Gromacs 5.0 for Primargy RX300/CX250
Webpage
Version
5.0
Tools for Compiling
- Intel Compiler 13.1.1
- Cuda compilation tools, release 5.0, V0.2.1221
- Intel MPI 4.1.0.030
- cmake 2.8.8
Necessary Files for Compiling
- gromacs-5.0.tar.gz
- no-gcc-version.patch
- int128.patch
Patch Files
no-gcc-version.patch
--- cmake/gmxManageNvccConfig.cmake.orig 2014-07-09 09:43:31.108489646 +0900
+++ cmake/gmxManageNvccConfig.cmake 2014-07-09 09:44:24.668688300 +0900
@@ -109,16 +109,16 @@
# as even with icc used as host compiler, when icc's gcc compatibility
# mode is higher than the max gcc version officially supported by CUDA,
# nvcc will freak out.
- if (UNIX AND CMAKE_C_COMPILER_ID MATCHES "Intel" AND
- CUDA_HOST_COMPILER_AUTOSET)
- if (CUDA_VERSION VERSION_LESS "4.1")
- message(STATUS "Setting Intel Compiler compatibity mode to gcc 4.4 for nvcc host compilation")
- set(CUDA_HOST_COMPILER_OPTIONS "${CUDA_HOST_COMPILER_OPTIONS};-Xcompiler;-gcc-version=440;")
- else()
- message(STATUS "Setting Intel Compiler compatibity mode to gcc 4.5 for nvcc host compilation")
- set(CUDA_HOST_COMPILER_OPTIONS "${CUDA_HOST_COMPILER_OPTIONS};-Xcompiler;-gcc-version=450;")
- endif()
- endif()
+# if (UNIX AND CMAKE_C_COMPILER_ID MATCHES "Intel" AND
+# CUDA_HOST_COMPILER_AUTOSET)
+# if (CUDA_VERSION VERSION_LESS "4.1")
+# message(STATUS "Setting Intel Compiler compatibity mode to gcc 4.4 for nvcc host compilation")
+# set(CUDA_HOST_COMPILER_OPTIONS "${CUDA_HOST_COMPILER_OPTIONS};-Xcompiler;-gcc-version=440;")
+# else()
+# message(STATUS "Setting Intel Compiler compatibity mode to gcc 4.5 for nvcc host compilation")
+# set(CUDA_HOST_COMPILER_OPTIONS "${CUDA_HOST_COMPILER_OPTIONS};-Xcompiler;-gcc-version=450;")
+# endif()
+# endif()
set(CUDA_HOST_COMPILER_OPTIONS "${CUDA_HOST_COMPILER_OPTIONS}"
CACHE STRING "Options for nvcc host compiler (do not edit!)." FORCE)
int128.patch
--- src/external/boost/boost/config/compiler/intel.hpp.orig 2014-06-18 00:14:19.000000000 +0900 +++ src/external/boost/boost/config/compiler/intel.hpp 2014-07-09 09:59:27.000000000 +0900 @@ -35,10 +35,14 @@ #endif #ifdef BOOST_INTEL_STDCXX0X +#ifndef BOOST_COMPILER #define BOOST_COMPILER "Intel C++ C++0x mode version " BOOST_STRINGIZE(BOOST_INTEL_CXX_VERSION) +#endif #else +#ifndef BOOST_COMPILER #define BOOST_COMPILER "Intel C++ version " BOOST_STRINGIZE(BOOST_INTEL_CXX_VERSION) #endif +#endif #define BOOST_INTEL BOOST_INTEL_CXX_VERSION #if defined(_WIN32) || defined(_WIN64) @@ -303,10 +307,6 @@ # define BOOST_HAS_STDINT_H #endif -#if defined(__LP64__) && defined(__GNUC__) && (BOOST_INTEL_CXX_VERSION >= 1310) -# define BOOST_HAS_INT128 -#endif - // // last known and checked version: #if (BOOST_INTEL_CXX_VERSION > 1310)
Attention
Setting GMX_CPU_ACCELERATION=AVX_256 makes two fails in freeenergy of regressiontests.
So, need preparation of SSE4.1 binary files.
Procedure of Compiling
#!/bin/csh -f
umask 022
set file_gromacs=/home/users/${USER}/build/gromacs500/gromacs-5.0.tar.gz
set file_patch1=/home/users/${USER}/build/gromacs500/no-gcc-version.patch
set file_patch2=/home/users/${USER}/build/gromacs500/int128.patch
set prefix_avx256=/local/apl/pg/gromacs500
set prefix_sse41=/local/apl/pg/gromacs500_sse41
set work=/work/users/${USER}
#------------------------------------------------------------------------------
cd ${work}
if (-d gromacs-5.0) then
mv gromacs-5.0 gromacs-erase
rm -rf gromacs-erase &
endif
tar xzf ${file_gromacs}
cd gromacs-5.0
patch -p0 < ${file_patch1}
patch -p0 < ${file_patch2}
#
setenv CC icc
setenv CXX icpc
setenv F77 ifort
setenv F90 ifort
setenv FC ifort
mkdir rccs-gpu
cd rccs-gpu
cmake28 .. -DCMAKE_INSTALL_PREFIX=${prefix_avx256} \
-DCMAKE_VERBOSE_MAKEFILE=ON \
-DGMX_MPI=OFF \
-DGMX_GPU=ON \
-DGMX_DOUBLE=OFF \
-DGMX_FFT_LIBRARY=mkl \
-DGMX_SYMLINK_OLD_BINARY_NAMES=OFF \
-DREGRESSIONTEST_DOWNLOAD=OFF
make -j 12
make install
cd ..
#
mkdir rccs-d
cd rccs-d
cmake28 .. -DCMAKE_INSTALL_PREFIX=${prefix_avx256} \
-DCMAKE_VERBOSE_MAKEFILE=ON \
-DGMX_MPI=OFF \
-DGMX_GPU=OFF \
-DGMX_DOUBLE=ON \
-DGMX_FFT_LIBRARY=mkl \
-DGMX_SYMLINK_OLD_BINARY_NAMES=OFF \
-DREGRESSIONTEST_DOWNLOAD=OFF
make -j 12
make install
cd ..
#
mkdir rccs-gpu-sse41
cd rccs-gpu-sse41
cmake28 .. -DCMAKE_INSTALL_PREFIX=${prefix_sse41} \
-DCMAKE_VERBOSE_MAKEFILE=ON \
-DGMX_MPI=OFF \
-DGMX_GPU=ON \
-DGMX_DOUBLE=OFF \
-DGMX_FFT_LIBRARY=mkl \
-DGMX_CPU_ACCELERATION=SSE4.1 \
-DGMX_SYMLINK_OLD_BINARY_NAMES=OFF \
-DREGRESSIONTEST_DOWNLOAD=OFF
make -j 12
make install
cd ..
#
mkdir rccs-d-sse41
cd rccs-d-sse41
cmake28 .. -DCMAKE_INSTALL_PREFIX=${prefix_sse41} \
-DCMAKE_VERBOSE_MAKEFILE=ON \
-DGMX_MPI=OFF \
-DGMX_GPU=OFF \
-DGMX_DOUBLE=ON \
-DGMX_FFT_LIBRARY=mkl \
-DGMX_CPU_ACCELERATION=SSE4.1 \
-DGMX_SYMLINK_OLD_BINARY_NAMES=OFF \
-DREGRESSIONTEST_DOWNLOAD=OFF
make -j 12
make install
cd ..
setenv CC mpiicc
setenv CXX mpiicpc
setenv F77 mpiifort
setenv F90 mpiifort
setenv FC mpiifort
mkdir rccs-mpi
cd rccs-mpi
cmake28 .. -DCMAKE_INSTALL_PREFIX=${prefix_avx256} \
-DCMAKE_VERBOSE_MAKEFILE=ON \
-DGMX_MPI=ON \
-DGMX_GPU=OFF \
-DGMX_DOUBLE=OFF \
-DGMX_FFT_LIBRARY=mkl \
-DMPIEXEC=/opt/intel/impi/4.1.0.030/intel64/bin/mpirun \
-DGMX_SYMLINK_OLD_BINARY_NAMES=OFF \
-DREGRESSIONTEST_DOWNLOAD=OFF
make -j 12
make install
cd ..
#
mkdir rccs-mpi-d
cd rccs-mpi-d
cmake28 .. -DCMAKE_INSTALL_PREFIX=${prefix_avx256} \
-DCMAKE_VERBOSE_MAKEFILE=ON \
-DGMX_MPI=ON \
-DGMX_GPU=OFF \
-DGMX_DOUBLE=ON \
-DGMX_FFT_LIBRARY=mkl \
-DMPIEXEC=/opt/intel/impi/4.1.0.030/intel64/bin/mpirun \
-DGMX_SYMLINK_OLD_BINARY_NAMES=OFF \
-DREGRESSIONTEST_DOWNLOAD=OFF
make -j 12
make install
cd ..
#
mkdir rccs-mpi-sse41
cd rccs-mpi-sse41
cmake28 .. -DCMAKE_INSTALL_PREFIX=${prefix_sse41} \
-DCMAKE_VERBOSE_MAKEFILE=ON \
-DGMX_MPI=ON \
-DGMX_GPU=OFF \
-DGMX_DOUBLE=OFF \
-DGMX_FFT_LIBRARY=mkl \
-DMPIEXEC=/opt/intel/impi/4.1.0.030/intel64/bin/mpirun \
-DGMX_CPU_ACCELERATION=SSE4.1 \
-DGMX_SYMLINK_OLD_BINARY_NAMES=OFF \
-DREGRESSIONTEST_DOWNLOAD=OFF
make -j 12
make install
cd ..
#
mkdir rccs-mpi-d-sse41
cd rccs-mpi-d-sse41
cmake28 .. -DCMAKE_INSTALL_PREFIX=${prefix_sse41} \
-DCMAKE_VERBOSE_MAKEFILE=ON \
-DGMX_MPI=ON \
-DGMX_GPU=OFF \
-DGMX_DOUBLE=ON \
-DGMX_FFT_LIBRARY=mkl \
-DMPIEXEC=/opt/intel/impi/4.1.0.030/intel64/bin/mpirun \
-DGMX_CPU_ACCELERATION=SSE4.1 \
-DGMX_SYMLINK_OLD_BINARY_NAMES=OFF \
-DREGRESSIONTEST_DOWNLOAD=OFF
make -j 12
make install
cd ..