From 391693f4a6d8698c0251bc2a7775529b08ce59fa Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Mon, 26 Oct 2020 16:49:13 +0100 Subject: [PATCH 1/4] fix LAMMPS-3Mar2020-intel installations on AMD CPUs --- ...MPS-3Mar2020-intel-2019b-Python-3.7.4-kokkos.eb | 2 ++ ...MPS-3Mar2020-intel-2020a-Python-3.8.2-kokkos.eb | 6 +++++- .../lammps-stable_3Mar2020_intel_ebflag.patch | 14 ++++++++++++++ 3 files changed, 21 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/l/LAMMPS/lammps-stable_3Mar2020_intel_ebflag.patch diff --git a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-3Mar2020-intel-2019b-Python-3.7.4-kokkos.eb b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-3Mar2020-intel-2019b-Python-3.7.4-kokkos.eb index a0a8ee53589..572b35ddbfe 100644 --- a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-3Mar2020-intel-2019b-Python-3.7.4-kokkos.eb +++ b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-3Mar2020-intel-2019b-Python-3.7.4-kokkos.eb @@ -25,9 +25,11 @@ sources = [ 'stable_%(version)s.tar.gz', {'filename': 'lammps_vs_yaff_test_single_point_energy.py', 'extract_cmd': "cp %s %(builddir)s"}, ] +patches = ['lammps-stable_3Mar2020_intel_ebflag.patch'] checksums = [ 'a1a2e3e763ef5baecea258732518d75775639db26e60af1634ab385ed89224d1', # stable_3Mar2020.tar.gz 'c28fa5a1ea9608e4fd8686937be501c3bed8cc03ce1956f1cf0a1efce2c75349', # lammps_vs_yaff_test_single_point_energy.py + '491a2da88f37960e0d9013bd28108bf3c6952733ab2664ea7395acfb2e7ccdf9', # lammps-stable_3Mar2020_intel_ebflag.patch ] local_source_dir_name = '%(namelower)s-%(version)s' diff --git a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-3Mar2020-intel-2020a-Python-3.8.2-kokkos.eb b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-3Mar2020-intel-2020a-Python-3.8.2-kokkos.eb index 9c903f6b9de..3752cd44de5 100644 --- a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-3Mar2020-intel-2020a-Python-3.8.2-kokkos.eb +++ b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-3Mar2020-intel-2020a-Python-3.8.2-kokkos.eb @@ -25,11 +25,15 @@ sources = [ 'stable_%(version)s.tar.gz', {'filename': 'lammps_vs_yaff_test_single_point_energy.py', 'extract_cmd': "cp %s %(builddir)s"}, ] -patches = ['LAMMPS-3Mar2020_fix-docs-build.patch'] +patches = [ + 'LAMMPS-3Mar2020_fix-docs-build.patch', + 'lammps-stable_3Mar2020_intel_ebflag.patch', +] checksums = [ 'a1a2e3e763ef5baecea258732518d75775639db26e60af1634ab385ed89224d1', # stable_3Mar2020.tar.gz 'c28fa5a1ea9608e4fd8686937be501c3bed8cc03ce1956f1cf0a1efce2c75349', # lammps_vs_yaff_test_single_point_energy.py '7f010853d81022f286cf32e3babe252d5cc7c0bfb274bee5a2c64e810e170239', # LAMMPS-3Mar2020_fix-docs-build.patch + '491a2da88f37960e0d9013bd28108bf3c6952733ab2664ea7395acfb2e7ccdf9', # lammps-stable_3Mar2020_intel_ebflag.patch ] local_source_dir_name = '%(namelower)s-%(version)s' diff --git a/easybuild/easyconfigs/l/LAMMPS/lammps-stable_3Mar2020_intel_ebflag.patch b/easybuild/easyconfigs/l/LAMMPS/lammps-stable_3Mar2020_intel_ebflag.patch new file mode 100644 index 00000000000..1156b6a7c3b --- /dev/null +++ b/easybuild/easyconfigs/l/LAMMPS/lammps-stable_3Mar2020_intel_ebflag.patch @@ -0,0 +1,14 @@ +# remove hard coded -xHost flag for intel compilers (useful on AMD systems, as -xHost may lead to mmx/sse code) +# OCT 26th 2020 by B. Hajgato (UGent) +diff -ru lammps-stable_3Mar2020.orig/src/MAKE/OPTIONS/Makefile.intel_cpu_intelmpi lammps-stable_3Mar2020/src/MAKE/OPTIONS/Makefile.intel_cpu_intelmpi +--- lammps-stable_3Mar2020.orig/src/MAKE/OPTIONS/Makefile.intel_cpu_intelmpi 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/src/MAKE/OPTIONS/Makefile.intel_cpu_intelmpi 2020-10-26 16:41:59.900088648 +0100 +@@ -7,7 +7,7 @@ + # specify flags and libraries needed for your compiler + + CC = mpiicpc -std=c++11 +-OPTFLAGS = -xHost -O2 -fp-model fast=2 -no-prec-div -qoverride-limits \ ++OPTFLAGS = ${EBVAROPTFLAGS} -fp-model fast=2 -no-prec-div -qoverride-limits \ + -qopt-zmm-usage=high + CCFLAGS = -qopenmp -qno-offload -ansi-alias -restrict \ + -DLMP_INTEL_USELRT -DLMP_USE_MKL_RNG $(OPTFLAGS) \ From 5dfd1a192d81bff102c83e5067f977d60797bc2c Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 27 Oct 2020 09:02:22 +0100 Subject: [PATCH 2/4] fix cmake -xHost --- ...AMMPS-3Mar2020-intel-2019b-Python-3.7.4-kokkos.eb | 2 +- ...AMMPS-3Mar2020-intel-2020a-Python-3.8.2-kokkos.eb | 4 +++- .../LAMMPS/lammps-stable_3Mar2020_intel_ebflag.patch | 12 ++++++++++++ 3 files changed, 16 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-3Mar2020-intel-2019b-Python-3.7.4-kokkos.eb b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-3Mar2020-intel-2019b-Python-3.7.4-kokkos.eb index 572b35ddbfe..fd0612cf229 100644 --- a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-3Mar2020-intel-2019b-Python-3.7.4-kokkos.eb +++ b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-3Mar2020-intel-2019b-Python-3.7.4-kokkos.eb @@ -29,7 +29,7 @@ patches = ['lammps-stable_3Mar2020_intel_ebflag.patch'] checksums = [ 'a1a2e3e763ef5baecea258732518d75775639db26e60af1634ab385ed89224d1', # stable_3Mar2020.tar.gz 'c28fa5a1ea9608e4fd8686937be501c3bed8cc03ce1956f1cf0a1efce2c75349', # lammps_vs_yaff_test_single_point_energy.py - '491a2da88f37960e0d9013bd28108bf3c6952733ab2664ea7395acfb2e7ccdf9', # lammps-stable_3Mar2020_intel_ebflag.patch + '3b04681bf8d5c60818a197905f68c83e477ef41824278ebc05d437ecac6d5c0a', # lammps-stable_3Mar2020_intel_ebflag.patch ] local_source_dir_name = '%(namelower)s-%(version)s' diff --git a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-3Mar2020-intel-2020a-Python-3.8.2-kokkos.eb b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-3Mar2020-intel-2020a-Python-3.8.2-kokkos.eb index 3752cd44de5..e9360befb8c 100644 --- a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-3Mar2020-intel-2020a-Python-3.8.2-kokkos.eb +++ b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-3Mar2020-intel-2020a-Python-3.8.2-kokkos.eb @@ -33,7 +33,7 @@ checksums = [ 'a1a2e3e763ef5baecea258732518d75775639db26e60af1634ab385ed89224d1', # stable_3Mar2020.tar.gz 'c28fa5a1ea9608e4fd8686937be501c3bed8cc03ce1956f1cf0a1efce2c75349', # lammps_vs_yaff_test_single_point_energy.py '7f010853d81022f286cf32e3babe252d5cc7c0bfb274bee5a2c64e810e170239', # LAMMPS-3Mar2020_fix-docs-build.patch - '491a2da88f37960e0d9013bd28108bf3c6952733ab2664ea7395acfb2e7ccdf9', # lammps-stable_3Mar2020_intel_ebflag.patch + '3b04681bf8d5c60818a197905f68c83e477ef41824278ebc05d437ecac6d5c0a', # lammps-stable_3Mar2020_intel_ebflag.patch ] local_source_dir_name = '%(namelower)s-%(version)s' @@ -106,6 +106,8 @@ user_packages = [ 'SCAFACOS', 'SMD', 'SMTBQ', 'SPH', 'TALLY', 'UEF', 'YAFF' ] +maxparallel = 1 + enhance_sanity_check = True # run short test case to make sure installation doesn't produce blatently incorrect results; diff --git a/easybuild/easyconfigs/l/LAMMPS/lammps-stable_3Mar2020_intel_ebflag.patch b/easybuild/easyconfigs/l/LAMMPS/lammps-stable_3Mar2020_intel_ebflag.patch index 1156b6a7c3b..51cc9e246a6 100644 --- a/easybuild/easyconfigs/l/LAMMPS/lammps-stable_3Mar2020_intel_ebflag.patch +++ b/easybuild/easyconfigs/l/LAMMPS/lammps-stable_3Mar2020_intel_ebflag.patch @@ -1,5 +1,17 @@ # remove hard coded -xHost flag for intel compilers (useful on AMD systems, as -xHost may lead to mmx/sse code) # OCT 26th 2020 by B. Hajgato (UGent) +diff -ru lammps-stable_3Mar2020.orig/cmake/Modules/Packages/USER-INTEL.cmake lammps-stable_3Mar2020/cmake/Modules/Packages/USER-INTEL.cmake +--- lammps-stable_3Mar2020.orig/cmake/Modules/Packages/USER-INTEL.cmake 2020-03-03 16:27:12.000000000 +0100 ++++ lammps-stable_3Mar2020/cmake/Modules/Packages/USER-INTEL.cmake 2020-10-27 08:54:15.816960998 +0100 +@@ -77,7 +77,7 @@ + if(CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.3 OR CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.4) + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -xCOMMON-AVX512") + else() +- set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -xHost") ++ set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ") + endif() + include(CheckCXXCompilerFlag) + foreach(_FLAG -O2 -fp-model fast=2 -no-prec-div -qoverride-limits -qopt-zmm-usage=high -qno-offload -fno-alias -ansi-alias -restrict) diff -ru lammps-stable_3Mar2020.orig/src/MAKE/OPTIONS/Makefile.intel_cpu_intelmpi lammps-stable_3Mar2020/src/MAKE/OPTIONS/Makefile.intel_cpu_intelmpi --- lammps-stable_3Mar2020.orig/src/MAKE/OPTIONS/Makefile.intel_cpu_intelmpi 2020-03-03 16:27:12.000000000 +0100 +++ lammps-stable_3Mar2020/src/MAKE/OPTIONS/Makefile.intel_cpu_intelmpi 2020-10-26 16:41:59.900088648 +0100 From 38ffb9a148172a60bf911ed7fae63bfb0f6bf8ce Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 27 Oct 2020 09:12:12 +0100 Subject: [PATCH 3/4] remove maxparallel --- .../l/LAMMPS/LAMMPS-3Mar2020-intel-2020a-Python-3.8.2-kokkos.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-3Mar2020-intel-2020a-Python-3.8.2-kokkos.eb b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-3Mar2020-intel-2020a-Python-3.8.2-kokkos.eb index e9360befb8c..03571e9e23b 100644 --- a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-3Mar2020-intel-2020a-Python-3.8.2-kokkos.eb +++ b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-3Mar2020-intel-2020a-Python-3.8.2-kokkos.eb @@ -106,8 +106,6 @@ user_packages = [ 'SCAFACOS', 'SMD', 'SMTBQ', 'SPH', 'TALLY', 'UEF', 'YAFF' ] -maxparallel = 1 - enhance_sanity_check = True # run short test case to make sure installation doesn't produce blatently incorrect results; From 3397a25bdc80312271353e490171f59827f3b7ea Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 3 Sep 2021 15:23:43 +0200 Subject: [PATCH 4/4] consistently apply fix-docs patch for LAMMPS 3Mar2020 --- .../LAMMPS-3Mar2020-foss-2019b-Python-3.7.4-kokkos.eb | 2 ++ .../LAMMPS-3Mar2020-foss-2020a-Python-3.8.2-kokkos.eb | 6 +++++- .../LAMMPS-3Mar2020-intel-2019b-Python-3.7.4-kokkos.eb | 6 +++++- 3 files changed, 12 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-3Mar2020-foss-2019b-Python-3.7.4-kokkos.eb b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-3Mar2020-foss-2019b-Python-3.7.4-kokkos.eb index b0941e89897..5649a33478f 100644 --- a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-3Mar2020-foss-2019b-Python-3.7.4-kokkos.eb +++ b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-3Mar2020-foss-2019b-Python-3.7.4-kokkos.eb @@ -25,9 +25,11 @@ sources = [ 'stable_%(version)s.tar.gz', {'filename': 'lammps_vs_yaff_test_single_point_energy.py', 'extract_cmd': "cp %s %(builddir)s"}, ] +patches = ['LAMMPS-3Mar2020_fix-docs-build.patch'] checksums = [ 'a1a2e3e763ef5baecea258732518d75775639db26e60af1634ab385ed89224d1', # stable_3Mar2020.tar.gz 'c28fa5a1ea9608e4fd8686937be501c3bed8cc03ce1956f1cf0a1efce2c75349', # lammps_vs_yaff_test_single_point_energy.py + '7f010853d81022f286cf32e3babe252d5cc7c0bfb274bee5a2c64e810e170239', # LAMMPS-3Mar2020_fix-docs-build.patch ] local_source_dir_name = '%(namelower)s-%(version)s' diff --git a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-3Mar2020-foss-2020a-Python-3.8.2-kokkos.eb b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-3Mar2020-foss-2020a-Python-3.8.2-kokkos.eb index 9cc825d8371..64fb76ca4d1 100644 --- a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-3Mar2020-foss-2020a-Python-3.8.2-kokkos.eb +++ b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-3Mar2020-foss-2020a-Python-3.8.2-kokkos.eb @@ -26,10 +26,14 @@ sources = [ {'filename': 'lammps_vs_yaff_test_single_point_energy.py', 'extract_cmd': "cp %s %(builddir)s"}, ] # see https://github.com/lammps/lammps/pull/1483 for why this is needed -patches = ['lammps-stable_3Mar2020_hack_openmp_gcc9.patch'] +patches = [ + 'LAMMPS-3Mar2020_fix-docs-build.patch', + 'lammps-stable_3Mar2020_hack_openmp_gcc9.patch', +] checksums = [ 'a1a2e3e763ef5baecea258732518d75775639db26e60af1634ab385ed89224d1', # stable_3Mar2020.tar.gz 'c28fa5a1ea9608e4fd8686937be501c3bed8cc03ce1956f1cf0a1efce2c75349', # lammps_vs_yaff_test_single_point_energy.py + '7f010853d81022f286cf32e3babe252d5cc7c0bfb274bee5a2c64e810e170239', # LAMMPS-3Mar2020_fix-docs-build.patch '41a0bcb828be22d38bb489bbd4b1fd7803d7771a2308371f01e961c52b8c869f', # lammps-stable_3Mar2020_hack_openmp_gcc9.patch ] diff --git a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-3Mar2020-intel-2019b-Python-3.7.4-kokkos.eb b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-3Mar2020-intel-2019b-Python-3.7.4-kokkos.eb index 41af48624a3..722f37b89e8 100644 --- a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-3Mar2020-intel-2019b-Python-3.7.4-kokkos.eb +++ b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-3Mar2020-intel-2019b-Python-3.7.4-kokkos.eb @@ -25,10 +25,14 @@ sources = [ 'stable_%(version)s.tar.gz', {'filename': 'lammps_vs_yaff_test_single_point_energy.py', 'extract_cmd': "cp %s %(builddir)s"}, ] -patches = ['lammps-stable_3Mar2020_intel_ebflag.patch'] +patches = [ + 'LAMMPS-3Mar2020_fix-docs-build.patch', + 'lammps-stable_3Mar2020_intel_ebflag.patch', +] checksums = [ 'a1a2e3e763ef5baecea258732518d75775639db26e60af1634ab385ed89224d1', # stable_3Mar2020.tar.gz 'c28fa5a1ea9608e4fd8686937be501c3bed8cc03ce1956f1cf0a1efce2c75349', # lammps_vs_yaff_test_single_point_energy.py + '7f010853d81022f286cf32e3babe252d5cc7c0bfb274bee5a2c64e810e170239', # LAMMPS-3Mar2020_fix-docs-build.patch '3b04681bf8d5c60818a197905f68c83e477ef41824278ebc05d437ecac6d5c0a', # lammps-stable_3Mar2020_intel_ebflag.patch ]