[gmx-users] Using several cores for MD production

Justin Lemkul 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

-Justin

> 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
>>> 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
>>
>> --
>> ==================================================
>>
>> 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.
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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