Gromacs 2020.2 with GPU (intel)
ウェブページ
バージョン
2020.2
ビルド環境
- Intel Parallel Studio XE 2018 update 4
- GCC 6.3.1 (Software Collections devtoolset-6)
- CUDA 10.1
- cmake 3.16.3
ビルドに必要なファイル
- gromacs-2020.2.tar.gz
- regressiontests-2020.2.tar.gz
- tests_CMakelists.patch
--- tests/CMakeLists.txt.org 2019-10-07 19:24:40.524863424 +0900
+++ tests/CMakeLists.txt 2019-10-07 19:25:13.736715189 +0900
@@ -125,6 +125,11 @@
endif()
#We should use MPIEXEC_NUMPROC_FLAG but gmxtest.pl doesn't let us pass it
endif()
+ if(GMX_THREAD_MPI)
+ set(GMX_TEST_NUMBER_PROCS 8 CACHE STRING "Number of processors used for testing")
+ mark_as_advanced(GMX_TEST_NUMBER_PROCS)
+ list(APPEND ARGS -nt ${GMX_TEST_NUMBER_PROCS})
+ endif()
if(GMX_BINARY_SUFFIX)
list(APPEND ARGS -suffix ${GMX_BINARY_SUFFIX})
endif()
(2019.4 で使ったものをそのまま流用。)
- fftw-3.3.8.tar.gz (ビルドを行った ccgpuv は fftw 配布サイトに直接アクセスできないため)
ビルド手順
#!/bin/sh
VERSION=2020.2
INSTALL_PREFIX=/local/apl/lx/gromacs${VERSION}-CUDABASEDIR=/home/users/${USER}/Software/Gromacs/${VERSION}/
GROMACS_TARBALL=${BASEDIR}/gromacs-${VERSION}.tar.gz
REGRESSION_TARBALL=${BASEDIR}/regressiontests-${VERSION}.tar.gz
WORKDIR=/work/users/${USER}
REGRESSION_PATH=${WORKDIR}/regressiontests-${VERSION}FFTW_VER=3.3.8
FFTW_PATH=${BASEDIR}/fftw-${FFTW_VER}.tar.gzPATCH_TEST=${BASEDIR}/tests_CMakelists.patch
PARALLEL=12
#---------------------------------------------------------------------
umask 0022module purge
module load scl/devtoolset-6
module load intel_parallelstudio/2018update4
module load cuda/10.1
module load cmake/3.16.3cd ${WORKDIR}
if [ -d gromacs-${VERSION} ]; then
mv gromacs-${VERSION} gromacs_erase
rm -rf gromacs_erase &
fiif [ -d regressiontests-${VERSION} ]; then
mv regressiontests-${VERSION} regressiontests_erase
rm -rf regressiontests_erase &
fitar xzf ${GROMACS_TARBALL}
tar xzf ${REGRESSION_TARBALL}
cd gromacs-${VERSION}
patch -p0 < ${PATCH_TEST}# compiler setting
export CC=icc
export CXX=icpc
export F77=ifort
export F90=ifort
export FC=ifort# single precision, no MPI
mkdir rccs-s
cd rccs-s
cmake .. \
-DCMAKE_INSTALL_PREFIX=${INSTALL_PREFIX} \
-DCMAKE_VERBOSE_MAKEFILE=ON \
-DGMX_MPI=OFF \
-DGMX_GPU=ON \
-DGMX_DOUBLE=OFF \
-DGMX_THREAD_MPI=ON \
-DGMX_BUILD_OWN_FFTW=ON \
-DGMX_BUILD_OWN_FFTW_URL=${FFTW_PATH} \
-DREGRESSIONTEST_DOWNLOAD=OFF \
-DREGRESSIONTEST_PATH=${REGRESSION_PATH}
make -j${PARALLEL} && make check && make install
cd ..# compiler setting for MPI versions
export CC=mpiicc
export CXX=mpiicpc
export F77=mpiifort
export F90=mpiifort
export FC=mpiifort# single precision, with MPI
mkdir rccs-mpi-s
cd rccs-mpi-s
cmake .. \
-DCMAKE_INSTALL_PREFIX=${INSTALL_PREFIX} \
-DCMAKE_VERBOSE_MAKEFILE=ON \
-DGMX_MPI=ON \
-DGMX_GPU=ON \
-DGMX_DOUBLE=OFF \
-DGMX_THREAD_MPI=OFF \
-DGMX_BUILD_OWN_FFTW=ON \
-DGMX_BUILD_OWN_FFTW_URL=${FFTW_PATH} \
-DREGRESSIONTEST_DOWNLOAD=OFF \
-DREGRESSIONTEST_PATH=${REGRESSION_PATH}
make -j${PARALLEL} && make check && make install
cd ..
メモ
- ccgpuv でビルド