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