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" 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 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
