Update ML related software #6649

riga · 2021-02-15T18:17:16Z

This PR updates software related to ML workflows. Details:

Update ONNXRuntime from 1.3.0 to 1.6.0. The current fork is at this branch and could be included to cms_externals/onnxruntime. When 1.6.0 is working properly, the race conditions mentioned in Apparent data race in onnxruntime on aarch64 cmssw#32899 should be checked again.
Add standalone XGBoost library to be used in C++. The Python3 bindings are linked to that version. The legacy Python2 bindings are pinned to an older XGBoost version and thus bring their own library as before.
Add the cmsml python package containing useful tools for working with ML in a cms-specific context. These tools are meant to work independently of cmssw, hence the externalization. Note: similar yet older versions of some of the tools are currently living in PhysicsTools/TensorFlow/python and should be removed (or properly deprecated) (Adapt python code to updated ML software cmssw#32942).
Add onnxmltools which contains several converters to onnx model format. I only added the Python3 tools as they dropped Python2 quite a while ago, and we should have the latest version available to support more models.
Minor version updates of other ml related software and add the luigi/law workflow tools (plus 2 dependencies) as they are used in some groups.

I tested with workflow 23424.0 (TTbar_13+2026D49PU): runTheMatrix.py -w upgrade -l 23424.0.

@mialiu149

cmsbuild · 2021-02-15T18:17:39Z

A new Pull Request was created by @riga (Marcel R.) for branch IB/CMSSW_11_3_X/master.

@cmsbuild, @smuzaffar, @mrodozov can you please review it and eventually sign? Thanks.
cms-bot commands are listed here

cmsbuild · 2021-02-15T18:31:17Z

Pull request #6649 was updated.

smuzaffar · 2021-02-15T18:31:36Z

thanks @riga for the updates. I have included your changes in cms-externals/onnxruntime repo now

smuzaffar · 2021-02-15T18:31:42Z

please test

smuzaffar · 2021-02-15T18:32:25Z

please test for slc7_aarch64_gcc9

smuzaffar · 2021-02-15T18:32:51Z

please test for slc7_ppc64le_gcc9

smuzaffar · 2021-02-15T18:33:13Z

please test for slc7_amd64_gcc10

cmsbuild · 2021-02-15T18:42:23Z

-1

Summary: https://cmssdt.cern.ch/SDT/jenkins-artifacts/pull-request-integration/PR-ae302a/12902/summary.html
COMMIT: 2e927cd
CMSSW: CMSSW_11_3_X_2021-02-14-2300/slc7_amd64_gcc10
User test area: For local testing, you can use /cvmfs/cms-ci.cern.ch/week0/cms-sw/cmsdist/6649/12902/install.sh to create a dev area with all the needed externals and cmssw changes.

External Build

I found compilation error when building:

FATAL: malformed spec found while quering it. Command: 
source /data/cmsbld/jenkins/workspace/ib-run-pr-tests/testBuildDir/slc7_amd64_gcc10/rpm-env.sh ;  rpm -q --specfile /data/cmsbld/jenkins/workspace/ib-run-pr-tests/testBuildDir/tmp/tmpspec-python_tools --info --define "cmsdist_directory /data/cmsbld/jenkins/workspace/ib-run-pr-tests/cmsdist" --define "compilerv 1020" --define "cmscompilerv 10" --define "cmsos slc7_amd64" --define "package_vectorization %{nil}" --define 'buildroot /foo'
Resulted in:

warning: Macro %rpmbuild_libdir defined but not used within scope
error: line 369: Unknown tag: <<<<<<< HEAD
error: query of specfile /data/cmsbld/jenkins/workspace/ib-run-pr-tests/testBuildDir/tmp/tmpspec-python_tools failed, can't parse
Traceback (most recent call last):
  File "./pkgtools/cmsBuild", line 4396, in 
    build(opts, args[1:], PKGFactory)
  File "./pkgtools/cmsBuild", line 3695, in build

cmsbuild · 2021-02-15T19:18:10Z

-1

Summary: https://cmssdt.cern.ch/SDT/jenkins-artifacts/pull-request-integration/PR-ae302a/12899/summary.html
COMMIT: 2e927cd
CMSSW: CMSSW_11_3_X_2021-02-15-1100/slc7_amd64_gcc900
User test area: For local testing, you can use /cvmfs/cms-ci.cern.ch/week0/cms-sw/cmsdist/6649/12899/install.sh to create a dev area with all the needed externals and cmssw changes.

External Build

I found compilation error when building:

call_subprocess(
File "/data/cmsbld/jenkins/workspace/ib-run-pr-tests/testBuildDir/slc7_amd64_gcc900/external/py3-pip/20.3.3/lib/python3.8/site-packages/pip/_internal/utils/subprocess.py", line 240, in call_subprocess
raise InstallationError(exc_msg)
pip._internal.exceptions.InstallationError: Command errored out with exit status 1: /data/cmsbld/jenkins/workspace/ib-run-pr-tests/testBuildDir/slc7_amd64_gcc900/external/python3/3.8.2-bcolbf/bin/python3 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/data/cmsbld/jenkins/workspace/ib-run-pr-tests/testBuildDir/BUILD/slc7_amd64_gcc900/external/py3-xgboost/1.3.3-532d7cb9a6d277c956517be10bbbf61e/cmsdist-tmp/pip-req-build-o8alg2k5/setup.py'"'"'; __file__='"'"'/data/cmsbld/jenkins/workspace/ib-run-pr-tests/testBuildDir/BUILD/slc7_amd64_gcc900/external/py3-xgboost/1.3.3-532d7cb9a6d277c956517be10bbbf61e/cmsdist-tmp/pip-req-build-o8alg2k5/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /data/cmsbld/jenkins/workspace/ib-run-pr-tests/testBuildDir/BUILD/slc7_amd64_gcc900/external/py3-xgboost/1.3.3-532d7cb9a6d277c956517be10bbbf61e/cmsdist-tmp/pip-record-1_72s80u/install-record.txt --single-version-externally-managed --user --prefix= --compile --install-headers /data/cmsbld/jenkins/workspace/ib-run-pr-tests/testBuildDir/tmp/BUILDROOT/532d7cb9a6d277c956517be10bbbf61e/opt/cmssw/slc7_amd64_gcc900/external/py3-xgboost/1.3.3-532d7cb9a6d277c956517be10bbbf61e/include/python3.8/xgboost --use-system-libxgboost Check the logs for full command output.
Removed build tracker: '/data/cmsbld/jenkins/workspace/ib-run-pr-tests/testBuildDir/BUILD/slc7_amd64_gcc900/external/py3-xgboost/1.3.3-532d7cb9a6d277c956517be10bbbf61e/cmsdist-tmp/pip-req-tracker-pd1s0gv2'
error: Bad exit status from /data/cmsbld/jenkins/workspace/ib-run-pr-tests/testBuildDir/tmp/rpm-tmp.LCH162 (%build)


RPM build errors:
Macro %rpmbuild_libdir defined but not used within scope
Bad exit status from /data/cmsbld/jenkins/workspace/ib-run-pr-tests/testBuildDir/tmp/rpm-tmp.LCH162 (%build)

cmsbuild · 2021-02-15T19:22:10Z

-1

Summary: https://cmssdt.cern.ch/SDT/jenkins-artifacts/pull-request-integration/PR-ae302a/12901/summary.html
COMMIT: 2e927cd
CMSSW: CMSSW_11_3_X_2021-02-14-2300/slc7_ppc64le_gcc9
User test area: For local testing, you can use /cvmfs/cms-ci.cern.ch/week0/cms-sw/cmsdist/6649/12901/install.sh to create a dev area with all the needed externals and cmssw changes.

External Build

I found compilation error when building:

call_subprocess(
File "/scratch/cmsbuild/jenkins_a/workspace/ib-run-pr-tests/testBuildDir/slc7_ppc64le_gcc9/external/py3-pip/20.3.3/lib/python3.8/site-packages/pip/_internal/utils/subprocess.py", line 240, in call_subprocess
raise InstallationError(exc_msg)
pip._internal.exceptions.InstallationError: Command errored out with exit status 1: /scratch/cmsbuild/jenkins_a/workspace/ib-run-pr-tests/testBuildDir/slc7_ppc64le_gcc9/external/python3/3.8.2-0923d45facc02c507f248eced2e49422/bin/python3 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/scratch/cmsbuild/jenkins_a/workspace/ib-run-pr-tests/testBuildDir/BUILD/slc7_ppc64le_gcc9/external/py3-xgboost/1.3.3-532d7cb9a6d277c956517be10bbbf61e/cmsdist-tmp/pip-req-build-sdz7_9oo/setup.py'"'"'; __file__='"'"'/scratch/cmsbuild/jenkins_a/workspace/ib-run-pr-tests/testBuildDir/BUILD/slc7_ppc64le_gcc9/external/py3-xgboost/1.3.3-532d7cb9a6d277c956517be10bbbf61e/cmsdist-tmp/pip-req-build-sdz7_9oo/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /scratch/cmsbuild/jenkins_a/workspace/ib-run-pr-tests/testBuildDir/BUILD/slc7_ppc64le_gcc9/external/py3-xgboost/1.3.3-532d7cb9a6d277c956517be10bbbf61e/cmsdist-tmp/pip-record-9vjbksf9/install-record.txt --single-version-externally-managed --user --prefix= --compile --install-headers /scratch/cmsbuild/jenkins_a/workspace/ib-run-pr-tests/testBuildDir/tmp/BUILDROOT/532d7cb9a6d277c956517be10bbbf61e/opt/cmssw/slc7_ppc64le_gcc9/external/py3-xgboost/1.3.3-532d7cb9a6d277c956517be10bbbf61e/include/python3.8/xgboost --use-system-libxgboost Check the logs for full command output.
Removed build tracker: '/scratch/cmsbuild/jenkins_a/workspace/ib-run-pr-tests/testBuildDir/BUILD/slc7_ppc64le_gcc9/external/py3-xgboost/1.3.3-532d7cb9a6d277c956517be10bbbf61e/cmsdist-tmp/pip-req-tracker-s_z3162t'
error: Bad exit status from /scratch/cmsbuild/jenkins_a/workspace/ib-run-pr-tests/testBuildDir/tmp/rpm-tmp.u8vSVa (%build)


RPM build errors:
Macro %rpmbuild_libdir defined but not used within scope
Bad exit status from /scratch/cmsbuild/jenkins_a/workspace/ib-run-pr-tests/testBuildDir/tmp/rpm-tmp.u8vSVa (%build)

cmsbuild · 2021-02-15T19:31:00Z

-1

Summary: https://cmssdt.cern.ch/SDT/jenkins-artifacts/pull-request-integration/PR-ae302a/12900/summary.html
COMMIT: 2e927cd
CMSSW: CMSSW_11_3_X_2021-02-15-1100/slc7_aarch64_gcc9
User test area: For local testing, you can use /cvmfs/cms-ci.cern.ch/week0/cms-sw/cmsdist/6649/12900/install.sh to create a dev area with all the needed externals and cmssw changes.

External Build

I found compilation error when building:

call_subprocess(
File "/home/cmsbld/jenkins_a/workspace/ib-run-pr-tests/testBuildDir/slc7_aarch64_gcc9/external/py3-pip/20.3.3/lib/python3.8/site-packages/pip/_internal/utils/subprocess.py", line 240, in call_subprocess
raise InstallationError(exc_msg)
pip._internal.exceptions.InstallationError: Command errored out with exit status 1: /home/cmsbld/jenkins_a/workspace/ib-run-pr-tests/testBuildDir/slc7_aarch64_gcc9/external/python3/3.8.2/bin/python3 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/home/cmsbld/jenkins_a/workspace/ib-run-pr-tests/testBuildDir/BUILD/slc7_aarch64_gcc9/external/py3-xgboost/1.3.3-532d7cb9a6d277c956517be10bbbf61e/cmsdist-tmp/pip-req-build-4plvzbys/setup.py'"'"'; __file__='"'"'/home/cmsbld/jenkins_a/workspace/ib-run-pr-tests/testBuildDir/BUILD/slc7_aarch64_gcc9/external/py3-xgboost/1.3.3-532d7cb9a6d277c956517be10bbbf61e/cmsdist-tmp/pip-req-build-4plvzbys/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /home/cmsbld/jenkins_a/workspace/ib-run-pr-tests/testBuildDir/BUILD/slc7_aarch64_gcc9/external/py3-xgboost/1.3.3-532d7cb9a6d277c956517be10bbbf61e/cmsdist-tmp/pip-record-nd4vkf49/install-record.txt --single-version-externally-managed --user --prefix= --compile --install-headers /home/cmsbld/jenkins_a/workspace/ib-run-pr-tests/testBuildDir/tmp/BUILDROOT/532d7cb9a6d277c956517be10bbbf61e/opt/cmssw/slc7_aarch64_gcc9/external/py3-xgboost/1.3.3-532d7cb9a6d277c956517be10bbbf61e/include/python3.8/xgboost --use-system-libxgboost Check the logs for full command output.
Removed build tracker: '/home/cmsbld/jenkins_a/workspace/ib-run-pr-tests/testBuildDir/BUILD/slc7_aarch64_gcc9/external/py3-xgboost/1.3.3-532d7cb9a6d277c956517be10bbbf61e/cmsdist-tmp/pip-req-tracker-mpeouj1_'
error: Bad exit status from /home/cmsbld/jenkins_a/workspace/ib-run-pr-tests/testBuildDir/tmp/rpm-tmp.COk8NR (%build)


RPM build errors:
Macro %rpmbuild_libdir defined but not used within scope
Bad exit status from /home/cmsbld/jenkins_a/workspace/ib-run-pr-tests/testBuildDir/tmp/rpm-tmp.COk8NR (%build)

smuzaffar · 2021-02-15T20:33:52Z

please test

cmsbuild · 2021-02-15T20:33:54Z

Pull request #6649 was updated.

smuzaffar · 2021-02-15T21:07:10Z

please test for slc7_ppc64le_gcc9

smuzaffar · 2021-02-15T21:07:36Z

please test for slc7_aarch64_gcc9

riga · 2021-02-16T14:20:52Z

The error in cms/6649/slc7_amd64_gcc10 looks like an unresolved merge conflict but I can't see where it comes from.

The failed cms/6649/slc7_ppc64le_gcc9/relvals test is due to a segfault in OscarMTProducer:g4SimHits, however, I can't see the connection to the changes in this PR yet.

smuzaffar · 2021-02-16T14:38:47Z

11634.911 for pcc64le is already failing in power IBs

smuzaffar · 2021-02-16T14:42:48Z

please test for CMSSW_11_3_PY3_X
lets hope there are no merge conflicts

mrodozov · 2021-02-16T14:48:15Z

It comes from python_tools which seems to be unmergeble into gcc10 (gcc900 to gcc10), fails to merge it with a conflict and then the .spec file remains with the conflict lines -> malformed spec.
I think we can get the rest in and fix gcc10 python_tools by hand and test it.

cmsbuild · 2021-02-16T19:32:01Z

-1

Failed Tests: UnitTests
Summary: https://cmssdt.cern.ch/SDT/jenkins-artifacts/pull-request-integration/PR-ae302a/12926/summary.html
COMMIT: 0a5f9e1
CMSSW: CMSSW_11_3_PY3_X_2021-02-15-2300/slc7_amd64_gcc900
User test area: For local testing, you can use /cvmfs/cms-ci.cern.ch/week0/cms-sw/cmsdist/6649/12926/install.sh to create a dev area with all the needed externals and cmssw changes.

Unit Tests

I found errors in the following unit tests:

---> test testhep_ml had ERRORS

Comparison Summary

@slava77 comparisons for the following workflows were not done due to missing matrix map:

/data/cmsbld/jenkins/workspace/compare-root-files-short-matrix/data/PR-ae302a/11634.911_TTbar_14TeV+2021_DD4hep+TTbar_14TeV_TuneCP5_GenSim+Digi+Reco+HARVEST+ALCA

Summary:

No significant changes to the logs found
Reco comparison results: 4822 differences found in the comparisons
DQMHistoTests: Total files compared: 37
DQMHistoTests: Total histograms compared: 2752246
DQMHistoTests: Total failures: 777
DQMHistoTests: Total nulls: 0
DQMHistoTests: Total successes: 2751469
DQMHistoTests: Total skipped: 0
DQMHistoTests: Total Missing objects: 0
DQMHistoSizes: Histogram memory added: 0.0 KiB( 36 files compared)
Checked 156 log files, 37 edm output root files, 37 DQM output files

riga · 2021-02-17T10:11:00Z

The failed unit test in PhysicsTools/PythonAnalysis/test/testhep_ml.py uses a wrong import in Python3 and is easy to fix. I will open a PR to CMSSW to change that. I can use the same PR to make the changes to the tools in PhysicsTools/TensorFlow/python/tools.py as mentioned above:

Note: similar yet older versions of some of the tools are currently living in PhysicsTools/TensorFlow/python and should be removed (or properly deprecated).

smuzaffar · 2021-02-17T10:11:52Z

please test

davidlange6 · 2021-02-17T10:49:11Z

Hum - there isn’t any history difference between these branches for python_tools.spec is there? Best we can keep it that way.

…

On Feb 16, 2021, at 3:48 PM, Mircho Rodozov ***@***.***> wrote: It comes from python_tools which seems to be unmergeble into gcc10 (gcc900 to gcc10), fails to merge it with a conflict and then the .spec file remains with the conflict lines -> malformed spec. I think we can get the rest in and fix gcc10 python_tools by hand and test it. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or unsubscribe.

smuzaffar · 2021-02-17T10:54:24Z

please test for slc7_amd64_gcc10
gcc10 branch was missing a new line in python_tools. It should be fine now

cmsbuild · 2021-02-17T11:01:29Z

-1

Summary: https://cmssdt.cern.ch/SDT/jenkins-artifacts/pull-request-integration/PR-ae302a/12952/summary.html
COMMIT: 0a5f9e1
CMSSW: CMSSW_11_3_X_2021-02-16-2300/slc7_amd64_gcc10
User test area: For local testing, you can use /cvmfs/cms-ci.cern.ch/week0/cms-sw/cmsdist/6649/12952/install.sh to create a dev area with all the needed externals and cmssw changes.

External Build

I found compilation warning when building: See details on the summary page.

cmsbuild · 2021-02-17T12:32:58Z

+1

Summary: https://cmssdt.cern.ch/SDT/jenkins-artifacts/pull-request-integration/PR-ae302a/12953/summary.html
COMMIT: 0a5f9e1
CMSSW: CMSSW_11_3_X_2021-02-16-2300/slc7_amd64_gcc10
User test area: For local testing, you can use /cvmfs/cms-ci.cern.ch/week0/cms-sw/cmsdist/6649/12953/install.sh to create a dev area with all the needed externals and cmssw changes.

cmsbuild · 2021-02-17T12:42:07Z

+1

Summary: https://cmssdt.cern.ch/SDT/jenkins-artifacts/pull-request-integration/PR-ae302a/12951/summary.html
COMMIT: 0a5f9e1
CMSSW: CMSSW_11_3_X_2021-02-16-2300/slc7_amd64_gcc900
User test area: For local testing, you can use /cvmfs/cms-ci.cern.ch/week0/cms-sw/cmsdist/6649/12951/install.sh to create a dev area with all the needed externals and cmssw changes.

smuzaffar · 2021-02-17T20:13:36Z

+externals
looks good to go. PY3 unit tests needs cmssw PR

cmsbuild · 2021-02-17T20:13:58Z

This pull request is fully signed and it will be integrated in one of the next IB/CMSSW_11_3_X/master IBs (tests are also fine). This pull request will now be reviewed by the release team before it's merged. @silviodonato, @dpiparo, @qliphy (and backports should be raised in the release meeting by the corresponding L2)

riga added 3 commits February 15, 2021 11:32

Update onnx, add xgboost cpp library, add cmsml.

eb80092

Fix cmsml installation.

14d69f5

Add further software.

4605014

cmsbuild added externals-pending orp-pending pending-signatures tests-pending labels Feb 15, 2021

use cms-externals repo

2e927cd

cmsbuild added tests-started and removed tests-pending labels Feb 15, 2021

cmsbuild added tests-rejected and removed tests-started labels Feb 15, 2021

Update py3-xgboost.file

d77091b

cmsbuild added tests-started and removed tests-rejected labels Feb 15, 2021

cmsbuild added the tests-approved label Feb 16, 2021

cmsbuild added tests-started and removed tests-approved labels Feb 17, 2021

cmsbuild added tests-approved tests-started and removed tests-started tests-approved labels Feb 17, 2021

cmsbuild added externals-approved fully-signed and removed externals-pending pending-signatures labels Feb 17, 2021

smuzaffar merged commit cc7078a into cms-sw:IB/CMSSW_11_3_X/master Feb 17, 2021

This was referenced Feb 18, 2021

reduce ML inference time in b-tag and related jet taggers: focus on ParticleNet cms-sw/cmssw#32883

Closed

Adapt python code to updated ML software cms-sw/cmssw#32942

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Update ML related software #6649

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Update ML related software #6649

Update ML related software #6649

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External Build

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External Build

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External Build

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External Build

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Unit Tests

Comparison Summary

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External Build

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