On Dec 4, 2012, at 2:45 PM, Chandan Choudhury <iitd...@gmail.com> wrote:
> 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? Typically mdrun allocates the PME and PP nodes in an interleaved way, meaning you would end up with 9 PME nodes on each of your two nodes. Check the -ddorder of mdrun. Interleaving is normally fastest unless you could have all PME processes exclusively on a single node. Carsten > > 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 -- 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