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[WIP] 6054 Integrate azureml for autorunner training #6088
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76f3737
➕ Add minimum requirements for triggering AzureML
peterhessey c762d9e
Set AzureML to SDK v1 only
peterhessey 6288cdc
🚧 Set up AzureML environment file
peterhessey 9d0b98f
✨ Enable job submission to run correct command
peterhessey dc8101b
📌 Add hi-ml to AzureML env
peterhessey 2b88637
📌 AzureML environment working
peterhessey 136ec66
🚧 Enable configuring training using task.yaml
peterhessey 49dbb04
🚧 Pass in azureml args as dict
peterhessey c4b8d4e
🚧 Fix AzureML training arg parsing
peterhessey ce16775
🐛 🚧 Fix training to work with AzureML dataroot
peterhessey f5ea9d6
🚧 Attempt to run on Prostate data
peterhessey 218cb8b
🔇 Remove old logs + configs
peterhessey f547930
🙈 Update gitignore for azureml_configs
peterhessey 9a1e7c7
🐛 Fix creating local work_dir when running in Azure
peterhessey 4c024bc
🙈 🐛 Update gitignore and fix work dir creation
peterhessey e6e3456
🚨 Pass linting tests
peterhessey b7cf860
Merge branch 'Project-MONAI:dev' into 6054-integrate-azureml-for-auto…
peterhessey d35d6e7
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] 2ed7ab0
🐛 Update optional imports
peterhessey 1d40819
Merge branch '6054-integrate-azureml-for-autorunner-training' of http…
peterhessey a3342e4
DCO Remediation Commit for Peter Hessey <[email protected]>
peterhessey 91d7320
Fix mypy
peterhessey 244cf81
📌 Pin packages to remove Azure warnings
peterhessey d7d2af8
✅ 🚧 Add azureml auto3dseg test for heart data
peterhessey dcfee01
🚧 Start building AzureML test using synthetic data
peterhessey 4145a78
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] aeec9f4
Merge branch 'Project-MONAI:dev' into 6054-integrate-azureml-for-auto…
peterhessey e3eacf4
🎨 Restructure auto3dseg synth data functions
peterhessey 9c0cc4d
✅ Add synthetic data test
peterhessey 0eb2cd5
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] 301dc7d
📌 Update azureml env and remove configs
peterhessey 53db45b
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] 1103209
Merge branch 'Project-MONAI:dev' into 6054-integrate-azureml-for-auto…
peterhessey 1d9c2f2
Update setup.py
peterhessey 0f39701
Merge branch '6054-integrate-azureml-for-autorunner-training' of http…
peterhessey 8a83655
💄 Fix styling
peterhessey b9e5bc7
💄 Fix styling
peterhessey 18237ae
DCO Remediation Commit for Peter Hessey <[email protected]>
peterhessey b63142c
Fix typing
peterhessey 3a098fa
Fix typing
peterhessey 4a8408b
Merge branch '6054-integrate-azureml-for-autorunner-training' of http…
peterhessey 5e9fa1c
Remove git merge content
peterhessey a53b32b
Merge branch 'dev' into 6054-integrate-azureml-for-autorunner-training
peterhessey 26bc937
Merge branch '6054-integrate-azureml-for-autorunner-training' of http…
peterhessey 8f8e63f
Merge branch 'dev' into 6054-integrate-azureml-for-autorunner-training
peterhessey 13456a2
Merge branch '6054-integrate-azureml-for-autorunner-training' of http…
peterhessey c96b66a
Add hi-ml-azure to dev reqs
peterhessey ac9ec8c
Test creating separate AML class
peterhessey 354fde1
✅ Pass Auto3dSeg AzureML test with subclass
peterhessey 3a60f6d
📝 Add docstrings
peterhessey a800423
📝 Add more docstrings
peterhessey 662c6b4
Add typing and docstrings
peterhessey 468f893
DCO Remediation Commit for Peter Hessey <[email protected]>
peterhessey 34f51b1
Merge branch 'dev' into 6054-integrate-azureml-for-autorunner-training
peterhessey 45e482f
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] 838abb7
Styling fixes
peterhessey 364f311
Merge branch '6054-integrate-azureml-for-autorunner-training' of http…
peterhessey b7292f4
Merge branch 'dev' into 6054-integrate-azureml-for-autorunner-training
peterhessey a073b76
Remove num_fold arg
peterhessey 229a48e
Remove need for --azureml flag
peterhessey a43bd9b
🚧 Reduce AzureML environment complexity
peterhessey fe49bee
Update env again
peterhessey 55d2aaf
DCO Remediation Commit for Peter Hessey <[email protected]>
peterhessey 2b642a5
Add fire to AzureML environment
peterhessey d66c65f
Remove num_fold arg from AMLAutoRunner
peterhessey 0967115
🚧 🐛 Bugfix and env update
peterhessey 345c191
DCO Remediation Commit for Peter Hessey <[email protected]>
peterhessey b8644ff
Merge remote-tracking branch 'upstream/dev' into 6054-integrate-azure…
peterhessey ff5c4f4
mypy fixes
peterhessey 4c275b3
Merge remote-tracking branch 'upstream/dev' into 6054-integrate-azure…
peterhessey 510b141
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] 643d713
Black fixes
peterhessey d81bf97
Merge branch 'dev' into 6054-integrate-azureml-for-autorunner-training
peterhessey 86adbdf
Merge branch 'dev' into 6054-integrate-azureml-for-autorunner-training
peterhessey 2e9c6a1
Merge remote-tracking branch 'upstream/dev' into 6054-integrate-azure…
peterhessey 4833e13
Minor fixes
peterhessey File filter
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,3 @@ | ||
| tests/ | ||
| docs/ | ||
| monai/ |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,240 @@ | ||
| name: monai-azureml | ||
| channels: | ||
| - pytorch | ||
| - nvidia | ||
| - defaults | ||
| dependencies: | ||
| - _libgcc_mutex=0.1=main | ||
| - _openmp_mutex=5.1=1_gnu | ||
| - blas=1.0=mkl | ||
| - brotlipy=0.7.0=py38h27cfd23_1003 | ||
| - bzip2=1.0.8=h7b6447c_0 | ||
| - ca-certificates=2023.01.10=h06a4308_0 | ||
| - certifi=2022.12.7=py38h06a4308_0 | ||
| - cffi=1.15.1=py38h5eee18b_3 | ||
| - charset-normalizer=2.0.4=pyhd3eb1b0_0 | ||
| - cryptography=39.0.1=py38h9ce1e76_0 | ||
| - cuda-cudart=11.7.99=0 | ||
| - cuda-cupti=11.7.101=0 | ||
| - cuda-libraries=11.7.1=0 | ||
| - cuda-nvrtc=11.7.99=0 | ||
| - cuda-nvtx=11.7.91=0 | ||
| - cuda-runtime=11.7.1=0 | ||
| - ffmpeg=4.3=hf484d3e_0 | ||
| - filelock=3.9.0=py38h06a4308_0 | ||
| - flit-core=3.8.0=py38h06a4308_0 | ||
| - freetype=2.12.1=h4a9f257_0 | ||
| - giflib=5.2.1=h5eee18b_3 | ||
| - gmp=6.2.1=h295c915_3 | ||
| - gmpy2=2.1.2=py38heeb90bb_0 | ||
| - gnutls=3.6.15=he1e5248_0 | ||
| - idna=3.4=py38h06a4308_0 | ||
| - intel-openmp=2021.4.0=h06a4308_3561 | ||
| - jinja2=3.1.2=py38h06a4308_0 | ||
| - jpeg=9e=h5eee18b_1 | ||
| - lame=3.100=h7b6447c_0 | ||
| - lcms2=2.12=h3be6417_0 | ||
| - ld_impl_linux-64=2.38=h1181459_1 | ||
| - lerc=3.0=h295c915_0 | ||
| - libcublas=11.10.3.66=0 | ||
| - libcufft=10.7.2.124=h4fbf590_0 | ||
| - libcufile=1.6.0.25=0 | ||
| - libcurand=10.3.2.56=0 | ||
| - libcusolver=11.4.0.1=0 | ||
| - libcusparse=11.7.4.91=0 | ||
| - libdeflate=1.17=h5eee18b_0 | ||
| - libffi=3.4.2=h6a678d5_6 | ||
| - libgcc-ng=11.2.0=h1234567_1 | ||
| - libgomp=11.2.0=h1234567_1 | ||
| - libiconv=1.16=h7f8727e_2 | ||
| - libidn2=2.3.2=h7f8727e_0 | ||
| - libnpp=11.7.4.75=0 | ||
| - libnvjpeg=11.8.0.2=0 | ||
| - libpng=1.6.39=h5eee18b_0 | ||
| - libstdcxx-ng=11.2.0=h1234567_1 | ||
| - libtasn1=4.19.0=h5eee18b_0 | ||
| - libtiff=4.5.0=h6a678d5_2 | ||
| - libunistring=0.9.10=h27cfd23_0 | ||
| - libwebp=1.2.4=h11a3e52_1 | ||
| - libwebp-base=1.2.4=h5eee18b_1 | ||
| - lz4-c=1.9.4=h6a678d5_0 | ||
| - markupsafe=2.1.1=py38h7f8727e_0 | ||
| - mkl=2021.4.0=h06a4308_640 | ||
| - mkl-service=2.4.0=py38h7f8727e_0 | ||
| - mkl_fft=1.3.1=py38hd3c417c_0 | ||
| - mkl_random=1.2.2=py38h51133e4_0 | ||
| - mpc=1.1.0=h10f8cd9_1 | ||
| - mpfr=4.0.2=hb69a4c5_1 | ||
| - mpmath=1.2.1=py38h06a4308_0 | ||
| - ncurses=6.4=h6a678d5_0 | ||
| - nettle=3.7.3=hbbd107a_1 | ||
| - networkx=2.8.4=py38h06a4308_1 | ||
| - numpy=1.23.5=py38h14f4228_0 | ||
| - numpy-base=1.23.5=py38h31eccc5_0 | ||
| - openh264=2.1.1=h4ff587b_0 | ||
| - openssl=1.1.1t=h7f8727e_0 | ||
| - pillow=9.4.0=py38h6a678d5_0 | ||
| - pip=23.0.1=py38h06a4308_0 | ||
| - pycparser=2.21=pyhd3eb1b0_0 | ||
| - pyopenssl=23.0.0=py38h06a4308_0 | ||
| - pysocks=1.7.1=py38h06a4308_0 | ||
| - python=3.8.16 | ||
| - pytorch=2.0.0=py3.8_cuda11.7_cudnn8.5.0_0 | ||
| - pytorch-cuda=11.7=h778d358_3 | ||
| - pytorch-mutex=1.0=cuda | ||
| - readline=8.2=h5eee18b_0 | ||
| - requests=2.28.1=py38h06a4308_1 | ||
| - setuptools=65.6.3=py38h06a4308_0 | ||
| - six=1.16.0=pyhd3eb1b0_1 | ||
| - sqlite=3.41.1=h5eee18b_0 | ||
| - sympy=1.11.1=py38h06a4308_0 | ||
| - tk=8.6.12=h1ccaba5_0 | ||
| - torchaudio=2.0.0=py38_cu117 | ||
| - torchtriton=2.0.0=py38 | ||
| - torchvision=0.15.0=py38_cu117 | ||
| - typing_extensions=4.4.0=py38h06a4308_0 | ||
| - urllib3=1.26.15=py38h06a4308_0 | ||
| - wheel=0.38.4=py38h06a4308_0 | ||
| - xz=5.2.10=h5eee18b_1 | ||
| - zlib=1.2.13=h5eee18b_0 | ||
| - zstd=1.5.4=hc292b87_0 | ||
| - pip: | ||
| - absl-py==1.4.0 | ||
| - adal==1.2.7 | ||
| - alembic==1.10.3 | ||
| - applicationinsights==0.11.10 | ||
| - argcomplete==2.1.2 | ||
| - attrs==22.2.0 | ||
| - azure-ai-ml==1.5.0 | ||
| - azure-common==1.1.28 | ||
| - azure-core==1.26.4 | ||
| - azure-graphrbac==0.61.1 | ||
| - azure-identity==1.12.0 | ||
| - azure-mgmt-authorization==3.0.0 | ||
| - azure-mgmt-containerregistry==10.1.0 | ||
| - azure-mgmt-core==1.4.0 | ||
| - azure-mgmt-keyvault==10.2.1 | ||
| - azure-mgmt-resource==21.2.1 | ||
| - azure-mgmt-storage==20.1.0 | ||
| - azure-storage-blob==12.10.0 | ||
| - azure-storage-file-datalake==12.6.0 | ||
| - azure-storage-file-share==12.11.1 | ||
| - azureml-core==1.49.0 | ||
| - azureml-dataprep==4.9.6 | ||
| - azureml-dataprep-native==38.0.0 | ||
| - azureml-dataprep-rslex==2.16.4 | ||
| - azureml-dataset-runtime==1.49.0 | ||
| - azureml-mlflow==1.49.0 | ||
| - azureml-telemetry==1.49.0 | ||
| - azureml-tensorboard==1.49.0 | ||
| - azureml-train-core==1.49.0.post1 | ||
| - azureml-train-restclients-hyperdrive==1.49.0 | ||
| - backports-tempfile==1.0 | ||
| - backports-weakref==1.0.post1 | ||
| - bcrypt==4.0.1 | ||
| - cachetools==5.3.0 | ||
| - click==8.1.3 | ||
| - cloudpickle==2.2.1 | ||
| - colorama==0.4.6 | ||
| - conda-merge==0.2.0 | ||
| - contextlib2==21.6.0 | ||
| - contourpy==1.0.7 | ||
| - cycler==0.11.0 | ||
| - databricks-cli==0.17.6 | ||
| - distro==1.8.0 | ||
| - docker==6.0.1 | ||
| - dotnetcore2==3.1.23 | ||
| - einops==0.6.0 | ||
| - entrypoints==0.4 | ||
| - fire==0.5.0 | ||
| - flask==2.2.3 | ||
| - fonttools==4.39.3 | ||
| - fusepy==3.0.1 | ||
| - gitdb==4.0.10 | ||
| - gitpython==3.1.31 | ||
| - google-api-core==2.11.0 | ||
| - google-auth==2.17.2 | ||
| - google-auth-oauthlib==1.0.0 | ||
| - googleapis-common-protos==1.59.0 | ||
| - greenlet==2.0.2 | ||
| - grpcio==1.53.0 | ||
| - gunicorn==20.1.0 | ||
| - hi-ml-azure==0.2.19 | ||
| - humanfriendly==10.0 | ||
| - importlib-metadata==6.3.0 | ||
| - importlib-resources==5.12.0 | ||
| - isodate==0.6.1 | ||
| - itsdangerous==2.1.2 | ||
| - jeepney==0.8.0 | ||
| - jmespath==1.0.1 | ||
| - joblib==1.2.0 | ||
| - jsonpickle==2.2.0 | ||
| - jsonschema==4.17.3 | ||
| - kiwisolver==1.4.4 | ||
| - knack==0.10.1 | ||
| - llvmlite==0.39.1 | ||
| - mako==1.2.4 | ||
| - markdown==3.4.3 | ||
| - marshmallow==3.19.0 | ||
| - matplotlib==3.7.1 | ||
| - mlflow==2.2.2 | ||
| - mlflow-skinny==2.2.2 | ||
| - git+https://github.com/peterhessey/MONAI.git@6054-integrate-azureml-for-autorunner-training | ||
| - msal==1.21.0 | ||
| - msal-extensions==1.0.0 | ||
| - msrest==0.7.1 | ||
| - msrestazure==0.6.4 | ||
| - ndg-httpsclient==0.5.1 | ||
| - nibabel==5.1.0 | ||
| - numba==0.56.4 | ||
| - oauthlib==3.2.2 | ||
| - opencensus==0.11.2 | ||
| - opencensus-context==0.1.3 | ||
| - opencensus-ext-azure==1.1.9 | ||
| - packaging==21.3 | ||
| - pandas==2.0.0 | ||
| - param==1.13.0 | ||
| - paramiko==2.12.0 | ||
| - pathspec==0.11.1 | ||
| - pkginfo==1.9.6 | ||
| - pkgutil-resolve-name==1.3.10 | ||
| - portalocker==2.7.0 | ||
| - protobuf==3.20.3 | ||
| - psutil==5.9.4 | ||
| - pyarrow==9.0.0 | ||
| - pyasn1==0.4.8 | ||
| - pyasn1-modules==0.2.8 | ||
| - pydash==5.1.2 | ||
| - pygments==2.14.0 | ||
| - pyjwt==2.6.0 | ||
| - pynacl==1.5.0 | ||
| - pyparsing==3.0.9 | ||
| - pyrsistent==0.19.3 | ||
| - python-dateutil==2.8.2 | ||
| - pytz==2022.7.1 | ||
| - pyyaml==6.0 | ||
| - querystring-parser==1.2.4 | ||
| - requests-oauthlib==1.3.1 | ||
| - rsa==4.9 | ||
| - ruamel-yaml==0.17.21 | ||
| - ruamel-yaml-clib==0.2.7 | ||
| - scikit-learn==1.2.2 | ||
| - scipy==1.10.1 | ||
| - secretstorage==3.3.3 | ||
| - shap==0.41.0 | ||
| - slicer==0.0.7 | ||
| - smmap==5.0.0 | ||
| - sqlalchemy==2.0.9 | ||
| - sqlparse==0.4.3 | ||
| - strictyaml==1.7.3 | ||
| - tabulate==0.9.0 | ||
| - tensorboard==2.12.1 | ||
| - tensorboard-data-server==0.7.0 | ||
| - tensorboard-plugin-wit==1.8.1 | ||
| - termcolor==2.2.0 | ||
| - threadpoolctl==3.1.0 | ||
| - tqdm==4.65.0 | ||
| - tzdata==2023.3 | ||
| - websocket-client==1.5.1 | ||
| - werkzeug==2.2.3 | ||
| - zipp==3.15.0 | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -10,5 +10,6 @@ dependencies: | |
| - torchvision | ||
| - pytorch-cuda=11.6 | ||
| - pip | ||
| - python>=3.8 | ||
| - pip: | ||
| - -r requirements-dev.txt | ||
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This needs to be reviewed and changed back to MONAI repo during PR approval