This version is outdated by a newer approved version.DiffThis version (2014/11/04 13:59) is a draft.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

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.1415109551.txt.gz
  • Last modified: 2014/11/04 13:59
  • by sh