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Preparing the Environment

There are lots of litte tweaks we need in order to prepate the environment for running specific software. We will try to describe the ones we use more regularly so we do not forget how to do it.

mvapich

Version 2.3.3 compiled wiht Intel 2020

module load intel/mvapich2/2.3.3
source $I_MPI_ROOT/intel64/bin/mpivars.sh intel64 -ofi_internal=0
export LD_PRELOAD="libmpi.so"

mpich

Version 3.2.2 compiled with Intel 2020

module load intel/mpich/3.3.2
##source $I_MPI_ROOT/intel64/bin/mpivars.sh intel64 -ofi_internal=0
export LD_PRELOAD="libmpi.so"

OpenMPI 4.0.3

Version 4.0.3 compiled with Intel 2019

module load intel/openmpi/4.0.3
#source $I_MPI_ROOT/intel64/bin/mpivars.sh intel64 -ofi_internal=0
export I_MPI_PMI_LIBRARY=/lib64/libpmi.so
#export LD_PRELOAD="libmpi.so"

openfoam

Version 1912 compiled wiht Intel 2020

module load intel/openfoami20/1912
source /cvmfs/sw.el7/ar/ix_es2680/i20/openfoami20/1912/build01/OpenFOAM-v1912/etc/bashrc
. /cvmfs/sw.el7/ar/ix_es2680/i20/openfoami20/1912/build01/OpenFOAM-v1912/bin/tools/RunFunctions

Version 1906 compiled wiht Intel 2020

module load intel/openfoami20/1906
source /cvmfs/sw.el7/ar/ix_es2680/i20/openfoami20/1906/build01/OpenFOAM-v1912/etc/bashrc
. /cvmfs/sw.el7/ar/ix_es2680/i20/openfoami20/1906/build01/OpenFOAM-v1912/bin/tools/RunFunctions

gromacs

intel/gromacs/2020.2

#module load gcc-6.3
#source /cvmfs/sw.el7/ar/ix_es2680/i20/gromacs/2020.2/build01/bin/GMXRC.bash
#source /cvmfs/sw.el7/intel/2020/bin/compilervars.sh intel64
#module load intel/gromacs/2020.2

intel/gromacs/2020.20-i20

module load gcc-7.5
source /cvmfs/sw.el7/ar/ix_es2680/i20/gromacs/2020.2/build02/bin/GMXRC.bash#source /cvmfs/sw.el7/intel/2020/bin/compilervars.sh intel64
source /cvmfs/sw.el7/intel/2020/bin/compilervars.sh intel64
module load intel/gromacs/2020.2

gromacs-4.6.7

module load gromacs-4.6.7
module load gcc63/openmpi/4.0.3
export GMX_MAXBACKUP=-1
mpirun -np 10 mdrun -s  benchMEM.tpr -nsteps 500000 -maxh 3.0 -resethway

Version 2020.2 compiled wiht Intel 2020

module load gcc-6.3
source /cvmfs/sw.el7/ar/ix_es2680/i20/gromacs/2020.2/build02/bin/GMXRC.bash
source /cvmfs/sw.el7/intel/2020/bin/compilervars.sh intel64
module load intel/gromacs/2020.2
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