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acelab:gromacs

General Info

GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. It is primarily designed for biochemical molecules like proteins, lipids and nucleic acids that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non-biological systems, e.g. polymers. source

Installation Guide

cd ~
mkdir GROMACS
cd GROMACS

Create a source file:

vim bashrc
source /data/opt/intel/bin/compilervars.sh intel64
source /data/opt/intel/mkl/bin/mklvars.sh intel64
export PATH=/data/opt/openmpi-1.8.7-ics2013/bin:$PATH
export LD_LIBRARY_PATH=/data/opt/openmpi-1.8.7-ics2013/lib:$LD_LIBRARY_PATH
export PATH=/home/$USER/GROMACS/libs/binutils/bin:$PATH
export LD_LIBRARY_PATH=/home/$USER/GROMACS/libs/binutils/lib:$LD_LIBRARY_PATH
export PATH=/home/$USER/GROMACS/libs/cmake/bin:$PATH
export CC=icc
export CXX=icpc
export CFLAGS='-O3'
export CXXFLAGS='-O3'
export F77=ifort
export FC=ifort
export F90=ifort
export FFLAGS='-O3'
export CPP='icc -E'
export CXXCPP='icpc -E'
source bashrc
mkdir tars
mkidr libs
mkdir tests
cd tars

Install dependencies from repository:

sudo yum install blas-devel lapack-devel atlas-devel libxml2-devel
CMAKE
cd ~/GROMACS/tars
wget http://www.cmake.org/files/v3.0/cmake-3.0.2.tar.gz
tar -xf cmake-3.0.2.tar.gz
cd cmake-3.0.2
./configure --prefix=/home/$USER/GROMACS/libs/cmake
make -j4
make install
BINUTILS
cd ~/GROMACS/tars
wget https://ftp.gnu.org/gnu/binutils/binutils-2.25.tar.gz
tar -xf binutils-2.25.tar.gz
cd binutils-2.25
./configure --prefix=/home/$USER/GROMACS/libs/binutils
make -j4
make install
GROMACS
cd ~/GROMACS/tars
wget https://kth.box.com/shared/static/7uwctwj33h4uo2f8d1tmdyj9afaj3hzy.gz
tar -xf 7uwctwj33h4uo2f8d1tmdyj9afaj3hzy.gz
cd gromacs-5.0.6
mkdir build
cd build
x86 build
cmake .. -DCMAKE_C_COMPILER=mpicc -DCMAKE_CXX_COMPILER=mpicxx -DGMX_GPU=off -DGMX_MPI=on -DGMX_SIMD=AVX2_256 -DCMAKE_INSTALL_PREFIX=/home/$USER/GROMACS/gromacs-x86/ -DGMX_BUILD_OWN_FFTW=ON -DGMX_BUILD_UNITTESTS=ON
make -j10
make install
CUDA build

The CUDA version requires a CUDA SDK of at least version 4.0, however the latest is recommended (version 7.0 was used for testing). If the SDK in not found in the default /usr/local/cuda directory, then source it.

cmake .. -DCMAKE_C_COMPILER=mpicc -DCMAKE_CXX_COMPILER=mpicxx -DGMX_GPU=on -DGMX_MPI=on -DGMX_SIMD=AVX2_256 -DCMAKE_INSTALL_PREFIX=/home/$USER/GROMACS/gromacs-cuda/ -DGMX_BUILD_UNITTESTS=ON
make -j10
make install

Test Installation

Source the GROMACS installation:

export PATH=/home/$USER/GROMACS/gromacs-x86/bin:$PATH

Test the installation by using the regression tests which ship with the release, available here: regressiontests.tar.gz

cd ~/GROMACS/tests
tar -xf Regressiontests.tar.gz
cd regressiontests
./gmxtest.pl -suffix _mpi all

Benchmark

/var/www/wiki/data/pages/acelab/gromacs.txt · Last modified: 2015/09/02 12:17 by mcawood