Differences

This shows you the differences between two versions of the page.

--- howto:bioinformatics:gromacs [2013/11/15 15:06]
dane
+++ — (current)
@@ Line 1: / Line 1: @@
-Before running your scripts remember to run((Note: Make sure the line:<code bash>export MODULEPATH=/opt/gridware/bioinformatics/modules:$MODULEPATH</code>exists in your //~/.profile// file)):<code bash>user@login01:~ $ module add gromacs/4.6.3</code>
-Then your job script called //my_job.msub// will look something like this:
-<file bash my_job.msub>
-#/bin/sh
-#MSUB -l procs=64
-#MSUB -l feature=dell
-#MSUB -l walltime=10:00:00
-#MSUB -m be
-#MSUB -V
-#MSUB -o ${HOME}/scratch5/GROMACS/stdout.txt
-#MSUB -e ${HOME}/scratch5/GROMACS/stderr.txt
-#MSUB -d ${HOME}/scratch5/GROMACS/
-#MSUB -N MyGromacsJob
-#MSUB -mb
-NP=`cat ${PBS_NODEFILE} | wc -l`
-EXE=mdrun
-ARGS="-s input.tpr -deffnm input.tpr"
-mpirun -np ${NP} -machinefile ${PBS_NODEFILE} ${EXE} ${ARGS}
-</file>
-Finally submit your job using:<code bash>user@login01:~ $ msub my_job.msub</code>

wiki.chpc.ac.za