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Add MPI_Finalize "detouring" mechanism #765

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Add MPI_Finalize "detouring" mechanism #765

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program--
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@program-- program-- commented Mar 15, 2024 •
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This PR resolves #748 by implementing a shim library that overrides MPI_Finalize calls to become no-op. Additionally, calls to MPI_Finalize from NGen code are modified to PMPI_Finalize to call the MPI library's actual implementation.

Adding everyone as reviewers for visibility on this change.

Additions

  • CMake target MPIDetour in utilities/mpi/ with the source file MPIDetour.c.

Changes

  • Both calls to MPI_Finalize in src/NGen.cpp are converted to PMPI_Finalize.

TODO

Checklist

  • PR has an informative and human-readable title
  • Changes are limited to a single goal (no scope creep)
  • Code can be automatically merged (no conflicts)
  • Code follows project standards (link if applicable)
  • Passes all existing automated tests
  • Any change in functionality is tested
  • New functions are documented (with a description, list of inputs, and expected output)
  • Placeholder code is flagged / future todos are captured in comments
  • Project documentation has been updated (including the "Unreleased" section of the CHANGELOG)
  • Reviewers requested with the Reviewers tool ➡️

Target Environment support

  • Linux
  • macOS

program-- and others added 2 commits March 15, 2024 12:04
@program-- @PhilMiller
mpi: add MPI detour library
e178f12 
Co-authored-by: Phil Miller - NOAA <[email protected]>
@program-- @PhilMiller
ngen: MPI_Finalize -> PMPI_Finalize
9821ac4 
Co-authored-by: Phil Miller - NOAA <[email protected]>
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Something needs to say target_link_library(ngen MPIDetour), too

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hellkite500 commented Mar 16, 2024 •
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Ubuntu linux tests failing due to a timeout running the tests. Downloading the logs and poking around, I see a LOT of these DEADLYSIGNAL messages comfing from running the test_bmi_c target

2024-03-15T22:38:01.4674964Z [100%] Linking CXX executable test_bmi_c
2024-03-15T22:38:02.1738113Z AddressSanitizer:DEADLYSIGNAL

and eventually the test times out

2024-03-15T22:38:17.3139827Z AddressSanitizer:DEADLYSIGNAL
2024-03-15T22:38:17.3140454Z CMake Error at /usr/local/share/cmake-3.28/Modules/GoogleTestAddTests.cmake:112 (message):
2024-03-15T22:38:17.3140582Z   Error running test executable.
2024-03-15T22:38:17.3140590Z 
2024-03-15T22:38:17.3140878Z     Path: '/home/runner/work/ngen/ngen/cmake_build/test/test_bmi_c'
2024-03-15T22:38:17.3141033Z     Result: Process terminated due to timeout
2024-03-15T22:38:17.3141126Z     Output:
2024-03-15T22:38:17.3141215Z       
2024-03-15T22:38:17.3141230Z 
2024-03-15T22:38:17.3141350Z Call Stack (most recent call first):
2024-03-15T22:38:17.3141791Z   /usr/local/share/cmake-3.28/Modules/GoogleTestAddTests.cmake:225 (gtest_discover_tests_impl)
2024-03-15T22:38:17.3141803Z 
2024-03-15T22:38:17.3141807Z 
2024-03-15T22:38:17.3142098Z gmake[3]: *** [test/CMakeFiles/test_bmi_c.dir/build.make:133: test/test_bmi_c] Error 1
2024-03-15T22:38:17.3142289Z gmake[3]: *** Deleting file 'test/test_bmi_c'
2024-03-15T22:38:17.3142567Z gmake[2]: *** [CMakeFiles/Makefile2:2163: test/CMakeFiles/test_bmi_c.dir/all] Error 2
2024-03-15T22:38:17.3142850Z gmake[1]: *** [CMakeFiles/Makefile2:2170: test/CMakeFiles/test_bmi_c.dir/rule] Error 2
2024-03-15T22:38:17.3142986Z gmake: *** [Makefile:921: test_bmi_c] Error 2
2024-03-15T22:38:17.3154227Z ##[error]Process completed with exit code 2.
2024-03-15T22:38:17.3379867Z Post job cleanup.

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program-- commented Mar 16, 2024 •
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Ubuntu linux tests failing due to a timeout running the tests. Downloading the logs and poking around, I see a LOT of these DEDLYSIGNAL messages comfing from running the test_bmi_c target
...

@hellkite500 Yeah this is happening across PR's and the master branch, see: #750 (comment). Not sure why this is happening, but it's not reproducible locally for neither Phil nor I

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Ah, I'm still catching up on a few things. Just wasn't sure if this was related to these changes or not...I looked at a few recent PR's and didn't see the failures. Might try getting an Ubuntu image spun up to test on.

@program-- program-- marked this pull request as ready for review March 18, 2024 16:42
program--
program-- commented Mar 21, 2024
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@PhilMiller PhilMiller marked this pull request as draft March 25, 2024 14:49
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Converting back to draft, since we may not need this for the time being if ESMF PR esmf-org/esmf#234 gets merged and released quickly. It could be useful for other uncooperative libraries that insist on acting like they own MPI, though.

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donaldwj commented Mar 25, 2024 •
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Where is the PMPI_Finalize coming from? I can not find documentation on It, I am guessing that it is directly called by the MPI library provided MPI_Finalize. Also is using this compatible across different MPI implementations? Ok this is the from section 15 of the MPI standard, documentation on this is not something easy to find. But It looks like this should be fine on all MPI implementations that meet the standard.

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@hellkite500 hellkite500 hellkite500 approved these changes

@PhilMiller PhilMiller Awaiting requested review from PhilMiller

@stcui007 stcui007 Awaiting requested review from stcui007

@christophertubbs christophertubbs Awaiting requested review from christophertubbs

@donaldwj donaldwj Awaiting requested review from donaldwj

@robertbartel robertbartel Awaiting requested review from robertbartel

@aaraney aaraney Awaiting requested review from aaraney

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Segfault thrown when Python is finalizing ESMF through pybind11
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