On Tue, Dec 4, 2012 at 7:18 PM, Carsten Kutzner <[email protected]> wrote:
> > On Dec 4, 2012, at 2:45 PM, Chandan Choudhury <[email protected]> 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. > Thanks Carsten for the explanation. Chandan > > Carsten > > > > > Chandan > > > > > > -- > > Chandan kumar Choudhury > > NCL, Pune > > INDIA > > > > > > On Tue, Dec 4, 2012 at 6:39 PM, Carsten Kutzner <[email protected]> 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 <[email protected]> > 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 <[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 > >> > >> > >> -- > >> 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 [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 > http://www.mpibpc.mpg.de/grubmueller/sppexa > > -- > 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. 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