[gmx-users] g_tune_pme for multiple nodes

[Chandan Choudhury]

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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