Merge pull request easybuilders#20439 from boegel/20240430110124_new_…

…pr_GROMACS20241 add patch for GROMACS 2024.1 to fix filesystem race in tests
satishskamath · Apr 30, 2024 · 9a09523 · 9a09523
2 parents 460062c + 231b705
commit 9a09523
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diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2024.1-foss-2023b.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2024.1-foss-2023b.eb
@@ -40,13 +40,16 @@ sources = [SOURCELOWER_TAR_GZ]
 patches = [
     'GROMACS-2023.1_set_omp_num_threads_env_for_ntomp_tests.patch',
     'GROMACS-2023.1_fix_tests_for_gmx_thread_mpi.patch',
+    'GROMACS-2024.1_fix-tests-filesystem-race.patch',
 ]
 checksums = [
     {'gromacs-2024.1.tar.gz': '937d8f12a36fffbf2af7add71adbb5aa5c5537892d46c9a76afbecab1aa0aac7'},
     {'GROMACS-2023.1_set_omp_num_threads_env_for_ntomp_tests.patch':
      '7f41bda16c9c2837624265dda4be252f655d1288ddc4486b1a2422af30d5d199'},
     {'GROMACS-2023.1_fix_tests_for_gmx_thread_mpi.patch':
      '6df844bb3bbc51180446a3595c61a4ef195e5f975533a04cef76841aa763aec1'},
+    {'GROMACS-2024.1_fix-tests-filesystem-race.patch':
+     '25b933b37bc40576ee25ebae24442ae15fafe7cd5ac4b066e1dc8de488d58b4c'},
 ]
 
 builddependencies = [

diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2024.1_fix-tests-filesystem-race.patch b/easybuild/easyconfigs/g/GROMACS/GROMACS-2024.1_fix-tests-filesystem-race.patch
@@ -0,0 +1,152 @@
+diff --git a/api/gmxapi/cpp/tests/CMakeLists.txt b/api/gmxapi/cpp/tests/CMakeLists.txt
+index ca741dc930b4ed9cbde2ba4c84e50d4579e1adc6..7c00e390a32e92926d08b006df4ad335273143fb 100644
+--- a/api/gmxapi/cpp/tests/CMakeLists.txt
++++ b/api/gmxapi/cpp/tests/CMakeLists.txt
+@@ -107,4 +107,10 @@ if (GMX_MPI)
+         set_tests_properties(GmxapiMpiTests PROPERTIES
+                              WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})
+     endif ()
++    if (TEST GmxapiExternalInterfaceTests AND TEST GmxapiMpiTests)
++        # Because the gmxapi tests depend on writing files whose names are not
++        # unique across test cases, prevent CTest from running these tests
++        # concurrently. See #4654
++        set_tests_properties(GmxapiMpiTests PROPERTIES DEPENDS GmxapiExternalInterfaceTests)
++    endif()
+ endif ()
+diff --git a/src/programs/mdrun/tests/CMakeLists.txt b/src/programs/mdrun/tests/CMakeLists.txt
+index 23dc2840aed9660f6fb84a4d5a295a2cb36feace..e24ae102d511b735257d60ce2c59e6a1d1956400 100644
+--- a/src/programs/mdrun/tests/CMakeLists.txt
++++ b/src/programs/mdrun/tests/CMakeLists.txt
+@@ -113,6 +113,12 @@ gmx_add_gtest_executable(${exename} MPI
+ target_link_libraries(${exename} PRIVATE mdrun_test_infrastructure)
+ gmx_register_gtest_test(MdrunTestsOneRank ${exename} MPI_RANKS 1 OPENMP_THREADS 2 INTEGRATION_TEST SLOW_TEST IGNORE_LEAKS SLOW_GPU_TEST)
+ gmx_register_gtest_test(MdrunTestsTwoRanks ${exename} MPI_RANKS 2 OPENMP_THREADS 2 INTEGRATION_TEST SLOW_TEST IGNORE_LEAKS SLOW_GPU_TEST)
++# Because the mdrun tests depend on writing files whose names are not
++# unique across test cases, prevent CTest from running these tests
++# concurrently. See #4654
++if (TEST MdrunTestsTwoRanks AND TEST MdrunTestsOneRank)
++    set_tests_properties(MdrunTestsTwoRanks PROPERTIES DEPENDS MdrunTestsOneRank)
++endif()
+
+ # The orires test is separate, as it supports only a single MPI rank
+ set(testname "MdrunSingleRankAlgorithmsTests")
+@@ -129,13 +135,31 @@ gmx_add_gtest_executable(${exename}
+ target_link_libraries(${exename} PRIVATE mdrun_test_infrastructure)
+ gmx_register_gtest_test(${testname} ${exename} OPENMP_THREADS 2 INTEGRATION_TEST IGNORE_LEAKS SLOW_GPU_TEST)
+
++set(exename "minimize-test")
++
++gmx_add_gtest_executable(${exename} MPI
++    CPP_SOURCE_FILES
++        # files with code for tests
++        minimize.cpp
++        # pseudo-library for code for mdrun
++        $<TARGET_OBJECTS:mdrun_objlib>
++        )
++target_link_libraries(${exename} PRIVATE mdrun_test_infrastructure)
++gmx_register_gtest_test(Minimize1RankTests ${exename} MPI_RANKS 1 OPENMP_THREADS 2 INTEGRATION_TEST IGNORE_LEAKS QUICK_GPU_TEST)
++gmx_register_gtest_test(Minimize2RankTests ${exename} MPI_RANKS 2 OPENMP_THREADS 2 INTEGRATION_TEST IGNORE_LEAKS QUICK_GPU_TEST)
++# Because the minimizer tests depend on writing files whose names are not
++# unique across test cases, prevent CTest from running these tests
++# concurrently. See #4654
++if (TEST Minimize2RankTests AND TEST Minimize1RankTests)
++    set_tests_properties(Minimize2RankTests PROPERTIES DEPENDS Minimize1RankTests)
++endif()
++
+ set(testname "MdrunNonIntegratorTests")
+ set(exename "mdrun-non-integrator-test")
+
+ gmx_add_gtest_executable(${exename}
+     CPP_SOURCE_FILES
+         # files with code for tests
+-        minimize.cpp
+         nonbonded_bench.cpp
+         normalmodes.cpp
+         rerun.cpp
+@@ -169,7 +193,6 @@ gmx_add_gtest_executable(${exename} MPI
+     CPP_SOURCE_FILES
+         # files with code for tests
+         domain_decomposition.cpp
+-        minimize.cpp
+         mimic.cpp
+         # pseudo-library for code for mdrun
+         $<TARGET_OBJECTS:mdrun_objlib>
+@@ -177,6 +200,13 @@ gmx_add_gtest_executable(${exename} MPI
+ target_link_libraries(${exename} PRIVATE mdrun_test_infrastructure)
+ gmx_register_gtest_test(${testname} ${exename} MPI_RANKS 2 OPENMP_THREADS 2 INTEGRATION_TEST IGNORE_LEAKS QUICK_GPU_TEST)
+
++# Because the mdrun tests depend on writing files whose names are not
++# unique across test cases, prevent CTest from running these tests
++# concurrently. See #4654. These test binaries both test aspects of MiMiC.
++if (TEST MdrunMpiTests AND TEST MdrunModulesTests)
++    set_tests_properties(MdrunMpiTests PROPERTIES DEPENDS MdrunModulesTests)
++endif()
++
+ # Multi sim only makes sense with real MPI, and ideally at least 4 ranks,
+ # to allow for multiple simulations (>= 2 sims) each using DD (>= 2 ranks per sim)
+ set(testname "MdrunMultiSimTests")
+@@ -235,6 +265,12 @@ gmx_add_gtest_executable(${exename} MPI
+ target_link_libraries(${exename} PRIVATE mdrun_test_infrastructure)
+ gmx_register_gtest_test(MdrunMpi1RankPmeTests ${exename} MPI_RANKS 1 OPENMP_THREADS 2 INTEGRATION_TEST IGNORE_LEAKS SLOW_GPU_TEST)
+ gmx_register_gtest_test(MdrunMpi2RankPmeTests ${exename} MPI_RANKS 2 OPENMP_THREADS 2 INTEGRATION_TEST IGNORE_LEAKS SLOW_GPU_TEST)
++# Because the mdrun tests depend on writing files whose names are not
++# unique across test cases, prevent CTest from running these tests
++# concurrently. See #4654
++if (TEST MdrunMpi2RankPmeTests AND TEST MdrunMpi1RankPmeTests)
++    set_tests_properties(MdrunMpi2RankPmeTests PROPERTIES DEPENDS MdrunMpi1RankPmeTests)
++endif()
+
+ # Slow-running tests that target testing multiple-rank coordination behaviors
+ # These tests are extremely slow without optimization or OpenMP, so only run them for
+@@ -256,6 +292,12 @@ if (CMAKE_BUILD_TYPE MATCHES "Rel" AND GMX_OPENMP)
+     gmx_register_gtest_test(${testname} ${exename} MPI_RANKS 1 SLOW_TEST IGNORE_LEAKS QUICK_GPU_TEST)
+     set(testname "MdrunCoordinationBasicTests2Ranks")
+     gmx_register_gtest_test(${testname} ${exename} MPI_RANKS 2 SLOW_TEST IGNORE_LEAKS QUICK_GPU_TEST)
++    # Because the mdrun tests depend on writing files whose names are not
++    # unique across test cases, prevent CTest from running these tests
++    # concurrently. See #4654
++    if (TEST MdrunCoordinationBasicTests2Ranks AND TEST MdrunCoordinationBasicTests1Rank)
++        set_tests_properties(MdrunCoordinationBasicTests2Ranks PROPERTIES DEPENDS MdrunCoordinationBasicTests1Rank)
++    endif()
+ endif()
+
+ set(exename "mdrun-coordination-coupling-test")
+@@ -274,6 +316,12 @@ if (CMAKE_BUILD_TYPE MATCHES "Rel" AND GMX_OPENMP)
+     gmx_register_gtest_test(${testname} ${exename} MPI_RANKS 1 SLOW_TEST IGNORE_LEAKS SLOW_GPU_TEST)
+     set(testname "MdrunCoordinationCouplingTests2Ranks")
+     gmx_register_gtest_test(${testname} ${exename} MPI_RANKS 2 SLOW_TEST IGNORE_LEAKS SLOW_GPU_TEST)
++    # Because the mdrun tests depend on writing files whose names are not
++    # unique across test cases, prevent CTest from running these tests
++    # concurrently. See #4654
++    if (TEST MdrunCoordinationCouplingTests2Ranks AND TEST MdrunCoordinationCouplingTests1Rank)
++        set_tests_properties(MdrunCoordinationCouplingTests2Ranks PROPERTIES DEPENDS MdrunCoordinationCouplingTests1Rank)
++    endif()
+ endif()
+
+ set(exename "mdrun-coordination-constraints-test")
+@@ -292,6 +340,12 @@ if (CMAKE_BUILD_TYPE MATCHES "Rel" AND GMX_OPENMP)
+     gmx_register_gtest_test(${testname} ${exename} MPI_RANKS 1 SLOW_TEST IGNORE_LEAKS SLOW_GPU_TEST)
+     set(testname "MdrunCoordinationConstraintsTests2Ranks")
+     gmx_register_gtest_test(${testname} ${exename} MPI_RANKS 2 SLOW_TEST IGNORE_LEAKS SLOW_GPU_TEST)
++    # Because the mdrun tests depend on writing files whose names are not
++    # unique across test cases, prevent CTest from running these tests
++    # concurrently. See #4654
++    if (TEST MdrunCoordinationConstraintsTests2Ranks AND TEST MdrunCoordinationConstraintsTests1Rank)
++        set_tests_properties(MdrunCoordinationConstraintsTests2Ranks PROPERTIES DEPENDS MdrunCoordinationConstraintsTests1Rank)
++    endif()
+ endif()
+
+ # Keeping the FEP tests separate for now to be able to judge runtime more easily
+diff --git a/src/testutils/testinit.cpp b/src/testutils/testinit.cpp
+index ca3ed8db2c52940a128701e2e5ae4999904a2802..5db9bb1af05631eab768c259e4e4f328e0efa7ff 100644
+--- a/src/testutils/testinit.cpp
++++ b/src/testutils/testinit.cpp
+@@ -191,7 +191,7 @@ void initTestUtils(const std::filesystem::path& dataPath,
+             {
+                 fprintf(stderr,
+                         "NOTE: You are running %s on %d MPI ranks, "
+-                        "but it is does not contain MPI-enabled tests. "
++                        "but it does not contain MPI-enabled tests. "
+                         "The test will now exit.\n",
+                         context.programName(),
+                         gmx_node_num());