On Wed, Jun 13, 2012 at 3:59 AM, Mark Abraham <mark.abra...@anu.edu.au>wrote:
> 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.abra...@anu.edu.**au <mark.abra...@anu.edu.au>> >>> Subject: Re: [gmx-users] GPU >>> To: Discussion list for GROMACS users<gmx-users@gromacs.org> >>> Message-ID:<4FD5881F.3040509@**anu.edu.au <4fd5881f.3040...@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 It does work and has been tested extensively. We are working on the final details, but you can get the code from the nbnxn_hybrid_acc branch -- it's pretty safe to use it for non-production purposes! The pages Mark linked are the resources you want to start with before you start using the NxN kernels. Cheers, -- Szilárd > understand. See http://www.gromacs.org/**Documentation/Acceleration_** > and_parallelization<http://www.gromacs.org/Documentation/Acceleration_and_parallelization>and > http://www.gromacs.org/**Documentation/Cut-off_schemes<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. :-) > > > Mark > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before > posting! > Please don't post (un)subscribe requests to the list. Use the www > interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >
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