Hi Chandan, On Nov 29, 2012, at 3:30 PM, Chandan Choudhury <iitd...@gmail.com> wrote:
> Hi Carsten, > > Thanks for your suggestion. > > I did try to pass to total number of cores with the np flag to the > g_tune_pme, but it didnot help. Hopefully I am doing something silliy. I > have pasted the snippet of the PBS script. > > #!/bin/csh > #PBS -l nodes=2:ppn=12:twelve > #PBS -N bilayer_tune > .... > .... > .... > > cd $PBS_O_WORKDIR > export MDRUN="/cm/shared/apps/gromacs/4.5.5/single/bin/mdrun_mpi_4.5.5" from here on you job file should read: export MPIRUN=`which mpirun` g_tune_pme_4.5.5 -np $NPROCS -s md0-200.tpr -c tune.pdb -x tune.xtc -e tune.edr -g tune.log > mpirun -np $NPROCS g_tune_pme_4.5.5 -np 24 -s md0-200.tpr -c tune.pdb -x > tune.xtc -e tune.edr -g tune.log -nice 0 this way you will get $NPROCS g_tune_pme instances, each trying to run an mdrun job on 24 cores, which is not what you want. g_tune_pme itself is a serial program, it just spawns the mdrun's. Carsten > > > Then I submit the script using qsub. > When I login to the compute nodes there I donot find and mdrun executable > running. > > I also tried using nodes=1 and np 12. It didnot work through qsub. > > Then I logged in to the compute nodes and executed g_tune_pme_4.5.5 -np 12 > -s md0-200.tpr -c tune.pdb -x tune.xtc -e tune.edr -g tune.log -nice 0 > > It worked. > > Also, if I just use > $g_tune_pme_4.5.5 -np 12 -s md0-200.tpr -c tune.pdb -x tune.xtc -e tune.edr > -g tune.log -nice 0 > g_tune_pme executes on the head node and writes various files. > > Kindly let me know what am I missing when I submit through qsub. > > Thanks > > Chandan > -- > Chandan kumar Choudhury > NCL, Pune > INDIA > > > On Mon, Sep 3, 2012 at 3:31 PM, Carsten Kutzner <ckut...@gwdg.de> wrote: > >> Hi Chandan, >> >> g_tune_pme also finds the optimal number of PME cores if the cores >> are distributed on multiple nodes. Simply pass the total number of >> cores to the -np option. Depending on the MPI and queue environment >> that you use, the distribution of the cores over the nodes may have >> to be specified in a hostfile / machinefile. Check g_tune_pme -h >> on how to set that. >> >> Best, >> Carsten >> >> >> On Aug 28, 2012, at 8:33 PM, Chandan Choudhury <iitd...@gmail.com> wrote: >> >>> Dear gmx users, >>> >>> I am using 4.5.5 of gromacs. >>> >>> I was trying to use g_tune_pme for a simulation. I intend to execute >>> mdrun at multiple nodes with 12 cores each. Therefore, I would like to >>> optimize the number of pme nodes. I could execute g_tune_pme -np 12 >>> md.tpr. But this will only find the optimal PME nodes for single nodes >>> run. How do I find the optimal PME nodes for multiple nodes. >>> >>> Any suggestion would be helpful. >>> >>> Chandan >>> >>> -- >>> Chandan kumar Choudhury >>> NCL, Pune >>> INDIA >>> -- >>> gmx-users mailing list gmx-users@gromacs.org >>> 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 gmx-users-requ...@gromacs.org. >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> >> -- >> Dr. Carsten Kutzner >> Max Planck Institute for Biophysical Chemistry >> Theoretical and Computational Biophysics >> Am Fassberg 11, 37077 Goettingen, Germany >> Tel. +49-551-2012313, Fax: +49-551-2012302 >> http://www3.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne >> >> -- >> gmx-users mailing list gmx-users@gromacs.org >> 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 gmx-users-requ...@gromacs.org. >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > -- > gmx-users mailing list gmx-users@gromacs.org > 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 gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/grubmueller/kutzner -- gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists