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>
Subject: Re: [gmx-users] GPU
To: Discussion list for GROMACS users<gmx-users@gromacs.org>
Message-ID:<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 understand. See
http://www.gromacs.org/Documentation/Acceleration_and_parallelization
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. :-)
Mark
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