Dear Carsten and Florian, Thanks for you useful suggestions. It did work. I still have a doubt regarding the execution :
export MPIRUN=`which mpirun` export MDRUN="/cm/shared/apps/gromacs/4.5.5/single/bin/mdrun_mpi_4.5.5" g_tune_pme_4.5.5 -np $NPROCS -s md0-200.tpr -c tune.pdb -x tune.xtc -e tune.edr -g tune.log I am suppling $NPROCS as 24 [2 (nodes)*12(ppn)], so that g_tune_pme tunes the no. of pme nodes. As I am executing it on a single node, mdrun never checks pme for greater than 12 ppn. So, how do I understand that the pme is tuned for 24 ppn spanning across the two nodes. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA On Thu, Nov 29, 2012 at 8:32 PM, Carsten Kutzner <[email protected]> wrote: > Hi Chandan, > > On Nov 29, 2012, at 3:30 PM, Chandan Choudhury <[email protected]> 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 <[email protected]> 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 <[email protected]> > 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 [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 > >> > >> > >> -- > >> 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 [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 > >> > > -- > > 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 > > > -- > 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 [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 > -- 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
