Shulou(Shulou.com)06/03 Report--

Installation preparation

Cmake2.8.8 or later

Cpene Centrum +

3.gromacs package

Http://www.gromacs.org/Downloads

Installation steps

Tar xfz gromacs.tar.gz

Cd gromacs

Mkdir build

Cmake.. /

-DCMAKE_INSTALL_PREFIX=/opt/software/gromacs specifies the installation directory

-DGMX_BINARY_SUFFIX=_5.0.7_s specifies that the execution file suffix defaults to gmx (serial single precision), gmx_mpi (parallel single precision), and gmx_mpi_d (parallel double precision).

-DGMX_LIBS_SUFFIX=_5.0.7_s library file suffix

-DGMX_MPI=ON uses the mpich compiler build

-DGMX_OPENMP=ON uses the openmpi compiler build

-DGMX_SIMD=None specify the level of SIMD support of the node on

Which mdrun will run

-DGMX_X11=ON

-DGMX_DEFAULT_SUFFIX=OFF turns off the default suffix

-DCMAKE_CXX_COMPILER=icpc specifies the C++ compiler

-DCMAKE_C_COMPILER=icc specifies the C compiler

-DBUILD_SHARED_LIBS=ON to build a shared library

-DGMX_BUILD_OWN_FFTW=ON-DGMX_BUILD_OWN_FFTW_MD5=2edab8c06b24feeb3b82bbb3ebf3e7b3-DGMX_BUILD_OWN_FFTW_URL=/backup/fftw-3.3.4.tar.gz-DGMX_GPU=OFF-DGMX_DOUBLE=ON turns on double precision default single precision

Parameters are required for CUDA version.

-DGMX_GPU=ON-DGMX_TOOLKIT_ROOT_DIR=/usr/local/cuda

2 > & 1 | tee cmake.log

Make & & makeinstall

There are more than 100 execution files in gromacs4.6.7 and previous versions. Between gromacs5.0 and 5.0.7, you should want to integrate execution commands step by step. All commands appear as soft links to gmx commands. After version 5.1, there is only gmx command.

Cpu version test command

Source / opt/software/gromacs-XXX/bin/GMXRC.bash # Environment variables

Mpirun-np 4 gmx_XXX_s mdrun-s md.tpr-ntomp 1

Cuda version test commands to be updated

Welcome to subscribe "Shulou Technology Information " to get latest news, interesting things and hot topics in the IT industry, and controls the hottest and latest Internet news, technology news and IT industry trends.