[gmx-users] error on running job in parallel

delara aghaie d_aghaie at yahoo.com
Wed Jan 1 10:05:32 CET 2014

Dear gromacs users,
here in our university the gromacs is installed parallel and now we are going to submit our simulation projects.
To do a protein simulation, we are in the step to submit nvt and npt runs. this is the job,sh file which we use to submit our jobs: below you can see the explanation sent by the instructor:
Right now you can submit a job to chemistry queue, please make a job journal file( for example job.sh). Here is the sample required scripts:

#$ -cwd
#$ -j y
#$ -S /bin/sh
#$ -pe orte 8
cd $HOME
mpirun -v mdrun -s topol.tpr

-pe orte 8 specifies the number of core assigned to your job. (in this case 8 cores)

After that submit your job to chemistry queue by this command:
qsub -q chemistry.q   job.sh
I have made the job.sh file and submitted the job using the above qsub command, but I get this error:
Unable to read script file because of the error: ERROR! invalid option argument "-s"
what should I do about this error???
Thanks in advance

More information about the gromacs.org_gmx-users mailing list