Gromacs 5.1.2 for UV2000

Webpage

http://www.gromacs.org/

Version

 5.1.2

Tools for Compiling

  • Intel Compiler 15.0.2
  • MPT 2.11
  • cmake 2.8.11

Necessary Files for Compiling

Patch Files

no-mpifinalized.patch

--- src/gromacs/utility/init.cpp.orig    2014-07-10 11:07:50.617514888 +0900
+++ src/gromacs/utility/init.cpp    2014-07-10 11:09:20.845939159 +0900
@@ -67,8 +67,6 @@
 {
 #ifdef GMX_LIB_MPI
     int isInitialized = 0, isFinalized = 0;
-    MPI_Finalized(&isFinalized);
-    GMX_RELEASE_ASSERT(!isFinalized, "Invalid attempt to initialize MPI after finalization");
     MPI_Initialized(&isInitialized);
     if (isInitialized)
     {

Procedure of Compiling

#!/bin/csh -f
umask 022
set file_gromacs=/home/users/${USER}/build/gromacs512/gromacs-5.1.2.tar.gz
set file_patch3=/home/users/${USER}/build/gromacs512/no-mpifinalized.patch
set prefix=/local/apl/uv/gromacs512
set work=/work/users/${USER}
source /opt/intel/composer_xe_2015.2.164/bin/compilervars.csh intel64
#------------------------------------------------------------------------------
cd ${work}
if (-d gromacs-5.1.2) then
  mv gromacs-5.1.2 gromacs-erase
  rm -rf gromacs-erase &
endif
tar xzf ${file_gromacs}
cd gromacs-5.1.2
patch -p0 < ${file_patch3}
#
setenv CC icc
setenv CXX icpc
setenv F77 ifort
setenv F90 ifort
setenv FC ifort
mkdir rccs-s
cd rccs-s
cmake .. -DCMAKE_INSTALL_PREFIX=${prefix} \
    -DCMAKE_VERBOSE_MAKEFILE=ON \
    -DGMX_MPI=OFF \
    -DGMX_THREAD_MPI=OFF \
    -DGMX_GPU=OFF \
    -DGMX_DOUBLE=OFF \
    -DGMX_FFT_LIBRARY=mkl \
    -DREGRESSIONTEST_DOWNLOAD=OFF
make -j 12
make install
cd ..
#
mkdir rccs-d
cd rccs-d
cmake .. -DCMAKE_INSTALL_PREFIX=${prefix} \
    -DCMAKE_VERBOSE_MAKEFILE=ON \
    -DGMX_MPI=OFF \
    -DGMX_THREAD_MPI=OFF \
    -DGMX_GPU=OFF \
    -DGMX_DOUBLE=ON \
    -DGMX_FFT_LIBRARY=mkl \
    -DREGRESSIONTEST_DOWNLOAD=OFF
make -j 12
make install
cd ..
#
#
setenv CC mpicc
setenv CXX mpicxx
setenv F77 mpif90
setenv F90 mpif90
setenv FC mpif90
mkdir rccs-mpi
cd rccs-mpi
cmake .. -DCMAKE_INSTALL_PREFIX=${prefix} \
    -DCMAKE_VERBOSE_MAKEFILE=ON \
    -DGMX_MPI=ON \
    -DGMX_THREAD_MPI=OFF \
    -DGMX_GPU=OFF \
    -DGMX_DOUBLE=OFF \
    -DGMX_FFT_LIBRARY=mkl \
    -DMPIEXEC=/opt/sgi/mpt/mpt-2.11/bin/mpirun \
    -DREGRESSIONTEST_DOWNLOAD=OFF
make -j 12
make install
cd ..
#
mkdir rccs-mpi-d
cd rccs-mpi-d
cmake .. -DCMAKE_INSTALL_PREFIX=${prefix} \
    -DCMAKE_VERBOSE_MAKEFILE=ON \
    -DGMX_MPI=ON \
    -DGMX_THREAD_MPI=OFF \
    -DGMX_GPU=OFF \
    -DGMX_DOUBLE=ON \
    -DGMX_FFT_LIBRARY=mkl \
    -DMPIEXEC=/opt/sgi/mpt/mpt-2.11/bin/mpirun \
    -DREGRESSIONTEST_DOWNLOAD=OFF
make -j 12
make install
cd ..
View PDF