Gromacs 2020.6 (gnu)

Webpage

http://www.gromacs.org/

Version

2020.6

Build Environment

• Intel Parallel Studio XE 2018 update 4 (for MKL & MPI)
• GCC 8.3.1 (Software Collections devtoolset-8)
• cmake 3.16.3

Files Required

• gromacs-2020.6.tar.gz
• regressiontests-2020.6.tar.gz

Build Procedure

#!/bin/sh

VERSION=2020.6
INSTALL_PREFIX=/local/apl/lx/gromacs${VERSION}-gnu

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

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

module purge
module load scl/devtoolset-8
module load intel_parallelstudio/2018update4
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=${INSTALL_PREFIX} \
   -DCMAKE_VERBOSE_MAKEFILE=ON \
   -DGMX_MPI=OFF \
   -DGMX_GPU=OFF \
   -DGMX_DOUBLE=OFF \
   -DGMX_THREAD_MPI=ON \
   -DGMX_BUILD_OWN_FFTW=ON \
   -DREGRESSIONTEST_DOWNLOAD=OFF \
   -DREGRESSIONTEST_PATH=${REGRESSION_PATH}
make -j${PARALLEL} && make check && make install
cd ..

# double precision, no MPI
mkdir rccs-d
cd rccs-d
cmake .. \
   -DCMAKE_INSTALL_PREFIX=${INSTALL_PREFIX} \
   -DCMAKE_VERBOSE_MAKEFILE=ON \
   -DGMX_MPI=OFF \
   -DGMX_GPU=OFF \
   -DGMX_DOUBLE=ON \
   -DGMX_THREAD_MPI=ON \
   -DGMX_BUILD_OWN_FFTW=mkl \
   -DMKL_LIBRARIES="-L${MKLROOT}/lib/intel64 -Wl,--no-as-needed -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -lpthread -lm -ldl" \
   -DMKL_INCLUDE_DIR="-m64 -I${MKLROOT}/include" \
   -DREGRESSIONTEST_DOWNLOAD=OFF \
   -DREGRESSIONTEST_PATH=${REGRESSION_PATH}
make -j${PARALLEL} && make check && make install
cd ..

# compiler setting for MPI versions
export CC=mpicc
export CXX=mpicxx
export F77=mpif90
export F90=mpif90
export FC=mpif90

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

# double precision, with MPI
mkdir rccs-mpi-d
cd rccs-mpi-d
cmake .. \
   -DCMAKE_INSTALL_PREFIX=${INSTALL_PREFIX} \
   -DCMAKE_VERBOSE_MAKEFILE=ON \
   -DGMX_MPI=ON \
   -DGMX_GPU=OFF \
   -DGMX_DOUBLE=ON \
   -DGMX_THREAD_MPI=mkl \
   -DMKL_LIBRARIES="-L${MKLROOT}/lib/intel64 -Wl,--no-as-needed -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -lpthread -lm -ldl" \
   -DMKL_INCLUDE_DIR="-m64 -I${MKLROOT}/include" \
   -DGMX_BUILD_OWN_FFTW=ON \
   -DREGRESSIONTEST_DOWNLOAD=OFF \
   -DREGRESSIONTEST_PATH=${REGRESSION_PATH}
make -j${PARALLEL} && make check && make install
cd ..

Notes

• Built and tested on ccfep; the same procedure as the previous version.