.jsx)(n.li,{children:"Introduce horizontal movement if Topology threshold is exceeded."}),"\n"]}),"\n",(0,r.jsx)(n.h2,{id:"experiments",children:"Experiments"}),"\n",(0,r.jsxs)(n.ul,{children:["\n",(0,r.jsxs)(n.li,{children:["Test the difference between flushing tier by tier vs skipping tiers. For example, a ",(0,r.jsx)(n.code,{children:"Blob"})," moving from RAM to burst buffer could go through NVMe as an intermediate tier, or skip it altogether."]}),"\n"]})]})}function d(e={}){const{wrapper:n}={...(0,s.a)(),...e.components};return n?(0,r.jsx)(n,{...e,children:(0,r.jsx)(h,{...e})}):h(e)}},5181:(e,n,i)=>{i.d(n,{Z:()=>r});const r=i.p+"assets/images/bo-9412e1ce05035896279ca164b1375068.png"},1506:(e,n,i)=>{i.d(n,{Z:()=>r});const r=i.p+"assets/images/bo_evict-f585db845536915d3efa4b9225efce29.png"},8418:(e,n,i)=>{i.d(n,{Z:()=>r});const r=i.p+"assets/images/hot_put-0d2d32fadedf6f594a46ecc415ad16d0.png"},1151:(e,n,i)=>{i.d(n,{Z:()=>o,a:()=>l});var r=i(7294);const s={},t=r.createContext(s);function l(e){const n=r.useContext(t);return r.useMemo((function(){return"function"==typeof e?e(n):{...n,...e}}),[n,e])}function o(e){let n;return n=e.disableParentContext?"function"==typeof e.components?e.components(s):e.components||s:l(e.components),r.createElement(t.Provider,{value:n},e.children)}}}]);
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diff --git a/assets/js/697644c6.f5e2565a.js b/assets/js/7b3f7c98.47261f2c.js
similarity index 98%
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rename to assets/js/7b3f7c98.47261f2c.js
index bdd15866..d52098c6 100644
--- a/assets/js/697644c6.f5e2565a.js
+++ b/assets/js/7b3f7c98.47261f2c.js
@@ -1 +1 @@
-"use strict";(self.webpackChunkgrc=self.webpackChunkgrc||[]).push([[1206],{9406:(e,n,s)=>{s.r(n),s.d(n,{assets:()=>c,contentTitle:()=>d,default:()=>o,frontMatter:()=>t,metadata:()=>l,toc:()=>h});var i=s(5893),r=s(1151);const t={},d="Examples",l={id:"hermes/components/examples",title:"Examples",description:"Ares (IIT)",source:"@site/docs/03-hermes/06-components/10-examples.md",sourceDirName:"03-hermes/06-components",slug:"/hermes/components/examples",permalink:"/docs/hermes/components/examples",draft:!1,unlisted:!1,tags:[],version:"current",sidebarPosition:10,frontMatter:{},sidebar:"tutorialSidebar",previous:{title:"Prefetcher",permalink:"/docs/hermes/components/prefetcher"},next:{title:"Tagging",permalink:"/docs/hermes/components/tagging"}},c={},h=[{value:"Ares (IIT)",id:"ares-iit",level:2},{value:"Performance",id:"performance",level:3},{value:"Memory",id:"memory",level:4},{value:"Storage",id:"storage",level:4},{value:"Networking",id:"networking",level:4},{value:"Chameleon (TACC)",id:"chameleon-tacc",level:2},{value:"Standard Cloud Units",id:"standard-cloud-units",level:3},{value:"Tier Characterization",id:"tier-characterization",level:2},{value:"Layer (Level?)",id:"layer-level",level:2}];function a(e){const n={a:"a",em:"em",h1:"h1",h2:"h2",h3:"h3",h4:"h4",img:"img",li:"li",p:"p",table:"table",tbody:"tbody",td:"td",th:"th",thead:"thead",tr:"tr",ul:"ul",...(0,r.a)(),...e.components};return(0,i.jsxs)(i.Fragment,{children:[(0,i.jsx)(n.h1,{id:"examples",children:"Examples"}),"\n",(0,i.jsx)(n.h2,{id:"ares-iit",children:"Ares (IIT)"}),"\n",(0,i.jsx)(n.p,{children:(0,i.jsx)(n.img,{alt:"Ares - simplified structure",src:s(9391).Z+"",width:"534",height:"489"})}),"\n",(0,i.jsx)(n.p,{children:(0,i.jsx)(n.img,{alt:"Ares - network topology",src:s(2252).Z+"",width:"1027",height:"771"})}),"\n",(0,i.jsxs)("table",{children:[(0,i.jsxs)("tr",{children:[(0,i.jsx)("th",{children:(0,i.jsx)("p",{children:"Compute Rack"})}),(0,i.jsx)("th",{children:(0,i.jsx)("p",{children:"Interconnect"})}),(0,i.jsx)("th",{children:(0,i.jsx)("p",{children:"Storage Rack"})})]}),(0,i.jsxs)("tr",{children:[(0,i.jsx)("td",{children:(0,i.jsxs)("p",{children:["8x ",(0,i.jsx)("strong",{children:"C1"})," nodes w/ Samsung 960 Evo 250GB NVMe SSD"]})}),(0,i.jsx)("td",{rowspan:"2",children:(0,i.jsxs)("ul",{children:[(0,i.jsx)("li",{children:"1x 40 Gbps ethernet port"}),(0,i.jsx)("li",{children:"1x 1 Gbps ethernet"}),(0,i.jsx)("li",{children:"200Gbps uplink switch"})]})}),(0,i.jsx)("td",{rowspan:"2",children:(0,i.jsxs)("ul",{children:[(0,i.jsx)("li",{children:"Seagate 1TB SATA HDD"}),(0,i.jsx)("li",{children:"Samsung 860 Evo 250GB SATA SSD"})]})})]}),(0,i.jsx)("tr",{children:(0,i.jsx)("td",{children:(0,i.jsxs)("p",{children:["24x ",(0,i.jsx)("strong",{children:"C2"})," nodes w/ Toshiba OCZ RD400 256GB NVMe SSD"]})})})]}),"\n",(0,i.jsxs)(n.ul,{children:["\n",(0,i.jsxs)(n.li,{children:["What kind of CPU(s)?","\n",(0,i.jsxs)(n.ul,{children:["\n",(0,i.jsx)(n.li,{children:"Intel Xeon silver 4114"}),"\n"]}),"\n"]}),"\n"]}),"\n",(0,i.jsxs)(n.ul,{children:["\n",(0,i.jsxs)(n.li,{children:["How much memory and what kind?","\n",(0,i.jsxs)(n.ul,{children:["\n",(0,i.jsx)(n.li,{children:"128GB DDR4-2400 (need to double check)"}),"\n"]}),"\n"]}),"\n",(0,i.jsxs)(n.li,{children:["What's the OS? (kernel version, etc.)","\n",(0,i.jsxs)(n.ul,{children:["\n",(0,i.jsx)(n.li,{children:"OpenHPC(GCC 4.8.5) on login and compute nodes, CentOS(GCC 7.3.0)\nand on storage nodes. (Need to double check)"}),"\n"]}),"\n"]}),"\n",(0,i.jsxs)(n.li,{children:["How is the system configured? (file systems, networking, etc.)","\n",(0,i.jsxs)(n.ul,{children:["\n",(0,i.jsx)(n.li,{children:"All nodes are equipped with one Mellanox 40Gbps adapter."}),"\n",(0,i.jsx)(n.li,{children:"Each compute/storage node has one high-speed (40Gbps) Ethernet\nand one low-speed (1Gbps) Ethernet."}),"\n",(0,i.jsx)(n.li,{children:"Compute node 31, 32 and the master node are connected to the\nhigh-speed switch in the storage rack."}),"\n",(0,i.jsx)(n.li,{children:"Compute and storage nodes are connected to different switches\nwhich are connected with a 200Gbps uplink."}),"\n",(0,i.jsx)(n.li,{children:"The network speed on the storage nodes are limited by the PCIe\n2.0 standard, which is around 1GB/s."}),"\n",(0,i.jsx)(n.li,{children:"OrangeFS 2.9.7 has been installed into /opt/ohpc/pub/orangefs.\nEvery user can run it and access it from MPI applications with\nproper configuration in the MPI library."}),"\n"]}),"\n"]}),"\n"]}),"\n",(0,i.jsx)(n.h3,{id:"performance",children:"Performance"}),"\n",(0,i.jsx)(n.h4,{id:"memory",children:"Memory"}),"\n",(0,i.jsx)(n.p,{children:"RDMA max bandwidth is around 37 Gb/s."}),"\n",(0,i.jsx)(n.p,{children:(0,i.jsx)(n.img,{alt:"ARES RDMA Bandwidth",src:s(4864).Z+"",width:"931",height:"604"})}),"\n",(0,i.jsxs)(n.p,{children:["Memory bandwidth (",(0,i.jsx)(n.a,{href:"https://www.cs.virginia.edu/stream/",children:"STREAM\nbenchmark"}),"):"]}),"\n",(0,i.jsxs)(n.ul,{children:["\n",(0,i.jsxs)(n.li,{children:["Compute node (Lenovo): 49 GB/s\n(",(0,i.jsx)(n.a,{href:"https://docs.google.com/document/d/1QQPs-NwI-tqaUmA3CnpztY3i2pkVujSAVoliSnTBlPQ/edit",children:"reference"}),")"]}),"\n",(0,i.jsxs)(n.li,{children:["Storage node (Sun): 7GB/s\n(",(0,i.jsx)(n.a,{href:"https://docs.google.com/document/d/1jkOKFvc7ueLkP6kjJgOhgK7k-LMq-jMIaTVuHmTzA5M/edit",children:"reference"}),")"]}),"\n"]}),"\n",(0,i.jsxs)(n.p,{children:["Memory latency (",(0,i.jsx)(n.a,{href:"https://github.com/torvalds/test-tlb",children:"TLB benchmark"}),"):"]}),"\n",(0,i.jsxs)(n.ul,{children:["\n",(0,i.jsx)(n.li,{children:"Huge/regular page seq: 7ns"}),"\n",(0,i.jsx)(n.li,{children:"Huge page rand: 92 ns"}),"\n",(0,i.jsx)(n.li,{children:"Regular page rand: 108 ns"}),"\n",(0,i.jsx)(n.li,{children:(0,i.jsx)(n.a,{href:"https://docs.google.com/spreadsheets/d/1piDh07T3fX5tlel4NdrsxvkFy_Ojopa1dbkN1X5AruE/edit#gid=0",children:"numbers are\nfrom"})}),"\n"]}),"\n",(0,i.jsx)(n.h4,{id:"storage",children:"Storage"}),"\n",(0,i.jsxs)(n.p,{children:["Disk bandwidth (",(0,i.jsx)(n.a,{href:"https://fio.readthedocs.io/en/latest/fio_doc.html",children:"fio"}),"\nbenchmark):"]}),"\n",(0,i.jsxs)(n.ul,{children:["\n",(0,i.jsx)(n.li,{children:(0,i.jsx)(n.a,{href:"https://ares.cs.iit.edu/baseline-perf/",children:"test script can be found"})}),"\n"]}),"\n",(0,i.jsxs)(n.ul,{children:["\n",(0,i.jsxs)(n.li,{children:[(0,i.jsx)(n.a,{href:"https://ares.cs.iit.edu/baseline-perf/local_disk/comp-samsung-nvme.html",children:"Compute node (Samsung\nNVMe)"}),"\n& ",(0,i.jsx)(n.a,{href:"https://ares.cs.iit.edu/baseline-perf/local_disk/comp-toshiba-nvme.html",children:"Compute node (Toshiba\nNVMe)"}),":","\n",(0,i.jsxs)(n.ul,{children:["\n",(0,i.jsx)(n.li,{children:"Read max: 2.5GB/s"}),"\n",(0,i.jsx)(n.li,{children:"Write max: 1GB/s"}),"\n"]}),"\n"]}),"\n"]}),"\n",(0,i.jsxs)(n.ul,{children:["\n",(0,i.jsxs)(n.li,{children:[(0,i.jsx)(n.a,{href:"https://ares.cs.iit.edu/baseline-perf/local_disk/stor-ssd-pcie-sata.html",children:"Storage node (Samsung SATA SSD) with PICe\nadapter"}),"\n",(0,i.jsxs)(n.ul,{children:["\n",(0,i.jsx)(n.li,{children:"Read/Write max: 400MB/s"}),"\n"]}),"\n"]}),"\n"]}),"\n",(0,i.jsxs)(n.ul,{children:["\n",(0,i.jsxs)(n.li,{children:[(0,i.jsx)(n.a,{href:"https://ares.cs.iit.edu/baseline-perf/local_disk/stor-hdd-sata.html",children:"Storage node (Samsung SATA)\nHDD"}),"\n",(0,i.jsxs)(n.ul,{children:["\n",(0,i.jsx)(n.li,{children:"Read/Write max: 180MB/s"}),"\n"]}),"\n"]}),"\n"]}),"\n",(0,i.jsx)(n.h4,{id:"networking",children:"Networking"}),"\n",(0,i.jsx)(n.p,{children:(0,i.jsx)(n.a,{href:"https://docs.google.com/spreadsheets/d/1bngw2dXIamtT7rvPcultBxF5lyhubNCmK2BkkIr5vAc/edit#gid=686223677",children:"Numbers are\nfrom"})}),"\n",(0,i.jsxs)(n.table,{children:[(0,i.jsx)(n.thead,{children:(0,i.jsxs)(n.tr,{children:[(0,i.jsx)(n.th,{children:"Direction"}),(0,i.jsx)(n.th,{children:"Latency (us)"}),(0,i.jsx)(n.th,{children:"Max Bandwidth (Gb/s)"})]})}),(0,i.jsxs)(n.tbody,{children:[(0,i.jsxs)(n.tr,{children:[(0,i.jsx)(n.td,{children:"Compute - compute node"}),(0,i.jsx)(n.td,{children:"2"}),(0,i.jsx)(n.td,{children:"37"})]}),(0,i.jsxs)(n.tr,{children:[(0,i.jsx)(n.td,{children:"Compute - storage node"}),(0,i.jsx)(n.td,{children:"6"}),(0,i.jsx)(n.td,{children:"10"})]}),(0,i.jsxs)(n.tr,{children:[(0,i.jsx)(n.td,{children:"Storage - storage node"}),(0,i.jsx)(n.td,{children:"5"}),(0,i.jsx)(n.td,{children:"12.5"})]})]})]}),"\n",(0,i.jsx)(n.h2,{id:"chameleon-tacc",children:"Chameleon (TACC)"}),"\n",(0,i.jsx)(n.p,{children:"The Chameleon architecture consists of a set of standard cloud units\n(SCUs)."}),"\n",(0,i.jsx)(n.p,{children:(0,i.jsx)(n.img,{alt:"Chameleon - One Unit of SCU Hardware Summary",src:s(26).Z+"",width:"693",height:"234"})}),"\n",(0,i.jsx)(n.h3,{id:"standard-cloud-units",children:"Standard Cloud Units"}),"\n",(0,i.jsxs)(n.ul,{children:["\n",(0,i.jsxs)(n.li,{children:["What kind of CPU(s)?","\n",(0,i.jsxs)(n.ul,{children:["\n",(0,i.jsx)(n.li,{children:"Each compute node is with 24 cores delivered in dual socket\nIntel Xeon E5-2670 v3 \u201cHaswell\u201d processors (each with 12 cores @\n2.3GHz)"}),"\n"]}),"\n"]}),"\n"]}),"\n",(0,i.jsxs)(n.ul,{children:["\n",(0,i.jsxs)(n.li,{children:["How much memory and what kind?","\n",(0,i.jsxs)(n.ul,{children:["\n",(0,i.jsx)(n.li,{children:"128 GiB of DDR4 RAM."}),"\n"]}),"\n"]}),"\n"]}),"\n",(0,i.jsxs)(n.ul,{children:["\n",(0,i.jsxs)(n.li,{children:["What's the OS? (kernel version, etc.)","\n",(0,i.jsxs)(n.ul,{children:["\n",(0,i.jsx)(n.li,{children:"OS is configurable by the user."}),"\n"]}),"\n"]}),"\n"]}),"\n",(0,i.jsxs)(n.ul,{children:["\n",(0,i.jsxs)(n.li,{children:["How is the system configured? (file systems, networking, etc.)","\n",(0,i.jsxs)(n.ul,{children:["\n",(0,i.jsx)(n.li,{children:"Every switch in the research network is a fully OpenFlow\ncompliant programmable Dell S6000-ON switch."}),"\n",(0,i.jsx)(n.li,{children:"Each node connects to this network at 10 Gbps, and each unit\nuplinks with 40Gbps per rack to the Chameleon core network."}),"\n",(0,i.jsx)(n.li,{children:"The core switches (Dell S6000-ON) are connected by 40 Gbps\nEthernet links, which connect to the backbone 100Gbps services\nat both UC and TACC."}),"\n",(0,i.jsx)(n.li,{children:"Chameleon also provides a shared storage system. The shared\nstorage provides more than 3.6PB of raw disk."}),"\n",(0,i.jsxs)(n.li,{children:["Heterogeneous Compute Hardware","\n",(0,i.jsxs)(n.ul,{children:["\n",(0,i.jsx)(n.li,{children:"The heterogeneous hardware includes various technologies:\nGPU and FPGA accelerators, SSD and NVMe storage, low-power\nARM, Atom, and Xeon systems-on-a-chip."}),"\n",(0,i.jsx)(n.li,{children:"The two storage hierarchy nodes have been designed to enable\nexperiments using multiple layers of caching: they are\nconfigured with 512 GiB of memory, two Intel P3700 NVMe of 2\nTB each, four Intel S3610 SSDs of 1.6 TB each, and four 15K\nSAS HDDs of 600 GB each."}),"\n"]}),"\n"]}),"\n"]}),"\n"]}),"\n"]}),"\n",(0,i.jsx)(n.h2,{id:"tier-characterization",children:"Tier Characterization"}),"\n",(0,i.jsx)(n.p,{children:"A tier is a class of storage devices that share certain characteristics\nincluding:"}),"\n",(0,i.jsxs)(n.table,{children:[(0,i.jsx)(n.thead,{children:(0,i.jsxs)(n.tr,{children:[(0,i.jsx)(n.th,{children:"Symbol"}),(0,i.jsx)(n.th,{children:"Description"}),(0,i.jsx)(n.th,{children:"Unit"}),(0,i.jsx)(n.th,{children:"Comment"})]})}),(0,i.jsxs)(n.tbody,{children:[(0,i.jsxs)(n.tr,{children:[(0,i.jsx)(n.td,{children:"L"}),(0,i.jsx)(n.td,{children:"Latency"}),(0,i.jsx)(n.td,{children:"ns"}),(0,i.jsx)(n.td,{children:"How is it measured?"})]}),(0,i.jsxs)(n.tr,{children:[(0,i.jsx)(n.td,{children:"B"}),(0,i.jsx)(n.td,{children:"Bandwidth"}),(0,i.jsx)(n.td,{children:"GB/s"}),(0,i.jsx)(n.td,{children:"How is it measured?"})]}),(0,i.jsxs)(n.tr,{children:[(0,i.jsx)(n.td,{children:"C"}),(0,i.jsx)(n.td,{children:"Total capacity"}),(0,i.jsx)(n.td,{children:"GB"}),(0,i.jsx)(n.td,{})]}),(0,i.jsxs)(n.tr,{children:[(0,i.jsx)(n.td,{children:"Q"}),(0,i.jsx)(n.td,{children:"Request queue depth"}),(0,i.jsx)(n.td,{children:"n/a"}),(0,i.jsx)(n.td,{})]})]})]}),"\n",(0,i.jsx)(n.p,{children:"The previous characteristics are considered constant during a Hermes\nsession. In addition, the following time-dependent characteristics are\nconsidered:"}),"\n",(0,i.jsxs)(n.table,{children:[(0,i.jsx)(n.thead,{children:(0,i.jsxs)(n.tr,{children:[(0,i.jsx)(n.th,{children:"Symbol"}),(0,i.jsx)(n.th,{children:"Description"}),(0,i.jsx)(n.th,{children:"Unit"}),(0,i.jsx)(n.th,{children:"Comment"})]})}),(0,i.jsxs)(n.tbody,{children:[(0,i.jsxs)(n.tr,{children:[(0,i.jsx)(n.td,{children:"R"}),(0,i.jsx)(n.td,{children:"Remaining capacity"}),(0,i.jsx)(n.td,{children:"GB"}),(0,i.jsx)(n.td,{})]}),(0,i.jsxs)(n.tr,{children:[(0,i.jsx)(n.td,{children:"F"}),(0,i.jsx)(n.td,{children:"Request queue fill"}),(0,i.jsx)(n.td,{children:"%"}),(0,i.jsx)(n.td,{})]})]})]}),"\n",(0,i.jsx)(n.p,{children:'To keep the terminology simple, we will refer to the storage devices of\na certain tier class collectively as "the tier."'}),"\n",(0,i.jsx)(n.p,{children:"Tiers are (pairwise) disjoint, i.e., no storage device can belong to\nmore than one tier."}),"\n",(0,i.jsx)(n.p,{children:"There are intra-tier and inter-tier connections (i.e., between tiers via\nsuitable buses or interconnects). Data transfer via these connections\nmay or may not require CPU intervention."}),"\n",(0,i.jsx)(n.p,{children:'The grouping of storage devices into tiers has nothing to do with the\nphysical distribution of the devices. For example, the fact that two\nstorage devices are of RAM-class doesn\'t say anything about their\n"proximity", which is defined by the intra-tier connectivity.'}),"\n",(0,i.jsx)(n.h2,{id:"layer-level",children:"Layer (Level?)"}),"\n",(0,i.jsxs)(n.p,{children:['In Hermes, it is intuitive to define the "storage device distance" of a\nstorage device from an application or permanent storage port, and\nstorage devices can be ranked or sorted by their distance from such a\nport. By grouping together storage devices of the same or similar\ndistance from a given port, one can identify ',(0,i.jsx)(n.em,{children:"layers"})," or ",(0,i.jsx)(n.em,{children:"levels."}),' The\ndistance is defined relative to a port: The storage world "looks"\ndifferent from different ports, i.e., the same storage device will\ngenerally have different distances from different ports. Since some of\nthe storage device characteristics which enter into the storage device\ndistance are time-dependent, the corrsponding layer structure is\ntime-dependent as well!']})]})}function o(e={}){const{wrapper:n}={...(0,r.a)(),...e.components};return n?(0,i.jsx)(n,{...e,children:(0,i.jsx)(a,{...e})}):a(e)}},9391:(e,n,s)=>{s.d(n,{Z:()=>i});const i=s.p+"assets/images/Ares_simplified_structure-138c68b13ac25cf2b2a1362901083bcc.png"},26:(e,n,s)=>{s.d(n,{Z:()=>i});const i=s.p+"assets/images/Chameleon_Hardware_Summary-005b894eae2701e8cfd0939325068578.png"},2252:(e,n,s)=>{s.d(n,{Z:()=>i});const i=s.p+"assets/images/Network_topology-d94e9a0ff17e966a7b09ccda04a06c7d.png"},4864:(e,n,s)=>{s.d(n,{Z:()=>i});const i=s.p+"assets/images/RDMA_bandwidth-4eab72d930c7b07f186f971fd24a2742.png"},1151:(e,n,s)=>{s.d(n,{Z:()=>l,a:()=>d});var i=s(7294);const r={},t=i.createContext(r);function d(e){const n=i.useContext(t);return i.useMemo((function(){return"function"==typeof e?e(n):{...n,...e}}),[n,e])}function l(e){let n;return n=e.disableParentContext?"function"==typeof e.components?e.components(r):e.components||r:d(e.components),i.createElement(t.Provider,{value:n},e.children)}}}]);
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(kernel version, etc.)","\n",(0,i.jsxs)(n.ul,{children:["\n",(0,i.jsx)(n.li,{children:"OpenHPC(GCC 4.8.5) on login and compute nodes, CentOS(GCC 7.3.0)\nand on storage nodes. (Need to double check)"}),"\n"]}),"\n"]}),"\n",(0,i.jsxs)(n.li,{children:["How is the system configured? (file systems, networking, etc.)","\n",(0,i.jsxs)(n.ul,{children:["\n",(0,i.jsx)(n.li,{children:"All nodes are equipped with one Mellanox 40Gbps adapter."}),"\n",(0,i.jsx)(n.li,{children:"Each compute/storage node has one high-speed (40Gbps) Ethernet\nand one low-speed (1Gbps) Ethernet."}),"\n",(0,i.jsx)(n.li,{children:"Compute node 31, 32 and the master node are connected to the\nhigh-speed switch in the storage rack."}),"\n",(0,i.jsx)(n.li,{children:"Compute and storage nodes are connected to different switches\nwhich are connected with a 200Gbps uplink."}),"\n",(0,i.jsx)(n.li,{children:"The network speed on the storage nodes are limited by the PCIe\n2.0 standard, which is around 1GB/s."}),"\n",(0,i.jsx)(n.li,{children:"OrangeFS 2.9.7 has been installed into /opt/ohpc/pub/orangefs.\nEvery user can run it and access it from MPI applications with\nproper configuration in the MPI library."}),"\n"]}),"\n"]}),"\n"]}),"\n",(0,i.jsx)(n.h3,{id:"performance",children:"Performance"}),"\n",(0,i.jsx)(n.h4,{id:"memory",children:"Memory"}),"\n",(0,i.jsx)(n.p,{children:"RDMA max bandwidth is around 37 Gb/s."}),"\n",(0,i.jsx)(n.p,{children:(0,i.jsx)(n.img,{alt:"ARES RDMA Bandwidth",src:s(4864).Z+"",width:"931",height:"604"})}),"\n",(0,i.jsxs)(n.p,{children:["Memory bandwidth (",(0,i.jsx)(n.a,{href:"https://www.cs.virginia.edu/stream/",children:"STREAM\nbenchmark"}),"):"]}),"\n",(0,i.jsxs)(n.ul,{children:["\n",(0,i.jsxs)(n.li,{children:["Compute node (Lenovo): 49 GB/s\n(",(0,i.jsx)(n.a,{href:"https://docs.google.com/document/d/1QQPs-NwI-tqaUmA3CnpztY3i2pkVujSAVoliSnTBlPQ/edit",children:"reference"}),")"]}),"\n",(0,i.jsxs)(n.li,{children:["Storage node (Sun): 7GB/s\n(",(0,i.jsx)(n.a,{href:"https://docs.google.com/document/d/1jkOKFvc7ueLkP6kjJgOhgK7k-LMq-jMIaTVuHmTzA5M/edit",children:"reference"}),")"]}),"\n"]}),"\n",(0,i.jsxs)(n.p,{children:["Memory latency (",(0,i.jsx)(n.a,{href:"https://github.com/torvalds/test-tlb",children:"TLB benchmark"}),"):"]}),"\n",(0,i.jsxs)(n.ul,{children:["\n",(0,i.jsx)(n.li,{children:"Huge/regular page seq: 7ns"}),"\n",(0,i.jsx)(n.li,{children:"Huge page rand: 92 ns"}),"\n",(0,i.jsx)(n.li,{children:"Regular page rand: 108 ns"}),"\n",(0,i.jsx)(n.li,{children:(0,i.jsx)(n.a,{href:"https://docs.google.com/spreadsheets/d/1piDh07T3fX5tlel4NdrsxvkFy_Ojopa1dbkN1X5AruE/edit#gid=0",children:"numbers are\nfrom"})}),"\n"]}),"\n",(0,i.jsx)(n.h4,{id:"storage",children:"Storage"}),"\n",(0,i.jsxs)(n.p,{children:["Disk bandwidth (",(0,i.jsx)(n.a,{href:"https://fio.readthedocs.io/en/latest/fio_doc.html",children:"fio"}),"\nbenchmark):"]}),"\n",(0,i.jsxs)(n.ul,{children:["\n",(0,i.jsx)(n.li,{children:(0,i.jsx)(n.a,{href:"https://ares.cs.iit.edu/baseline-perf/",children:"test script can be found"})}),"\n"]}),"\n",(0,i.jsxs)(n.ul,{children:["\n",(0,i.jsxs)(n.li,{children:[(0,i.jsx)(n.a,{href:"https://ares.cs.iit.edu/baseline-perf/local_disk/comp-samsung-nvme.html",children:"Compute node (Samsung\nNVMe)"}),"\n& ",(0,i.jsx)(n.a,{href:"https://ares.cs.iit.edu/baseline-perf/local_disk/comp-toshiba-nvme.html",children:"Compute node (Toshiba\nNVMe)"}),":","\n",(0,i.jsxs)(n.ul,{children:["\n",(0,i.jsx)(n.li,{children:"Read max: 2.5GB/s"}),"\n",(0,i.jsx)(n.li,{children:"Write max: 1GB/s"}),"\n"]}),"\n"]}),"\n"]}),"\n",(0,i.jsxs)(n.ul,{children:["\n",(0,i.jsxs)(n.li,{children:[(0,i.jsx)(n.a,{href:"https://ares.cs.iit.edu/baseline-perf/local_disk/stor-ssd-pcie-sata.html",children:"Storage node (Samsung SATA SSD) with PICe\nadapter"}),"\n",(0,i.jsxs)(n.ul,{children:["\n",(0,i.jsx)(n.li,{children:"Read/Write max: 400MB/s"}),"\n"]}),"\n"]}),"\n"]}),"\n",(0,i.jsxs)(n.ul,{children:["\n",(0,i.jsxs)(n.li,{children:[(0,i.jsx)(n.a,{href:"https://ares.cs.iit.edu/baseline-perf/local_disk/stor-hdd-sata.html",children:"Storage node (Samsung SATA)\nHDD"}),"\n",(0,i.jsxs)(n.ul,{children:["\n",(0,i.jsx)(n.li,{children:"Read/Write max: 180MB/s"}),"\n"]}),"\n"]}),"\n"]}),"\n",(0,i.jsx)(n.h4,{id:"networking",children:"Networking"}),"\n",(0,i.jsx)(n.p,{children:(0,i.jsx)(n.a,{href:"https://docs.google.com/spreadsheets/d/1bngw2dXIamtT7rvPcultBxF5lyhubNCmK2BkkIr5vAc/edit#gid=686223677",children:"Numbers are\nfrom"})}),"\n",(0,i.jsxs)(n.table,{children:[(0,i.jsx)(n.thead,{children:(0,i.jsxs)(n.tr,{children:[(0,i.jsx)(n.th,{children:"Direction"}),(0,i.jsx)(n.th,{children:"Latency (us)"}),(0,i.jsx)(n.th,{children:"Max Bandwidth (Gb/s)"})]})}),(0,i.jsxs)(n.tbody,{children:[(0,i.jsxs)(n.tr,{children:[(0,i.jsx)(n.td,{children:"Compute - compute node"}),(0,i.jsx)(n.td,{children:"2"}),(0,i.jsx)(n.td,{children:"37"})]}),(0,i.jsxs)(n.tr,{children:[(0,i.jsx)(n.td,{children:"Compute - storage node"}),(0,i.jsx)(n.td,{children:"6"}),(0,i.jsx)(n.td,{children:"10"})]}),(0,i.jsxs)(n.tr,{children:[(0,i.jsx)(n.td,{children:"Storage - storage node"}),(0,i.jsx)(n.td,{children:"5"}),(0,i.jsx)(n.td,{children:"12.5"})]})]})]}),"\n",(0,i.jsx)(n.h2,{id:"chameleon-tacc",children:"Chameleon (TACC)"}),"\n",(0,i.jsx)(n.p,{children:"The Chameleon architecture consists of a set of standard cloud units\n(SCUs)."}),"\n",(0,i.jsx)(n.p,{children:(0,i.jsx)(n.img,{alt:"Chameleon - One Unit of SCU Hardware Summary",src:s(26).Z+"",width:"693",height:"234"})}),"\n",(0,i.jsx)(n.h3,{id:"standard-cloud-units",children:"Standard Cloud Units"}),"\n",(0,i.jsxs)(n.ul,{children:["\n",(0,i.jsxs)(n.li,{children:["What kind of CPU(s)?","\n",(0,i.jsxs)(n.ul,{children:["\n",(0,i.jsx)(n.li,{children:"Each compute node is with 24 cores delivered in dual socket\nIntel Xeon E5-2670 v3 \u201cHaswell\u201d processors (each with 12 cores @\n2.3GHz)"}),"\n"]}),"\n"]}),"\n"]}),"\n",(0,i.jsxs)(n.ul,{children:["\n",(0,i.jsxs)(n.li,{children:["How much memory and what kind?","\n",(0,i.jsxs)(n.ul,{children:["\n",(0,i.jsx)(n.li,{children:"128 GiB of DDR4 RAM."}),"\n"]}),"\n"]}),"\n"]}),"\n",(0,i.jsxs)(n.ul,{children:["\n",(0,i.jsxs)(n.li,{children:["What's the OS? (kernel version, etc.)","\n",(0,i.jsxs)(n.ul,{children:["\n",(0,i.jsx)(n.li,{children:"OS is configurable by the user."}),"\n"]}),"\n"]}),"\n"]}),"\n",(0,i.jsxs)(n.ul,{children:["\n",(0,i.jsxs)(n.li,{children:["How is the system configured? (file systems, networking, etc.)","\n",(0,i.jsxs)(n.ul,{children:["\n",(0,i.jsx)(n.li,{children:"Every switch in the research network is a fully OpenFlow\ncompliant programmable Dell S6000-ON switch."}),"\n",(0,i.jsx)(n.li,{children:"Each node connects to this network at 10 Gbps, and each unit\nuplinks with 40Gbps per rack to the Chameleon core network."}),"\n",(0,i.jsx)(n.li,{children:"The core switches (Dell S6000-ON) are connected by 40 Gbps\nEthernet links, which connect to the backbone 100Gbps services\nat both UC and TACC."}),"\n",(0,i.jsx)(n.li,{children:"Chameleon also provides a shared storage system. The shared\nstorage provides more than 3.6PB of raw disk."}),"\n",(0,i.jsxs)(n.li,{children:["Heterogeneous Compute Hardware","\n",(0,i.jsxs)(n.ul,{children:["\n",(0,i.jsx)(n.li,{children:"The heterogeneous hardware includes various technologies:\nGPU and FPGA accelerators, SSD and NVMe storage, low-power\nARM, Atom, and Xeon systems-on-a-chip."}),"\n",(0,i.jsx)(n.li,{children:"The two storage hierarchy nodes have been designed to enable\nexperiments using multiple layers of caching: they are\nconfigured with 512 GiB of memory, two Intel P3700 NVMe of 2\nTB each, four Intel S3610 SSDs of 1.6 TB each, and four 15K\nSAS HDDs of 600 GB each."}),"\n"]}),"\n"]}),"\n"]}),"\n"]}),"\n"]}),"\n",(0,i.jsx)(n.h2,{id:"tier-characterization",children:"Tier Characterization"}),"\n",(0,i.jsx)(n.p,{children:"A tier is a class of storage devices that share certain characteristics\nincluding:"}),"\n",(0,i.jsxs)(n.table,{children:[(0,i.jsx)(n.thead,{children:(0,i.jsxs)(n.tr,{children:[(0,i.jsx)(n.th,{children:"Symbol"}),(0,i.jsx)(n.th,{children:"Description"}),(0,i.jsx)(n.th,{children:"Unit"}),(0,i.jsx)(n.th,{children:"Comment"})]})}),(0,i.jsxs)(n.tbody,{children:[(0,i.jsxs)(n.tr,{children:[(0,i.jsx)(n.td,{children:"L"}),(0,i.jsx)(n.td,{children:"Latency"}),(0,i.jsx)(n.td,{children:"ns"}),(0,i.jsx)(n.td,{children:"How is it measured?"})]}),(0,i.jsxs)(n.tr,{children:[(0,i.jsx)(n.td,{children:"B"}),(0,i.jsx)(n.td,{children:"Bandwidth"}),(0,i.jsx)(n.td,{children:"GB/s"}),(0,i.jsx)(n.td,{children:"How is it measured?"})]}),(0,i.jsxs)(n.tr,{children:[(0,i.jsx)(n.td,{children:"C"}),(0,i.jsx)(n.td,{children:"Total capacity"}),(0,i.jsx)(n.td,{children:"GB"}),(0,i.jsx)(n.td,{})]}),(0,i.jsxs)(n.tr,{children:[(0,i.jsx)(n.td,{children:"Q"}),(0,i.jsx)(n.td,{children:"Request queue depth"}),(0,i.jsx)(n.td,{children:"n/a"}),(0,i.jsx)(n.td,{})]})]})]}),"\n",(0,i.jsx)(n.p,{children:"The previous characteristics are considered constant during a Hermes\nsession. In addition, the following time-dependent characteristics are\nconsidered:"}),"\n",(0,i.jsxs)(n.table,{children:[(0,i.jsx)(n.thead,{children:(0,i.jsxs)(n.tr,{children:[(0,i.jsx)(n.th,{children:"Symbol"}),(0,i.jsx)(n.th,{children:"Description"}),(0,i.jsx)(n.th,{children:"Unit"}),(0,i.jsx)(n.th,{children:"Comment"})]})}),(0,i.jsxs)(n.tbody,{children:[(0,i.jsxs)(n.tr,{children:[(0,i.jsx)(n.td,{children:"R"}),(0,i.jsx)(n.td,{children:"Remaining capacity"}),(0,i.jsx)(n.td,{children:"GB"}),(0,i.jsx)(n.td,{})]}),(0,i.jsxs)(n.tr,{children:[(0,i.jsx)(n.td,{children:"F"}),(0,i.jsx)(n.td,{children:"Request queue fill"}),(0,i.jsx)(n.td,{children:"%"}),(0,i.jsx)(n.td,{})]})]})]}),"\n",(0,i.jsx)(n.p,{children:'To keep the terminology simple, we will refer to the storage devices of\na certain tier class collectively as "the tier."'}),"\n",(0,i.jsx)(n.p,{children:"Tiers are (pairwise) disjoint, i.e., no storage device can belong to\nmore than one tier."}),"\n",(0,i.jsx)(n.p,{children:"There are intra-tier and inter-tier connections (i.e., between tiers via\nsuitable buses or interconnects). Data transfer via these connections\nmay or may not require CPU intervention."}),"\n",(0,i.jsx)(n.p,{children:'The grouping of storage devices into tiers has nothing to do with the\nphysical distribution of the devices. For example, the fact that two\nstorage devices are of RAM-class doesn\'t say anything about their\n"proximity", which is defined by the intra-tier connectivity.'}),"\n",(0,i.jsx)(n.h2,{id:"layer-level",children:"Layer (Level?)"}),"\n",(0,i.jsxs)(n.p,{children:['In Hermes, it is intuitive to define the "storage device distance" of a\nstorage device from an application or permanent storage port, and\nstorage devices can be ranked or sorted by their distance from such a\nport. By grouping together storage devices of the same or similar\ndistance from a given port, one can identify ',(0,i.jsx)(n.em,{children:"layers"})," or ",(0,i.jsx)(n.em,{children:"levels."}),' The\ndistance is defined relative to a port: The storage world "looks"\ndifferent from different ports, i.e., the same storage device will\ngenerally have different distances from different ports. Since some of\nthe storage device characteristics which enter into the storage device\ndistance are time-dependent, the corrsponding layer structure is\ntime-dependent as well!']})]})}function o(e={}){const{wrapper:n}={...(0,r.a)(),...e.components};return n?(0,i.jsx)(n,{...e,children:(0,i.jsx)(a,{...e})}):a(e)}},9391:(e,n,s)=>{s.d(n,{Z:()=>i});const i=s.p+"assets/images/Ares_simplified_structure-138c68b13ac25cf2b2a1362901083bcc.png"},26:(e,n,s)=>{s.d(n,{Z:()=>i});const i=s.p+"assets/images/Chameleon_Hardware_Summary-005b894eae2701e8cfd0939325068578.png"},2252:(e,n,s)=>{s.d(n,{Z:()=>i});const i=s.p+"assets/images/Network_topology-d94e9a0ff17e966a7b09ccda04a06c7d.png"},4864:(e,n,s)=>{s.d(n,{Z:()=>i});const i=s.p+"assets/images/RDMA_bandwidth-4eab72d930c7b07f186f971fd24a2742.png"},1151:(e,n,s)=>{s.d(n,{Z:()=>l,a:()=>d});var i=s(7294);const r={},t=i.createContext(r);function d(e){const n=i.useContext(t);return i.useMemo((function(){return"function"==typeof e?e(n):{...n,...e}}),[n,e])}function l(e){let n;return n=e.disableParentContext?"function"==typeof e.components?e.components(r):e.components||r:d(e.components),i.createElement(t.Provider,{value:n},e.children)}}}]);
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diff --git a/assets/js/82cb9cb5.c8189fcd.js b/assets/js/82cb9cb5.c8189fcd.js
deleted file mode 100644
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--- a/assets/js/82cb9cb5.c8189fcd.js
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-"use strict";(self.webpackChunkgrc=self.webpackChunkgrc||[]).push([[527],{5233:(e,n,i)=>{i.r(n),i.d(n,{assets:()=>c,contentTitle:()=>l,default:()=>d,frontMatter:()=>t,metadata:()=>o,toc:()=>a});var r=i(5893),s=i(1151);const t={},l="Buffer Organizer",o={id:"hermes/components/buffer-organizer",title:"Buffer Organizer",description:'The Buffer Organizer is the "corrector" half of our',source:"@site/docs/03-hermes/06-components/01-buffer-organizer.md",sourceDirName:"03-hermes/06-components",slug:"/hermes/components/buffer-organizer",permalink:"/docs/hermes/components/buffer-organizer",draft:!1,unlisted:!1,tags:[],version:"current",sidebarPosition:1,frontMatter:{},sidebar:"tutorialSidebar",previous:{title:"Configuration",permalink:"/docs/hermes/configuration"},next:{title:"Buffer Pool",permalink:"/docs/hermes/components/buffer-pool"}},c={},a=[{value:"Objectives",id:"objectives",level:2},{value:"Blob Scoring",id:"blob-scoring",level:2},{value:"Importance Score",id:"importance-score",level:3},{value:"Variables that might contribute to the importance score",id:"variables-that-might-contribute-to-the-importance-score",level:4},{value:"Access Score",id:"access-score",level:3},{value:"Variables that contribute to the access score",id:"variables-that-contribute-to-the-access-score",level:4},{value:"How the scores are used",id:"how-the-scores-are-used",level:3},{value:"Ideas",id:"ideas",level:2},{value:"Operations",id:"operations",level:2},{value:"Transfer",id:"transfer",level:3},{value:"Who can initiate Transfer tasks?",id:"who-can-initiate-transfer-tasks",level:4},{value:"Evict(size_t bytes, Targets[])",id:"evictsize_t-bytes-targets",level:3},{value:"Who can initiate Eviction tasks?",id:"who-can-initiate-eviction-tasks",level:4},{value:"Who translates an Eviction into a series of Transfers?",id:"who-translates-an-eviction-into-a-series-of-transfers",level:4},{value:"Single shared file pros",id:"single-shared-file-pros",level:4},{value:"File per rank pros",id:"file-per-rank-pros",level:4},{value:"File per node",id:"file-per-node",level:4},{value:"Triggers",id:"triggers",level:2},{value:"Periodic",id:"periodic",level:3},{value:"Client-triggered",id:"client-triggered",level:3},{value:"System-triggered",id:"system-triggered",level:3},{value:"Requirements for Queue implementation",id:"requirements-for-queue-implementation",level:3},{value:"Design Details",id:"design-details",level:2},{value:"BO RPC Server",id:"bo-rpc-server",level:3},{value:"Buffer Organizer",id:"buffer-organizer-1",level:3},{value:"Work Queues",id:"work-queues",level:4},{value:"Schedulers",id:"schedulers",level:4},{value:"Threads",id:"threads",level:4},{value:"Example Flows",id:"example-flows",level:2},{value:"Hot Put",id:"hot-put",level:3},{value:"BO Eviction Flow",id:"bo-eviction-flow",level:3},{value:"Ideas",id:"ideas-1",level:2},{value:"Experiments",id:"experiments",level:2}];function h(e){const n={code:"code",h1:"h1",h2:"h2",h3:"h3",h4:"h4",img:"img",li:"li",ol:"ol",p:"p",pre:"pre",strong:"strong",ul:"ul",...(0,s.a)(),...e.components};return(0,r.jsxs)(r.Fragment,{children:[(0,r.jsx)(n.h1,{id:"buffer-organizer",children:"Buffer Organizer"}),"\n",(0,r.jsxs)(n.p,{children:["The ",(0,r.jsx)(n.strong,{children:"Buffer Organizer"}),' is the "corrector" half of our\npredictor/corrector model. It attempts to correct sub-optimal DPE\nplacements by moving data among buffers.']}),"\n",(0,r.jsx)(n.h2,{id:"objectives",children:"Objectives"}),"\n",(0,r.jsxs)(n.ul,{children:["\n",(0,r.jsxs)(n.li,{children:["Management of hierarchical buffering space","\n",(0,r.jsxs)(n.ul,{children:["\n",(0,r.jsx)(n.li,{children:"Data flushing"}),"\n",(0,r.jsx)(n.li,{children:"Read acceleration"}),"\n"]}),"\n"]}),"\n",(0,r.jsxs)(n.li,{children:["Manage data life cycle, or journey","\n",(0,r.jsxs)(n.ul,{children:["\n",(0,r.jsx)(n.li,{children:"When is the blob in equilibrium?"}),"\n",(0,r.jsx)(n.li,{children:"How do we eliminate unnecessary data movement?"}),"\n"]}),"\n"]}),"\n"]}),"\n",(0,r.jsx)(n.h2,{id:"blob-scoring",children:"Blob Scoring"}),"\n",(0,r.jsxs)(n.p,{children:["We attempt to meet the above objectives via a ",(0,r.jsx)(n.code,{children:"Blob"})," scoring system. Each ",(0,r.jsx)(n.code,{children:"Blob"})," has two different scores associated with it: the ",(0,r.jsx)(n.strong,{children:"importance score"})," and the ",(0,r.jsx)(n.strong,{children:"access score"}),"."]}),"\n",(0,r.jsx)(n.h3,{id:"importance-score",children:"Importance Score"}),"\n",(0,r.jsxs)(n.p,{children:["The importance score is a real number in the range [0, 1] where 0 represents a ",(0,r.jsx)(n.code,{children:"Blob"})," that is not important to the user (i.e., it will not be accessed) and 1 represents a ",(0,r.jsx)(n.code,{children:"Blob"})," that will be accessed either very frequently, very soon, or both."]}),"\n",(0,r.jsx)(n.h4,{id:"variables-that-might-contribute-to-the-importance-score",children:"Variables that might contribute to the importance score"}),"\n",(0,r.jsxs)(n.ul,{children:["\n",(0,r.jsx)(n.li,{children:"Blob Size"}),"\n",(0,r.jsx)(n.li,{children:"Blob Name"}),"\n",(0,r.jsx)(n.li,{children:"Recency of Blob access"}),"\n",(0,r.jsx)(n.li,{children:"Frequency of Blob access"}),"\n",(0,r.jsx)(n.li,{children:"User-supplied priority (this is only a hint, not a guarantee)."}),"\n"]}),"\n",(0,r.jsx)(n.h3,{id:"access-score",children:"Access Score"}),"\n",(0,r.jsxs)(n.p,{children:["This is a real number in the range [0, 1] where 0 represents a ",(0,r.jsx)(n.code,{children:"Blob"})," with the slowest access time (i.e., all its ",(0,r.jsx)(n.code,{children:"Buffer"}),"s are in the slowest tier) and 1 represents a ",(0,r.jsx)(n.code,{children:"Blob"})," with the quickest access time (all the ",(0,r.jsx)(n.code,{children:"Buffer"}),"s are in the fastest tier)."]}),"\n",(0,r.jsx)(n.h4,{id:"variables-that-contribute-to-the-access-score",children:"Variables that contribute to the access score"}),"\n",(0,r.jsxs)(n.ul,{children:["\n",(0,r.jsxs)(n.li,{children:["Bandwidth of the tiers that contain the ",(0,r.jsx)(n.code,{children:"Blob"}),"'s ",(0,r.jsx)(n.code,{children:"Buffer"}),"s."]}),"\n",(0,r.jsxs)(n.li,{children:["The ",(0,r.jsx)(n.code,{children:"Blob"})," distribution (i.e., is all the data in a single ",(0,r.jsx)(n.code,{children:"Buffer"}),", or is it spread out among multiple ",(0,r.jsx)(n.code,{children:"Buffer"}),"s on multiple nodes?)."]}),"\n"]}),"\n",(0,r.jsx)(n.h3,{id:"how-the-scores-are-used",children:"How the scores are used"}),"\n",(0,r.jsxs)(n.p,{children:["The goal of the ",(0,r.jsx)(n.code,{children:"BufferOrganizer"})," is to ensure that each ",(0,r.jsx)(n.code,{children:"Blob"}),"'s access score is closely aligned to its importance score."]}),"\n",(0,r.jsx)(n.h2,{id:"ideas",children:"Ideas"}),"\n",(0,r.jsxs)(n.ul,{children:["\n",(0,r.jsxs)(n.li,{children:["If a ",(0,r.jsx)(n.code,{children:"Blob"}),"'s ",(0,r.jsx)(n.code,{children:"Bucket"})," has a reference count of 0 (i.e., no process has an open handle to the ",(0,r.jsx)(n.code,{children:"Bucket"}),") then the importance score should be 0. The score is only calculated once at least one process opens the ",(0,r.jsx)(n.code,{children:"Bucket"}),"."]}),"\n"]}),"\n",(0,r.jsx)(n.h2,{id:"operations",children:"Operations"}),"\n",(0,r.jsxs)(n.p,{children:["All ",(0,r.jsx)(n.code,{children:"BufferOrganizer"})," operations are implemented in terms of 3 simple\noperators"]}),"\n",(0,r.jsxs)(n.ul,{children:["\n",(0,r.jsx)(n.li,{children:"MOVE(BufferID, TargetID)"}),"\n",(0,r.jsx)(n.li,{children:"COPY(BufferID, TargetID)"}),"\n",(0,r.jsx)(n.li,{children:"DELETE(BufferID)"}),"\n"]}),"\n",(0,r.jsx)(n.p,{children:"With these operators, we can build more complex tasks:"}),"\n",(0,r.jsx)(n.h3,{id:"transfer",children:"Transfer"}),"\n",(0,r.jsxs)(n.p,{children:["Move a ",(0,r.jsx)(n.code,{children:"BufferID"})," from one set of ",(0,r.jsx)(n.code,{children:"Target"}),"s to another."]}),"\n",(0,r.jsx)(n.h4,{id:"who-can-initiate-transfer-tasks",children:"Who can initiate Transfer tasks?"}),"\n",(0,r.jsxs)(n.ul,{children:["\n",(0,r.jsx)(n.li,{children:"The System (load balancing)"}),"\n",(0,r.jsx)(n.li,{children:"The User (producer/consumer)"}),"\n"]}),"\n",(0,r.jsx)(n.h3,{id:"evictsize_t-bytes-targets",children:"Evict(size_t bytes, Targets[])"}),"\n",(0,r.jsxs)(n.p,{children:["Move a set of ",(0,r.jsx)(n.code,{children:"BufferId"}),"s from one set of ",(0,r.jsx)(n.code,{children:"Target"}),"s to an unspecified\nlocation (could even be swap space)."]}),"\n",(0,r.jsx)(n.h4,{id:"who-can-initiate-eviction-tasks",children:"Who can initiate Eviction tasks?"}),"\n",(0,r.jsxs)(n.ul,{children:["\n",(0,r.jsx)(n.li,{children:"Put (DPE)"}),"\n",(0,r.jsx)(n.li,{children:"Get (Prefetcher)"}),"\n",(0,r.jsxs)(n.li,{children:["Thread that updates the ",(0,r.jsx)(n.code,{children:"SystemViewState"})," (enforces a minimum\ncapacity threshold passed in through the config)."]}),"\n"]}),"\n",(0,r.jsx)(n.h4,{id:"who-translates-an-eviction-into-a-series-of-transfers",children:"Who translates an Eviction into a series of Transfers?"}),"\n",(0,r.jsxs)(n.ul,{children:["\n",(0,r.jsx)(n.li,{children:"DPE?"}),"\n",(0,r.jsx)(n.li,{children:"BO?"}),"\n"]}),"\n",(0,r.jsx)(n.h4,{id:"single-shared-file-pros",children:"Single shared file pros"}),"\n",(0,r.jsxs)(n.ul,{children:["\n",(0,r.jsx)(n.li,{children:"Could theoretically reap performance benefits of collective IO\noperations, although I don't think we'll ever be able to capitalize\non this because each rank must act independently and can't\nsynchronize with the other ranks."}),"\n",(0,r.jsx)(n.li,{children:"Less stress on the PFS metadata server."}),"\n"]}),"\n",(0,r.jsx)(n.h4,{id:"file-per-rank-pros",children:"File per rank pros"}),"\n",(0,r.jsxs)(n.ul,{children:["\n",(0,r.jsx)(n.li,{children:"Don't have to worry about reserving size for each rank."}),"\n",(0,r.jsx)(n.li,{children:"Don't have to worry about locking."}),"\n"]}),"\n",(0,r.jsx)(n.h4,{id:"file-per-node",children:"File per node"}),"\n",(0,r.jsxs)(n.ul,{children:["\n",(0,r.jsx)(n.li,{children:"We'll go with this for the initial implementation."}),"\n",(0,r.jsxs)(n.li,{children:["Don't have to worry about locking or reserving size with respect to\nthe buffer organizer. However, since multiple ranks could\npotentially write to the same swap file, we need to either","\n",(0,r.jsxs)(n.ul,{children:["\n",(0,r.jsx)(n.li,{children:"Filter all swap traffic through the buffer organizer"}),"\n",(0,r.jsx)(n.li,{children:"Synchronize all access to the file"}),"\n"]}),"\n"]}),"\n",(0,r.jsx)(n.li,{children:"Won't overload the metadata servers as bad as file per rank."}),"\n"]}),"\n",(0,r.jsx)(n.h2,{id:"triggers",children:"Triggers"}),"\n",(0,r.jsx)(n.p,{children:"The Buffer Organizer can be triggered in 3 ways:"}),"\n",(0,r.jsx)(n.h3,{id:"periodic",children:"Periodic"}),"\n",(0,r.jsx)(n.p,{children:"The period can be controlled by a configuration variable."}),"\n",(0,r.jsx)(n.h3,{id:"client-triggered",children:"Client-triggered"}),"\n",(0,r.jsxs)(n.ul,{children:["\n",(0,r.jsx)(n.li,{children:"If, for any reason, a client DPE places data to the swap target, it\nwill also trigger the buffer organizer by adding an event to the\nbuffer organizer's queue."}),"\n",(0,r.jsx)(n.li,{children:"We store the blob name, the offset into the swap target (for\nfile-based targets), and the blob size."}),"\n",(0,r.jsx)(n.li,{children:"When the buffer organizer processes an event, it"}),"\n"]}),"\n",(0,r.jsxs)(n.ol,{children:["\n",(0,r.jsx)(n.li,{children:"Reads the blob from the swap target into memory."}),"\n",(0,r.jsxs)(n.li,{children:["Calls ",(0,r.jsx)(n.code,{children:"Put"})," to place the blob into the hierarchy. If the ",(0,r.jsx)(n.code,{children:"Put"}),"\nfails, it tries again, up to ",(0,r.jsx)(n.code,{children:"num_buffer_organizer_retries"}),"\n(configurable) times."]}),"\n"]}),"\n",(0,r.jsx)(n.h3,{id:"system-triggered",children:"System-triggered"}),"\n",(0,r.jsxs)(n.ul,{children:["\n",(0,r.jsx)(n.li,{children:"Nothing is implemented yet."}),"\n",(0,r.jsx)(n.li,{children:"Should the BO constantly monitor the buffering hierarchy and attempt\nto maintain a set of rules (remaining capacity percentage,\nthresholds, etc.)?"}),"\n",(0,r.jsx)(n.li,{children:'Should the BO simply carry out "orders" and not attempt to make its\nown decisions? If so, who gives the orders?'}),"\n",(0,r.jsx)(n.li,{children:"Should the BO be available for other asynchronous tasks?"}),"\n"]}),"\n",(0,r.jsx)(n.h3,{id:"requirements-for-queue-implementation",children:"Requirements for Queue implementation"}),"\n",(0,r.jsxs)(n.ul,{children:["\n",(0,r.jsx)(n.li,{children:"(At least) 2 different priority lanes"}),"\n",(0,r.jsx)(n.li,{children:"Node local and remote queues (but only for neighborhoods, not global\nqueues)."}),"\n",(0,r.jsx)(n.li,{children:"Need ability to restrict queue length"}),"\n"]}),"\n",(0,r.jsx)(n.h2,{id:"design-details",children:"Design Details"}),"\n",(0,r.jsx)(n.h3,{id:"bo-rpc-server",children:"BO RPC Server"}),"\n",(0,r.jsxs)(n.ul,{children:["\n",(0,r.jsxs)(n.li,{children:["RPC is used to route ",(0,r.jsx)(n.code,{children:"BoTask"}),"s to the appropriate Hermes core."]}),"\n"]}),"\n",(0,r.jsxs)(n.ul,{children:["\n",(0,r.jsxs)(n.li,{children:["The ",(0,r.jsx)(n.code,{children:"BO"})," RPC server only has one function:","\n",(0,r.jsx)(n.pre,{children:(0,r.jsx)(n.code,{className:"language-cpp",children:"bool EnqueueBoTask(BoTask task, Priority priority);\n"})}),"\n"]}),"\n"]}),"\n",(0,r.jsx)(n.p,{children:"[[../images/bo_rpc.png]]"}),"\n",(0,r.jsx)(n.h3,{id:"buffer-organizer-1",children:"Buffer Organizer"}),"\n",(0,r.jsx)(n.h4,{id:"work-queues",children:"Work Queues"}),"\n",(0,r.jsxs)(n.ul,{children:["\n",(0,r.jsxs)(n.li,{children:["Argobots ",(0,r.jsx)(n.strong,{children:"pool"}),"s"]}),"\n",(0,r.jsx)(n.li,{children:"High and low priorities"}),"\n",(0,r.jsx)(n.li,{children:"Basic FIFO queue by default"}),"\n",(0,r.jsx)(n.li,{children:"Completely customizable (e.g., could be a priority queue, min-heap,\netc.)"}),"\n"]}),"\n",(0,r.jsx)(n.h4,{id:"schedulers",children:"Schedulers"}),"\n",(0,r.jsxs)(n.ul,{children:["\n",(0,r.jsxs)(n.li,{children:["Argobots ",(0,r.jsx)(n.strong,{children:"scheduler"}),"s"]}),"\n",(0,r.jsx)(n.li,{children:"Takes tasks from the queues and runs them on OS threads as user\nlevel threads (basically coroutines)."}),"\n",(0,r.jsx)(n.li,{children:"Completely customizable."}),"\n",(0,r.jsx)(n.li,{children:"By default, one scheduler is associated with a single execution\nstream (OS thread)."}),"\n",(0,r.jsx)(n.li,{children:"Only take tasks from low priority queue if high priority queue is\nempty?"}),"\n"]}),"\n",(0,r.jsx)(n.h4,{id:"threads",children:"Threads"}),"\n",(0,r.jsxs)(n.ul,{children:["\n",(0,r.jsxs)(n.li,{children:["Argobots ",(0,r.jsx)(n.strong,{children:"execution stream"}),"s"]}),"\n",(0,r.jsxs)(n.li,{children:["Bound to a ",(0,r.jsx)(n.strong,{children:"processing element"})," (CPU core or hyperthread), and\nshouldn't be oversubscribed."]}),"\n"]}),"\n",(0,r.jsx)(n.p,{children:(0,r.jsx)(n.img,{src:i(5181).Z+"",width:"643",height:"495"})}),"\n",(0,r.jsx)(n.h2,{id:"example-flows",children:"Example Flows"}),"\n",(0,r.jsx)(n.h3,{id:"hot-put",children:"Hot Put"}),"\n",(0,r.jsx)(n.p,{children:(0,r.jsx)(n.img,{src:i(8418).Z+"",width:"378",height:"956"})}),"\n",(0,r.jsx)(n.h3,{id:"bo-eviction-flow",children:"BO Eviction Flow"}),"\n",(0,r.jsx)(n.p,{children:(0,r.jsx)(n.img,{src:i(1506).Z+"",width:"553",height:"524"})}),"\n",(0,r.jsx)(n.h2,{id:"ideas-1",children:"Ideas"}),"\n",(0,r.jsxs)(n.ul,{children:["\n",(0,r.jsxs)(n.li,{children:["An importance score of 0 could be the signal to flush a ",(0,r.jsx)(n.code,{children:"Blob"})," to the PFS."]}),"\n",(0,r.jsxs)(n.li,{children:[(0,r.jsx)(n.code,{children:"StageIn"})," and ",(0,r.jsx)(n.code,{children:"StageOut"})," APIs"]}),"\n",(0,r.jsxs)(n.li,{children:['Reverse "gravity" for read heavy workloads. ',(0,r.jsx)(n.code,{children:"Blobs"})," trickle up to higher tiers."]}),"\n",(0,r.jsx)(n.li,{children:"Explicitly maintain Target capacity thresholds."}),"\n",(0,r.jsx)(n.li,{children:"Introduce horizontal movement if Topology threshold is exceeded."}),"\n"]}),"\n",(0,r.jsx)(n.h2,{id:"experiments",children:"Experiments"}),"\n",(0,r.jsxs)(n.ul,{children:["\n",(0,r.jsxs)(n.li,{children:["Test the difference between flushing tier by tier vs skipping tiers. For example, a ",(0,r.jsx)(n.code,{children:"Blob"})," moving from RAM to burst buffer could go through NVMe as an intermediate tier, or skip it altogether."]}),"\n"]})]})}function d(e={}){const{wrapper:n}={...(0,s.a)(),...e.components};return n?(0,r.jsx)(n,{...e,children:(0,r.jsx)(h,{...e})}):h(e)}},5181:(e,n,i)=>{i.d(n,{Z:()=>r});const r=i.p+"assets/images/bo-9412e1ce05035896279ca164b1375068.png"},1506:(e,n,i)=>{i.d(n,{Z:()=>r});const r=i.p+"assets/images/bo_evict-f585db845536915d3efa4b9225efce29.png"},8418:(e,n,i)=>{i.d(n,{Z:()=>r});const r=i.p+"assets/images/hot_put-0d2d32fadedf6f594a46ecc415ad16d0.png"},1151:(e,n,i)=>{i.d(n,{Z:()=>o,a:()=>l});var r=i(7294);const s={},t=r.createContext(s);function l(e){const n=r.useContext(t);return r.useMemo((function(){return"function"==typeof e?e(n):{...n,...e}}),[n,e])}function o(e){let n;return n=e.disableParentContext?"function"==typeof e.components?e.components(s):e.components||s:l(e.components),r.createElement(t.Provider,{value:n},e.children)}}}]);
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+"use strict";(self.webpackChunkgrc=self.webpackChunkgrc||[]).push([[726],{5125:(e,t,n)=>{n.r(t),n.d(t,{assets:()=>o,contentTitle:()=>r,default:()=>c,frontMatter:()=>a,metadata:()=>d,toc:()=>l});var s=n(5893),i=n(1151);const a={},r="Distributed Metadata",d={id:"hermes/components/distributed-metadata",title:"Distributed Metadata",description:"Metadata is stored in a distributed hash map. In each Hermes Daemon, we",source:"@site/docs/03-hermes/08-components/08-distributed-metadata.md",sourceDirName:"03-hermes/08-components",slug:"/hermes/components/distributed-metadata",permalink:"/docs/hermes/components/distributed-metadata",draft:!1,unlisted:!1,tags:[],version:"current",sidebarPosition:8,frontMatter:{},sidebar:"tutorialSidebar",previous:{title:"Runtime",permalink:"/docs/hermes/components/runtime"},next:{title:"Prefetcher",permalink:"/docs/hermes/components/prefetcher"}},o={},l=[{value:"User View",id:"user-view",level:2},{value:"System View",id:"system-view",level:2},{value:"UniqueId",id:"uniqueid",level:2},{value:"Storage Method",id:"storage-method",level:2},{value:"Maps and ID Lists",id:"maps-and-id-lists",level:2},{value:"Pros",id:"pros",level:3},{value:"Cons",id:"cons",level:3},{value:"Walkthrough of <code>Bucket.Put()</code>",id:"walkthrough-of-bucketput",level:2},{value:"Walkthrough of <code>Bucket.Get()</code>",id:"walkthrough-of-bucketget",level:2},{value:"Limits",id:"limits",level:2}];function h(e){const t={code:"code",h1:"h1",h2:"h2",h3:"h3",li:"li",p:"p",strong:"strong",ul:"ul",...(0,i.a)(),...e.components};return(0,s.jsxs)(s.Fragment,{children:[(0,s.jsx)(t.h1,{id:"distributed-metadata",children:"Distributed Metadata"}),"\n",(0,s.jsxs)(t.p,{children:["Metadata is stored in a distributed hash map. In each Hermes Daemon, we\ninitialize an ",(0,s.jsx)(t.code,{children:"hipc::unordered_map"}),". The main metadata structures we store\nare as follows: Tag Map (note, Buckets are represented as Tags), Blob Map,\nand Trait Map. These maps typically map an integer ID to an\ninformation structure. For example, the Blob Map maps a ",(0,s.jsx)(t.code,{children:"BlobId"})," (a 96-bit int)\nto a ",(0,s.jsx)(t.code,{children:"BlobInfo"})," struct. In addition, we have separate maps for mapping semantic\nstrings to integer IDs. For example, we have a map from a ",(0,s.jsx)(t.code,{children:"hipc::string"})," to\na ",(0,s.jsx)(t.code,{children:"BlobId"}),"."]}),"\n",(0,s.jsx)(t.p,{children:"At this time, metadata is not replicated on nodes and we assume that metadata\ndoesn't grow so large that it exceeds the bounds of main memory."}),"\n",(0,s.jsx)(t.h2,{id:"user-view",children:"User View"}),"\n",(0,s.jsx)(t.p,{children:"Metadata (e.g., Blobs and Tags) can be given semantic names using hipc::strings\nor std::strings. hipc::string is what is eventually stored in Hermes, since it's\ncompatible with shared memory."}),"\n",(0,s.jsx)(t.h2,{id:"system-view",children:"System View"}),"\n",(0,s.jsx)(t.p,{children:"User primitives are referred to by unsigned 96-bit integers (IDs)."}),"\n",(0,s.jsx)(t.p,{children:"Each ID encodes the data it needs to access its metadata."}),"\n",(0,s.jsx)(t.h2,{id:"uniqueid",children:"UniqueId"}),"\n",(0,s.jsx)(t.p,{children:"TagIds, BlobIds, and TraitIds all are instances of a UniqueId. UniqueIds are\nrepresented as follows:"}),"\n",(0,s.jsxs)(t.ul,{children:["\n",(0,s.jsx)(t.li,{children:"Node ID: The identifier of the node the metadata is on (32-bit)"}),"\n",(0,s.jsx)(t.li,{children:"Unique: The unique number of the metadata object (64-bit)"}),"\n"]}),"\n",(0,s.jsx)(t.p,{children:"The unique field is a 64-bit integer which is atomically incremented every time\nthe program creates a new metadata object. 64-bit is large enough that the\nprogram should never be able to use all 2^64 combos."}),"\n",(0,s.jsx)(t.h2,{id:"storage-method",children:"Storage Method"}),"\n",(0,s.jsx)(t.h2,{id:"maps-and-id-lists",children:"Maps and ID Lists"}),"\n",(0,s.jsx)(t.p,{children:"All metadata is distributed among nodes by first hashing the key to\ndetermine the node, then hashing again to determine the slot."}),"\n",(0,s.jsx)(t.h3,{id:"pros",children:"Pros"}),"\n",(0,s.jsxs)(t.ul,{children:["\n",(0,s.jsx)(t.li,{children:"Better load balancing"}),"\n"]}),"\n",(0,s.jsx)(t.h3,{id:"cons",children:"Cons"}),"\n",(0,s.jsxs)(t.ul,{children:["\n",(0,s.jsxs)(t.li,{children:["May require extra RPC calls. Initial tests show that this\nindirection should be avoided. ",(0,s.jsx)(t.strong,{children:"TODO:"})," We need to revisit this."]}),"\n"]}),"\n",(0,s.jsxs)(t.h2,{id:"walkthrough-of-bucketput",children:["Walkthrough of ",(0,s.jsx)(t.code,{children:"Bucket.Put()"})]}),"\n",(0,s.jsxs)(t.p,{children:["1. Create a new ",(0,s.jsx)(t.code,{children:"BlobID"}),". The ID's node index (top 32 bits) is created\nby hashing the blob name, and the ID's offset to a list of ",(0,s.jsx)(t.code,{children:"BufferID"}),"s\n(bottom 32 bits) is allocated from the MDM shared memory segment on the\ntarget node."]}),"\n",(0,s.jsxs)(t.p,{children:["2. Add the new ",(0,s.jsx)(t.code,{children:"BlobID"})," to the ",(0,s.jsx)(t.strong,{children:"IdMap"}),". This could be local, or an\nRPC."]}),"\n",(0,s.jsxs)(t.p,{children:["3. Add the ",(0,s.jsx)(t.code,{children:"BlobID"})," to the ",(0,s.jsx)(t.code,{children:"Bucket"}),"'s list of blobs."]}),"\n",(0,s.jsxs)(t.h2,{id:"walkthrough-of-bucketget",children:["Walkthrough of ",(0,s.jsx)(t.code,{children:"Bucket.Get()"})]}),"\n",(0,s.jsxs)(t.p,{children:["1. Hash the blob name to get the ",(0,s.jsx)(t.code,{children:"BlobID"}),"."]}),"\n",(0,s.jsxs)(t.p,{children:["2. Get the list of ",(0,s.jsx)(t.code,{children:"BufferID"}),"s from the ",(0,s.jsx)(t.code,{children:"BlobID"}),"."]}),"\n",(0,s.jsxs)(t.p,{children:["3. Read each ",(0,s.jsx)(t.code,{children:"BufferID"}),"'s data into a user buffer."]}),"\n",(0,s.jsx)(t.h2,{id:"limits",children:"Limits"}),"\n",(0,s.jsx)(t.p,{children:"There can be a total of 2^64 unique metadata objects. I.e., there can be\na total of 2^64 Tags, Buckets, and Traits."})]})}function c(e={}){const{wrapper:t}={...(0,i.a)(),...e.components};return t?(0,s.jsx)(t,{...e,children:(0,s.jsx)(h,{...e})}):h(e)}},1151:(e,t,n)=>{n.d(t,{Z:()=>d,a:()=>r});var s=n(7294);const i={},a=s.createContext(i);function r(e){const t=s.useContext(a);return s.useMemo((function(){return"function"==typeof e?e(t):{...t,...e}}),[t,e])}function d(e){let t;return t=e.disableParentContext?"function"==typeof e.components?e.components(i):e.components||i:r(e.components),s.createElement(a.Provider,{value:t},e.children)}}}]);
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diff --git a/assets/js/904b44e2.14ac8ffd.js b/assets/js/904b44e2.14ac8ffd.js
deleted file mode 100644
index 8a2f019e..00000000
--- a/assets/js/904b44e2.14ac8ffd.js
+++ /dev/null
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-"use strict";(self.webpackChunkgrc=self.webpackChunkgrc||[]).push([[571],{7411:(e,t,n)=>{n.r(t),n.d(t,{assets:()=>l,contentTitle:()=>r,default:()=>u,frontMatter:()=>s,metadata:()=>o,toc:()=>c});var a=n(5893),i=n(1151);const s={},r="Data Staging",o={id:"hermes/components/data-staging",title:"Data Staging",description:"Stage-in is the ability to load external datasets into Hermes.",source:"@site/docs/03-hermes/06-components/06-data-staging.md",sourceDirName:"03-hermes/06-components",slug:"/hermes/components/data-staging",permalink:"/docs/hermes/components/data-staging",draft:!1,unlisted:!1,tags:[],version:"current",sidebarPosition:6,frontMatter:{},sidebar:"tutorialSidebar",previous:{title:"Data Placement",permalink:"/docs/hermes/components/data-placement"},next:{title:"Runtime",permalink:"/docs/hermes/components/runtime"}},l={},c=[{value:"Use Case",id:"use-case",level:2},{value:"Current Status",id:"current-status",level:2},{value:"Utility Script",id:"utility-script",level:2},{value:"Native API",id:"native-api",level:2}];function d(e){const t={code:"code",h1:"h1",h2:"h2",p:"p",pre:"pre",strong:"strong",...(0,i.a)(),...e.components};return(0,a.jsxs)(a.Fragment,{children:[(0,a.jsx)(t.h1,{id:"data-staging",children:"Data Staging"}),"\n",(0,a.jsxs)(t.p,{children:["Stage-in is the ability to load ",(0,a.jsx)(t.strong,{children:"external"})," datasets into Hermes.\nStage-out is the ability export data out of Hermes."]}),"\n",(0,a.jsx)(t.h2,{id:"use-case",children:"Use Case"}),"\n",(0,a.jsx)(t.p,{children:"Data Staging is frequently used for extracting information from large datasets during scientific simulations and workflows.\nThis approach shifts the burden of synchronization, aggregation, validation, cleaning, and processing from the PFS and main memory to the high-performance staging area. I/O stalls are reduced by overlapping compute phases with asynchronous I/O, utilizing the high-performance compute network, and leveraging storage tiering."}),"\n",(0,a.jsx)(t.h2,{id:"current-status",children:"Current Status"}),"\n",(0,a.jsx)(t.p,{children:"Currently, stage-in and stage-out can be applied to POSIX files. Stage-in/stage-out can be used to load directories, specific files, or fractions of files into Hermes to be processed by the application.\nNote: The ability to stage-in and stage-out HDF5 datasets (as opposed to the entire HDF5 file) is currently under development."}),"\n",(0,a.jsx)(t.h2,{id:"utility-script",children:"Utility Script"}),"\n",(0,a.jsx)(t.p,{children:"The stage-in / stage-out utility scripts provide the following API:"}),"\n",(0,a.jsx)(t.pre,{children:(0,a.jsx)(t.code,{className:"language-bash",children:"./stage-in [url] [offset] [size] [dpe]\n./stage-out [url]\n"})}),"\n",(0,a.jsx)(t.p,{children:'The [url] parameter for now is just a POSIX path (e.g., "/home/user/hi.txt"). When [size] is 0, the size of the file will be determined automatically. In the future, this parameter could represent an HDF5 dataset using a different schema (e.g., "hdf5::/[dataset-group1]/[dataset-name1]").'}),"\n",(0,a.jsx)(t.p,{children:"An example of a typical stage-in / stage-out workflow is as follows:"}),"\n",(0,a.jsx)(t.pre,{children:(0,a.jsx)(t.code,{className:"language-bash",children:'# Create a 4GB file (1GB / proc)\nmpirun -n 4 ior -w -k -b 1048576 -o /tmp/hi.txt\n# Start the Hermes Daemon\nmpirun -n 1 ${HERMES_INSTALL}/hermes_daemon\n# Stage-in the entire 4GB file\nmpirun -n 4 ${HERMES_INSTALL}/stage_in /tmp/hi.txt 0 0 kRoundRobin\n# Read the 4GB file in IOR\nmpirun -n 4 \\\n-genv HERMES_CONF=${HERMES_CONF} \\\n-genv LD_PRELOAD "${HERMES_INSTALL}/libhermes_posix.so" \\\n-genv HERMES_STOP_DAEMON 0 \\\n-genv ADAPTER_MODE WORKFLOW \\\n-genv HERMES_CLIENT 1 \\\n-genv HERMES_PAGE_SIZE 1048576 \\\nior -r -b 1048576 -o /tmp/hi.txt\n# Stage the file back out\nmpirun -n 4 ${HERMES_INSTALL/stage_out /tmp/hi.txt\n'})}),"\n",(0,a.jsx)(t.h2,{id:"native-api",children:"Native API"}),"\n",(0,a.jsx)(t.p,{children:"Stage-in / stage-out can also be applied in a native Hermes program."}),"\n",(0,a.jsx)(t.pre,{children:(0,a.jsx)(t.code,{className:"language-cpp",children:"#include <hermes/staging.h>\n\nint main(int argc, char **argv) {\n  auto stager = DataStagerFactory::Get(url);\n  stager->StageIn(url, PlacementEngine::kRoundRobin);\n  stager->StageOut(url);\n}\n"})})]})}function u(e={}){const{wrapper:t}={...(0,i.a)(),...e.components};return t?(0,a.jsx)(t,{...e,children:(0,a.jsx)(d,{...e})}):d(e)}},1151:(e,t,n)=>{n.d(t,{Z:()=>o,a:()=>r});var a=n(7294);const i={},s=a.createContext(i);function r(e){const t=a.useContext(s);return a.useMemo((function(){return"function"==typeof e?e(t):{...t,...e}}),[t,e])}function o(e){let t;return t=e.disableParentContext?"function"==typeof e.components?e.components(i):e.components||i:r(e.components),a.createElement(s.Provider,{value:t},e.children)}}}]);
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diff --git a/assets/js/90fa0cb6.07940709.js b/assets/js/90fa0cb6.07940709.js
new file mode 100644
index 00000000..24762228
--- /dev/null
+++ b/assets/js/90fa0cb6.07940709.js
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diff --git a/assets/js/935f2afb.0a7348b3.js b/assets/js/935f2afb.3e7fdc42.js
similarity index 58%
rename from assets/js/935f2afb.0a7348b3.js
rename to assets/js/935f2afb.3e7fdc42.js
index ab06fedb..25241640 100644
--- a/assets/js/935f2afb.0a7348b3.js
+++ b/assets/js/935f2afb.3e7fdc42.js
@@ -1 +1 @@
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Tier 1 represents the "best" targets according to the\nprioritized characteristics, and the tiers get "worse" as the tier\nnumber increases. For example, tier 1 might be a local RAM target when\nbandwidth is the ordering characteristic, but it might be a burst buffer\ntarget when remaining capacity is prioritized.']}),"\n",(0,n.jsx)(i.p,{children:"When the DPE runs, it is given an appropriate list of targets. If a\nplacement fails, it can request an extended list of targets\n(neighborhood or global)."}),"\n",(0,n.jsxs)(i.p,{children:["For now we map 1 ",(0,n.jsx)(i.code,{children:"TargetID"})," to 1 (NodeID, VirtualDevice) pair, but the\noption is open for 1 to ",(0,n.jsx)(i.em,{children:"n"})," and ",(0,n.jsx)(i.em,{children:"n"})," to ",(0,n.jsx)(i.em,{children:"m"}),"."]}),"\n",(0,n.jsx)(i.hr,{}),"\n",(0,n.jsxs)(i.p,{children:["The set of targets can be partitioned in the form of ",(0,n.jsx)(i.em,{children:"topologies"}),". In\nsome cases, the aggregate characteristics of such partitions can be\ndefined based on the characteristics of the underlying targets."]}),"\n",(0,n.jsx)(i.hr,{}),"\n",(0,n.jsx)(i.h2,{id:"user-view",children:"User View"}),"\n",(0,n.jsxs)(i.p,{children:["Buffering targets are exposed in the [[Hermes Configuration]] file as the variables ",(0,n.jsx)(i.code,{children:"num_targets"})," and ",(0,n.jsx)(i.code,{children:"num_devices"}),". 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Assume a neighborhood is any 2 of the three nodes. This\nmeans a local target list will consist of 3 targets, a neighborhood target list of\n6, and the global target list of 9."}),"\n",(0,n.jsx)(i.h2,{id:"kitchen-sink",children:"Kitchen Sink"}),"\n",(0,n.jsx)("table",{children:(0,n.jsx)("tbody",{children:(0,n.jsxs)("tr",{class:"odd",children:[(0,n.jsxs)("td",{children:[(0,n.jsxs)("p",{children:["From the ",(0,n.jsx)("a",{href:"https://www.cut.ac.cy/digitalAssets/122/122275_100sigmod.pdf",children:"OctopusFS paper"}),":"]}),(0,n.jsxs)("ul",{children:[(0,n.jsxs)("li",{children:["Tiers ",(0,n.jsxs)("span",{class:"math inline",children:[(0,n.jsx)("em",{children:"T"}),(0,n.jsx)("sub",{children:"1"}),",\u2006\u2026,\u2006",(0,n.jsx)("em",{children:"T"}),(0,n.jsx)("sub",{children:(0,n.jsx)("em",{children:"k"})})]})]}),(0,n.jsxs)("li",{children:[(0,n.jsxs)(i.p,{children:["Media ",(0,n.jsxs)("span",{class:"math inline",children:[(0,n.jsx)("em",{children:"m"}),(0,n.jsx)("sub",{children:(0,n.jsx)("em",{children:"i"})})]})]}),(0,n.jsxs)("ul",{children:[(0,n.jsxs)("li",{children:[(0,n.jsxs)("span",{class:"math inline",children:[(0,n.jsx)("em",{children:"T"}),(0,n.jsx)("em",{children:"i"}),(0,n.jsx)("em",{children:"e"}),(0,n.jsx)("em",{children:"r"}),"[",(0,n.jsx)("em",{children:"m"}),(0,n.jsx)("sub",{children:(0,n.jsx)("em",{children:"i"})}),"]"]})," - the tier of medium ",(0,n.jsxs)("span",{class:"math inline",children:[(0,n.jsx)("em",{children:"m"}),(0,n.jsx)("sub",{children:(0,n.jsx)("em",{children:"i"})})]})]}),(0,n.jsxs)("li",{children:[(0,n.jsxs)("span",{class:"math inline",children:[(0,n.jsx)("em",{children:"C"}),(0,n.jsx)("em",{children:"a"}),(0,n.jsx)("em",{children:"p"}),"[",(0,n.jsx)("em",{children:"m"}),(0,n.jsx)("sub",{children:(0,n.jsx)("em",{children:"i"})}),"]"]})," - the total capacity of medium ",(0,n.jsxs)("span",{class:"math inline",children:[(0,n.jsx)("em",{children:"m"}),(0,n.jsx)("sub",{children:(0,n.jsx)("em",{children:"i"})})]})]}),(0,n.jsxs)("li",{children:[(0,n.jsxs)("span",{class:"math inline",children:[(0,n.jsx)("em",{children:"R"}),(0,n.jsx)("em",{children:"e"}),(0,n.jsx)("em",{children:"m"}),"[",(0,n.jsx)("em",{children:"m"}),(0,n.jsx)("sub",{children:(0,n.jsx)("em",{children:"i"})}),"]"]})," - the remaining capacity of medium ",(0,n.jsxs)("span",{class:"math inline",children:[(0,n.jsx)("em",{children:"m"}),(0,n.jsx)("sub",{children:(0,n.jsx)("em",{children:"i"})})]})]}),(0,n.jsxs)("li",{children:[(0,n.jsxs)("span",{class:"math inline",children:[(0,n.jsx)("em",{children:"N"}),(0,n.jsx)("em",{children:"r"}),(0,n.jsx)("em",{children:"C"}),(0,n.jsx)("em",{children:"o"}),(0,n.jsx)("em",{children:"n"}),(0,n.jsx)("em",{children:"n"}),"[",(0,n.jsx)("em",{children:"m"}),(0,n.jsx)("sub",{children:(0,n.jsx)("em",{children:"i"})}),"]"]})," - 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+"use strict";(self.webpackChunkgrc=self.webpackChunkgrc||[]).push([[2232],{8695:(e,i,s)=>{s.r(i),s.d(i,{assets:()=>d,contentTitle:()=>t,default:()=>o,frontMatter:()=>l,metadata:()=>c,toc:()=>h});var n=s(5893),r=s(1151);const l={},t="Buffering Target",c={id:"hermes/components/buffering-target",title:"Buffering Target",description:"A buffering target represents a logical target of data placement, i.e.,",source:"@site/docs/03-hermes/08-components/03-buffering-target.md",sourceDirName:"03-hermes/08-components",slug:"/hermes/components/buffering-target",permalink:"/docs/hermes/components/buffering-target",draft:!1,unlisted:!1,tags:[],version:"current",sidebarPosition:3,frontMatter:{},sidebar:"tutorialSidebar",previous:{title:"Buffer Pool",permalink:"/docs/hermes/components/buffer-pool"},next:{title:"Data Placement",permalink:"/docs/hermes/components/data-placement"}},d={},h=[{value:"Terminology",id:"terminology",level:2},{value:"Virtual Device",id:"virtual-device",level:3},{value:"NodeID",id:"nodeid",level:3},{value:"User View",id:"user-view",level:2},{value:"Goals",id:"goals",level:2},{value:"Charateristics",id:"charateristics",level:2},{value:"Example",id:"example",level:2},{value:"Kitchen Sink",id:"kitchen-sink",level:2}];function a(e){const i={code:"code",em:"em",h1:"h1",h2:"h2",h3:"h3",hr:"hr",li:"li",p:"p",strong:"strong",ul:"ul",...(0,r.a)(),...e.components};return(0,n.jsxs)(n.Fragment,{children:[(0,n.jsx)(i.h1,{id:"buffering-target",children:"Buffering Target"}),"\n",(0,n.jsx)(i.p,{children:"A buffering target represents a logical target of data placement, i.e.,\nparts of or a full BLOB can be placed there by the DPE. Buffering\ntargets are logical constructs that are statically mapped by Hermes to\nunderlying physical resources."}),"\n",(0,n.jsx)(i.h2,{id:"terminology",children:"Terminology"}),"\n",(0,n.jsx)(i.p,{children:"A buffering target consists of two components:"}),"\n",(0,n.jsx)(i.h3,{id:"virtual-device",children:"Virtual Device"}),"\n",(0,n.jsx)(i.p,{children:"This represents a way to get to the actual storage. It could be a file handle and an offset, a memory address, a partition of a drive, etc."}),"\n",(0,n.jsx)(i.h3,{id:"nodeid",children:"NodeID"}),"\n",(0,n.jsx)(i.p,{children:"The identifier of the node that is responsible for the virtual device."}),"\n",(0,n.jsxs)(i.p,{children:[(0,n.jsx)(i.strong,{children:"Tiers"}),' are the partitions of a partitioned set of targets order by a\nscore, which is calculated based on a set of prioritized\ncharacteristics. Tier 1 represents the "best" targets according to the\nprioritized characteristics, and the tiers get "worse" as the tier\nnumber increases. For example, tier 1 might be a local RAM target when\nbandwidth is the ordering characteristic, but it might be a burst buffer\ntarget when remaining capacity is prioritized.']}),"\n",(0,n.jsx)(i.p,{children:"When the DPE runs, it is given an appropriate list of targets. If a\nplacement fails, it can request an extended list of targets\n(neighborhood or global)."}),"\n",(0,n.jsxs)(i.p,{children:["For now we map 1 ",(0,n.jsx)(i.code,{children:"TargetID"})," to 1 (NodeID, VirtualDevice) pair, but the\noption is open for 1 to ",(0,n.jsx)(i.em,{children:"n"})," and ",(0,n.jsx)(i.em,{children:"n"})," to ",(0,n.jsx)(i.em,{children:"m"}),"."]}),"\n",(0,n.jsx)(i.hr,{}),"\n",(0,n.jsxs)(i.p,{children:["The set of targets can be partitioned in the form of ",(0,n.jsx)(i.em,{children:"topologies"}),". In\nsome cases, the aggregate characteristics of such partitions can be\ndefined based on the characteristics of the underlying targets."]}),"\n",(0,n.jsx)(i.hr,{}),"\n",(0,n.jsx)(i.h2,{id:"user-view",children:"User View"}),"\n",(0,n.jsxs)(i.p,{children:["Buffering targets are exposed in the [[Hermes Configuration]] file as the variables ",(0,n.jsx)(i.code,{children:"num_targets"})," and ",(0,n.jsx)(i.code,{children:"num_devices"}),". Currently, the number of targets must equal the number of devices."]}),"\n",(0,n.jsx)(i.h2,{id:"goals",children:"Goals"}),"\n",(0,n.jsxs)(i.ul,{children:["\n",(0,n.jsx)(i.li,{children:"Provide a way for the DPE to operate on a reduced (or custom) set of\nresources."}),"\n",(0,n.jsx)(i.li,{children:"Remove certain resources from DPE consideration."}),"\n",(0,n.jsx)(i.li,{children:"Create orderings of resources based on characteristics (i.e., tiered\ngroups)."}),"\n"]}),"\n",(0,n.jsx)(i.h2,{id:"charateristics",children:"Charateristics"}),"\n",(0,n.jsx)(i.p,{children:"Each buffering target has the following characteristics."}),"\n",(0,n.jsxs)(i.ul,{children:["\n",(0,n.jsxs)(i.li,{children:["Targets $",(0,n.jsx)(i.code,{children:"d_i, i=1,\\ldots,D"}),"$","\n",(0,n.jsxs)(i.ul,{children:["\n",(0,n.jsxs)(i.li,{children:["Target configuration/specs.","\n",(0,n.jsxs)(i.ul,{children:["\n",(0,n.jsxs)(i.li,{children:["$",(0,n.jsx)(i.code,{children:"Cap[d_i]"}),"$ - the total capacity of target $",(0,n.jsx)(i.code,{children:"d_i"}),"$"]}),"\n",(0,n.jsxs)(i.li,{children:["$",(0,n.jsx)(i.code,{children:"Wbw[d_i]"}),"$ - the HW max. write bandwidth of target $",(0,n.jsx)(i.code,{children:"d_i"}),"$"]}),"\n",(0,n.jsxs)(i.li,{children:["$",(0,n.jsx)(i.code,{children:"Rbw[d_i]"}),"$ - the HW max. read bandwidth of target $",(0,n.jsx)(i.code,{children:"d_i"}),"$"]}),"\n",(0,n.jsxs)(i.li,{children:["$",(0,n.jsx)(i.code,{children:"Alat[d_i]"}),"$ - the average HW access latency of target\n$",(0,n.jsx)(i.code,{children:"d_i"}),"$ (measured as time)"]}),"\n",(0,n.jsxs)(i.li,{children:["$",(0,n.jsx)(i.code,{children:"Pwr[d_i]"}),"$ - the energy consumption of target $",(0,n.jsx)(i.code,{children:"d_i"}),"$\n(measured in Watts)"]}),"\n",(0,n.jsxs)(i.li,{children:["$",(0,n.jsx)(i.code,{children:"Concy[d_i]"}),"$ - the HW concurrency of target $",(0,n.jsx)(i.code,{children:"d_i"}),"$\n(measured in lane count)"]}),"\n",(0,n.jsxs)(i.li,{children:["$",(0,n.jsx)(i.code,{children:"End[d_i]"}),"$ - the endurance (wear and tear) of target\n$",(0,n.jsx)(i.code,{children:"d_i"}),"$ (measured as percentage of the expected storage\ncycles over the life time)"]}),"\n",(0,n.jsxs)(i.li,{children:["$",(0,n.jsx)(i.code,{children:"Rrat[d_i]"}),"$ - the reliability rating of target $",(0,n.jsx)(i.code,{children:"d_i"}),"$\n(measured as test-retest reliability)"]}),"\n",(0,n.jsxs)(i.li,{children:["$",(0,n.jsx)(i.code,{children:"Speed[d_i]"}),"$ - the average I/O speed of target $",(0,n.jsx)(i.code,{children:"d_i"}),"$\n(measured as MB/s)"]}),"\n"]}),"\n"]}),"\n",(0,n.jsxs)(i.li,{children:["Variables","\n",(0,n.jsxs)(i.ul,{children:["\n",(0,n.jsxs)(i.li,{children:["$",(0,n.jsx)(i.code,{children:"Avail[d_i]"}),"$ - the availability of target $",(0,n.jsx)(i.code,{children:"d_i"}),"$\n(Boolean)"]}),"\n",(0,n.jsxs)(i.li,{children:["$",(0,n.jsx)(i.code,{children:"Rem[d_i]"}),"$ - the remaining capacity of target $",(0,n.jsx)(i.code,{children:"d_i"}),"$"]}),"\n",(0,n.jsxs)(i.li,{children:["$",(0,n.jsx)(i.code,{children:"Load[d_i]"}),"$ - the expected completion time of outstanding\nrequests on target $",(0,n.jsx)(i.code,{children:"d_i"}),"$"]}),"\n"]}),"\n"]}),"\n"]}),"\n"]}),"\n"]}),"\n",(0,n.jsx)(i.h2,{id:"example",children:"Example"}),"\n",(0,n.jsx)(i.p,{children:"Assume a system with 3 nodes, each with three targets (RAM, NVMe, and\nburst buffer). Assume a neighborhood is any 2 of the three nodes. This\nmeans a local target list will consist of 3 targets, a neighborhood target list of\n6, and the global target list of 9."}),"\n",(0,n.jsx)(i.h2,{id:"kitchen-sink",children:"Kitchen Sink"}),"\n",(0,n.jsx)("table",{children:(0,n.jsx)("tbody",{children:(0,n.jsxs)("tr",{class:"odd",children:[(0,n.jsxs)("td",{children:[(0,n.jsxs)("p",{children:["From the ",(0,n.jsx)("a",{href:"https://www.cut.ac.cy/digitalAssets/122/122275_100sigmod.pdf",children:"OctopusFS paper"}),":"]}),(0,n.jsxs)("ul",{children:[(0,n.jsxs)("li",{children:["Tiers ",(0,n.jsxs)("span",{class:"math inline",children:[(0,n.jsx)("em",{children:"T"}),(0,n.jsx)("sub",{children:"1"}),",\u2006\u2026,\u2006",(0,n.jsx)("em",{children:"T"}),(0,n.jsx)("sub",{children:(0,n.jsx)("em",{children:"k"})})]})]}),(0,n.jsxs)("li",{children:[(0,n.jsxs)(i.p,{children:["Media ",(0,n.jsxs)("span",{class:"math inline",children:[(0,n.jsx)("em",{children:"m"}),(0,n.jsx)("sub",{children:(0,n.jsx)("em",{children:"i"})})]})]}),(0,n.jsxs)("ul",{children:[(0,n.jsxs)("li",{children:[(0,n.jsxs)("span",{class:"math inline",children:[(0,n.jsx)("em",{children:"T"}),(0,n.jsx)("em",{children:"i"}),(0,n.jsx)("em",{children:"e"}),(0,n.jsx)("em",{children:"r"}),"[",(0,n.jsx)("em",{children:"m"}),(0,n.jsx)("sub",{children:(0,n.jsx)("em",{children:"i"})}),"]"]})," - 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the number of active I/O connections to medium ",(0,n.jsxs)("span",{class:"math inline",children:[(0,n.jsx)("em",{children:"m"}),(0,n.jsx)("sub",{children:(0,n.jsx)("em",{children:"i"})})]})]}),(0,n.jsxs)("li",{children:[(0,n.jsxs)("span",{class:"math inline",children:[(0,n.jsx)("em",{children:"W"}),(0,n.jsx)("em",{children:"T"}),(0,n.jsx)("em",{children:"h"}),(0,n.jsx)("em",{children:"r"}),(0,n.jsx)("em",{children:"u"}),"[",(0,n.jsx)("em",{children:"m"}),(0,n.jsx)("sub",{children:(0,n.jsx)("em",{children:"i"})}),"]"]})," - the sustained write throughput of medium ",(0,n.jsxs)("span",{class:"math inline",children:[(0,n.jsx)("em",{children:"m"}),(0,n.jsx)("sub",{children:(0,n.jsx)("em",{children:"i"})})]})]}),(0,n.jsxs)("li",{children:[(0,n.jsxs)("span",{class:"math inline",children:[(0,n.jsx)("em",{children:"R"}),(0,n.jsx)("em",{children:"T"}),(0,n.jsx)("em",{children:"h"}),(0,n.jsx)("em",{children:"r"}),(0,n.jsx)("em",{children:"u"}),"[",(0,n.jsx)("em",{children:"m"}),(0,n.jsx)("sub",{children:(0,n.jsx)("em",{children:"i"})}),"]"]})," - the sustained read throughput of medium ",(0,n.jsxs)("span",{class:"math inline",children:[(0,n.jsx)("em",{children:"m"}),(0,n.jsx)("sub",{children:(0,n.jsx)("em",{children:"i"})})]})]})]})]}),(0,n.jsxs)("li",{children:[(0,n.jsxs)(i.p,{children:["Workers ",(0,n.jsxs)("span",{class:"math inline",children:[(0,n.jsx)("em",{children:"W"}),(0,n.jsx)("sub",{children:"1"}),",\u2006\u2026,\u2006",(0,n.jsx)("em",{children:"W"}),(0,n.jsx)("sub",{children:(0,n.jsx)("em",{children:"n"})})]})]}),(0,n.jsx)("ul",{children:(0,n.jsxs)("li",{children:[(0,n.jsx)(i.p,{children:"Slightly different concept"}),(0,n.jsxs)("ul",{children:[(0,n.jsx)("li",{children:"Stores and manages file blocks on storage media"}),(0,n.jsx)("li",{children:"Serves read and write requests from clients"}),(0,n.jsx)("li",{children:"Block creation, deletion, replication (instructed by name nodes HDFS...)"})]})]})})]})]})]}),(0,n.jsxs)("td",{children:[(0,n.jsxs)("p",{children:["From ",(0,n.jsx)("a",{href:"https://www.wrike.com/open.htm?id=416733774",children:"Wrike"}),":"]}),(0,n.jsxs)("ul",{children:[(0,n.jsx)("li",{children:(0,n.jsxs)("span",{class:"math inline",children:[(0,n.jsx)("em",{children:"W"}),(0,n.jsx)("sub",{children:(0,n.jsx)("em",{children:"i"})}),"\u2004=\u2004\u2004<\u2004",(0,n.jsx)("em",{children:"n"}),(0,n.jsx)("em",{children:"o"}),(0,n.jsx)("em",{children:"d"}),(0,n.jsx)("em",{children:"e"}),",\u2006",(0,n.jsx)("em",{children:"t"}),(0,n.jsx)("em",{children:"i"}),(0,n.jsx)("em",{children:"e"}),(0,n.jsx)("em",{children:"r"}),">"]})}),(0,n.jsx)("li",{children:"Workers are a dedicated thread per tier available on the node"}),(0,n.jsxs)("li",{children:[(0,n.jsx)(i.p,{children:"Worker characteristics:"}),(0,n.jsxs)("ul",{children:[(0,n.jsx)("li",{children:"Capacity"}),(0,n.jsx)("li",{children:"BW"}),(0,n.jsx)("li",{children:"Latency"}),(0,n.jsx)("li",{children:"Energy consumption"}),(0,n.jsx)("li",{children:"Concurrency (expressed as the number of lanes of the bus e.g., PCIex8 or SATA)"}),(0,n.jsxs)("li",{children:[(0,n.jsx)(i.p,{children:"Queue pressure (outstanding requests)"}),(0,n.jsxs)("ul",{children:[(0,n.jsx)("li",{children:"Aggregate data size in queue"}),(0,n.jsx)("li",{children:"Number of pending requests"})]})]})]})]})]})]})]})})})]})}function o(e={}){const{wrapper:i}={...(0,r.a)(),...e.components};return i?(0,n.jsx)(i,{...e,children:(0,n.jsx)(a,{...e})}):a(e)}},1151:(e,i,s)=>{s.d(i,{Z:()=>c,a:()=>t});var n=s(7294);const r={},l=n.createContext(r);function t(e){const i=n.useContext(l);return n.useMemo((function(){return"function"==typeof e?e(i):{...i,...e}}),[i,e])}function c(e){let i;return i=e.disableParentContext?"function"==typeof e.components?e.components(r):e.components||r:t(e.components),n.createElement(l.Provider,{value:i},e.children)}}}]);
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-"use strict";(self.webpackChunkgrc=self.webpackChunkgrc||[]).push([[5945],{4785:(e,n,t)=>{t.r(n),t.d(n,{assets:()=>l,contentTitle:()=>a,default:()=>h,frontMatter:()=>s,metadata:()=>o,toc:()=>c});var i=t(5893),r=t(1151);const s={},a="Debugging",o={id:"hermes/debugging",title:"Debugging",description:"Hermes can be complicated to debug due to its distributed and asynchronous",source:"@site/docs/03-hermes/09-debugging.md",sourceDirName:"03-hermes",slug:"/hermes/debugging",permalink:"/docs/hermes/debugging",draft:!1,unlisted:!1,tags:[],version:"current",sidebarPosition:9,frontMatter:{},sidebar:"tutorialSidebar",previous:{title:"Quick Start Guide",permalink:"/docs/hermes/quick-start"},next:{title:"Doxygen",permalink:"/docs/hermes/doxygen"}},l={},c=[{value:"Preparing For Release",id:"preparing-for-release",level:2},{value:"Preparing Pull Request (PR)",id:"preparing-pull-request-pr",level:3},{value:"PR Check Failure",id:"pr-check-failure",level:3},{value:"Introduction to our Continuous Integration (CI)",id:"introduction-to-our-continuous-integration-ci",level:2},{value:"API Test",id:"api-test",level:3},{value:"Adding a New Adapter",id:"adding-a-new-adapter",level:2},{value:"Customizing Data Placement Engine",id:"customizing-data-placement-engine",level:2},{value:"Codes for Testing DPE",id:"codes-for-testing-dpe",level:3}];function d(e){const n={a:"a",code:"code",em:"em",h1:"h1",h2:"h2",h3:"h3",li:"li",ol:"ol",p:"p",pre:"pre",ul:"ul",...(0,r.a)(),...e.components};return(0,i.jsxs)(i.Fragment,{children:[(0,i.jsx)(n.h1,{id:"debugging",children:"Debugging"}),"\n",(0,i.jsx)(n.p,{children:"Hermes can be complicated to debug due to its distributed and asynchronous\nnature. Faults can happen in the client program, or in the Hermes daemon.\nThe first step when encountering problems is to compile in Debug mode."}),"\n",(0,i.jsx)(n.pre,{children:(0,i.jsx)(n.code,{className:"language-cmake",children:"cmake .. -DCMAKE_BUILD_TYPE=Debug\n"})}),"\n",(0,i.jsx)(n.p,{children:"The Debug mode will increase the number of logging statements the program\nuses to give you a stronger hint as to where the problem occurs. These\nstatements are typically compiled out for performance reasons."}),"\n",(0,i.jsx)(n.p,{children:"Secondly, make sure to use an IDE which supports visual debugging. Debugging\nusing a terminal with gdb can be very cumbersome, especially when multi-process\ncases come along."}),"\n",(0,i.jsx)(n.h2,{id:"preparing-for-release",children:"Preparing For Release"}),"\n",(0,i.jsxs)(n.ol,{children:["\n",(0,i.jsxs)(n.li,{children:["Create a GitHub Project for the ",(0,i.jsx)(n.em,{children:"next"})," release"]}),"\n",(0,i.jsxs)(n.li,{children:["Update the ",(0,i.jsx)(n.code,{children:"HERMES_VERSION_*"})," variables in ",(0,i.jsx)(n.code,{children:"CMakeLists.txt"})]}),"\n",(0,i.jsxs)(n.li,{children:["Update ",(0,i.jsx)(n.code,{children:"PROJECT_NUMBER"})," in ",(0,i.jsx)(n.code,{children:"Doxyfile.in"}),"."]}),"\n",(0,i.jsx)(n.li,{children:"To make release note generation as automated as possible, make sure\nrelevant pull requests that are part of the release have proper labels and and\ntitles, as that information will show up directly in the generated release\nnotes in the next step."}),"\n",(0,i.jsxs)(n.li,{children:["Draft a release on Github. Click ",(0,i.jsx)(n.code,{children:"auto-generate release notes"}),' and edit\nthe result as necessary. Fill in the new tag, and select "Create new tag x.x.x\non publish" so that Github will automatically tag the release when it is\npublished.']}),"\n",(0,i.jsx)(n.li,{children:"The docker containers will be automatically built and pushed to docker hub\nwhenever a new tag is added. Check the CI actions to make sure there were no\nerrors."}),"\n",(0,i.jsx)(n.li,{children:"Copy/move ideas to the project for the next release"}),"\n",(0,i.jsxs)(n.li,{children:["Close and archive the project for the ",(0,i.jsx)(n.em,{children:"current"})," release"]}),"\n",(0,i.jsxs)(n.li,{children:["Merge the latest release branch (if one exists) of the wiki into the ",(0,i.jsx)(n.code,{children:"master"})," branch."]}),"\n",(0,i.jsx)(n.li,{children:"Make an announcement in the Hermes topic of the HDF forum."}),"\n",(0,i.jsx)(n.li,{children:"Send Lori a note for the next HDF5 newsletter."}),"\n"]}),"\n",(0,i.jsx)(n.h3,{id:"preparing-pull-request-pr",children:"Preparing Pull Request (PR)"}),"\n",(0,i.jsx)(n.p,{children:"Please run these two steps and remove all warnings."}),"\n",(0,i.jsx)(n.pre,{children:(0,i.jsx)(n.code,{className:"language-bash",children:"make dox\nmake lint\n"})}),"\n",(0,i.jsx)(n.h3,{id:"pr-check-failure",children:"PR Check Failure"}),"\n",(0,i.jsxs)(n.p,{children:['GitHub Actions for PR check may fail because it uses a Spack cache.\nThe cache does not have to change often (unless you\'ve added dependencies),\nso this should be done only in this case. To refresh the github cache,\nmodify the file "ci/install_deps.sh" in some way. For\nexample, by adding a comment. If you check the ',(0,i.jsx)(n.a,{href:"https://github.com/HDFGroup/hermes/blob/master/.github/workflows/main.yml",children:"github workflow which produces\nthe cache"}),", it uses a hash\nof install_deps.sh to locate a cache."]}),"\n",(0,i.jsx)(n.h2,{id:"introduction-to-our-continuous-integration-ci",children:"Introduction to our Continuous Integration (CI)"}),"\n",(0,i.jsxs)(n.p,{children:["We are primarily using Python for managing for running unit tests. Under\n",(0,i.jsx)(n.a,{href:"https://github.com/HDFGroup/hermes/blob/master/CMakeLists.txt",children:"our root CMakeList"}),", we implement a\nCMake function called pytest, which wraps around the Python testing\nframework called py_hermes_ci, which is located under ci/py_hermes_ci."]}),"\n",(0,i.jsx)(n.p,{children:"Fundamentally, py_hermes_ci relies on our library jarvis-util,\n(located under ci/jarvis-util), which provides utilities to execute\nbinaries in Python."}),"\n",(0,i.jsx)(n.h3,{id:"api-test",children:"API Test"}),"\n",(0,i.jsxs)(n.p,{children:["Update ",(0,i.jsx)(n.code,{children:"test/CMakeLists.txt"})," with your new .cc test code name.\nFor example, if you add ",(0,i.jsx)(n.code,{children:"trait_order.cc"}),", add ",(0,i.jsx)(n.code,{children:"trait_order"})," as follows:"]}),"\n",(0,i.jsx)(n.pre,{children:(0,i.jsx)(n.code,{children:"set(API_TESTS dpe_optimization_test dpe_random_test\n    dpe_roundrobin_test end_to_end_test vbucket_test trait_order)\n"})}),"\n",(0,i.jsx)(n.h2,{id:"adding-a-new-adapter",children:"Adding a New Adapter"}),"\n",(0,i.jsxs)(n.ol,{children:["\n",(0,i.jsxs)(n.li,{children:["Create a new directory under the ",(0,i.jsx)(n.code,{children:"adapter"})," directory."]}),"\n"]}),"\n",(0,i.jsx)(n.h2,{id:"customizing-data-placement-engine",children:"Customizing Data Placement Engine"}),"\n",(0,i.jsx)(n.p,{children:"Data Placement Engine (DPE) is the heart of Hermes performance.\nDevelopers may want to replace the default engine using different optimization algorithms."}),"\n",(0,i.jsx)(n.h3,{id:"codes-for-testing-dpe",children:"Codes for Testing DPE"}),"\n",(0,i.jsx)(n.p,{children:"You can quickly check how DPE is tested."}),"\n",(0,i.jsxs)(n.ul,{children:["\n",(0,i.jsx)(n.li,{children:(0,i.jsx)(n.a,{href:"https://github.com/HDFGroup/hermes/blob/master/test/dpe_optimization_test.cc",children:"test/dpe_optimization_test.cc"})}),"\n"]})]})}function h(e={}){const{wrapper:n}={...(0,r.a)(),...e.components};return n?(0,i.jsx)(n,{...e,children:(0,i.jsx)(d,{...e})}):d(e)}},1151:(e,n,t)=>{t.d(n,{Z:()=>o,a:()=>a});var i=t(7294);const r={},s=i.createContext(r);function a(e){const n=i.useContext(s);return i.useMemo((function(){return"function"==typeof e?e(n):{...n,...e}}),[n,e])}function o(e){let n;return n=e.disableParentContext?"function"==typeof e.components?e.components(r):e.components||r:a(e.components),i.createElement(s.Provider,{value:n},e.children)}}}]);
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+"use strict";(self.webpackChunkgrc=self.webpackChunkgrc||[]).push([[8737],{5316:(e,n,i)=>{i.r(n),i.d(n,{assets:()=>c,contentTitle:()=>r,default:()=>h,frontMatter:()=>o,metadata:()=>l,toc:()=>a});var s=i(5893),t=i(1151);const o={},r="Topology",l={id:"hermes/components/topology",title:"Topology",description:"The TopologyManager is responsible for maintaining sets of Targets",source:"@site/docs/03-hermes/08-components/12-topology.md",sourceDirName:"03-hermes/08-components",slug:"/hermes/components/topology",permalink:"/docs/hermes/components/topology",draft:!1,unlisted:!1,tags:[],version:"current",sidebarPosition:12,frontMatter:{},sidebar:"tutorialSidebar",previous:{title:"Tagging",permalink:"/docs/hermes/components/tagging"},next:{title:"Containers",permalink:"/docs/hermes/containers"}},c={},a=[{value:"API",id:"api",level:2},{value:"Requirements",id:"requirements",level:3},{value:"Scoring System",id:"scoring-system",level:2},{value:"Pre-built Partitions",id:"pre-built-partitions",level:2}];function d(e){const n={code:"code",h1:"h1",h2:"h2",h3:"h3",li:"li",p:"p",pre:"pre",ul:"ul",...(0,t.a)(),...e.components};return(0,s.jsxs)(s.Fragment,{children:[(0,s.jsx)(n.h1,{id:"topology",children:"Topology"}),"\n",(0,s.jsxs)(n.p,{children:["The ",(0,s.jsx)(n.code,{children:"TopologyManager"})," is responsible for maintaining sets of ",(0,s.jsx)(n.code,{children:"Target"}),"s\nas metadata."]}),"\n",(0,s.jsx)(n.h2,{id:"api",children:"API"}),"\n",(0,s.jsx)(n.pre,{children:(0,s.jsx)(n.code,{className:"language-c++",children:"  - std::vector<TargetID> GetTop(size_t num_targets, Critera criteria)\n"})}),"\n",(0,s.jsx)(n.h3,{id:"requirements",children:"Requirements"}),"\n",(0,s.jsxs)(n.ul,{children:["\n",(0,s.jsx)(n.li,{children:"O(1) insert"}),"\n",(0,s.jsx)(n.li,{children:"Fast find."}),"\n"]}),"\n",(0,s.jsx)(n.h2,{id:"scoring-system",children:"Scoring System"}),"\n",(0,s.jsx)(n.h2,{id:"pre-built-partitions",children:"Pre-built Partitions"}),"\n",(0,s.jsxs)(n.ul,{children:["\n",(0,s.jsxs)(n.li,{children:["Remaining Capacity","\n",(0,s.jsxs)(n.ul,{children:["\n",(0,s.jsx)(n.li,{children:"Global"}),"\n",(0,s.jsx)(n.li,{children:"Neighborhood"}),"\n",(0,s.jsx)(n.li,{children:"Local"}),"\n"]}),"\n"]}),"\n",(0,s.jsxs)(n.li,{children:["Bandwidth","\n",(0,s.jsxs)(n.ul,{children:["\n",(0,s.jsx)(n.li,{children:"Global"}),"\n",(0,s.jsx)(n.li,{children:"Neighborhood"}),"\n",(0,s.jsx)(n.li,{children:"Local"}),"\n"]}),"\n"]}),"\n"]})]})}function h(e={}){const{wrapper:n}={...(0,t.a)(),...e.components};return n?(0,s.jsx)(n,{...e,children:(0,s.jsx)(d,{...e})}):d(e)}},1151:(e,n,i)=>{i.d(n,{Z:()=>l,a:()=>r});var s=i(7294);const t={},o=s.createContext(t);function r(e){const n=s.useContext(o);return s.useMemo((function(){return"function"==typeof e?e(n):{...n,...e}}),[n,e])}function l(e){let n;return n=e.disableParentContext?"function"==typeof e.components?e.components(t):e.components||t:r(e.components),s.createElement(o.Provider,{value:n},e.children)}}}]);
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diff --git a/assets/js/a5e346b8.b1610c43.js b/assets/js/a5e346b8.b1610c43.js
deleted file mode 100644
index f81dc150..00000000
--- a/assets/js/a5e346b8.b1610c43.js
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-"use strict";(self.webpackChunkgrc=self.webpackChunkgrc||[]).push([[5105],{7356:(e,n,t)=>{t.r(n),t.d(n,{assets:()=>l,contentTitle:()=>s,default:()=>d,frontMatter:()=>o,metadata:()=>a,toc:()=>c});var i=t(5893),r=t(1151);const o={},s="Programming",a={id:"hermes/programming",title:"Programming",description:"In this section, we will discuss the general steps of building a program",source:"@site/docs/03-hermes/06-programming.md",sourceDirName:"03-hermes",slug:"/hermes/programming",permalink:"/docs/hermes/programming",draft:!1,unlisted:!1,tags:[],version:"current",sidebarPosition:6,frontMatter:{},sidebar:"tutorialSidebar",previous:{title:"Topology",permalink:"/docs/hermes/components/topology"},next:{title:"Adapters",permalink:"/docs/hermes/adapters"}},l={},c=[{value:"Basic API Example",id:"basic-api-example",level:2},{value:"Basic Deployment",id:"basic-deployment",level:2},{value:"Create a server configuration",id:"create-a-server-configuration",level:3},{value:"Launch the Hermes Daemon",id:"launch-the-hermes-daemon",level:3},{value:"Launch your application",id:"launch-your-application",level:3}];function h(e){const n={a:"a",code:"code",h1:"h1",h2:"h2",h3:"h3",li:"li",p:"p",pre:"pre",ul:"ul",...(0,r.a)(),...e.components};return(0,i.jsxs)(i.Fragment,{children:[(0,i.jsx)(n.h1,{id:"programming",children:"Programming"}),"\n",(0,i.jsx)(n.p,{children:"In this section, we will discuss the general steps of building a program\non top of the Hermes native API. We will focus on the core data structures\nprovided by Hermes -- Buckets and Blobs."}),"\n",(0,i.jsx)(n.h2,{id:"basic-api-example",children:"Basic API Example"}),"\n",(0,i.jsx)(n.pre,{children:(0,i.jsx)(n.code,{className:"language-cpp",children:'#include <hermes.h>\n#include <bucket.h>\n\nint main() {\n  HERMES->Create(hermes::HermesType::kClient);\n  Bucket bkt = hermes->GetBucket("hello");\n  size_t blob_size = KILOBYTES(4);\n  Context ctx;\n\n  for (size_t i = 0; i < num_blobs; ++i) {\n    hermes::Blob blob(blob_size);\n    std::string name = std::to_string(i);\n    char nonce = i % 256;\n    memset(blob.data(), nonce, blob_size);\n    bkt.Put(name, blob, blob_id, ctx);\n  }\n\n  for (size_t i = 0; i < num_blobs; ++i) {\n    std::string name = std::to_string(i);\n    char nonce = i % 256;\n    hermes::Blob blob;\n    bkt.GetBlobId(name, blob_id);\n    bkt.Get(blob_id, blob, ctx);\n  }\n}\n'})}),"\n",(0,i.jsxs)(n.ul,{children:["\n",(0,i.jsx)(n.li,{children:"HERMES is a singleton macro provided in hermes.h."}),"\n",(0,i.jsx)(n.li,{children:"GetBucket will either create a bucket or get the bucket if it exists.\nThis operation is concurrency-safe. I.e., it is guaranteed only one\nthread or process calling this function will create the bucket if it\nDNE."}),"\n",(0,i.jsx)(n.li,{children:"Context is optional. It contains the ability to override\ndefaults defined in the server and client configuration files. For\nexample, you can set a custom DPE to use for a blob Put."}),"\n",(0,i.jsxs)(n.li,{children:[(0,i.jsx)(n.code,{children:"hermes::Blob analagous to and std::vector<char>"}),". It's not quite the\nsame thing, but we won't go into detail here."]}),"\n",(0,i.jsx)(n.li,{children:"bkt.Put will put a blob into the bucket. Put destroys all content\nif the blob previously existed. At this time, blobs are considered\nimmutable."}),"\n",(0,i.jsx)(n.li,{children:"bkt.Get will get the contents of an entire blob."}),"\n"]}),"\n",(0,i.jsx)(n.h2,{id:"basic-deployment",children:"Basic Deployment"}),"\n",(0,i.jsx)(n.p,{children:"Here we will describe the basic flow of deploying a Hermes program."}),"\n",(0,i.jsx)(n.h3,{id:"create-a-server-configuration",children:"Create a server configuration"}),"\n",(0,i.jsxs)(n.p,{children:["Technically, this is optional. Hermes has a\n",(0,i.jsx)(n.a,{href:"https://github.com/HDFGroup/hermes/blob/master/config/hermes_server_default.yaml",children:"default server\nconfiguration"}),".\nThe main important thing here is defining the storage devices on your machines.\nThe example file has more details."]}),"\n",(0,i.jsx)(n.p,{children:"The Hermes server configuration is also described in Section 3."}),"\n",(0,i.jsx)(n.h3,{id:"launch-the-hermes-daemon",children:"Launch the Hermes Daemon"}),"\n",(0,i.jsx)(n.p,{children:"To launch the daemon on a single node, do the following:"}),"\n",(0,i.jsx)(n.pre,{children:(0,i.jsx)(n.code,{className:"language-bash",children:"HERMES_CONF=/path/to/your/hermes_server.yaml \\\nhermes_daemon\n"})}),"\n",(0,i.jsx)(n.p,{children:"If you need the daemon on multiple nodes, we support MPI"}),"\n",(0,i.jsx)(n.pre,{children:(0,i.jsx)(n.code,{className:"language-bash",children:"mpirun -n 4 -ppn 1 --hostfile=hostfile.txt \\\n-genv HERMES_CONF /path/to/your/hermes_server.yaml \\\nhermes_daemon\n"})}),"\n",(0,i.jsx)(n.p,{children:"Make sure to only spawn one daemon per node."}),"\n",(0,i.jsx)(n.h3,{id:"launch-your-application",children:"Launch your application"}),"\n",(0,i.jsx)(n.pre,{children:(0,i.jsx)(n.code,{className:"language-bash",children:"HERMES_CONF=/path/to/your/hermes_server.yaml \\\nHERMES_CLEINT_CONF=/path/to/your/hermes_client.yaml \\\n./myprogram\n"})})]})}function d(e={}){const{wrapper:n}={...(0,r.a)(),...e.components};return n?(0,i.jsx)(n,{...e,children:(0,i.jsx)(h,{...e})}):h(e)}},1151:(e,n,t)=>{t.d(n,{Z:()=>a,a:()=>s});var i=t(7294);const r={},o=i.createContext(r);function s(e){const n=i.useContext(o);return i.useMemo((function(){return"function"==typeof e?e(n):{...n,...e}}),[n,e])}function a(e){let n;return n=e.disableParentContext?"function"==typeof e.components?e.components(r):e.components||r:s(e.components),i.createElement(o.Provider,{value:n},e.children)}}}]);
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diff --git a/assets/js/b8ffec82.e124a715.js b/assets/js/b8ffec82.e124a715.js
new file mode 100644
index 00000000..f14820f2
--- /dev/null
+++ b/assets/js/b8ffec82.e124a715.js
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+"use strict";(self.webpackChunkgrc=self.webpackChunkgrc||[]).push([[1542],{9162:(e,t,n)=>{n.r(t),n.d(t,{assets:()=>l,contentTitle:()=>r,default:()=>u,frontMatter:()=>s,metadata:()=>o,toc:()=>c});var a=n(5893),i=n(1151);const s={},r="Data Staging",o={id:"hermes/components/data-staging",title:"Data Staging",description:"Stage-in is the ability to load external datasets into Hermes.",source:"@site/docs/03-hermes/08-components/06-data-staging.md",sourceDirName:"03-hermes/08-components",slug:"/hermes/components/data-staging",permalink:"/docs/hermes/components/data-staging",draft:!1,unlisted:!1,tags:[],version:"current",sidebarPosition:6,frontMatter:{},sidebar:"tutorialSidebar",previous:{title:"Data Placement",permalink:"/docs/hermes/components/data-placement"},next:{title:"Runtime",permalink:"/docs/hermes/components/runtime"}},l={},c=[{value:"Use Case",id:"use-case",level:2},{value:"Current Status",id:"current-status",level:2},{value:"Utility Script",id:"utility-script",level:2},{value:"Native API",id:"native-api",level:2}];function d(e){const t={code:"code",h1:"h1",h2:"h2",p:"p",pre:"pre",strong:"strong",...(0,i.a)(),...e.components};return(0,a.jsxs)(a.Fragment,{children:[(0,a.jsx)(t.h1,{id:"data-staging",children:"Data Staging"}),"\n",(0,a.jsxs)(t.p,{children:["Stage-in is the ability to load ",(0,a.jsx)(t.strong,{children:"external"})," datasets into Hermes.\nStage-out is the ability export data out of Hermes."]}),"\n",(0,a.jsx)(t.h2,{id:"use-case",children:"Use Case"}),"\n",(0,a.jsx)(t.p,{children:"Data Staging is frequently used for extracting information from large datasets during scientific simulations and workflows.\nThis approach shifts the burden of synchronization, aggregation, validation, cleaning, and processing from the PFS and main memory to the high-performance staging area. I/O stalls are reduced by overlapping compute phases with asynchronous I/O, utilizing the high-performance compute network, and leveraging storage tiering."}),"\n",(0,a.jsx)(t.h2,{id:"current-status",children:"Current Status"}),"\n",(0,a.jsx)(t.p,{children:"Currently, stage-in and stage-out can be applied to POSIX files. Stage-in/stage-out can be used to load directories, specific files, or fractions of files into Hermes to be processed by the application.\nNote: The ability to stage-in and stage-out HDF5 datasets (as opposed to the entire HDF5 file) is currently under development."}),"\n",(0,a.jsx)(t.h2,{id:"utility-script",children:"Utility Script"}),"\n",(0,a.jsx)(t.p,{children:"The stage-in / stage-out utility scripts provide the following API:"}),"\n",(0,a.jsx)(t.pre,{children:(0,a.jsx)(t.code,{className:"language-bash",children:"./stage-in [url] [offset] [size] [dpe]\n./stage-out [url]\n"})}),"\n",(0,a.jsx)(t.p,{children:'The [url] parameter for now is just a POSIX path (e.g., "/home/user/hi.txt"). When [size] is 0, the size of the file will be determined automatically. In the future, this parameter could represent an HDF5 dataset using a different schema (e.g., "hdf5::/[dataset-group1]/[dataset-name1]").'}),"\n",(0,a.jsx)(t.p,{children:"An example of a typical stage-in / stage-out workflow is as follows:"}),"\n",(0,a.jsx)(t.pre,{children:(0,a.jsx)(t.code,{className:"language-bash",children:'# Create a 4GB file (1GB / proc)\nmpirun -n 4 ior -w -k -b 1048576 -o /tmp/hi.txt\n# Start the Hermes Daemon\nmpirun -n 1 ${HERMES_INSTALL}/hermes_daemon\n# Stage-in the entire 4GB file\nmpirun -n 4 ${HERMES_INSTALL}/stage_in /tmp/hi.txt 0 0 kRoundRobin\n# Read the 4GB file in IOR\nmpirun -n 4 \\\n-genv HERMES_CONF=${HERMES_CONF} \\\n-genv LD_PRELOAD "${HERMES_INSTALL}/libhermes_posix.so" \\\n-genv HERMES_STOP_DAEMON 0 \\\n-genv ADAPTER_MODE WORKFLOW \\\n-genv HERMES_CLIENT 1 \\\n-genv HERMES_PAGE_SIZE 1048576 \\\nior -r -b 1048576 -o /tmp/hi.txt\n# Stage the file back out\nmpirun -n 4 ${HERMES_INSTALL/stage_out /tmp/hi.txt\n'})}),"\n",(0,a.jsx)(t.h2,{id:"native-api",children:"Native API"}),"\n",(0,a.jsx)(t.p,{children:"Stage-in / stage-out can also be applied in a native Hermes program."}),"\n",(0,a.jsx)(t.pre,{children:(0,a.jsx)(t.code,{className:"language-cpp",children:"#include <hermes/staging.h>\n\nint main(int argc, char **argv) {\n  auto stager = DataStagerFactory::Get(url);\n  stager->StageIn(url, PlacementEngine::kRoundRobin);\n  stager->StageOut(url);\n}\n"})})]})}function u(e={}){const{wrapper:t}={...(0,i.a)(),...e.components};return t?(0,a.jsx)(t,{...e,children:(0,a.jsx)(d,{...e})}):d(e)}},1151:(e,t,n)=>{n.d(t,{Z:()=>o,a:()=>r});var a=n(7294);const i={},s=a.createContext(i);function r(e){const t=a.useContext(s);return a.useMemo((function(){return"function"==typeof e?e(t):{...t,...e}}),[t,e])}function o(e){let t;return t=e.disableParentContext?"function"==typeof e.components?e.components(i):e.components||i:r(e.components),a.createElement(s.Provider,{value:t},e.children)}}}]);
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diff --git a/assets/js/cdffcd68.b5e363ec.js b/assets/js/cdffcd68.b5e363ec.js
new file mode 100644
index 00000000..4c522074
--- /dev/null
+++ b/assets/js/cdffcd68.b5e363ec.js
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+"use strict";(self.webpackChunkgrc=self.webpackChunkgrc||[]).push([[9513],{1684:(e,s,n)=>{n.r(s),n.d(s,{assets:()=>o,contentTitle:()=>a,default:()=>h,frontMatter:()=>r,metadata:()=>c,toc:()=>d});var t=n(5893),i=n(1151);const r={},a="Adapters",c={id:"hermes/adapters",title:"Adapters",description:"Hermes Ecosystem",source:"@site/docs/03-hermes/06-adapters.md",sourceDirName:"03-hermes",slug:"/hermes/adapters",permalink:"/docs/hermes/adapters",draft:!1,unlisted:!1,tags:[],version:"current",sidebarPosition:6,frontMatter:{},sidebar:"tutorialSidebar",previous:{title:"Configuration",permalink:"/docs/hermes/configuration"},next:{title:"Programming",permalink:"/docs/hermes/programming"}},o={},d=[{value:"Filesystem Base Class (FSBC)",id:"filesystem-base-class-fsbc",level:2},{value:"Design",id:"design",level:3},{value:"VFD",id:"vfd",level:3},{value:"PubSub Adapter",id:"pubsub-adapter",level:2},{value:"Suported API",id:"suported-api",level:3},{value:"<code>connect</code>",id:"connect",level:4},{value:"<code>attach</code>",id:"attach",level:4},{value:"<code>detach</code>",id:"detach",level:4},{value:"<code>publish</code>",id:"publish",level:4},{value:"<code>subscribe</code>",id:"subscribe",level:4},{value:"Current Limitations",id:"current-limitations",level:2},{value:"Future Work",id:"future-work",level:2},{value:"References",id:"references",level:2}];function l(e){const s={a:"a",code:"code",em:"em",h1:"h1",h2:"h2",h3:"h3",h4:"h4",img:"img",li:"li",ol:"ol",p:"p",pre:"pre",ul:"ul",...(0,i.a)(),...e.components};return(0,t.jsxs)(t.Fragment,{children:[(0,t.jsx)(s.h1,{id:"adapters",children:"Adapters"}),"\n",(0,t.jsx)(s.p,{children:(0,t.jsx)(s.img,{alt:"Hermes Ecosystem",src:n(8194).Z+"",width:"522",height:"727"})}),"\n",(0,t.jsxs)(s.p,{children:["Instead of the ",(0,t.jsx)(s.a,{href:"/docs/hermes/programming",children:"Hermes primitives"}),", existing applications\nuse I/O libraries and middleware such as the C standard I/O library,\nMPI-IO, or HDF5. Since Hermes is intended to be a seamless I/O\nbuffering solution, a set of ",(0,t.jsx)(s.em,{children:"adapters"})," is provided in the form of\n",(0,t.jsx)(s.code,{children:"LD_PRELOAD"}),"-able shared libraries. These adapters perform the task of\nmapping between the application view of I/O primitives (e.g., files)\nand the Hermes primitives. An exemplary discussion of such mappings\ncan be found in ",(0,t.jsx)(s.a,{href:"http://www.cs.iit.edu/~scs/assets/files/Enosis.pdf",children:"Enosis: Bridging the Semantic Gap between File-based\nand Object-based Data Models"})," and ",(0,t.jsx)(s.a,{href:"http://www.cs.iit.edu/~scs/assets/files/Syndesis.pdf",children:"Syndesis: Mapping Objects to Files for a Unified Data Access\nSystem"}),"."]}),"\n",(0,t.jsx)(s.p,{children:"Another important task of Hermes adapters is to collect I/O profiling\nthat supports the detection of I/O patterns."}),"\n",(0,t.jsx)(s.h2,{id:"filesystem-base-class-fsbc",children:"Filesystem Base Class (FSBC)"}),"\n",(0,t.jsx)(s.p,{children:"The Filesystem Base Class (FSBC) is used by all filesystem-based APIs. This\nincludes STDIO, POSIX, and MPIIO. The FSBC implements all necessary APIs for\nbuffering files within Hermes."}),"\n",(0,t.jsx)(s.p,{children:"The FSBC provides basic filesystem overrides, including:"}),"\n",(0,t.jsxs)(s.ul,{children:["\n",(0,t.jsx)(s.li,{children:"Opening a file"}),"\n",(0,t.jsx)(s.li,{children:"Writing to a file"}),"\n",(0,t.jsx)(s.li,{children:"Reading from a file"}),"\n",(0,t.jsx)(s.li,{children:"Getting the size of a file"}),"\n",(0,t.jsx)(s.li,{children:"Removing a file"}),"\n"]}),"\n",(0,t.jsx)(s.p,{children:"Currently, we have four filesystem adapters:"}),"\n",(0,t.jsxs)(s.ol,{children:["\n",(0,t.jsx)(s.li,{children:"STDIO"}),"\n",(0,t.jsx)(s.li,{children:"POSIX"}),"\n",(0,t.jsx)(s.li,{children:"MPI-IO"}),"\n",(0,t.jsx)(s.li,{children:"HDF5 VFD"}),"\n"]}),"\n",(0,t.jsx)(s.h3,{id:"design",children:"Design"}),"\n",(0,t.jsx)(s.p,{children:"When reading/writing to a file, the FSBC will divide the I/O request into\nfixed-size pages. This is a configurable value, but the default is 1MB."}),"\n",(0,t.jsx)(s.p,{children:"As opposed to locking, Hermes uses queuing to ensure that I/O to the same regions\nof a file are strongly consistent. I/O to the same blob will be placed in the\nsame queue, ensuring sequencing."}),"\n",(0,t.jsx)(s.h3,{id:"vfd",children:"VFD"}),"\n",(0,t.jsx)(s.p,{children:"The HDF5 VFD is used to interface HDF5 with Hermes natively. To use the Hermes\nVFD in HDF5, you must define the following environment variables:"}),"\n",(0,t.jsx)(s.pre,{children:(0,t.jsx)(s.code,{className:"language-bash",children:"export HDF5_PLUGIN_PATH=/path/to/hermes/lib\nexport HDF5_DRIVER=hdf5_hermes_vfd\n"})}),"\n",(0,t.jsx)(s.p,{children:"HDF5_PLUGIN_PATH indicates the directory to search for the HDF5_DRIVER. In\nthis case, HDF5 will search for libhdf5_hermes_vfd.so."}),"\n",(0,t.jsx)(s.h2,{id:"pubsub-adapter",children:"PubSub Adapter"}),"\n",(0,t.jsx)(s.p,{children:"The PubSub adapter for Hermes stands a bit different from other adapters due to the diverse nature of pub/sub APIs on the market. For example, here are two examples of starting programs for two different queue/broker systems."}),"\n",(0,t.jsx)(s.p,{children:"A simple example of, one of, the ZeroMQ C++ API."}),"\n",(0,t.jsx)(s.pre,{children:(0,t.jsx)(s.code,{className:"language-cpp",children:'#include <string>\n#include <zmq.hpp>\nint main()\n{\n   zmq::context_t ctx;\n   zmq::socket_t sock(ctx, zmq::socket_type::push);\n   sock.bind("inproc://test");\n   const std::string_view m = "Hello, world";\n   sock.send(zmq::buffer(m), zmq::send_flags::dontwait);\n}\n'})}),"\n",(0,t.jsx)(s.p,{children:"And an example of the Kafka C++ API."}),"\n",(0,t.jsx)(s.pre,{children:(0,t.jsx)(s.code,{className:"language-cpp",children:'#include "kafka/KafkaProducer.h"\n#include <iostream>\n#include <string>\nint main(int argc, char **argv)\n{\n  std::string brokers = argv[1];\n  kafka::Topic topic  = argv[2];\n  string line\'\n\n  kafka::Properties props({\n    {"bootstrap.servers", brokers},\n    {"enable.idempotence", "true"},\n  });\n  kafka::KafkaSyncProducer producer(props);\n  std::cin >> line;\n  auto record = kafka::ProducerRecord(topic, kafka::NullKey, kafka::Value(line.c_str(), line.size()));\n  kafka::Producer::RecordMetadata metadata = producer.send(record);\n}\n'})}),"\n",(0,t.jsx)(s.p,{children:"Both examples highlight the diversity of APIs present on the pub/sub market.\nAs such, the adapter API is intended to present a common and sharable lower interface to Hermes to which all other used API can be intercepted and redirected."}),"\n",(0,t.jsx)(s.h3,{id:"suported-api",children:"Suported API"}),"\n",(0,t.jsxs)(s.p,{children:["In all functions ",(0,t.jsx)(s.code,{children:"hapi"})," stands for objects under the ",(0,t.jsx)(s.code,{children:"hermes::api"})," namespace."]}),"\n",(0,t.jsx)(s.h4,{id:"connect",children:(0,t.jsx)(s.code,{children:"connect"})}),"\n",(0,t.jsx)(s.pre,{children:(0,t.jsx)(s.code,{className:"language-cpp",children:"hapi::Status connect(const std::string &config_file);\nhapi::Status connect();\n    - Connects to the Hermes instance\n    - One option accepts, config_file: Path to the config file of Hermes\n    - The other, assumes that path is loaded into an environment variable defined in constants.h under kHermesConf\n"})}),"\n",(0,t.jsx)(s.h4,{id:"attach",children:(0,t.jsx)(s.code,{children:"attach"})}),"\n",(0,t.jsx)(s.pre,{children:(0,t.jsx)(s.code,{className:"language-cpp",children:"hapi::Status attach(const std::string& topic);\n    - Attaches to a topic, creating it if it doesn't exist\n    - topic: The name of the topic\n"})}),"\n",(0,t.jsx)(s.h4,{id:"detach",children:(0,t.jsx)(s.code,{children:"detach"})}),"\n",(0,t.jsx)(s.pre,{children:(0,t.jsx)(s.code,{className:"language-cpp",children:"hapi::Status detach(const std::string& topic);\n    - Detaches from the topic cleaning up all client-local metadata\n    - topic: The name of the topic\n    - Note, detaching doesn't delete the topic\n"})}),"\n",(0,t.jsx)(s.h4,{id:"publish",children:(0,t.jsx)(s.code,{children:"publish"})}),"\n",(0,t.jsx)(s.pre,{children:(0,t.jsx)(s.code,{className:"language-cpp",children:"hapi::Status publish(const std::string& topic,  const std::vector<unsigned char>& message);\n    - Puts a message to a topic\n    - topic: The name of the topic\n    - message: the data buffer\n    - Note, the function uses std::vector<unsigned char> which is equivalent to hermes::api::Blob\n"})}),"\n",(0,t.jsx)(s.h4,{id:"subscribe",children:(0,t.jsx)(s.code,{children:"subscribe"})}),"\n",(0,t.jsx)(s.pre,{children:(0,t.jsx)(s.code,{className:"language-cpp",children:" std::pair<std::vector<unsigned char>, hapi::Status> subscribe( const std::string& topic);\n    - Retrieves the next message from the topic\n    - topic: The name of the topic\n    - returns: a pair of the return code/status and, if successful, the subscribed message.\n"})}),"\n",(0,t.jsx)(s.h2,{id:"current-limitations",children:"Current Limitations"}),"\n",(0,t.jsxs)(s.ul,{children:["\n",(0,t.jsx)(s.li,{children:"Currently on Hermes, Blob deletions causes the latest Blob to be placed in it's place, this is intended to save memory space and provide an O(1) deletion complexity. Nevertheless, this destroys the ordering of messages expected but the pub/sub API, as such, message/Blob deletions is not possible, currently."}),"\n",(0,t.jsx)(s.li,{children:"Multi-threaded support of the API has not been fully tested. All tests have been performed under multi-process, MPI-driven tests."}),"\n"]}),"\n",(0,t.jsx)(s.h2,{id:"future-work",children:"Future Work"}),"\n",(0,t.jsxs)(s.ul,{children:["\n",(0,t.jsx)(s.li,{children:"Current work is being focused in expanding the library to support the use of traits to support in-transit transformations of the data"}),"\n"]}),"\n",(0,t.jsx)(s.h2,{id:"references",children:"References"}),"\n",(0,t.jsxs)(s.ul,{children:["\n",(0,t.jsx)(s.li,{children:(0,t.jsx)(s.a,{href:"https://github.com/LLNL/GOTCHA",children:"GOTCHA is a library for wrapping function calls in shared libraries"})}),"\n"]})]})}function h(e={}){const{wrapper:s}={...(0,i.a)(),...e.components};return s?(0,t.jsx)(s,{...e,children:(0,t.jsx)(l,{...e})}):l(e)}},8194:(e,s,n)=>{n.d(s,{Z:()=>t});const t=n.p+"assets/images/Hermes_Ecosystem-bcc2b31f697fea047fc773fbf10d2dbb.jpg"},1151:(e,s,n)=>{n.d(s,{Z:()=>c,a:()=>a});var t=n(7294);const i={},r=t.createContext(i);function a(e){const s=t.useContext(r);return t.useMemo((function(){return"function"==typeof e?e(s):{...s,...e}}),[s,e])}function c(e){let s;return s=e.disableParentContext?"function"==typeof e.components?e.components(i):e.components||i:a(e.components),t.createElement(r.Provider,{value:s},e.children)}}}]);
\ No newline at end of file
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-"use strict";(self.webpackChunkgrc=self.webpackChunkgrc||[]).push([[5429],{6304:(e,n,i)=>{i.r(n),i.d(n,{assets:()=>o,contentTitle:()=>l,default:()=>h,frontMatter:()=>a,metadata:()=>r,toc:()=>c});var s=i(5893),t=i(1151);const a={},l="Data Placement",r={id:"hermes/components/data-placement",title:"Data Placement",description:"Every Hermes system instance includes one or more Hermes nodes.",source:"@site/docs/03-hermes/06-components/04-data-placement.md",sourceDirName:"03-hermes/06-components",slug:"/hermes/components/data-placement",permalink:"/docs/hermes/components/data-placement",draft:!1,unlisted:!1,tags:[],version:"current",sidebarPosition:4,frontMatter:{},sidebar:"tutorialSidebar",previous:{title:"Buffering Target",permalink:"/docs/hermes/components/buffering-target"},next:{title:"Data Staging",permalink:"/docs/hermes/components/data-staging"}},o={},c=[{value:"The Data Placement Problem",id:"the-data-placement-problem",level:2},{value:"The Data Placement Loop",id:"the-data-placement-loop",level:2},{value:"Problem to Solve in DPE",id:"problem-to-solve-in-dpe",level:2},{value:"Data Placement Solution",id:"data-placement-solution",level:2},{value:"Error Handling",id:"error-handling",level:3},{value:"Data Placement Solution Implementation",id:"data-placement-solution-implementation",level:2},{value:"Experimental Setup",id:"experimental-setup",level:2},{value:"Experimental Results",id:"experimental-results",level:2},{value:"Conclusions",id:"conclusions",level:2}];function d(e){const n={code:"code",em:"em",h1:"h1",h2:"h2",h3:"h3",img:"img",li:"li",ol:"ol",p:"p",strong:"strong",ul:"ul",...(0,t.a)(),...e.components};return(0,s.jsxs)(s.Fragment,{children:[(0,s.jsx)(n.h1,{id:"data-placement",children:"Data Placement"}),"\n",(0,s.jsxs)(n.p,{children:["Every Hermes system instance includes one or more Hermes ",(0,s.jsx)(n.em,{children:"nodes"}),"."]}),"\n",(0,s.jsxs)(n.p,{children:["A ",(0,s.jsx)(n.em,{children:"destination"}),' is a buffering resource that can be identified by a pair\nof node + target "coordinates."']}),"\n",(0,s.jsxs)(n.p,{children:["Each target $",(0,s.jsx)(n.code,{children:"t_k"}),"$ has characteristics such as the following:"]}),"\n",(0,s.jsxs)(n.ul,{children:["\n",(0,s.jsxs)(n.li,{children:["A capacity $",(0,s.jsx)(n.code,{children:"Cap[t_k]"}),"$"]}),"\n",(0,s.jsxs)(n.li,{children:["A remaining capacity $",(0,s.jsx)(n.code,{children:"Rem[t_k]"}),"$"]}),"\n",(0,s.jsxs)(n.li,{children:["A speed (or throughput) $",(0,s.jsx)(n.code,{children:"Speed[...,t_k]"}),"$","\n",(0,s.jsxs)(n.ul,{children:["\n",(0,s.jsx)(n.li,{children:"This is the mean of the throughputs of all ranks associated with\nthe destination's node."}),"\n",(0,s.jsxs)(n.li,{children:[(0,s.jsx)(n.strong,{children:"Fix this!"})," Speed is really a function of the origin."]}),"\n"]}),"\n"]}),"\n"]}),"\n",(0,s.jsxs)(n.p,{children:[(0,s.jsx)(n.strong,{children:"Note:"})," At any point in time, there's a degree of ",(0,s.jsx)(n.em,{children:"uncertainty"})," to\nsome of the destination characteristics. For example, the remaining\ncapacity of a destination is typically obtained from a global metadata (MD)\nstructure that is updated asynchronously. Only the Hermes node buffer\npool managers have the precise value(s) for the pool under their\nmanagement."]}),"\n",(0,s.jsx)(n.h2,{id:"the-data-placement-problem",children:"The Data Placement Problem"}),"\n",(0,s.jsxs)(n.p,{children:["Given ",(0,s.jsx)(n.em,{children:"N"})," storage targets, a data placement policy ",(0,s.jsx)(n.em,{children:"P"}),", a cost function ",(0,s.jsx)(n.em,{children:"F"}),", and a ",(0,s.jsx)(n.em,{children:"BLOB"}),",\na data placement consists of a BLOB partitioning and an assignment of those parts to storage targets\nthat satisfies the constraints of the data placement policy and that minimizes the cost function."]}),"\n",(0,s.jsxs)(n.ul,{children:["\n",(0,s.jsxs)(n.li,{children:["Epoch - interval within which we update targets (status).","\n",(0,s.jsxs)(n.ul,{children:["\n",(0,s.jsx)(n.li,{children:"Static (e.g., time interval or number of operations)"}),"\n",(0,s.jsx)(n.li,{children:"Dynamic, i.e., computed by the delta of status"}),"\n"]}),"\n"]}),"\n"]}),"\n",(0,s.jsx)(n.p,{children:"[optional] Placement window - interval within which we make data\nplacement decisions."}),"\n",(0,s.jsxs)(n.ul,{children:["\n",(0,s.jsx)(n.li,{children:"Timer expired or I/O operation count reached, which ever comes\nfirst."}),"\n",(0,s.jsx)(n.li,{children:"Static (e.g., time interval or number of operations)"}),"\n",(0,s.jsx)(n.li,{children:"Dynamic, i.e., number of put operations"}),"\n"]}),"\n",(0,s.jsx)(n.p,{children:"Epoch and placement window could be aligned (static mode)."}),"\n",(0,s.jsx)(n.p,{children:"The data placement is done within Data Placement Engine (DPE) component\nin HERMES."}),"\n",(0,s.jsx)(n.h2,{id:"the-data-placement-loop",children:"The Data Placement Loop"}),"\n",(0,s.jsxs)(n.p,{children:["A ",(0,s.jsx)(n.em,{children:"placement schema"})," $",(0,s.jsx)(n.code,{children:"PS(b)"}),"$ of a BLOB $",(0,s.jsx)(n.code,{children:"b (>0)"}),"$ is a decomposition\n$",(0,s.jsx)(n.code,{children:"b = s_1+\\cdots+s_k,\\; s_i\\in\\mathbb{N}\\setminus\\{0\\}"}),"$ together with a\ntarget mapping $",(0,s.jsx)(n.code,{children:"(s_1,\\ldots,s_k)\\mapsto(t_1(s_1),\\ldots,t_k(s_k))"}),"$."]}),"\n",(0,s.jsxs)(n.p,{children:["A sequence of buffer IDs $",(0,s.jsx)(n.code,{children:"(ID_1,\\ldots,ID_A)"}),"$ ",(0,s.jsx)(n.em,{children:"conforms"})," to a target\nassignment $",(0,s.jsx)(n.code,{children:"(s, t)"}),"$, iff $",(0,s.jsx)(n.code,{children:"s = \\sum_{i=1}^A Size(ID_i)"}),"$ and\n$",(0,s.jsx)(n.code,{children:"\\forall i\\;Target(ID_i) = t"}),"$."]}),"\n",(0,s.jsxs)(n.p,{children:["An ",(0,s.jsx)(n.em,{children:"allocation of a placement schema"})," is a sequence of buffer IDs which\nis the concatenation of conforming target assignments."]}),"\n",(0,s.jsxs)(n.ol,{children:["\n",(0,s.jsxs)(n.li,{children:["Given: a vector of BLOBs $",(0,s.jsx)(n.code,{children:"(b_1, b_2,\\ldots, b_B)"}),"$"]}),"\n",(0,s.jsxs)(n.li,{children:["The DPE creates placement schemas $",(0,s.jsx)(n.code,{children:"PS(b_i),\\;1\\leq i\\leq B"}),"$."]}),"\n",(0,s.jsx)(n.li,{children:"The placement schemas are presented to the buffer manager, which,\nfor each placement schema, returns an allocation of that schema (or\nan error), and updates the underlying metadata structures."}),"\n",(0,s.jsx)(n.li,{children:"I/O clients transfer data from the BLOBs to the buffers."}),"\n"]}),"\n",(0,s.jsx)(n.h2,{id:"problem-to-solve-in-dpe",children:"Problem to Solve in DPE"}),"\n",(0,s.jsx)(n.p,{children:"Input:"}),"\n",(0,s.jsxs)(n.ul,{children:["\n",(0,s.jsxs)(n.li,{children:["Vector of BLOBs $",(0,s.jsx)(n.code,{children:"(b_1, b_2,\\ldots, b_B)"}),"$."]}),"\n",(0,s.jsxs)(n.li,{children:["Vector of targets $",(0,s.jsx)(n.code,{children:"(t_1, t_2,\\ldots, t_D)"}),"$."]}),"\n",(0,s.jsxs)(n.li,{children:["Vector of target remaining capacities $",(0,s.jsx)(n.code,{children:"Rem[t_k], \\;1\\leq k\\leq D"}),"$."]}),"\n",(0,s.jsxs)(n.li,{children:["Vector of target speed $",(0,s.jsx)(n.code,{children:"Speed[t_k], \\;1\\leq k\\leq D"}),"$."]}),"\n"]}),"\n",(0,s.jsx)(n.p,{children:"Output:"}),"\n",(0,s.jsxs)(n.ul,{children:["\n",(0,s.jsxs)(n.li,{children:["Placement schema\n$",(0,s.jsx)(n.code,{children:"(s_1,\\ldots,s_k)\\mapsto(t_1(s_1),\\ldots,t_k(s_k))"}),"$, where\n$",(0,s.jsx)(n.code,{children:"b (>0)"}),"$ is a decomposition\n$",(0,s.jsx)(n.code,{children:"b = s_1+\\cdots+s_k,\\; s_i\\in\\mathbb{N}\\setminus\\{0\\}"}),"$"]}),"\n"]}),"\n",(0,s.jsx)(n.h2,{id:"data-placement-solution",children:"Data Placement Solution"}),"\n",(0,s.jsxs)(n.ol,{children:["\n",(0,s.jsxs)(n.li,{children:["Pick a DP solver to obtain a ",(0,s.jsx)(n.em,{children:"placement schema"}),".","\n",(0,s.jsxs)(n.ul,{children:["\n",(0,s.jsxs)(n.li,{children:["Linear programming","\n",(0,s.jsxs)(n.ul,{children:["\n",(0,s.jsx)(n.li,{children:"Constraints"}),"\n",(0,s.jsx)(n.li,{children:"Objective function"}),"\n"]}),"\n"]}),"\n",(0,s.jsxs)(n.li,{children:["Round-robin","\n",(0,s.jsxs)(n.ul,{children:["\n",(0,s.jsx)(n.li,{children:"Granularity"}),"\n"]}),"\n"]}),"\n",(0,s.jsxs)(n.li,{children:["Random","\n",(0,s.jsxs)(n.ul,{children:["\n",(0,s.jsx)(n.li,{children:"Distribution(s)"}),"\n"]}),"\n"]}),"\n"]}),"\n"]}),"\n",(0,s.jsx)(n.li,{children:'Use the buffer pool\'s "coin selector" to convert into buffer IDs.'}),"\n",(0,s.jsxs)(n.li,{children:["Handle two types of potential errors.","\n",(0,s.jsxs)(n.ul,{children:["\n",(0,s.jsxs)(n.li,{children:["DP solver failure: This can happen because of outdated target\nstatus, i.e., insufficient capacity, constraint infeasibility,\netc.","\n",(0,s.jsxs)(n.ul,{children:["\n",(0,s.jsx)(n.li,{children:"Solution to insufficient capacity: epoch, decision windows,\nswap space."}),"\n",(0,s.jsx)(n.li,{children:"Solution to constraint infeasibility: buffer reorganization,\ntarget filtering."}),"\n"]}),"\n"]}),"\n",(0,s.jsxs)(n.li,{children:["Coin selection failure: This can happen because of outdated\nstate view information, e.g., outdated remaining capacities.","\n",(0,s.jsxs)(n.ul,{children:["\n",(0,s.jsx)(n.li,{children:"Solution: epoch, decision windows, swap space."}),"\n"]}),"\n"]}),"\n"]}),"\n"]}),"\n"]}),"\n",(0,s.jsx)(n.h3,{id:"error-handling",children:"Error Handling"}),"\n",(0,s.jsx)(n.p,{children:"In both cases, the list of targets is inappropriate and needs to be\nupdated or changed."}),"\n",(0,s.jsxs)(n.p,{children:['The list of "relevant destinations" for a rank is assembled by the\nHermes node ',(0,s.jsx)(n.em,{children:"topology generator"}),'. It gets triggered when DP fails. The\ninitial topology consists of "node-local" destinations (Plan A) plus a\nbackup list of neighbors (Plan B) to consult when a rank gets in\ntrouble. If both plans fail, the topology generator invokes the\n',(0,s.jsx)(n.em,{children:"application-level"}),' "rebalancer" to redraw neighborhood boundaries\n(Plan C). In the past, we used to call these components node- and\napplication-level DPEs, but they aren\'t directly involved in DP\ndecisions, and we need maybe a clearer terminology.']}),"\n",(0,s.jsx)(n.h2,{id:"data-placement-solution-implementation",children:"Data Placement Solution Implementation"}),"\n",(0,s.jsx)(n.p,{children:"LP solver"}),"\n",(0,s.jsxs)(n.ul,{children:["\n",(0,s.jsxs)(n.li,{children:["Pick Google OR-Tools as a linear optimization tool to obtain\na\xa0",(0,s.jsx)(n.em,{children:"placement schema"}),".","\n",(0,s.jsxs)(n.ul,{children:["\n",(0,s.jsx)(n.li,{children:"Minimize client I/O time."}),"\n"]}),"\n"]}),"\n"]}),"\n",(0,s.jsx)(n.p,{children:"Round-robin solver"}),"\n",(0,s.jsxs)(n.ul,{children:["\n",(0,s.jsxs)(n.li,{children:["Pick the next ",(0,s.jsx)(n.em,{children:"target"})," if the remaining capacity is greater or equal\nto the BLOB size, otherwise check the one after the next target\nuntil a target with enough capacity is found."]}),"\n"]}),"\n",(0,s.jsx)(n.p,{children:"Random solver"}),"\n",(0,s.jsxs)(n.ul,{children:["\n",(0,s.jsx)(n.li,{children:"Randomly pick a target from all targets which have the capacity\ngreater or equal to the BLOB size."}),"\n"]}),"\n",(0,s.jsx)(n.h2,{id:"experimental-setup",children:"Experimental Setup"}),"\n",(0,s.jsx)(n.p,{children:"Scaling the number of BLOBs, 10 GB total BLOB size"}),"\n",(0,s.jsxs)(n.ul,{children:["\n",(0,s.jsx)(n.li,{children:"Small size BLOBs: random within the range of 4KB to 64KB"}),"\n",(0,s.jsx)(n.li,{children:"Medium size BLOBs: random within the range of 64KB to 1MB"}),"\n",(0,s.jsx)(n.li,{children:"Large size BLOBs: random within the range of 1MB to 4MB"}),"\n",(0,s.jsx)(n.li,{children:"Extra large size BLOBs: random with the range 4MB to 64MB"}),"\n",(0,s.jsx)(n.li,{children:"Huge size BLOBs: fixed 1GB"}),"\n"]}),"\n",(0,s.jsx)(n.p,{children:"Scaling the BLOB size, 1,000 and 8,192 BLOBs in total"}),"\n",(0,s.jsxs)(n.ul,{children:["\n",(0,s.jsx)(n.li,{children:"Fixed BLOB size of 4KB, 64KB, 1MB, 4MB, 64MB"}),"\n"]}),"\n",(0,s.jsx)(n.h2,{id:"experimental-results",children:"Experimental Results"}),"\n",(0,s.jsx)(n.p,{children:"The DPE time of three different solvers with 10GB BLOBs in total."}),"\n",(0,s.jsx)(n.p,{children:(0,s.jsx)(n.img,{src:i(5990).Z+"",width:"360",height:"216"})}),"\n",(0,s.jsx)(n.p,{children:(0,s.jsx)(n.img,{src:i(2593).Z+"",width:"360",height:"216"})}),"\n",(0,s.jsx)(n.p,{children:(0,s.jsx)(n.img,{src:i(5935).Z+"",width:"360",height:"216"})}),"\n",(0,s.jsx)(n.p,{children:"The associated I/O time of placement schema from three different solvers\nwith 10GB BLOBs in total."}),"\n",(0,s.jsx)(n.p,{children:(0,s.jsx)(n.img,{src:i(5140).Z+"",width:"360",height:"216"})}),"\n",(0,s.jsx)(n.p,{children:(0,s.jsx)(n.img,{src:i(5135).Z+"",width:"360",height:"216"})}),"\n",(0,s.jsx)(n.p,{children:(0,s.jsx)(n.img,{src:i(4307).Z+"",width:"360",height:"216"})}),"\n",(0,s.jsx)(n.p,{children:"The DPE time of three different solvers with 1,000 BLOBs in total."}),"\n",(0,s.jsx)(n.p,{children:(0,s.jsx)(n.img,{src:i(2838).Z+"",width:"360",height:"216"})}),"\n",(0,s.jsx)(n.p,{children:(0,s.jsx)(n.img,{src:i(1163).Z+"",width:"360",height:"216"})}),"\n",(0,s.jsx)(n.p,{children:(0,s.jsx)(n.img,{src:i(9017).Z+"",width:"360",height:"216"})}),"\n",(0,s.jsx)(n.p,{children:"The associated I/O time by placement schema by three different solvers\nwith 1,000 BLOBs in total."}),"\n",(0,s.jsx)(n.p,{children:(0,s.jsx)(n.img,{src:i(334).Z+"",width:"360",height:"216"})}),"\n",(0,s.jsx)(n.p,{children:(0,s.jsx)(n.img,{src:i(6996).Z+"",width:"360",height:"216"})}),"\n",(0,s.jsx)(n.p,{children:(0,s.jsx)(n.img,{src:i(4065).Z+"",width:"360",height:"216"})}),"\n",(0,s.jsx)(n.h2,{id:"conclusions",children:"Conclusions"}),"\n",(0,s.jsx)(n.p,{children:"For a fixed total size of many BLOBs, DPE time is increasing with the\nnumber of BLOBs for all solvers."}),"\n",(0,s.jsx)(n.p,{children:"Round-robin and random solver can quickly calculate targets for a BLOB\nthan LP solver, while not considering optimizing I/O time."}),"\n",(0,s.jsx)(n.p,{children:"LP solver is efficient when the search space (number of targets) is not\ntoo large (for example, less than 1,024)."}),"\n",(0,s.jsx)(n.p,{children:"LP solver is a good candidate to place large size BLOBs, where the DPE\ntime has less impact than the I/O time to the overall performance."}),"\n",(0,s.jsx)(n.p,{children:"One of the possible policies is that size 64KB could be a boundary for\nBLOB aggregation. BLOB size less than 64KB will be aggregated within a\nplacement window and than placed together to mitigate DPE impact."}),"\n",(0,s.jsx)(n.p,{children:"Another possible policy is to use round-robin or random for small blobs\nand LP solver for large blobs."})]})}function h(e={}){const{wrapper:n}={...(0,t.a)(),...e.components};return n?(0,s.jsx)(n,{...e,children:(0,s.jsx)(d,{...e})}):d(e)}},5990:(e,n,i)=>{i.d(n,{Z:()=>s});const s=i.p+"assets/images/Picture1_11-39073f55ead305e54d26b2b807186055.jpg"},2593:(e,n,i)=>{i.d(n,{Z:()=>s});const s=i.p+"assets/images/Picture2_1-f69c2af98fae3901d36a25d21d472764.jpg"},5935:(e,n,i)=>{i.d(n,{Z:()=>s});const s=i.p+"assets/images/Picture3_1-39a88339cbe63ca25ee0724ee6299d49.jpg"},4307:(e,n,i)=>{i.d(n,{Z:()=>s});const s=i.p+"assets/images/Picture4_1-bdcb34596dad2684fa7489a9f7f6fe79.jpg"},5135:(e,n,i)=>{i.d(n,{Z:()=>s});const s=i.p+"assets/images/Picture5_1-7b8f1d4f1bc3d69d054d170c0f451bc6.jpg"},5140:(e,n,i)=>{i.d(n,{Z:()=>s});const s=i.p+"assets/images/Picture6_1-7d429d3b8b75eaaa90a68ec6e0cd8692.jpg"},9017:(e,n,i)=>{i.d(n,{Z:()=>s});const s=i.p+"assets/images/or_dpe-ff86d9273ff956678a5c2bff993bda19.jpg"},4065:(e,n,i)=>{i.d(n,{Z:()=>s});const s=i.p+"assets/images/ortools_io-2cba299e1b353b03c824eb11a917648f.jpg"},1163:(e,n,i)=>{i.d(n,{Z:()=>s});const s=i.p+"assets/images/random_dpe-11c7b726ae0dc701735a1e96486d1d1e.jpg"},6996:(e,n,i)=>{i.d(n,{Z:()=>s});const s=i.p+"assets/images/random_io-e4637d3689e4881e30360ebf78458381.jpg"},2838:(e,n,i)=>{i.d(n,{Z:()=>s});const s=i.p+"assets/images/rr_dpe-ced03cee3e9901af631e3114a92b44f0.jpg"},334:(e,n,i)=>{i.d(n,{Z:()=>s});const s=i.p+"assets/images/rr_io-e0ca102ee0c5e9e2e15303dcb58c11a1.jpg"},1151:(e,n,i)=>{i.d(n,{Z:()=>r,a:()=>l});var s=i(7294);const t={},a=s.createContext(t);function l(e){const n=s.useContext(a);return s.useMemo((function(){return"function"==typeof e?e(n):{...n,...e}}),[n,e])}function r(e){let n;return n=e.disableParentContext?"function"==typeof e.components?e.components(t):e.components||t:l(e.components),s.createElement(a.Provider,{value:n},e.children)}}}]);
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+"use strict";(self.webpackChunkgrc=self.webpackChunkgrc||[]).push([[9905],{8763:(e,n,i)=>{i.r(n),i.d(n,{assets:()=>o,contentTitle:()=>l,default:()=>h,frontMatter:()=>a,metadata:()=>r,toc:()=>c});var s=i(5893),t=i(1151);const a={},l="Data Placement",r={id:"hermes/components/data-placement",title:"Data Placement",description:"Every Hermes system instance includes one or more Hermes nodes.",source:"@site/docs/03-hermes/08-components/04-data-placement.md",sourceDirName:"03-hermes/08-components",slug:"/hermes/components/data-placement",permalink:"/docs/hermes/components/data-placement",draft:!1,unlisted:!1,tags:[],version:"current",sidebarPosition:4,frontMatter:{},sidebar:"tutorialSidebar",previous:{title:"Buffering Target",permalink:"/docs/hermes/components/buffering-target"},next:{title:"Data Staging",permalink:"/docs/hermes/components/data-staging"}},o={},c=[{value:"The Data Placement Problem",id:"the-data-placement-problem",level:2},{value:"The Data Placement Loop",id:"the-data-placement-loop",level:2},{value:"Problem to Solve in DPE",id:"problem-to-solve-in-dpe",level:2},{value:"Data Placement Solution",id:"data-placement-solution",level:2},{value:"Error Handling",id:"error-handling",level:3},{value:"Data Placement Solution Implementation",id:"data-placement-solution-implementation",level:2},{value:"Experimental Setup",id:"experimental-setup",level:2},{value:"Experimental Results",id:"experimental-results",level:2},{value:"Conclusions",id:"conclusions",level:2}];function d(e){const n={code:"code",em:"em",h1:"h1",h2:"h2",h3:"h3",img:"img",li:"li",ol:"ol",p:"p",strong:"strong",ul:"ul",...(0,t.a)(),...e.components};return(0,s.jsxs)(s.Fragment,{children:[(0,s.jsx)(n.h1,{id:"data-placement",children:"Data Placement"}),"\n",(0,s.jsxs)(n.p,{children:["Every Hermes system instance includes one or more Hermes ",(0,s.jsx)(n.em,{children:"nodes"}),"."]}),"\n",(0,s.jsxs)(n.p,{children:["A ",(0,s.jsx)(n.em,{children:"destination"}),' is a buffering resource that can be identified by a pair\nof node + target "coordinates."']}),"\n",(0,s.jsxs)(n.p,{children:["Each target $",(0,s.jsx)(n.code,{children:"t_k"}),"$ has characteristics such as the following:"]}),"\n",(0,s.jsxs)(n.ul,{children:["\n",(0,s.jsxs)(n.li,{children:["A capacity $",(0,s.jsx)(n.code,{children:"Cap[t_k]"}),"$"]}),"\n",(0,s.jsxs)(n.li,{children:["A remaining capacity $",(0,s.jsx)(n.code,{children:"Rem[t_k]"}),"$"]}),"\n",(0,s.jsxs)(n.li,{children:["A speed (or throughput) $",(0,s.jsx)(n.code,{children:"Speed[...,t_k]"}),"$","\n",(0,s.jsxs)(n.ul,{children:["\n",(0,s.jsx)(n.li,{children:"This is the mean of the throughputs of all ranks associated with\nthe destination's node."}),"\n",(0,s.jsxs)(n.li,{children:[(0,s.jsx)(n.strong,{children:"Fix this!"})," Speed is really a function of the origin."]}),"\n"]}),"\n"]}),"\n"]}),"\n",(0,s.jsxs)(n.p,{children:[(0,s.jsx)(n.strong,{children:"Note:"})," At any point in time, there's a degree of ",(0,s.jsx)(n.em,{children:"uncertainty"})," to\nsome of the destination characteristics. For example, the remaining\ncapacity of a destination is typically obtained from a global metadata (MD)\nstructure that is updated asynchronously. Only the Hermes node buffer\npool managers have the precise value(s) for the pool under their\nmanagement."]}),"\n",(0,s.jsx)(n.h2,{id:"the-data-placement-problem",children:"The Data Placement Problem"}),"\n",(0,s.jsxs)(n.p,{children:["Given ",(0,s.jsx)(n.em,{children:"N"})," storage targets, a data placement policy ",(0,s.jsx)(n.em,{children:"P"}),", a cost function ",(0,s.jsx)(n.em,{children:"F"}),", and a ",(0,s.jsx)(n.em,{children:"BLOB"}),",\na data placement consists of a BLOB partitioning and an assignment of those parts to storage targets\nthat satisfies the constraints of the data placement policy and that minimizes the cost function."]}),"\n",(0,s.jsxs)(n.ul,{children:["\n",(0,s.jsxs)(n.li,{children:["Epoch - interval within which we update targets (status).","\n",(0,s.jsxs)(n.ul,{children:["\n",(0,s.jsx)(n.li,{children:"Static (e.g., time interval or number of operations)"}),"\n",(0,s.jsx)(n.li,{children:"Dynamic, i.e., computed by the delta of status"}),"\n"]}),"\n"]}),"\n"]}),"\n",(0,s.jsx)(n.p,{children:"[optional] Placement window - interval within which we make data\nplacement decisions."}),"\n",(0,s.jsxs)(n.ul,{children:["\n",(0,s.jsx)(n.li,{children:"Timer expired or I/O operation count reached, which ever comes\nfirst."}),"\n",(0,s.jsx)(n.li,{children:"Static (e.g., time interval or number of operations)"}),"\n",(0,s.jsx)(n.li,{children:"Dynamic, i.e., number of put operations"}),"\n"]}),"\n",(0,s.jsx)(n.p,{children:"Epoch and placement window could be aligned (static mode)."}),"\n",(0,s.jsx)(n.p,{children:"The data placement is done within Data Placement Engine (DPE) component\nin HERMES."}),"\n",(0,s.jsx)(n.h2,{id:"the-data-placement-loop",children:"The Data Placement Loop"}),"\n",(0,s.jsxs)(n.p,{children:["A ",(0,s.jsx)(n.em,{children:"placement schema"})," $",(0,s.jsx)(n.code,{children:"PS(b)"}),"$ of a BLOB $",(0,s.jsx)(n.code,{children:"b (>0)"}),"$ is a decomposition\n$",(0,s.jsx)(n.code,{children:"b = s_1+\\cdots+s_k,\\; s_i\\in\\mathbb{N}\\setminus\\{0\\}"}),"$ together with a\ntarget mapping $",(0,s.jsx)(n.code,{children:"(s_1,\\ldots,s_k)\\mapsto(t_1(s_1),\\ldots,t_k(s_k))"}),"$."]}),"\n",(0,s.jsxs)(n.p,{children:["A sequence of buffer IDs $",(0,s.jsx)(n.code,{children:"(ID_1,\\ldots,ID_A)"}),"$ ",(0,s.jsx)(n.em,{children:"conforms"})," to a target\nassignment $",(0,s.jsx)(n.code,{children:"(s, t)"}),"$, iff $",(0,s.jsx)(n.code,{children:"s = \\sum_{i=1}^A Size(ID_i)"}),"$ and\n$",(0,s.jsx)(n.code,{children:"\\forall i\\;Target(ID_i) = t"}),"$."]}),"\n",(0,s.jsxs)(n.p,{children:["An ",(0,s.jsx)(n.em,{children:"allocation of a placement schema"})," is a sequence of buffer IDs which\nis the concatenation of conforming target assignments."]}),"\n",(0,s.jsxs)(n.ol,{children:["\n",(0,s.jsxs)(n.li,{children:["Given: a vector of BLOBs $",(0,s.jsx)(n.code,{children:"(b_1, b_2,\\ldots, b_B)"}),"$"]}),"\n",(0,s.jsxs)(n.li,{children:["The DPE creates placement schemas $",(0,s.jsx)(n.code,{children:"PS(b_i),\\;1\\leq i\\leq B"}),"$."]}),"\n",(0,s.jsx)(n.li,{children:"The placement schemas are presented to the buffer manager, which,\nfor each placement schema, returns an allocation of that schema (or\nan error), and updates the underlying metadata structures."}),"\n",(0,s.jsx)(n.li,{children:"I/O clients transfer data from the BLOBs to the buffers."}),"\n"]}),"\n",(0,s.jsx)(n.h2,{id:"problem-to-solve-in-dpe",children:"Problem to Solve in DPE"}),"\n",(0,s.jsx)(n.p,{children:"Input:"}),"\n",(0,s.jsxs)(n.ul,{children:["\n",(0,s.jsxs)(n.li,{children:["Vector of BLOBs $",(0,s.jsx)(n.code,{children:"(b_1, b_2,\\ldots, b_B)"}),"$."]}),"\n",(0,s.jsxs)(n.li,{children:["Vector of targets $",(0,s.jsx)(n.code,{children:"(t_1, t_2,\\ldots, t_D)"}),"$."]}),"\n",(0,s.jsxs)(n.li,{children:["Vector of target remaining capacities $",(0,s.jsx)(n.code,{children:"Rem[t_k], \\;1\\leq k\\leq D"}),"$."]}),"\n",(0,s.jsxs)(n.li,{children:["Vector of target speed $",(0,s.jsx)(n.code,{children:"Speed[t_k], \\;1\\leq k\\leq D"}),"$."]}),"\n"]}),"\n",(0,s.jsx)(n.p,{children:"Output:"}),"\n",(0,s.jsxs)(n.ul,{children:["\n",(0,s.jsxs)(n.li,{children:["Placement schema\n$",(0,s.jsx)(n.code,{children:"(s_1,\\ldots,s_k)\\mapsto(t_1(s_1),\\ldots,t_k(s_k))"}),"$, where\n$",(0,s.jsx)(n.code,{children:"b (>0)"}),"$ is a decomposition\n$",(0,s.jsx)(n.code,{children:"b = s_1+\\cdots+s_k,\\; s_i\\in\\mathbb{N}\\setminus\\{0\\}"}),"$"]}),"\n"]}),"\n",(0,s.jsx)(n.h2,{id:"data-placement-solution",children:"Data Placement Solution"}),"\n",(0,s.jsxs)(n.ol,{children:["\n",(0,s.jsxs)(n.li,{children:["Pick a DP solver to obtain a ",(0,s.jsx)(n.em,{children:"placement schema"}),".","\n",(0,s.jsxs)(n.ul,{children:["\n",(0,s.jsxs)(n.li,{children:["Linear programming","\n",(0,s.jsxs)(n.ul,{children:["\n",(0,s.jsx)(n.li,{children:"Constraints"}),"\n",(0,s.jsx)(n.li,{children:"Objective function"}),"\n"]}),"\n"]}),"\n",(0,s.jsxs)(n.li,{children:["Round-robin","\n",(0,s.jsxs)(n.ul,{children:["\n",(0,s.jsx)(n.li,{children:"Granularity"}),"\n"]}),"\n"]}),"\n",(0,s.jsxs)(n.li,{children:["Random","\n",(0,s.jsxs)(n.ul,{children:["\n",(0,s.jsx)(n.li,{children:"Distribution(s)"}),"\n"]}),"\n"]}),"\n"]}),"\n"]}),"\n",(0,s.jsx)(n.li,{children:'Use the buffer pool\'s "coin selector" to convert into buffer IDs.'}),"\n",(0,s.jsxs)(n.li,{children:["Handle two types of potential errors.","\n",(0,s.jsxs)(n.ul,{children:["\n",(0,s.jsxs)(n.li,{children:["DP solver failure: This can happen because of outdated target\nstatus, i.e., insufficient capacity, constraint infeasibility,\netc.","\n",(0,s.jsxs)(n.ul,{children:["\n",(0,s.jsx)(n.li,{children:"Solution to insufficient capacity: epoch, decision windows,\nswap space."}),"\n",(0,s.jsx)(n.li,{children:"Solution to constraint infeasibility: buffer reorganization,\ntarget filtering."}),"\n"]}),"\n"]}),"\n",(0,s.jsxs)(n.li,{children:["Coin selection failure: This can happen because of outdated\nstate view information, e.g., outdated remaining capacities.","\n",(0,s.jsxs)(n.ul,{children:["\n",(0,s.jsx)(n.li,{children:"Solution: epoch, decision windows, swap space."}),"\n"]}),"\n"]}),"\n"]}),"\n"]}),"\n"]}),"\n",(0,s.jsx)(n.h3,{id:"error-handling",children:"Error Handling"}),"\n",(0,s.jsx)(n.p,{children:"In both cases, the list of targets is inappropriate and needs to be\nupdated or changed."}),"\n",(0,s.jsxs)(n.p,{children:['The list of "relevant destinations" for a rank is assembled by the\nHermes node ',(0,s.jsx)(n.em,{children:"topology generator"}),'. It gets triggered when DP fails. The\ninitial topology consists of "node-local" destinations (Plan A) plus a\nbackup list of neighbors (Plan B) to consult when a rank gets in\ntrouble. If both plans fail, the topology generator invokes the\n',(0,s.jsx)(n.em,{children:"application-level"}),' "rebalancer" to redraw neighborhood boundaries\n(Plan C). In the past, we used to call these components node- and\napplication-level DPEs, but they aren\'t directly involved in DP\ndecisions, and we need maybe a clearer terminology.']}),"\n",(0,s.jsx)(n.h2,{id:"data-placement-solution-implementation",children:"Data Placement Solution Implementation"}),"\n",(0,s.jsx)(n.p,{children:"LP solver"}),"\n",(0,s.jsxs)(n.ul,{children:["\n",(0,s.jsxs)(n.li,{children:["Pick Google OR-Tools as a linear optimization tool to obtain\na\xa0",(0,s.jsx)(n.em,{children:"placement schema"}),".","\n",(0,s.jsxs)(n.ul,{children:["\n",(0,s.jsx)(n.li,{children:"Minimize client I/O time."}),"\n"]}),"\n"]}),"\n"]}),"\n",(0,s.jsx)(n.p,{children:"Round-robin solver"}),"\n",(0,s.jsxs)(n.ul,{children:["\n",(0,s.jsxs)(n.li,{children:["Pick the next ",(0,s.jsx)(n.em,{children:"target"})," if the remaining capacity is greater or equal\nto the BLOB size, otherwise check the one after the next target\nuntil a target with enough capacity is found."]}),"\n"]}),"\n",(0,s.jsx)(n.p,{children:"Random solver"}),"\n",(0,s.jsxs)(n.ul,{children:["\n",(0,s.jsx)(n.li,{children:"Randomly pick a target from all targets which have the capacity\ngreater or equal to the BLOB size."}),"\n"]}),"\n",(0,s.jsx)(n.h2,{id:"experimental-setup",children:"Experimental Setup"}),"\n",(0,s.jsx)(n.p,{children:"Scaling the number of BLOBs, 10 GB total BLOB size"}),"\n",(0,s.jsxs)(n.ul,{children:["\n",(0,s.jsx)(n.li,{children:"Small size BLOBs: random within the range of 4KB to 64KB"}),"\n",(0,s.jsx)(n.li,{children:"Medium size BLOBs: random within the range of 64KB to 1MB"}),"\n",(0,s.jsx)(n.li,{children:"Large size BLOBs: random within the range of 1MB to 4MB"}),"\n",(0,s.jsx)(n.li,{children:"Extra large size BLOBs: random with the range 4MB to 64MB"}),"\n",(0,s.jsx)(n.li,{children:"Huge size BLOBs: fixed 1GB"}),"\n"]}),"\n",(0,s.jsx)(n.p,{children:"Scaling the BLOB size, 1,000 and 8,192 BLOBs in total"}),"\n",(0,s.jsxs)(n.ul,{children:["\n",(0,s.jsx)(n.li,{children:"Fixed BLOB size of 4KB, 64KB, 1MB, 4MB, 64MB"}),"\n"]}),"\n",(0,s.jsx)(n.h2,{id:"experimental-results",children:"Experimental Results"}),"\n",(0,s.jsx)(n.p,{children:"The DPE time of three different solvers with 10GB BLOBs in total."}),"\n",(0,s.jsx)(n.p,{children:(0,s.jsx)(n.img,{src:i(5990).Z+"",width:"360",height:"216"})}),"\n",(0,s.jsx)(n.p,{children:(0,s.jsx)(n.img,{src:i(2593).Z+"",width:"360",height:"216"})}),"\n",(0,s.jsx)(n.p,{children:(0,s.jsx)(n.img,{src:i(5935).Z+"",width:"360",height:"216"})}),"\n",(0,s.jsx)(n.p,{children:"The associated I/O time of placement schema from three different solvers\nwith 10GB BLOBs in total."}),"\n",(0,s.jsx)(n.p,{children:(0,s.jsx)(n.img,{src:i(5140).Z+"",width:"360",height:"216"})}),"\n",(0,s.jsx)(n.p,{children:(0,s.jsx)(n.img,{src:i(5135).Z+"",width:"360",height:"216"})}),"\n",(0,s.jsx)(n.p,{children:(0,s.jsx)(n.img,{src:i(4307).Z+"",width:"360",height:"216"})}),"\n",(0,s.jsx)(n.p,{children:"The DPE time of three different solvers with 1,000 BLOBs in total."}),"\n",(0,s.jsx)(n.p,{children:(0,s.jsx)(n.img,{src:i(2838).Z+"",width:"360",height:"216"})}),"\n",(0,s.jsx)(n.p,{children:(0,s.jsx)(n.img,{src:i(1163).Z+"",width:"360",height:"216"})}),"\n",(0,s.jsx)(n.p,{children:(0,s.jsx)(n.img,{src:i(9017).Z+"",width:"360",height:"216"})}),"\n",(0,s.jsx)(n.p,{children:"The associated I/O time by placement schema by three different solvers\nwith 1,000 BLOBs in total."}),"\n",(0,s.jsx)(n.p,{children:(0,s.jsx)(n.img,{src:i(334).Z+"",width:"360",height:"216"})}),"\n",(0,s.jsx)(n.p,{children:(0,s.jsx)(n.img,{src:i(6996).Z+"",width:"360",height:"216"})}),"\n",(0,s.jsx)(n.p,{children:(0,s.jsx)(n.img,{src:i(4065).Z+"",width:"360",height:"216"})}),"\n",(0,s.jsx)(n.h2,{id:"conclusions",children:"Conclusions"}),"\n",(0,s.jsx)(n.p,{children:"For a fixed total size of many BLOBs, DPE time is increasing with the\nnumber of BLOBs for all solvers."}),"\n",(0,s.jsx)(n.p,{children:"Round-robin and random solver can quickly calculate targets for a BLOB\nthan LP solver, while not considering optimizing I/O time."}),"\n",(0,s.jsx)(n.p,{children:"LP solver is efficient when the search space (number of targets) is not\ntoo large (for example, less than 1,024)."}),"\n",(0,s.jsx)(n.p,{children:"LP solver is a good candidate to place large size BLOBs, where the DPE\ntime has less impact than the I/O time to the overall performance."}),"\n",(0,s.jsx)(n.p,{children:"One of the possible policies is that size 64KB could be a boundary for\nBLOB aggregation. BLOB size less than 64KB will be aggregated within a\nplacement window and than placed together to mitigate DPE impact."}),"\n",(0,s.jsx)(n.p,{children:"Another possible policy is to use round-robin or random for small blobs\nand LP solver for large blobs."})]})}function h(e={}){const{wrapper:n}={...(0,t.a)(),...e.components};return n?(0,s.jsx)(n,{...e,children:(0,s.jsx)(d,{...e})}):d(e)}},5990:(e,n,i)=>{i.d(n,{Z:()=>s});const s=i.p+"assets/images/Picture1_11-39073f55ead305e54d26b2b807186055.jpg"},2593:(e,n,i)=>{i.d(n,{Z:()=>s});const s=i.p+"assets/images/Picture2_1-f69c2af98fae3901d36a25d21d472764.jpg"},5935:(e,n,i)=>{i.d(n,{Z:()=>s});const s=i.p+"assets/images/Picture3_1-39a88339cbe63ca25ee0724ee6299d49.jpg"},4307:(e,n,i)=>{i.d(n,{Z:()=>s});const s=i.p+"assets/images/Picture4_1-bdcb34596dad2684fa7489a9f7f6fe79.jpg"},5135:(e,n,i)=>{i.d(n,{Z:()=>s});const s=i.p+"assets/images/Picture5_1-7b8f1d4f1bc3d69d054d170c0f451bc6.jpg"},5140:(e,n,i)=>{i.d(n,{Z:()=>s});const s=i.p+"assets/images/Picture6_1-7d429d3b8b75eaaa90a68ec6e0cd8692.jpg"},9017:(e,n,i)=>{i.d(n,{Z:()=>s});const s=i.p+"assets/images/or_dpe-ff86d9273ff956678a5c2bff993bda19.jpg"},4065:(e,n,i)=>{i.d(n,{Z:()=>s});const s=i.p+"assets/images/ortools_io-2cba299e1b353b03c824eb11a917648f.jpg"},1163:(e,n,i)=>{i.d(n,{Z:()=>s});const s=i.p+"assets/images/random_dpe-11c7b726ae0dc701735a1e96486d1d1e.jpg"},6996:(e,n,i)=>{i.d(n,{Z:()=>s});const s=i.p+"assets/images/random_io-e4637d3689e4881e30360ebf78458381.jpg"},2838:(e,n,i)=>{i.d(n,{Z:()=>s});const s=i.p+"assets/images/rr_dpe-ced03cee3e9901af631e3114a92b44f0.jpg"},334:(e,n,i)=>{i.d(n,{Z:()=>s});const s=i.p+"assets/images/rr_io-e0ca102ee0c5e9e2e15303dcb58c11a1.jpg"},1151:(e,n,i)=>{i.d(n,{Z:()=>r,a:()=>l});var s=i(7294);const t={},a=s.createContext(t);function l(e){const n=s.useContext(a);return s.useMemo((function(){return"function"==typeof e?e(n):{...n,...e}}),[n,e])}function r(e){let n;return n=e.disableParentContext?"function"==typeof e.components?e.components(t):e.components||t:l(e.components),s.createElement(a.Provider,{value:n},e.children)}}}]);
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-"use strict";(self.webpackChunkgrc=self.webpackChunkgrc||[]).push([[5243],{8221:(e,t,n)=>{n.r(t),n.d(t,{assets:()=>l,contentTitle:()=>i,default:()=>b,frontMatter:()=>s,metadata:()=>r,toc:()=>c});var o=n(5893),a=n(1151);const s={},i="Tagging",r={id:"hermes/components/tagging",title:"Tagging",description:"Tags enable users to semantically define associations between blobs and provide",source:"@site/docs/03-hermes/06-components/11-tagging.md",sourceDirName:"03-hermes/06-components",slug:"/hermes/components/tagging",permalink:"/docs/hermes/components/tagging",draft:!1,unlisted:!1,tags:[],version:"current",sidebarPosition:11,frontMatter:{},sidebar:"tutorialSidebar",previous:{title:"Examples",permalink:"/docs/hermes/components/examples"},next:{title:"Topology",permalink:"/docs/hermes/components/topology"}},l={},c=[{value:"The tagging API",id:"the-tagging-api",level:2}];function g(e){const t={code:"code",h1:"h1",h2:"h2",p:"p",pre:"pre",...(0,a.a)(),...e.components};return(0,o.jsxs)(o.Fragment,{children:[(0,o.jsx)(t.h1,{id:"tagging",children:"Tagging"}),"\n",(0,o.jsx)(t.p,{children:"Tags enable users to semantically define associations between blobs and provide\nan intuitive way of locating blobs which are related. Tags can be used\ninternally by Hermes to provide enhanced data placement decisions based on the\nlogical grouping of data. Operations (known as Traits) can be associated with\ntags to define a set of operations to perform based."}),"\n",(0,o.jsx)(t.h2,{id:"the-tagging-api",children:"The tagging API"}),"\n",(0,o.jsx)(t.p,{children:"The tag API supports the ability to tag and untag a blob. There are two general\nuse cases of tags: locating related blobs, and defining a set of operations to\nperform on a blob. In the below example, we show how to use tags to locate\nblobs. We discuss the use of tagging for operating on blobs through the use of\nTraits."}),"\n",(0,o.jsx)(t.pre,{children:(0,o.jsx)(t.code,{className:"language-cpp",children:'int main() {\n  size_t blob_size = KILOBYTES(4);\n  hermes::api::Context ctx;\n  BlobId blob_id[2];\n\n  auto bkt1 = HERMES->GetBucket("hello1");\n  auto bkt2 = HERMES->GetBucket("hello2");\n\n  Blob blob(blob_size);\n  bkt1->Put("1", blob, blob_id[0], ctx);\n  bkt2->Put("2", blob, blob_id[1], ctx);\n\n  TagId tag = HERMES->CreateTag("equivalent");\n  bkt1->TagBlob(blob_id[0], tag);\n  bkt2->TagBlob(blob_id[1], tag);\n  std::vector<BlobId> tags = HERMES->GroupBy(tag);\n  REQUIRE(tags.size() == 2);\n}\n'})}),"\n",(0,o.jsx)(t.p,{children:'In this example, we create two buckets and one blob (of size 4KB) in each\nbucket. Both blobs have the same value. We create the tag "equivalent" to\nindicate that blobs with this tag are all equal. Note, the name of the tag is\nonly relevant to the user, and has no internal meaning to Hermes itself. Hermes\ndoes not know the blobs are equivalent.'}),"\n",(0,o.jsx)(t.p,{children:'Next, we tag the two blobs, which are in separate buckets, with the "equivalent"\ntag. We then group all blobs which have the tag. We verify that the number of\nblobs apart of this tag is two and then return.'})]})}function b(e={}){const{wrapper:t}={...(0,a.a)(),...e.components};return t?(0,o.jsx)(t,{...e,children:(0,o.jsx)(g,{...e})}):g(e)}},1151:(e,t,n)=>{n.d(t,{Z:()=>r,a:()=>i});var o=n(7294);const a={},s=o.createContext(a);function i(e){const t=o.useContext(s);return o.useMemo((function(){return"function"==typeof e?e(t):{...t,...e}}),[t,e])}function r(e){let t;return t=e.disableParentContext?"function"==typeof e.components?e.components(a):e.components||a:i(e.components),o.createElement(s.Provider,{value:t},e.children)}}}]);
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-"use strict";(self.webpackChunkgrc=self.webpackChunkgrc||[]).push([[9636],{4607:(e,s,n)=>{n.r(s),n.d(s,{assets:()=>o,contentTitle:()=>a,default:()=>h,frontMatter:()=>r,metadata:()=>c,toc:()=>d});var t=n(5893),i=n(1151);const r={},a="Adapters",c={id:"hermes/adapters",title:"Adapters",description:"Hermes Ecosystem",source:"@site/docs/03-hermes/07-adapters.md",sourceDirName:"03-hermes",slug:"/hermes/adapters",permalink:"/docs/hermes/adapters",draft:!1,unlisted:!1,tags:[],version:"current",sidebarPosition:7,frontMatter:{},sidebar:"tutorialSidebar",previous:{title:"Programming",permalink:"/docs/hermes/programming"},next:{title:"Quick Start Guide",permalink:"/docs/hermes/quick-start"}},o={},d=[{value:"Filesystem Base Class (FSBC)",id:"filesystem-base-class-fsbc",level:2},{value:"Design",id:"design",level:3},{value:"VFD",id:"vfd",level:3},{value:"PubSub Adapter",id:"pubsub-adapter",level:2},{value:"Suported API",id:"suported-api",level:3},{value:"<code>connect</code>",id:"connect",level:4},{value:"<code>attach</code>",id:"attach",level:4},{value:"<code>detach</code>",id:"detach",level:4},{value:"<code>publish</code>",id:"publish",level:4},{value:"<code>subscribe</code>",id:"subscribe",level:4},{value:"Current Limitations",id:"current-limitations",level:2},{value:"Future Work",id:"future-work",level:2},{value:"References",id:"references",level:2}];function l(e){const s={a:"a",code:"code",em:"em",h1:"h1",h2:"h2",h3:"h3",h4:"h4",img:"img",li:"li",ol:"ol",p:"p",pre:"pre",ul:"ul",...(0,i.a)(),...e.components};return(0,t.jsxs)(t.Fragment,{children:[(0,t.jsx)(s.h1,{id:"adapters",children:"Adapters"}),"\n",(0,t.jsx)(s.p,{children:(0,t.jsx)(s.img,{alt:"Hermes Ecosystem",src:n(8194).Z+"",width:"522",height:"727"})}),"\n",(0,t.jsxs)(s.p,{children:["Instead of the ",(0,t.jsx)(s.a,{href:"/docs/hermes/programming",children:"Hermes primitives"}),", existing applications\nuse I/O libraries and middleware such as the C standard I/O library,\nMPI-IO, or HDF5. Since Hermes is intended to be a seamless I/O\nbuffering solution, a set of ",(0,t.jsx)(s.em,{children:"adapters"})," is provided in the form of\n",(0,t.jsx)(s.code,{children:"LD_PRELOAD"}),"-able shared libraries. These adapters perform the task of\nmapping between the application view of I/O primitives (e.g., files)\nand the Hermes primitives. An exemplary discussion of such mappings\ncan be found in ",(0,t.jsx)(s.a,{href:"http://www.cs.iit.edu/~scs/assets/files/Enosis.pdf",children:"Enosis: Bridging the Semantic Gap between File-based\nand Object-based Data Models"})," and ",(0,t.jsx)(s.a,{href:"http://www.cs.iit.edu/~scs/assets/files/Syndesis.pdf",children:"Syndesis: Mapping Objects to Files for a Unified Data Access\nSystem"}),"."]}),"\n",(0,t.jsx)(s.p,{children:"Another important task of Hermes adapters is to collect I/O profiling\nthat supports the detection of I/O patterns."}),"\n",(0,t.jsx)(s.h2,{id:"filesystem-base-class-fsbc",children:"Filesystem Base Class (FSBC)"}),"\n",(0,t.jsx)(s.p,{children:"The Filesystem Base Class (FSBC) is used by all filesystem-based APIs. This\nincludes STDIO, POSIX, and MPIIO. The FSBC implements all necessary APIs for\nbuffering files within Hermes."}),"\n",(0,t.jsx)(s.p,{children:"The FSBC provides basic filesystem overrides, including:"}),"\n",(0,t.jsxs)(s.ul,{children:["\n",(0,t.jsx)(s.li,{children:"Opening a file"}),"\n",(0,t.jsx)(s.li,{children:"Writing to a file"}),"\n",(0,t.jsx)(s.li,{children:"Reading from a file"}),"\n",(0,t.jsx)(s.li,{children:"Getting the size of a file"}),"\n",(0,t.jsx)(s.li,{children:"Removing a file"}),"\n"]}),"\n",(0,t.jsx)(s.p,{children:"Currently, we have four filesystem adapters:"}),"\n",(0,t.jsxs)(s.ol,{children:["\n",(0,t.jsx)(s.li,{children:"STDIO"}),"\n",(0,t.jsx)(s.li,{children:"POSIX"}),"\n",(0,t.jsx)(s.li,{children:"MPI-IO"}),"\n",(0,t.jsx)(s.li,{children:"HDF5 VFD"}),"\n"]}),"\n",(0,t.jsx)(s.h3,{id:"design",children:"Design"}),"\n",(0,t.jsx)(s.p,{children:"When reading/writing to a file, the FSBC will divide the I/O request into\nfixed-size pages. This is a configurable value, but the default is 1MB."}),"\n",(0,t.jsx)(s.p,{children:"When extending the size of a file, the FSBC relies on a lock to ensure that\nthe size of the file is coherent. This lock is a problem for workloads which\nperform shared I/O to a single file. FPP workloads are generally better."}),"\n",(0,t.jsx)(s.p,{children:"A solution to this problem would be a log-structured merge tree, but this\nwill require significant changes to the Hermes data model."}),"\n",(0,t.jsx)(s.h3,{id:"vfd",children:"VFD"}),"\n",(0,t.jsx)(s.p,{children:"The HDF5 VFD is used to interface HDF5 with Hermes natively. To use the Hermes\nVFD in HDF5, you must define the following environment variables:"}),"\n",(0,t.jsx)(s.pre,{children:(0,t.jsx)(s.code,{className:"language-bash",children:"export HDF5_PLUGIN_PATH=/path/to/hermes/lib\nexport HDF5_DRIVER=hdf5_hermes_vfd\n"})}),"\n",(0,t.jsx)(s.p,{children:"HDF5_PLUGIN_PATH indicates the directory to search for the HDF5_DRIVER. In\nthis case, HDF5 will search for libhdf5_hermes_vfd.so."}),"\n",(0,t.jsx)(s.h2,{id:"pubsub-adapter",children:"PubSub Adapter"}),"\n",(0,t.jsx)(s.p,{children:"The PubSub adapter for Hermes stands a bit different from other adapters due to the diverse nature of pub/sub APIs on the market. For example, here are two examples of starting programs for two different queue/broker systems."}),"\n",(0,t.jsx)(s.p,{children:"A simple example of, one of, the ZeroMQ C++ API."}),"\n",(0,t.jsx)(s.pre,{children:(0,t.jsx)(s.code,{className:"language-cpp",children:'#include <string>\n#include <zmq.hpp>\nint main()\n{\n   zmq::context_t ctx;\n   zmq::socket_t sock(ctx, zmq::socket_type::push);\n   sock.bind("inproc://test");\n   const std::string_view m = "Hello, world";\n   sock.send(zmq::buffer(m), zmq::send_flags::dontwait);\n}\n'})}),"\n",(0,t.jsx)(s.p,{children:"And an example of the Kafka C++ API."}),"\n",(0,t.jsx)(s.pre,{children:(0,t.jsx)(s.code,{className:"language-cpp",children:'#include "kafka/KafkaProducer.h"\n#include <iostream>\n#include <string>\nint main(int argc, char **argv)\n{\n  std::string brokers = argv[1];\n  kafka::Topic topic  = argv[2];\n  string line\'\n\n  kafka::Properties props({\n    {"bootstrap.servers", brokers},\n    {"enable.idempotence", "true"},\n  });\n  kafka::KafkaSyncProducer producer(props);\n  std::cin >> line;\n  auto record = kafka::ProducerRecord(topic, kafka::NullKey, kafka::Value(line.c_str(), line.size()));\n  kafka::Producer::RecordMetadata metadata = producer.send(record);\n}\n'})}),"\n",(0,t.jsx)(s.p,{children:"Both examples highlight the diversity of APIs present on the pub/sub market.\nAs such, the adapter API is intended to present a common and sharable lower interface to Hermes to which all other used API can be intercepted and redirected."}),"\n",(0,t.jsx)(s.h3,{id:"suported-api",children:"Suported API"}),"\n",(0,t.jsxs)(s.p,{children:["In all functions ",(0,t.jsx)(s.code,{children:"hapi"})," stands for objects under the ",(0,t.jsx)(s.code,{children:"hermes::api"})," namespace."]}),"\n",(0,t.jsx)(s.h4,{id:"connect",children:(0,t.jsx)(s.code,{children:"connect"})}),"\n",(0,t.jsx)(s.pre,{children:(0,t.jsx)(s.code,{className:"language-cpp",children:"hapi::Status connect(const std::string &config_file);\nhapi::Status connect();\n    - Connects to the Hermes instance\n    - One option accepts, config_file: Path to the config file of Hermes\n    - The other, assumes that path is loaded into an environment variable defined in constants.h under kHermesConf\n"})}),"\n",(0,t.jsx)(s.h4,{id:"attach",children:(0,t.jsx)(s.code,{children:"attach"})}),"\n",(0,t.jsx)(s.pre,{children:(0,t.jsx)(s.code,{className:"language-cpp",children:"hapi::Status attach(const std::string& topic);\n    - Attaches to a topic, creating it if it doesn't exist\n    - topic: The name of the topic\n"})}),"\n",(0,t.jsx)(s.h4,{id:"detach",children:(0,t.jsx)(s.code,{children:"detach"})}),"\n",(0,t.jsx)(s.pre,{children:(0,t.jsx)(s.code,{className:"language-cpp",children:"hapi::Status detach(const std::string& topic);\n    - Detaches from the topic cleaning up all client-local metadata\n    - topic: The name of the topic\n    - Note, detaching doesn't delete the topic\n"})}),"\n",(0,t.jsx)(s.h4,{id:"publish",children:(0,t.jsx)(s.code,{children:"publish"})}),"\n",(0,t.jsx)(s.pre,{children:(0,t.jsx)(s.code,{className:"language-cpp",children:"hapi::Status publish(const std::string& topic,  const std::vector<unsigned char>& message);\n    - Puts a message to a topic\n    - topic: The name of the topic\n    - message: the data buffer\n    - Note, the function uses std::vector<unsigned char> which is equivalent to hermes::api::Blob\n"})}),"\n",(0,t.jsx)(s.h4,{id:"subscribe",children:(0,t.jsx)(s.code,{children:"subscribe"})}),"\n",(0,t.jsx)(s.pre,{children:(0,t.jsx)(s.code,{className:"language-cpp",children:" std::pair<std::vector<unsigned char>, hapi::Status> subscribe( const std::string& topic);\n    - Retrieves the next message from the topic\n    - topic: The name of the topic\n    - returns: a pair of the return code/status and, if successful, the subscribed message.\n"})}),"\n",(0,t.jsx)(s.h2,{id:"current-limitations",children:"Current Limitations"}),"\n",(0,t.jsxs)(s.ul,{children:["\n",(0,t.jsx)(s.li,{children:"Currently on Hermes, Blob deletions causes the latest Blob to be placed in it's place, this is intended to save memory space and provide an O(1) deletion complexity. Nevertheless, this destroys the ordering of messages expected but the pub/sub API, as such, message/Blob deletions is not possible, currently."}),"\n",(0,t.jsx)(s.li,{children:"Multi-threaded support of the API has not been fully tested. All tests have been performed under multi-process, MPI-driven tests."}),"\n"]}),"\n",(0,t.jsx)(s.h2,{id:"future-work",children:"Future Work"}),"\n",(0,t.jsxs)(s.ul,{children:["\n",(0,t.jsx)(s.li,{children:"Current work is being focused in expanding the library to support the use of traits to support in-transit transformations of the data"}),"\n"]}),"\n",(0,t.jsx)(s.h2,{id:"references",children:"References"}),"\n",(0,t.jsxs)(s.ul,{children:["\n",(0,t.jsx)(s.li,{children:(0,t.jsx)(s.a,{href:"https://github.com/LLNL/GOTCHA",children:"GOTCHA is a library for wrapping function calls in shared libraries"})}),"\n"]})]})}function h(e={}){const{wrapper:s}={...(0,i.a)(),...e.components};return s?(0,t.jsx)(s,{...e,children:(0,t.jsx)(l,{...e})}):l(e)}},8194:(e,s,n)=>{n.d(s,{Z:()=>t});const t=n.p+"assets/images/Hermes_Ecosystem-bcc2b31f697fea047fc773fbf10d2dbb.jpg"},1151:(e,s,n)=>{n.d(s,{Z:()=>c,a:()=>a});var t=n(7294);const i={},r=t.createContext(i);function a(e){const s=t.useContext(r);return t.useMemo((function(){return"function"==typeof e?e(s):{...s,...e}}),[s,e])}function c(e){let s;return s=e.disableParentContext?"function"==typeof e.components?e.components(i):e.components||i:a(e.components),t.createElement(r.Provider,{value:s},e.children)}}}]);
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diff --git a/assets/js/e5318f16.cf6e9ebb.js b/assets/js/e5318f16.b23d5d3c.js
similarity index 97%
rename from assets/js/e5318f16.cf6e9ebb.js
rename to assets/js/e5318f16.b23d5d3c.js
index 58cb5437..f1c966c0 100644
--- a/assets/js/e5318f16.cf6e9ebb.js
+++ b/assets/js/e5318f16.b23d5d3c.js
@@ -1 +1 @@
-"use strict";(self.webpackChunkgrc=self.webpackChunkgrc||[]).push([[3837],{9162:(e,t,n)=>{n.r(t),n.d(t,{assets:()=>c,contentTitle:()=>i,default:()=>d,frontMatter:()=>o,metadata:()=>s,toc:()=>l});var r=n(5893),a=n(1151);const o={},i="LD_LIBRARY_PATH",s={id:"hpc-tutorials/important-environment-variables/ld-library-path",title:"LD_LIBRARY_PATH",description:"LDLIBRARYPATH is used by Linux to locate shared objects at runtime (as opposed to compile-time).",source:"@site/docs/02-hpc-tutorials/03-important-environment-variables/ld-library-path.md",sourceDirName:"02-hpc-tutorials/03-important-environment-variables",slug:"/hpc-tutorials/important-environment-variables/ld-library-path",permalink:"/docs/hpc-tutorials/important-environment-variables/ld-library-path",draft:!1,unlisted:!1,tags:[],version:"current",frontMatter:{},sidebar:"tutorialSidebar",previous:{title:"JAVA_HOME",permalink:"/docs/hpc-tutorials/important-environment-variables/java-home"},next:{title:"LD_PRELOAD",permalink:"/docs/hpc-tutorials/important-environment-variables/ld-preload"}},c={},l=[];function p(e){const t={code:"code",h1:"h1",p:"p",pre:"pre",...(0,a.a)(),...e.components};return(0,r.jsxs)(r.Fragment,{children:[(0,r.jsx)(t.h1,{id:"ld_library_path",children:(0,r.jsx)(t.code,{children:"LD_LIBRARY_PATH"})}),"\n",(0,r.jsxs)(t.p,{children:[(0,r.jsx)(t.code,{children:"LD_LIBRARY_PATH"})," is used by Linux to locate shared objects at runtime (as opposed to compile-time).\nShared objects need to be found all over again when starting your program."]}),"\n",(0,r.jsxs)(t.p,{children:[(0,r.jsx)(t.code,{children:"LD_LIBRARY_PATH"})," is organized as a colon-separated list."]}),"\n",(0,r.jsx)(t.pre,{children:(0,r.jsx)(t.code,{className:"language-bash",children:'export LD_LIBRARY_PATH="/path1:/path2:/path3"\n'})}),"\n",(0,r.jsxs)(t.p,{children:[(0,r.jsx)(t.code,{children:"LD_LIBRARY_PATH"})," contains three paths in this example."]})]})}function d(e={}){const{wrapper:t}={...(0,a.a)(),...e.components};return t?(0,r.jsx)(t,{...e,children:(0,r.jsx)(p,{...e})}):p(e)}},1151:(e,t,n)=>{n.d(t,{Z:()=>s,a:()=>i});var r=n(7294);const a={},o=r.createContext(a);function i(e){const t=r.useContext(o);return r.useMemo((function(){return"function"==typeof e?e(t):{...t,...e}}),[t,e])}function s(e){let t;return t=e.disableParentContext?"function"==typeof e.components?e.components(a):e.components||a:i(e.components),r.createElement(o.Provider,{value:t},e.children)}}}]);
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+"use strict";(self.webpackChunkgrc=self.webpackChunkgrc||[]).push([[3837],{3490:(e,t,n)=>{n.r(t),n.d(t,{assets:()=>c,contentTitle:()=>i,default:()=>d,frontMatter:()=>o,metadata:()=>s,toc:()=>l});var r=n(5893),a=n(1151);const o={},i="LD_LIBRARY_PATH",s={id:"hpc-tutorials/important-environment-variables/ld-library-path",title:"LD_LIBRARY_PATH",description:"LDLIBRARYPATH is used by Linux to locate shared objects at runtime (as opposed to compile-time).",source:"@site/docs/02-hpc-tutorials/03-important-environment-variables/ld-library-path.md",sourceDirName:"02-hpc-tutorials/03-important-environment-variables",slug:"/hpc-tutorials/important-environment-variables/ld-library-path",permalink:"/docs/hpc-tutorials/important-environment-variables/ld-library-path",draft:!1,unlisted:!1,tags:[],version:"current",frontMatter:{},sidebar:"tutorialSidebar",previous:{title:"JAVA_HOME",permalink:"/docs/hpc-tutorials/important-environment-variables/java-home"},next:{title:"LD_PRELOAD",permalink:"/docs/hpc-tutorials/important-environment-variables/ld-preload"}},c={},l=[];function p(e){const t={code:"code",h1:"h1",p:"p",pre:"pre",...(0,a.a)(),...e.components};return(0,r.jsxs)(r.Fragment,{children:[(0,r.jsx)(t.h1,{id:"ld_library_path",children:(0,r.jsx)(t.code,{children:"LD_LIBRARY_PATH"})}),"\n",(0,r.jsxs)(t.p,{children:[(0,r.jsx)(t.code,{children:"LD_LIBRARY_PATH"})," is used by Linux to locate shared objects at runtime (as opposed to compile-time).\nShared objects need to be found all over again when starting your program."]}),"\n",(0,r.jsxs)(t.p,{children:[(0,r.jsx)(t.code,{children:"LD_LIBRARY_PATH"})," is organized as a colon-separated list."]}),"\n",(0,r.jsx)(t.pre,{children:(0,r.jsx)(t.code,{className:"language-bash",children:'export LD_LIBRARY_PATH="/path1:/path2:/path3"\n'})}),"\n",(0,r.jsxs)(t.p,{children:[(0,r.jsx)(t.code,{children:"LD_LIBRARY_PATH"})," contains three paths in this example."]})]})}function d(e={}){const{wrapper:t}={...(0,a.a)(),...e.components};return t?(0,r.jsx)(t,{...e,children:(0,r.jsx)(p,{...e})}):p(e)}},1151:(e,t,n)=>{n.d(t,{Z:()=>s,a:()=>i});var r=n(7294);const a={},o=r.createContext(a);function i(e){const t=r.useContext(o);return r.useMemo((function(){return"function"==typeof e?e(t):{...t,...e}}),[t,e])}function s(e){let t;return t=e.disableParentContext?"function"==typeof e.components?e.components(a):e.components||a:i(e.components),r.createElement(o.Provider,{value:t},e.children)}}}]);
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diff --git a/assets/js/f3c6a837.55ff94c1.js b/assets/js/f3c6a837.55ff94c1.js
new file mode 100644
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--- /dev/null
+++ b/assets/js/f3c6a837.55ff94c1.js
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+"use strict";(self.webpackChunkgrc=self.webpackChunkgrc||[]).push([[6154],{3848:(e,t,n)=>{n.r(t),n.d(t,{assets:()=>c,contentTitle:()=>i,default:()=>h,frontMatter:()=>s,metadata:()=>a,toc:()=>d});var o=n(5893),r=n(1151);const s={},i="Doxygen",a={id:"hermes/doxygen",title:"Doxygen",description:"The Doxygen portion of the Hermes documentation can be built as follows:",source:"@site/docs/03-hermes/11-doxygen.md",sourceDirName:"03-hermes",slug:"/hermes/doxygen",permalink:"/docs/hermes/doxygen",draft:!1,unlisted:!1,tags:[],version:"current",sidebarPosition:11,frontMatter:{},sidebar:"tutorialSidebar",previous:{title:"Developer Guide",permalink:"/docs/hermes/developer-guide"},next:{title:"Frequently Asked Questions",permalink:"/docs/hermes/faq"}},c={},d=[];function l(e){const t={a:"a",code:"code",h1:"h1",p:"p",pre:"pre",...(0,r.a)(),...e.components};return(0,o.jsxs)(o.Fragment,{children:[(0,o.jsx)(t.h1,{id:"doxygen",children:"Doxygen"}),"\n",(0,o.jsxs)(t.p,{children:["The ",(0,o.jsx)(t.a,{href:"https://www.doxygen.nl/index.html",children:"Doxygen"})," portion of the Hermes documentation can be built as follows:"]}),"\n",(0,o.jsx)(t.pre,{children:(0,o.jsx)(t.code,{className:"language-bash",children:"cmake -D <Other Hermes CMake build options> -DHERMES_ENABLE_DOXYGEN=ON ../\nmake dox\n"})}),"\n",(0,o.jsxs)(t.p,{children:["The HTML version of the documentation will be placed into the ",(0,o.jsx)(t.code,{children:"_build/html"})," subfolder of the build directory."]}),"\n",(0,o.jsxs)(t.p,{children:["An online version for the latest release is available at ",(0,o.jsx)(t.a,{href:"https://hdfgroup.github.io/hermes/html/",children:"https://hdfgroup.github.io/hermes/html/"}),"."]}),"\n",(0,o.jsxs)(t.p,{children:["The official version for the stable release is available at ",(0,o.jsx)(t.a,{href:"https://docs.hdfgroup.org/hermes/",children:"https://docs.hdfgroup.org/hermes/"}),"."]})]})}function h(e={}){const{wrapper:t}={...(0,r.a)(),...e.components};return t?(0,o.jsx)(t,{...e,children:(0,o.jsx)(l,{...e})}):l(e)}},1151:(e,t,n)=>{n.d(t,{Z:()=>a,a:()=>i});var o=n(7294);const r={},s=o.createContext(r);function i(e){const t=o.useContext(s);return o.useMemo((function(){return"function"==typeof e?e(t):{...t,...e}}),[t,e])}function a(e){let t;return t=e.disableParentContext?"function"==typeof e.components?e.components(r):e.components||r:i(e.components),o.createElement(s.Provider,{value:t},e.children)}}}]);
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diff --git a/assets/js/fdbe0d49.bfd16a7c.js b/assets/js/fdbe0d49.bfd16a7c.js
new file mode 100644
index 00000000..ca1641a9
--- /dev/null
+++ b/assets/js/fdbe0d49.bfd16a7c.js
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+"use strict";(self.webpackChunkgrc=self.webpackChunkgrc||[]).push([[5437],{339:(e,t,n)=>{n.r(t),n.d(t,{assets:()=>l,contentTitle:()=>i,default:()=>b,frontMatter:()=>s,metadata:()=>r,toc:()=>c});var o=n(5893),a=n(1151);const s={},i="Tagging",r={id:"hermes/components/tagging",title:"Tagging",description:"Tags enable users to semantically define associations between blobs and provide",source:"@site/docs/03-hermes/08-components/11-tagging.md",sourceDirName:"03-hermes/08-components",slug:"/hermes/components/tagging",permalink:"/docs/hermes/components/tagging",draft:!1,unlisted:!1,tags:[],version:"current",sidebarPosition:11,frontMatter:{},sidebar:"tutorialSidebar",previous:{title:"Examples",permalink:"/docs/hermes/components/examples"},next:{title:"Topology",permalink:"/docs/hermes/components/topology"}},l={},c=[{value:"The tagging API",id:"the-tagging-api",level:2}];function g(e){const t={code:"code",h1:"h1",h2:"h2",p:"p",pre:"pre",...(0,a.a)(),...e.components};return(0,o.jsxs)(o.Fragment,{children:[(0,o.jsx)(t.h1,{id:"tagging",children:"Tagging"}),"\n",(0,o.jsx)(t.p,{children:"Tags enable users to semantically define associations between blobs and provide\nan intuitive way of locating blobs which are related. Tags can be used\ninternally by Hermes to provide enhanced data placement decisions based on the\nlogical grouping of data. Operations (known as Traits) can be associated with\ntags to define a set of operations to perform based."}),"\n",(0,o.jsx)(t.h2,{id:"the-tagging-api",children:"The tagging API"}),"\n",(0,o.jsx)(t.p,{children:"The tag API supports the ability to tag and untag a blob. There are two general\nuse cases of tags: locating related blobs, and defining a set of operations to\nperform on a blob. In the below example, we show how to use tags to locate\nblobs. We discuss the use of tagging for operating on blobs through the use of\nTraits."}),"\n",(0,o.jsx)(t.pre,{children:(0,o.jsx)(t.code,{className:"language-cpp",children:'int main() {\n  size_t blob_size = KILOBYTES(4);\n  hermes::api::Context ctx;\n  BlobId blob_id[2];\n\n  auto bkt1 = HERMES->GetBucket("hello1");\n  auto bkt2 = HERMES->GetBucket("hello2");\n\n  Blob blob(blob_size);\n  bkt1->Put("1", blob, blob_id[0], ctx);\n  bkt2->Put("2", blob, blob_id[1], ctx);\n\n  TagId tag = HERMES->CreateTag("equivalent");\n  bkt1->TagBlob(blob_id[0], tag);\n  bkt2->TagBlob(blob_id[1], tag);\n  std::vector<BlobId> tags = HERMES->GroupBy(tag);\n  REQUIRE(tags.size() == 2);\n}\n'})}),"\n",(0,o.jsx)(t.p,{children:'In this example, we create two buckets and one blob (of size 4KB) in each\nbucket. Both blobs have the same value. We create the tag "equivalent" to\nindicate that blobs with this tag are all equal. Note, the name of the tag is\nonly relevant to the user, and has no internal meaning to Hermes itself. Hermes\ndoes not know the blobs are equivalent.'}),"\n",(0,o.jsx)(t.p,{children:'Next, we tag the two blobs, which are in separate buckets, with the "equivalent"\ntag. We then group all blobs which have the tag. We verify that the number of\nblobs apart of this tag is two and then return.'})]})}function b(e={}){const{wrapper:t}={...(0,a.a)(),...e.components};return t?(0,o.jsx)(t,{...e,children:(0,o.jsx)(g,{...e})}):g(e)}},1151:(e,t,n)=>{n.d(t,{Z:()=>r,a:()=>i});var o=n(7294);const a={},s=o.createContext(a);function i(e){const t=o.useContext(s);return o.useMemo((function(){return"function"==typeof e?e(t):{...t,...e}}),[t,e])}function r(e){let t;return t=e.disableParentContext?"function"==typeof e.components?e.components(a):e.components||a:i(e.components),o.createElement(s.Provider,{value:t},e.children)}}}]);
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diff --git a/assets/js/fdf52e69.e8e2d294.js b/assets/js/fdf52e69.e8e2d294.js
new file mode 100644
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--- /dev/null
+++ b/assets/js/fdf52e69.e8e2d294.js
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+"use strict";(self.webpackChunkgrc=self.webpackChunkgrc||[]).push([[5865],{4995:(A,e,t)=>{t.r(e),t.d(e,{assets:()=>i,contentTitle:()=>r,default:()=>f,frontMatter:()=>a,metadata:()=>o,toc:()=>l});var n=t(5893),s=t(1151);const a={},r="Buffer Pool",o={id:"hermes/components/buffer-pool",title:"Buffer Pool",description:"The main idea behind the Buffer Pool is to avoid the runtime",source:"@site/docs/03-hermes/08-components/02-buffer-pool.md",sourceDirName:"03-hermes/08-components",slug:"/hermes/components/buffer-pool",permalink:"/docs/hermes/components/buffer-pool",draft:!1,unlisted:!1,tags:[],version:"current",sidebarPosition:2,frontMatter:{},sidebar:"tutorialSidebar",previous:{title:"Buffer Organizer",permalink:"/docs/hermes/components/buffer-organizer"},next:{title:"Buffering Target",permalink:"/docs/hermes/components/buffering-target"}},i={},l=[{value:"Buffers and BufferIDs",id:"buffers-and-bufferids",level:2},{value:"Buffer Pool Layout",id:"buffer-pool-layout",level:2},{value:"Initialization",id:"initialization",level:3},{value:"API",id:"api",level:2},{value:"Buffer Pool Visualizer",id:"buffer-pool-visualizer",level:2}];function d(A){const e={code:"code",em:"em",h1:"h1",h2:"h2",h3:"h3",img:"img",li:"li",p:"p",pre:"pre",strong:"strong",ul:"ul",...(0,s.a)(),...A.components};return(0,n.jsxs)(n.Fragment,{children:[(0,n.jsx)(e.h1,{id:"buffer-pool",children:"Buffer Pool"}),"\n",(0,n.jsxs)(e.p,{children:["The main idea behind the ",(0,n.jsx)(e.strong,{children:"Buffer Pool"})," is to avoid the runtime\noverhead of memory allocation each time Hermes wishes to buffer data.\nInstead, we pre-allocate a pool of fixed sized (though the size groups\nare configurable) buffers that can be reused throughout an application\nrun. We allocate memory and reserve file system space on startup and\ndivide the available resources into buffers which the system can\nrequest. We deploy one buffer pool per node for a given Hermes instance."]}),"\n",(0,n.jsx)(e.h2,{id:"buffers-and-bufferids",children:"Buffers and BufferIDs"}),"\n",(0,n.jsxs)(e.p,{children:["A ",(0,n.jsx)(e.strong,{children:(0,n.jsx)(e.em,{children:"Buffer"})})," represents a portion of storage that Hermes is aware of\nand is allowed to buffer data in. It can be backed by various storage\ndevices (RAM, NVMe, SSD, burst buffer, parallel file system, object\nstore, etc.). Each ",(0,n.jsx)(e.strong,{children:(0,n.jsx)(e.em,{children:"Buffer"})})," is identified by a globally unique (per\nHermes application instance) ",(0,n.jsx)(e.code,{children:"BufferID"})," which is an unsigned 64 bit\ninteger divided into the following sections:"]}),"\n",(0,n.jsxs)(e.ul,{children:["\n",(0,n.jsx)(e.li,{children:"32 bits for the node ID. Each node is assigned a unique integer\nindex (starting at 1, not 0) during Hermes initialization."}),"\n",(0,n.jsx)(e.li,{children:"32 bits for header index. This is an index into the array of buffer\nheaders on the corresponding node."}),"\n"]}),"\n",(0,n.jsxs)(e.p,{children:["A ",(0,n.jsx)(e.code,{children:"BufferID"})," of 0 (node id = 0 and header index = 0) signifies the NULL\n",(0,n.jsx)(e.code,{children:"BufferID"}),"."]}),"\n",(0,n.jsx)(e.h2,{id:"buffer-pool-layout",children:"Buffer Pool Layout"}),"\n",(0,n.jsxs)(e.ul,{children:["\n",(0,n.jsxs)(e.li,{children:["Terminology\nBlock : A ",(0,n.jsx)(e.strong,{children:"block"})," is the smallest buffering unit available to\nHermes. It defaults to the system's page size (usually 4 KiB on\nLinux) but can be configured to be any value.\nSlab : A ",(0,n.jsx)(e.strong,{children:"slab"})," is the collection of all buffers of the same block\nsize. A typical setup would be a buffer pool with 4 slabs where the\nfirst slab is a collection of buffers that are 1 block each, the\nnext slab consists of buffers of 4 blocks each, then 16-block\nbuffers, and 32-block buffers. The number of slabs and number of\nblocks for each slab is configurable through a Hermes configuration\nfile so that it can be tailored to each application's I/O pattern."]}),"\n"]}),"\n",(0,n.jsx)(e.p,{children:(0,n.jsx)(e.img,{alt:"Buffer Pool Layout",src:t(8241).Z+"",width:"769",height:"469"})}),"\n",(0,n.jsx)(e.h3,{id:"initialization",children:"Initialization"}),"\n",(0,n.jsx)(e.p,{children:"When Hermes initializes, it will read from the Hermes configuration file\nhow much space is available for buffering in each tier. The amount of\nRAM available is allocated as 1 contiguous address space and split into\nslabs and buffer pool metadata. The total amount of metadata is\ncalculated and reserved. The remaining space is split up into slabs,\naccording to the parameters in the configuration file. A free list is\nmaintained for each slab of buffers. Buffers are marked as in use or\nnot. When the system requests buffers, the buffer pool simply returns\nthe first item from the free list, and freeing buffers translates to\npushing them onto the head of the free list."}),"\n",(0,n.jsx)(e.h2,{id:"api",children:"API"}),"\n",(0,n.jsxs)(e.p,{children:["The primary consumer of the buffer pool API is the Hermes API.\n",(0,n.jsx)(e.code,{children:"Bucket::Put"})," is the primary path that will request buffers, and\n",(0,n.jsx)(e.code,{children:"Bucket::Delete"})," will release buffers."]}),"\n",(0,n.jsx)(e.pre,{children:(0,n.jsx)(e.code,{className:"language-cpp",children:"std::vector<hermes::BufferID> GetBuffers(const hermes::PlacementSchema &schema);\nvoid ReleaseBuffers(const std::vector<hermes::BufferID> &buffer_ids);\n"})}),"\n",(0,n.jsxs)(e.p,{children:["Most operations deal with ",(0,n.jsx)(e.code,{children:"BufferID"}),"s, but when the data itself must be\naccessed (e.g., when an I/O client wises to flush buffers to the PFS)\neach ID contains all the information required to get to the actual data."]}),"\n",(0,n.jsxs)(e.ul,{children:["\n",(0,n.jsx)(e.li,{children:"Split and Merge"}),"\n"]}),"\n",(0,n.jsx)(e.p,{children:"In addition, if the system finds that small buffers are underutilized\nwhile large buffers are exhausted, it can merge unused small buffers\ninto larger buffers for better utilization. Conversely, if large buffers\nare underutilized, it can split large buffers into small buffers."}),"\n",(0,n.jsx)(e.h2,{id:"buffer-pool-visualizer",children:"Buffer Pool Visualizer"}),"\n",(0,n.jsx)(e.p,{children:"To facilitate testing and debugging, we've developed a tool to display a\ngraphical view of the state of a buffer pool. The buffer visualization\nupdates in real time by simply reading the buffer pool shared memory, so\nwe can watch how buffers get used and freed as an application executes,\nand it can be attached and detached to/from any running application.\nBelow is a visualization of a buffer pool with 4 slabs. The red slab is\nmade of 1-block (4 KiB in this case) buffers, the yellow of 4-block\nbuffers, the green of 16 block buffers, and the blue of 32-block\nbuffers. Note that the relative sizes are preserved. The space above the\nmagenta line is directly mapped to the RAM buffers in shared memory.\nBelow the magenta line we see the total headers, including those in use\n(green) and unused (grey). In the initial state, we have some unused\nheaders to facilitate splitting buffers."}),"\n",(0,n.jsx)(e.p,{children:(0,n.jsx)(e.img,{alt:"Buffer Pool Visualizer",src:t(7823).Z+"",width:"1200",height:"633"})}),"\n",(0,n.jsx)(e.p,{children:"Here we have merged the yellow 4-block slab into the green 16-block\nslab. We can also see that fewer headers are in use because we now have\nfewer buffers."}),"\n",(0,n.jsx)(e.p,{children:(0,n.jsx)(e.img,{alt:"Buffer Pool Visualizer Merge",src:t(2724).Z+"",width:"1200",height:"516"})}),"\n",(0,n.jsx)(e.p,{children:"Here we have split all slabs into the smallest possible buffers,\nresulting in one slab of 1-block buffers. Here every header is used, and\nthis is the maximum number of buffers the system can support for this\nparticular configuration."}),"\n",(0,n.jsx)(e.p,{children:(0,n.jsx)(e.img,{alt:"Buffer Pool Visualizer Split",src:t(5464).Z+"",width:"1200",height:"508"})}),"\n",(0,n.jsx)(e.p,{children:"Development on the visualizer occurs on an as-needed basis, but should\nthe need arise, it would be great to be able to zoom in and out, and\nhover over buffers to see actual data."})]})}function f(A={}){const{wrapper:e}={...(0,s.a)(),...A.components};return e?(0,n.jsx)(e,{...A,children:(0,n.jsx)(d,{...A})}):d(A)}},8241:(A,e,t)=>{t.d(e,{Z:()=>n});const n=t.p+"assets/images/BufferPoolLayout-6ad491f91329f6452cba250510eeb74f.jpg"},7823:(A,e,t)=>{t.d(e,{Z:()=>n});const n=t.p+"assets/images/buffer_pool_visualizer_default-4f856358bcbb7a8ee79889853c0d1238.png"},2724:(A,e,t)=>{t.d(e,{Z:()=>n});const 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e.languages.tsx["literal-property"],e.languages.tsx.tag)).pattern=RegExp(/(^|[^\w$]|(?=<\/))/.source+"(?:"+t.pattern.source+")",t.pattern.flags),t.lookbehind=!0}(C),C.languages.swift={comment:{pattern:/(^|[^\\:])(?:\/\/.*|\/\*(?:[^/*]|\/(?!\*)|\*(?!\/)|\/\*(?:[^*]|\*(?!\/))*\*\/)*\*\/)/,lookbehind:!0,greedy:!0},"string-literal":[{pattern:RegExp(/(^|[^"#])/.source+"(?:"+/"(?:\\(?:\((?:[^()]|\([^()]*\))*\)|\r\n|[^(])|[^\\\r\n"])*"/.source+"|"+/"""(?:\\(?:\((?:[^()]|\([^()]*\))*\)|[^(])|[^\\"]|"(?!""))*"""/.source+")"+/(?!["#])/.source),lookbehind:!0,greedy:!0,inside:{interpolation:{pattern:/(\\\()(?:[^()]|\([^()]*\))*(?=\))/,lookbehind:!0,inside:null},"interpolation-punctuation":{pattern:/^\)|\\\($/,alias:"punctuation"},punctuation:/\\(?=[\r\n])/,string:/[\s\S]+/}},{pattern:RegExp(/(^|[^"#])(#+)/.source+"(?:"+/"(?:\\(?:#+\((?:[^()]|\([^()]*\))*\)|\r\n|[^#])|[^\\\r\n])*?"/.source+"|"+/"""(?:\\(?:#+\((?:[^()]|\([^()]*\))*\)|[^#])|[^\\])*?"""/.source+")\\2"),lookbehind:!0,greedy:!0,inside:{interpolation:{pattern:/(\\#+\()(?:[^()]|\([^()]*\))*(?=\))/,lookbehind:!0,inside:null},"interpolation-punctuation":{pattern:/^\)|\\#+\($/,alias:"punctuation"},string:/[\s\S]+/}}],directive:{pattern:RegExp(/#/.source+"(?:"+/(?:elseif|if)\b/.source+"(?:[ 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\t]*(?:&&|\|\|))?/.source+")+|"+/(?:else|endif)\b/.source+")"),alias:"property",inside:{"directive-name":/^#\w+/,boolean:/\b(?:false|true)\b/,number:/\b\d+(?:\.\d+)*\b/,operator:/!|&&|\|\||[<>]=?/,punctuation:/[(),]/}},literal:{pattern:/#(?:colorLiteral|column|dsohandle|file(?:ID|Literal|Path)?|function|imageLiteral|line)\b/,alias:"constant"},"other-directive":{pattern:/#\w+\b/,alias:"property"},attribute:{pattern:/@\w+/,alias:"atrule"},"function-definition":{pattern:/(\bfunc\s+)\w+/,lookbehind:!0,alias:"function"},label:{pattern:/\b(break|continue)\s+\w+|\b[a-zA-Z_]\w*(?=\s*:\s*(?:for|repeat|while)\b)/,lookbehind:!0,alias:"important"},keyword:/\b(?:Any|Protocol|Self|Type|actor|as|assignment|associatedtype|associativity|async|await|break|case|catch|class|continue|convenience|default|defer|deinit|didSet|do|dynamic|else|enum|extension|fallthrough|fileprivate|final|for|func|get|guard|higherThan|if|import|in|indirect|infix|init|inout|internal|is|isolated|lazy|left|let|lowerThan|mutating|none|nonisolated|nonmutating|open|operator|optional|override|postfix|precedencegroup|prefix|private|protocol|public|repeat|required|rethrows|return|right|safe|self|set|some|static|struct|subscript|super|switch|throw|throws|try|typealias|unowned|unsafe|var|weak|where|while|willSet)\b/,boolean:/\b(?:false|true)\b/,nil:{pattern:/\bnil\b/,alias:"constant"},"short-argument":/\$\d+\b/,omit:{pattern:/\b_\b/,alias:"keyword"},number:/\b(?:[\d_]+(?:\.[\de_]+)?|0x[a-f0-9_]+(?:\.[a-f0-9p_]+)?|0b[01_]+|0o[0-7_]+)\b/i,"class-name":/\b[A-Z](?:[A-Z_\d]*[a-z]\w*)?\b/,function:/\b[a-z_]\w*(?=\s*\()/i,constant:/\b(?:[A-Z_]{2,}|k[A-Z][A-Za-z_]+)\b/,operator:/[-+*/%=!<>&|^~?]+|\.[.\-+*/%=!<>&|^~?]+/,punctuation:/[{}[\]();,.:\\]/},C.languages.swift["string-literal"].forEach((function(e){e.inside.interpolation.inside=C.languages.swift})),function(e){e.languages.kotlin=e.languages.extend("clike",{keyword:{pattern:/(^|[^.])\b(?:abstract|actual|annotation|as|break|by|catch|class|companion|const|constructor|continue|crossinline|data|do|dynamic|else|enum|expect|external|final|finally|for|fun|get|if|import|in|infix|init|inline|inner|interface|internal|is|lateinit|noinline|null|object|open|operator|out|override|package|private|protected|public|reified|return|sealed|set|super|suspend|tailrec|this|throw|to|try|typealias|val|var|vararg|when|where|while)\b/,lookbehind:!0},function:[{pattern:/(?:`[^\r\n`]+`|\b\w+)(?=\s*\()/,greedy:!0},{pattern:/(\.)(?:`[^\r\n`]+`|\w+)(?=\s*\{)/,lookbehind:!0,greedy:!0}],number:/\b(?:0[xX][\da-fA-F]+(?:_[\da-fA-F]+)*|0[bB][01]+(?:_[01]+)*|\d+(?:_\d+)*(?:\.\d+(?:_\d+)*)?(?:[eE][+-]?\d+(?:_\d+)*)?[fFL]?)\b/,operator:/\+[+=]?|-[-=>]?|==?=?|!(?:!|==?)?|[\/*%<>]=?|[?:]:?|\.\.|&&|\|\||\b(?:and|inv|or|shl|shr|ushr|xor)\b/}),delete e.languages.kotlin["class-name"];var t={"interpolation-punctuation":{pattern:/^\$\{?|\}$/,alias:"punctuation"},expression:{pattern:/[\s\S]+/,inside:e.languages.kotlin}};e.languages.insertBefore("kotlin","string",{"string-literal":[{pattern:/"""(?:[^$]|\$(?:(?!\{)|\{[^{}]*\}))*?"""/,alias:"multiline",inside:{interpolation:{pattern:/\$(?:[a-z_]\w*|\{[^{}]*\})/i,inside:t},string:/[\s\S]+/}},{pattern:/"(?:[^"\\\r\n$]|\\.|\$(?:(?!\{)|\{[^{}]*\}))*"/,alias:"singleline",inside:{interpolation:{pattern:/((?:^|[^\\])(?:\\{2})*)\$(?:[a-z_]\w*|\{[^{}]*\})/i,lookbehind:!0,inside:t},string:/[\s\S]+/}}],char:{pattern:/'(?:[^'\\\r\n]|\\(?:.|u[a-fA-F0-9]{0,4}))'/,greedy:!0}}),delete e.languages.kotlin.string,e.languages.insertBefore("kotlin","keyword",{annotation:{pattern:/\B@(?:\w+:)?(?:[A-Z]\w*|\[[^\]]+\])/,alias:"builtin"}}),e.languages.insertBefore("kotlin","function",{label:{pattern:/\b\w+@|@\w+\b/,alias:"symbol"}}),e.languages.kt=e.languages.kotlin,e.languages.kts=e.languages.kotlin}(C),C.languages.c=C.languages.extend("clike",{comment:{pattern:/\/\/(?:[^\r\n\\]|\\(?:\r\n?|\n|(?![\r\n])))*|\/\*[\s\S]*?(?:\*\/|$)/,greedy:!0},string:{pattern:/"(?:\\(?:\r\n|[\s\S])|[^"\\\r\n])*"/,greedy:!0},"class-name":{pattern:/(\b(?:enum|struct)\s+(?:__attribute__\s*\(\([\s\S]*?\)\)\s*)?)\w+|\b[a-z]\w*_t\b/,lookbehind:!0},keyword:/\b(?:_Alignas|_Alignof|_Atomic|_Bool|_Complex|_Generic|_Imaginary|_Noreturn|_Static_assert|_Thread_local|__attribute__|asm|auto|break|case|char|const|continue|default|do|double|else|enum|extern|float|for|goto|if|inline|int|long|register|return|short|signed|sizeof|static|struct|switch|typedef|typeof|union|unsigned|void|volatile|while)\b/,function:/\b[a-z_]\w*(?=\s*\()/i,number:/(?:\b0x(?:[\da-f]+(?:\.[\da-f]*)?|\.[\da-f]+)(?:p[+-]?\d+)?|(?:\b\d+(?:\.\d*)?|\B\.\d+)(?:e[+-]?\d+)?)[ful]{0,4}/i,operator:/>>=?|<<=?|->|([-+&|:])\1|[?:~]|[-+*/%&|^!=<>]=?/}),C.languages.insertBefore("c","string",{char:{pattern:/'(?:\\(?:\r\n|[\s\S])|[^'\\\r\n]){0,32}'/,greedy:!0}}),C.languages.insertBefore("c","string",{macro:{pattern:/(^[\t ]*)#\s*[a-z](?:[^\r\n\\/]|\/(?!\*)|\/\*(?:[^*]|\*(?!\/))*\*\/|\\(?:\r\n|[\s\S]))*/im,lookbehind:!0,greedy:!0,alias:"property",inside:{string:[{pattern:/^(#\s*include\s*)<[^>]+>/,lookbehind:!0},C.languages.c.string],char:C.languages.c.char,comment:C.languages.c.comment,"macro-name":[{pattern:/(^#\s*define\s+)\w+\b(?!\()/i,lookbehind:!0},{pattern:/(^#\s*define\s+)\w+\b(?=\()/i,lookbehind:!0,alias:"function"}],directive:{pattern:/^(#\s*)[a-z]+/,lookbehind:!0,alias:"keyword"},"directive-hash":/^#/,punctuation:/##|\\(?=[\r\n])/,expression:{pattern:/\S[\s\S]*/,inside:C.languages.c}}}}),C.languages.insertBefore("c","function",{constant:/\b(?:EOF|NULL|SEEK_CUR|SEEK_END|SEEK_SET|__DATE__|__FILE__|__LINE__|__TIMESTAMP__|__TIME__|__func__|stderr|stdin|stdout)\b/}),delete C.languages.c.boolean,C.languages.objectivec=C.languages.extend("c",{string:{pattern:/@?"(?:\\(?:\r\n|[\s\S])|[^"\\\r\n])*"/,greedy:!0},keyword:/\b(?:asm|auto|break|case|char|const|continue|default|do|double|else|enum|extern|float|for|goto|if|in|inline|int|long|register|return|self|short|signed|sizeof|static|struct|super|switch|typedef|typeof|union|unsigned|void|volatile|while)\b|(?:@interface|@end|@implementation|@protocol|@class|@public|@protected|@private|@property|@try|@catch|@finally|@throw|@synthesize|@dynamic|@selector)\b/,operator:/-[->]?|\+\+?|!=?|<<?=?|>>?=?|==?|&&?|\|\|?|[~^%?*\/@]/}),delete C.languages.objectivec["class-name"],C.languages.objc=C.languages.objectivec,C.languages.reason=C.languages.extend("clike",{string:{pattern:/"(?:\\(?:\r\n|[\s\S])|[^\\\r\n"])*"/,greedy:!0},"class-name":/\b[A-Z]\w*/,keyword:/\b(?:and|as|assert|begin|class|constraint|do|done|downto|else|end|exception|external|for|fun|function|functor|if|in|include|inherit|initializer|lazy|let|method|module|mutable|new|nonrec|object|of|open|or|private|rec|sig|struct|switch|then|to|try|type|val|virtual|when|while|with)\b/,operator:/\.{3}|:[:=]|\|>|->|=(?:==?|>)?|<=?|>=?|[|^?'#!~`]|[+\-*\/]\.?|\b(?:asr|land|lor|lsl|lsr|lxor|mod)\b/}),C.languages.insertBefore("reason","class-name",{char:{pattern:/'(?:\\x[\da-f]{2}|\\o[0-3][0-7][0-7]|\\\d{3}|\\.|[^'\\\r\n])'/,greedy:!0},constructor:/\b[A-Z]\w*\b(?!\s*\.)/,label:{pattern:/\b[a-z]\w*(?=::)/,alias:"symbol"}}),delete C.languages.reason.function,function(e){for(var t=/\/\*(?:[^*/]|\*(?!\/)|\/(?!\*)|<self>)*\*\//.source,n=0;n<2;n++)t=t.replace(/<self>/g,(function(){return t}));t=t.replace(/<self>/g,(function(){return/[^\s\S]/.source})),e.languages.rust={comment:[{pattern:RegExp(/(^|[^\\])/.source+t),lookbehind:!0,greedy:!0},{pattern:/(^|[^\\:])\/\/.*/,lookbehind:!0,greedy:!0}],string:{pattern:/b?"(?:\\[\s\S]|[^\\"])*"|b?r(#*)"(?:[^"]|"(?!\1))*"\1/,greedy:!0},char:{pattern:/b?'(?:\\(?:x[0-7][\da-fA-F]|u\{(?:[\da-fA-F]_*){1,6}\}|.)|[^\\\r\n\t'])'/,greedy:!0},attribute:{pattern:/#!?\[(?:[^\[\]"]|"(?:\\[\s\S]|[^\\"])*")*\]/,greedy:!0,alias:"attr-name",inside:{string:null}},"closure-params":{pattern:/([=(,:]\s*|\bmove\s*)\|[^|]*\||\|[^|]*\|(?=\s*(?:\{|->))/,lookbehind:!0,greedy:!0,inside:{"closure-punctuation":{pattern:/^\||\|$/,alias:"punctuation"},rest:null}},"lifetime-annotation":{pattern:/'\w+/,alias:"symbol"},"fragment-specifier":{pattern:/(\$\w+:)[a-z]+/,lookbehind:!0,alias:"punctuation"},variable:/\$\w+/,"function-definition":{pattern:/(\bfn\s+)\w+/,lookbehind:!0,alias:"function"},"type-definition":{pattern:/(\b(?:enum|struct|trait|type|union)\s+)\w+/,lookbehind:!0,alias:"class-name"},"module-declaration":[{pattern:/(\b(?:crate|mod)\s+)[a-z][a-z_\d]*/,lookbehind:!0,alias:"namespace"},{pattern:/(\b(?:crate|self|super)\s*)::\s*[a-z][a-z_\d]*\b(?:\s*::(?:\s*[a-z][a-z_\d]*\s*::)*)?/,lookbehind:!0,alias:"namespace",inside:{punctuation:/::/}}],keyword:[/\b(?:Self|abstract|as|async|await|become|box|break|const|continue|crate|do|dyn|else|enum|extern|final|fn|for|if|impl|in|let|loop|macro|match|mod|move|mut|override|priv|pub|ref|return|self|static|struct|super|trait|try|type|typeof|union|unsafe|unsized|use|virtual|where|while|yield)\b/,/\b(?:bool|char|f(?:32|64)|[ui](?:8|16|32|64|128|size)|str)\b/],function:/\b[a-z_]\w*(?=\s*(?:::\s*<|\())/,macro:{pattern:/\b\w+!/,alias:"property"},constant:/\b[A-Z_][A-Z_\d]+\b/,"class-name":/\b[A-Z]\w*\b/,namespace:{pattern:/(?:\b[a-z][a-z_\d]*\s*::\s*)*\b[a-z][a-z_\d]*\s*::(?!\s*<)/,inside:{punctuation:/::/}},number:/\b(?:0x[\dA-Fa-f](?:_?[\dA-Fa-f])*|0o[0-7](?:_?[0-7])*|0b[01](?:_?[01])*|(?:(?:\d(?:_?\d)*)?\.)?\d(?:_?\d)*(?:[Ee][+-]?\d+)?)(?:_?(?:f32|f64|[iu](?:8|16|32|64|size)?))?\b/,boolean:/\b(?:false|true)\b/,punctuation:/->|\.\.=|\.{1,3}|::|[{}[\];(),:]/,operator:/[-+*\/%!^]=?|=[=>]?|&[&=]?|\|[|=]?|<<?=?|>>?=?|[@?]/},e.languages.rust["closure-params"].inside.rest=e.languages.rust,e.languages.rust.attribute.inside.string=e.languages.rust.string}(C),C.languages.go=C.languages.extend("clike",{string:{pattern:/(^|[^\\])"(?:\\.|[^"\\\r\n])*"|`[^`]*`/,lookbehind:!0,greedy:!0},keyword:/\b(?:break|case|chan|const|continue|default|defer|else|fallthrough|for|func|go(?:to)?|if|import|interface|map|package|range|return|select|struct|switch|type|var)\b/,boolean:/\b(?:_|false|iota|nil|true)\b/,number:[/\b0(?:b[01_]+|o[0-7_]+)i?\b/i,/\b0x(?:[a-f\d_]+(?:\.[a-f\d_]*)?|\.[a-f\d_]+)(?:p[+-]?\d+(?:_\d+)*)?i?(?!\w)/i,/(?:\b\d[\d_]*(?:\.[\d_]*)?|\B\.\d[\d_]*)(?:e[+-]?[\d_]+)?i?(?!\w)/i],operator:/[*\/%^!=]=?|\+[=+]?|-[=-]?|\|[=|]?|&(?:=|&|\^=?)?|>(?:>=?|=)?|<(?:<=?|=|-)?|:=|\.\.\./,builtin:/\b(?:append|bool|byte|cap|close|complex|complex(?:64|128)|copy|delete|error|float(?:32|64)|u?int(?:8|16|32|64)?|imag|len|make|new|panic|print(?:ln)?|real|recover|rune|string|uintptr)\b/}),C.languages.insertBefore("go","string",{char:{pattern:/'(?:\\.|[^'\\\r\n]){0,10}'/,greedy:!0}}),delete C.languages.go["class-name"],function(e){var t=/\b(?:alignas|alignof|asm|auto|bool|break|case|catch|char|char16_t|char32_t|char8_t|class|co_await|co_return|co_yield|compl|concept|const|const_cast|consteval|constexpr|constinit|continue|decltype|default|delete|do|double|dynamic_cast|else|enum|explicit|export|extern|final|float|for|friend|goto|if|import|inline|int|int16_t|int32_t|int64_t|int8_t|long|module|mutable|namespace|new|noexcept|nullptr|operator|override|private|protected|public|register|reinterpret_cast|requires|return|short|signed|sizeof|static|static_assert|static_cast|struct|switch|template|this|thread_local|throw|try|typedef|typeid|typename|uint16_t|uint32_t|uint64_t|uint8_t|union|unsigned|using|virtual|void|volatile|wchar_t|while)\b/,n=/\b(?!<keyword>)\w+(?:\s*\.\s*\w+)*\b/.source.replace(/<keyword>/g,(function(){return t.source}));e.languages.cpp=e.languages.extend("c",{"class-name":[{pattern:RegExp(/(\b(?:class|concept|enum|struct|typename)\s+)(?!<keyword>)\w+/.source.replace(/<keyword>/g,(function(){return t.source}))),lookbehind:!0},/\b[A-Z]\w*(?=\s*::\s*\w+\s*\()/,/\b[A-Z_]\w*(?=\s*::\s*~\w+\s*\()/i,/\b\w+(?=\s*<(?:[^<>]|<(?:[^<>]|<[^<>]*>)*>)*>\s*::\s*\w+\s*\()/],keyword:t,number:{pattern:/(?:\b0b[01']+|\b0x(?:[\da-f']+(?:\.[\da-f']*)?|\.[\da-f']+)(?:p[+-]?[\d']+)?|(?:\b[\d']+(?:\.[\d']*)?|\B\.[\d']+)(?:e[+-]?[\d']+)?)[ful]{0,4}/i,greedy:!0},operator:/>>=?|<<=?|->|--|\+\+|&&|\|\||[?:~]|<=>|[-+*/%&|^!=<>]=?|\b(?:and|and_eq|bitand|bitor|not|not_eq|or|or_eq|xor|xor_eq)\b/,boolean:/\b(?:false|true)\b/}),e.languages.insertBefore("cpp","string",{module:{pattern:RegExp(/(\b(?:import|module)\s+)/.source+"(?:"+/"(?:\\(?:\r\n|[\s\S])|[^"\\\r\n])*"|<[^<>\r\n]*>/.source+"|"+/<mod-name>(?:\s*:\s*<mod-name>)?|:\s*<mod-name>/.source.replace(/<mod-name>/g,(function(){return n}))+")"),lookbehind:!0,greedy:!0,inside:{string:/^[<"][\s\S]+/,operator:/:/,punctuation:/\./}},"raw-string":{pattern:/R"([^()\\ 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\t]+)[a-zA-Z_]\w*(?=\s*\()/g,lookbehind:!0},"class-name":{pattern:/(\bclass\s+)\w+/i,lookbehind:!0},decorator:{pattern:/(^[\t 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e.languages.tsx["literal-property"],e.languages.tsx.tag)).pattern=RegExp(/(^|[^\w$]|(?=<\/))/.source+"(?:"+t.pattern.source+")",t.pattern.flags),t.lookbehind=!0}(C),C.languages.swift={comment:{pattern:/(^|[^\\:])(?:\/\/.*|\/\*(?:[^/*]|\/(?!\*)|\*(?!\/)|\/\*(?:[^*]|\*(?!\/))*\*\/)*\*\/)/,lookbehind:!0,greedy:!0},"string-literal":[{pattern:RegExp(/(^|[^"#])/.source+"(?:"+/"(?:\\(?:\((?:[^()]|\([^()]*\))*\)|\r\n|[^(])|[^\\\r\n"])*"/.source+"|"+/"""(?:\\(?:\((?:[^()]|\([^()]*\))*\)|[^(])|[^\\"]|"(?!""))*"""/.source+")"+/(?!["#])/.source),lookbehind:!0,greedy:!0,inside:{interpolation:{pattern:/(\\\()(?:[^()]|\([^()]*\))*(?=\))/,lookbehind:!0,inside:null},"interpolation-punctuation":{pattern:/^\)|\\\($/,alias:"punctuation"},punctuation:/\\(?=[\r\n])/,string:/[\s\S]+/}},{pattern:RegExp(/(^|[^"#])(#+)/.source+"(?:"+/"(?:\\(?:#+\((?:[^()]|\([^()]*\))*\)|\r\n|[^#])|[^\\\r\n])*?"/.source+"|"+/"""(?:\\(?:#+\((?:[^()]|\([^()]*\))*\)|[^#])|[^\\])*?"""/.source+")\\2"),lookbehind:!0,greedy:!0,inside:{interpolation:{pattern:/(\\#+\()(?:[^()]|\([^()]*\))*(?=\))/,lookbehind:!0,inside:null},"interpolation-punctuation":{pattern:/^\)|\\#+\($/,alias:"punctuation"},string:/[\s\S]+/}}],directive:{pattern:RegExp(/#/.source+"(?:"+/(?:elseif|if)\b/.source+"(?:[ 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\t]*(?:&&|\|\|))?/.source+")+|"+/(?:else|endif)\b/.source+")"),alias:"property",inside:{"directive-name":/^#\w+/,boolean:/\b(?:false|true)\b/,number:/\b\d+(?:\.\d+)*\b/,operator:/!|&&|\|\||[<>]=?/,punctuation:/[(),]/}},literal:{pattern:/#(?:colorLiteral|column|dsohandle|file(?:ID|Literal|Path)?|function|imageLiteral|line)\b/,alias:"constant"},"other-directive":{pattern:/#\w+\b/,alias:"property"},attribute:{pattern:/@\w+/,alias:"atrule"},"function-definition":{pattern:/(\bfunc\s+)\w+/,lookbehind:!0,alias:"function"},label:{pattern:/\b(break|continue)\s+\w+|\b[a-zA-Z_]\w*(?=\s*:\s*(?:for|repeat|while)\b)/,lookbehind:!0,alias:"important"},keyword:/\b(?:Any|Protocol|Self|Type|actor|as|assignment|associatedtype|associativity|async|await|break|case|catch|class|continue|convenience|default|defer|deinit|didSet|do|dynamic|else|enum|extension|fallthrough|fileprivate|final|for|func|get|guard|higherThan|if|import|in|indirect|infix|init|inout|internal|is|isolated|lazy|left|let|lowerThan|mutating|none|nonisolated|nonmutating|open|operator|optional|override|postfix|precedencegroup|prefix|private|protocol|public|repeat|required|rethrows|return|right|safe|self|set|some|static|struct|subscript|super|switch|throw|throws|try|typealias|unowned|unsafe|var|weak|where|while|willSet)\b/,boolean:/\b(?:false|true)\b/,nil:{pattern:/\bnil\b/,alias:"constant"},"short-argument":/\$\d+\b/,omit:{pattern:/\b_\b/,alias:"keyword"},number:/\b(?:[\d_]+(?:\.[\de_]+)?|0x[a-f0-9_]+(?:\.[a-f0-9p_]+)?|0b[01_]+|0o[0-7_]+)\b/i,"class-name":/\b[A-Z](?:[A-Z_\d]*[a-z]\w*)?\b/,function:/\b[a-z_]\w*(?=\s*\()/i,constant:/\b(?:[A-Z_]{2,}|k[A-Z][A-Za-z_]+)\b/,operator:/[-+*/%=!<>&|^~?]+|\.[.\-+*/%=!<>&|^~?]+/,punctuation:/[{}[\]();,.:\\]/},C.languages.swift["string-literal"].forEach((function(e){e.inside.interpolation.inside=C.languages.swift})),function(e){e.languages.kotlin=e.languages.extend("clike",{keyword:{pattern:/(^|[^.])\b(?:abstract|actual|annotation|as|break|by|catch|class|companion|const|constructor|continue|crossinline|data|do|dynamic|else|enum|expect|external|final|finally|for|fun|get|if|import|in|infix|init|inline|inner|interface|internal|is|lateinit|noinline|null|object|open|operator|out|override|package|private|protected|public|reified|return|sealed|set|super|suspend|tailrec|this|throw|to|try|typealias|val|var|vararg|when|where|while)\b/,lookbehind:!0},function:[{pattern:/(?:`[^\r\n`]+`|\b\w+)(?=\s*\()/,greedy:!0},{pattern:/(\.)(?:`[^\r\n`]+`|\w+)(?=\s*\{)/,lookbehind:!0,greedy:!0}],number:/\b(?:0[xX][\da-fA-F]+(?:_[\da-fA-F]+)*|0[bB][01]+(?:_[01]+)*|\d+(?:_\d+)*(?:\.\d+(?:_\d+)*)?(?:[eE][+-]?\d+(?:_\d+)*)?[fFL]?)\b/,operator:/\+[+=]?|-[-=>]?|==?=?|!(?:!|==?)?|[\/*%<>]=?|[?:]:?|\.\.|&&|\|\||\b(?:and|inv|or|shl|shr|ushr|xor)\b/}),delete e.languages.kotlin["class-name"];var t={"interpolation-punctuation":{pattern:/^\$\{?|\}$/,alias:"punctuation"},expression:{pattern:/[\s\S]+/,inside:e.languages.kotlin}};e.languages.insertBefore("kotlin","string",{"string-literal":[{pattern:/"""(?:[^$]|\$(?:(?!\{)|\{[^{}]*\}))*?"""/,alias:"multiline",inside:{interpolation:{pattern:/\$(?:[a-z_]\w*|\{[^{}]*\})/i,inside:t},string:/[\s\S]+/}},{pattern:/"(?:[^"\\\r\n$]|\\.|\$(?:(?!\{)|\{[^{}]*\}))*"/,alias:"singleline",inside:{interpolation:{pattern:/((?:^|[^\\])(?:\\{2})*)\$(?:[a-z_]\w*|\{[^{}]*\})/i,lookbehind:!0,inside:t},string:/[\s\S]+/}}],char:{pattern:/'(?:[^'\\\r\n]|\\(?:.|u[a-fA-F0-9]{0,4}))'/,greedy:!0}}),delete e.languages.kotlin.string,e.languages.insertBefore("kotlin","keyword",{annotation:{pattern:/\B@(?:\w+:)?(?:[A-Z]\w*|\[[^\]]+\])/,alias:"builtin"}}),e.languages.insertBefore("kotlin","function",{label:{pattern:/\b\w+@|@\w+\b/,alias:"symbol"}}),e.languages.kt=e.languages.kotlin,e.languages.kts=e.languages.kotlin}(C),C.languages.c=C.languages.extend("clike",{comment:{pattern:/\/\/(?:[^\r\n\\]|\\(?:\r\n?|\n|(?![\r\n])))*|\/\*[\s\S]*?(?:\*\/|$)/,greedy:!0},string:{pattern:/"(?:\\(?:\r\n|[\s\S])|[^"\\\r\n])*"/,greedy:!0},"class-name":{pattern:/(\b(?:enum|struct)\s+(?:__attribute__\s*\(\([\s\S]*?\)\)\s*)?)\w+|\b[a-z]\w*_t\b/,lookbehind:!0},keyword:/\b(?:_Alignas|_Alignof|_Atomic|_Bool|_Complex|_Generic|_Imaginary|_Noreturn|_Static_assert|_Thread_local|__attribute__|asm|auto|break|case|char|const|continue|default|do|double|else|enum|extern|float|for|goto|if|inline|int|long|register|return|short|signed|sizeof|static|struct|switch|typedef|typeof|union|unsigned|void|volatile|while)\b/,function:/\b[a-z_]\w*(?=\s*\()/i,number:/(?:\b0x(?:[\da-f]+(?:\.[\da-f]*)?|\.[\da-f]+)(?:p[+-]?\d+)?|(?:\b\d+(?:\.\d*)?|\B\.\d+)(?:e[+-]?\d+)?)[ful]{0,4}/i,operator:/>>=?|<<=?|->|([-+&|:])\1|[?:~]|[-+*/%&|^!=<>]=?/}),C.languages.insertBefore("c","string",{char:{pattern:/'(?:\\(?:\r\n|[\s\S])|[^'\\\r\n]){0,32}'/,greedy:!0}}),C.languages.insertBefore("c","string",{macro:{pattern:/(^[\t ]*)#\s*[a-z](?:[^\r\n\\/]|\/(?!\*)|\/\*(?:[^*]|\*(?!\/))*\*\/|\\(?:\r\n|[\s\S]))*/im,lookbehind:!0,greedy:!0,alias:"property",inside:{string:[{pattern:/^(#\s*include\s*)<[^>]+>/,lookbehind:!0},C.languages.c.string],char:C.languages.c.char,comment:C.languages.c.comment,"macro-name":[{pattern:/(^#\s*define\s+)\w+\b(?!\()/i,lookbehind:!0},{pattern:/(^#\s*define\s+)\w+\b(?=\()/i,lookbehind:!0,alias:"function"}],directive:{pattern:/^(#\s*)[a-z]+/,lookbehind:!0,alias:"keyword"},"directive-hash":/^#/,punctuation:/##|\\(?=[\r\n])/,expression:{pattern:/\S[\s\S]*/,inside:C.languages.c}}}}),C.languages.insertBefore("c","function",{constant:/\b(?:EOF|NULL|SEEK_CUR|SEEK_END|SEEK_SET|__DATE__|__FILE__|__LINE__|__TIMESTAMP__|__TIME__|__func__|stderr|stdin|stdout)\b/}),delete C.languages.c.boolean,C.languages.objectivec=C.languages.extend("c",{string:{pattern:/@?"(?:\\(?:\r\n|[\s\S])|[^"\\\r\n])*"/,greedy:!0},keyword:/\b(?:asm|auto|break|case|char|const|continue|default|do|double|else|enum|extern|float|for|goto|if|in|inline|int|long|register|return|self|short|signed|sizeof|static|struct|super|switch|typedef|typeof|union|unsigned|void|volatile|while)\b|(?:@interface|@end|@implementation|@protocol|@class|@public|@protected|@private|@property|@try|@catch|@finally|@throw|@synthesize|@dynamic|@selector)\b/,operator:/-[->]?|\+\+?|!=?|<<?=?|>>?=?|==?|&&?|\|\|?|[~^%?*\/@]/}),delete C.languages.objectivec["class-name"],C.languages.objc=C.languages.objectivec,C.languages.reason=C.languages.extend("clike",{string:{pattern:/"(?:\\(?:\r\n|[\s\S])|[^\\\r\n"])*"/,greedy:!0},"class-name":/\b[A-Z]\w*/,keyword:/\b(?:and|as|assert|begin|class|constraint|do|done|downto|else|end|exception|external|for|fun|function|functor|if|in|include|inherit|initializer|lazy|let|method|module|mutable|new|nonrec|object|of|open|or|private|rec|sig|struct|switch|then|to|try|type|val|virtual|when|while|with)\b/,operator:/\.{3}|:[:=]|\|>|->|=(?:==?|>)?|<=?|>=?|[|^?'#!~`]|[+\-*\/]\.?|\b(?:asr|land|lor|lsl|lsr|lxor|mod)\b/}),C.languages.insertBefore("reason","class-name",{char:{pattern:/'(?:\\x[\da-f]{2}|\\o[0-3][0-7][0-7]|\\\d{3}|\\.|[^'\\\r\n])'/,greedy:!0},constructor:/\b[A-Z]\w*\b(?!\s*\.)/,label:{pattern:/\b[a-z]\w*(?=::)/,alias:"symbol"}}),delete C.languages.reason.function,function(e){for(var t=/\/\*(?:[^*/]|\*(?!\/)|\/(?!\*)|<self>)*\*\//.source,n=0;n<2;n++)t=t.replace(/<self>/g,(function(){return t}));t=t.replace(/<self>/g,(function(){return/[^\s\S]/.source})),e.languages.rust={comment:[{pattern:RegExp(/(^|[^\\])/.source+t),lookbehind:!0,greedy:!0},{pattern:/(^|[^\\:])\/\/.*/,lookbehind:!0,greedy:!0}],string:{pattern:/b?"(?:\\[\s\S]|[^\\"])*"|b?r(#*)"(?:[^"]|"(?!\1))*"\1/,greedy:!0},char:{pattern:/b?'(?:\\(?:x[0-7][\da-fA-F]|u\{(?:[\da-fA-F]_*){1,6}\}|.)|[^\\\r\n\t'])'/,greedy:!0},attribute:{pattern:/#!?\[(?:[^\[\]"]|"(?:\\[\s\S]|[^\\"])*")*\]/,greedy:!0,alias:"attr-name",inside:{string:null}},"closure-params":{pattern:/([=(,:]\s*|\bmove\s*)\|[^|]*\||\|[^|]*\|(?=\s*(?:\{|->))/,lookbehind:!0,greedy:!0,inside:{"closure-punctuation":{pattern:/^\||\|$/,alias:"punctuation"},rest:null}},"lifetime-annotation":{pattern:/'\w+/,alias:"symbol"},"fragment-specifier":{pattern:/(\$\w+:)[a-z]+/,lookbehind:!0,alias:"punctuation"},variable:/\$\w+/,"function-definition":{pattern:/(\bfn\s+)\w+/,lookbehind:!0,alias:"function"},"type-definition":{pattern:/(\b(?:enum|struct|trait|type|union)\s+)\w+/,lookbehind:!0,alias:"class-name"},"module-declaration":[{pattern:/(\b(?:crate|mod)\s+)[a-z][a-z_\d]*/,lookbehind:!0,alias:"namespace"},{pattern:/(\b(?:crate|self|super)\s*)::\s*[a-z][a-z_\d]*\b(?:\s*::(?:\s*[a-z][a-z_\d]*\s*::)*)?/,lookbehind:!0,alias:"namespace",inside:{punctuation:/::/}}],keyword:[/\b(?:Self|abstract|as|async|await|become|box|break|const|continue|crate|do|dyn|else|enum|extern|final|fn|for|if|impl|in|let|loop|macro|match|mod|move|mut|override|priv|pub|ref|return|self|static|struct|super|trait|try|type|typeof|union|unsafe|unsized|use|virtual|where|while|yield)\b/,/\b(?:bool|char|f(?:32|64)|[ui](?:8|16|32|64|128|size)|str)\b/],function:/\b[a-z_]\w*(?=\s*(?:::\s*<|\())/,macro:{pattern:/\b\w+!/,alias:"property"},constant:/\b[A-Z_][A-Z_\d]+\b/,"class-name":/\b[A-Z]\w*\b/,namespace:{pattern:/(?:\b[a-z][a-z_\d]*\s*::\s*)*\b[a-z][a-z_\d]*\s*::(?!\s*<)/,inside:{punctuation:/::/}},number:/\b(?:0x[\dA-Fa-f](?:_?[\dA-Fa-f])*|0o[0-7](?:_?[0-7])*|0b[01](?:_?[01])*|(?:(?:\d(?:_?\d)*)?\.)?\d(?:_?\d)*(?:[Ee][+-]?\d+)?)(?:_?(?:f32|f64|[iu](?:8|16|32|64|size)?))?\b/,boolean:/\b(?:false|true)\b/,punctuation:/->|\.\.=|\.{1,3}|::|[{}[\];(),:]/,operator:/[-+*\/%!^]=?|=[=>]?|&[&=]?|\|[|=]?|<<?=?|>>?=?|[@?]/},e.languages.rust["closure-params"].inside.rest=e.languages.rust,e.languages.rust.attribute.inside.string=e.languages.rust.string}(C),C.languages.go=C.languages.extend("clike",{string:{pattern:/(^|[^\\])"(?:\\.|[^"\\\r\n])*"|`[^`]*`/,lookbehind:!0,greedy:!0},keyword:/\b(?:break|case|chan|const|continue|default|defer|else|fallthrough|for|func|go(?:to)?|if|import|interface|map|package|range|return|select|struct|switch|type|var)\b/,boolean:/\b(?:_|false|iota|nil|true)\b/,number:[/\b0(?:b[01_]+|o[0-7_]+)i?\b/i,/\b0x(?:[a-f\d_]+(?:\.[a-f\d_]*)?|\.[a-f\d_]+)(?:p[+-]?\d+(?:_\d+)*)?i?(?!\w)/i,/(?:\b\d[\d_]*(?:\.[\d_]*)?|\B\.\d[\d_]*)(?:e[+-]?[\d_]+)?i?(?!\w)/i],operator:/[*\/%^!=]=?|\+[=+]?|-[=-]?|\|[=|]?|&(?:=|&|\^=?)?|>(?:>=?|=)?|<(?:<=?|=|-)?|:=|\.\.\./,builtin:/\b(?:append|bool|byte|cap|close|complex|complex(?:64|128)|copy|delete|error|float(?:32|64)|u?int(?:8|16|32|64)?|imag|len|make|new|panic|print(?:ln)?|real|recover|rune|string|uintptr)\b/}),C.languages.insertBefore("go","string",{char:{pattern:/'(?:\\.|[^'\\\r\n]){0,10}'/,greedy:!0}}),delete C.languages.go["class-name"],function(e){var t=/\b(?:alignas|alignof|asm|auto|bool|break|case|catch|char|char16_t|char32_t|char8_t|class|co_await|co_return|co_yield|compl|concept|const|const_cast|consteval|constexpr|constinit|continue|decltype|default|delete|do|double|dynamic_cast|else|enum|explicit|export|extern|final|float|for|friend|goto|if|import|inline|int|int16_t|int32_t|int64_t|int8_t|long|module|mutable|namespace|new|noexcept|nullptr|operator|override|private|protected|public|register|reinterpret_cast|requires|return|short|signed|sizeof|static|static_assert|static_cast|struct|switch|template|this|thread_local|throw|try|typedef|typeid|typename|uint16_t|uint32_t|uint64_t|uint8_t|union|unsigned|using|virtual|void|volatile|wchar_t|while)\b/,n=/\b(?!<keyword>)\w+(?:\s*\.\s*\w+)*\b/.source.replace(/<keyword>/g,(function(){return t.source}));e.languages.cpp=e.languages.extend("c",{"class-name":[{pattern:RegExp(/(\b(?:class|concept|enum|struct|typename)\s+)(?!<keyword>)\w+/.source.replace(/<keyword>/g,(function(){return t.source}))),lookbehind:!0},/\b[A-Z]\w*(?=\s*::\s*\w+\s*\()/,/\b[A-Z_]\w*(?=\s*::\s*~\w+\s*\()/i,/\b\w+(?=\s*<(?:[^<>]|<(?:[^<>]|<[^<>]*>)*>)*>\s*::\s*\w+\s*\()/],keyword:t,number:{pattern:/(?:\b0b[01']+|\b0x(?:[\da-f']+(?:\.[\da-f']*)?|\.[\da-f']+)(?:p[+-]?[\d']+)?|(?:\b[\d']+(?:\.[\d']*)?|\B\.[\d']+)(?:e[+-]?[\d']+)?)[ful]{0,4}/i,greedy:!0},operator:/>>=?|<<=?|->|--|\+\+|&&|\|\||[?:~]|<=>|[-+*/%&|^!=<>]=?|\b(?:and|and_eq|bitand|bitor|not|not_eq|or|or_eq|xor|xor_eq)\b/,boolean:/\b(?:false|true)\b/}),e.languages.insertBefore("cpp","string",{module:{pattern:RegExp(/(\b(?:import|module)\s+)/.source+"(?:"+/"(?:\\(?:\r\n|[\s\S])|[^"\\\r\n])*"|<[^<>\r\n]*>/.source+"|"+/<mod-name>(?:\s*:\s*<mod-name>)?|:\s*<mod-name>/.source.replace(/<mod-name>/g,(function(){return n}))+")"),lookbehind:!0,greedy:!0,inside:{string:/^[<"][\s\S]+/,operator:/:/,punctuation:/\./}},"raw-string":{pattern:/R"([^()\\ 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\t]+)[a-zA-Z_]\w*(?=\s*\()/g,lookbehind:!0},"class-name":{pattern:/(\bclass\s+)\w+/i,lookbehind:!0},decorator:{pattern:/(^[\t 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Lorem ipsum dolor sit amet"><header><h1 class="title_f1Hy" itemprop="headline">First Blog Post</h1><div class="container_mt6G margin-vert--md"><time datetime="2019-05-28T00:00:00.000Z" itemprop="datePublished">May 28, 2019</time> · <!-- -->One min read</div><div class="margin-top--md margin-bottom--sm row"><div class="col col--6 authorCol_Hf19"><div class="avatar margin-bottom--sm"><a href="https://github.com/wgao19" target="_blank" rel="noopener noreferrer" class="avatar__photo-link"><img class="avatar__photo" src="https://github.com/wgao19.png" alt="Gao Wei" itemprop="image"></a><div class="avatar__intro" itemprop="author" itemscope="" itemtype="https://schema.org/Person"><div class="avatar__name"><a href="https://github.com/wgao19" target="_blank" rel="noopener noreferrer" itemprop="url"><span itemprop="name">Gao Wei</span></a></div><small class="avatar__subtitle" itemprop="description">Docusaurus Core Team</small></div></div></div></div></header><div id="__blog-post-container" class="markdown" itemprop="articleBody"><p>Lorem ipsum dolor sit amet, consectetur adipiscing elit. 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class="sidebarItemLink_mo7H" href="/blog/first-blog-post">First Blog Post</a></li></ul></nav></aside><main class="col col--7" itemscope="" itemtype="https://schema.org/Blog"><article class="margin-bottom--xl" itemprop="blogPost" itemscope="" itemtype="https://schema.org/BlogPosting"><meta itemprop="description" content="Docusaurus blogging features are powered by the blog plugin."><header><h2 class="title_f1Hy" itemprop="headline"><a itemprop="url" href="/blog/welcome">Welcome</a></h2><div class="container_mt6G margin-vert--md"><time datetime="2021-08-26T00:00:00.000Z" itemprop="datePublished">August 26, 2021</time> · <!-- -->One min read</div><div class="margin-top--md margin-bottom--sm row"><div class="col col--6 authorCol_Hf19"><div class="avatar margin-bottom--sm"><a href="https://sebastienlorber.com" target="_blank" rel="noopener noreferrer" class="avatar__photo-link"><img class="avatar__photo" src="https://github.com/slorber.png" alt="Sébastien Lorber" itemprop="image"></a><div class="avatar__intro" itemprop="author" itemscope="" itemtype="https://schema.org/Person"><div class="avatar__name"><a href="https://sebastienlorber.com" target="_blank" rel="noopener noreferrer" itemprop="url"><span itemprop="name">Sébastien Lorber</span></a></div><small class="avatar__subtitle" itemprop="description">Docusaurus maintainer</small></div></div></div><div class="col col--6 authorCol_Hf19"><div class="avatar margin-bottom--sm"><a href="https://github.com/yangshun" target="_blank" rel="noopener noreferrer" class="avatar__photo-link"><img class="avatar__photo" src="https://github.com/yangshun.png" alt="Yangshun Tay" itemprop="image"></a><div class="avatar__intro" itemprop="author" itemscope="" itemtype="https://schema.org/Person"><div class="avatar__name"><a href="https://github.com/yangshun" target="_blank" rel="noopener noreferrer" itemprop="url"><span itemprop="name">Yangshun Tay</span></a></div><small class="avatar__subtitle" itemprop="description">Front End Engineer @ Facebook</small></div></div></div></div></header><div class="markdown" itemprop="articleBody"><p><a href="https://docusaurus.io/docs/blog" target="_blank" rel="noopener noreferrer">Docusaurus blogging features</a> are powered by the <a href="https://docusaurus.io/docs/api/plugins/@docusaurus/plugin-content-blog" target="_blank" rel="noopener noreferrer">blog plugin</a>.</p>
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index 4e1d8a1f..0b8d7b1b 100644
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Post</a></li><li class="sidebarItem__DBe"><a class="sidebarItemLink_mo7H" href="/blog/first-blog-post">First Blog Post</a></li></ul></nav></aside><main class="col col--7" itemscope="" itemtype="https://schema.org/Blog"><article itemprop="blogPost" itemscope="" itemtype="https://schema.org/BlogPosting"><meta itemprop="description" content="This is the summary of a very long blog post,"><header><h1 class="title_f1Hy" itemprop="headline">Long Blog Post</h1><div class="container_mt6G margin-vert--md"><time datetime="2019-05-29T00:00:00.000Z" itemprop="datePublished">May 29, 2019</time> · <!-- -->3 min read</div><div class="margin-top--md margin-bottom--sm row"><div class="col col--6 authorCol_Hf19"><div class="avatar margin-bottom--sm"><a href="https://github.com/endiliey" target="_blank" rel="noopener noreferrer" class="avatar__photo-link"><img class="avatar__photo" src="https://github.com/endiliey.png" alt="Endilie Yacop Sucipto" itemprop="image"></a><div class="avatar__intro" itemprop="author" itemscope="" itemtype="https://schema.org/Person"><div class="avatar__name"><a href="https://github.com/endiliey" target="_blank" rel="noopener noreferrer" itemprop="url"><span itemprop="name">Endilie Yacop Sucipto</span></a></div><small class="avatar__subtitle" itemprop="description">Maintainer of Docusaurus</small></div></div></div></div></header><div id="__blog-post-container" class="markdown" itemprop="articleBody"><p>This is the summary of a very long blog post,</p>
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Post</a></li><li class="sidebarItem__DBe"><a class="sidebarItemLink_mo7H" href="/blog/first-blog-post">First Blog Post</a></li></ul></nav></aside><main class="col col--7" itemscope="" itemtype="https://schema.org/Blog"><article itemprop="blogPost" itemscope="" itemtype="https://schema.org/BlogPosting"><meta itemprop="description" content="Blog posts support Docusaurus Markdown features, such as MDX."><header><h1 class="title_f1Hy" itemprop="headline">MDX Blog Post</h1><div class="container_mt6G margin-vert--md"><time datetime="2021-08-01T00:00:00.000Z" itemprop="datePublished">August 1, 2021</time> · <!-- -->One min read</div><div class="margin-top--md margin-bottom--sm row"><div class="col col--6 authorCol_Hf19"><div class="avatar margin-bottom--sm"><a href="https://sebastienlorber.com" target="_blank" rel="noopener noreferrer" class="avatar__photo-link"><img class="avatar__photo" src="https://github.com/slorber.png" alt="Sébastien Lorber" itemprop="image"></a><div class="avatar__intro" itemprop="author" itemscope="" itemtype="https://schema.org/Person"><div class="avatar__name"><a href="https://sebastienlorber.com" target="_blank" rel="noopener noreferrer" itemprop="url"><span itemprop="name">Sébastien Lorber</span></a></div><small class="avatar__subtitle" itemprop="description">Docusaurus maintainer</small></div></div></div></div></header><div id="__blog-post-container" class="markdown" itemprop="articleBody"><p>Blog posts support <a href="https://docusaurus.io/docs/markdown-features" target="_blank" rel="noopener noreferrer">Docusaurus Markdown features</a>, such as <a href="https://mdxjs.com/" target="_blank" rel="noopener noreferrer">MDX</a>.</p>
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class="sidebarItemLink_mo7H" href="/blog/first-blog-post">First Blog Post</a></li></ul></nav></aside><main class="col col--7" itemscope="" itemtype="https://schema.org/Blog"><header class="margin-bottom--xl"><h1>4 posts tagged with &quot;docusaurus&quot;</h1><a href="/blog/tags">View All Tags</a></header><article class="margin-bottom--xl" itemprop="blogPost" itemscope="" itemtype="https://schema.org/BlogPosting"><meta itemprop="description" content="Docusaurus blogging features are powered by the blog plugin."><header><h2 class="title_f1Hy" itemprop="headline"><a itemprop="url" href="/blog/welcome">Welcome</a></h2><div class="container_mt6G margin-vert--md"><time datetime="2021-08-26T00:00:00.000Z" itemprop="datePublished">August 26, 2021</time> · <!-- -->One min read</div><div class="margin-top--md margin-bottom--sm row"><div class="col col--6 authorCol_Hf19"><div class="avatar margin-bottom--sm"><a href="https://sebastienlorber.com" target="_blank" rel="noopener noreferrer" class="avatar__photo-link"><img class="avatar__photo" src="https://github.com/slorber.png" alt="Sébastien Lorber" itemprop="image"></a><div class="avatar__intro" itemprop="author" itemscope="" itemtype="https://schema.org/Person"><div class="avatar__name"><a href="https://sebastienlorber.com" target="_blank" rel="noopener noreferrer" itemprop="url"><span itemprop="name">Sébastien Lorber</span></a></div><small class="avatar__subtitle" itemprop="description">Docusaurus maintainer</small></div></div></div><div class="col col--6 authorCol_Hf19"><div class="avatar margin-bottom--sm"><a href="https://github.com/yangshun" target="_blank" rel="noopener noreferrer" class="avatar__photo-link"><img class="avatar__photo" src="https://github.com/yangshun.png" alt="Yangshun Tay" itemprop="image"></a><div class="avatar__intro" itemprop="author" itemscope="" itemtype="https://schema.org/Person"><div class="avatar__name"><a href="https://github.com/yangshun" target="_blank" rel="noopener noreferrer" itemprop="url"><span itemprop="name">Yangshun Tay</span></a></div><small class="avatar__subtitle" itemprop="description">Front End Engineer @ Facebook</small></div></div></div></div></header><div class="markdown" itemprop="articleBody"><p><a href="https://docusaurus.io/docs/blog" target="_blank" rel="noopener noreferrer">Docusaurus blogging features</a> are powered by the <a href="https://docusaurus.io/docs/api/plugins/@docusaurus/plugin-content-blog" target="_blank" rel="noopener noreferrer">blog plugin</a>.</p>
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class="sidebarItemLink_mo7H" href="/blog/first-blog-post">First Blog Post</a></li></ul></nav></aside><main class="col col--7" itemscope="" itemtype="https://schema.org/Blog"><header class="margin-bottom--xl"><h1>One post tagged with &quot;facebook&quot;</h1><a href="/blog/tags">View All Tags</a></header><article class="margin-bottom--xl" itemprop="blogPost" itemscope="" itemtype="https://schema.org/BlogPosting"><meta itemprop="description" content="Docusaurus blogging features are powered by the blog plugin."><header><h2 class="title_f1Hy" itemprop="headline"><a itemprop="url" href="/blog/welcome">Welcome</a></h2><div class="container_mt6G margin-vert--md"><time datetime="2021-08-26T00:00:00.000Z" itemprop="datePublished">August 26, 2021</time> · <!-- -->One min read</div><div class="margin-top--md margin-bottom--sm row"><div class="col col--6 authorCol_Hf19"><div class="avatar margin-bottom--sm"><a href="https://sebastienlorber.com" target="_blank" rel="noopener noreferrer" class="avatar__photo-link"><img class="avatar__photo" src="https://github.com/slorber.png" alt="Sébastien Lorber" itemprop="image"></a><div class="avatar__intro" itemprop="author" itemscope="" itemtype="https://schema.org/Person"><div class="avatar__name"><a href="https://sebastienlorber.com" target="_blank" rel="noopener noreferrer" itemprop="url"><span itemprop="name">Sébastien Lorber</span></a></div><small class="avatar__subtitle" itemprop="description">Docusaurus maintainer</small></div></div></div><div class="col col--6 authorCol_Hf19"><div class="avatar margin-bottom--sm"><a href="https://github.com/yangshun" target="_blank" rel="noopener noreferrer" class="avatar__photo-link"><img class="avatar__photo" src="https://github.com/yangshun.png" alt="Yangshun Tay" itemprop="image"></a><div class="avatar__intro" itemprop="author" itemscope="" itemtype="https://schema.org/Person"><div class="avatar__name"><a href="https://github.com/yangshun" target="_blank" rel="noopener noreferrer" itemprop="url"><span itemprop="name">Yangshun Tay</span></a></div><small class="avatar__subtitle" itemprop="description">Front End Engineer @ Facebook</small></div></div></div></div></header><div class="markdown" itemprop="articleBody"><p><a href="https://docusaurus.io/docs/blog" target="_blank" rel="noopener noreferrer">Docusaurus blogging features</a> are powered by the <a href="https://docusaurus.io/docs/api/plugins/@docusaurus/plugin-content-blog" target="_blank" rel="noopener noreferrer">blog plugin</a>.</p>
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class="sidebarItemLink_mo7H" href="/blog/first-blog-post">First Blog Post</a></li></ul></nav></aside><main class="col col--7" itemscope="" itemtype="https://schema.org/Blog"><header class="margin-bottom--xl"><h1>2 posts tagged with &quot;hello&quot;</h1><a href="/blog/tags">View All Tags</a></header><article class="margin-bottom--xl" itemprop="blogPost" itemscope="" itemtype="https://schema.org/BlogPosting"><meta itemprop="description" content="Docusaurus blogging features are powered by the blog plugin."><header><h2 class="title_f1Hy" itemprop="headline"><a itemprop="url" href="/blog/welcome">Welcome</a></h2><div class="container_mt6G margin-vert--md"><time datetime="2021-08-26T00:00:00.000Z" itemprop="datePublished">August 26, 2021</time> · <!-- -->One min read</div><div class="margin-top--md margin-bottom--sm row"><div class="col col--6 authorCol_Hf19"><div class="avatar margin-bottom--sm"><a href="https://sebastienlorber.com" target="_blank" rel="noopener noreferrer" class="avatar__photo-link"><img class="avatar__photo" src="https://github.com/slorber.png" alt="Sébastien Lorber" itemprop="image"></a><div class="avatar__intro" itemprop="author" itemscope="" itemtype="https://schema.org/Person"><div class="avatar__name"><a href="https://sebastienlorber.com" target="_blank" rel="noopener noreferrer" itemprop="url"><span itemprop="name">Sébastien Lorber</span></a></div><small class="avatar__subtitle" itemprop="description">Docusaurus maintainer</small></div></div></div><div class="col col--6 authorCol_Hf19"><div class="avatar margin-bottom--sm"><a href="https://github.com/yangshun" target="_blank" rel="noopener noreferrer" class="avatar__photo-link"><img class="avatar__photo" src="https://github.com/yangshun.png" alt="Yangshun Tay" itemprop="image"></a><div class="avatar__intro" itemprop="author" itemscope="" itemtype="https://schema.org/Person"><div class="avatar__name"><a href="https://github.com/yangshun" target="_blank" rel="noopener noreferrer" itemprop="url"><span itemprop="name">Yangshun Tay</span></a></div><small class="avatar__subtitle" itemprop="description">Front End Engineer @ Facebook</small></div></div></div></div></header><div class="markdown" itemprop="articleBody"><p><a href="https://docusaurus.io/docs/blog" target="_blank" rel="noopener noreferrer">Docusaurus blogging features</a> are powered by the <a href="https://docusaurus.io/docs/api/plugins/@docusaurus/plugin-content-blog" target="_blank" rel="noopener noreferrer">blog plugin</a>.</p>
diff --git a/blog/tags/hola/index.html b/blog/tags/hola/index.html
index af22f0ff..fa571912 100644
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Lorem ipsum dolor sit amet"><header><h2 class="title_f1Hy" itemprop="headline"><a itemprop="url" href="/blog/first-blog-post">First Blog Post</a></h2><div class="container_mt6G margin-vert--md"><time datetime="2019-05-28T00:00:00.000Z" itemprop="datePublished">May 28, 2019</time> · <!-- -->One min read</div><div class="margin-top--md margin-bottom--sm row"><div class="col col--6 authorCol_Hf19"><div class="avatar margin-bottom--sm"><a href="https://github.com/wgao19" target="_blank" rel="noopener noreferrer" class="avatar__photo-link"><img class="avatar__photo" src="https://github.com/wgao19.png" alt="Gao Wei" itemprop="image"></a><div class="avatar__intro" itemprop="author" itemscope="" itemtype="https://schema.org/Person"><div class="avatar__name"><a href="https://github.com/wgao19" target="_blank" rel="noopener noreferrer" itemprop="url"><span itemprop="name">Gao Wei</span></a></div><small class="avatar__subtitle" itemprop="description">Docusaurus Core Team</small></div></div></div></div></header><div class="markdown" itemprop="articleBody"><p>Lorem ipsum dolor sit amet, consectetur adipiscing elit. 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title="Main Scenario">📄️<!-- --> <!-- -->Main Scenario</h2><p class="text--truncate cardDescription_PWke" title="Hermes 1.1.0 is now available! [Download">Hermes 1.1.0 is now available! [Download</p></a></article><article class="col col--6 margin-bottom--lg"><a class="card padding--lg cardContainer_fWXF" href="/docs/hermes/building-hermes"><h2 class="text--truncate cardTitle_rnsV" title="Building Hermes">📄️<!-- --> <!-- -->Building Hermes</h2><p class="text--truncate cardDescription_PWke" title="Dependencies">Dependencies</p></a></article><article class="col col--6 margin-bottom--lg"><a class="card padding--lg cardContainer_fWXF" href="/docs/hermes/deploying-hermes"><h2 class="text--truncate cardTitle_rnsV" title="Deploying Hermes">📄️<!-- --> <!-- -->Deploying Hermes</h2><p class="text--truncate cardDescription_PWke" title="Configuring + Deploying Hermes">Configuring + Deploying Hermes</p></a></article><article class="col col--6 margin-bottom--lg"><a class="card padding--lg cardContainer_fWXF" href="/docs/hermes/configuration"><h2 class="text--truncate cardTitle_rnsV" title="Configuration">📄️<!-- --> <!-- -->Configuration</h2><p class="text--truncate cardDescription_PWke" title="Before deploying an application, you need to configure Hermes. Hermes has two types of configurations: server configuration and client configuration. They">Before deploying an application, you need to configure Hermes. Hermes has two types of configurations: server configuration and client configuration. They</p></a></article><article class="col col--6 margin-bottom--lg"><a class="card padding--lg cardContainer_fWXF" href="/docs/hermes/components/buffer-organizer"><h2 class="text--truncate cardTitle_rnsV" title="Components">🗃️<!-- --> <!-- -->Components</h2><p class="text--truncate cardDescription_PWke" title="11 items">11 items</p></a></article><article class="col col--6 margin-bottom--lg"><a class="card padding--lg cardContainer_fWXF" href="/docs/hermes/programming"><h2 class="text--truncate cardTitle_rnsV" title="Programming">📄️<!-- --> <!-- -->Programming</h2><p class="text--truncate cardDescription_PWke" title="In this section, we will discuss the general steps of building a program">In this section, we will discuss the general steps of building a program</p></a></article><article class="col col--6 margin-bottom--lg"><a class="card padding--lg cardContainer_fWXF" href="/docs/hermes/adapters"><h2 class="text--truncate cardTitle_rnsV" title="Adapters">📄️<!-- --> <!-- -->Adapters</h2><p class="text--truncate cardDescription_PWke" title="Hermes Ecosystem">Hermes Ecosystem</p></a></article><article class="col col--6 margin-bottom--lg"><a class="card padding--lg cardContainer_fWXF" href="/docs/hermes/quick-start"><h2 class="text--truncate cardTitle_rnsV" title="Quick Start Guide">📄️<!-- --> <!-- -->Quick Start Guide</h2><p class="text--truncate cardDescription_PWke" title="CAUTION: The image from DockerHub may throw Illegal Instruction for Spack-installed binaries.">CAUTION: The image from DockerHub may throw Illegal Instruction for Spack-installed binaries.</p></a></article><article class="col col--6 margin-bottom--lg"><a class="card padding--lg cardContainer_fWXF" href="/docs/hermes/debugging"><h2 class="text--truncate cardTitle_rnsV" title="Debugging">📄️<!-- --> <!-- -->Debugging</h2><p class="text--truncate cardDescription_PWke" title="Hermes can be complicated to debug due to its distributed and asynchronous">Hermes can be complicated to debug due to its distributed and asynchronous</p></a></article><article class="col col--6 margin-bottom--lg"><a class="card padding--lg cardContainer_fWXF" href="/docs/hermes/doxygen"><h2 class="text--truncate cardTitle_rnsV" title="Doxygen">📄️<!-- --> <!-- -->Doxygen</h2><p class="text--truncate cardDescription_PWke" title="The Doxygen portion of the Hermes documentation can be built as follows:">The Doxygen portion of the Hermes documentation can be built as follows:</p></a></article><article class="col col--6 margin-bottom--lg"><a class="card padding--lg cardContainer_fWXF" href="/docs/hermes/faq"><h2 class="text--truncate cardTitle_rnsV" title="Frequently Asked Questions">📄️<!-- --> <!-- -->Frequently Asked Questions</h2><p class="text--truncate cardDescription_PWke" title="What is the minimum version for GCC?">What is the minimum version for GCC?</p></a></article></section></article><footer class="margin-top--lg"><nav class="pagination-nav docusaurus-mt-lg" aria-label="Docs pages"><a class="pagination-nav__link pagination-nav__link--prev" href="/docs/hpc-tutorials/cpp-introduction/hello-world"><div class="pagination-nav__sublabel">Previous</div><div class="pagination-nav__label">Hello World</div></a><a class="pagination-nav__link pagination-nav__link--next" href="/docs/hermes/main-scenario"><div class="pagination-nav__sublabel">Next</div><div class="pagination-nav__label">Main Scenario</div></a></nav></footer></div></div></main></div></div></div><footer class="footer"><div class="container container-fluid"><div class="row footer__links"><div class="col footer__col"><div class="footer__title">Gnosis Research Center</div><ul class="footer__items clean-list"><li class="footer__item">
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aria-label="Home page" class="breadcrumbs__link" href="/"><svg viewBox="0 0 24 24" class="breadcrumbHomeIcon_YNFT"><path d="M10 19v-5h4v5c0 .55.45 1 1 1h3c.55 0 1-.45 1-1v-7h1.7c.46 0 .68-.57.33-.87L12.67 3.6c-.38-.34-.96-.34-1.34 0l-8.36 7.53c-.34.3-.13.87.33.87H5v7c0 .55.45 1 1 1h3c.55 0 1-.45 1-1z" fill="currentColor"></path></svg></a></li><li itemscope="" itemprop="itemListElement" itemtype="https://schema.org/ListItem" class="breadcrumbs__item breadcrumbs__item--active"><span class="breadcrumbs__link" itemprop="name">Hermes</span><meta itemprop="position" content="1"></li></ul></nav><header><h1 class="title_kItE">Hermes</h1><p>Hermes is a middeware library that automatically manages buffering in heterogeneous storage environments.</p></header><article class="margin-top--lg"><section class="row list_eTzJ"><article class="col col--6 margin-bottom--lg"><a class="card padding--lg cardContainer_fWXF" href="/docs/hermes/main-scenario"><h2 class="text--truncate cardTitle_rnsV" title="Main Scenario">📄️<!-- --> <!-- -->Main Scenario</h2><p class="text--truncate cardDescription_PWke" title="Hermes 1.1.0 is now available! [Download">Hermes 1.1.0 is now available! [Download</p></a></article><article class="col col--6 margin-bottom--lg"><a class="card padding--lg cardContainer_fWXF" href="/docs/hermes/building-hermes"><h2 class="text--truncate cardTitle_rnsV" title="Building Hermes">📄️<!-- --> <!-- -->Building Hermes</h2><p class="text--truncate cardDescription_PWke" title="Dependencies">Dependencies</p></a></article><article class="col col--6 margin-bottom--lg"><a class="card padding--lg cardContainer_fWXF" href="/docs/hermes/deploying-hermes"><h2 class="text--truncate cardTitle_rnsV" title="Deploying Hermes">📄️<!-- --> <!-- -->Deploying Hermes</h2><p class="text--truncate cardDescription_PWke" title="Configuring + Deploying Hermes">Configuring + Deploying Hermes</p></a></article><article class="col col--6 margin-bottom--lg"><a class="card padding--lg cardContainer_fWXF" href="/docs/hermes/configuration"><h2 class="text--truncate cardTitle_rnsV" title="Configuration">📄️<!-- --> <!-- -->Configuration</h2><p class="text--truncate cardDescription_PWke" title="Before deploying an application, you need to configure Hermes. Hermes has two types of configurations: server configuration and client configuration. They">Before deploying an application, you need to configure Hermes. Hermes has two types of configurations: server configuration and client configuration. They</p></a></article><article class="col col--6 margin-bottom--lg"><a class="card padding--lg cardContainer_fWXF" href="/docs/hermes/adapters"><h2 class="text--truncate cardTitle_rnsV" title="Adapters">📄️<!-- --> <!-- -->Adapters</h2><p class="text--truncate cardDescription_PWke" title="Hermes Ecosystem">Hermes Ecosystem</p></a></article><article class="col col--6 margin-bottom--lg"><a class="card padding--lg cardContainer_fWXF" href="/docs/hermes/programming"><h2 class="text--truncate cardTitle_rnsV" title="Programming">📄️<!-- --> <!-- -->Programming</h2><p class="text--truncate cardDescription_PWke" title="In this section, we will discuss the general steps of building a program">In this section, we will discuss the general steps of building a program</p></a></article><article class="col col--6 margin-bottom--lg"><a class="card padding--lg cardContainer_fWXF" href="/docs/hermes/components/buffer-organizer"><h2 class="text--truncate cardTitle_rnsV" title="Components">🗃️<!-- --> <!-- -->Components</h2><p class="text--truncate cardDescription_PWke" title="11 items">11 items</p></a></article><article class="col col--6 margin-bottom--lg"><a class="card padding--lg cardContainer_fWXF" href="/docs/hermes/containers"><h2 class="text--truncate cardTitle_rnsV" title="Containers">📄️<!-- --> <!-- -->Containers</h2><p class="text--truncate cardDescription_PWke" title="Dockerfiles">Dockerfiles</p></a></article><article class="col col--6 margin-bottom--lg"><a class="card padding--lg cardContainer_fWXF" href="/docs/hermes/developer-guide"><h2 class="text--truncate cardTitle_rnsV" title="Developer Guide">📄️<!-- --> <!-- -->Developer Guide</h2><p class="text--truncate cardDescription_PWke" title="Hermes can be complicated to debug due to its distributed and asynchronous">Hermes can be complicated to debug due to its distributed and asynchronous</p></a></article><article class="col col--6 margin-bottom--lg"><a class="card padding--lg cardContainer_fWXF" href="/docs/hermes/doxygen"><h2 class="text--truncate cardTitle_rnsV" title="Doxygen">📄️<!-- --> <!-- -->Doxygen</h2><p class="text--truncate cardDescription_PWke" title="The Doxygen portion of the Hermes documentation can be built as follows:">The Doxygen portion of the Hermes documentation can be built as follows:</p></a></article><article class="col col--6 margin-bottom--lg"><a class="card padding--lg cardContainer_fWXF" href="/docs/hermes/faq"><h2 class="text--truncate cardTitle_rnsV" title="Frequently Asked Questions">📄️<!-- --> <!-- -->Frequently Asked Questions</h2><p class="text--truncate cardDescription_PWke" title="What is the minimum version for GCC?">What is the minimum version for GCC?</p></a></article></section></article><footer class="margin-top--lg"><nav class="pagination-nav docusaurus-mt-lg" aria-label="Docs pages"><a class="pagination-nav__link pagination-nav__link--prev" href="/docs/hpc-tutorials/cpp-introduction/hello-world"><div class="pagination-nav__sublabel">Previous</div><div class="pagination-nav__label">Hello World</div></a><a class="pagination-nav__link pagination-nav__link--next" href="/docs/hermes/main-scenario"><div class="pagination-nav__sublabel">Next</div><div class="pagination-nav__label">Main Scenario</div></a></nav></footer></div></div></main></div></div></div><footer class="footer"><div class="container container-fluid"><div class="row footer__links"><div class="col footer__col"><div class="footer__title">Gnosis Research Center</div><ul class="footer__items clean-list"><li class="footer__item">
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used by CMake to identify the location of CMake modules.">CMAKEMODULEPATH is used by CMake to identify the location of CMake modules.</p></a></article><article class="col col--6 margin-bottom--lg"><a class="card padding--lg cardContainer_fWXF" href="/docs/hpc-tutorials/important-environment-variables/cmake-prefix-path"><h2 class="text--truncate cardTitle_rnsV" title="CMAKE_PREFIX_PATH">📄️<!-- --> <!-- -->CMAKE_PREFIX_PATH</h2><p class="text--truncate cardDescription_PWke" title="CMAKEPREFIXPATH is used by CMake to identify the location of CMake package configurations.">CMAKEPREFIXPATH is used by CMake to identify the location of CMake package configurations.</p></a></article><article class="col col--6 margin-bottom--lg"><a class="card padding--lg cardContainer_fWXF" href="/docs/hpc-tutorials/important-environment-variables/cpath"><h2 class="text--truncate cardTitle_rnsV" title="CPATH">📄️<!-- --> <!-- -->CPATH</h2><p class="text--truncate cardDescription_PWke" title="GCC and Clang search each path in CPATH and sometimes INCLUDE_PATH for header files.">GCC and Clang search each path in CPATH and sometimes INCLUDE_PATH for header files.</p></a></article><article class="col col--6 margin-bottom--lg"><a class="card padding--lg cardContainer_fWXF" href="/docs/hpc-tutorials/important-environment-variables/java-home"><h2 class="text--truncate cardTitle_rnsV" title="JAVA_HOME">📄️<!-- --> <!-- -->JAVA_HOME</h2><p class="text--truncate cardDescription_PWke" title="JAVA_HOME is frequently used as the environment variable to specify the current java installation.">JAVA_HOME is frequently used as the environment variable to specify the current java installation.</p></a></article><article class="col col--6 margin-bottom--lg"><a class="card padding--lg cardContainer_fWXF" href="/docs/hpc-tutorials/important-environment-variables/ld-library-path"><h2 class="text--truncate cardTitle_rnsV" title="LD_LIBRARY_PATH">📄️<!-- --> <!-- -->LD_LIBRARY_PATH</h2><p class="text--truncate cardDescription_PWke" title="LDLIBRARYPATH is used by Linux to locate shared objects at runtime (as opposed to compile-time).">LDLIBRARYPATH is used by Linux to locate shared objects at runtime (as opposed to compile-time).</p></a></article><article class="col col--6 margin-bottom--lg"><a class="card padding--lg cardContainer_fWXF" href="/docs/hpc-tutorials/important-environment-variables/ld-preload"><h2 class="text--truncate cardTitle_rnsV" title="LD_PRELOAD">📄️<!-- --> <!-- -->LD_PRELOAD</h2><p class="text--truncate cardDescription_PWke" title="LD_PRELOAD is used by Linux to intercept functions in a program and replace their">LD_PRELOAD is used by Linux to intercept functions in a program and replace their</p></a></article><article class="col col--6 margin-bottom--lg"><a class="card padding--lg cardContainer_fWXF" href="/docs/hpc-tutorials/important-environment-variables/library-path"><h2 class="text--truncate cardTitle_rnsV" title="LIBRARY_PATH">📄️<!-- --> <!-- -->LIBRARY_PATH</h2><p class="text--truncate cardDescription_PWke" title="GCC and Clang search each path in LIBRARY_PATH for shared objects and archives.">GCC and Clang search each path in LIBRARY_PATH for shared objects and archives.</p></a></article><article class="col col--6 margin-bottom--lg"><a class="card padding--lg cardContainer_fWXF" href="/docs/hpc-tutorials/important-environment-variables/path"><h2 class="text--truncate cardTitle_rnsV" title="PATH">📄️<!-- --> <!-- -->PATH</h2><p class="text--truncate cardDescription_PWke" title="The PATH variable is used to locate executable objects. 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tocMobile_ITEo"><button type="button" class="clean-btn tocCollapsibleButton_TO0P">On this page</button></div><div class="theme-doc-markdown markdown"><h1>Adapters</h1>
 <p><img loading="lazy" alt="Hermes Ecosystem" src="/assets/images/Hermes_Ecosystem-bcc2b31f697fea047fc773fbf10d2dbb.jpg" width="522" height="727" class="img_ev3q"></p>
 <p>Instead of the <a href="/docs/hermes/programming">Hermes primitives</a>, existing applications
 use I/O libraries and middleware such as the C standard I/O library,
@@ -50,11 +50,9 @@ <h2 class="anchor anchorWithStickyNavbar_LWe7" id="filesystem-base-class-fsbc">F
 <h3 class="anchor anchorWithStickyNavbar_LWe7" id="design">Design<a href="#design" class="hash-link" aria-label="Direct link to Design" title="Direct link to Design">​</a></h3>
 <p>When reading/writing to a file, the FSBC will divide the I/O request into
 fixed-size pages. This is a configurable value, but the default is 1MB.</p>
-<p>When extending the size of a file, the FSBC relies on a lock to ensure that
-the size of the file is coherent. This lock is a problem for workloads which
-perform shared I/O to a single file. FPP workloads are generally better.</p>
-<p>A solution to this problem would be a log-structured merge tree, but this
-will require significant changes to the Hermes data model.</p>
+<p>As opposed to locking, Hermes uses queuing to ensure that I/O to the same regions
+of a file are strongly consistent. I/O to the same blob will be placed in the
+same queue, ensuring sequencing.</p>
 <h3 class="anchor anchorWithStickyNavbar_LWe7" id="vfd">VFD<a href="#vfd" class="hash-link" aria-label="Direct link to VFD" title="Direct link to VFD">​</a></h3>
 <p>The HDF5 VFD is used to interface HDF5 with Hermes natively. To use the Hermes
 VFD in HDF5, you must define the following environment variables:</p>
@@ -93,7 +91,7 @@ <h2 class="anchor anchorWithStickyNavbar_LWe7" id="future-work">Future Work<a hr
 <h2 class="anchor anchorWithStickyNavbar_LWe7" id="references">References<a href="#references" class="hash-link" aria-label="Direct link to References" title="Direct link to References">​</a></h2>
 <ul>
 <li><a href="https://github.com/LLNL/GOTCHA" target="_blank" rel="noopener noreferrer">GOTCHA is a library for wrapping function calls in shared libraries</a></li>
-</ul></div></article><nav class="pagination-nav docusaurus-mt-lg" aria-label="Docs pages"><a class="pagination-nav__link pagination-nav__link--prev" href="/docs/hermes/programming"><div class="pagination-nav__sublabel">Previous</div><div class="pagination-nav__label">Programming</div></a><a class="pagination-nav__link pagination-nav__link--next" href="/docs/hermes/quick-start"><div class="pagination-nav__sublabel">Next</div><div class="pagination-nav__label">Quick Start Guide</div></a></nav></div></div><div class="col col--3"><div class="tableOfContents_bqdL thin-scrollbar theme-doc-toc-desktop"><ul class="table-of-contents table-of-contents__left-border"><li><a href="#filesystem-base-class-fsbc" class="table-of-contents__link toc-highlight">Filesystem Base Class (FSBC)</a><ul><li><a href="#design" class="table-of-contents__link toc-highlight">Design</a></li><li><a href="#vfd" class="table-of-contents__link toc-highlight">VFD</a></li></ul></li><li><a href="#pubsub-adapter" class="table-of-contents__link toc-highlight">PubSub Adapter</a><ul><li><a href="#suported-api" class="table-of-contents__link toc-highlight">Suported API</a></li></ul></li><li><a href="#current-limitations" class="table-of-contents__link toc-highlight">Current Limitations</a></li><li><a href="#future-work" class="table-of-contents__link toc-highlight">Future Work</a></li><li><a href="#references" class="table-of-contents__link toc-highlight">References</a></li></ul></div></div></div></div></main></div></div></div><footer class="footer"><div class="container container-fluid"><div class="row footer__links"><div class="col footer__col"><div class="footer__title">Gnosis Research Center</div><ul class="footer__items clean-list"><li class="footer__item">
+</ul></div></article><nav class="pagination-nav docusaurus-mt-lg" aria-label="Docs pages"><a class="pagination-nav__link pagination-nav__link--prev" href="/docs/hermes/configuration"><div class="pagination-nav__sublabel">Previous</div><div class="pagination-nav__label">Configuration</div></a><a class="pagination-nav__link pagination-nav__link--next" href="/docs/hermes/programming"><div class="pagination-nav__sublabel">Next</div><div class="pagination-nav__label">Programming</div></a></nav></div></div><div class="col col--3"><div class="tableOfContents_bqdL thin-scrollbar theme-doc-toc-desktop"><ul class="table-of-contents table-of-contents__left-border"><li><a href="#filesystem-base-class-fsbc" class="table-of-contents__link toc-highlight">Filesystem Base Class (FSBC)</a><ul><li><a href="#design" class="table-of-contents__link toc-highlight">Design</a></li><li><a href="#vfd" class="table-of-contents__link toc-highlight">VFD</a></li></ul></li><li><a href="#pubsub-adapter" class="table-of-contents__link toc-highlight">PubSub Adapter</a><ul><li><a href="#suported-api" class="table-of-contents__link toc-highlight">Suported API</a></li></ul></li><li><a href="#current-limitations" class="table-of-contents__link toc-highlight">Current Limitations</a></li><li><a href="#future-work" class="table-of-contents__link toc-highlight">Future Work</a></li><li><a href="#references" class="table-of-contents__link toc-highlight">References</a></li></ul></div></div></div></div></main></div></div></div><footer class="footer"><div class="container container-fluid"><div class="row footer__links"><div class="col footer__col"><div class="footer__title">Gnosis Research Center</div><ul class="footer__items clean-list"><li class="footer__item">
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diff --git a/docs/hermes/building-hermes/index.html b/docs/hermes/building-hermes/index.html
index e1b75a1a..19d746aa 100644
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itemtype="https://schema.org/BreadcrumbList"><li class="breadcrumbs__item"><a aria-label="Home page" class="breadcrumbs__link" href="/"><svg viewBox="0 0 24 24" class="breadcrumbHomeIcon_YNFT"><path d="M10 19v-5h4v5c0 .55.45 1 1 1h3c.55 0 1-.45 1-1v-7h1.7c.46 0 .68-.57.33-.87L12.67 3.6c-.38-.34-.96-.34-1.34 0l-8.36 7.53c-.34.3-.13.87.33.87H5v7c0 .55.45 1 1 1h3c.55 0 1-.45 1-1z" fill="currentColor"></path></svg></a></li><li itemscope="" itemprop="itemListElement" itemtype="https://schema.org/ListItem" class="breadcrumbs__item"><a class="breadcrumbs__link" itemprop="item" href="/docs/category/hermes"><span itemprop="name">Hermes</span></a><meta itemprop="position" content="1"></li><li itemscope="" itemprop="itemListElement" itemtype="https://schema.org/ListItem" class="breadcrumbs__item breadcrumbs__item--active"><span class="breadcrumbs__link" itemprop="name">Building Hermes</span><meta itemprop="position" content="2"></li></ul></nav><div class="tocCollapsible_ETCw theme-doc-toc-mobile tocMobile_ITEo"><button type="button" class="clean-btn tocCollapsibleButton_TO0P">On this page</button></div><div class="theme-doc-markdown markdown"><h1>Building Hermes</h1>
 <h2 class="anchor anchorWithStickyNavbar_LWe7" id="dependencies">Dependencies<a href="#dependencies" class="hash-link" aria-label="Direct link to Dependencies" title="Direct link to Dependencies">​</a></h2>
 <ul>
-<li>A C++ compiler that supports C++ 17. GCC 9.4 is the minimum version of GCC
-that Hermes was tested with.</li>
+<li>A C++ compiler that supports C++ 17. GCC 9.4 is the minimum version of GCC that Hermes was tested with.</li>
 <li><a href="https://mochi.readthedocs.io/en/latest/installing.html" target="_blank" rel="noopener noreferrer">Thallium</a> - RPC library for HPC. Use a version greater than <code>0.5</code> for RoCE support.</li>
 <li><a href="https://github.com/jbeder/yaml-cpp" target="_blank" rel="noopener noreferrer">yaml-cpp</a> - YAML file parser</li>
 <li><a href="https://github.com/lukemartinlogan/hermes_shm" target="_blank" rel="noopener noreferrer">hermes_shm</a>: A library containing shared-memory data structures, configuration parsing, and various helper utilities</li>
diff --git a/docs/hermes/components/buffer-organizer/index.html b/docs/hermes/components/buffer-organizer/index.html
index df1b88ed..17dd0485 100644
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class="breadcrumbs__link">Components</span><meta itemprop="position" content="2"></li><li itemscope="" itemprop="itemListElement" itemtype="https://schema.org/ListItem" class="breadcrumbs__item breadcrumbs__item--active"><span class="breadcrumbs__link" itemprop="name">Buffer Organizer</span><meta itemprop="position" content="3"></li></ul></nav><div class="tocCollapsible_ETCw theme-doc-toc-mobile tocMobile_ITEo"><button type="button" class="clean-btn tocCollapsibleButton_TO0P">On this page</button></div><div class="theme-doc-markdown markdown"><h1>Buffer Organizer</h1>
 <p>The <strong>Buffer Organizer</strong> is the &quot;corrector&quot; half of our
 predictor/corrector model. It attempts to correct sub-optimal DPE
 placements by moving data among buffers.</p>
@@ -205,7 +205,7 @@ <h2 class="anchor anchorWithStickyNavbar_LWe7" id="ideas-1">Ideas<a href="#ideas
 <h2 class="anchor anchorWithStickyNavbar_LWe7" id="experiments">Experiments<a href="#experiments" class="hash-link" aria-label="Direct link to Experiments" title="Direct link to Experiments">​</a></h2>
 <ul>
 <li>Test the difference between flushing tier by tier vs skipping tiers. For example, a <code>Blob</code> moving from RAM to burst buffer could go through NVMe as an intermediate tier, or skip it altogether.</li>
-</ul></div></article><nav class="pagination-nav docusaurus-mt-lg" aria-label="Docs pages"><a class="pagination-nav__link pagination-nav__link--prev" href="/docs/hermes/configuration"><div class="pagination-nav__sublabel">Previous</div><div class="pagination-nav__label">Configuration</div></a><a class="pagination-nav__link pagination-nav__link--next" href="/docs/hermes/components/buffer-pool"><div class="pagination-nav__sublabel">Next</div><div class="pagination-nav__label">Buffer Pool</div></a></nav></div></div><div class="col col--3"><div class="tableOfContents_bqdL thin-scrollbar theme-doc-toc-desktop"><ul class="table-of-contents table-of-contents__left-border"><li><a href="#objectives" class="table-of-contents__link toc-highlight">Objectives</a></li><li><a href="#blob-scoring" class="table-of-contents__link toc-highlight">Blob Scoring</a><ul><li><a href="#importance-score" class="table-of-contents__link toc-highlight">Importance Score</a></li><li><a href="#access-score" class="table-of-contents__link toc-highlight">Access Score</a></li><li><a href="#how-the-scores-are-used" class="table-of-contents__link toc-highlight">How the scores are used</a></li></ul></li><li><a href="#ideas" class="table-of-contents__link toc-highlight">Ideas</a></li><li><a href="#operations" class="table-of-contents__link toc-highlight">Operations</a><ul><li><a href="#transfer" class="table-of-contents__link toc-highlight">Transfer</a></li><li><a href="#evictsize_t-bytes-targets" class="table-of-contents__link toc-highlight">Evict(size_t bytes, Targets[])</a></li></ul></li><li><a href="#triggers" class="table-of-contents__link toc-highlight">Triggers</a><ul><li><a href="#periodic" class="table-of-contents__link toc-highlight">Periodic</a></li><li><a href="#client-triggered" class="table-of-contents__link toc-highlight">Client-triggered</a></li><li><a href="#system-triggered" class="table-of-contents__link toc-highlight">System-triggered</a></li><li><a href="#requirements-for-queue-implementation" class="table-of-contents__link toc-highlight">Requirements for Queue implementation</a></li></ul></li><li><a href="#design-details" class="table-of-contents__link toc-highlight">Design Details</a><ul><li><a href="#bo-rpc-server" class="table-of-contents__link toc-highlight">BO RPC Server</a></li><li><a href="#buffer-organizer-1" class="table-of-contents__link toc-highlight">Buffer Organizer</a></li></ul></li><li><a href="#example-flows" class="table-of-contents__link toc-highlight">Example Flows</a><ul><li><a href="#hot-put" class="table-of-contents__link toc-highlight">Hot Put</a></li><li><a href="#bo-eviction-flow" class="table-of-contents__link toc-highlight">BO Eviction Flow</a></li></ul></li><li><a href="#ideas-1" class="table-of-contents__link toc-highlight">Ideas</a></li><li><a href="#experiments" class="table-of-contents__link toc-highlight">Experiments</a></li></ul></div></div></div></div></main></div></div></div><footer class="footer"><div class="container container-fluid"><div class="row footer__links"><div class="col footer__col"><div class="footer__title">Gnosis Research Center</div><ul class="footer__items clean-list"><li class="footer__item">
+</ul></div></article><nav class="pagination-nav docusaurus-mt-lg" aria-label="Docs pages"><a class="pagination-nav__link pagination-nav__link--prev" href="/docs/hermes/programming"><div class="pagination-nav__sublabel">Previous</div><div class="pagination-nav__label">Programming</div></a><a class="pagination-nav__link pagination-nav__link--next" href="/docs/hermes/components/buffer-pool"><div class="pagination-nav__sublabel">Next</div><div class="pagination-nav__label">Buffer Pool</div></a></nav></div></div><div class="col col--3"><div class="tableOfContents_bqdL thin-scrollbar theme-doc-toc-desktop"><ul class="table-of-contents table-of-contents__left-border"><li><a href="#objectives" class="table-of-contents__link toc-highlight">Objectives</a></li><li><a href="#blob-scoring" class="table-of-contents__link toc-highlight">Blob Scoring</a><ul><li><a href="#importance-score" class="table-of-contents__link toc-highlight">Importance Score</a></li><li><a href="#access-score" class="table-of-contents__link toc-highlight">Access Score</a></li><li><a href="#how-the-scores-are-used" class="table-of-contents__link toc-highlight">How the scores are used</a></li></ul></li><li><a href="#ideas" class="table-of-contents__link toc-highlight">Ideas</a></li><li><a href="#operations" class="table-of-contents__link toc-highlight">Operations</a><ul><li><a href="#transfer" class="table-of-contents__link toc-highlight">Transfer</a></li><li><a href="#evictsize_t-bytes-targets" class="table-of-contents__link toc-highlight">Evict(size_t bytes, Targets[])</a></li></ul></li><li><a href="#triggers" class="table-of-contents__link toc-highlight">Triggers</a><ul><li><a href="#periodic" class="table-of-contents__link toc-highlight">Periodic</a></li><li><a href="#client-triggered" class="table-of-contents__link toc-highlight">Client-triggered</a></li><li><a href="#system-triggered" class="table-of-contents__link toc-highlight">System-triggered</a></li><li><a href="#requirements-for-queue-implementation" class="table-of-contents__link toc-highlight">Requirements for Queue implementation</a></li></ul></li><li><a href="#design-details" class="table-of-contents__link toc-highlight">Design Details</a><ul><li><a href="#bo-rpc-server" class="table-of-contents__link toc-highlight">BO RPC Server</a></li><li><a href="#buffer-organizer-1" class="table-of-contents__link toc-highlight">Buffer Organizer</a></li></ul></li><li><a href="#example-flows" class="table-of-contents__link toc-highlight">Example Flows</a><ul><li><a href="#hot-put" class="table-of-contents__link toc-highlight">Hot Put</a></li><li><a href="#bo-eviction-flow" class="table-of-contents__link toc-highlight">BO Eviction Flow</a></li></ul></li><li><a href="#ideas-1" class="table-of-contents__link toc-highlight">Ideas</a></li><li><a href="#experiments" class="table-of-contents__link toc-highlight">Experiments</a></li></ul></div></div></div></div></main></div></div></div><footer class="footer"><div class="container container-fluid"><div class="row footer__links"><div class="col footer__col"><div class="footer__title">Gnosis Research Center</div><ul class="footer__items clean-list"><li class="footer__item">
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 <p>The main idea behind the <strong>Buffer Pool</strong> is to avoid the runtime
 overhead of memory allocation each time Hermes wishes to buffer data.
 Instead, we pre-allocate a pool of fixed sized (though the size groups
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 <p>A buffering target represents a logical target of data placement, i.e.,
 parts of or a full BLOB can be placed there by the DPE. Buffering
 targets are logical constructs that are statically mapped by Hermes to
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 <p>Every Hermes system instance includes one or more Hermes <em>nodes</em>.</p>
 <p>A <em>destination</em> is a buffering resource that can be identified by a pair
 of node + target &quot;coordinates.&quot;</p>
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itemprop="position" content="2"></li><li itemscope="" itemprop="itemListElement" itemtype="https://schema.org/ListItem" class="breadcrumbs__item breadcrumbs__item--active"><span class="breadcrumbs__link" itemprop="name">Data Staging</span><meta itemprop="position" content="3"></li></ul></nav><div class="tocCollapsible_ETCw theme-doc-toc-mobile tocMobile_ITEo"><button type="button" class="clean-btn tocCollapsibleButton_TO0P">On this page</button></div><div class="theme-doc-markdown markdown"><h1>Data Staging</h1>
 <p>Stage-in is the ability to load <strong>external</strong> datasets into Hermes.
 Stage-out is the ability export data out of Hermes.</p>
 <h2 class="anchor anchorWithStickyNavbar_LWe7" id="use-case">Use Case<a href="#use-case" class="hash-link" aria-label="Direct link to Use Case" title="Direct link to Use Case">​</a></h2>
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itemprop="position" content="2"></li><li itemscope="" itemprop="itemListElement" itemtype="https://schema.org/ListItem" class="breadcrumbs__item breadcrumbs__item--active"><span class="breadcrumbs__link" itemprop="name">Distributed Metadata</span><meta itemprop="position" content="3"></li></ul></nav><div class="tocCollapsible_ETCw theme-doc-toc-mobile tocMobile_ITEo"><button type="button" class="clean-btn tocCollapsibleButton_TO0P">On this page</button></div><div class="theme-doc-markdown markdown"><h1>Distributed Metadata</h1>
 <p>Metadata is stored in a distributed hash map. In each Hermes Daemon, we
 initialize an <code>hipc::unordered_map</code>. The main metadata structures we store
 are as follows: Tag Map (note, Buckets are represented as Tags), Blob Map,
@@ -55,7 +55,7 @@ <h3 class="anchor anchorWithStickyNavbar_LWe7" id="cons">Cons<a href="#cons" cla
 <li>May require extra RPC calls. Initial tests show that this
 indirection should be avoided. <strong>TODO:</strong> We need to revisit this.</li>
 </ul>
-<h2 class="anchor anchorWithStickyNavbar_LWe7" id="walkthrough-of-bucketput">Walkthrough of <code>Bucket.Put()</code><a href="#walkthrough-of-bucketput" class="hash-link" aria-label="Direct link to walkthrough-of-bucketput" title="Direct link to walkthrough-of-bucketput">​</a></h2>
+<h2 class="anchor anchorWithStickyNavbar_LWe7" id="walkthrough-of-bucketput">Walkthrough of <code>Bucket.Put()</code><a href="#walkthrough-of-bucketput" class="hash-link" aria-label="Direct link to walkthrough-of-bucketput" title="Direct link to walkthrough-of-bucketput">​</a></h2>
 <p>1. Create a new <code>BlobID</code>. The ID&#x27;s node index (top 32 bits) is created
 by hashing the blob name, and the ID&#x27;s offset to a list of <code>BufferID</code>s
 (bottom 32 bits) is allocated from the MDM shared memory segment on the
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 <h2 class="anchor anchorWithStickyNavbar_LWe7" id="ares-iit">Ares (IIT)<a href="#ares-iit" class="hash-link" aria-label="Direct link to Ares (IIT)" title="Direct link to Ares (IIT)">​</a></h2>
 <p><img loading="lazy" alt="Ares - simplified structure" src="/assets/images/Ares_simplified_structure-138c68b13ac25cf2b2a1362901083bcc.png" width="534" height="489" class="img_ev3q"></p>
 <p><img loading="lazy" alt="Ares - network topology" src="/assets/images/Network_topology-d94e9a0ff17e966a7b09ccda04a06c7d.png" width="1027" height="771" class="img_ev3q"></p>
diff --git a/docs/hermes/components/prefetcher/index.html b/docs/hermes/components/prefetcher/index.html
index 9a0d1ac0..3893edb9 100644
--- a/docs/hermes/components/prefetcher/index.html
+++ b/docs/hermes/components/prefetcher/index.html
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itemprop="position" content="2"></li><li itemscope="" itemprop="itemListElement" itemtype="https://schema.org/ListItem" class="breadcrumbs__item breadcrumbs__item--active"><span class="breadcrumbs__link" itemprop="name">Prefetcher</span><meta itemprop="position" content="3"></li></ul></nav><div class="tocCollapsible_ETCw theme-doc-toc-mobile tocMobile_ITEo"><button type="button" class="clean-btn tocCollapsibleButton_TO0P">On this page</button></div><div class="theme-doc-markdown markdown"><h1>Prefetcher</h1>
 <p>The objective of the <strong>Prefetcher</strong> is to promote and demote content which is
 expected to be used in the near future or frequently. The prefetcher only
 applies to data which is already staged within Hermes. In order to activate
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 <p>Hermes is built as a plugin to the Hermes Runtime, a distributed task processing framework
 capable of scheduling, replicating, distributing, processing, monitoring, and
 load balancing arbitrary tasks. Tasks define various properties which provide
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 <p>Tags enable users to semantically define associations between blobs and provide
 an intuitive way of locating blobs which are related. Tags can be used
 internally by Hermes to provide enhanced data placement decisions based on the
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itemprop="position" content="2"></li><li itemscope="" itemprop="itemListElement" itemtype="https://schema.org/ListItem" class="breadcrumbs__item breadcrumbs__item--active"><span class="breadcrumbs__link" itemprop="name">Topology</span><meta itemprop="position" content="3"></li></ul></nav><div class="tocCollapsible_ETCw theme-doc-toc-mobile tocMobile_ITEo"><button type="button" class="clean-btn tocCollapsibleButton_TO0P">On this page</button></div><div class="theme-doc-markdown markdown"><h1>Topology</h1>
 <p>The <code>TopologyManager</code> is responsible for maintaining sets of <code>Target</code>s
 as metadata.</p>
 <h2 class="anchor anchorWithStickyNavbar_LWe7" id="api">API<a href="#api" class="hash-link" aria-label="Direct link to API" title="Direct link to API">​</a></h2>
@@ -41,7 +41,7 @@ <h2 class="anchor anchorWithStickyNavbar_LWe7" id="pre-built-partitions">Pre-bui
 <li>Local</li>
 </ul>
 </li>
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theme-doc-sidebar-item-category-level-1 menu__list-item menu__list-item--collapsed"><div class="menu__list-item-collapsible"><a class="menu__link menu__link--sublist menu__link--sublist-caret" aria-expanded="false" href="/docs/category/linux-introduction">HPC Tutorials</a></div></li><li class="theme-doc-sidebar-item-category theme-doc-sidebar-item-category-level-1 menu__list-item"><div class="menu__list-item-collapsible"><a class="menu__link menu__link--sublist menu__link--active" aria-expanded="true" href="/docs/category/hermes">Hermes</a><button aria-label="Collapse sidebar category &#x27;Hermes&#x27;" type="button" class="clean-btn menu__caret"></button></div><ul style="display:block;overflow:visible;height:auto" class="menu__list"><li class="theme-doc-sidebar-item-link theme-doc-sidebar-item-link-level-2 menu__list-item"><a class="menu__link" tabindex="0" href="/docs/hermes/main-scenario">Main Scenario</a></li><li class="theme-doc-sidebar-item-link 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itemtype="https://schema.org/BreadcrumbList"><li class="breadcrumbs__item"><a aria-label="Home page" class="breadcrumbs__link" href="/"><svg viewBox="0 0 24 24" class="breadcrumbHomeIcon_YNFT"><path d="M10 19v-5h4v5c0 .55.45 1 1 1h3c.55 0 1-.45 1-1v-7h1.7c.46 0 .68-.57.33-.87L12.67 3.6c-.38-.34-.96-.34-1.34 0l-8.36 7.53c-.34.3-.13.87.33.87H5v7c0 .55.45 1 1 1h3c.55 0 1-.45 1-1z" fill="currentColor"></path></svg></a></li><li itemscope="" itemprop="itemListElement" itemtype="https://schema.org/ListItem" class="breadcrumbs__item"><a class="breadcrumbs__link" itemprop="item" href="/docs/category/hermes"><span itemprop="name">Hermes</span></a><meta itemprop="position" content="1"></li><li itemscope="" itemprop="itemListElement" itemtype="https://schema.org/ListItem" class="breadcrumbs__item breadcrumbs__item--active"><span class="breadcrumbs__link" itemprop="name">Configuration</span><meta itemprop="position" content="2"></li></ul></nav><div class="tocCollapsible_ETCw theme-doc-toc-mobile tocMobile_ITEo"><button type="button" class="clean-btn tocCollapsibleButton_TO0P">On this page</button></div><div class="theme-doc-markdown markdown"><h1>Configuration</h1>
 <p>Before deploying an application, you need to configure Hermes. Hermes has two types of configurations: server configuration and client configuration. They
 are represented as YAML files. We will describe the contents of these YAML
 files here.</p>
@@ -239,7 +239,7 @@ <h2 class="anchor anchorWithStickyNavbar_LWe7" id="how-to-avoid-repeating-the-de
 <p>Many parameters in Hermes can be left as default. Any parameters which
 you would like to leave as default can be removed from your configuration
 file completely. Hermes will fill in missing values based on the values
-in our default configurations.</p></div></article><nav class="pagination-nav docusaurus-mt-lg" aria-label="Docs pages"><a class="pagination-nav__link pagination-nav__link--prev" href="/docs/hermes/deploying-hermes"><div class="pagination-nav__sublabel">Previous</div><div class="pagination-nav__label">Deploying Hermes</div></a><a class="pagination-nav__link pagination-nav__link--next" href="/docs/hermes/components/buffer-organizer"><div class="pagination-nav__sublabel">Next</div><div class="pagination-nav__label">Buffer Organizer</div></a></nav></div></div><div class="col col--3"><div class="tableOfContents_bqdL thin-scrollbar theme-doc-toc-desktop"><ul class="table-of-contents table-of-contents__left-border"><li><a href="#server-configuration" class="table-of-contents__link toc-highlight">Server Configuration</a><ul><li><a href="#defining-storage-targets" class="table-of-contents__link toc-highlight">Defining Storage Targets</a></li><li><a href="#device-names" class="table-of-contents__link toc-highlight">Device Names</a></li><li><a href="#mount_point" class="table-of-contents__link toc-highlight"><code>mount_point</code></a></li><li><a href="#capacity" class="table-of-contents__link toc-highlight"><code>capacity</code></a></li><li><a href="#block_size" class="table-of-contents__link toc-highlight"><code>block_size</code></a></li><li><a href="#slab_sizes" class="table-of-contents__link toc-highlight"><code>slab_sizes</code></a></li><li><a href="#bandwidth-latency" class="table-of-contents__link toc-highlight"><code>bandwidth</code>, <code>latency</code></a></li><li><a href="#is_shared_device" class="table-of-contents__link toc-highlight"><code>is_shared_device</code></a></li><li><a href="#borg_capacity_thresh" class="table-of-contents__link toc-highlight"><code>borg_capacity_thresh</code></a></li></ul></li><li><a href="#buffer-organizer-borg" class="table-of-contents__link toc-highlight">Buffer Organizer (BORG)</a></li><li><a href="#prefetcher" class="table-of-contents__link toc-highlight">Prefetcher</a></li><li><a href="#traits" class="table-of-contents__link toc-highlight">Traits</a></li><li><a href="#shared-memory" class="table-of-contents__link toc-highlight">Shared Memory</a></li><li><a href="#system-view-state" class="table-of-contents__link toc-highlight">System View State</a></li><li><a href="#bounding-memory-utilization" class="table-of-contents__link toc-highlight">Bounding Memory Utilization</a><ul><li><a href="#using-ram-as-a-buffering-device" class="table-of-contents__link toc-highlight">Using RAM as a buffering device</a></li><li><a href="#hashtables-for-storing-blobs--buckets" class="table-of-contents__link toc-highlight">Hashtables for storing blobs + buckets</a></li><li><a href="#bounding-non-buffering-tasks" class="table-of-contents__link toc-highlight">Bounding Non-Buffering Tasks</a></li><li><a href="#calculating-total-amount-of-memory" class="table-of-contents__link toc-highlight">Calculating Total Amount of Memory</a></li></ul></li><li><a href="#client-configuration" class="table-of-contents__link toc-highlight">Client Configuration</a><ul><li><a href="#path-inclusion--exclusion" class="table-of-contents__link toc-highlight">Path Inclusion / Exclusion</a></li><li><a href="#adapter-mode" class="table-of-contents__link toc-highlight">Adapter Mode</a></li><li><a href="#file-page-size" class="table-of-contents__link toc-highlight">File Page Size</a></li><li><a href="#flushing-mode" class="table-of-contents__link toc-highlight">Flushing Mode</a></li><li><a href="#adapter-config" class="table-of-contents__link toc-highlight">Adapter Config</a></li></ul></li><li><a href="#provided-configurations" class="table-of-contents__link toc-highlight">Provided Configurations</a></li><li><a href="#how-to-avoid-repeating-the-default-configurations" class="table-of-contents__link toc-highlight">How To Avoid Repeating the Default Configurations</a></li></ul></div></div></div></div></main></div></div></div><footer class="footer"><div class="container container-fluid"><div class="row footer__links"><div class="col footer__col"><div class="footer__title">Gnosis Research Center</div><ul class="footer__items clean-list"><li class="footer__item">
+in our default configurations.</p></div></article><nav class="pagination-nav docusaurus-mt-lg" aria-label="Docs pages"><a class="pagination-nav__link pagination-nav__link--prev" href="/docs/hermes/deploying-hermes"><div class="pagination-nav__sublabel">Previous</div><div class="pagination-nav__label">Deploying Hermes</div></a><a class="pagination-nav__link pagination-nav__link--next" href="/docs/hermes/adapters"><div class="pagination-nav__sublabel">Next</div><div class="pagination-nav__label">Adapters</div></a></nav></div></div><div class="col col--3"><div class="tableOfContents_bqdL thin-scrollbar theme-doc-toc-desktop"><ul class="table-of-contents table-of-contents__left-border"><li><a href="#server-configuration" class="table-of-contents__link toc-highlight">Server Configuration</a><ul><li><a href="#defining-storage-targets" class="table-of-contents__link toc-highlight">Defining Storage Targets</a></li><li><a href="#device-names" class="table-of-contents__link toc-highlight">Device Names</a></li><li><a href="#mount_point" class="table-of-contents__link toc-highlight"><code>mount_point</code></a></li><li><a href="#capacity" class="table-of-contents__link toc-highlight"><code>capacity</code></a></li><li><a href="#block_size" class="table-of-contents__link toc-highlight"><code>block_size</code></a></li><li><a href="#slab_sizes" class="table-of-contents__link toc-highlight"><code>slab_sizes</code></a></li><li><a href="#bandwidth-latency" class="table-of-contents__link toc-highlight"><code>bandwidth</code>, <code>latency</code></a></li><li><a href="#is_shared_device" class="table-of-contents__link toc-highlight"><code>is_shared_device</code></a></li><li><a href="#borg_capacity_thresh" class="table-of-contents__link toc-highlight"><code>borg_capacity_thresh</code></a></li></ul></li><li><a href="#buffer-organizer-borg" class="table-of-contents__link toc-highlight">Buffer Organizer (BORG)</a></li><li><a href="#prefetcher" class="table-of-contents__link toc-highlight">Prefetcher</a></li><li><a href="#traits" class="table-of-contents__link toc-highlight">Traits</a></li><li><a href="#shared-memory" class="table-of-contents__link toc-highlight">Shared Memory</a></li><li><a href="#system-view-state" class="table-of-contents__link toc-highlight">System View State</a></li><li><a href="#bounding-memory-utilization" class="table-of-contents__link toc-highlight">Bounding Memory Utilization</a><ul><li><a href="#using-ram-as-a-buffering-device" class="table-of-contents__link toc-highlight">Using RAM as a buffering device</a></li><li><a href="#hashtables-for-storing-blobs--buckets" class="table-of-contents__link toc-highlight">Hashtables for storing blobs + buckets</a></li><li><a href="#bounding-non-buffering-tasks" class="table-of-contents__link toc-highlight">Bounding Non-Buffering Tasks</a></li><li><a href="#calculating-total-amount-of-memory" class="table-of-contents__link toc-highlight">Calculating Total Amount of Memory</a></li></ul></li><li><a href="#client-configuration" class="table-of-contents__link toc-highlight">Client Configuration</a><ul><li><a href="#path-inclusion--exclusion" class="table-of-contents__link toc-highlight">Path Inclusion / Exclusion</a></li><li><a href="#adapter-mode" class="table-of-contents__link toc-highlight">Adapter Mode</a></li><li><a href="#file-page-size" class="table-of-contents__link toc-highlight">File Page Size</a></li><li><a href="#flushing-mode" class="table-of-contents__link toc-highlight">Flushing Mode</a></li><li><a href="#adapter-config" class="table-of-contents__link toc-highlight">Adapter Config</a></li></ul></li><li><a href="#provided-configurations" class="table-of-contents__link toc-highlight">Provided Configurations</a></li><li><a href="#how-to-avoid-repeating-the-default-configurations" class="table-of-contents__link toc-highlight">How To Avoid Repeating the Default Configurations</a></li></ul></div></div></div></div></main></div></div></div><footer class="footer"><div class="container container-fluid"><div class="row footer__links"><div class="col footer__col"><div class="footer__title">Gnosis Research Center</div><ul class="footer__items clean-list"><li class="footer__item">
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diff --git a/docs/hermes/quick-start/index.html b/docs/hermes/containers/index.html
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-<div class="language-bash codeBlockContainer_Ckt0 theme-code-block" style="--prism-color:#393A34;--prism-background-color:#f6f8fa"><div class="codeBlockContent_biex"><pre tabindex="0" class="prism-code language-bash codeBlock_bY9V thin-scrollbar" style="color:#393A34;background-color:#f6f8fa"><code class="codeBlockLines_e6Vv"><span class="token-line" style="color:#393A34"><span class="token plain">docker pull hdfgroup/hermes</span><br></span><span class="token-line" style="color:#393A34"><span class="token plain">docker run -it hdfgroup/hermes</span><br></span><span class="token-line" style="color:#393A34"><span class="token plain">hermes@6bcfd7679b0a:~$ stage_in</span><br></span><span class="token-line" style="color:#393A34"><span class="token plain">Usage: mpirun -n [nprocs] ./stage_in [url] [offset] [size] [dpe]</span><br></span></code></pre><div class="buttonGroup__atx"><button type="button" aria-label="Copy code to clipboard" title="Copy" class="clean-btn"><span class="copyButtonIcons_eSgA" aria-hidden="true"><svg viewBox="0 0 24 24" class="copyButtonIcon_y97N"><path fill="currentColor" d="M19,21H8V7H19M19,5H8A2,2 0 0,0 6,7V21A2,2 0 0,0 8,23H19A2,2 0 0,0 21,21V7A2,2 0 0,0 19,5M16,1H4A2,2 0 0,0 2,3V17H4V3H16V1Z"></path></svg><svg viewBox="0 0 24 24" class="copyButtonSuccessIcon_LjdS"><path fill="currentColor" d="M21,7L9,19L3.5,13.5L4.91,12.09L9,16.17L19.59,5.59L21,7Z"></path></svg></span></button></div></div></div>
-<p>CAUTION: The image from DockerHub may throw <strong>Illegal Instruction</strong> for Spack-installed binaries.
-See <a href="https://github.com/HDFGroup/hermes/issues/483" target="_blank" rel="noopener noreferrer">#483</a>.</p>
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itemtype="https://schema.org/BreadcrumbList"><li class="breadcrumbs__item"><a aria-label="Home page" class="breadcrumbs__link" href="/"><svg viewBox="0 0 24 24" class="breadcrumbHomeIcon_YNFT"><path d="M10 19v-5h4v5c0 .55.45 1 1 1h3c.55 0 1-.45 1-1v-7h1.7c.46 0 .68-.57.33-.87L12.67 3.6c-.38-.34-.96-.34-1.34 0l-8.36 7.53c-.34.3-.13.87.33.87H5v7c0 .55.45 1 1 1h3c.55 0 1-.45 1-1z" fill="currentColor"></path></svg></a></li><li itemscope="" itemprop="itemListElement" itemtype="https://schema.org/ListItem" class="breadcrumbs__item"><a class="breadcrumbs__link" itemprop="item" href="/docs/category/hermes"><span itemprop="name">Hermes</span></a><meta itemprop="position" content="1"></li><li itemscope="" itemprop="itemListElement" itemtype="https://schema.org/ListItem" class="breadcrumbs__item breadcrumbs__item--active"><span class="breadcrumbs__link" itemprop="name">Containers</span><meta itemprop="position" content="2"></li></ul></nav><div class="tocCollapsible_ETCw theme-doc-toc-mobile tocMobile_ITEo"><button type="button" class="clean-btn tocCollapsibleButton_TO0P">On this page</button></div><div class="theme-doc-markdown markdown"><h1>Containers</h1>
+<div class="language-bash codeBlockContainer_Ckt0 theme-code-block" style="--prism-color:#393A34;--prism-background-color:#f6f8fa"><div class="codeBlockContent_biex"><pre tabindex="0" class="prism-code language-bash codeBlock_bY9V thin-scrollbar" style="color:#393A34;background-color:#f6f8fa"><code class="codeBlockLines_e6Vv"><span class="token-line" style="color:#393A34"><span class="token plain">docker pull hdfgroup/hermes</span><br></span><span class="token-line" style="color:#393A34"><span class="token plain">docker run -it hdfgroup/hermes</span><br></span></code></pre><div class="buttonGroup__atx"><button type="button" aria-label="Copy code to clipboard" title="Copy" class="clean-btn"><span class="copyButtonIcons_eSgA" aria-hidden="true"><svg viewBox="0 0 24 24" class="copyButtonIcon_y97N"><path fill="currentColor" d="M19,21H8V7H19M19,5H8A2,2 0 0,0 6,7V21A2,2 0 0,0 8,23H19A2,2 0 0,0 21,21V7A2,2 0 0,0 19,5M16,1H4A2,2 0 0,0 2,3V17H4V3H16V1Z"></path></svg><svg viewBox="0 0 24 24" class="copyButtonSuccessIcon_LjdS"><path fill="currentColor" d="M21,7L9,19L3.5,13.5L4.91,12.09L9,16.17L19.59,5.59L21,7Z"></path></svg></span></button></div></div></div>
 <h2 class="anchor anchorWithStickyNavbar_LWe7" id="dockerfiles">Dockerfiles<a href="#dockerfiles" class="hash-link" aria-label="Direct link to Dockerfiles" title="Direct link to Dockerfiles">​</a></h2>
-<p>There are <a href="https://github.com/HDFGroup/hermes/tree/master/docker" target="_blank" rel="noopener noreferrer">four Dockerfiles</a> at the top level of the Hermes repository.
+<p>There are <a href="https://github.com/HDFGroup/hermes/tree/master/docker" target="_blank" rel="noopener noreferrer">two Dockerfiles</a> at the top level of the Hermes repository.
 Three Docker images built from these Dockerfiles are available on <a href="https://hub.docker.com/r/hdfgroup/hermes" target="_blank" rel="noopener noreferrer">Docker Hub</a>:</p>
 <ul>
+<li><a href="https://hub.docker.com/repository/docker/hdfgroup/hermes-deps" target="_blank" rel="noopener noreferrer"><code>hdfgroup/hermes-deps:latest</code></a> - The Hermes dependencies for developers.</li>
 <li><a href="https://hub.docker.com/repository/docker/hdfgroup/hermes" target="_blank" rel="noopener noreferrer"><code>hdfgroup/hermes:latest</code></a> - Hermes pre-built &amp; ready to go</li>
-<li><a href="https://hub.docker.com/repository/docker/hdfgroup/hermes-dev" target="_blank" rel="noopener noreferrer"><code>hdfgroup/hermes-dev:latest</code></a> - For Hermes developers; it clones Hermes repo.</li>
-<li><a href="https://hub.docker.com/repository/docker/hdfgroup/hermes-deps" target="_blank" rel="noopener noreferrer"><code>hdfgroup/hermes-deps:latest</code></a> - For testers; this is used by the two images above.</li>
 </ul>
 <p>Running one of these docker containers usually involves mounting volumes or directories of the host system in the docker container via the <code>-v</code> option of the <code>docker run</code> command, for example:</p>
 <div class="language-bash codeBlockContainer_Ckt0 theme-code-block" style="--prism-color:#393A34;--prism-background-color:#f6f8fa"><div class="codeBlockContent_biex"><pre tabindex="0" class="prism-code language-bash codeBlock_bY9V thin-scrollbar" style="color:#393A34;background-color:#f6f8fa"><code class="codeBlockLines_e6Vv"><span class="token-line" style="color:#393A34"><span class="token plain">docker run --rm -it -v &lt;host mount point1&gt;:&lt;container mount point1&gt; \</span><br></span><span class="token-line" style="color:#393A34"><span class="token plain">                    -v &lt;host mount point2&gt;:&lt;container mount point2&gt; \</span><br></span><span class="token-line" style="color:#393A34"><span class="token plain">                    ... \</span><br></span><span class="token-line" style="color:#393A34"><span class="token plain">           --entrypoint bash &lt;container image ID&gt;</span><br></span></code></pre><div class="buttonGroup__atx"><button type="button" aria-label="Copy code to clipboard" title="Copy" class="clean-btn"><span class="copyButtonIcons_eSgA" aria-hidden="true"><svg viewBox="0 0 24 24" class="copyButtonIcon_y97N"><path fill="currentColor" d="M19,21H8V7H19M19,5H8A2,2 0 0,0 6,7V21A2,2 0 0,0 8,23H19A2,2 0 0,0 21,21V7A2,2 0 0,0 19,5M16,1H4A2,2 0 0,0 2,3V17H4V3H16V1Z"></path></svg><svg viewBox="0 0 24 24" class="copyButtonSuccessIcon_LjdS"><path fill="currentColor" d="M21,7L9,19L3.5,13.5L4.91,12.09L9,16.17L19.59,5.59L21,7Z"></path></svg></span></button></div></div></div>
@@ -33,7 +30,7 @@ <h2 class="anchor anchorWithStickyNavbar_LWe7" id="for-emacs-users">For Emacs Us
 <p><img loading="lazy" src="https://img.shields.io/badge/Emacs-%237F5AB6.svg?&amp;style=for-the-badge&amp;logo=gnu-emacs&amp;logoColor=white" alt="Emacs" class="img_ev3q"></p>
 <p>Editing files in a running container in Emacs (running on a host) is rather convenient with <a href="https://www.emacswiki.org/emacs/TrampAndDocker" target="_blank" rel="noopener noreferrer">Tramp</a> and <a href="https://github.com/emacs-pe/docker-tramp.el" target="_blank" rel="noopener noreferrer"><code>docker-tramp.el</code></a>. For example:</p>
 <div class="language-bash codeBlockContainer_Ckt0 theme-code-block" style="--prism-color:#393A34;--prism-background-color:#f6f8fa"><div class="codeBlockContent_biex"><pre tabindex="0" class="prism-code language-bash codeBlock_bY9V thin-scrollbar" style="color:#393A34;background-color:#f6f8fa"><code class="codeBlockLines_e6Vv"><span class="token-line" style="color:#393A34"><span class="token plain">C-x C-f /docker:user@container:/path/to/file</span><br></span><span class="token-line" style="color:#393A34"><span class="token plain" style="display:inline-block"></span><br></span><span class="token-line" style="color:#393A34"><span class="token plain">where</span><br></span><span class="token-line" style="color:#393A34"><span class="token plain">  user           is the user that you want to use inside the container (optional)</span><br></span><span class="token-line" style="color:#393A34"><span class="token plain">  container      is the id or name of the container</span><br></span></code></pre><div class="buttonGroup__atx"><button type="button" aria-label="Copy code to clipboard" title="Copy" class="clean-btn"><span class="copyButtonIcons_eSgA" aria-hidden="true"><svg viewBox="0 0 24 24" class="copyButtonIcon_y97N"><path fill="currentColor" d="M19,21H8V7H19M19,5H8A2,2 0 0,0 6,7V21A2,2 0 0,0 8,23H19A2,2 0 0,0 21,21V7A2,2 0 0,0 19,5M16,1H4A2,2 0 0,0 2,3V17H4V3H16V1Z"></path></svg><svg viewBox="0 0 24 24" class="copyButtonSuccessIcon_LjdS"><path fill="currentColor" d="M21,7L9,19L3.5,13.5L4.91,12.09L9,16.17L19.59,5.59L21,7Z"></path></svg></span></button></div></div></div>
-<p>Multiple hops are supported as well.</p></div></article><nav class="pagination-nav docusaurus-mt-lg" aria-label="Docs pages"><a class="pagination-nav__link pagination-nav__link--prev" href="/docs/hermes/adapters"><div class="pagination-nav__sublabel">Previous</div><div class="pagination-nav__label">Adapters</div></a><a class="pagination-nav__link pagination-nav__link--next" href="/docs/hermes/debugging"><div class="pagination-nav__sublabel">Next</div><div class="pagination-nav__label">Debugging</div></a></nav></div></div><div class="col col--3"><div class="tableOfContents_bqdL thin-scrollbar theme-doc-toc-desktop"><ul class="table-of-contents table-of-contents__left-border"><li><a href="#dockerfiles" class="table-of-contents__link toc-highlight">Dockerfiles</a></li><li><a href="#for-emacs-users" class="table-of-contents__link toc-highlight">For Emacs Users</a></li></ul></div></div></div></div></main></div></div></div><footer class="footer"><div class="container container-fluid"><div class="row footer__links"><div class="col footer__col"><div class="footer__title">Gnosis Research Center</div><ul class="footer__items clean-list"><li class="footer__item">
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class="theme-doc-sidebar-item-category theme-doc-sidebar-item-category-level-1 menu__list-item menu__list-item--collapsed"><div class="menu__list-item-collapsible"><a class="menu__link menu__link--sublist menu__link--sublist-caret" aria-expanded="false" href="/docs/chronolog/index">ChronoLog</a></div></li><li class="theme-doc-sidebar-item-category theme-doc-sidebar-item-category-level-1 menu__list-item menu__list-item--collapsed"><div class="menu__list-item-collapsible"><a class="menu__link menu__link--sublist menu__link--sublist-caret" aria-expanded="false" href="/docs/jarvis/jarvis-util/index">Jarvis</a></div></li></ul></nav></div></div></aside><main class="docMainContainer_TBSr"><div class="container padding-top--md padding-bottom--lg"><div class="row"><div class="col docItemCol_VOVn"><div class="docItemContainer_Djhp"><article><nav class="theme-doc-breadcrumbs breadcrumbsContainer_Z_bl" aria-label="Breadcrumbs"><ul class="breadcrumbs" itemscope="" itemtype="https://schema.org/BreadcrumbList"><li class="breadcrumbs__item"><a aria-label="Home page" class="breadcrumbs__link" href="/"><svg viewBox="0 0 24 24" class="breadcrumbHomeIcon_YNFT"><path d="M10 19v-5h4v5c0 .55.45 1 1 1h3c.55 0 1-.45 1-1v-7h1.7c.46 0 .68-.57.33-.87L12.67 3.6c-.38-.34-.96-.34-1.34 0l-8.36 7.53c-.34.3-.13.87.33.87H5v7c0 .55.45 1 1 1h3c.55 0 1-.45 1-1z" fill="currentColor"></path></svg></a></li><li itemscope="" itemprop="itemListElement" itemtype="https://schema.org/ListItem" class="breadcrumbs__item"><a class="breadcrumbs__link" itemprop="item" href="/docs/category/hermes"><span itemprop="name">Hermes</span></a><meta itemprop="position" content="1"></li><li itemscope="" itemprop="itemListElement" itemtype="https://schema.org/ListItem" class="breadcrumbs__item breadcrumbs__item--active"><span class="breadcrumbs__link" itemprop="name">Debugging</span><meta itemprop="position" content="2"></li></ul></nav><div class="tocCollapsible_ETCw theme-doc-toc-mobile tocMobile_ITEo"><button type="button" class="clean-btn tocCollapsibleButton_TO0P">On this page</button></div><div class="theme-doc-markdown markdown"><h1>Debugging</h1>
-<p>Hermes can be complicated to debug due to its distributed and asynchronous
-nature. Faults can happen in the client program, or in the Hermes daemon.
-The first step when encountering problems is to compile in Debug mode.</p>
-<div class="language-cmake codeBlockContainer_Ckt0 theme-code-block" style="--prism-color:#393A34;--prism-background-color:#f6f8fa"><div class="codeBlockContent_biex"><pre tabindex="0" class="prism-code language-cmake codeBlock_bY9V thin-scrollbar" style="color:#393A34;background-color:#f6f8fa"><code class="codeBlockLines_e6Vv"><span class="token-line" style="color:#393A34"><span class="token plain">cmake .. -DCMAKE_BUILD_TYPE=Debug</span><br></span></code></pre><div class="buttonGroup__atx"><button type="button" aria-label="Copy code to clipboard" title="Copy" class="clean-btn"><span class="copyButtonIcons_eSgA" aria-hidden="true"><svg viewBox="0 0 24 24" class="copyButtonIcon_y97N"><path fill="currentColor" d="M19,21H8V7H19M19,5H8A2,2 0 0,0 6,7V21A2,2 0 0,0 8,23H19A2,2 0 0,0 21,21V7A2,2 0 0,0 19,5M16,1H4A2,2 0 0,0 2,3V17H4V3H16V1Z"></path></svg><svg viewBox="0 0 24 24" class="copyButtonSuccessIcon_LjdS"><path fill="currentColor" d="M21,7L9,19L3.5,13.5L4.91,12.09L9,16.17L19.59,5.59L21,7Z"></path></svg></span></button></div></div></div>
-<p>The Debug mode will increase the number of logging statements the program
-uses to give you a stronger hint as to where the problem occurs. These
-statements are typically compiled out for performance reasons.</p>
-<p>Secondly, make sure to use an IDE which supports visual debugging. Debugging
-using a terminal with gdb can be very cumbersome, especially when multi-process
-cases come along.</p>
-<h2 class="anchor anchorWithStickyNavbar_LWe7" id="preparing-for-release">Preparing For Release<a href="#preparing-for-release" class="hash-link" aria-label="Direct link to Preparing For Release" title="Direct link to Preparing For Release">​</a></h2>
-<ol>
-<li>Create a GitHub Project for the <em>next</em> release</li>
-<li>Update the <code>HERMES_VERSION_*</code> variables in <code>CMakeLists.txt</code></li>
-<li>Update <code>PROJECT_NUMBER</code> in <code>Doxyfile.in</code>.</li>
-<li>To make release note generation as automated as possible, make sure
-relevant pull requests that are part of the release have proper labels and and
-titles, as that information will show up directly in the generated release
-notes in the next step.</li>
-<li>Draft a release on Github. Click <code>auto-generate release notes</code> and edit
-the result as necessary. Fill in the new tag, and select &quot;Create new tag x.x.x
-on publish&quot; so that Github will automatically tag the release when it is
-published.</li>
-<li>The docker containers will be automatically built and pushed to docker hub
-whenever a new tag is added. Check the CI actions to make sure there were no
-errors.</li>
-<li>Copy/move ideas to the project for the next release</li>
-<li>Close and archive the project for the <em>current</em> release</li>
-<li>Merge the latest release branch (if one exists) of the wiki into the <code>master</code> branch.</li>
-<li>Make an announcement in the Hermes topic of the HDF forum.</li>
-<li>Send Lori a note for the next HDF5 newsletter.</li>
-</ol>
-<h3 class="anchor anchorWithStickyNavbar_LWe7" id="preparing-pull-request-pr">Preparing Pull Request (PR)<a href="#preparing-pull-request-pr" class="hash-link" aria-label="Direct link to Preparing Pull Request (PR)" title="Direct link to Preparing Pull Request (PR)">​</a></h3>
-<p>Please run these two steps and remove all warnings.</p>
-<div class="language-bash codeBlockContainer_Ckt0 theme-code-block" style="--prism-color:#393A34;--prism-background-color:#f6f8fa"><div class="codeBlockContent_biex"><pre tabindex="0" class="prism-code language-bash codeBlock_bY9V thin-scrollbar" style="color:#393A34;background-color:#f6f8fa"><code class="codeBlockLines_e6Vv"><span class="token-line" style="color:#393A34"><span class="token plain">make dox</span><br></span><span class="token-line" style="color:#393A34"><span class="token plain">make lint</span><br></span></code></pre><div class="buttonGroup__atx"><button type="button" aria-label="Copy code to clipboard" title="Copy" class="clean-btn"><span class="copyButtonIcons_eSgA" aria-hidden="true"><svg viewBox="0 0 24 24" class="copyButtonIcon_y97N"><path fill="currentColor" d="M19,21H8V7H19M19,5H8A2,2 0 0,0 6,7V21A2,2 0 0,0 8,23H19A2,2 0 0,0 21,21V7A2,2 0 0,0 19,5M16,1H4A2,2 0 0,0 2,3V17H4V3H16V1Z"></path></svg><svg viewBox="0 0 24 24" class="copyButtonSuccessIcon_LjdS"><path fill="currentColor" d="M21,7L9,19L3.5,13.5L4.91,12.09L9,16.17L19.59,5.59L21,7Z"></path></svg></span></button></div></div></div>
-<h3 class="anchor anchorWithStickyNavbar_LWe7" id="pr-check-failure">PR Check Failure<a href="#pr-check-failure" class="hash-link" aria-label="Direct link to PR Check Failure" title="Direct link to PR Check Failure">​</a></h3>
-<p>GitHub Actions for PR check may fail because it uses a Spack cache.
-The cache does not have to change often (unless you&#x27;ve added dependencies),
-so this should be done only in this case. To refresh the github cache,
-modify the file &quot;ci/install_deps.sh&quot; in some way. For
-example, by adding a comment. If you check the <a href="https://github.com/HDFGroup/hermes/blob/master/.github/workflows/main.yml" target="_blank" rel="noopener noreferrer">github workflow which produces
-the cache</a>, it uses a hash
-of install_deps.sh to locate a cache.</p>
-<h2 class="anchor anchorWithStickyNavbar_LWe7" id="introduction-to-our-continuous-integration-ci">Introduction to our Continuous Integration (CI)<a href="#introduction-to-our-continuous-integration-ci" class="hash-link" aria-label="Direct link to Introduction to our Continuous Integration (CI)" title="Direct link to Introduction to our Continuous Integration (CI)">​</a></h2>
-<p>We are primarily using Python for managing for running unit tests. Under
-<a href="https://github.com/HDFGroup/hermes/blob/master/CMakeLists.txt" target="_blank" rel="noopener noreferrer">our root CMakeList</a>, we implement a
-CMake function called pytest, which wraps around the Python testing
-framework called py_hermes_ci, which is located under ci/py_hermes_ci.</p>
-<p>Fundamentally, py_hermes_ci relies on our library jarvis-util,
-(located under ci/jarvis-util), which provides utilities to execute
-binaries in Python.</p>
-<h3 class="anchor anchorWithStickyNavbar_LWe7" id="api-test">API Test<a href="#api-test" class="hash-link" aria-label="Direct link to API Test" title="Direct link to API Test">​</a></h3>
-<p>Update <code>test/CMakeLists.txt</code> with your new .cc test code name.
-For example, if you add <code>trait_order.cc</code>, add <code>trait_order</code> as follows:</p>
-<div class="codeBlockContainer_Ckt0 theme-code-block" style="--prism-color:#393A34;--prism-background-color:#f6f8fa"><div class="codeBlockContent_biex"><pre tabindex="0" class="prism-code language-text codeBlock_bY9V thin-scrollbar" style="color:#393A34;background-color:#f6f8fa"><code class="codeBlockLines_e6Vv"><span class="token-line" style="color:#393A34"><span class="token plain">set(API_TESTS dpe_optimization_test dpe_random_test</span><br></span><span class="token-line" style="color:#393A34"><span class="token plain">    dpe_roundrobin_test end_to_end_test vbucket_test trait_order)</span><br></span></code></pre><div class="buttonGroup__atx"><button type="button" aria-label="Copy code to clipboard" title="Copy" class="clean-btn"><span class="copyButtonIcons_eSgA" aria-hidden="true"><svg viewBox="0 0 24 24" class="copyButtonIcon_y97N"><path fill="currentColor" d="M19,21H8V7H19M19,5H8A2,2 0 0,0 6,7V21A2,2 0 0,0 8,23H19A2,2 0 0,0 21,21V7A2,2 0 0,0 19,5M16,1H4A2,2 0 0,0 2,3V17H4V3H16V1Z"></path></svg><svg viewBox="0 0 24 24" class="copyButtonSuccessIcon_LjdS"><path fill="currentColor" d="M21,7L9,19L3.5,13.5L4.91,12.09L9,16.17L19.59,5.59L21,7Z"></path></svg></span></button></div></div></div>
-<h2 class="anchor anchorWithStickyNavbar_LWe7" id="adding-a-new-adapter">Adding a New Adapter<a href="#adding-a-new-adapter" class="hash-link" aria-label="Direct link to Adding a New Adapter" title="Direct link to Adding a New Adapter">​</a></h2>
-<ol>
-<li>Create a new directory under the <code>adapter</code> directory.</li>
-</ol>
-<h2 class="anchor anchorWithStickyNavbar_LWe7" id="customizing-data-placement-engine">Customizing Data Placement Engine<a href="#customizing-data-placement-engine" class="hash-link" aria-label="Direct link to Customizing Data Placement Engine" title="Direct link to Customizing Data Placement Engine">​</a></h2>
-<p>Data Placement Engine (DPE) is the heart of Hermes performance.
-Developers may want to replace the default engine using different optimization algorithms.</p>
-<h3 class="anchor anchorWithStickyNavbar_LWe7" id="codes-for-testing-dpe">Codes for Testing DPE<a href="#codes-for-testing-dpe" class="hash-link" aria-label="Direct link to Codes for Testing DPE" title="Direct link to Codes for Testing DPE">​</a></h3>
-<p>You can quickly check how DPE is tested.</p>
-<ul>
-<li><a href="https://github.com/HDFGroup/hermes/blob/master/test/dpe_optimization_test.cc" target="_blank" rel="noopener noreferrer">test/dpe_optimization_test.cc</a></li>
-</ul></div></article><nav class="pagination-nav docusaurus-mt-lg" aria-label="Docs pages"><a class="pagination-nav__link pagination-nav__link--prev" href="/docs/hermes/quick-start"><div class="pagination-nav__sublabel">Previous</div><div class="pagination-nav__label">Quick Start Guide</div></a><a class="pagination-nav__link pagination-nav__link--next" href="/docs/hermes/doxygen"><div class="pagination-nav__sublabel">Next</div><div class="pagination-nav__label">Doxygen</div></a></nav></div></div><div class="col col--3"><div class="tableOfContents_bqdL thin-scrollbar theme-doc-toc-desktop"><ul class="table-of-contents table-of-contents__left-border"><li><a href="#preparing-for-release" class="table-of-contents__link toc-highlight">Preparing For Release</a><ul><li><a href="#preparing-pull-request-pr" class="table-of-contents__link toc-highlight">Preparing Pull Request (PR)</a></li><li><a href="#pr-check-failure" class="table-of-contents__link toc-highlight">PR Check Failure</a></li></ul></li><li><a href="#introduction-to-our-continuous-integration-ci" class="table-of-contents__link toc-highlight">Introduction to our Continuous Integration (CI)</a><ul><li><a href="#api-test" class="table-of-contents__link toc-highlight">API Test</a></li></ul></li><li><a href="#adding-a-new-adapter" class="table-of-contents__link toc-highlight">Adding a New Adapter</a></li><li><a href="#customizing-data-placement-engine" class="table-of-contents__link toc-highlight">Customizing Data Placement Engine</a><ul><li><a href="#codes-for-testing-dpe" class="table-of-contents__link toc-highlight">Codes for Testing DPE</a></li></ul></li></ul></div></div></div></div></main></div></div></div><footer class="footer"><div class="container container-fluid"><div class="row footer__links"><div class="col footer__col"><div class="footer__title">Gnosis Research Center</div><ul class="footer__items clean-list"><li class="footer__item">
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tocMobile_ITEo"><button type="button" class="clean-btn tocCollapsibleButton_TO0P">On this page</button></div><div class="theme-doc-markdown markdown"><h1>Deploying Hermes</h1>
 <h2 class="anchor anchorWithStickyNavbar_LWe7" id="configuring--deploying-hermes">Configuring + Deploying Hermes<a href="#configuring--deploying-hermes" class="hash-link" aria-label="Direct link to Configuring + Deploying Hermes" title="Direct link to Configuring + Deploying Hermes">​</a></h2>
 <p>The Hermes daemon is responsible for tracking various metadata, and it is
 required to be launched before your application. There should only be
@@ -34,17 +34,18 @@ <h3 class="anchor anchorWithStickyNavbar_LWe7" id="initialize-jarvis">Initialize
 objects are <strong>never</strong> intended to be stored in these directories.</p>
 <p>There are three places where configuration data is stored:</p>
 <ul>
-<li>CONFIG_DIR: A directory where jarvis metadata for pkgs and pipelines are stored. This
-directory can be anywhere that the current user can access.</li>
-<li>PRIVATE_DIR: A directory which is common across all machines, but stores data locally to the
-machine. Some jarvis pkgs require certain data to be stored per-machine. /tmp
-would be an example.</li>
-<li>SHARED_DIR: A directory which is common across all machines, where each machine has the same
+<li><strong>CONFIG_DIR:</strong> A directory where jarvis metadata for pkgs and pipelines are stored. This
+directory can be anywhere that the current user can access. <code>${HOME}/jarvis_config</code> would be an example.</li>
+<li><strong>PRIVATE_DIR:</strong> A directory which is common across all machines, but stores data locally to the
+machine. Some jarvis pkgs require certain data to be stored per-machine. <code>/tmp/jarvis_priv</code> would be an example.</li>
+<li><strong>SHARED_DIR:</strong> A directory which is common across all machines, where each machine has the same
 view of data in the directory. In a supercomputing site, this would typically be
-in your home directory.</li>
+in your home directory. For example <code>${HOME}/jarvis_shared</code></li>
 </ul>
-<p>Make sure that all these paths are absolute paths.</p>
+<p>Make sure that all these paths are absolute paths. Environment variables can be used to make absolute paths less cumbersome. This command will automatically create the directories if they don&#x27;t exist.</p>
 <div class="language-bash codeBlockContainer_Ckt0 theme-code-block" style="--prism-color:#393A34;--prism-background-color:#f6f8fa"><div class="codeBlockContent_biex"><pre tabindex="0" class="prism-code language-bash codeBlock_bY9V thin-scrollbar" style="color:#393A34;background-color:#f6f8fa"><code class="codeBlockLines_e6Vv"><span class="token-line" style="color:#393A34"><span class="token plain">jarvis init [CONFIG_DIR] [PRIVATE_DIR] [SHARED_DIR]</span><br></span></code></pre><div class="buttonGroup__atx"><button type="button" aria-label="Copy code to clipboard" title="Copy" class="clean-btn"><span class="copyButtonIcons_eSgA" aria-hidden="true"><svg viewBox="0 0 24 24" class="copyButtonIcon_y97N"><path fill="currentColor" d="M19,21H8V7H19M19,5H8A2,2 0 0,0 6,7V21A2,2 0 0,0 8,23H19A2,2 0 0,0 21,21V7A2,2 0 0,0 19,5M16,1H4A2,2 0 0,0 2,3V17H4V3H16V1Z"></path></svg><svg viewBox="0 0 24 24" class="copyButtonSuccessIcon_LjdS"><path fill="currentColor" d="M21,7L9,19L3.5,13.5L4.91,12.09L9,16.17L19.59,5.59L21,7Z"></path></svg></span></button></div></div></div>
+<p>This above command produces the jarvis configuration and store it here:</p>
+<div class="language-bash codeBlockContainer_Ckt0 theme-code-block" style="--prism-color:#393A34;--prism-background-color:#f6f8fa"><div class="codeBlockContent_biex"><pre tabindex="0" class="prism-code language-bash codeBlock_bY9V thin-scrollbar" style="color:#393A34;background-color:#f6f8fa"><code class="codeBlockLines_e6Vv"><span class="token-line" style="color:#393A34"><span class="token plain">${JARVIS_PATH}/config/jarvis_config.yaml</span><br></span></code></pre><div class="buttonGroup__atx"><button type="button" aria-label="Copy code to clipboard" title="Copy" class="clean-btn"><span class="copyButtonIcons_eSgA" aria-hidden="true"><svg viewBox="0 0 24 24" class="copyButtonIcon_y97N"><path fill="currentColor" d="M19,21H8V7H19M19,5H8A2,2 0 0,0 6,7V21A2,2 0 0,0 8,23H19A2,2 0 0,0 21,21V7A2,2 0 0,0 19,5M16,1H4A2,2 0 0,0 2,3V17H4V3H16V1Z"></path></svg><svg viewBox="0 0 24 24" class="copyButtonSuccessIcon_LjdS"><path fill="currentColor" d="M21,7L9,19L3.5,13.5L4.91,12.09L9,16.17L19.59,5.59L21,7Z"></path></svg></span></button></div></div></div>
 <h3 class="anchor anchorWithStickyNavbar_LWe7" id="build-a-resource-graph">Build a Resource Graph<a href="#build-a-resource-graph" class="hash-link" aria-label="Direct link to Build a Resource Graph" title="Direct link to Build a Resource Graph">​</a></h3>
 <p>A resource graph contains the storage and networking configuration
 of the machines you intend to deploy Hermes on.</p>
@@ -108,7 +109,9 @@ <h4 class="anchor anchorWithStickyNavbar_LWe7" id="add-hermes-runtime">Add Herme
 <p>Jarvis will automatically produce a Hermes client and server configuration that
 contains all storage devices and fastest available network defined in the
 resource graph. These configurations will be located in:</p>
-<div class="codeBlockContainer_Ckt0 theme-code-block" style="--prism-color:#393A34;--prism-background-color:#f6f8fa"><div class="codeBlockContent_biex"><pre tabindex="0" class="prism-code language-text codeBlock_bY9V thin-scrollbar" style="color:#393A34;background-color:#f6f8fa"><code class="codeBlockLines_e6Vv"><span class="token-line" style="color:#393A34"><span class="token plain">$(jarvis path +shared)/hermes_run/hermes_server.yaml</span><br></span><span class="token-line" style="color:#393A34"><span class="token plain">$(jarvis path +shared)/hermes_run/hermes_client.yaml</span><br></span></code></pre><div class="buttonGroup__atx"><button type="button" aria-label="Copy code to clipboard" title="Copy" class="clean-btn"><span class="copyButtonIcons_eSgA" aria-hidden="true"><svg viewBox="0 0 24 24" class="copyButtonIcon_y97N"><path fill="currentColor" d="M19,21H8V7H19M19,5H8A2,2 0 0,0 6,7V21A2,2 0 0,0 8,23H19A2,2 0 0,0 21,21V7A2,2 0 0,0 19,5M16,1H4A2,2 0 0,0 2,3V17H4V3H16V1Z"></path></svg><svg viewBox="0 0 24 24" class="copyButtonSuccessIcon_LjdS"><path fill="currentColor" d="M21,7L9,19L3.5,13.5L4.91,12.09L9,16.17L19.59,5.59L21,7Z"></path></svg></span></button></div></div></div>
+<div class="language-bash codeBlockContainer_Ckt0 theme-code-block" style="--prism-color:#393A34;--prism-background-color:#f6f8fa"><div class="codeBlockContent_biex"><pre tabindex="0" class="prism-code language-bash codeBlock_bY9V thin-scrollbar" style="color:#393A34;background-color:#f6f8fa"><code class="codeBlockLines_e6Vv"><span class="token-line" style="color:#393A34"><span class="token plain">$(jarvis path +shared)/hermes_run/hermes_server.yaml</span><br></span><span class="token-line" style="color:#393A34"><span class="token plain">$(jarvis path +shared)/hermes_run/hermes_client.yaml</span><br></span></code></pre><div class="buttonGroup__atx"><button type="button" aria-label="Copy code to clipboard" title="Copy" class="clean-btn"><span class="copyButtonIcons_eSgA" aria-hidden="true"><svg viewBox="0 0 24 24" class="copyButtonIcon_y97N"><path fill="currentColor" d="M19,21H8V7H19M19,5H8A2,2 0 0,0 6,7V21A2,2 0 0,0 8,23H19A2,2 0 0,0 21,21V7A2,2 0 0,0 19,5M16,1H4A2,2 0 0,0 2,3V17H4V3H16V1Z"></path></svg><svg viewBox="0 0 24 24" class="copyButtonSuccessIcon_LjdS"><path fill="currentColor" d="M21,7L9,19L3.5,13.5L4.91,12.09L9,16.17L19.59,5.59L21,7Z"></path></svg></span></button></div></div></div>
+<p>To view all parameters of the Hermes package, you can run:</p>
+<div class="language-bash codeBlockContainer_Ckt0 theme-code-block" style="--prism-color:#393A34;--prism-background-color:#f6f8fa"><div class="codeBlockContent_biex"><pre tabindex="0" class="prism-code language-bash codeBlock_bY9V thin-scrollbar" style="color:#393A34;background-color:#f6f8fa"><code class="codeBlockLines_e6Vv"><span class="token-line" style="color:#393A34"><span class="token plain">jarvis pkg help hermes_run</span><br></span></code></pre><div class="buttonGroup__atx"><button type="button" aria-label="Copy code to clipboard" title="Copy" class="clean-btn"><span class="copyButtonIcons_eSgA" aria-hidden="true"><svg viewBox="0 0 24 24" class="copyButtonIcon_y97N"><path fill="currentColor" d="M19,21H8V7H19M19,5H8A2,2 0 0,0 6,7V21A2,2 0 0,0 8,23H19A2,2 0 0,0 21,21V7A2,2 0 0,0 19,5M16,1H4A2,2 0 0,0 2,3V17H4V3H16V1Z"></path></svg><svg viewBox="0 0 24 24" class="copyButtonSuccessIcon_LjdS"><path fill="currentColor" d="M21,7L9,19L3.5,13.5L4.91,12.09L9,16.17L19.59,5.59L21,7Z"></path></svg></span></button></div></div></div>
 <h3 class="anchor anchorWithStickyNavbar_LWe7" id="starting--stopping-hermes">Starting + Stopping Hermes<a href="#starting--stopping-hermes" class="hash-link" aria-label="Direct link to Starting + Stopping Hermes" title="Direct link to Starting + Stopping Hermes">​</a></h3>
 <p>To start Hermes:</p>
 <div class="language-bash codeBlockContainer_Ckt0 theme-code-block" style="--prism-color:#393A34;--prism-background-color:#f6f8fa"><div class="codeBlockContent_biex"><pre tabindex="0" class="prism-code language-bash codeBlock_bY9V thin-scrollbar" style="color:#393A34;background-color:#f6f8fa"><code class="codeBlockLines_e6Vv"><span class="token-line" style="color:#393A34"><span class="token plain">jarvis pipeline start</span><br></span></code></pre><div class="buttonGroup__atx"><button type="button" aria-label="Copy code to clipboard" title="Copy" class="clean-btn"><span class="copyButtonIcons_eSgA" aria-hidden="true"><svg viewBox="0 0 24 24" class="copyButtonIcon_y97N"><path fill="currentColor" d="M19,21H8V7H19M19,5H8A2,2 0 0,0 6,7V21A2,2 0 0,0 8,23H19A2,2 0 0,0 21,21V7A2,2 0 0,0 19,5M16,1H4A2,2 0 0,0 2,3V17H4V3H16V1Z"></path></svg><svg viewBox="0 0 24 24" class="copyButtonSuccessIcon_LjdS"><path fill="currentColor" d="M21,7L9,19L3.5,13.5L4.91,12.09L9,16.17L19.59,5.59L21,7Z"></path></svg></span></button></div></div></div>
@@ -148,6 +151,8 @@ <h3 class="anchor anchorWithStickyNavbar_LWe7" id="add-hermes-mpi-io-interceptor
 <p>This will automatically locate the interceptor library by
 traversing various environment variables. This will ensure
 that MPI-IO is intercepted by Hermes.</p>
+<p>hermes_api includes other interceptors that can be used: posix, stdio, vfd. To view the set of options:</p>
+<div class="language-bash codeBlockContainer_Ckt0 theme-code-block" style="--prism-color:#393A34;--prism-background-color:#f6f8fa"><div class="codeBlockContent_biex"><pre tabindex="0" class="prism-code language-bash codeBlock_bY9V thin-scrollbar" style="color:#393A34;background-color:#f6f8fa"><code class="codeBlockLines_e6Vv"><span class="token-line" style="color:#393A34"><span class="token plain">jarvis pkg help hermes_run</span><br></span></code></pre><div class="buttonGroup__atx"><button type="button" aria-label="Copy code to clipboard" title="Copy" class="clean-btn"><span class="copyButtonIcons_eSgA" aria-hidden="true"><svg viewBox="0 0 24 24" class="copyButtonIcon_y97N"><path fill="currentColor" d="M19,21H8V7H19M19,5H8A2,2 0 0,0 6,7V21A2,2 0 0,0 8,23H19A2,2 0 0,0 21,21V7A2,2 0 0,0 19,5M16,1H4A2,2 0 0,0 2,3V17H4V3H16V1Z"></path></svg><svg viewBox="0 0 24 24" class="copyButtonSuccessIcon_LjdS"><path fill="currentColor" d="M21,7L9,19L3.5,13.5L4.91,12.09L9,16.17L19.59,5.59L21,7Z"></path></svg></span></button></div></div></div>
 <h3 class="anchor anchorWithStickyNavbar_LWe7" id="add-ior">Add IOR<a href="#add-ior" class="hash-link" aria-label="Direct link to Add IOR" title="Direct link to Add IOR">​</a></h3>
 <div class="language-bash codeBlockContainer_Ckt0 theme-code-block" style="--prism-color:#393A34;--prism-background-color:#f6f8fa"><div class="codeBlockContent_biex"><pre tabindex="0" class="prism-code language-bash codeBlock_bY9V thin-scrollbar" style="color:#393A34;background-color:#f6f8fa"><code class="codeBlockLines_e6Vv"><span class="token-line" style="color:#393A34"><span class="token plain">jarvis pipeline append ior</span><br></span><span class="token-line" style="color:#393A34"><span class="token plain">jarvis pkg configure ior \</span><br></span><span class="token-line" style="color:#393A34"><span class="token plain">xfer=1m \</span><br></span><span class="token-line" style="color:#393A34"><span class="token plain">block=1g \</span><br></span><span class="token-line" style="color:#393A34"><span class="token plain">nprocs=64 \</span><br></span><span class="token-line" style="color:#393A34"><span class="token plain">ppn=16 \</span><br></span><span class="token-line" style="color:#393A34"><span class="token plain">+write +read \</span><br></span><span class="token-line" style="color:#393A34"><span class="token plain">out=${HOME}/ior_data/ior.bin \</span><br></span><span class="token-line" style="color:#393A34"><span class="token plain">api=mpiio</span><br></span></code></pre><div class="buttonGroup__atx"><button type="button" aria-label="Copy code to clipboard" title="Copy" class="clean-btn"><span class="copyButtonIcons_eSgA" aria-hidden="true"><svg viewBox="0 0 24 24" class="copyButtonIcon_y97N"><path fill="currentColor" d="M19,21H8V7H19M19,5H8A2,2 0 0,0 6,7V21A2,2 0 0,0 8,23H19A2,2 0 0,0 21,21V7A2,2 0 0,0 19,5M16,1H4A2,2 0 0,0 2,3V17H4V3H16V1Z"></path></svg><svg viewBox="0 0 24 24" class="copyButtonSuccessIcon_LjdS"><path fill="currentColor" d="M21,7L9,19L3.5,13.5L4.91,12.09L9,16.17L19.59,5.59L21,7Z"></path></svg></span></button></div></div></div>
 <p>This IOR will perform 1GB of I/O per-process (block) in units of 1m (xfer) and
@@ -165,9 +170,11 @@ <h3 class="anchor anchorWithStickyNavbar_LWe7" id="cleanup-1">Cleanup<a href="#c
 <h2 class="anchor anchorWithStickyNavbar_LWe7" id="why-is-my-application-hanging">Why is my application hanging?<a href="#why-is-my-application-hanging" class="hash-link" aria-label="Direct link to Why is my application hanging?" title="Direct link to Why is my application hanging?">​</a></h2>
 <h3 class="anchor anchorWithStickyNavbar_LWe7" id="resource-graph-misconfiguration">Resource Graph Misconfiguration<a href="#resource-graph-misconfiguration" class="hash-link" aria-label="Direct link to Resource Graph Misconfiguration" title="Direct link to Resource Graph Misconfiguration">​</a></h3>
 <p>Commonly, the cause is a misconfiguration in the resource graph, specifically
-with the network section. Make sure that the domain, provider, and fabric
-are valid. To view the Hermes configuration to see which network was selected
-from your resource graph, you can run:</p>
+with the network section. If the resource graph is misconfigured, Hermes may
+crash with a <code>mercury-&gt;fatal</code> error and ultimately cause the program to stall
+forever. Make sure that the domain, provider, and fabric are valid. To view the
+Hermes configuration to see which network was selected from your resource graph,
+you can run:</p>
 <div class="language-bash codeBlockContainer_Ckt0 theme-code-block" style="--prism-color:#393A34;--prism-background-color:#f6f8fa"><div class="codeBlockContent_biex"><pre tabindex="0" class="prism-code language-bash codeBlock_bY9V thin-scrollbar" style="color:#393A34;background-color:#f6f8fa"><code class="codeBlockLines_e6Vv"><span class="token-line" style="color:#393A34"><span class="token plain">cat $(jarvis path)/hermes_run/hermes_server.yaml</span><br></span></code></pre><div class="buttonGroup__atx"><button type="button" aria-label="Copy code to clipboard" title="Copy" class="clean-btn"><span class="copyButtonIcons_eSgA" aria-hidden="true"><svg viewBox="0 0 24 24" class="copyButtonIcon_y97N"><path fill="currentColor" d="M19,21H8V7H19M19,5H8A2,2 0 0,0 6,7V21A2,2 0 0,0 8,23H19A2,2 0 0,0 21,21V7A2,2 0 0,0 19,5M16,1H4A2,2 0 0,0 2,3V17H4V3H16V1Z"></path></svg><svg viewBox="0 0 24 24" class="copyButtonSuccessIcon_LjdS"><path fill="currentColor" d="M21,7L9,19L3.5,13.5L4.91,12.09L9,16.17L19.59,5.59L21,7Z"></path></svg></span></button></div></div></div>
 <h3 class="anchor anchorWithStickyNavbar_LWe7" id="dependency-problems">Dependency Problems<a href="#dependency-problems" class="hash-link" aria-label="Direct link to Dependency Problems" title="Direct link to Dependency Problems">​</a></h3>
 <p>If you are using the MPI-IO interceptor, make sure that the MPI that Hermes
diff --git a/docs/hermes/developer-guide/index.html b/docs/hermes/developer-guide/index.html
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tocMobile_ITEo"><button type="button" class="clean-btn tocCollapsibleButton_TO0P">On this page</button></div><div class="theme-doc-markdown markdown"><h1>Developer Guide</h1>
+<p>Hermes can be complicated to debug due to its distributed and asynchronous
+nature. Faults can happen in the client program, or in the Hermes daemon.
+The first step when encountering problems is to compile in Debug mode.</p>
+<div class="language-cmake codeBlockContainer_Ckt0 theme-code-block" style="--prism-color:#393A34;--prism-background-color:#f6f8fa"><div class="codeBlockContent_biex"><pre tabindex="0" class="prism-code language-cmake codeBlock_bY9V thin-scrollbar" style="color:#393A34;background-color:#f6f8fa"><code class="codeBlockLines_e6Vv"><span class="token-line" style="color:#393A34"><span class="token plain">cmake .. -DCMAKE_BUILD_TYPE=Debug</span><br></span></code></pre><div class="buttonGroup__atx"><button type="button" aria-label="Copy code to clipboard" title="Copy" class="clean-btn"><span class="copyButtonIcons_eSgA" aria-hidden="true"><svg viewBox="0 0 24 24" class="copyButtonIcon_y97N"><path fill="currentColor" d="M19,21H8V7H19M19,5H8A2,2 0 0,0 6,7V21A2,2 0 0,0 8,23H19A2,2 0 0,0 21,21V7A2,2 0 0,0 19,5M16,1H4A2,2 0 0,0 2,3V17H4V3H16V1Z"></path></svg><svg viewBox="0 0 24 24" class="copyButtonSuccessIcon_LjdS"><path fill="currentColor" d="M21,7L9,19L3.5,13.5L4.91,12.09L9,16.17L19.59,5.59L21,7Z"></path></svg></span></button></div></div></div>
+<p>The Debug mode will increase the number of logging statements the program
+uses to give you a stronger hint as to where the problem occurs. These
+statements are typically compiled out for performance reasons.</p>
+<p>Secondly, make sure to use an IDE which supports visual debugging. Debugging
+using a terminal with gdb can be very cumbersome, especially when multi-process cases come along.</p>
+<h2 class="anchor anchorWithStickyNavbar_LWe7" id="hermes-repo-structure">Hermes Repo Structure<a href="#hermes-repo-structure" class="hash-link" aria-label="Direct link to Hermes Repo Structure" title="Direct link to Hermes Repo Structure">​</a></h2>
+<p>The Hermes repo is organized as follows:</p>
+<ol>
+<li><code>hrun</code> is the Hermes runtime and contains all source files / includes for it. This includes queuing and network code.</li>
+<li><code>tasks</code> contains the majority of Hermes implementation. These are tasks that execute in the Hermes runtime</li>
+<li><code>src</code> contains a single source file that is used to construct the Hermes library object that applications link to. Very little code is here, as most implementation is executed in the runtime.</li>
+<li><code>codegen</code> contains python code to help with generating and maintaining hrun tasks.</li>
+<li><code>hermes_adapters</code> includes all code relating to the adapters, such as  POSIX, STDIO, and MPI-IO interception</li>
+<li><code>config</code> contains default configurations of Hermes.</li>
+<li><code>docker</code> contains dockerfiles for building Hermes container.</li>
+<li><code>wrapper</code> contains all code for binding Hermes to other languages.</li>
+<li><code>external</code> contains git submodules of repos external to Hermes.</li>
+<li><code>test</code> includes all unit tests</li>
+<li><code>benchmark</code> includes some performance benchmark kernels</li>
+<li><code>ci</code> includes all code for continuous integration</li>
+</ol>
+<h2 class="anchor anchorWithStickyNavbar_LWe7" id="preparing-pull-request-pr">Preparing Pull Request (PR)<a href="#preparing-pull-request-pr" class="hash-link" aria-label="Direct link to Preparing Pull Request (PR)" title="Direct link to Preparing Pull Request (PR)">​</a></h2>
+<p>Please run these two steps and remove all warnings.</p>
+<div class="language-bash codeBlockContainer_Ckt0 theme-code-block" style="--prism-color:#393A34;--prism-background-color:#f6f8fa"><div class="codeBlockContent_biex"><pre tabindex="0" class="prism-code language-bash codeBlock_bY9V thin-scrollbar" style="color:#393A34;background-color:#f6f8fa"><code class="codeBlockLines_e6Vv"><span class="token-line" style="color:#393A34"><span class="token plain">make dox</span><br></span><span class="token-line" style="color:#393A34"><span class="token plain">make lint</span><br></span></code></pre><div class="buttonGroup__atx"><button type="button" aria-label="Copy code to clipboard" title="Copy" class="clean-btn"><span class="copyButtonIcons_eSgA" aria-hidden="true"><svg viewBox="0 0 24 24" class="copyButtonIcon_y97N"><path fill="currentColor" d="M19,21H8V7H19M19,5H8A2,2 0 0,0 6,7V21A2,2 0 0,0 8,23H19A2,2 0 0,0 21,21V7A2,2 0 0,0 19,5M16,1H4A2,2 0 0,0 2,3V17H4V3H16V1Z"></path></svg><svg viewBox="0 0 24 24" class="copyButtonSuccessIcon_LjdS"><path fill="currentColor" d="M21,7L9,19L3.5,13.5L4.91,12.09L9,16.17L19.59,5.59L21,7Z"></path></svg></span></button></div></div></div>
+<h2 class="anchor anchorWithStickyNavbar_LWe7" id="pr-check-failure">PR Check Failure<a href="#pr-check-failure" class="hash-link" aria-label="Direct link to PR Check Failure" title="Direct link to PR Check Failure">​</a></h2>
+<p>We use the <a href="https://github.com/HDFGroup/hermes/blob/master/docker/deps.Dockerfile" target="_blank" rel="noopener noreferrer">deps.Dockerfile</a>
+to avoid reinstalling packages in the github action. While github has a cache action,
+we find it somewhat cumbersome. This way, we get the benefit of both a maintained
+dockerfile and a fast github action.</p>
+<h2 class="anchor anchorWithStickyNavbar_LWe7" id="containerized-hermes">Containerized Hermes<a href="#containerized-hermes" class="hash-link" aria-label="Direct link to Containerized Hermes" title="Direct link to Containerized Hermes">​</a></h2>
+<p>As a developer, it may be beneficial to use Hermes inside of a container to
+avoid differences in machines.</p>
+<p>First, cd into your Hermes directory:</p>
+<div class="language-bash codeBlockContainer_Ckt0 theme-code-block" style="--prism-color:#393A34;--prism-background-color:#f6f8fa"><div class="codeBlockContent_biex"><pre tabindex="0" class="prism-code language-bash codeBlock_bY9V thin-scrollbar" style="color:#393A34;background-color:#f6f8fa"><code class="codeBlockLines_e6Vv"><span class="token-line" style="color:#393A34"><span class="token plain">cd /path/to/hermes</span><br></span></code></pre><div class="buttonGroup__atx"><button type="button" aria-label="Copy code to clipboard" title="Copy" class="clean-btn"><span class="copyButtonIcons_eSgA" aria-hidden="true"><svg viewBox="0 0 24 24" class="copyButtonIcon_y97N"><path fill="currentColor" d="M19,21H8V7H19M19,5H8A2,2 0 0,0 6,7V21A2,2 0 0,0 8,23H19A2,2 0 0,0 21,21V7A2,2 0 0,0 19,5M16,1H4A2,2 0 0,0 2,3V17H4V3H16V1Z"></path></svg><svg viewBox="0 0 24 24" class="copyButtonSuccessIcon_LjdS"><path fill="currentColor" d="M21,7L9,19L3.5,13.5L4.91,12.09L9,16.17L19.59,5.59L21,7Z"></path></svg></span></button></div></div></div>
+<p>Then either build the container from scratch or pull (but not both):</p>
+<p>From scratch:</p>
+<div class="language-bash codeBlockContainer_Ckt0 theme-code-block" style="--prism-color:#393A34;--prism-background-color:#f6f8fa"><div class="codeBlockContent_biex"><pre tabindex="0" class="prism-code language-bash codeBlock_bY9V thin-scrollbar" style="color:#393A34;background-color:#f6f8fa"><code class="codeBlockLines_e6Vv"><span class="token-line" style="color:#393A34"><span class="token plain">docker build -t lukemartinlogan/hermes_deps . -f docker/deps.Dockerfile</span><br></span></code></pre><div class="buttonGroup__atx"><button type="button" aria-label="Copy code to clipboard" title="Copy" class="clean-btn"><span class="copyButtonIcons_eSgA" aria-hidden="true"><svg viewBox="0 0 24 24" class="copyButtonIcon_y97N"><path fill="currentColor" d="M19,21H8V7H19M19,5H8A2,2 0 0,0 6,7V21A2,2 0 0,0 8,23H19A2,2 0 0,0 21,21V7A2,2 0 0,0 19,5M16,1H4A2,2 0 0,0 2,3V17H4V3H16V1Z"></path></svg><svg viewBox="0 0 24 24" class="copyButtonSuccessIcon_LjdS"><path fill="currentColor" d="M21,7L9,19L3.5,13.5L4.91,12.09L9,16.17L19.59,5.59L21,7Z"></path></svg></span></button></div></div></div>
+<p>Pull:</p>
+<div class="language-bash codeBlockContainer_Ckt0 theme-code-block" style="--prism-color:#393A34;--prism-background-color:#f6f8fa"><div class="codeBlockContent_biex"><pre tabindex="0" class="prism-code language-bash codeBlock_bY9V thin-scrollbar" style="color:#393A34;background-color:#f6f8fa"><code class="codeBlockLines_e6Vv"><span class="token-line" style="color:#393A34"><span class="token plain">docker pull lukemartinlogan/hermes_deps:latest</span><br></span></code></pre><div class="buttonGroup__atx"><button type="button" aria-label="Copy code to clipboard" title="Copy" class="clean-btn"><span class="copyButtonIcons_eSgA" aria-hidden="true"><svg viewBox="0 0 24 24" class="copyButtonIcon_y97N"><path fill="currentColor" d="M19,21H8V7H19M19,5H8A2,2 0 0,0 6,7V21A2,2 0 0,0 8,23H19A2,2 0 0,0 21,21V7A2,2 0 0,0 19,5M16,1H4A2,2 0 0,0 2,3V17H4V3H16V1Z"></path></svg><svg viewBox="0 0 24 24" class="copyButtonSuccessIcon_LjdS"><path fill="currentColor" d="M21,7L9,19L3.5,13.5L4.91,12.09L9,16.17L19.59,5.59L21,7Z"></path></svg></span></button></div></div></div>
+<p>Then, run the container. This command will mount the Hermes directory
+as /hermes. It will make it so that the container has 4GB of memory and
+4GB of shared memory. By default, containers don&#x27;t have shared memory, but
+Hermes requires it. We then also forward ports 4000 and 4001 to support remote
+debugging from those ports.</p>
+<div class="language-bash codeBlockContainer_Ckt0 theme-code-block" style="--prism-color:#393A34;--prism-background-color:#f6f8fa"><div class="codeBlockContent_biex"><pre tabindex="0" class="prism-code language-bash codeBlock_bY9V thin-scrollbar" style="color:#393A34;background-color:#f6f8fa"><code class="codeBlockLines_e6Vv"><span class="token-line" style="color:#393A34"><span class="token plain">docker run -it --mount src=${PWD},target=/hermes,type=bind \</span><br></span><span class="token-line" style="color:#393A34"><span class="token plain">--name hermes_deps_c \</span><br></span><span class="token-line" style="color:#393A34"><span class="token plain">--network host \</span><br></span><span class="token-line" style="color:#393A34"><span class="token plain">--memory=8G \</span><br></span><span class="token-line" style="color:#393A34"><span class="token plain">--shm-size=8G \</span><br></span><span class="token-line" style="color:#393A34"><span class="token plain">-p 4000:4000 \</span><br></span><span class="token-line" style="color:#393A34"><span class="token plain">-p 4001:4001 \</span><br></span><span class="token-line" style="color:#393A34"><span class="token plain">lukemartinlogan/hermes_deps</span><br></span></code></pre><div class="buttonGroup__atx"><button type="button" aria-label="Copy code to clipboard" title="Copy" class="clean-btn"><span class="copyButtonIcons_eSgA" aria-hidden="true"><svg viewBox="0 0 24 24" class="copyButtonIcon_y97N"><path fill="currentColor" d="M19,21H8V7H19M19,5H8A2,2 0 0,0 6,7V21A2,2 0 0,0 8,23H19A2,2 0 0,0 21,21V7A2,2 0 0,0 19,5M16,1H4A2,2 0 0,0 2,3V17H4V3H16V1Z"></path></svg><svg viewBox="0 0 24 24" class="copyButtonSuccessIcon_LjdS"><path fill="currentColor" d="M21,7L9,19L3.5,13.5L4.91,12.09L9,16.17L19.59,5.59L21,7Z"></path></svg></span></button></div></div></div>
+<p>To run the github action:</p>
+<div class="language-bash codeBlockContainer_Ckt0 theme-code-block" style="--prism-color:#393A34;--prism-background-color:#f6f8fa"><div class="codeBlockContent_biex"><pre tabindex="0" class="prism-code language-bash codeBlock_bY9V thin-scrollbar" style="color:#393A34;background-color:#f6f8fa"><code class="codeBlockLines_e6Vv"><span class="token-line" style="color:#393A34"><span class="token plain">bash /hermes/ci/build_hermes.sh</span><br></span></code></pre><div class="buttonGroup__atx"><button type="button" aria-label="Copy code to clipboard" title="Copy" class="clean-btn"><span class="copyButtonIcons_eSgA" aria-hidden="true"><svg viewBox="0 0 24 24" class="copyButtonIcon_y97N"><path fill="currentColor" d="M19,21H8V7H19M19,5H8A2,2 0 0,0 6,7V21A2,2 0 0,0 8,23H19A2,2 0 0,0 21,21V7A2,2 0 0,0 19,5M16,1H4A2,2 0 0,0 2,3V17H4V3H16V1Z"></path></svg><svg viewBox="0 0 24 24" class="copyButtonSuccessIcon_LjdS"><path fill="currentColor" d="M21,7L9,19L3.5,13.5L4.91,12.09L9,16.17L19.59,5.59L21,7Z"></path></svg></span></button></div></div></div>
+<p>Within the container, build Hermes:</p>
+<div class="language-bash codeBlockContainer_Ckt0 theme-code-block" style="--prism-color:#393A34;--prism-background-color:#f6f8fa"><div class="codeBlockContent_biex"><pre tabindex="0" class="prism-code language-bash codeBlock_bY9V thin-scrollbar" style="color:#393A34;background-color:#f6f8fa"><code class="codeBlockLines_e6Vv"><span class="token-line" style="color:#393A34"><span class="token plain"># Load spack and other modules</span><br></span><span class="token-line" style="color:#393A34"><span class="token plain">. /module_load.sh</span><br></span><span class="token-line" style="color:#393A34"><span class="token plain">. &quot;${SPACK_DIR}/share/spack/setup-env.sh&quot;</span><br></span><span class="token-line" style="color:#393A34"><span class="token plain"># Load hermes_shm</span><br></span><span class="token-line" style="color:#393A34"><span class="token plain">spack load hermes_shm</span><br></span><span class="token-line" style="color:#393A34"><span class="token plain"># Build hermes</span><br></span><span class="token-line" style="color:#393A34"><span class="token plain">cd /hermes</span><br></span><span class="token-line" style="color:#393A34"><span class="token plain">mkdir build</span><br></span><span class="token-line" style="color:#393A34"><span class="token plain">cd build</span><br></span><span class="token-line" style="color:#393A34"><span class="token plain">cmake ../</span><br></span><span class="token-line" style="color:#393A34"><span class="token plain">make -j8</span><br></span></code></pre><div class="buttonGroup__atx"><button type="button" aria-label="Copy code to clipboard" title="Copy" class="clean-btn"><span class="copyButtonIcons_eSgA" aria-hidden="true"><svg viewBox="0 0 24 24" class="copyButtonIcon_y97N"><path fill="currentColor" d="M19,21H8V7H19M19,5H8A2,2 0 0,0 6,7V21A2,2 0 0,0 8,23H19A2,2 0 0,0 21,21V7A2,2 0 0,0 19,5M16,1H4A2,2 0 0,0 2,3V17H4V3H16V1Z"></path></svg><svg viewBox="0 0 24 24" class="copyButtonSuccessIcon_LjdS"><path fill="currentColor" d="M21,7L9,19L3.5,13.5L4.91,12.09L9,16.17L19.59,5.59L21,7Z"></path></svg></span></button></div></div></div>
+<p>If you make changes to the dependencies container:</p>
+<div class="language-bash codeBlockContainer_Ckt0 theme-code-block" style="--prism-color:#393A34;--prism-background-color:#f6f8fa"><div class="codeBlockContent_biex"><pre tabindex="0" class="prism-code language-bash codeBlock_bY9V thin-scrollbar" style="color:#393A34;background-color:#f6f8fa"><code class="codeBlockLines_e6Vv"><span class="token-line" style="color:#393A34"><span class="token plain">docker commit hermes_deps_c lukemartinlogan/hermes_deps</span><br></span><span class="token-line" style="color:#393A34"><span class="token plain">docker push lukemartinlogan/hermes_deps</span><br></span><span class="token-line" style="color:#393A34"><span class="token plain">docker stop /hermes_deps_c</span><br></span><span class="token-line" style="color:#393A34"><span class="token plain">docker rm /hermes_deps_c</span><br></span></code></pre><div class="buttonGroup__atx"><button type="button" aria-label="Copy code to clipboard" title="Copy" class="clean-btn"><span class="copyButtonIcons_eSgA" aria-hidden="true"><svg viewBox="0 0 24 24" class="copyButtonIcon_y97N"><path fill="currentColor" d="M19,21H8V7H19M19,5H8A2,2 0 0,0 6,7V21A2,2 0 0,0 8,23H19A2,2 0 0,0 21,21V7A2,2 0 0,0 19,5M16,1H4A2,2 0 0,0 2,3V17H4V3H16V1Z"></path></svg><svg viewBox="0 0 24 24" class="copyButtonSuccessIcon_LjdS"><path fill="currentColor" d="M21,7L9,19L3.5,13.5L4.91,12.09L9,16.17L19.59,5.59L21,7Z"></path></svg></span></button></div></div></div>
+<h2 class="anchor anchorWithStickyNavbar_LWe7" id="remote-debugging">Remote Debugging<a href="#remote-debugging" class="hash-link" aria-label="Direct link to Remote Debugging" title="Direct link to Remote Debugging">​</a></h2>
+<p>At some point, you may have to do a remote debug. The following code will
+forward SSH connections so that you can remotely connect a debugger.</p>
+<p>Let&#x27;s say that you are running Hermes on a machine <a href="mailto:myusername@myip.org" target="_blank" rel="noopener noreferrer">myusername@myip.org</a> on
+port 4000. You can connect to that by forwarding a local port to that address.
+A debugger would connect to localhost:4000, which will then be routed to
+<a href="mailto:myusername@myip.org" target="_blank" rel="noopener noreferrer">myusername@myip.org</a>:4000.</p>
+<div class="language-bash codeBlockContainer_Ckt0 theme-code-block" style="--prism-color:#393A34;--prism-background-color:#f6f8fa"><div class="codeBlockContent_biex"><pre tabindex="0" class="prism-code language-bash codeBlock_bY9V thin-scrollbar" style="color:#393A34;background-color:#f6f8fa"><code class="codeBlockLines_e6Vv"><span class="token-line" style="color:#393A34"><span class="token plain">remote_machine_login=myusername@myip.org</span><br></span><span class="token-line" style="color:#393A34"><span class="token plain" style="display:inline-block"></span><br></span><span class="token-line" style="color:#393A34"><span class="token plain">local_port=4000</span><br></span><span class="token-line" style="color:#393A34"><span class="token plain">remote_port=4000</span><br></span><span class="token-line" style="color:#393A34"><span class="token plain">ssh -L ${local_port}:localhost:${remote_port} -fN ${ares_node}</span><br></span><span class="token-line" style="color:#393A34"><span class="token plain" style="display:inline-block"></span><br></span><span class="token-line" style="color:#393A34"><span class="token plain">local_port=4001</span><br></span><span class="token-line" style="color:#393A34"><span class="token plain">remote_port=4001</span><br></span><span class="token-line" style="color:#393A34"><span class="token plain">ssh -L ${local_port}:localhost:${remote_port} -fN ${ares_node}</span><br></span></code></pre><div class="buttonGroup__atx"><button type="button" aria-label="Copy code to clipboard" title="Copy" class="clean-btn"><span class="copyButtonIcons_eSgA" aria-hidden="true"><svg viewBox="0 0 24 24" class="copyButtonIcon_y97N"><path fill="currentColor" d="M19,21H8V7H19M19,5H8A2,2 0 0,0 6,7V21A2,2 0 0,0 8,23H19A2,2 0 0,0 21,21V7A2,2 0 0,0 19,5M16,1H4A2,2 0 0,0 2,3V17H4V3H16V1Z"></path></svg><svg viewBox="0 0 24 24" class="copyButtonSuccessIcon_LjdS"><path fill="currentColor" d="M21,7L9,19L3.5,13.5L4.91,12.09L9,16.17L19.59,5.59L21,7Z"></path></svg></span></button></div></div></div>
+<p>To shutdown this forwarding, you kill all routed SSH connections as follows:</p>
+<div class="language-bash codeBlockContainer_Ckt0 theme-code-block" style="--prism-color:#393A34;--prism-background-color:#f6f8fa"><div class="codeBlockContent_biex"><pre tabindex="0" class="prism-code language-bash codeBlock_bY9V thin-scrollbar" style="color:#393A34;background-color:#f6f8fa"><code class="codeBlockLines_e6Vv"><span class="token-line" style="color:#393A34"><span class="token plain">pkill -f &quot;ssh -L&quot;</span><br></span></code></pre><div class="buttonGroup__atx"><button type="button" aria-label="Copy code to clipboard" title="Copy" class="clean-btn"><span class="copyButtonIcons_eSgA" aria-hidden="true"><svg viewBox="0 0 24 24" class="copyButtonIcon_y97N"><path fill="currentColor" d="M19,21H8V7H19M19,5H8A2,2 0 0,0 6,7V21A2,2 0 0,0 8,23H19A2,2 0 0,0 21,21V7A2,2 0 0,0 19,5M16,1H4A2,2 0 0,0 2,3V17H4V3H16V1Z"></path></svg><svg viewBox="0 0 24 24" class="copyButtonSuccessIcon_LjdS"><path fill="currentColor" d="M21,7L9,19L3.5,13.5L4.91,12.09L9,16.17L19.59,5.59L21,7Z"></path></svg></span></button></div></div></div>
+<p>If the machine you are running Hermes on has a head/login node, you
+will have to forward the connection from your head node to the node actually
+running the code (the compute nodes). If this is the case, just repeat the
+above steps on the head node, replacing remote_machine_login with the address
+of the compute node.</p>
+<h2 class="anchor anchorWithStickyNavbar_LWe7" id="preparing-for-release">Preparing For Release<a href="#preparing-for-release" class="hash-link" aria-label="Direct link to Preparing For Release" title="Direct link to Preparing For Release">​</a></h2>
+<ol>
+<li>Create a GitHub Project for the <em>next</em> release</li>
+<li>Update the <code>HERMES_VERSION_*</code> variables in <code>CMakeLists.txt</code></li>
+<li>Update <code>PROJECT_NUMBER</code> in <code>Doxyfile.in</code>.</li>
+<li>To make release note generation as automated as possible, make sure
+relevant pull requests that are part of the release have proper labels and and
+titles, as that information will show up directly in the generated release
+notes in the next step.</li>
+<li>Draft a release on Github. Click <code>auto-generate release notes</code> and edit
+the result as necessary. Fill in the new tag, and select &quot;Create new tag x.x.x
+on publish&quot; so that Github will automatically tag the release when it is
+published.</li>
+<li>The docker containers will be automatically built and pushed to docker hub
+whenever a new tag is added. Check the CI actions to make sure there were no
+errors.</li>
+<li>Copy/move ideas to the project for the next release</li>
+<li>Close and archive the project for the <em>current</em> release</li>
+<li>Merge the latest release branch (if one exists) of the wiki into the <code>master</code> branch.</li>
+<li>Make an announcement in the Hermes topic of the HDF forum.</li>
+<li>Send Lori a note for the next HDF5 newsletter.</li>
+</ol>
+<h2 class="anchor anchorWithStickyNavbar_LWe7" id="introduction-to-our-continuous-integration-ci">Introduction to our Continuous Integration (CI)<a href="#introduction-to-our-continuous-integration-ci" class="hash-link" aria-label="Direct link to Introduction to our Continuous Integration (CI)" title="Direct link to Introduction to our Continuous Integration (CI)">​</a></h2>
+<p>We are primarily using Python for managing for running unit tests. Under
+<a href="https://github.com/HDFGroup/hermes/blob/master/CMakeLists.txt" target="_blank" rel="noopener noreferrer">our root CMakeList</a>, we implement a
+CMake function called jarvis_test, which uses <a href="https://github.com/grc-iit/jarvis-cd.git" target="_blank" rel="noopener noreferrer">Jarvis</a>
+and its <a href="https://github.com/HDFGroup/hermes/tree/master/test/unit/pipelines" target="_blank" rel="noopener noreferrer">pipelines</a> concept.</p>
+<h2 class="anchor anchorWithStickyNavbar_LWe7" id="adding-a-new-adapter">Adding a New Adapter<a href="#adding-a-new-adapter" class="hash-link" aria-label="Direct link to Adding a New Adapter" title="Direct link to Adding a New Adapter">​</a></h2>
+<ol>
+<li>Create a new directory under the <code>adapter</code> directory.</li>
+</ol></div></article><nav class="pagination-nav docusaurus-mt-lg" aria-label="Docs pages"><a class="pagination-nav__link pagination-nav__link--prev" href="/docs/hermes/containers"><div class="pagination-nav__sublabel">Previous</div><div class="pagination-nav__label">Containers</div></a><a class="pagination-nav__link pagination-nav__link--next" href="/docs/hermes/doxygen"><div class="pagination-nav__sublabel">Next</div><div class="pagination-nav__label">Doxygen</div></a></nav></div></div><div class="col col--3"><div class="tableOfContents_bqdL thin-scrollbar theme-doc-toc-desktop"><ul class="table-of-contents table-of-contents__left-border"><li><a href="#hermes-repo-structure" class="table-of-contents__link toc-highlight">Hermes Repo Structure</a></li><li><a href="#preparing-pull-request-pr" class="table-of-contents__link toc-highlight">Preparing Pull Request (PR)</a></li><li><a href="#pr-check-failure" class="table-of-contents__link toc-highlight">PR Check Failure</a></li><li><a href="#containerized-hermes" class="table-of-contents__link toc-highlight">Containerized Hermes</a></li><li><a href="#remote-debugging" class="table-of-contents__link toc-highlight">Remote Debugging</a></li><li><a href="#preparing-for-release" class="table-of-contents__link toc-highlight">Preparing For Release</a></li><li><a href="#introduction-to-our-continuous-integration-ci" class="table-of-contents__link toc-highlight">Introduction to our Continuous Integration (CI)</a></li><li><a href="#adding-a-new-adapter" class="table-of-contents__link toc-highlight">Adding a New Adapter</a></li></ul></div></div></div></div></main></div></div></div><footer class="footer"><div class="container container-fluid"><div class="row footer__links"><div class="col footer__col"><div class="footer__title">Gnosis Research Center</div><ul class="footer__items clean-list"><li class="footer__item">
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itemtype="https://schema.org/BreadcrumbList"><li class="breadcrumbs__item"><a aria-label="Home page" class="breadcrumbs__link" href="/"><svg viewBox="0 0 24 24" class="breadcrumbHomeIcon_YNFT"><path d="M10 19v-5h4v5c0 .55.45 1 1 1h3c.55 0 1-.45 1-1v-7h1.7c.46 0 .68-.57.33-.87L12.67 3.6c-.38-.34-.96-.34-1.34 0l-8.36 7.53c-.34.3-.13.87.33.87H5v7c0 .55.45 1 1 1h3c.55 0 1-.45 1-1z" fill="currentColor"></path></svg></a></li><li itemscope="" itemprop="itemListElement" itemtype="https://schema.org/ListItem" class="breadcrumbs__item"><a class="breadcrumbs__link" itemprop="item" href="/docs/category/hermes"><span itemprop="name">Hermes</span></a><meta itemprop="position" content="1"></li><li itemscope="" itemprop="itemListElement" itemtype="https://schema.org/ListItem" class="breadcrumbs__item breadcrumbs__item--active"><span class="breadcrumbs__link" itemprop="name">Doxygen</span><meta itemprop="position" content="2"></li></ul></nav><div class="theme-doc-markdown markdown"><h1>Doxygen</h1>
 <p>The <a href="https://www.doxygen.nl/index.html" target="_blank" rel="noopener noreferrer">Doxygen</a> portion of the Hermes documentation can be built as follows:</p>
 <div class="language-bash codeBlockContainer_Ckt0 theme-code-block" style="--prism-color:#393A34;--prism-background-color:#f6f8fa"><div class="codeBlockContent_biex"><pre tabindex="0" class="prism-code language-bash codeBlock_bY9V thin-scrollbar" style="color:#393A34;background-color:#f6f8fa"><code class="codeBlockLines_e6Vv"><span class="token-line" style="color:#393A34"><span class="token plain">cmake -D &lt;Other Hermes CMake build options&gt; -DHERMES_ENABLE_DOXYGEN=ON ../</span><br></span><span class="token-line" style="color:#393A34"><span class="token plain">make dox</span><br></span></code></pre><div class="buttonGroup__atx"><button type="button" aria-label="Copy code to clipboard" title="Copy" class="clean-btn"><span class="copyButtonIcons_eSgA" aria-hidden="true"><svg viewBox="0 0 24 24" class="copyButtonIcon_y97N"><path fill="currentColor" d="M19,21H8V7H19M19,5H8A2,2 0 0,0 6,7V21A2,2 0 0,0 8,23H19A2,2 0 0,0 21,21V7A2,2 0 0,0 19,5M16,1H4A2,2 0 0,0 2,3V17H4V3H16V1Z"></path></svg><svg viewBox="0 0 24 24" class="copyButtonSuccessIcon_LjdS"><path fill="currentColor" d="M21,7L9,19L3.5,13.5L4.91,12.09L9,16.17L19.59,5.59L21,7Z"></path></svg></span></button></div></div></div>
 <p>The HTML version of the documentation will be placed into the <code>_build/html</code> subfolder of the build directory.</p>
 <p>An online version for the latest release is available at <a href="https://hdfgroup.github.io/hermes/html/" target="_blank" rel="noopener noreferrer">https://hdfgroup.github.io/hermes/html/</a>.</p>
-<p>The official version for the stable release is available at <a href="https://docs.hdfgroup.org/hermes/" target="_blank" rel="noopener noreferrer">https://docs.hdfgroup.org/hermes/</a>.</p></div></article><nav class="pagination-nav docusaurus-mt-lg" aria-label="Docs pages"><a class="pagination-nav__link pagination-nav__link--prev" href="/docs/hermes/debugging"><div class="pagination-nav__sublabel">Previous</div><div class="pagination-nav__label">Debugging</div></a><a class="pagination-nav__link pagination-nav__link--next" href="/docs/hermes/faq"><div class="pagination-nav__sublabel">Next</div><div class="pagination-nav__label">Frequently Asked Questions</div></a></nav></div></div></div></div></main></div></div></div><footer class="footer"><div class="container container-fluid"><div class="row footer__links"><div class="col footer__col"><div class="footer__title">Gnosis Research Center</div><ul class="footer__items clean-list"><li class="footer__item">
+<p>The official version for the stable release is available at <a href="https://docs.hdfgroup.org/hermes/" target="_blank" rel="noopener noreferrer">https://docs.hdfgroup.org/hermes/</a>.</p></div></article><nav class="pagination-nav docusaurus-mt-lg" aria-label="Docs pages"><a class="pagination-nav__link pagination-nav__link--prev" href="/docs/hermes/developer-guide"><div class="pagination-nav__sublabel">Previous</div><div class="pagination-nav__label">Developer Guide</div></a><a class="pagination-nav__link pagination-nav__link--next" href="/docs/hermes/faq"><div class="pagination-nav__sublabel">Next</div><div class="pagination-nav__label">Frequently Asked Questions</div></a></nav></div></div></div></div></main></div></div></div><footer class="footer"><div class="container container-fluid"><div class="row footer__links"><div class="col footer__col"><div class="footer__title">Gnosis Research Center</div><ul class="footer__items clean-list"><li class="footer__item">
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diff --git a/docs/hermes/faq/index.html b/docs/hermes/faq/index.html
index 64dd4439..19203b11 100644
--- a/docs/hermes/faq/index.html
+++ b/docs/hermes/faq/index.html
@@ -10,13 +10,13 @@
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 <h2 class="anchor anchorWithStickyNavbar_LWe7" id="what-is-the-minimum-version-for-gcc">What is the minimum version for GCC?<a href="#what-is-the-minimum-version-for-gcc" class="hash-link" aria-label="Direct link to What is the minimum version for GCC?" title="Direct link to What is the minimum version for GCC?">​</a></h2>
-<p>GCC 11. Hermes requires C++17 features that are only available since GCC 7.3. C++17 support is enabled by default in GCC 11; it can be explicitly selected in earlier versions with the <code>-std=c++17</code> command-line flag or <code>-std=gnu++17</code> to enable GNU extensions as well. See <a href="https://gcc.gnu.org/projects/cxx-status.html#cxx17" target="_blank" rel="noopener noreferrer">C++17 Support in GCC</a> for the details. Use <code>spack install gcc</code> first if your system has GCC 4. It will install GCC 12.2.0 by default. Then, run <code>spack compiler find</code> to use the newly installed gcc.</p>
+<p>GCC 9.4. C++17 support is enabled by default in GCC 11; it can be explicitly selected in earlier versions with the <code>-std=c++17</code> command-line flag or <code>-std=gnu++17</code> to enable GNU extensions as well. See <a href="https://gcc.gnu.org/projects/cxx-status.html#cxx17" target="_blank" rel="noopener noreferrer">C++17 Support in GCC</a> for the details. Use <code>spack install gcc</code> first if your system has GCC 4. It will install GCC 12.2.0 by default. Then, run <code>spack compiler find</code> to use the newly installed gcc.</p>
 <h2 class="anchor anchorWithStickyNavbar_LWe7" id="can-i-run-hermes-on-mac">Can I run Hermes on Mac?<a href="#can-i-run-hermes-on-mac" class="hash-link" aria-label="Direct link to Can I run Hermes on Mac?" title="Direct link to Can I run Hermes on Mac?">​</a></h2>
 <p>No. macOS lacks several system calls that Hermes components use:</p>
 <ul>
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diff --git a/docs/hermes/programming/index.html b/docs/hermes/programming/index.html
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tocMobile_ITEo"><button type="button" class="clean-btn tocCollapsibleButton_TO0P">On this page</button></div><div class="theme-doc-markdown markdown"><h1>Programming</h1>
 <p>In this section, we will discuss the general steps of building a program
 on top of the Hermes native API. We will focus on the core data structures
 provided by Hermes -- Buckets and Blobs.</p>
+<p>To see demonstrations of the API, check out our <a href="https://github.com/HDFGroup/hermes/blob/master/test/unit/hermes/test_bucket.cc" target="_blank" rel="noopener noreferrer">API tests</a></p>
 <h2 class="anchor anchorWithStickyNavbar_LWe7" id="basic-api-example">Basic API Example<a href="#basic-api-example" class="hash-link" aria-label="Direct link to Basic API Example" title="Direct link to Basic API Example">​</a></h2>
-<div class="language-cpp codeBlockContainer_Ckt0 theme-code-block" style="--prism-color:#393A34;--prism-background-color:#f6f8fa"><div class="codeBlockContent_biex"><pre tabindex="0" class="prism-code language-cpp codeBlock_bY9V thin-scrollbar" style="color:#393A34;background-color:#f6f8fa"><code class="codeBlockLines_e6Vv"><span class="token-line" style="color:#393A34"><span class="token macro property directive-hash" style="color:#36acaa">#</span><span class="token macro property directive keyword" style="color:#00009f">include</span><span class="token macro property" style="color:#36acaa"> </span><span class="token macro property string" style="color:#e3116c">&lt;hermes.h&gt;</span><span class="token plain"></span><br></span><span class="token-line" style="color:#393A34"><span class="token plain"></span><span class="token macro property directive-hash" style="color:#36acaa">#</span><span class="token macro property directive keyword" style="color:#00009f">include</span><span class="token macro property" style="color:#36acaa"> </span><span class="token macro property string" style="color:#e3116c">&lt;bucket.h&gt;</span><span class="token plain"></span><br></span><span class="token-line" style="color:#393A34"><span class="token plain" style="display:inline-block"></span><br></span><span class="token-line" style="color:#393A34"><span class="token plain"></span><span class="token keyword" style="color:#00009f">int</span><span class="token plain"> </span><span class="token function" style="color:#d73a49">main</span><span class="token punctuation" style="color:#393A34">(</span><span class="token punctuation" style="color:#393A34">)</span><span class="token plain"> </span><span class="token punctuation" style="color:#393A34">{</span><span class="token plain"></span><br></span><span class="token-line" style="color:#393A34"><span class="token plain">  HERMES</span><span class="token operator" style="color:#393A34">-&gt;</span><span class="token function" style="color:#d73a49">Create</span><span class="token punctuation" style="color:#393A34">(</span><span class="token plain">hermes</span><span class="token double-colon punctuation" style="color:#393A34">::</span><span class="token plain">HermesType</span><span class="token double-colon punctuation" style="color:#393A34">::</span><span class="token plain">kClient</span><span class="token punctuation" style="color:#393A34">)</span><span class="token punctuation" style="color:#393A34">;</span><span class="token plain"></span><br></span><span class="token-line" style="color:#393A34"><span class="token plain">  Bucket bkt </span><span class="token operator" style="color:#393A34">=</span><span class="token plain"> hermes</span><span class="token operator" style="color:#393A34">-&gt;</span><span class="token function" style="color:#d73a49">GetBucket</span><span class="token punctuation" style="color:#393A34">(</span><span class="token string" style="color:#e3116c">&quot;hello&quot;</span><span class="token punctuation" style="color:#393A34">)</span><span class="token punctuation" style="color:#393A34">;</span><span class="token plain"></span><br></span><span class="token-line" style="color:#393A34"><span class="token plain">  size_t blob_size </span><span class="token operator" style="color:#393A34">=</span><span class="token plain"> </span><span class="token function" style="color:#d73a49">KILOBYTES</span><span class="token punctuation" style="color:#393A34">(</span><span class="token number" style="color:#36acaa">4</span><span class="token punctuation" style="color:#393A34">)</span><span class="token punctuation" style="color:#393A34">;</span><span class="token plain"></span><br></span><span class="token-line" style="color:#393A34"><span class="token plain">  Context ctx</span><span class="token punctuation" style="color:#393A34">;</span><span class="token plain"></span><br></span><span class="token-line" style="color:#393A34"><span class="token plain" style="display:inline-block"></span><br></span><span class="token-line" style="color:#393A34"><span class="token plain">  </span><span class="token keyword" style="color:#00009f">for</span><span class="token plain"> </span><span class="token punctuation" style="color:#393A34">(</span><span class="token plain">size_t i </span><span class="token operator" style="color:#393A34">=</span><span class="token plain"> </span><span class="token number" style="color:#36acaa">0</span><span class="token punctuation" style="color:#393A34">;</span><span class="token plain"> i </span><span class="token operator" style="color:#393A34">&lt;</span><span class="token plain"> num_blobs</span><span class="token punctuation" style="color:#393A34">;</span><span class="token plain"> </span><span class="token operator" style="color:#393A34">++</span><span class="token plain">i</span><span class="token punctuation" style="color:#393A34">)</span><span class="token plain"> </span><span class="token punctuation" style="color:#393A34">{</span><span class="token plain"></span><br></span><span class="token-line" style="color:#393A34"><span class="token plain">    hermes</span><span class="token double-colon punctuation" style="color:#393A34">::</span><span class="token plain">Blob </span><span class="token function" style="color:#d73a49">blob</span><span class="token punctuation" style="color:#393A34">(</span><span class="token plain">blob_size</span><span class="token punctuation" style="color:#393A34">)</span><span class="token punctuation" style="color:#393A34">;</span><span class="token plain"></span><br></span><span class="token-line" style="color:#393A34"><span class="token plain">    std</span><span class="token double-colon punctuation" style="color:#393A34">::</span><span class="token plain">string name </span><span class="token operator" style="color:#393A34">=</span><span class="token plain"> std</span><span class="token double-colon punctuation" style="color:#393A34">::</span><span class="token function" style="color:#d73a49">to_string</span><span class="token punctuation" style="color:#393A34">(</span><span class="token plain">i</span><span class="token punctuation" style="color:#393A34">)</span><span class="token punctuation" style="color:#393A34">;</span><span class="token plain"></span><br></span><span class="token-line" style="color:#393A34"><span class="token plain">    </span><span class="token keyword" style="color:#00009f">char</span><span class="token plain"> nonce </span><span class="token operator" style="color:#393A34">=</span><span class="token plain"> i </span><span class="token operator" style="color:#393A34">%</span><span class="token plain"> </span><span class="token number" style="color:#36acaa">256</span><span class="token punctuation" style="color:#393A34">;</span><span class="token plain"></span><br></span><span class="token-line" style="color:#393A34"><span class="token plain">    </span><span class="token function" style="color:#d73a49">memset</span><span class="token punctuation" style="color:#393A34">(</span><span class="token plain">blob</span><span class="token punctuation" style="color:#393A34">.</span><span class="token function" style="color:#d73a49">data</span><span class="token punctuation" style="color:#393A34">(</span><span class="token punctuation" style="color:#393A34">)</span><span class="token punctuation" style="color:#393A34">,</span><span class="token plain"> nonce</span><span class="token punctuation" style="color:#393A34">,</span><span class="token plain"> blob_size</span><span class="token punctuation" style="color:#393A34">)</span><span class="token punctuation" style="color:#393A34">;</span><span class="token plain"></span><br></span><span class="token-line" style="color:#393A34"><span class="token plain">    bkt</span><span class="token punctuation" style="color:#393A34">.</span><span class="token function" style="color:#d73a49">Put</span><span class="token punctuation" style="color:#393A34">(</span><span class="token plain">name</span><span class="token punctuation" style="color:#393A34">,</span><span class="token plain"> blob</span><span class="token punctuation" style="color:#393A34">,</span><span class="token plain"> blob_id</span><span class="token punctuation" style="color:#393A34">,</span><span class="token plain"> ctx</span><span class="token punctuation" style="color:#393A34">)</span><span class="token punctuation" style="color:#393A34">;</span><span class="token plain"></span><br></span><span class="token-line" style="color:#393A34"><span class="token plain">  </span><span class="token punctuation" style="color:#393A34">}</span><span class="token plain"></span><br></span><span class="token-line" style="color:#393A34"><span class="token plain" style="display:inline-block"></span><br></span><span class="token-line" style="color:#393A34"><span class="token plain">  </span><span class="token keyword" style="color:#00009f">for</span><span class="token plain"> </span><span class="token punctuation" style="color:#393A34">(</span><span class="token plain">size_t i </span><span class="token operator" style="color:#393A34">=</span><span class="token plain"> </span><span class="token number" style="color:#36acaa">0</span><span class="token punctuation" style="color:#393A34">;</span><span class="token plain"> i </span><span class="token operator" style="color:#393A34">&lt;</span><span class="token plain"> num_blobs</span><span class="token punctuation" style="color:#393A34">;</span><span class="token plain"> </span><span class="token operator" style="color:#393A34">++</span><span class="token plain">i</span><span class="token punctuation" style="color:#393A34">)</span><span class="token plain"> </span><span class="token punctuation" style="color:#393A34">{</span><span class="token plain"></span><br></span><span class="token-line" style="color:#393A34"><span class="token plain">    std</span><span class="token double-colon punctuation" style="color:#393A34">::</span><span class="token plain">string name </span><span class="token operator" style="color:#393A34">=</span><span class="token plain"> std</span><span class="token double-colon punctuation" style="color:#393A34">::</span><span class="token function" style="color:#d73a49">to_string</span><span class="token punctuation" style="color:#393A34">(</span><span class="token plain">i</span><span class="token punctuation" style="color:#393A34">)</span><span class="token punctuation" style="color:#393A34">;</span><span class="token plain"></span><br></span><span class="token-line" style="color:#393A34"><span class="token plain">    </span><span class="token keyword" style="color:#00009f">char</span><span class="token plain"> nonce </span><span class="token operator" style="color:#393A34">=</span><span class="token plain"> i </span><span class="token operator" style="color:#393A34">%</span><span class="token plain"> </span><span class="token number" style="color:#36acaa">256</span><span class="token punctuation" style="color:#393A34">;</span><span class="token plain"></span><br></span><span class="token-line" style="color:#393A34"><span class="token plain">    hermes</span><span class="token double-colon punctuation" style="color:#393A34">::</span><span class="token plain">Blob blob</span><span class="token punctuation" style="color:#393A34">;</span><span class="token plain"></span><br></span><span class="token-line" style="color:#393A34"><span class="token plain">    bkt</span><span class="token punctuation" style="color:#393A34">.</span><span class="token function" style="color:#d73a49">GetBlobId</span><span class="token punctuation" style="color:#393A34">(</span><span class="token plain">name</span><span class="token punctuation" style="color:#393A34">,</span><span class="token plain"> blob_id</span><span class="token punctuation" style="color:#393A34">)</span><span class="token punctuation" style="color:#393A34">;</span><span class="token plain"></span><br></span><span class="token-line" style="color:#393A34"><span class="token plain">    bkt</span><span class="token punctuation" style="color:#393A34">.</span><span class="token function" style="color:#d73a49">Get</span><span class="token punctuation" style="color:#393A34">(</span><span class="token plain">blob_id</span><span class="token punctuation" style="color:#393A34">,</span><span class="token plain"> blob</span><span class="token punctuation" style="color:#393A34">,</span><span class="token plain"> ctx</span><span class="token punctuation" style="color:#393A34">)</span><span class="token punctuation" style="color:#393A34">;</span><span class="token plain"></span><br></span><span class="token-line" style="color:#393A34"><span class="token plain">  </span><span class="token punctuation" style="color:#393A34">}</span><span class="token plain"></span><br></span><span class="token-line" style="color:#393A34"><span class="token plain"></span><span class="token punctuation" style="color:#393A34">}</span><br></span></code></pre><div class="buttonGroup__atx"><button type="button" aria-label="Copy code to clipboard" title="Copy" class="clean-btn"><span class="copyButtonIcons_eSgA" aria-hidden="true"><svg viewBox="0 0 24 24" class="copyButtonIcon_y97N"><path fill="currentColor" d="M19,21H8V7H19M19,5H8A2,2 0 0,0 6,7V21A2,2 0 0,0 8,23H19A2,2 0 0,0 21,21V7A2,2 0 0,0 19,5M16,1H4A2,2 0 0,0 2,3V17H4V3H16V1Z"></path></svg><svg viewBox="0 0 24 24" class="copyButtonSuccessIcon_LjdS"><path fill="currentColor" d="M21,7L9,19L3.5,13.5L4.91,12.09L9,16.17L19.59,5.59L21,7Z"></path></svg></span></button></div></div></div>
+<p>This example will place a blob into the DMSH and then retrieve that blob.</p>
+<div class="language-cpp codeBlockContainer_Ckt0 theme-code-block" style="--prism-color:#393A34;--prism-background-color:#f6f8fa"><div class="codeBlockContent_biex"><pre tabindex="0" class="prism-code language-cpp codeBlock_bY9V thin-scrollbar" style="color:#393A34;background-color:#f6f8fa"><code class="codeBlockLines_e6Vv"><span class="token-line" style="color:#393A34"><span class="token macro property directive-hash" style="color:#36acaa">#</span><span class="token macro property directive keyword" style="color:#00009f">include</span><span class="token macro property" style="color:#36acaa"> </span><span class="token macro property string" style="color:#e3116c">&lt;hermes.h&gt;</span><span class="token plain"></span><br></span><span class="token-line" style="color:#393A34"><span class="token plain"></span><span class="token macro property directive-hash" style="color:#36acaa">#</span><span class="token macro property directive keyword" style="color:#00009f">include</span><span class="token macro property" style="color:#36acaa"> </span><span class="token macro property string" style="color:#e3116c">&lt;bucket.h&gt;</span><span class="token plain"></span><br></span><span class="token-line" style="color:#393A34"><span class="token plain" style="display:inline-block"></span><br></span><span class="token-line" style="color:#393A34"><span class="token plain"></span><span class="token keyword" style="color:#00009f">int</span><span class="token plain"> </span><span class="token function" style="color:#d73a49">main</span><span class="token punctuation" style="color:#393A34">(</span><span class="token punctuation" style="color:#393A34">)</span><span class="token plain"> </span><span class="token punctuation" style="color:#393A34">{</span><span class="token plain"></span><br></span><span class="token-line" style="color:#393A34"><span class="token plain">  </span><span class="token function" style="color:#d73a49">TRANSPARENT_HERMES</span><span class="token punctuation" style="color:#393A34">(</span><span class="token punctuation" style="color:#393A34">)</span><span class="token punctuation" style="color:#393A34">;</span><span class="token plain"></span><br></span><span class="token-line" style="color:#393A34"><span class="token plain">  Bucket bkt </span><span class="token operator" style="color:#393A34">=</span><span class="token plain"> HERMES</span><span class="token operator" style="color:#393A34">-&gt;</span><span class="token function" style="color:#d73a49">GetBucket</span><span class="token punctuation" style="color:#393A34">(</span><span class="token string" style="color:#e3116c">&quot;hello&quot;</span><span class="token punctuation" style="color:#393A34">)</span><span class="token punctuation" style="color:#393A34">;</span><span class="token plain"></span><br></span><span class="token-line" style="color:#393A34"><span class="token plain">  size_t blob_size </span><span class="token operator" style="color:#393A34">=</span><span class="token plain"> </span><span class="token function" style="color:#d73a49">KILOBYTES</span><span class="token punctuation" style="color:#393A34">(</span><span class="token number" style="color:#36acaa">4</span><span class="token punctuation" style="color:#393A34">)</span><span class="token punctuation" style="color:#393A34">;</span><span class="token plain"></span><br></span><span class="token-line" style="color:#393A34"><span class="token plain">  Context ctx</span><span class="token punctuation" style="color:#393A34">;</span><span class="token plain"></span><br></span><span class="token-line" style="color:#393A34"><span class="token plain" style="display:inline-block"></span><br></span><span class="token-line" style="color:#393A34"><span class="token plain">  std</span><span class="token double-colon punctuation" style="color:#393A34">::</span><span class="token plain">vector</span><span class="token operator" style="color:#393A34">&lt;</span><span class="token keyword" style="color:#00009f">int</span><span class="token operator" style="color:#393A34">&gt;</span><span class="token plain"> </span><span class="token function" style="color:#d73a49">data_put</span><span class="token punctuation" style="color:#393A34">(</span><span class="token number" style="color:#36acaa">1024</span><span class="token punctuation" style="color:#393A34">,</span><span class="token plain"> i</span><span class="token punctuation" style="color:#393A34">)</span><span class="token punctuation" style="color:#393A34">;</span><span class="token plain"></span><br></span><span class="token-line" style="color:#393A34"><span class="token plain">  bkt</span><span class="token punctuation" style="color:#393A34">.</span><span class="token generic-function function" style="color:#d73a49">Put</span><span class="token generic-function generic class-name operator" style="color:#393A34">&lt;</span><span class="token generic-function generic class-name">std</span><span class="token generic-function generic class-name double-colon punctuation" style="color:#393A34">::</span><span class="token generic-function generic class-name">vector</span><span class="token generic-function generic class-name operator" style="color:#393A34">&lt;</span><span class="token generic-function generic class-name keyword" style="color:#00009f">int</span><span class="token generic-function generic class-name operator" style="color:#393A34">&gt;&gt;</span><span class="token punctuation" style="color:#393A34">(</span><span class="token string" style="color:#e3116c">&quot;0&quot;</span><span class="token punctuation" style="color:#393A34">,</span><span class="token plain"> data_put</span><span class="token punctuation" style="color:#393A34">,</span><span class="token plain"> ctx</span><span class="token punctuation" style="color:#393A34">)</span><span class="token punctuation" style="color:#393A34">;</span><span class="token plain"></span><br></span><span class="token-line" style="color:#393A34"><span class="token plain" style="display:inline-block"></span><br></span><span class="token-line" style="color:#393A34"><span class="token plain">  std</span><span class="token double-colon punctuation" style="color:#393A34">::</span><span class="token plain">vector</span><span class="token operator" style="color:#393A34">&lt;</span><span class="token keyword" style="color:#00009f">int</span><span class="token operator" style="color:#393A34">&gt;</span><span class="token plain"> </span><span class="token function" style="color:#d73a49">data_get</span><span class="token punctuation" style="color:#393A34">(</span><span class="token number" style="color:#36acaa">1024</span><span class="token punctuation" style="color:#393A34">,</span><span class="token plain"> i</span><span class="token punctuation" style="color:#393A34">)</span><span class="token punctuation" style="color:#393A34">;</span><span class="token plain"></span><br></span><span class="token-line" style="color:#393A34"><span class="token plain">  bkt</span><span class="token punctuation" style="color:#393A34">.</span><span class="token generic-function function" style="color:#d73a49">Get</span><span class="token generic-function generic class-name operator" style="color:#393A34">&lt;</span><span class="token generic-function generic class-name">std</span><span class="token generic-function generic class-name double-colon punctuation" style="color:#393A34">::</span><span class="token generic-function generic class-name">vector</span><span class="token generic-function generic class-name operator" style="color:#393A34">&lt;</span><span class="token generic-function generic class-name keyword" style="color:#00009f">int</span><span class="token generic-function generic class-name operator" style="color:#393A34">&gt;&gt;</span><span class="token punctuation" style="color:#393A34">(</span><span class="token string" style="color:#e3116c">&quot;0&quot;</span><span class="token punctuation" style="color:#393A34">,</span><span class="token plain"> data_get</span><span class="token punctuation" style="color:#393A34">,</span><span class="token plain"> ctx</span><span class="token punctuation" style="color:#393A34">)</span><span class="token punctuation" style="color:#393A34">;</span><span class="token plain"></span><br></span><span class="token-line" style="color:#393A34"><span class="token plain" style="display:inline-block"></span><br></span><span class="token-line" style="color:#393A34"><span class="token plain">  </span><span class="token function" style="color:#d73a49">REQUIRE</span><span class="token punctuation" style="color:#393A34">(</span><span class="token plain">data_put </span><span class="token operator" style="color:#393A34">==</span><span class="token plain"> data_get</span><span class="token punctuation" style="color:#393A34">)</span><span class="token punctuation" style="color:#393A34">;</span><span class="token plain"></span><br></span><span class="token-line" style="color:#393A34"><span class="token plain"></span><span class="token punctuation" style="color:#393A34">}</span><br></span></code></pre><div class="buttonGroup__atx"><button type="button" aria-label="Copy code to clipboard" title="Copy" class="clean-btn"><span class="copyButtonIcons_eSgA" aria-hidden="true"><svg viewBox="0 0 24 24" class="copyButtonIcon_y97N"><path fill="currentColor" d="M19,21H8V7H19M19,5H8A2,2 0 0,0 6,7V21A2,2 0 0,0 8,23H19A2,2 0 0,0 21,21V7A2,2 0 0,0 19,5M16,1H4A2,2 0 0,0 2,3V17H4V3H16V1Z"></path></svg><svg viewBox="0 0 24 24" class="copyButtonSuccessIcon_LjdS"><path fill="currentColor" d="M21,7L9,19L3.5,13.5L4.91,12.09L9,16.17L19.59,5.59L21,7Z"></path></svg></span></button></div></div></div>
 <ul>
-<li>HERMES is a singleton macro provided in hermes.h.</li>
-<li>GetBucket will either create a bucket or get the bucket if it exists.
+<li><code>TRANSPARENT_HERMES()</code> will initialize your connection to Hermes</li>
+<li><code>HERMES</code> is a singleton macro provided in hermes.h.</li>
+<li><code>GetBucket</code> will either create a bucket or get the bucket if it exists.
 This operation is concurrency-safe. I.e., it is guaranteed only one
 thread or process calling this function will create the bucket if it
 DNE.</li>
-<li>Context is optional. It contains the ability to override
+<li><code>Context</code> is optional. It contains the ability to override
 defaults defined in the server and client configuration files. For
 example, you can set a custom DPE to use for a blob Put.</li>
 <li><code>hermes::Blob analagous to and std::vector&lt;char&gt;</code>. It&#x27;s not quite the
 same thing, but we won&#x27;t go into detail here.</li>
-<li>bkt.Put will put a blob into the bucket. Put destroys all content
-if the blob previously existed. At this time, blobs are considered
-immutable.</li>
-<li>bkt.Get will get the contents of an entire blob.</li>
-</ul>
-<h2 class="anchor anchorWithStickyNavbar_LWe7" id="basic-deployment">Basic Deployment<a href="#basic-deployment" class="hash-link" aria-label="Direct link to Basic Deployment" title="Direct link to Basic Deployment">​</a></h2>
-<p>Here we will describe the basic flow of deploying a Hermes program.</p>
-<h3 class="anchor anchorWithStickyNavbar_LWe7" id="create-a-server-configuration">Create a server configuration<a href="#create-a-server-configuration" class="hash-link" aria-label="Direct link to Create a server configuration" title="Direct link to Create a server configuration">​</a></h3>
-<p>Technically, this is optional. Hermes has a
-<a href="https://github.com/HDFGroup/hermes/blob/master/config/hermes_server_default.yaml" target="_blank" rel="noopener noreferrer">default server
-configuration</a>.
-The main important thing here is defining the storage devices on your machines.
-The example file has more details.</p>
-<p>The Hermes server configuration is also described in Section 3.</p>
-<h3 class="anchor anchorWithStickyNavbar_LWe7" id="launch-the-hermes-daemon">Launch the Hermes Daemon<a href="#launch-the-hermes-daemon" class="hash-link" aria-label="Direct link to Launch the Hermes Daemon" title="Direct link to Launch the Hermes Daemon">​</a></h3>
-<p>To launch the daemon on a single node, do the following:</p>
-<div class="language-bash codeBlockContainer_Ckt0 theme-code-block" style="--prism-color:#393A34;--prism-background-color:#f6f8fa"><div class="codeBlockContent_biex"><pre tabindex="0" class="prism-code language-bash codeBlock_bY9V thin-scrollbar" style="color:#393A34;background-color:#f6f8fa"><code class="codeBlockLines_e6Vv"><span class="token-line" style="color:#393A34"><span class="token plain">HERMES_CONF=/path/to/your/hermes_server.yaml \</span><br></span><span class="token-line" style="color:#393A34"><span class="token plain">hermes_daemon</span><br></span></code></pre><div class="buttonGroup__atx"><button type="button" aria-label="Copy code to clipboard" title="Copy" class="clean-btn"><span class="copyButtonIcons_eSgA" aria-hidden="true"><svg viewBox="0 0 24 24" class="copyButtonIcon_y97N"><path fill="currentColor" d="M19,21H8V7H19M19,5H8A2,2 0 0,0 6,7V21A2,2 0 0,0 8,23H19A2,2 0 0,0 21,21V7A2,2 0 0,0 19,5M16,1H4A2,2 0 0,0 2,3V17H4V3H16V1Z"></path></svg><svg viewBox="0 0 24 24" class="copyButtonSuccessIcon_LjdS"><path fill="currentColor" d="M21,7L9,19L3.5,13.5L4.91,12.09L9,16.17L19.59,5.59L21,7Z"></path></svg></span></button></div></div></div>
-<p>If you need the daemon on multiple nodes, we support MPI</p>
-<div class="language-bash codeBlockContainer_Ckt0 theme-code-block" style="--prism-color:#393A34;--prism-background-color:#f6f8fa"><div class="codeBlockContent_biex"><pre tabindex="0" class="prism-code language-bash codeBlock_bY9V thin-scrollbar" style="color:#393A34;background-color:#f6f8fa"><code class="codeBlockLines_e6Vv"><span class="token-line" style="color:#393A34"><span class="token plain">mpirun -n 4 -ppn 1 --hostfile=hostfile.txt \</span><br></span><span class="token-line" style="color:#393A34"><span class="token plain">-genv HERMES_CONF /path/to/your/hermes_server.yaml \</span><br></span><span class="token-line" style="color:#393A34"><span class="token plain">hermes_daemon</span><br></span></code></pre><div class="buttonGroup__atx"><button type="button" aria-label="Copy code to clipboard" title="Copy" class="clean-btn"><span class="copyButtonIcons_eSgA" aria-hidden="true"><svg viewBox="0 0 24 24" class="copyButtonIcon_y97N"><path fill="currentColor" d="M19,21H8V7H19M19,5H8A2,2 0 0,0 6,7V21A2,2 0 0,0 8,23H19A2,2 0 0,0 21,21V7A2,2 0 0,0 19,5M16,1H4A2,2 0 0,0 2,3V17H4V3H16V1Z"></path></svg><svg viewBox="0 0 24 24" class="copyButtonSuccessIcon_LjdS"><path fill="currentColor" d="M21,7L9,19L3.5,13.5L4.91,12.09L9,16.17L19.59,5.59L21,7Z"></path></svg></span></button></div></div></div>
-<p>Make sure to only spawn one daemon per node.</p>
-<h3 class="anchor anchorWithStickyNavbar_LWe7" id="launch-your-application">Launch your application<a href="#launch-your-application" class="hash-link" aria-label="Direct link to Launch your application" title="Direct link to Launch your application">​</a></h3>
-<div class="language-bash codeBlockContainer_Ckt0 theme-code-block" style="--prism-color:#393A34;--prism-background-color:#f6f8fa"><div class="codeBlockContent_biex"><pre tabindex="0" class="prism-code language-bash codeBlock_bY9V thin-scrollbar" style="color:#393A34;background-color:#f6f8fa"><code class="codeBlockLines_e6Vv"><span class="token-line" style="color:#393A34"><span class="token plain">HERMES_CONF=/path/to/your/hermes_server.yaml \</span><br></span><span class="token-line" style="color:#393A34"><span class="token plain">HERMES_CLEINT_CONF=/path/to/your/hermes_client.yaml \</span><br></span><span class="token-line" style="color:#393A34"><span class="token plain">./myprogram</span><br></span></code></pre><div class="buttonGroup__atx"><button type="button" aria-label="Copy code to clipboard" title="Copy" class="clean-btn"><span class="copyButtonIcons_eSgA" aria-hidden="true"><svg viewBox="0 0 24 24" class="copyButtonIcon_y97N"><path fill="currentColor" d="M19,21H8V7H19M19,5H8A2,2 0 0,0 6,7V21A2,2 0 0,0 8,23H19A2,2 0 0,0 21,21V7A2,2 0 0,0 19,5M16,1H4A2,2 0 0,0 2,3V17H4V3H16V1Z"></path></svg><svg viewBox="0 0 24 24" class="copyButtonSuccessIcon_LjdS"><path fill="currentColor" d="M21,7L9,19L3.5,13.5L4.91,12.09L9,16.17L19.59,5.59L21,7Z"></path></svg></span></button></div></div></div></div></article><nav class="pagination-nav docusaurus-mt-lg" aria-label="Docs pages"><a class="pagination-nav__link pagination-nav__link--prev" href="/docs/hermes/components/topology"><div class="pagination-nav__sublabel">Previous</div><div class="pagination-nav__label">Topology</div></a><a class="pagination-nav__link pagination-nav__link--next" href="/docs/hermes/adapters"><div class="pagination-nav__sublabel">Next</div><div class="pagination-nav__label">Adapters</div></a></nav></div></div><div class="col col--3"><div class="tableOfContents_bqdL thin-scrollbar theme-doc-toc-desktop"><ul class="table-of-contents table-of-contents__left-border"><li><a href="#basic-api-example" class="table-of-contents__link toc-highlight">Basic API Example</a></li><li><a href="#basic-deployment" class="table-of-contents__link toc-highlight">Basic Deployment</a><ul><li><a href="#create-a-server-configuration" class="table-of-contents__link toc-highlight">Create a server configuration</a></li><li><a href="#launch-the-hermes-daemon" class="table-of-contents__link toc-highlight">Launch the Hermes Daemon</a></li><li><a href="#launch-your-application" class="table-of-contents__link toc-highlight">Launch your application</a></li></ul></li></ul></div></div></div></div></main></div></div></div><footer class="footer"><div class="container container-fluid"><div class="row footer__links"><div class="col footer__col"><div class="footer__title">Gnosis Research Center</div><ul class="footer__items clean-list"><li class="footer__item">
+<li><code>bkt.Put</code> will put a blob into the bucket. Put replaces all content
+if the blob previously existed.</li>
+<li><code>bkt.Get</code> will get the contents of an entire blob.</li>
+</ul></div></article><nav class="pagination-nav docusaurus-mt-lg" aria-label="Docs pages"><a class="pagination-nav__link pagination-nav__link--prev" href="/docs/hermes/adapters"><div class="pagination-nav__sublabel">Previous</div><div class="pagination-nav__label">Adapters</div></a><a class="pagination-nav__link pagination-nav__link--next" href="/docs/hermes/components/buffer-organizer"><div class="pagination-nav__sublabel">Next</div><div class="pagination-nav__label">Buffer Organizer</div></a></nav></div></div><div class="col col--3"><div class="tableOfContents_bqdL thin-scrollbar theme-doc-toc-desktop"><ul class="table-of-contents table-of-contents__left-border"><li><a href="#basic-api-example" class="table-of-contents__link toc-highlight">Basic API Example</a></li></ul></div></div></div></div></main></div></div></div><footer class="footer"><div class="container container-fluid"><div class="row footer__links"><div class="col footer__col"><div class="footer__title">Gnosis Research Center</div><ul class="footer__items clean-list"><li class="footer__item">
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index 728c245f..f3bd789c 100644
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href="/docs/chronolog/index">ChronoLog</a></div></li><li class="theme-doc-sidebar-item-category theme-doc-sidebar-item-category-level-1 menu__list-item menu__list-item--collapsed"><div class="menu__list-item-collapsible"><a class="menu__link menu__link--sublist menu__link--sublist-caret" aria-expanded="false" href="/docs/jarvis/jarvis-util/index">Jarvis</a></div></li></ul></nav></div></div></aside><main class="docMainContainer_TBSr"><div class="container padding-top--md padding-bottom--lg"><div class="row"><div class="col docItemCol_VOVn"><div class="docItemContainer_Djhp"><article><nav class="theme-doc-breadcrumbs breadcrumbsContainer_Z_bl" aria-label="Breadcrumbs"><ul class="breadcrumbs" itemscope="" itemtype="https://schema.org/BreadcrumbList"><li class="breadcrumbs__item"><a aria-label="Home page" class="breadcrumbs__link" href="/"><svg viewBox="0 0 24 24" class="breadcrumbHomeIcon_YNFT"><path d="M10 19v-5h4v5c0 .55.45 1 1 1h3c.55 0 1-.45 1-1v-7h1.7c.46 0 .68-.57.33-.87L12.67 3.6c-.38-.34-.96-.34-1.34 0l-8.36 7.53c-.34.3-.13.87.33.87H5v7c0 .55.45 1 1 1h3c.55 0 1-.45 1-1z" fill="currentColor"></path></svg></a></li><li class="breadcrumbs__item"><span class="breadcrumbs__link">HPC Tutorials</span><meta itemprop="position" content="1"></li><li itemscope="" itemprop="itemListElement" itemtype="https://schema.org/ListItem" class="breadcrumbs__item"><a class="breadcrumbs__link" itemprop="item" href="/docs/category/important-environment-variables"><span itemprop="name">Important Environment Variables</span></a><meta itemprop="position" content="2"></li><li itemscope="" itemprop="itemListElement" itemtype="https://schema.org/ListItem" class="breadcrumbs__item breadcrumbs__item--active"><span class="breadcrumbs__link" itemprop="name">CMAKE_MODULE_PATH</span><meta itemprop="position" content="3"></li></ul></nav><div class="theme-doc-markdown markdown"><h1><code>CMAKE_MODULE_PATH</code></h1>
diff --git a/docs/hpc-tutorials/important-environment-variables/cmake-prefix-path/index.html b/docs/hpc-tutorials/important-environment-variables/cmake-prefix-path/index.html
index d3dffd7b..2933bd66 100644
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markdown"><h1><code>CMAKE_PREFIX_PATH</code></h1>
diff --git a/docs/hpc-tutorials/important-environment-variables/cpath/index.html b/docs/hpc-tutorials/important-environment-variables/cpath/index.html
index 18b76fbf..3ffd5663 100644
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href="/docs/hpc-tutorials/important-environment-variables/cmake-module-path">CMAKE_MODULE_PATH</a></li><li class="theme-doc-sidebar-item-link theme-doc-sidebar-item-link-level-3 menu__list-item"><a class="menu__link" tabindex="0" href="/docs/hpc-tutorials/important-environment-variables/cmake-prefix-path">CMAKE_PREFIX_PATH</a></li><li class="theme-doc-sidebar-item-link theme-doc-sidebar-item-link-level-3 menu__list-item"><a class="menu__link" tabindex="0" href="/docs/hpc-tutorials/important-environment-variables/cpath">CPATH</a></li><li class="theme-doc-sidebar-item-link theme-doc-sidebar-item-link-level-3 menu__list-item"><a class="menu__link menu__link--active" aria-current="page" tabindex="0" href="/docs/hpc-tutorials/important-environment-variables/java-home">JAVA_HOME</a></li><li class="theme-doc-sidebar-item-link theme-doc-sidebar-item-link-level-3 menu__list-item"><a class="menu__link" tabindex="0" 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class="breadcrumbHomeIcon_YNFT"><path d="M10 19v-5h4v5c0 .55.45 1 1 1h3c.55 0 1-.45 1-1v-7h1.7c.46 0 .68-.57.33-.87L12.67 3.6c-.38-.34-.96-.34-1.34 0l-8.36 7.53c-.34.3-.13.87.33.87H5v7c0 .55.45 1 1 1h3c.55 0 1-.45 1-1z" fill="currentColor"></path></svg></a></li><li class="breadcrumbs__item"><span class="breadcrumbs__link">HPC Tutorials</span><meta itemprop="position" content="1"></li><li itemscope="" itemprop="itemListElement" itemtype="https://schema.org/ListItem" class="breadcrumbs__item"><a class="breadcrumbs__link" itemprop="item" href="/docs/category/important-environment-variables"><span itemprop="name">Important Environment Variables</span></a><meta itemprop="position" content="2"></li><li itemscope="" itemprop="itemListElement" itemtype="https://schema.org/ListItem" class="breadcrumbs__item breadcrumbs__item--active"><span class="breadcrumbs__link" itemprop="name">JAVA_HOME</span><meta itemprop="position" content="3"></li></ul></nav><div class="theme-doc-markdown 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class="breadcrumbHomeIcon_YNFT"><path d="M10 19v-5h4v5c0 .55.45 1 1 1h3c.55 0 1-.45 1-1v-7h1.7c.46 0 .68-.57.33-.87L12.67 3.6c-.38-.34-.96-.34-1.34 0l-8.36 7.53c-.34.3-.13.87.33.87H5v7c0 .55.45 1 1 1h3c.55 0 1-.45 1-1z" fill="currentColor"></path></svg></a></li><li class="breadcrumbs__item"><span class="breadcrumbs__link">HPC Tutorials</span><meta itemprop="position" content="1"></li><li itemscope="" itemprop="itemListElement" itemtype="https://schema.org/ListItem" class="breadcrumbs__item"><a class="breadcrumbs__link" itemprop="item" href="/docs/category/important-environment-variables"><span itemprop="name">Important Environment Variables</span></a><meta itemprop="position" content="2"></li><li itemscope="" itemprop="itemListElement" itemtype="https://schema.org/ListItem" class="breadcrumbs__item breadcrumbs__item--active"><span class="breadcrumbs__link" itemprop="name">LD_LIBRARY_PATH</span><meta itemprop="position" content="3"></li></ul></nav><div class="theme-doc-markdown markdown"><h1><code>LD_LIBRARY_PATH</code></h1>
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diff --git a/docs/hpc-tutorials/important-environment-variables/path/index.html b/docs/hpc-tutorials/important-environment-variables/path/index.html
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.68-.57.33-.87L12.67 3.6c-.38-.34-.96-.34-1.34 0l-8.36 7.53c-.34.3-.13.87.33.87H5v7c0 .55.45 1 1 1h3c.55 0 1-.45 1-1z" fill="currentColor"></path></svg></a></li><li class="breadcrumbs__item"><span class="breadcrumbs__link">HPC Tutorials</span><meta itemprop="position" content="1"></li><li itemscope="" itemprop="itemListElement" itemtype="https://schema.org/ListItem" class="breadcrumbs__item"><a class="breadcrumbs__link" itemprop="item" href="/docs/category/important-environment-variables"><span itemprop="name">Important Environment Variables</span></a><meta itemprop="position" content="2"></li><li itemscope="" itemprop="itemListElement" itemtype="https://schema.org/ListItem" class="breadcrumbs__item breadcrumbs__item--active"><span class="breadcrumbs__link" itemprop="name">PATH</span><meta itemprop="position" content="3"></li></ul></nav><div class="theme-doc-markdown markdown"><h1><code>PATH</code></h1>
diff --git a/docs/hpc-tutorials/important-environment-variables/pythonpath/index.html b/docs/hpc-tutorials/important-environment-variables/pythonpath/index.html
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c-0.98,1.37-2.58,2.26-4.4,2.26c-2.98,0-5.4-2.42-5.4-5.4c0-1.81,0.89-3.42,2.26-4.4C12.92,3.04,12.46,3,12,3L12,3z"></path></svg></button></div><div class="navbarSearchContainer_Bca1"></div></div></div><div role="presentation" class="navbar-sidebar__backdrop"></div></nav><div id="__docusaurus_skipToContent_fallback" class="main-wrapper mainWrapper_z2l0"><main class="container container--fluid margin-vert--lg"><div class="row mdxPageWrapper_j9I6"><div class="col"><article><h1>Projects</h1>
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c-0.98,1.37-2.58,2.26-4.4,2.26c-2.98,0-5.4-2.42-5.4-5.4c0-1.81,0.89-3.42,2.26-4.4C12.92,3.04,12.46,3,12,3L12,3z"></path></svg></button></div><div class="navbarSearchContainer_Bca1"></div></div></div><div role="presentation" class="navbar-sidebar__backdrop"></div></nav><div id="__docusaurus_skipToContent_fallback" class="main-wrapper mainWrapper_z2l0"><main class="container container--fluid margin-vert--lg"><div class="row mdxPageWrapper_j9I6"><div class="col col--8"><article><h1>IRIS: I/O Redirection Via Integrated Storage</h1>
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