On Wed, Jun 13, 2012 at 3:59 AM, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>></span> wrote:<br><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div class="im">On 12/06/2012 10:49 PM, Ehud Schreiber wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Message: 4<br>
Date: Mon, 11 Jun 2012 15:54:39 +1000<br>
From: Mark Abraham<<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.<u></u>au</a>><br>
Subject: Re: [gmx-users] GPU<br>
To: Discussion list for GROMACS users<<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><br>
Message-ID:<<a href="mailto:4FD5881F.3040509@anu.edu.au" target="_blank">4FD5881F.3040509@<u></u>anu.edu.au</a>><br>
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<br>
On 11/06/2012 2:32 AM, ifat shub wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi,<br>
<br>
<br>
<br>
If I understand correctly, currently the Gromacs GPU acceleration does<br>
not support energy minimization. Is this so? Are there any plans to<br>
include it in the 4.6 version or in a later one (i.e. to allow, say,<br>
integrator = steep or cg in mdrun-gpu)? I would find such options<br>
extremely useful.<br>
</blockquote>
EM is normally so quick that it's not worth putting much effort into<br>
accelerating it, compared to the CPU-months that are spent doing<br>
subsequent MD.<br>
<br>
Mark<br>
</blockquote>
Currently, my main use of Gromacs entails running multiple minimizations on an ensemble of states.<br>
Moreover, these states are not obtained using molecular dynamics but rather using the Concoord algorithm.<br>
Therefore, for me the bottleneck is not md but rather minimizations (specifically, cg) and so their acceleration on GPUs would be very advantageous.<br>
If such usage is not totally idiosyncratic, I hope the development team would reconsider GPU accelerating also minimizations.<br>
I suspect this would not be technically too complex given the work already done on dynamics.<br>
</blockquote>
<br></div>
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 </blockquote>
<div><br></div><div>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!</div>
<div><br></div><div>The pages Mark linked are the resources you want to start with before you start using the NxN kernels.</div><div><br></div><div>Cheers,</div><div>--<br>Szilárd<br></div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
understand. See <a href="http://www.gromacs.org/Documentation/Acceleration_and_parallelization" target="_blank">http://www.gromacs.org/<u></u>Documentation/Acceleration_<u></u>and_parallelization</a> and <a href="http://www.gromacs.org/Documentation/Cut-off_schemes" target="_blank">http://www.gromacs.org/<u></u>Documentation/Cut-off_schemes</a> for some advance details. When you hear a call for alpha testers in the next few</blockquote>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">months, you might want to spend some time on that so that you're sure GROMACS will best meet your future needs. :-)</blockquote>
<div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><span class="HOEnZb"><font color="#888888"><br>
<br>
Mark</font></span><div class="HOEnZb"><div class="h5"><br>
-- <br>
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