Sample submission scripts

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[edit] Serial Job for ccd

#!/bin/bash 
#$ -S /bin/bash 
#$ -N cat2.5 
#$ -l arch=lx24-x86 
#$ -cwd 
#$ -R yes 
#$ -pe pe_mpich2_onehost 1 
#$ -l mem_free=1G 
#$ -V 
#$ -e err 
echo cat_2.5uM_1.params | /netapp/home/lilipeng/ccd/ccd > cat_2.5uM_1_3.log


[edit] Parallel Job for ccd

#!/bin/tcsh
#$ -S /bin/tcsh
#$ -N GFP_2
#$ -l arch=lx24-amd64
#$ -cwd
#$ -R yes
#$ -pe pe_mpich2_onehost 4
#$ -l mem_free=1G
#$ -V
#$ -e err
echo Sph_1.params | /netapp/home/lilipeng/ccd_chris/ccd > Sph1.log


[edit] Parallel Job for GROMACS

#!/bin/tcsh 
#$ -S /bin/tcsh 
#$ -N protein 
#$ -l arch=lx24-amd64 
#$ -cwd 
#$ -R yes 
#$ -pe pe_mpich2_onehost 8 
#$ -l mem_free=1G 
#$ -V 
#$ -e err 
#source ${HOME}/.tcshrc
setenv PASCALHOME "/netapp/home/pwassam" setenv GROMACSHOME "${PASCALHOME}/local/gromacs-4.5.3" setenv MPI_HOME "/netopt/mpi/mpich2" setenv MDRUN "${GROMACSHOME}/bin/mdrun" setenv TPBCONV "${GROMACSHOME}/bin/tpbconv" setenv GROMPP "${GROMACSHOME}/bin/grompp" setenv GMX ${PASCALHOME}/local/gromacs-4.5.3 setenv PATH "${GMX}/bin:${MPI_HOME}/bin:${PATH}" setenv LD_LIBRARY_PATH ${PASCALHOME}/mkl/10.0.1.014/lib/em64t setenv MPIRUN ""
${MPIRUN} ${MDRUN} -n ${NSLOTS} \ -s protein.tpr \ -o protein.trr \ -c protein.gro \ -g fulllog.log \ -n index.ndx \ -x protein.xtc \ -e protein.edr
${TPBCONV} -s protein.tpr \ -f protein.trr \ -extend 200000 \ -o protein_2.tpr

[edit] Parallel Job for GROMACS with PLUMED

#!/bin/tcsh
#$ -S /bin/tcsh
#$ -N frame0_14
#$ -l arch=lx24-amd64 
#$ -cwd
#$ -R yes
#$ -pe pe_mpich2_onehost 2
#$ -l mem_free=1G
#$ -V
#$ -e err
#source ${HOME}/.tcshrc
setenv GROMACSHOME "/netapp/home/lilipeng/gromacs/bin" setenv MPIRUN "/netapp/home/lilipeng/openmpi/bin/mpirun" setenv MDRUN "${GROMACSHOME}/mdrun"
${MPIRUN} ${MDRUN} -n 2 \ -s frame0_id.tpr \ -g fulllog.log \ -plumed plumed.dat \ -x frame0_id.xtc \ -n index.ndx
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