[gmx-users] parallel running

mohsen ramezanpour ramezanpour.mohsen at gmail.com
Tue Mar 8 11:53:09 CET 2011

On Tue, Mar 8, 2011 at 1:36 PM, Jianguo Li <ljggmx at yahoo.com.sg> wrote:

> You don't use qsub or bsub?

No,What is these?How can I prepare and use them?
Thanks in advance

> usually you should submit a script file containing the gromacs command,
> then bsub/qsub will allocate the required resource to your job.
> Jianguo
> ------------------------------
> *From:* mohsen ramezanpour <ramezanpour.mohsen at gmail.com>
> *To:* Discussion list for GROMACS users <gmx-users at gromacs.org>
> *Sent:* Tuesday, 8 March 2011 17:26:19
> *Subject:* [gmx-users] parallel running
> Dear All
> I want to run gromacs in parallel on cluster.for this I follow below steps:
> 1-I connect to a node with ssh comand,fro example: ssh compute-o-1
> 2-cd scratch
> 3-grompp     -f   md.mdp    -c   input.gro    -o   output.tpr   -p
> topol.top     -n  index.ndx
> 4- nohup   mpirun  -np  8   mdrun  -deffnm  output   &
> The result is running mdrun on one node(compute-0-1) (on its 4 CPUs)
> Besides when I used the following command I get an executeable Error:
> mpirun   -np   8   mdrun_mpi     -deffnm   output  &
> The Error is related to mdrun_mpi
> I think is related to my cluster,because both of above commands work in my
> laptop
> Please let me know how can I run mdrun on all of CPUs of my cluster.
> Thanks in advance
> Mohsen
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