[gmx-users] Using several cores for MD production
jalemkul at vt.edu
Tue Dec 3 17:45:39 CET 2013
On 12/3/13 10:58 AM, MUSYOKA THOMMAS wrote:
> Dear Justin,
> Well it seems i am the first one to do MD simulations in my lab and i am
> using a chemistry department cluster and nobody has prior knowledge on
> GROMACS. I can use all the cores in the cluster but need to know if there
> is a specific mdrun command that can allow me specify the number of cores
> to be used for the MD run.
It still depends entirely on the architecture and how mdrun was compiled (which
can be checked with ldd), but if it's standard MPI:
mpirun -np 64 mdrun_mpi -whatever_else
> Thank you
> On Tue, Dec 3, 2013 at 5:37 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>> On 12/3/13 10:23 AM, MUSYOKA THOMMAS wrote:
>>> Dear Users,
>>> I am using a cluster of 64 cores to perform my MD simulations using
>>> version 4.5.5.
>>> I would be glad to know the exact mdrun command that will allow me use the
>>> available resources.
>> The answer depends entirely on the architecture of the cluster. Your sys
>> admin should know.
>> 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
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Justin A. Lemkul, Ph.D.
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
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