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add patch for GROMACS 2019.3 easyconfigs using CMake 3.15.3 to fix CPU detection #14212

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Merged
merged 1 commit into from
Oct 27, 2021
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add patch for GROMACS 2019.3 easyconfigs using CMake 3.15.3 to fix CPU detection #14212

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4 changes: 3 additions & 1 deletion easybuild/easyconfigs/g/GROMACS/GROMACS-2019.3-foss-2019b.eb
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Original file line number Diff line number Diff line change
Expand Up @@ -37,13 +37,15 @@ sources = [SOURCELOWER_TAR_GZ]
patches = [
'GROMACS-2019_fix_omp_num_threads_and_google_test_death_style_in_tests.patch',
'GROMACS-2018_dont_do_gpu_tests_on_cpu_build.patch',
'GROMACS-2019_fix_cpu_detection.patch',
]
checksums = [
'4211a598bf3b7aca2b14ad991448947da9032566f13239b1a05a2d4824357573', # gromacs-2019.3.tar.gz
# GROMACS-2019_fix_omp_num_threads_and_google_test_death_style_in_tests.patch
'406f5edd204be812f095a6f07ebc2673c5f6ddf1b1c1428fd336a80b9c629275',
# GROMACS-2018_dont_do_gpu_tests_on_cpu_build.patch
'727cc1afd9061002390e474b01aeb40efd984e6b7febd1cfe5e69a0a82b21f06'
'727cc1afd9061002390e474b01aeb40efd984e6b7febd1cfe5e69a0a82b21f06',
'6e305416773639e050f8cef6195e9de6f4555b213d093210bb0b2c0f37e9ef91', # GROMACS-2019_fix_cpu_detection.patch
]

builddependencies = [
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2 changes: 2 additions & 0 deletions easybuild/easyconfigs/g/GROMACS/GROMACS-2019.3-fosscuda-2019b.eb
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Original file line number Diff line number Diff line change
Expand Up @@ -37,13 +37,15 @@ sources = [SOURCELOWER_TAR_GZ]
patches = [
'GROMACS-2019_fix_omp_num_threads_and_google_test_death_style_in_tests.patch',
'GROMACS-2019_increase_test_timeout_for_GPU.patch',
'GROMACS-2019_fix_cpu_detection.patch',
]
checksums = [
'4211a598bf3b7aca2b14ad991448947da9032566f13239b1a05a2d4824357573', # gromacs-2019.3.tar.gz
# GROMACS-2019_fix_omp_num_threads_and_google_test_death_style_in_tests.patch
'406f5edd204be812f095a6f07ebc2673c5f6ddf1b1c1428fd336a80b9c629275',
# GROMACS-2019_increase_test_timeout_for_GPU.patch
'0d16f53d428155197a0ed0b0974ce03422f199d7c463c4a9156a3b99e3c86234',
'6e305416773639e050f8cef6195e9de6f4555b213d093210bb0b2c0f37e9ef91', # GROMACS-2019_fix_cpu_detection.patch
]

builddependencies = [
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47 changes: 47 additions & 0 deletions easybuild/easyconfigs/g/GROMACS/GROMACS-2019_fix_cpu_detection.patch
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Original file line number Diff line number Diff line change
@@ -0,0 +1,47 @@
There is a bug in the CPU detection when using CMake from 2019b toolchain.
Taking the diff between 2019 and 2019.4 makes the problem go away.

Åke Sandgren, 20211026
diff -ru gromacs-2019/cmake/gmxDetectCpu.cmake gromacs-2019.4/cmake/gmxDetectCpu.cmake
--- gromacs-2019/cmake/gmxDetectCpu.cmake 2017-07-23 18:42:23.000000000 +0200
+++ gromacs-2019.4/cmake/gmxDetectCpu.cmake 2019-10-02 08:23:32.000000000 +0200
@@ -1,7 +1,7 @@
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
+# Copyright (c) 2012,2013,2014,2015,2016,2017,2019, 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.
@@ -78,13 +78,13 @@
# for x86 we need inline assembly to use cpuid
gmx_test_inline_asm_gcc_x86(GMX_X86_GCC_INLINE_ASM)
if(GMX_X86_GCC_INLINE_ASM)
- set(GCC_INLINE_ASM_DEFINE "-DGMX_X86_GCC_INLINE_ASM=1")
+ set(GCC_INLINE_ASM_DEFINE -DGMX_X86_GCC_INLINE_ASM=1)
else()
- set(GCC_INLINE_ASM_DEFINE "-DGMX_X86_GCC_INLINE_ASM=0")
+ set(GCC_INLINE_ASM_DEFINE -DGMX_X86_GCC_INLINE_ASM=0)
endif()

- set(_compile_definitions "${GCC_INLINE_ASM_DEFINE} -I${PROJECT_SOURCE_DIR}/src -DGMX_CPUINFO_STANDALONE ${GMX_STDLIB_CXX_FLAGS} -DGMX_TARGET_X86=${GMX_TARGET_X86_VALUE}")
- set(LINK_LIBRARIES "${GMX_STDLIB_LIBRARIES}")
+ set(_compile_definitions ${GCC_INLINE_ASM_DEFINE};-I${PROJECT_SOURCE_DIR}/src;-DGMX_CPUINFO_STANDALONE=1;-DGMX_TARGET_X86=${GMX_TARGET_X86_VALUE})
+ set(LINK_LIBRARIES ${GMX_STDLIB_LIBRARIES})
try_compile(CPU_DETECTION_COMPILED
"${PROJECT_BINARY_DIR}"
"${PROJECT_SOURCE_DIR}/src/gromacs/hardware/cpuinfo.cpp"
@@ -93,7 +93,11 @@
OUTPUT_VARIABLE CPU_DETECTION_COMPILED_OUTPUT
COPY_FILE ${CPU_DETECTION_BINARY})
if(NOT CPU_DETECTION_COMPILED AND NOT RUN_CPU_DETECTION_COMPILATION_QUIETLY)
- message(STATUS "Did not detect build CPU ${LOWERTYPE} - detection program did not compile")
+ if(GMX_TARGET_X86)
+ message(WARNING "CPU detection program did not compile on x86 host - this should never happen. It is VERY bad for performance, since you will lose all SIMD support. Please file a bug report.")
+ else()
+ message(WARNING "Did not detect build CPU ${LOWERTYPE} - detection program did not compile. Please file a bug report if this is a common platform.")
+ endif()
endif()
set(RUN_CPU_DETECTION_COMPILATION_QUIETLY TRUE CACHE INTERNAL "Keep quiet on any future compilation attempts")
endif()