GENESIS 2.1.6.1

Webpage

https://mdgenesis.org/
https://github.com/genesis-release-r-ccs/genesis

Version

2.1.6.1

Build Environment

  • Intel oneAPI Compiler 2025.3.2 (oneAPI 2025.3.1)
  • MKL 2025.3 (oneAPI 2025.3.1)
  • Intel MPI 2021.17.2 (oneAPI 2025.3.1)

Files Required

  • genesis-2.1.6.1.tar.gz

Build Procedure

#!/bin/sh

VERSION=2.1.6.1
BASEDIR=/home/users/${USER}/Software/GENESIS/${VERSION}
TARBALL=${BASEDIR}/genesis-${VERSION}.tar.gz

INSTALL_DIR=/apl/genesis/2.1.6.1

WORKDIR=/gwork/users/${USER}

PARALLEL_TESTS=8

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

module -s purge
. ~/intel/oneapi/compiler/latest/env/vars.sh # oneAPI 2025.3.1
module -s load compiler-rt/2025.3.2
module -s load mkl/2025.3
module -s load intelmpi/2021.17.2

export LANG=C
export LC_ALL=C
export OMP_NUM_THREADS=1
#MKL_LIBS="$(mkl_link_tool --quiet -libs -c ifx)"
ulimit -s unlimited

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

tar xf ${TARBALL}
cd genesis-${VERSION}

sed -i -e 975i'FARCFLAGS=" -march=core-avx2"' configure.ac

autoreconf
FC=mpiifx CC=mpiicx ./configure --prefix=${INSTALL_DIR}
make && make install

# tests
ATDYN=${INSTALL_DIR}/bin/atdyn
SPDYN=${INSTALL_DIR}/bin/spdyn

cd tests/regression_test
for f in test.py test_remd.py test_fep.py test_rpath.py \
                test_vib.py test_gamd.py \
                test_analysis/test_analysis.py \
                test_spana/test_spana.py; do
 sed -i -e "s/env python/env python3/" $f
done

# atdyn tests
./test.py           "mpirun -np ${PARALLEL_TESTS} $ATDYN"
./test_remd.py      "mpirun -np ${PARALLEL_TESTS} $ATDYN"
./test_rpath.py     "mpirun -np ${PARALLEL_TESTS} $ATDYN"
./test_vib.py       "mpirun -np ${PARALLEL_TESTS} $ATDYN"
./test_gamd.py      "mpirun -np ${PARALLEL_TESTS} $ATDYN"
#./test_fep.py       "mpirun -np ${PARALLEL_TESTS} $ATDYN" # spdyn only

# spdyn tests
./test.py           "mpirun -np ${PARALLEL_TESTS} $SPDYN"
./test_remd.py      "mpirun -np ${PARALLEL_TESTS} $SPDYN"
./test_rpath.py     "mpirun -np ${PARALLEL_TESTS} $SPDYN"
./test_gamd.py      "mpirun -np ${PARALLEL_TESTS} $SPDYN"
./test_fep.py       "mpirun -np ${PARALLEL_TESTS} $SPDYN"

cd test_analysis
./test_analysis.py ${INSTALL_DIR}/bin
cd ../

cd test_spana
sed -i -e '/ref_fobj =/s/"r"/"r", encoding="utf-8"/' test_spana.py
sed -i -e '/out_fobj =/s/"r"/"r", encoding="utf-8"/' test_spana.py
./test_spana.py ${INSTALL_DIR}/bin
cd ..

Tests

All the tests have passed successfully.

Notes

  • Intel Compiler 2025.3.2 (oneAPI 2025.3.1) version shows a slightly better performance than gcc13/gcc15 version.
    • On the other hand, Intel Compiler 2025.0.4 (oneAPI 2025.0.1) version is not so good.
  • Intel MPI version shows slightly better performance than Open MPI 4.1.8 version.