[gmx-users] g_tune_pme for multiple nodes
Chandan Choudhury
iitdckc at gmail.com
Tue Dec 4 14:45:16 CET 2012
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 <ckutzne at 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 <iitdckc at 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 <ckutzne at gwdg.de>
> wrote:
> >
> >> Hi Chandan,
> >>
> >> On Nov 29, 2012, at 3:30 PM, Chandan Choudhury <iitdckc at 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 <ckutzne at 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 <iitdckc at 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 at gromacs.org
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> >>>>
> >>>>
> >>>> --
> >>>> 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
> >>>>
> >>>> --
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> >>
> >> --
> >> 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
> >>
> >> --
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>
> --
> 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
>
> --
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