Submitting a GROMACS Job to SGE

New Environment Fall 2009

#!/bin/csh
#$ -pe mpi-8 32
#$ -q *@@nehalem
module load gromacs
setenv WORK_DIR /afs/nd.edu/user27/apaluch/Public/gromacs/bin
setenv IN_DIR /sandbox/apaluch/DMPIm_TFSA/bulk_Buck/T_22/equil_anneal

mpirun  -np $NSLOTS `which mdrun_mpi_d` -s $IN_DIR/$inputfile

Old Environment

#!/bin/csh
#$ -M apaluch@nd.edu
#$ -N DMPIm-TFSA
#$ -m e
#$ -r n
#$ -pe mpi-4 4 

setenv WORK_DIR /afs/nd.edu/i386_linux24/opt/und/gromacs/x86_64/path/gromacs-4.0.5/bin
setenv IN_DIR /dscratch/apaluch/DMPIm_TFSA/bulk_LJ/T_22/equil_NVT

set inputfile = topol.tpr
set executable = mdrun_mpi

fsync $SGE_STDOUT_PATH &

module load  mpich/x86_64/1.2.7-ch_p4-path
module load gromacs/4.0.5

mpirun -np $NSLOTS $WORK_DIR/$executable -s  $IN_DIR/$inputfile