AW: [gmx-users] g_tune_pme for multiple nodes

[Florian Dommert]

> -----Ursprüngliche Nachricht-----
> Von: gmx-users-bounces at gromacs.org [mailto:gmx-users-
> bounces at gromacs.org] Im Auftrag von Chandan Choudhury
> Gesendet: Donnerstag, 29. November 2012 15:31
> An: Discussion list for GROMACS users
> Betreff: Re: [gmx-users] g_tune_pme for multiple nodes
> 
> 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

Hi,

 Don't start an MPI process. Run:

g_tune_pme_4.5.5 -np 24 -s md0-200.tpr -c tune.pdb -x

and everything should work fine.

/Flo
> 
> 
> 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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