[gmx-users] g_tune_pme for multiple nodes

Carsten Kutzner ckutzne at gwdg.de
Tue Dec 4 14:09:12 CET 2012 

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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