Hi Carsten, Thanks for the reply.
If PME nodes for the g_tune is half of np, then if it exceeds the ppn of of a node, how would g_tune perform. What I mean if $NPROCS=36, the its half is 18 ppn, but 18 ppns are not present in a single node (max. ppn = 12 per node). How would g_tune function in such scenario? Chandan -- Chandan kumar Choudhury NCL, Pune INDIA On Tue, Dec 4, 2012 at 6:39 PM, Carsten Kutzner <ckut...@gwdg.de> wrote: > Hi Chandan, > > the number of separate PME nodes in Gromacs must be larger than two and > smaller or equal to half the number of MPI processes (=np). Thus, > g_tune_pme > checks only up to npme = np/2 PME nodes. > > Best, > Carsten > > > On Dec 4, 2012, at 1:54 PM, Chandan Choudhury <iitd...@gmail.com> wrote: > > > 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 <ckut...@gwdg.de> > wrote: > > > >> 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 > >> > > -- > > 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 > http://www.mpibpc.mpg.de/grubmueller/sppexa > > -- > 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
