2018.3
(テストはインストール後に実行)
#!/bin/sh
VERSION=2018.3
INSTALL_PREFIX=/local/apl/lx/gromacs2018.3-CUDABASEDIR=/home/users/${USER}
GROMACS_TARBALL=${BASEDIR}/gromacs-${VERSION}.tar.gz
WORKDIR=/work/users/${USER}PARALLEL=12
#---------------------------------------------------------------------
umask 0022module purge
module load intel_parallelstudio/2017update4
module load cuda/9.1
module load cmake/3.8.2cd ${WORKDIR}
if [ -d gromacs-${VERSION} ]; then
mv gromacs-${VERSION} gromacs_erase
rm -rf gromacs_erase &
fitar xzf ${GROMACS_TARBALL}
cd gromacs-${VERSION}# 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=${INSTALL_PREFIX} \
-DCMAKE_VERBOSE_MAKEFILE=ON \
-DGMX_MPI=OFF \
-DGMX_GPU=ON \
-DGMX_DOUBLE=OFF \
-DGMX_THREAD_MPI=ON \
-DGMX_FFT_LIBRARY=mkl \
-DREGRESSIONTEST_DOWNLOAD=OFF
make -j${PARALLEL} && 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=${INSTALL_PREFIX} \
-DCMAKE_VERBOSE_MAKEFILE=ON \
-DGMX_MPI=ON \
-DGMX_GPU=ON \
-DGMX_DOUBLE=OFF \
-DGMX_THREAD_MPI=OFF \
-DGMX_FFT_LIBRARY=mkl \
-DREGRESSIONTEST_DOWNLOAD=OFF
make -j${PARALLEL} && make install
cd ..
#!/bin/sh
#PBS -l select=ncpus=12:mpiprocs=12:ompthreads=1:jobtype=gpu:ngpus=1
#PBS -l walltime=00:30:00if [ -d "${PBS_O_WORKDIR}" ]; then
cd ${PBS_O_WORKDIR}
fimodule purge
module load intel_parallelstudio/2017update4
module load cuda/9.1GMXBASE=/local/apl/lx/gromacs2018.3-CUDA
REGRESSIONS=/work/users/${USER}/regressiontests-2018.3
MPIRUN=`which mpirun`cd $REGRESSIONS
. ${GMXBASE}/bin/GMXRC.bash# MPI test
PARALLEL="-np 12"
./gmxtest.pl ${PARALLEL} \
-ntomp 1 \
-mpirun ${MPIRUN} \
all# thread MPI test
PARALLEL="-nt 12"
./gmxtest.pl ${PARALLEL} \
-ntomp 1 \
all