[gmx-developers] Regression test GmxapiMpiTests fails for GROMACS 2020.1

[Eric Irrgang]

Thank you, Christoph. That is very helpful confirmation.

We are still investigating some related test configuration logic and failure cases, but it is good to know we're on the right track and that we have logic that addresses your use case.

You can continue to follow #3845 or just look for it in the release notes for 2020.2.

Cheers!

> On Apr 16, 2020, at 11:40 AM, Christoph Pospiech <cpospiech at lenovo.com> wrote:
> 
> On Mittwoch, 15. April 2020 22:46:55 CEST Eric Irrgang <ericirrgang at gmail.com> 
> wrote:
>>> On Apr 15, 2020, at 5:52 PM, Christoph Pospiech <cpospiech at lenovo.com>
>>> wrote:
>>> 
>>> Can someone point me to the magic line, where to insert '-ntomp 2' into
>>> the
>>> regression test for GmxapiMpiTests? I would try on my local git clone,
>>> report back and share a 'git diff' (which you then can take, alter or
>>> reject).
>> 
>> Actually, that's the problem.
>> 
>> The CMake infrastructure is already set up to tell GmxapiMpiTests how many
>> threads to use by giving it "-ntomp 2".
>> 
>> But the executable used by GmxapiMpiTests is not based on `gmx mdrun` and so
>> does not know to do something with the "-ntomp 2" command line option.
>> 
>> The issue should be resolved in
>> https://gitlab.com/gromacs/gromacs/-/merge_requests/83 by
>> https://gitlab.com/gromacs/gromacs/-/tree/3485-gmxapimpitests-should-not-au
>> tomatically-choose-its-number-of-threads
>> 
>> Please confirm and review.
> 
> Eric,
> 
> while I was able to see the branch 
> 3485-gmxapimpitests-should-not-automatically-choose-its-number-of-threads
> in https://gitlab.com/, I couldn't see it in my local git clone, presumably 
> because I cloned as anonymous.
> 
> I therefore downloaded 17c2cebc and a735d3c2 as plain diff and scratched the 
> changes for release notes 2020.2 (which didn't exist on my 2020.1-derived 
> local branch either). Next, I patched the remaining changes in.
> $ patch -p1 < ../2020_fix3485_part1.patch
> $ patch -p1 < ../2020_fix3485_part2.patch
> $ git commit
> [v2020.1_CTT f1642fa] Manually adding patches 17c2cebc and a735d3c2 to fix 
> #3485.
> 2 files changed, 10 insertions(+), 4 deletions(-)
> $ git diff HEAD~
> diff --git a/src/api/cpp/tests/CMakeLists.txt b/src/api/cpp/tests/
> CMakeLists.txt
> index f0ea2ce..d87d830 100644
> --- a/src/api/cpp/tests/CMakeLists.txt
> +++ b/src/api/cpp/tests/CMakeLists.txt
> @@ -1,7 +1,7 @@
> #
> # This file is part of the GROMACS molecular simulation package.
> #
> -# Copyright (c) 2018,2019, by the GROMACS development team, led by
> +# Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
> # Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
> # and including many others, as listed in the AUTHORS file in the
> # top-level source directory and at http://www.gromacs.org.
> @@ -71,7 +71,7 @@ target_include_directories(gmxapi-test PRIVATE
> # Link against the gmxapi libraries and get access to its public (installed) 
> headers.
> target_link_libraries(gmxapi-test PRIVATE Gromacs::gmxapi 
> mdrun_test_infrastructure)
> 
> -gmx_register_gtest_test(GmxapiExternalInterfaceTests gmxapi-test 
> OPENMP_THREADS 2 INTEGRATION_TEST)
> +gmx_register_gtest_test(GmxapiExternalInterfaceTests gmxapi-test 
> INTEGRATION_TEST)
> 
> set_tests_properties(GmxapiExternalInterfaceTests PROPERTIES
>                      WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})
> @@ -101,4 +101,8 @@ target_include_directories(gmxapi-mpi-test PRIVATE
>                            ${CMAKE_CURRENT_SOURCE_DIR})
> target_link_libraries(gmxapi-mpi-test PRIVATE Gromacs::gmxapi 
> mdrun_test_infrastructure)
> 
> -gmx_register_gtest_test(GmxapiMpiTests gmxapi-mpi-test MPI_RANKS 2 
> OPENMP_THREADS 2 INTEGRATION_TEST)
> +# Note that gmxapi-mpi-test does not have a command line argument processor,
> +# so some of the information that is supposed to be conveyed through this 
> macro
> +# is not transmitted in the usual way. For instance, OPENMP_THREADS may have 
> no
> +# effect. See testingconfiguration.h
> +gmx_register_gtest_test(GmxapiMpiTests gmxapi-mpi-test MPI_RANKS 2 
> INTEGRATION_TEST)
> diff --git a/src/api/cpp/tests/testingconfiguration.h b/src/api/cpp/tests/
> testingconfiguration.h
> index f3bef5f..611ab87 100644
> --- a/src/api/cpp/tests/testingconfiguration.h
> +++ b/src/api/cpp/tests/testingconfiguration.h
> @@ -1,7 +1,7 @@
> /*
>  * This file is part of the GROMACS molecular simulation package.
>  *
> - * Copyright (c) 2018,2019, by the GROMACS development team, led by
> + * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
>  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
>  * and including many others, as listed in the AUTHORS file in the
>  * top-level source directory and at http://www.gromacs.org.
> @@ -115,6 +115,8 @@ public:
>     {
>         std::vector<std::string> mdArgs;
> 
> +        mdArgs.emplace_back("-ntomp");
> +        mdArgs.emplace_back("1");
>         mdArgs.emplace_back("-o");
>         mdArgs.emplace_back(runner_.fullPrecisionTrajectoryFileName_);
>         mdArgs.emplace_back("-x");
> 
> 
> I can confirm that after adding the patches detailed above, all regression 
> tests are passed and issue #3845 is now resolved.
> 
> I didn't patch in "42fce43f Explain a parameter choice.", because it moved two 
> code lines and added a comment. While necessary for the GROMACS release, I 
> regarded it optional for my "quick and dirty" test above. My understanding is 
> that 2020.2 will have that patch included - and properly documented in the 
> release notes for 2020.2 . 
> -- 
> Dr. Christoph Pospiech
> Senior HPC & AI Performance Engineer
> 
> T +49 (351) 86269826
> M +49 (171) 7655871
> E cpospiech at lenovo.com
> 
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