[gmx-users] Gromacs on GPU

[Justin Lemkul]

On 6/16/17 2:35 PM, Mohsen Ramezanpour wrote:
> Thanks Stephane,
> 
> Sure, but how if I am in the middle of simulation and must switch to GPU?
> 
> I have 50 systems each around 100 ns, but I need 500 ns of each. :-)
> 
> What would you suggest in this case?
> 

The physics should be independent of the hardware.  Be sure to check release 
notes in case there's any bug that might affect things.  5.1.4 is not the most 
current release.

-Justin

> Cheers,
> Mohsen
> 
> On Fri, Jun 16, 2017 at 12:20 PM, Téletchéa Stéphane <
> stephane.teletchea at univ-nantes.fr> wrote:
> 
>> Le 16/06/2017 à 20:07, Mohsen Ramezanpour a écrit :
>>
>>> Thanks Justin.
>>>
>>> So, can we say that simulation on CPU and GPU (as far as we use the same
>>> version of Gromacs) are compatible?
>>>
>>> If yes, is that okay to continue a simulation which was done with CPU (say
>>> till 100 ns) to 500 ns (using GPU)?
>>> Or I should start from t=0 with GPU?
>>>
>>> It is important for my case as the allocations on supercomputers change
>>> from CPU to GPU. So, not sure if I should start all again or it is fine to
>>> continue.
>>>
>>> Cheers
>>>
>>
>> Dear Moshen,
>>
>> What I'm doing daily is using my "small" workstation with CPU then
>> continue once equilibration and primary production has worked well.
>>
>> Go for GPU for a boost in performance (big) once the primary steps are ok
>> :-)
>>
>> Best,
>>
>> Stéphane
>>
>> --
>> Assistant Professor in BioInformatics, UFIP, UMR 6286 CNRS, Team Protein
>> Design In Silico
>> UFR Sciences et Techniques, 2, rue de la Houssinière, Bât. 25, 44322
>> Nantes cedex 03, France
>> Tél : +33 251 125 636 / Fax : +33 251 125 632
>> http://www.ufip.univ-nantes.fr/ - http://www.steletch.org
>>
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> 
> 
> 

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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