Gromacs 2021.2 - GCC9

Webpage

http://www.gromacs.org/

Version

2021.2

Build Environment

• Intel MPI 2019.0.8 (2019.8.254)
• Intel MKL 2020.0.2
• 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}

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 mpi/intelmpi/2019.8.254
module load mkl/2020.0.2
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=${INSTALL_PREFIX} \
   -DCMAKE_VERBOSE_MAKEFILE=ON \
   -DCMAKE_C_COMPILER=gcc \
   -DCMAKE_CXX_COMPILER=g++ \
   -DGMX_MPI=OFF \
   -DGMX_GPU=OFF \
   -DGMX_DOUBLE=OFF \
   -DGMX_THREAD_MPI=ON \
   -DGMX_BUILD_OWN_FFTW=ON \
   -DREGRESSIONTEST_DOWNLOAD=OFF \
   -DREGRESSIONTEST_PATH=${REGRESSION_PATH}
make -j${PARALLEL} && make check && make install
cd ..

# double precision, no MPI
module unload mkl
mkdir rccs-d
cd rccs-d
cmake .. \
   -DCMAKE_INSTALL_PREFIX=${INSTALL_PREFIX} \
   -DCMAKE_VERBOSE_MAKEFILE=ON \
   -DCMAKE_C_COMPILER=gcc \
   -DCMAKE_CXX_COMPILER=g++ \
   -DGMX_MPI=OFF \
   -DGMX_GPU=OFF \
   -DGMX_DOUBLE=ON \
   -DGMX_THREAD_MPI=ON \
   -DGMX_BUILD_OWN_FFTW=ON \
   -DREGRESSIONTEST_DOWNLOAD=OFF \
   -DREGRESSIONTEST_PATH=${REGRESSION_PATH}
make -j${PARALLEL} && make check && make install
cd ..

# single precision, with MPI
module load mkl/2020.0.2
mkdir rccs-mpi-s
cd rccs-mpi-s
cmake .. \
   -DCMAKE_INSTALL_PREFIX=${INSTALL_PREFIX} \
   -DCMAKE_VERBOSE_MAKEFILE=ON \
   -DCMAKE_C_COMPILER=mpicc \
   -DCMAKE_CXX_COMPILER=mpicxx \
   -DGMX_MPI=ON \
   -DGMX_GPU=OFF \
   -DGMX_DOUBLE=OFF \
   -DGMX_THREAD_MPI=OFF \
   -DGMX_BUILD_OWN_FFTW=ON \
   -DREGRESSIONTEST_DOWNLOAD=OFF \
   -DREGRESSIONTEST_PATH=${REGRESSION_PATH}
make -j${PARALLEL} && make check && make install
cd ..

# double precision, with MPI
module unload mkl
mkdir rccs-mpi-d
cd rccs-mpi-d
cmake .. \
   -DCMAKE_INSTALL_PREFIX=${INSTALL_PREFIX} \
   -DCMAKE_VERBOSE_MAKEFILE=ON \
   -DCMAKE_C_COMPILER=mpicc \
   -DCMAKE_CXX_COMPILER=mpicxx \
   -DGMX_MPI=ON \
   -DGMX_GPU=OFF \
   -DGMX_DOUBLE=ON \
   -DGMX_THREAD_MPI=OFF \
   -DGMX_BUILD_OWN_FFTW=ON \
   -DREGRESSIONTEST_DOWNLOAD=OFF \
   -DREGRESSIONTEST_PATH=${REGRESSION_PATH}
make -j${PARALLEL} && make check && make install
cd ..

Notes

• This GCC build is the default version of 2021.2.
• Double precision thread-mpi version failed on nmode tests if MKL is available. We thus avoid MKL for double precision version. (OpenBLAS is used instaed.)
  • (Double precision MPI version passed the nmode test. However, I am not sure if it would work correcly. Therefore, we don't use MKL for that build.)
  • If MKL is disabled for single precision versions, it will degrade the performance slightly.
• (For small scale calculations, gcc-8 version might show a slightly better performance.)