Difference between revisions of "How to compile Gromacs"
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| + | ==Gromacs 5.0.4 MPI (double)== | ||
| + | Download source code to /share/apps/download | ||
| + | |||
| + | See the Installation_Instructions | ||
| + | |||
| + | <code> | ||
| + | tar -zxvf ../gromacs-5.0.4.tar.gz <br/> | ||
| + | cd gromacs-5.0.4 <br/> | ||
| + | mkdir build-gmx <br/> | ||
| + | cd build-gmx <br/> | ||
| + | export MPICCDIR=/share/apps/openmpi/bin <br/> | ||
| + | <br/> | ||
| + | CMAKE_PREFIX_PATH=/share/apps/fftw3 \ <br/> | ||
| + | cmake .. \ <br/> | ||
| + | -DGMX_DOUBLE=ON \ <br/> | ||
| + | -DCMAKE_INSTALL_PREFIX=/share/apps/gmx-double-MPI <br/> | ||
| + | -DGMX_X11=OFF \ <br/> | ||
| + | -DCMAKE_CXX_COMPILER=${MPICCDIR}/mpicxx \ <br/> | ||
| + | -DCMAKE_C_COMPILER=${MPICCDIR}/mpicc \ <br/> | ||
| + | -DGMX_MPI=ON \ <br/> | ||
| + | -DGMX_PREFER_STATIC_LIBS=ON <br/> | ||
| + | <br/> | ||
| + | make -j 8 <br/> | ||
| + | make install <br/> | ||
| + | </code> <br/> | ||
| + | |||
| + | ==Gromacs 5.0.4 CUDA (single)== | ||
| + | Download source code to /share/apps/download | ||
| + | |||
| + | See the Installation_Instructions | ||
| + | |||
| + | <code> | ||
| + | tar -zxvf ../gromacs-5.0.4.tar.gz <br/> | ||
| + | cd gromacs-5.0.4 <br/> | ||
| + | mkdir build-gmx-cuda <br/> | ||
| + | cd build-gmx-cuda <br/> | ||
| + | <br/> | ||
| + | cmake .. \ <br/> | ||
| + | -DGMX_DOUBLE=ON \ <br/> | ||
| + | -DCMAKE_INSTALL_PREFIX=/share/apps/gmx-single-CUDA <br/> | ||
| + | -DGMX_GPU=ON <br/> | ||
| + | -DCUDA_TOOLKIT_ROOT_DIR=/share/apps/cuda <br/> | ||
| + | -DGMX_BUILD_OWN_FFTW=ON <br/> | ||
| + | <br/> | ||
| + | make -j 8 <br/> | ||
| + | make install <br/> | ||
| + | </code> <br/> | ||
| + | |||
| + | ==Gromacs 5.0.4 multicore (double)== | ||
| + | Download source code to /share/apps/download | ||
| + | |||
| + | See the Installation_Instructions | ||
| + | |||
| + | <code> | ||
| + | tar -zxvf ../gromacs-5.0.4.tar.gz <br/> | ||
| + | cd gromacs-5.0.4 <br/> | ||
| + | mkdir build-gmx <br/> | ||
| + | cd build-gmx <br/> | ||
| + | <br/> | ||
| + | CMAKE_PREFIX_PATH=/share/apps/fftw3 \ <br/> | ||
| + | cmake .. \ <br/> | ||
| + | -DGMX_DOUBLE=ON \ <br/> | ||
| + | -DCMAKE_INSTALL_PREFIX=/share/apps/gmx-double-multicore <br/> | ||
| + | <br/> | ||
| + | make -j 8 <br/> | ||
| + | make install <br/> | ||
| + | </code> <br/> | ||
| + | |||
==Gromacs MPI Compilation== | ==Gromacs MPI Compilation== | ||
Download gromacs-4.5.5.tar.gz into /usr/local/src/gromacs | Download gromacs-4.5.5.tar.gz into /usr/local/src/gromacs | ||
Revision as of 18:21, 24 December 2014
Contents
[hide]Gromacs 5.0.4 MPI (double)
Download source code to /share/apps/download
See the Installation_Instructions
tar -zxvf ../gromacs-5.0.4.tar.gz
cd gromacs-5.0.4
mkdir build-gmx
cd build-gmx
export MPICCDIR=/share/apps/openmpi/bin
CMAKE_PREFIX_PATH=/share/apps/fftw3 \
cmake .. \
-DGMX_DOUBLE=ON \
-DCMAKE_INSTALL_PREFIX=/share/apps/gmx-double-MPI
-DGMX_X11=OFF \
-DCMAKE_CXX_COMPILER=${MPICCDIR}/mpicxx \
-DCMAKE_C_COMPILER=${MPICCDIR}/mpicc \
-DGMX_MPI=ON \
-DGMX_PREFER_STATIC_LIBS=ON
make -j 8
make install
Gromacs 5.0.4 CUDA (single)
Download source code to /share/apps/download
See the Installation_Instructions
tar -zxvf ../gromacs-5.0.4.tar.gz
cd gromacs-5.0.4
mkdir build-gmx-cuda
cd build-gmx-cuda
cmake .. \
-DGMX_DOUBLE=ON \
-DCMAKE_INSTALL_PREFIX=/share/apps/gmx-single-CUDA
-DGMX_GPU=ON
-DCUDA_TOOLKIT_ROOT_DIR=/share/apps/cuda
-DGMX_BUILD_OWN_FFTW=ON
make -j 8
make install
Gromacs 5.0.4 multicore (double)
Download source code to /share/apps/download
See the Installation_Instructions
tar -zxvf ../gromacs-5.0.4.tar.gz
cd gromacs-5.0.4
mkdir build-gmx
cd build-gmx
CMAKE_PREFIX_PATH=/share/apps/fftw3 \
cmake .. \
-DGMX_DOUBLE=ON \
-DCMAKE_INSTALL_PREFIX=/share/apps/gmx-double-multicore
make -j 8
make install
Gromacs MPI Compilation
Download gromacs-4.5.5.tar.gz into /usr/local/src/gromacs
See the Installation_Instructions
1. Load Environment Modules:
module add intel/compiler/64/11.1/075
module add mvapich/intel/64/1.1
module add fftw3/intel/64/3.2.2
2. Set environment variables
export CCDIR=/cm/shared/apps/intel/Compiler/11.1/075/bin/intel64
export FFTW_LOCATION=/cm/shared/apps/fftw/intel/64/3.2.2
export MPICCDIR=/cm/shared/apps/mvapich/intel/64/1.1/bin
export CXX=mpicxx
export CC=mpicc
3. Setup the build environment
cd /usr/local/src/gromacs/
tar -zxvf ../gromacs-4.5.5.tar.gz
mv gromacs-4.5.5 gromacs-4.5.5-serial
mkdir build-serial
cd build-serial
4. Make the servial version
cmake ../gromacs-4.5.5-mpi \
-DFFTW3F_INCLUDE_DIR=$FFTW_LOCATION/include \
-DFFTW3F_LIBRARIES=$FFTW_LOCATION/lib/libfftw3f.a \
-DCMAKE_INSTALL_PREFIX=/cm/shared/apps/gromacs \
-DGMX_X11=OFF \
-DCMAKE_CXX_COMPILER=${MPICCDIR}/mpicxx \
-DCMAKE_C_COMPILER=${MPICCDIR}/mpicc \
-DGMX_MPI=ON \
-DGMX_PREFER_STATIC_LIBS=ON
make
make install-mdrun (WORKS & Installed)
