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Gromacs 5.1.5 for LX (intel compiler)

Webpage

http://www.gromacs.org/

Version

5.1.5

Build Environment

  • Intel Compiler 2018.2.199
  • Intel MKL 2018 Update 2
  • Intel MPI 2017.3.196
  • cmake 2.8.12.2

Files Required

  • gromacs-5.1.5.tar.gz
  • (regressiontests-5.1.5.tar.gz; testset)

Build Procedure

#!/bin/sh

VERSION=5.1.5

GROMACS_TARBALL=/home/users/${USER}/gromacs-${VERSION}.tar.gz
#REGRESSION=/home/users/${USER}/regressiontests-${VERSION} # unpacked

INSTALL_PREFIX=/local/apl/lx/gromacs515
WORKDIR=/work/users/${USER}

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

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

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

# compiler setting for single node versions
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=OFF \
    -DGMX_DOUBLE=OFF \
    -DGMX_THREAD_MPI=ON \
    -DGMX_FFT_LIBRARY=mkl \
    -DREGRESSIONTEST_DOWNLOAD=OFF
make -j12 && 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_FFT_LIBRARY=mkl \
    -DREGRESSIONTEST_DOWNLOAD=OFF
make -j12 && 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=OFF \
    -DGMX_DOUBLE=OFF \
    -DGMX_THREAD_MPI=OFF \
    -DGMX_FFT_LIBRARY=mkl \
    -DREGRESSIONTEST_DOWNLOAD=OFF
make -j12 && 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=OFF \
    -DGMX_FFT_LIBRARY=mkl \
    -DREGRESSIONTEST_DOWNLOAD=OFF
make -j12 && make install
cd ..

Notice

Single precision versions failed on SelectionCollectionDataTest.HandlesCharge unittest due to a tricky numerical error (in comparison of 5(int)/10.0(float) < 0.5(float; read from str)). Double precision version can pass the test.