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
-Justin
Thank you
On Tue, Dec 3, 2013 at 5:37 PM, Justin Lemkul <jalem...@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
GROMACS
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
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Justin A. Lemkul, Ph.D.
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Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
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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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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