This version is outdated by a newer approved version.This version (2014/11/04 11:19) is a draft.
Approvals: 0/1
Approvals: 0/1
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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. Here the focus is on the standard MPI implementation; Instructions-Cmake
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 */