[gmx-users] g_tune_pme for multiple nodes

[Chandan Choudhury]

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"
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


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
> > --
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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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