wiki.chpc.ac.za

GROMACS (GROningen MAchine for Chemical Simulations) is a molecular dynamics package primarily designed for simulations of proteins, lipids and nucleic acids.

HPCAC Guide [http://www.hpcadvisorycouncil.com/pdf/GROMACS_Best_Practices.pdf]
Acceleration and parallelization [http://www.gromacs.org/Documentation/Acceleration_and_parallelization]

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

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

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

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

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

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

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: http://www.ace.chpc.ac.za/tars/regressiontests.tar.gz

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