On Tue, Mar 8, 2011 at 1:36 PM, Jianguo Li <[email protected]> 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 <[email protected]> > *To:* Discussion list for GROMACS users <[email protected]> > *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 > > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
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