GENESIS 2.1.4 with GPU support

ウェブページ

https://www.r-ccs.riken.jp/labs/cbrt/

バージョン

2.1.4

ビルド環境

  • gcc 13.1.1 (gcc-toolset/13)
  • MKL 2025.0.0.1 (oneAPI 2025.0.1)
  • Intel MPI 2021.14.1 (oneAPI 2025.0.1)
  • CUDA 12.6 Update 2

ビルドに必要なファイル

  • genesis-2.1.4.tar.bz2
  • tests-2.1.4.tar.bz2

ビルド手順

#!/bin/sh

VERSION=2.1.4
BASEDIR=/home/users/${USER}/Software/GENESIS/${VERSION}
SRC_TARBALL=${BASEDIR}/genesis-${VERSION}.tar.bz2
TESTS_TARBALL=${BASEDIR}/tests-${VERSION}.tar.bz2

INSTALLDIR=/apl/genesis/2.1.4-CUDA

WORKDIR=/gwork/users/${USER}
BUILDDIR=${WORKDIR}/genesis-${VERSION}
TESTSDIR=${WORKDIR}/tests-${VERSION}

PARALLEL_TESTS=8

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

module -s purge
module -s load gcc-toolset/13
module -s load mkl/2025.0.0.1
module -s load intelmpi/2021.14.1
module -s load cuda/12.6u2

export LANG=C
export LC_ALL=C
export OMP_NUM_THREADS=1
ulimit -s unlimited

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

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

tar jxf ${SRC_TARBALL}
tar jxf ${TESTS_TARBALL}

cd ${BUILDDIR}
FC=mpif90 CC=mpicc \
LAPACK_LIBS=" -L${MKLROOT}/lib/intel64 -Wl,--no-as-needed -lmkl_gf_lp64 -lmkl_gnu_thread -lmkl_core -lgomp -lpthread -lm -ldl" \
 ./configure --prefix=${INSTALLDIR} \
             --enable-gpu \
             --enable-single \
             --with-cuda=/apl/cuda/12.6u2

make && make install

SPDYN=${INSTALLDIR}/bin/spdyn

cd ${TESTSDIR}/regression_test

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

# 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"

メモ

  • 上記スクリプトは ccgpu で実行。別途、計算ノードの A100 でも動作確認を実行済。
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