This version is outdated by a newer approved version.DiffThis version (2014/11/04 14:49) is a draft.
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1. Make sure we use a recent version of the Intel MPI toolchain.

mpi-selector --query
mpi-selector --list 
... in case 
mpi-selector --set intel_mpi_intel64-4.1.1.036
exit
relogin

2. Follow Instructions-Cmake and prepare for two separate directories, one for building the other for the actual installation.

cd /opt/sw/
wget ftp://ftp.gromacs.org/pub/gromacs/gromacs-5.0.1.tar.gz
gunzip ./gromacs-5.0.1.tar.gz
tar xvf ./gromacs-5.0.1.tar
gzip gromacs-5.0.1.tar
mv ./gromacs-5.0.1 ./gromacs-5.0.1_mpi
chown -R root ./gromacs-5.0.1_mpi 
chgrp -R root ./gromacs-5.0.1_mpi
rm -rf ./gromacs-5.0.1_mpi_build   ( delete all previous attempts and restart from scratch )
mkdir  ./gromacs-5.0.1_mpi_build
cd ./gromacs-5.0.1_mpi_build

3. Download the latest version of fftw and install single and double precision versions of it. For future compatibility with CUDA, gcc is preferred over icc for this step.

cd /opt/sw/fftw
cp from/where/ever/it/is/fftw-3.3.4.tar.gz  ./
gunzip ./fftw-3.3.4.tar.gz
tar xvf ./fftw-3.3.4.tar
gzip fftw-3.3.4.tar
cd ./fftw-3.3.4
./configure --help
export CC=gcc
export F77=gfortran
./configure --prefix=/opt/sw/fftw/fftw-3.3.4 --enable-shared --enable-single --enable-openmp  --enable-sse2
make clean
make
make install

4.

cd /opt/sw/gromacs-5.0.1_mpi_build

up to version 4.5.x openmm is needed for gpu support. For versions from 4.6.x on gpu support is included in gromaces source already.

On VSC-1 Gromacs was built with this cmake command (specifying mpiiccc and mpiicpc did not work here, -DGMX_MPI=ON is enough for compiling with MPI support):

CC=icc CXX=icpc /opt/sw/cmake/2.8.11/bin/cmake -DGMX_GPU=ON -DGMX_MPI=ON -DCMAKE_INSTALL_PREFIX=/opt/sw/gromacs/4.6.5_gpu -DFFTWF_LIBRARY=/opt/sw/fftw/3.3.3_sp/lib/libfftw3f.so -DFFTWF_INCLUDE_DIR=/opt/sw/fftw/3.3.3_sp/include .. 

There might be a problem coming from CUDA, where the intel compiler version is checked. In this case uncomment this part in the /opt/sw/cuda-5.5/include/host_config.h file

//#if defined(__ICC)

//#if !(__INTEL_COMPILER == 9999 && __INTEL_COMPILER_BUILD_DATE == 20110811) || !defined(__GNUC__) || !defined(__LP64__)

//#error -- unsupported ICC configuration! Only ICC 12.1 on Linux x86_64 is supported!

//#endif /* !(__INTEL_COMPILER == 9999 && __INTEL_COMPILER_BUILD_DATE == 20110811) || !__GNUC__ || !__LP64__ */

//#endif /* __ICC */ 
  • doku/gromacs.1415112554.txt.gz
  • Last modified: 2014/11/04 14:49
  • by sh