Gromacs 5.0 for UV2000
ウェブページ
バージョン
5.0
ビルド環境
- Intel Compiler 13.1.1
- MPT 2.0.7
- cmake 2.8.11
ビルドに必要なファイル
- gromacs-5.0.tar.gz
- no-gcc-version.patch
- no-mpifinalized.patch
パッチファイル
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 "${CUDA_HOST_COMPILER_OPTIONS}"
CACHE STRING "Options for nvcc host compiler (do not edit!)." FORCE)
no-mpifinalized.patch
--- src/gromacs/utility/init.cpp.orig 2014-07-10 11:07:50.617514888 +0900
+++ src/gromacs/utility/init.cpp 2014-07-10 11:09:20.845939159 +0900
@@ -67,8 +67,6 @@
{
#ifdef GMX_LIB_MPI
int isInitialized = 0, isFinalized = 0;
- MPI_Finalized(&isFinalized);
- GMX_RELEASE_ASSERT(!isFinalized, "Invalid attempt to initialize MPI after finalization");
MPI_Initialized(&isInitialized);
if (isInitialized)
{
注意事項
GMX_CPU_ACCELERATION=AVX_256にするとregressiontestsのfreeenergyの2つのテストでFailとなる。
そのため、SSE4.1も別途用意した。
ビルド手順
#!/bin/csh -f
umask 022
set file_gromacs=/home/users/${USER}/build/gromacs500/gromacs-5.0.tar.gz
set file_patch1=/home/users/${USER}/build/gromacs500/no-gcc-version.patch
set file_patch3=/home/users/${USER}/build/gromacs500/no-mpifinalized.patch
set prefix_avx256=/local/apl/uv/gromacs500
set prefix_sse41=/local/apl/uv/gromacs500_sse41
set work=/work/users/${USER}
source /opt/intel/composer_xe_2013.3.163/bin/compilervars.csh intel64
#------------------------------------------------------------------------------
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 < ${file_patch3}
#
setenv CC icc
setenv CXX icpc
setenv F77 ifort
setenv F90 ifort
setenv FC ifort
mkdir rccs-s
cd rccs-s
cmake .. -DCMAKE_INSTALL_PREFIX=${prefix_avx256} \
-DCMAKE_VERBOSE_MAKEFILE=ON \
-DGMX_MPI=OFF \
-DGMX_GPU=OFF \
-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
cmake .. -DCMAKE_INSTALL_PREFIX=${prefix_avx256} \
-DCMAKE_VERBOSE_MAKEFILE=ON \
-DGMX_MPI=OFF \
-DGMX_GPU=OFF \
-DGMX_DOUBLE=ON \
-DGMX_FFT_LIBRARY=mkl \
-DGMX_SYMLINK_OLD_BINARY_NAMES=OFF \
-DREGRESSIONTEST_DOWNLOAD=OFF
make -j 12
make install
cd ..
#
mkdir rccs-s-sse41
cd rccs-s-sse41
cmake .. -DCMAKE_INSTALL_PREFIX=${prefix_sse41} \
-DCMAKE_VERBOSE_MAKEFILE=ON \
-DGMX_MPI=OFF \
-DGMX_GPU=OFF \
-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
cmake .. -DCMAKE_INSTALL_PREFIX=${prefix_sse41} \
-DCMAKE_VERBOSE_MAKEFILE=ON \
-DGMX_MPI=OFF \
-DGMX_GPU=OFF \
-DGMX_DOUBLE=ON \
-DGMX_FFT_LIBRARY=mkl \
-DGMX_CPU_ACCELERATION=SSE4.1 \
-DGMX_SYMLINK_OLD_BINARY_NAMES=OFF \
-DREGRESSIONTEST_DOWNLOAD=OFF
make -j 12
make install
cd ..
#
setenv CC mpicc
setenv CXX mpicxx
setenv F77 mpif90
setenv F90 mpif90
setenv FC mpif90
mkdir rccs-mpi
cd rccs-mpi
cmake .. -DCMAKE_INSTALL_PREFIX=${prefix_avx256} \
-DCMAKE_VERBOSE_MAKEFILE=ON \
-DGMX_MPI=ON \
-DGMX_GPU=OFF \
-DGMX_DOUBLE=OFF \
-DGMX_FFT_LIBRARY=mkl \
-DMPIEXEC=/opt/sgi/mpt/mpt-2.07/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
cmake .. -DCMAKE_INSTALL_PREFIX=${prefix_avx256} \
-DCMAKE_VERBOSE_MAKEFILE=ON \
-DGMX_MPI=ON \
-DGMX_GPU=OFF \
-DGMX_DOUBLE=ON \
-DGMX_FFT_LIBRARY=mkl \
-DMPIEXEC=/opt/sgi/mpt/mpt-2.07/bin/mpirun \
-DGMX_SYMLINK_OLD_BINARY_NAMES=OFF \
-DREGRESSIONTEST_DOWNLOAD=OFF
make -j 12
make install
cd ..
mkdir rccs-mpi-sse41
cd rccs-mpi-sse41
cmake .. -DCMAKE_INSTALL_PREFIX=${prefix_sse41} \
-DCMAKE_VERBOSE_MAKEFILE=ON \
-DGMX_MPI=ON \
-DGMX_GPU=OFF \
-DGMX_DOUBLE=OFF \
-DGMX_FFT_LIBRARY=mkl \
-DGMX_CPU_ACCELERATION=SSE4.1 \
-DMPIEXEC=/opt/sgi/mpt/mpt-2.07/bin/mpirun \
-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
cmake .. -DCMAKE_INSTALL_PREFIX=${prefix_sse41} \
-DCMAKE_VERBOSE_MAKEFILE=ON \
-DGMX_MPI=ON \
-DGMX_GPU=OFF \
-DGMX_DOUBLE=ON \
-DGMX_FFT_LIBRARY=mkl \
-DGMX_CPU_ACCELERATION=SSE4.1 \
-DMPIEXEC=/opt/sgi/mpt/mpt-2.07/bin/mpirun \
-DGMX_SYMLINK_OLD_BINARY_NAMES=OFF \
-DREGRESSIONTEST_DOWNLOAD=OFF
make -j 12
make install
cd ..