【3.1】gromacs的安装

一、安装(g01)

1.1 部署环境

sudo mkdir -p /opt/fastone/softwares/hpc-kits
sudo tar xvf hpc-kits-v1.tar.gz -C /opt/fastone/softwares/hpc-kits
source /opt/fastone/softwares/hpc-kits/hpc-kits.sh

1.2 安装普通版本

cd /mnt/nfs/data/software/gromacs/src/gromacs-2020.3/

mkdir build
cd build


cd /mnt/nfs/data/software/gromacs/src/gromacs-2020.3/build2

BUILD_FLAGS=" -DGMX_FFT_LIBRARY=mkl -DMKL_LIBRARIES=${MKLROOT}/lib/intel64/libmkl_intel_lp64.so;${MKLROOT}/lib/intel64/libmkl_sequential.so;${MKLROOT}/lib/intel64/libmkl_core.so;${MKLROOT}/lib/intel64/libmkl_blacs_openmpi_lp64.so -DMKL_INCLUDE_DIR=$MKLROOT/include  -DGMX_SIMD=AVX2_256  -DCMAKE_INSTALL_PREFIX=/data/software/gromacs/gromacs-2020.3 -DCMAKE_C_COMPILER=mpicc -DCMAKE_CXX_COMPILER=mpicxx "

cmake .. $BUILD_FLAGS

make -j 32 2>&1 | tee make.log
make install

1.3 安装gpu版本

cd /mnt/nfs/data/software/gromacs/src/gromacs-2020.3/build

BUILD_FLAGS="-DGMX_GPU=ON -DGMX_FFT_LIBRARY=mkl -DMKL_LIBRARIES=${MKLROOT}/lib/intel64/libmkl_intel_lp64.so;${MKLROOT}/lib/intel64/libmkl_sequential.so;${MKLROOT}/lib/intel64/libmkl_core.so;${MKLROOT}/lib/intel64/libmkl_blacs_openmpi_lp64.so -DMKL_INCLUDE_DIR=$MKLROOT/include -DGMX_DEFAULT_SUFFIX=OFF -DGMX_BINARY_SUFFIX=_gpu_mpi -DGMX_LIBS_SUFFIX=_gpu_mpi -DGMX_SIMD=AVX2_256 -DGMX_BUILD_MDRUN_ONLY=on -DCMAKE_INSTALL_PREFIX=/data/software/gromacs/gromacs-2020.3 -DCMAKE_C_COMPILER=mpicc -DCMAKE_CXX_COMPILER=mpicxx -DGMX_MPI=on -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON"

cmake .. $BUILD_FLAGS

make -j 32 2>&1 | tee make.log
make install

二、使用

使用

source /opt/fastone/softwares/hpc-kits/hpc-kits.sh
source /data/software/gromacs/gromacs-2020.3/bin/GMXRC

查看帮助：

gmx  help commands

或者：

gmx  help selections