[gmx-users] error on running job in parallel

Mark Abraham mark.j.abraham at gmail.com
Wed Jan 1 10:46:30 CET 2014


It's not a GROMACS error, so you'll have to solve that one yourself.
Leading suspect is that the above example does not work with that mpirun,
because mpirun is trying to interpret "-s" (and giving an error) rather
than passing the argument to mdrun. See the mpirun docs and talk more to
the admins!


On Wed, Jan 1, 2014 at 8:02 PM, delara aghaie <d_aghaie at yahoo.com> wrote:

> Dear gromacs users,
> Hello,
> 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:
> #!/bin/sh
> #$ -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
> Regards
> D.M
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