安装GROMACS

1、编译器最低要求

GNU (gcc) 5.1
CMake 3.9.6

2、安装GCC-7.3

# yum install -y gcc gcc-c++ gcc-gfortran texinfo
# wget http://mirrors.ustc.edu.cn/gnu/gcc/gcc-7.3.0/gcc-7.3.0.tar.gz
# tar zxvf gcc-7.3.0.tar.gz
# cd gcc-7.3.0
# sh ./contrib/download_prerequisites
# mkdir build && cd build
# ../configure --prefix=/usr/local/gcc-7.3 --disable-bootstrap --enable-languages=c,c++,fortran --disable-multilib
# make -j
# make install
# vim ~/.bashrc
export GCC_HOME=/usr/local/gcc-7.3
export PATH=$GCC_HOME/bin:$PATH
export MANPATH=$GCC_HOME/share/man
export CPATH=$GCC_HOME/include:$CPANT
export LD_LIBRARY_PATH=$GCC_HOME/lib:$GCC_HOME/lib64:$LD_LIBARAY_PATH
export LIBRARY_PATH=$GCC_HOME/lib:$GCC_HOME/lib64:$LIBRARY_PATH

 

3、安装CMake 3.15

# wget https://cmake.org/files/v3.15/cmake-3.15.6.tar.gz
# tar zxvf cmake-3.15.6.tar.gz
# cd cmake-3.15.6
# ./bootstrap --prefix=/usr/local/cmake --parallel=4 --sphinx-man
# make -j4
# make install
# vim ~/.bashrc
export PATH=/usr/local/cmake/bin:$PATH

 

4、安装OpenMPI

# wget https://download.open-mpi.org/release/open-mpi/v4.0/openmpi-4.0.4.tar.bz2
# tar jxvf openmpi-4.0.4.tar.bz2
# cd openmpi-4.0.4 && # mkdir build && cd build
# ../configure --prefix=/usr/local/openmpi
# make -j4
# make install
# vim ~/.bashrc
export PATH=/usr/local/openmpi/bin:$PATH
export LD_LIBRARY_PATH=/usr/local/openmpi/lib:$LD_LIBRARY_PATH

 

5、安装GROMACS

# wget http://ftp.gromacs.org/pub/gromacs/gromacs-2020.3.tar.gz
# tar zxvf gromacs-2020.3.tar.gz
# cd gromacs-2020.3
# mkdir build && cd build
# cmake .. -DGMX_MPI=ON -DGMX_OPENMP=ON -DCMAKE_C_COMPILER=mpicc -DCMAKE_CXX_COMPILER=mpicxx -DGMX_BUILD_OWN_FFTW=ON \
    -DGMX_FFT_LIBRARY=fftw3 -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=/usr/local/gromacs
# make -j
# make check
# make install
# source /usr/local/gromacs/bin/GMXRC

 

6、基准测试

# wget https://www.mpibpc.mpg.de/15101317/benchMEM.zip
# mkdir benchmake_case && cd benchmake_case
# unzip ../benchMEM.zip
# mpirun -np 4 gmx_mpi mdrun -s benchMEM.tpr