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GROMACS 5.0.1
Installation VSC-1 (MPI-parallel)
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
GROMACS with gpu support
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 */