How to compile Gromacs

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1 Gromacs on College Cluster
2 Gromacs 5.1.1 MPI, single
3 Gromacs 5.0.6 MPI, single, GPU
4 Gromacs 5.0.4 MPI, single, GPU
5 Gromacs 5.0.4 MPI, double
6 Gromacs 5.0.4 CUDA, single
7 Gromacs 5.0.4 thread-MPI, double
8 [Oldest]Gromacs MPI Compilation

Gromacs on College Cluster

I am sorry to inform you (formally) that one of the College Cluster account that you are using - cchan2242 is currently not suitable for running MPI jobs. I have done some test runs with accounts jialema2 and xinhonliu2 and they are both fine. I attach you the simple pbs script and please read carefully the comments:

#PBS -S /bin/bash 
#PBS -N test
#PBS -l nodes=2:ppn=16
#PBS -r n
#PBS -q fast
#

# Though Intel libraries are either not used or accessed in another way (described below), it is still safer to source them first
source /home/intel/composerxe/bin/compilervars.sh intel64
source /home/intel/composer_xe_2013.3.163/mkl/bin/mklvars.sh intel64

# As it is a shared library, you may save your time by accessing a pre-compiled fftw library instead of compiling a new one
export LD_LIBRARY_PATH=/nfs/disk3/cchan2242/opt/fftw-3.3.4-shared/lib:$LD_LIBRARY_PATH

# This part comes directly from your old pbs
cd $PBS_O_WORKDIR
cat $PBS_NODEFILE >> /tmp/nodefile.$$
NP=`cat $PBS_NODEFILE | wc -l`
NN=`cat $PBS_NODEFILE | sort | uniq | tee /tmp/nodes.$$ | wc -l`
 
# Define variables so you will actually use an absolute path to call the commands
# Note that you have to compile a new openmpi for each account
# For GMX commands, you can access one that compiled by another user (Just note the permission stuff)
MPIRUN=/nfs/disk3/xinhonliu2/opt/openmpi-1.8.6/bin/mpirun
GMXDIR=/nfs/disk3/cchan2242/opt/gromacs-4.6.3-MPI-double/bin

$MPIRUN -hostfile $PBS_NODEFILE $GMXDIR/mdrun_mpi_d -v -deffnm md

As we have tested out during this afternoon, some mkl libraries have to be placed under the submission directory and they are from /home/intel/composer_xe_2013.3.163/composer_xe_2013.3.163/mkl/lib/intel64:

libmkl_core.so
libmkl_gnu_thread.so
libmkl_intel_lp64.so

Gromacs 5.1.1 MPI, single

cmake .. \
-DGMX_DOUBLE=OFF \
-DCMAKE_INSTALL_PREFIX= \
# Specify where you install at -DGMX_MPI=ON \
-DCMAKE_CXX_COMPILER=g++ \
# !!Very important!! -DMPI_CXX_COMPILER=${MPICCDIR}mpicxx \
# While DMPI options must point to MPI binaries -DCMAKE_C_COMPILER=gcc \
# DCMAKE options must point to g++/gcc -DMPI_C_COMPILER=${MPICCDIR}mpicc \
-DGMX_BUILD_OWN_FFTW=ON
# You may specify your own fftw library path make -j16
make install

Gromacs 5.0.6 MPI, single, GPU

Download source code to /share/apps/download

Read the Installation_Instructions

tar -zxvf ../gromacs-5.0.6.tar.gz cd gromacs-5.0.4 mkdir build-gmx cd build-gmx export MPICCDIR=/share/apps/openmpi/bin/ cmake .. \ -DGMX_DOUBLE=OFF \ -DCMAKE_INSTALL_PREFIX=/share/apps/gmx-single-MPI-CUDA \ -DGMX_GPU=ON \ -DCUDA_TOOLKIT_ROOT_DIR=/share/apps/cuda/ \ -DGMX_MPI=ON \ -DCMAKE_CXX_COMPILER=g++ \ -DCMAKE_CXX_COMPILER=${MPICCDIR}mpicxx \ -DCMAKE_C_COMPILER=gcc \ -DCMAKE_C_COMPILER=${MPICCDIR}mpicc \ -DGMX_BUILD_OWN_FFTW=ON make -j16 make install

Gromacs 5.0.4 MPI, single, GPU

Download source code to /share/apps/download

Read 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 .. \ -DGMX_DOUBLE=OFF \ -DCMAKE_INSTALL_PREFIX=/share/apps/gmx-single-MPI-CUDA \ -DGMX_GPU=ON \ -DCUDA_TOOLKIT_ROOT_DIR=/share/apps/cuda/ \ -DGMX_MPI=ON \ -DCMAKE_CXX_COMPILER=${MPICCDIR}mpicxx \ -DCMAKE_C_COMPILER=${MPICCDIR}mpicc \ -DGMX_BUILD_OWN_FFTW=ON make -j 8 make install

Points to note:
* As we only have fftw3 library compiled with double precision so we have to add -DGMX_BUILD_OWN_FFTW=ON
* Version info at here

Gromacs 5.0.4 MPI, double

Download source code to /share/apps/download

Read 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

Points to note:
* Version info at here

Gromacs 5.0.4 CUDA, single

Download source code to /share/apps/download

Read 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=OFF \ -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

Points to note:
* As we only have fftw3 library compiled with double precision so we have to add -DGMX_BUILD_OWN_FFTW=ON
* As MPI was not enabled, this build runs only on single machine. It is about to be replaced by MPI-enabled GPU-enabled build. 
* Version info at here

Gromacs 5.0.4 thread-MPI, double

Download source code to /share/apps/download

Read 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

Points to note:
* This is the safest build and only runs on a single machine but multiple cores.
* Version info at here

[Oldest]Gromacs MPI Compilation

Download gromacs-4.5.5.tar.gz into /usr/local/src/gromacs

Read 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)

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