From b245b4b27d8bcd5930db0afe64ab7e5a781ffc93 Mon Sep 17 00:00:00 2001 From: Joshua Nadeau Date: Tue, 18 Jun 2024 12:37:54 -0400 Subject: [PATCH 1/3] Add helpers for starting custom Dataproc cluster --- .../deployctl/subcommands/dataproc_cluster.py | 165 ++++++++++++++++++ 1 file changed, 165 insertions(+) diff --git a/deploy/deployctl/subcommands/dataproc_cluster.py b/deploy/deployctl/subcommands/dataproc_cluster.py index e6f5249d3..5fba452a0 100644 --- a/deploy/deployctl/subcommands/dataproc_cluster.py +++ b/deploy/deployctl/subcommands/dataproc_cluster.py @@ -1,4 +1,5 @@ import argparse +import json import os import subprocess import sys @@ -10,6 +11,70 @@ DATA_PIPELINE_DIRECTORY = os.path.abspath(os.path.join(os.path.dirname(__file__), "../../../data-pipeline")) +# The below regions and properties constantsare specified in +# the hailctl command to start a Dataproc cluster for Hail. +# They are necessary here for starting clusters using a custom OS images, +# in which case they would not use hailctl. +VEP_SUPPORTED_REGIONS = {"us-central1", "europe-west1", "europe-west2", "australia-southeast1"} +DATAPROC_PROPERTIES = ( + # NOTE: ^#^ specifies # as the delimiter + # Spark properties + "^#^spark:spark.dynamicAllocation.enabled=true" + "#spark:spark.executorEnv.PYTHONHASHSEED=0" + "#spark:spark.app.name=Hail" + # Per Hail docs: the below are necessary to make 'submit' work + "#spark:spark.jars=/opt/conda/miniconda3/lib/python3.10/site-packages/hail/backend/hail-all-spark.jar" + "#spark:spark.driver.extraClassPath=/opt/conda/miniconda3/lib/python3.10/site-packages/hail/backend/hail-all-spark.jar" + "#spark:spark.executor.extraClassPath=./hail-all-spark.jar" + # Spark environment variables + "#spark-env:PYTHONHASHSEED=0" + "#spark-env:PYTHONPATH=/usr/lib/spark/python/lib/py4j-0.10.9.5-src.zip:/usr/lib/spark/python/lib/pyspark.zip" + "#spark-env:SPARK_HOME=/usr/lib/spark/" + "#spark-env:PYSPARK_PYTHON=/opt/conda/default/bin/python" + "#spark-env:PYSPARK_DRIVER_PYTHON=/opt/conda/default/bin/python" + "#spark-env:HAIL_LOG_DIR=/home/hail" + "#spark-env:HAIL_DATAPROC=1" +) + + +def _parse_flags(flags: typing.List[str]) -> typing.Dict: + """Parse a list of string cli flags into dict. + + This function checks both the "--flag=value" and + "--flag value" formats. The former appears in the + "flags" list as: + ["--flag1=val1", "--flag2=val2"...] + which is a little easier to work with than the + second format, which is: + ["--flag1", "val1", "--flag2", "val2", ...] + + It will ignore any flags/values that do not follow + the above two formats. + """ + flags_dict = {} + key = "" + value = "" + for flag in flags: + flag_split = flag.split("=") + if len(flag_split) == 2: + key = flag_split[0].replace("--", "") + if len(flag_split) > 1: + value = flag_split[1] + else: + value = None + + elif flag.startswith("--"): + key = flag.replace("--", "") + elif key: + value = flag + + if key and value: + flags_dict[key] = value + key = "" + value = "" + + return flags_dict + def list_clusters() -> None: if not config.project: @@ -20,10 +85,110 @@ def list_clusters() -> None: ) +def _prep_vep_cluster_options( + cluster_args_dict: typing.Dict, +) -> typing.Dict: + """Adjust cluster creation arguments for VEP. + + Recreates steps from hailctl as seen below: + https://github.com/hail-is/hail/blob/main/hail/python/hailtop/hailctl/dataproc/start.py#L249 + + Necessary for when clusters are created using + custom OS images, which do not use hailctl. + """ + region = cluster_args_dict.get("region", config.region) + if region not in VEP_SUPPORTED_REGIONS: + supported_regions = ", ".join(VEP_SUPPORTED_REGIONS) + raise RuntimeError(f"VEP is only supported in the following regions: {supported_regions}") + + vep_options_dict = { + "secondary-worker-boot-disk-size": "200GB", + "worker-boot-disk-size": "200GB", + "worker-machine-type": "n1-highmem-8", + } + + metadata_value = cluster_args_dict.get("metadata", "") + metadata_list = metadata_value.split(",") if metadata_value else [] + vep_config_path = "/vep_data/vep-gcloud.json" + metadata_list += [ + f"VEP_CONFIG_PATH={vep_config_path}", + f"VEP_CONFIG_URI=file://{vep_config_path}", + f"VEP_REPLICATE={region}", + ] + vep_options_dict["metadata"] = ",".join(metadata_list) + + vep = cluster_args_dict["vep"] + custom_image = cluster_args_dict["image"] + cli_output = subprocess.run( + ["gcloud", "compute", "images", "describe", custom_image, "--format=json"], + capture_output=True, + text=True, + check=True, + ) + image_described = json.loads(cli_output.stdout) + hail_version = image_described["labels"]["hail-version"].replace("-", ".") + vep_gcs_path = f"gs://hail-common/hailctl/dataproc/{hail_version}/vep-{vep}.sh" + init_actions_value = cluster_args_dict.get("initialization-actions", "") + init_actions_list = init_actions_value.split(",") if init_actions_value else [] + init_actions_list = [val for val in init_actions_list if val] + init_actions_list.append(vep_gcs_path) + vep_options_dict["initialization-actions"] = ",".join(init_actions_list) + + return vep_options_dict + + +def start_custom_image_cluster( + name: str, + cluster_args_dict: typing.Dict, +) -> None: + if "vep" in cluster_args_dict: + vep_args_dict = _prep_vep_cluster_options(cluster_args_dict) + cluster_args_dict.update(vep_args_dict) + del cluster_args_dict["vep"] # Not an actual valid gcloud flag + + cluster_args_list = [] + for k, v in cluster_args_dict.items(): + cluster_arg = f"--{k}={v}" + cluster_args_list.append(cluster_arg) + + subprocess.check_output( + [ + "gcloud", + "dataproc", + "clusters", + "create", + name, + f"--project={config.project}", + f"--region={config.region}", + f"--zone={config.zone}", + f"--subnet={config.network_name}-dataproc", + "--tags=dataproc-node", + "--max-idle=1h", + f"--service-account=gnomad-data-pipeline@{config.project}.iam.gserviceaccount.com", + "--scopes=cloud-platform", + f"--properties={DATAPROC_PROPERTIES}", + # Default cluster configs + "--master-machine-type=n1-highmem-8", + "--master-boot-disk-size=100GB", + "--num-masters=1", + "--worker-machine-type=n1-standard-8", + "--worker-boot-disk-size=40GB", + "--num-workers=2", + "--num-secondary-workers=0", + ] + + cluster_args_list # Image flag is included in this var + ) + + def start_cluster(name: str, cluster_args: typing.List[str]) -> None: if not config.project: raise RuntimeError("project configuration is required") + cluster_args_dict = _parse_flags(cluster_args) + if "image" in cluster_args_dict: + return start_custom_image_cluster(name, cluster_args_dict) + # TODO: Add "else" block to confirm with user to use legacy hailctl initialization + with open(os.path.join(DATA_PIPELINE_DIRECTORY, "requirements.txt")) as requirements_file: requirements_hail_version = next( (line.strip().split("==")[1] for line in requirements_file if line.strip().startswith("hail==")), None From 8b2b2ebaa99774a96230e1fcb25b4003627b2d4c Mon Sep 17 00:00:00 2001 From: Joshua Nadeau Date: Tue, 18 Jun 2024 12:38:29 -0400 Subject: [PATCH 2/3] Add note on starting Dataproc with custom img --- data-pipeline/README.md | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/data-pipeline/README.md b/data-pipeline/README.md index eba25ff99..e3d9f6cfb 100644 --- a/data-pipeline/README.md +++ b/data-pipeline/README.md @@ -58,6 +58,11 @@ The ClinVar pipelines must be run on clusters with an appropriate version of VEP ./deployctl dataproc-cluster start ``` + NOTE: Starting with `gnomad version 4.1`, it is highly recommended to specify a + custom OS image that was built for that gnomAD version. To see these images, run + `gcloud compute images list --filter="family=dataproc-custom-image"`. You can then + pass the desired image name to the above `start` command using the `--image` flag. + - Run a pipeline. A list of all pipelines can be seen with `./deployctl data-pipeline run --help`. From 775719461d07b42aadff6e2a010245f9da5f3654 Mon Sep 17 00:00:00 2001 From: Joshua Nadeau Date: Tue, 18 Jun 2024 12:39:26 -0400 Subject: [PATCH 3/3] Remove poetry from data-pipeline src --- data-pipeline/poetry.lock | 3395 -------------------------- data-pipeline/pyproject.toml | 27 - data-pipeline/update-requirements.sh | 3 - 3 files changed, 3425 deletions(-) delete mode 100644 data-pipeline/poetry.lock delete mode 100755 data-pipeline/update-requirements.sh diff --git a/data-pipeline/poetry.lock b/data-pipeline/poetry.lock deleted file mode 100644 index e09be346d..000000000 --- a/data-pipeline/poetry.lock +++ /dev/null @@ -1,3395 +0,0 @@ -[[package]] -name = "aiodns" -version = "2.0.0" -description = "Simple DNS resolver for asyncio" -category = "dev" -optional = false -python-versions = "*" - -[package.dependencies] -pycares = ">=3.0.0" - -[[package]] -name = "aiohttp" -version = "3.8.5" -description = "Async http client/server framework (asyncio)" -category = "dev" -optional = false -python-versions = ">=3.6" - 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-[tool.poetry.dependencies] -python = "^3.9" -elasticsearch = "7.17.9" -tqdm = "^4.66.1" -loguru = "^0.7.2" -attrs = "^23.1.0" -cattrs = "^23.1.2" - -[tool.poetry.group.dev.dependencies] -hail = "^0.2.122" -pytest = "^7.4.2" -ipython = "^8.15.0" -ruff = "^0.0.290" -black = "^23.9.1" -pyright = "^1.1.327" - -[build-system] -requires = ["poetry-core"] -build-backend = "poetry.core.masonry.api" - [tool.black] line-length = 120 diff --git a/data-pipeline/update-requirements.sh b/data-pipeline/update-requirements.sh deleted file mode 100755 index a44236630..000000000 --- a/data-pipeline/update-requirements.sh +++ /dev/null @@ -1,3 +0,0 @@ -#!/usr/bin/env bash -# -poetry export --without-hashes --with dev >requirements.txt