Gromacs 2021.2 - Intel+CUDA

Webpage

http://www.gromacs.org/

Version

2021.2

Build Environment

• Intel Parallel Studio 2020 update 2
• cuda 11.1
• GCC 9.3.1 (Software Collections devtoolset-9)
• cmake 3.16.3

Files Required

• gromacs-2021.2.tar.gz
• regressiontests-2021.2.tar.gz

Build Procedure

#!/bin/sh

VERSION=2021.2
INSTALL_PREFIX=/local/apl/lx/gromacs${VERSION}-intel-CUDA

BASEDIR=/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}

PARALLEL=12
export LANG=C

#---------------------------------------------------------------------
umask 0022

module purge
module load scl/devtoolset-9
module load intel_parallelstudio/2020update2
module load cuda/11.1
module load cmake/3.16.3

cd ${WORKDIR}
if [ -d gromacs-${VERSION} ]; then
  mv gromacs-${VERSION} gromacs_erase
  rm -rf gromacs_erase &
fi

if [ -d regressiontests-${VERSION} ]; then
  mv regressiontests-${VERSION} regressiontests_erase
  rm -rf regressiontests_erase &
fi

tar xzf ${GROMACS_TARBALL}
tar xzf ${REGRESSION_TARBALL}
cd gromacs-${VERSION}

# single precision, no MPI
mkdir rccs-s
cd rccs-s
cmake .. \
   -DCMAKE_INSTALL_PREFIX=${INSTALL_PREFIX} \
   -DCMAKE_VERBOSE_MAKEFILE=ON \
   -DCMAKE_C_COMPILER=icc \
   -DCMAKE_CXX_COMPILER=icpc \
   -DGMX_MPI=OFF \
   -DGMX_GPU=CUDA \
   -DGMX_DOUBLE=OFF \
   -DGMX_THREAD_MPI=ON \
   -DGMX_BUILD_OWN_FFTW=ON \
   -DREGRESSIONTEST_DOWNLOAD=OFF \
   -DREGRESSIONTEST_PATH=${REGRESSION_PATH}
make -j${PARALLEL} && make check && make install
cd ..

# single precision, with MPI
mkdir rccs-mpi-s
cd rccs-mpi-s
cmake .. \
   -DCMAKE_INSTALL_PREFIX=${INSTALL_PREFIX} \
   -DCMAKE_VERBOSE_MAKEFILE=ON \
   -DCMAKE_C_COMPILER=mpiicc \
   -DCMAKE_CXX_COMPILER=mpiicpc \
   -DGMX_MPI=ON \
   -DGMX_GPU=CUDA \
   -DGMX_DOUBLE=OFF \
   -DGMX_THREAD_MPI=OFF \
   -DGMX_BUILD_OWN_FFTW=ON \
   -DREGRESSIONTEST_DOWNLOAD=OFF \
   -DREGRESSIONTEST_PATH=${REGRESSION_PATH}
make -j${PARALLEL} && make check && make install
cd ..