Gromacs 4.6.5 for Primargy RX300/CX250

Webpage

http://www.gromacs.org/

Version

 4.6.5

Tools for Compiling

  • Intel Compiler 13.1.1
  • Cuda compilation tools, release 5.0, V0.2.1221
  • Intel MPI 4.1.3.049
  • cmake 2.8

Necessary Files for Compiling

  • gromacs-4.6.5.tar.gz

Attention

Setting GMX_CPU_ACCELERATION=AVX_256 makes two fails in freeenergy of regressiontests.

Procedure of Compiling

#!/bin/csh -f
umask 022
set file_gromacs=/home/users/${USER}/build/gromacs465/gromacs-4.6.5.tar.gz
set work=/work/users/${USER}
set prefix=/local/apl/pg/gromacs465
set sse41_prefix=/local/apl/pg/gromacs465_sse41
#------------------------------------------------------------------------------
cd ${work}
if (-d gromacs-4.6.5) then
  mv gromacs-4.6.5 gromacs-4.6.5-erase
  rm -rf gromacs-4.6.5-erase &
endif
tar xzf ${file_gromacs}
cd gromacs-4.6.5
#
setenv CC icc
setenv CXX icpc
setenv F77 ifort
setenv F90 ifort
setenv FC ifort
mkdir rccs-gpu
cd rccs-gpu
cmake28 .. -DCMAKE_INSTALL_PREFIX=${prefix} \
    -DCMAKE_VERBOSE_MAKEFILE=ON \
    -DGMX_MPI=OFF \
    -DGMX_GPU=ON \
    -DGMX_DOUBLE=OFF \
    -DGMX_FFT_LIBRARY=mkl \
    -DREGRESSIONTEST_DOWNLOAD=OFF
make -j 12
make install
cd ..
#
mkdir rccs-d
cd rccs-d
cmake28 .. -DCMAKE_INSTALL_PREFIX=${prefix} \
    -DCMAKE_VERBOSE_MAKEFILE=ON \
    -DGMX_MPI=OFF \
    -DGMX_GPU=OFF \
    -DGMX_DOUBLE=ON \
    -DGMX_FFT_LIBRARY=mkl \
    -DREGRESSIONTEST_DOWNLOAD=OFF
make -j 12
make install
cd ..
#
mkdir rccs-d-sse41
cd rccs-d-sse41
cmake28 .. -DCMAKE_INSTALL_PREFIX=${sse41_prefix} \
    -DCMAKE_VERBOSE_MAKEFILE=ON \
    -DGMX_MPI=OFF \
    -DGMX_GPU=OFF \
    -DGMX_DOUBLE=ON \
    -DGMX_FFT_LIBRARY=mkl \
    -DGMX_CPU_ACCELERATION=SSE4.1 \
    -DREGRESSIONTEST_DOWNLOAD=OFF
make -j 12
make install
cd ..
#
setenv CC mpiicc
setenv CXX mpiicpc
setenv F77 mpiifort
setenv F90 mpiifort
setenv FC mpiifort
mkdir rccs-mpi
cd rccs-mpi
cmake28 .. -DCMAKE_INSTALL_PREFIX=${prefix} \
    -DCMAKE_VERBOSE_MAKEFILE=ON \
    -DGMX_MPI=ON \
    -DGMX_GPU=OFF \
    -DGMX_DOUBLE=OFF \
    -DGMX_FFT_LIBRARY=mkl \
    -DMPIEXEC=/opt/intel/impi/4.1.3.049/intel64/bin/mpirun \
    -DREGRESSIONTEST_DOWNLOAD=OFF
make -j 12
make install
cd ..
#
mkdir rccs-mpi-d
cd rccs-mpi-d
cmake28 .. -DCMAKE_INSTALL_PREFIX=${prefix} \
    -DCMAKE_VERBOSE_MAKEFILE=ON \
    -DGMX_MPI=ON \
    -DGMX_GPU=OFF \
    -DGMX_DOUBLE=ON \
    -DGMX_FFT_LIBRARY=mkl \
    -DMPIEXEC=/opt/intel/impi/4.1.3.049/intel64/bin/mpirun \
    -DREGRESSIONTEST_DOWNLOAD=OFF
make -j 12
make install
cd ..
#
mkdir rccs-mpi-d-sse41
cd rccs-mpi-d-sse41
cmake28 .. -DCMAKE_INSTALL_PREFIX=${sse41_prefix} \
    -DCMAKE_VERBOSE_MAKEFILE=ON \
    -DGMX_MPI=ON \
    -DGMX_GPU=OFF \
    -DGMX_DOUBLE=ON \
    -DGMX_FFT_LIBRARY=mkl \
    -DGMX_CPU_ACCELERATION=SSE4.1 \
    -DMPIEXEC=/opt/intel/impi/4.1.3.049/intel64/bin/mpirun \
    -DREGRESSIONTEST_DOWNLOAD=OFF
make -j 12
make install
cd ..
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