[gmx-users] g_tune_pme for multiple nodes

[Carsten Kutzner]

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
>>> 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 gmx-users-request at gromacs.org.
>>> * 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    gmx-users at gromacs.org
>> 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 gmx-users-request at gromacs.org.
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> 
> -- 
> gmx-users mailing list    gmx-users at gromacs.org
> 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 gmx-users-request at gromacs.org.
> * 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