From c9a03a867bd6c28325d64a0db0c0ec7eaffb13ed Mon Sep 17 00:00:00 2001 From: Cameron Smith Date: Wed, 17 May 2023 13:28:29 -0400 Subject: [PATCH] add draft for distributed pipeline (#264) * add gitignore * add argo pipeline dependencies * add environment log component * add pipeline construction method * add run pipeline script * add envrc example --- .github/workflows/cml.yml | 3 - poetry.lock | 897 ++++++++++++++++-- pyproject.toml | 80 +- reproducibility/pipelines/argo/.envrc.example | 7 + reproducibility/pipelines/argo/.gitignore | 4 + reproducibility/pipelines/argo/__init__.py | 0 .../components/environment_log_component.py | 75 ++ .../pipelines/argo/construct_pipeline.py | 39 + .../pipelines/argo/run_pipeline.py | 79 ++ 9 files changed, 1082 insertions(+), 102 deletions(-) create mode 100644 reproducibility/pipelines/argo/.envrc.example create mode 100644 reproducibility/pipelines/argo/.gitignore create mode 100644 reproducibility/pipelines/argo/__init__.py create mode 100644 reproducibility/pipelines/argo/components/environment_log_component.py create mode 100644 reproducibility/pipelines/argo/construct_pipeline.py create mode 100644 reproducibility/pipelines/argo/run_pipeline.py diff --git a/.github/workflows/cml.yml b/.github/workflows/cml.yml index 28ddd734a..57840c91c 100644 --- a/.github/workflows/cml.yml +++ b/.github/workflows/cml.yml @@ -21,9 +21,6 @@ on: - "reproducibility/figures/*.py" - "reproducibility/figures/dvc.*" - "reproducibility/figures/config.yaml" - pull_request: - branches: - - master # Review/set variables via gh CLI: # diff --git a/poetry.lock b/poetry.lock index 77c58da63..8facb1673 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry and should not be changed by hand. +# This file is automatically @generated by Poetry 1.4.2 and should not be changed by hand. [[package]] name = "absl-py" @@ -1249,6 +1249,24 @@ files = [ {file = "decorator-5.1.1.tar.gz", hash = "sha256:637996211036b6385ef91435e4fae22989472f9d571faba8927ba8253acbc330"}, ] +[[package]] +name = "deprecated" +version = "1.2.13" +description = "Python @deprecated decorator to deprecate old python classes, functions or methods." +category = "main" +optional = true +python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" +files = [ + {file = "Deprecated-1.2.13-py2.py3-none-any.whl", hash = "sha256:64756e3e14c8c5eea9795d93c524551432a0be75629f8f29e67ab8caf076c76d"}, + {file = "Deprecated-1.2.13.tar.gz", hash = "sha256:43ac5335da90c31c24ba028af536a91d41d53f9e6901ddb021bcc572ce44e38d"}, +] + +[package.dependencies] +wrapt = ">=1.10,<2" + +[package.extras] +dev = ["PyTest", "PyTest (<5)", "PyTest-Cov", "PyTest-Cov (<2.6)", "bump2version (<1)", "configparser (<5)", "importlib-metadata (<3)", "importlib-resources (<4)", "sphinx (<2)", "sphinxcontrib-websupport (<2)", "tox", "zipp (<2)"] + [[package]] name = "desert" version = "2022.9.22" @@ -1409,6 +1427,18 @@ files = [ [package.dependencies] six = "*" +[[package]] +name = "docstring-parser" +version = "0.15" +description = "Parse Python docstrings in reST, Google and Numpydoc format" +category = "main" +optional = true +python-versions = ">=3.6,<4.0" +files = [ + {file = "docstring_parser-0.15-py3-none-any.whl", hash = "sha256:d1679b86250d269d06a99670924d6bce45adc00b08069dae8c47d98e89b667a9"}, + {file = "docstring_parser-0.15.tar.gz", hash = "sha256:48ddc093e8b1865899956fcc03b03e66bb7240c310fac5af81814580c55bf682"}, +] + [[package]] name = "docutils" version = "0.19" @@ -1921,6 +1951,21 @@ files = [ docs = ["furo (>=2023.3.27)", "sphinx (>=6.1.3)", "sphinx-autodoc-typehints (>=1.22,!=1.23.4)"] testing = ["covdefaults (>=2.3)", "coverage (>=7.2.2)", "diff-cover (>=7.5)", "pytest (>=7.2.2)", "pytest-cov (>=4)", "pytest-mock (>=3.10)", "pytest-timeout (>=2.1)"] +[[package]] +name = "fire" +version = "0.5.0" +description = "A library for automatically generating command line interfaces." +category = "main" +optional = true +python-versions = "*" +files = [ + {file = "fire-0.5.0.tar.gz", hash = "sha256:a6b0d49e98c8963910021f92bba66f65ab440da2982b78eb1bbf95a0a34aacc6"}, +] + +[package.dependencies] +six = "*" +termcolor = "*" + [[package]] name = "flake8" version = "6.0.0" @@ -2340,6 +2385,8 @@ files = [ [package.dependencies] google-auth = ">=2.14.1,<3.0dev" googleapis-common-protos = ">=1.56.2,<2.0dev" +grpcio = {version = ">=1.33.2,<2.0dev", optional = true, markers = "extra == \"grpc\""} +grpcio-status = {version = ">=1.33.2,<2.0dev", optional = true, markers = "extra == \"grpc\""} protobuf = ">=3.19.5,<3.20.0 || >3.20.0,<3.20.1 || >3.20.1,<4.21.0 || >4.21.0,<4.21.1 || >4.21.1,<4.21.2 || >4.21.2,<4.21.3 || >4.21.3,<4.21.4 || >4.21.4,<4.21.5 || >4.21.5,<5.0.0dev" requests = ">=2.18.0,<3.0.0dev" @@ -2348,6 +2395,26 @@ grpc = ["grpcio (>=1.33.2,<2.0dev)", "grpcio (>=1.49.1,<2.0dev)", "grpcio-status grpcgcp = ["grpcio-gcp (>=0.2.2,<1.0dev)"] grpcio-gcp = ["grpcio-gcp (>=0.2.2,<1.0dev)"] +[[package]] +name = "google-api-python-client" +version = "1.12.11" +description = "Google API Client Library for Python" +category = "main" +optional = true +python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*" +files = [ + {file = "google-api-python-client-1.12.11.tar.gz", hash = "sha256:1b4bd42a46321e13c0542a9e4d96fa05d73626f07b39f83a73a947d70ca706a9"}, + {file = "google_api_python_client-1.12.11-py2.py3-none-any.whl", hash = "sha256:7e0a1a265c8d3088ee1987778c72683fcb376e32bada8d7767162bd9c503fd9b"}, +] + +[package.dependencies] +google-api-core = {version = ">=1.21.0,<3dev", markers = "python_version >= \"3\""} +google-auth = {version = ">=1.16.0,<3dev", markers = "python_version >= \"3\""} +google-auth-httplib2 = ">=0.0.3" +httplib2 = ">=0.15.0,<1dev" +six = ">=1.13.0,<2dev" +uritemplate = ">=3.0.0,<4dev" + [[package]] name = "google-auth" version = "2.17.3" @@ -2373,6 +2440,23 @@ pyopenssl = ["cryptography (>=38.0.3)", "pyopenssl (>=20.0.0)"] reauth = ["pyu2f (>=0.1.5)"] requests = ["requests (>=2.20.0,<3.0.0dev)"] +[[package]] +name = "google-auth-httplib2" +version = "0.1.0" +description = "Google Authentication Library: httplib2 transport" +category = "main" +optional = true +python-versions = "*" +files = [ + {file = "google-auth-httplib2-0.1.0.tar.gz", hash = "sha256:a07c39fd632becacd3f07718dfd6021bf396978f03ad3ce4321d060015cc30ac"}, + {file = "google_auth_httplib2-0.1.0-py2.py3-none-any.whl", hash = "sha256:31e49c36c6b5643b57e82617cb3e021e3e1d2df9da63af67252c02fa9c1f4a10"}, +] + +[package.dependencies] +google-auth = "*" +httplib2 = ">=0.15.0" +six = "*" + [[package]] name = "google-auth-oauthlib" version = "1.0.0" @@ -2392,6 +2476,77 @@ requests-oauthlib = ">=0.7.0" [package.extras] tool = ["click (>=6.0.0)"] +[[package]] +name = "google-cloud-aiplatform" +version = "1.25.0" +description = "Vertex AI API client library" +category = "main" +optional = true +python-versions = ">=3.7" +files = [ + {file = "google-cloud-aiplatform-1.25.0.tar.gz", hash = "sha256:766d545890bee7fa15bc76ef363089fd7a2964e9a0abc2e1bbca1f32055da3cf"}, + {file = "google_cloud_aiplatform-1.25.0-py2.py3-none-any.whl", hash = "sha256:a0fa7e58e5d5a3f7b29d0698216d79babc8402da7c19a4ee83a6ef590a8fe14f"}, +] + +[package.dependencies] +google-api-core = {version = ">=1.32.0,<2.0.0 || >=2.8.0,<3.0.0dev", extras = ["grpc"]} +google-cloud-bigquery = ">=1.15.0,<4.0.0dev" +google-cloud-resource-manager = ">=1.3.3,<3.0.0dev" +google-cloud-storage = ">=1.32.0,<3.0.0dev" +packaging = ">=14.3" +proto-plus = ">=1.22.0,<2.0.0dev" +protobuf = ">=3.19.5,<3.20.0 || >3.20.0,<3.20.1 || >3.20.1,<4.21.0 || >4.21.0,<4.21.1 || >4.21.1,<4.21.2 || >4.21.2,<4.21.3 || >4.21.3,<4.21.4 || >4.21.4,<4.21.5 || >4.21.5,<5.0.0dev" +shapely = "<2.0.0" + +[package.extras] +autologging = ["mlflow (>=1.27.0,<=2.1.1)"] +cloud-profiler = ["tensorboard-plugin-profile (>=2.4.0,<3.0.0dev)", 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">=1.25.0,<3.0dev" [package.extras] grpc = ["grpcio (>=1.38.0,<2.0dev)"] +[[package]] +name = "google-cloud-notebooks" +version = "1.7.0" +description = "Google Cloud Notebooks API client library" +category = "main" +optional = true +python-versions = ">=3.7" +files = [ + {file = "google-cloud-notebooks-1.7.0.tar.gz", hash = "sha256:dac73a5cd983a4344d1fa96f9a8e5849b0ff75d7a5fdde921023a2ef4566e75e"}, + {file = "google_cloud_notebooks-1.7.0-py2.py3-none-any.whl", hash = "sha256:8fbffb7ba535fc02c61f135d8863324a5a2d20dd58cafaae592f0b0172d6bdab"}, +] + +[package.dependencies] +google-api-core = {version = ">=1.34.0,<2.0.0 || >=2.11.0,<3.0.0dev", extras = ["grpc"]} +grpc-google-iam-v1 = ">=0.12.4,<1.0.0dev" +proto-plus = ">=1.22.0,<2.0.0dev" +protobuf = ">=3.19.5,<3.20.0 || >3.20.0,<3.20.1 || >3.20.1,<4.21.0 || >4.21.0,<4.21.1 || >4.21.1,<4.21.2 || >4.21.2,<4.21.3 || >4.21.3,<4.21.4 || >4.21.4,<4.21.5 || >4.21.5,<5.0.0dev" + +[[package]] +name = "google-cloud-pipeline-components" +version = 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lock-version = "2.0" python-versions = ">=3.9, <3.11" -content-hash = "5fff82b8b9b5dd7414ac1c042edc61439ccc41bf762a87cdf968fcec7a630406" +content-hash = "eda4e6b49c6452dbc19e4c502944ec402ac172a81ae8c0f778d1421357b1f41e" diff --git a/pyproject.toml b/pyproject.toml index e0d2ed066..8bfd06d91 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -86,6 +86,10 @@ dvc-gs = { version = ">=2.20.0", optional = true } jupyter-core = { version = ">=5.1.3", optional = true, source = "pypi" } pyvis = { version = ">=0.3.2", optional = true } hypothesis = {version = ">=6.71.0", optional = true } +kfp = { version = ">=1.8.18", optional = true } +google-cloud-aiplatform = { version = ">=1.24.1", optional = true } +google-cloud-pipeline-components = { version = ">=1.0.43", optional = true } +python-dotenv = { version = ">=1.0.0", optional = true } [tool.conda-lock.dependencies] seaborn = { version = "0.11.2", source = "conda-forge" } @@ -104,39 +108,49 @@ platforms = [ [tool.poetry.extras] dev = [ - "Pygments", - "black", - "coverage", - "darglint", - "flake8", - "flake8-bandit", - "flake8-bugbear", - "flake8-docstrings", - "flake8-rst-docstrings", - "furo", - "hypothesis", - "isort", - "ipython", - "mypy", - "pep8-naming", - "pre-commit", - "pre-commit-hooks", - "pytest", - "pyupgrade", - "pyvis", - "safety", - "sphinx", - "sphinx-autobuild", - "sphinx-click", - "typeguard", - "xdoctest", - "myst-parser", - "dparse", - "pytest-cov", - "pytest-mock", - "poethepoet", - "dvc-gs", - "jupyter-core" + "black", + "coverage", + "darglint", + "dparse", + "dvc-gs", + "flake8-bandit", + "flake8-bugbear", + "flake8-docstrings", + "flake8-rst-docstrings", + "flake8", + "hypothesis", + "ipython", + "isort", + "jupyter-core", + "mypy", + "pep8-naming", + "poethepoet", + "pre-commit-hooks", + "pre-commit", + "Pygments", + "pytest-cov", + "pytest-mock", + "pytest", + "pyupgrade", + "pyvis", + "safety", + "typeguard", + "xdoctest", + ] + + docs = [ + "furo", + "myst-parser", + "sphinx-autobuild", + "sphinx-click", + "sphinx", + ] + + pipeline = [ + "google-cloud-aiplatform", + "google-cloud-pipeline-components", + "kfp", + "python-dotenv", ] diff --git a/reproducibility/pipelines/argo/.envrc.example b/reproducibility/pipelines/argo/.envrc.example new file mode 100644 index 000000000..af774c85e --- /dev/null +++ b/reproducibility/pipelines/argo/.envrc.example @@ -0,0 +1,7 @@ +export ARGO_PIPELINE_BASE_IMAGE=us-central1-docker.pkg.dev/project/package/image:hash +export ARGO_PIPELINE_ROOT=gs://storagebucket +export ARGO_ENVIRONMENT_LOG_MACHINE_TYPE=n1-standard-4 +export ARGO_ACCELERATOR_TYPE=NVIDIA_TESLA_T4 +export ARGO_ACCELERATOR_COUNT=1 +export ARGO_GCP_PROJECT_ID=project +export ARGO_GCP_REGION=us-central1 diff --git a/reproducibility/pipelines/argo/.gitignore b/reproducibility/pipelines/argo/.gitignore new file mode 100644 index 000000000..07d0df61e --- /dev/null +++ b/reproducibility/pipelines/argo/.gitignore @@ -0,0 +1,4 @@ +outputs/ +multirun/ +testing/ +.envrc diff --git a/reproducibility/pipelines/argo/__init__.py b/reproducibility/pipelines/argo/__init__.py new file mode 100644 index 000000000..e69de29bb diff --git a/reproducibility/pipelines/argo/components/environment_log_component.py b/reproducibility/pipelines/argo/components/environment_log_component.py new file mode 100644 index 000000000..75d021fca --- /dev/null +++ b/reproducibility/pipelines/argo/components/environment_log_component.py @@ -0,0 +1,75 @@ +from google_cloud_pipeline_components.v1.custom_job import ( + create_custom_training_job_from_component, +) +from kfp.v2 import dsl +from kfp.v2.dsl import Dataset # , Input, Model, Artifact +from kfp.v2.dsl import Output + + +def create_environment_log_component( + base_image: str, + display_name: str, + machine_type: str, + accelerator_type: str, + accelerator_count: int, +): + @dsl.component( + base_image=base_image, + ) + def environment_log(message: str, environment_info: Output[Dataset]): + print(message) + print("Active conda environment and installed packages:") + import os + import subprocess + + commands = [ + ["ls", "-alh"], + ["pwd"], + ["which", "python"], + ["python", "--version"], + ["mamba", "info"], + ["mamba", "info", "--envs"], + ["mamba", "list"], + ["pip", "list"], + ["pip", "freeze"], + ["ls", "-alh", "/usr/local/nvidia/lib64"], + ["/usr/local/nvidia/bin/nvidia-smi"], + ] + + env_variables = ["NVIDIA_VISIBLE_DEVICES", "PATH", "LD_LIBRARY_PATH"] + + with open(environment_info.path, "a") as f: + for command in commands: + f.write(" ".join(command) + "\n") + result = subprocess.run(command, capture_output=True, text=True) + f.write(result.stdout + "\n" + result.stderr + "\n") + print(result.stdout) + print(result.stderr) + + for var in env_variables: + f.write(f"{var}: {os.environ.get(var, 'Not Found')}\n") + print(f"{var}: {os.environ.get(var, 'Not Found')}") + + import torch + + print(torch.__version__) + + if torch.cuda.is_available(): + print("A CUDA-enabled GPU is available.") + for device in range(torch.cuda.device_count()): + print(f" Device: {device}") + print(f" Name: {torch.cuda.get_device_name(device)}") + print( + f" Compute capability: {torch.cuda.get_device_capability(device)}" + ) + print(f" Properties: {torch.cuda.get_device_properties(device)}") + else: + print("A CUDA-enabled GPU is not available.") + + return create_custom_training_job_from_component( + environment_log, + display_name=display_name, + machine_type=machine_type, + accelerator_type=accelerator_type, + accelerator_count=accelerator_count, + ) diff --git a/reproducibility/pipelines/argo/construct_pipeline.py b/reproducibility/pipelines/argo/construct_pipeline.py new file mode 100644 index 000000000..b2a56a810 --- /dev/null +++ b/reproducibility/pipelines/argo/construct_pipeline.py @@ -0,0 +1,39 @@ +import os +from typing import Callable + +from dotenv import load_dotenv +from hydra_zen import make_custom_builds_fn +from kfp.v2 import dsl +from kfp.v2.dsl import Dataset # Output, Input, Model, Artifact + + +load_dotenv(".envrc") + + +base_image = os.getenv("ARGO_PIPELINE_BASE_IMAGE") +pipeline_root = os.getenv("ARGO_PIPELINE_ROOT") + +builds = make_custom_builds_fn(populate_full_signature=True) + + +def create_complete_pipeline( + pipeline_root: str, + environment_log_component: Callable, +): + @dsl.pipeline( + name="complete pipeline", + description="complete run of pipeline", + pipeline_root=pipeline_root, + ) + def complete_pipeline( + project: str, + location: str, + message: str, + ) -> Dataset: + return environment_log_component( + project=project, + location=location, + message=message, + ).outputs["environment_info"] + + return complete_pipeline diff --git a/reproducibility/pipelines/argo/run_pipeline.py b/reproducibility/pipelines/argo/run_pipeline.py new file mode 100644 index 000000000..d818597ff --- /dev/null +++ b/reproducibility/pipelines/argo/run_pipeline.py @@ -0,0 +1,79 @@ +import os +from typing import Callable + +from components.environment_log_component import create_environment_log_component +from construct_pipeline import create_complete_pipeline +from dotenv import load_dotenv +from google.cloud import aiplatform +from hydra_zen import instantiate +from hydra_zen import make_config +from hydra_zen import make_custom_builds_fn +from hydra_zen import store +from hydra_zen import zen +from kfp.v2 import dsl +from kfp.v2.dsl import Dataset # Output, Input, Model, Artifact + + +load_dotenv(".envrc") + + +base_image = os.getenv("ARGO_PIPELINE_BASE_IMAGE") +pipeline_root = os.getenv("ARGO_PIPELINE_ROOT") + +builds = make_custom_builds_fn(populate_full_signature=True) +pbuilds = make_custom_builds_fn(zen_partial=True, populate_full_signature=True) + +EnvironmentLogComponentConf = builds(create_environment_log_component) +base_envlog = EnvironmentLogComponentConf( + base_image=base_image, + display_name="environment_log_component", + machine_type=os.environ["ARGO_ENVIRONMENT_LOG_MACHINE_TYPE"], + accelerator_type=os.environ["ARGO_ACCELERATOR_TYPE"], + accelerator_count=int(os.environ["ARGO_ACCELERATOR_COUNT"]), +) +envlog_store = store(group="job/environment_log_component") +envlog_store(base_envlog, name="base_for_envlog_component") + + +PipelineConf = builds( + create_complete_pipeline, +) +base_pipeline = PipelineConf( + pipeline_root=pipeline_root, + environment_log_component=base_envlog, +) + +pipeline_store = store(group="job/pipeline") +pipeline_store(base_pipeline, name="base_pipeline") + +aiplatform.pipeline_jobs = aiplatform.PipelineJob +JobConf = builds( + aiplatform.PipelineJob.from_pipeline_func, +) +base_job = JobConf( + pipeline_func=base_pipeline, + parameter_values={ + "project": os.environ["ARGO_GCP_PROJECT_ID"], + "location": os.environ["ARGO_GCP_REGION"], + "message": "message text", + }, +) + +job_store = store(group="job") +job_store(base_job, name="base_job") + + +@store(name="distributed_pipeline", hydra_defaults=["_self_", {"job": "base_job"}]) +def task_function(job): + print("submitting pipeline") + print(job) + job.submit() + + +if __name__ == "__main__": + store.add_to_hydra_store() + zen(task_function).hydra_main( + config_name="distributed_pipeline", + version_base="1.1", + config_path=".", + )