Merge pull request #12 from osg-htc/xalim-text-fixes

Text fixes for exercises

docs/materials/data/part1-ex1-data-needs.md

@@ -35,8 +35,8 @@ genome information.
 1. Copy the BLAST executables:
 
         :::console
-        user@ap40 $ wget http://proxy.chtc.wisc.edu/SQUID/osg-school-2023/ncbi-blast-2.12.0+-x64-linux.tar.gz
-        user@ap40 $ tar -xzvf ncbi-blast-2.12.0+-x64-linux.tar.gz
+        user@ap40 $ wget http://proxy.chtc.wisc.edu/SQUID/osg-school-2023/ncbi-blast-2.15.0+-x64-linux.tar.gz
+        user@ap40 $ tar -xzvf ncbi-blast-2.15.0+-x64-linux.tar.gz
 
 1.  Download these files to your current directory:
 
@@ -55,7 +55,7 @@ Understanding BLAST
 Remember that `blastx` is executed in a command like the following:
 
 ``` console
-user@ap40 $ ./ncbi-blast-2.12.0+/bin/blastx -db <DATABASE ROOTNAME> -query <INPUT FILE> -out <RESULTS FILE>
+user@ap40 $ ./ncbi-blast-2.15.0+/bin/blastx -db <DATABASE ROOTNAME> -query <INPUT FILE> -out <RESULTS FILE>
 ```
 
 In the above, the `<INPUT FILE>` is the name of a file containing a number of genetic sequences (e.g. `mouse.fa`), and

docs/materials/data/part1-ex2-file-transfer.md

@@ -209,7 +209,7 @@ destination `science-results/mouse.fa.result`. Remember
 that the `transfer_output_remaps` value requires double
 quotes around it.
 
-Submit the job, and wait for it to complete. Was there
+Submit the job, and wait for it to complete. Are there
 any errors? Can you find mouse.fa.result?
 
 Conclusions

docs/materials/htcondor/part1-ex1-login.md

@@ -52,7 +52,7 @@ In the exercises, we will show commands that you are supposed to type or copy in
 
 ``` console
 username@ap1 $ hostname
-ap1.facility.path-cc.io
+path-ap2001
 ```
 
 !!! note
@@ -92,7 +92,7 @@ HTCondor is installed on this server. But what version? You can ask HTCondor its
 
 ``` console
 username@ap1 $ condor_version
-$CondorVersion: 10.7.0 2023-07-10 BuildID: 659788 PackageID: 10.7.0-0.659788 RC $
+$CondorVersion: 23.9.0 2024-06-27 BuildID: 742143 PackageID: 23.9.0-0.742143 GitSHA: 68fde429 RC $
 $CondorPlatform: x86_64_AlmaLinux8 $
 ```
 

docs/materials/htcondor/part1-ex3-jobs.md

@@ -159,13 +159,13 @@ or perhaps a shell script of commands that you'd like to run within a job. In th
 1. Test your script from the command line:
 
         :::console
-        username@ap1 $ ./test-script.sh hello 42 
-        Date: Mon Jul 17 10:02:20 CDT 2017 
-        Host: learn.chtc.wisc.edu 
-        System: Linux x86_64 GNU/Linux 
+        username@ap1 $ ./test-script.sh hello 42
+        Date:  Mon Jul 1 14:03:56 CDT 2024
+        Host:  path-ap2001
+        System:  Linux x86_64 GNU/Linux
         Program: ./test-script.sh
         Args: hello 42
-        ls: hostname.sub montage hostname.err hostname.log hostname.out test-script.sh
+        ls:  hostname.err hostname.log hostname.out hostname.sub sleep.log sleep.sub test-script.sh
 
     This step is **really** important! If you cannot run your executable from the command-line, HTCondor probably cannot run it on another machine, either. 
     Further, debugging problems like this one is surprisingly difficult. 

docs/materials/htcondor/part1-ex4-logs.md

@@ -23,15 +23,15 @@ For this exercise, we can examine a log file for any previous job that you have
 A job log file is updated throughout the life of a job, usually at key events. Each event starts with a heading that indicates what happened and when. Here are **all** of the event headings from the `sleep` job log (detailed output in between headings has been omitted here):
 
 ``` file
-000 (5739.000.000) 2023-07-10 10:44:20 Job submitted from host: <128.104.100.43:9618?addrs=...>
-040 (5739.000.000) 2023-07-10 10:45:10 Started transferring input files
-040 (5739.000.000) 2023-07-10 10:45:10 Finished transferring input files
-001 (5739.000.000) 2023-07-10 10:45:11 Job executing on host: <128.104.55.42:9618?addrs=...>
-006 (5739.000.000) 2023-07-10 10:45:20 Image size of job updated: 72
-040 (5739.000.000) 2023-07-10 10:45:20 Started transferring output files
-040 (5739.000.000) 2023-07-10 10:45:20 Finished transferring output files
-006 (5739.000.000) 2023-07-10 10:46:11 Image size of job updated: 4072
-005 (5739.000.000) 2023-07-10 10:46:11 Job terminated.
+000 (5739.000.000) 2024-07-10 10:44:20 Job submitted from host: <128.104.100.43:9618?addrs=...>
+040 (5739.000.000) 2024-07-10 10:45:10 Started transferring input files
+040 (5739.000.000) 2024-07-10 10:45:10 Finished transferring input files
+001 (5739.000.000) 2024-07-10 10:45:11 Job executing on host: <128.104.55.42:9618?addrs=...>
+006 (5739.000.000) 2024-07-10 10:45:20 Image size of job updated: 72
+040 (5739.000.000) 2024-07-10 10:45:20 Started transferring output files
+040 (5739.000.000) 2024-07-10 10:45:20 Finished transferring output files
+006 (5739.000.000) 2024-07-10 10:46:11 Image size of job updated: 4072
+005 (5739.000.000) 2024-07-10 10:46:11 Job terminated.
 ```
 
 There is a lot of extra information in those lines, but you can see:
@@ -43,7 +43,7 @@ There is a lot of extra information in those lines, but you can see:
 Some events provide no information in addition to the heading. For example:
 
 ``` file
-000 (5739.000.000) 2020-07-10 10:44:20 Job submitted from host: <128.104.100.43:9618?addrs=...>
+000 (5739.000.000) 2024-07-10 10:44:20 Job submitted from host: <128.104.100.43:9618?addrs=...>
 ...
 ```
 
@@ -53,7 +53,7 @@ Some events provide no information in addition to the heading. For example:
 However, some lines have additional information to help you quickly understand where and how your job is running. For example:  
 
 ``` file
-001 (5739.000.000) 2020-07-10 10:45:11 Job executing on host: <128.104.55.42:9618?addrs=...>
+001 (5739.000.000) 2024-07-10 10:45:11 Job executing on host: <128.104.55.42:9618?addrs=...>
 	SlotName: [email protected]
 	CondorScratchDir = "/pilot/osgvo-pilot-2q71K9/execute/dir_9316"
 	Cpus = 1
@@ -70,7 +70,7 @@ However, some lines have additional information to help you quickly understand w
 Another example of is the periodic update:
 
 ``` file
-006 (5739.000.000) 2020-07-10 10:45:20 Image size of job updated: 72
+006 (5739.000.000) 2024-07-10 10:45:20 Image size of job updated: 72
     1  -  MemoryUsage of job (MB)
     72  -  ResidentSetSize of job (KB)
 ...
@@ -81,7 +81,7 @@ These updates record the amount of memory that the job is using on the execute m
 The job termination event includes a lot of very useful information:
 
 ``` file
-005 (5739.000.000) 2023-07-10 10:46:11 Job terminated.
+005 (5739.000.000) 2024-07-10 10:46:11 Job terminated.
     (1) Normal termination (return value 0)
         Usr 0 00:00:00, Sys 0 00:00:00  -  Run Remote Usage
         Usr 0 00:00:00, Sys 0 00:00:00  -  Run Local Usage
@@ -95,7 +95,7 @@ The job termination event includes a lot of very useful information:
        Cpus                 :                 1         1
        Disk (KB)            :       40       30   4203309
        Memory (MB)          :        1        1         1
-Job terminated of its own accord at 2023-07-10 10:46:11 with exit-code 0.
+Job terminated of its own accord at 2024-07-10 10:46:11 with exit-code 0.
 ...
 ```
 

docs/materials/htcondor/part1-ex5-request.md

@@ -44,7 +44,7 @@ On Mac and Windows, for example, the "Activity Monitor" and "Task Manager" appli
 Using `ps`:
 
 ``` console
-username@learn $ ps ux
+username@ap1 $ ps ux
 USER       PID %CPU %MEM    VSZ   RSS TTY      STAT START   TIME COMMAND
 alice      24342  0.0  0.0  90224  1864 ?        S    13:39   0:00 sshd: alice@pts/0  
 alice      24343  0.0  0.0  66096  1580 pts/0    Ss   13:39   0:00 -bash

docs/materials/htcondor/part1-ex7-compile.md

@@ -48,19 +48,19 @@ Save that code to a file, for example, `simple.c`.
 Compile the program with static linking:
 
 ``` console
-username@learn $ gcc -static -o simple simple.c
+username@ap1 $ gcc -static -o simple simple.c
 ```
 
 As always, test that you can run your command from the command line first. First, without arguments to make sure it fails correctly:
 
 ``` console
-username@learn $ ./simple
+username@ap1 $ ./simple
 ```
 
 and then with valid arguments:
 
 ``` console
-username@learn $ ./simple 5 21
+username@ap1 $ ./simple 5 21
 ```
 
 Running a Compiled C Program

docs/materials/htcondor/part1-ex8-queue.md

@@ -17,40 +17,40 @@ Selecting Jobs
 The `condor_q` program has many options for selecting which jobs are listed. You have already seen that the default mode is to show only your jobs in "batch" mode:
 
 ``` console
-username@learn $ condor_q
+username@ap1 $ condor_q
 ```
 
 You've seen that you can view all jobs (all users) in the submit node's queue by using the `-all` argument:
 
 ``` console
-username@learn $ condor_q -all
+username@ap1 $ condor_q -all
 ```
 
 And you've seen that you can view more details about queued jobs, with each separate job on a single line using the `-nobatch` option:
 
 ``` console
-username@learn $ condor_q -nobatch
-username@learn $ condor_q -all -nobatch
+username@ap1 $ condor_q -nobatch
+username@ap1 $ condor_q -all -nobatch
 ```
 
 Did you know you can also name one or more user IDs on the command line, in which case jobs for all of the named users are listed at once?
 
 ``` console
-username@learn $ condor_q <USERNAME1> <USERNAME2> <USERNAME3>
+username@ap1 $ condor_q <USERNAME1> <USERNAME2> <USERNAME3>
 ```
 
 To list just the jobs associated with a single cluster number:
 
 ``` console
-username@learn $ condor_q <CLUSTER>
+username@ap1 $ condor_q <CLUSTER>
 ```
 
 For example, if you want to see the jobs in cluster 5678 (i.e., `5678.0`, `5678.1`, etc.), you use `condor_q 5678`.
 
 To list a specific job (i.e., cluster.process, as in 5678.0):
 
 ``` console
-username@learn $ condor_q <JOB.ID>
+username@ap1 $ condor_q <JOB.ID>
 ```
 
 For example, to see job ID 5678.1, you use `condor_q 5678.1`.
@@ -79,7 +79,7 @@ You may have wondered why it is useful to be able to list a single job ID using
 If you add the `-long` option to `condor_q` (or its short form, `-l`), it will show the complete ClassAd for each selected job, instead of the one-line summary that you have seen so far. Because job ClassAds may have 80–90 attributes (or more), it probably makes the most sense to show the ClassAd for a single job at a time. And you know how to show just one job! Here is what the command looks like:
 
 ``` console
-username@learn $ condor_q -long <JOB.ID>
+username@ap1 $ condor_q -long <JOB.ID>
 ```
 
 The output from this command is long and complex. Most of the attributes that HTCondor adds to a job are arcane and uninteresting for us now. But here are some examples of common, interesting attributes taken directly from `condor_q` output (except with some line breaks added to the `Requirements` attribute):
@@ -138,7 +138,7 @@ Sometimes, you submit a job and it just sits in the queue in Idle state, never r
 To ask HTCondor why your job is not running, add the `-better-analyze` option to `condor_q` for the specific job. For example, for job ID 2423.0, the command is:
 
 ``` console
-username@learn $ condor_q -better-analyze 2423.0
+username@ap1 $ condor_q -better-analyze 2423.0
 ```
 
 Of course, replace the job ID with your own.
@@ -166,7 +166,7 @@ There is a lot of output, but a few items are worth highlighting. Here is a samp
 
 ``` file
 
--- Schedd: learn.chtc.wisc.edu : <128.104.100.148:9618?...
+-- Schedd: ap1.facility.path-cc.io : <128.105.68.66:9618?...
 ...
 
 Job 98096.000 defines the following attributes:
@@ -215,7 +215,7 @@ There is a way to select the specific job attributes you want `condor_q` to tell
 To use autoformatting, use the `-af` option followed by the attribute name, for each attribute that you want to output:
 
 ``` console
-username@learn $ condor_q -all -af Owner ClusterId Cmd
+username@ap1 $ condor_q -all -af Owner ClusterId Cmd
 moate 2418 /share/test.sh
 cat 2421 /bin/sleep
 cat 2422 /bin/sleep
@@ -228,7 +228,7 @@ References
 
 As suggested above, if you want to learn more about `condor_q`, you can do some reading:
 
--   Read the `condor_q` man page or HTCondor Manual section (same text) to learn about more options
--   Read about ClassAd attributes in Appendix A of the HTCondor Manual
+-   Read the `condor_q` man page or [HTCondor Manual section](https://htcondor.readthedocs.io/en/latest/man-pages/condor_q.html) (same text) to learn about more options
+-   Read about [ClassAd attributes](https://htcondor.readthedocs.io/en/latest/classad-attributes/job-classad-attributes.html) in the HTCondor Manual
 
 

docs/materials/htcondor/part1-ex9-status.md

@@ -19,33 +19,33 @@ The `condor_status` program has many options for selecting which slots are liste
 Another convenient option is to list only those slots that are available now:
 
 ``` console
-username@learn $ condor_status -avail
+username@ap1 $ condor_status -avail
 ```
 
 Of course, the individual execute machines only report their slots to the collector at certain time intervals, so this list will not reflect the up-to-the-second reality of all slots. But this limitation is true of all `condor_status` output, not just with the `-avail` option.
 
 Similar to `condor_q`, you can limit the slots that are listed in two easy ways. To list just the slots on a specific machine:
 
 ``` console
-username@learn $ condor_status <hostname>
+username@ap1 $ condor_status <hostname>
 ```
 
 For example, if you want to see the slots on `e2337.chtc.wisc.edu` (in the CHTC pool):
 
 ``` console
-username@learn $ condor_status e2337.chtc.wisc.edu
+username@ap1 $ condor_status e2337.chtc.wisc.edu
 ```
 
 To list a specific slot on a machine:
 
 ``` console
-username@learn $ condor_status <slot>@<hostname>
+username@ap1 $ condor_status <slot>@<hostname>
 ```
 
 For example, to see the “first” slot on the machine above:
 
 ``` console
-username@learn $ condor_status [email protected]
+username@ap1 $ condor_status [email protected]
 ```
 
 !!! note
@@ -68,7 +68,7 @@ Viewing a Slot ClassAd
 Just as with `condor_q`, you can use `condor_status` to view the complete ClassAd for a given slot (often confusingly called the “machine” ad):
 
 ``` console
-username@learn $ condor_status -long <slot>@<hostname>
+username@ap1 $ condor_status -long <slot>@<hostname>
 ```
 
 Because slot ClassAds may have 150–200 attributes (or more), it probably makes the most sense to show the ClassAd for a single slot at a time, as shown above.
@@ -91,7 +91,7 @@ Memory = 1024
 
 As you may be able to tell, there is a mix of attributes about the machine as a whole (hence the name “machine ad”) and about the slot in particular.
 
-Go ahead and examine a machine ClassAd now. I suggest looking at one of the slots on, say, `e2337.chtc.wisc.edu` because of its relatively simple configuration.
+Go ahead and examine a machine ClassAd now.
 
 Viewing Slots by ClassAd Expression
 -----------------------------------
@@ -101,15 +101,15 @@ Often, it is helpful to view slots that meet some particular criteria. For examp
 For example, suppose we want to list all slots that are running Scientific Linux 7 (operating system) and have at least 16 GB memory available. Note that memory is reported in units of Megabytes. The command is:
 
 ``` console
-username@learn $ condor_status -constraint 'OpSysAndVer == "CentOS7" && Memory >= 16000'
+username@ap1 $ condor_status -constraint 'OpSysAndVer == "CentOS7" && Memory >= 16000'
 ```
 
 !!! note
     Be very careful with using quote characters appropriately in these commands.
     In the example above, the single quotes (`'`) are for the shell, so that the entire expression is passed to
     `condor_status` untouched, and the double quotes (`"`) surround a string value within the expression itself.
 
-Currently on CHTC, there are only a few slots that meet these criteria (our high-memory servers, mainly used for metagenomics assemblies).
+Currently on PATh, there are only a few slots that meet these criteria (our high-memory servers, mainly used for metagenomics assemblies).
 
 If you are interested in learning more about writing ClassAd expressions, look at section 4.1 and especially 4.1.4 of the HTCondor Manual. This is definitely advanced material, so if you do not want to read it, that is fine. But if you do, take some time to practice writing expressions for the `condor_status -constraint` command.
 
@@ -125,7 +125,7 @@ The `condor_status` command accepts the same `-autoformat` (`-af`) options that
 For example, I was curious about the host name and operating system of the slots with more than 32GB of memory:
 
 ``` console
-username@learn $ condor_status -af Machine -af OpSysAndVer -constraint 'Memory >= 32000'
+username@ap1 $ condor_status -af Machine -af OpSysAndVer -constraint 'Memory >= 32000'
 ```
 
 If you like, spend a few minutes now or later experimenting with `condor_status` formatting.

docs/materials/osg/part1-ex3-hardware-diffs.md

@@ -66,7 +66,7 @@ we will create a **new** submit file with the queue…in syntax
 and change the value of our parameter (`request_memory`) for each batch of jobs.
 
 1.  Log in or switch back to `ap1.facility.path-cc.io` (yes, back to PATh!)
-1.  Create and change into a new subdirectory called `osg-ex14`
+1.  Create and change into a new subdirectory called `osg-ex13`
 1.  Create a submit file named `sleep.sub` that executes the command `/bin/sleep 300`.
 
     !!! note
@@ -108,7 +108,7 @@ Now you will do essentially the same thing on the OSPool.
 
 1.  Log in or switch to `ap40.uw.osg-htc.org`
 
-1.  Copy the `osg-ex14` directory from the [section above](#checking-chtc-memory-availability)
+1.  Copy the `osg-ex13` directory from the [section above](#checking-chtc-memory-availability)
     from `ap1.facility.path-cc.io` to `ap40.uw.osg-htc.org`
 
     If you get stuck during the copying process, refer to [OSG exercise 1.1](part1-ex1-login-scp.md).

docs/materials/scaling/part1-ex1-organization.md

@@ -16,7 +16,7 @@ Make sure you are logged into `ap40.uw.osg-htc.org`.
 
 To get the files for this exercise:
 
-1.  Type `wget https://github.com/osg-htc/user-school-2023/raw/main/docs/materials/scaling/files/osgus23-day4-ex11-organizing-files.tar.gz` to download the tarball.
+1.  Type `wget https://github.com/osg-htc/school-2024/raw/main/docs/materials/scaling/files/osgus23-day4-ex11-organizing-files.tar.gz` to download the tarball.
 1.  As you learned earlier, expand this tarball file; it will create a `organizing-files` directory.
 1.  Change to that directory, or create a separate one for this exercise and copy the files in.
 

docs/materials/software/part1-ex4-apptainer-build.md

@@ -93,7 +93,7 @@ allow us to test our new container.
 1. Try running: 
 
 		:::console
-		$ singularity shell first-image.sif
+		$ singularity shell py-cowsay.sif
 
 1. Then try running the `hello-cow.py` script: 
 

docs/materials/software/part3-ex1-apptainer-recipes.md

@@ -16,8 +16,8 @@ the basic options and syntax of the "build" or definition file.
 |---------|
 | [Bootstrap/From](#where-to-start) | 
 | [%files](#files-needed-for-building-or-running) | 
-| [%files](#commnds-to-install) | 
-| [%files](#environment) | 
+| [%post](#commands-to-install) | 
+| [%env](#environment) | 
 
 
 Where to start