[gmx-users] GPU

Mark Abraham Mark.Abraham at anu.edu.au
Wed Jun 13 03:59:24 CEST 2012

On 12/06/2012 10:49 PM, Ehud Schreiber wrote:
>> Message: 4
>> Date: Mon, 11 Jun 2012 15:54:39 +1000
>> From: Mark Abraham<Mark.Abraham at anu.edu.au>
>> Subject: Re: [gmx-users] GPU
>> To: Discussion list for GROMACS users<gmx-users at gromacs.org>
>> Message-ID:<4FD5881F.3040509 at anu.edu.au>
>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>> On 11/06/2012 2:32 AM, ifat shub wrote:
>>> Hi,
>>> If I understand correctly, currently the Gromacs GPU acceleration does
>>> not support energy minimization. Is this so? Are there any plans to
>>> include it in the 4.6 version or in a later one (i.e. to allow, say,
>>> integrator = steep or cg in mdrun-gpu)? I would find such options
>>> extremely useful.
>> EM is normally so quick that it's not worth putting much effort into
>> accelerating it, compared to the CPU-months that are spent doing
>> subsequent MD.
>> Mark
> Currently, my main use of Gromacs entails running multiple minimizations on an ensemble of states.
> Moreover, these states are not obtained using molecular dynamics but rather using the Concoord algorithm.
> Therefore, for me the bottleneck is not md but rather minimizations (specifically, cg) and so their acceleration on GPUs would be very advantageous.
> If such usage is not totally idiosyncratic, I hope the development team would reconsider GPU accelerating also minimizations.
> I suspect this would not be technically too complex given the work already done on dynamics.

I suspect the upcoming 4.6 release will have GPU-accelerated EM 
available as a side effect of the new Verlet pair-list scheme for 
computing non-bonded interactions. This development is unrelated to 
previous GPU efforts, I understand. See 
and http://www.gromacs.org/Documentation/Cut-off_schemes for some 
advance details. When you hear a call for alpha testers in the next few 
months, you might want to spend some time on that so that you're sure 
GROMACS will best meet your future needs. :-)


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