[gmx-users] REMD run on higher nodes.

[Justin Lemkul]

On 8/5/13 6:36 AM, suhani nagpal wrote:
> Sir
>
> Yeah, I meant to use twice the hardware and i have already invoked
> mpiexec_mpt.
>
> the pbs script works fine if i start afresh mdrun of the tprs but if i
> extend the simulation run by -cpi filename -noappend the run doesnt take
> place.
>

AFAIK, you can't change the number of processors mid-job and then try to use 
mdrun -cpi since information related to DD, etc is stored in the checkpoint 
files, which now do not match the previous run.

-Justin

>
>
>
> On Mon, Aug 5, 2013 at 3:22 PM, Mark Abraham <mark.j.abraham at gmail.com>wrote:
>
>> Not sure what you're asking, but if you're providing twice as much
>> hardware, then invoke mpiexec_mpt suitably to tell it to use all of
>> that. Then, if you invoke mdrun_mpi the same way as you do now, it
>> will work out it can use twice as much hardware per replica.
>>
>> Mark
>>
>> On Mon, Aug 5, 2013 at 7:55 AM, suhani nagpal <suhani.nagpal at gmail.com>
>> wrote:
>>> Greetings
>>>
>>> I'm running REMD of 96 replicas where the run.pbs is the following:
>>>
>>> #!/bin/tcsh
>>> #PBS -S /bin/tcsh
>>> #PBS -l walltime=00:15:00
>>> #PBS -q workq
>>> #PBS -l select=8:ncpus=12:mpiprocs=12
>>> #PBS -l place=scatter:excl
>>> #PBS -V
>>>
>>> # Go to the directory from which you submitted the job
>>> cd $PBS_O_WORKDIR
>>> setenv MPI_GROUP_MAX 1024
>>> setenv MPI_UNBUFFERED_STDIO 1
>>>
>>> #mpiexec_mpt -np 24 ./exefile
>>> mpiexec_mpt -np 96
>> /lustre/applications/GROMACS/gromacs-4.5.5/bin/mdrun_mpi
>>> -s md_.tpr -multi 96 -replex 2000 -cpi state_.cpt -noappend
>>>
>>>
>>> So each replica runs at one processor.
>>>
>>> Now, I want to run the remd at 16 nodes ( double ) so that each replica
>> is
>>> subjected to 2 processors.
>>>
>>>
>>> Kindly assist !
>>>
>>> Thanks
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-- 
==================================================

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

==================================================