[gmx-users] GROMACS 4.6-beta2 released

[Mark Abraham]

Speed-up depends what you measure against, what precision GROMACS is using,
and what your AVX hardware is. There is no single number worth mentioning.
GROMACS has different AVX kernels for single vs double, and Intel Sandy
Bridge / Ivy Bridge vs AMD's Opteron / Bulldozer. I haven't seen any
numbers because the author of the kernels hasn't produced them yet, but
they will be considerably faster than anything you might compare them with.

Mark

On Fri, Dec 7, 2012 at 4:37 AM, Yorquant Wang <wangykoo at gmail.com> wrote:

> Hi Roland:
>      Based on your test, how many speed-up you get?
> Yorquant
>
> 2012/12/7 Roland Schulz <roland at utk.edu>
>
> > On Thu, Dec 6, 2012 at 9:42 PM, Yorquant Wang <wangykoo at gmail.com>
> wrote:
> >
> > > Hi Mark:
> > >     There is a new instruction set architecture (*Advanced Vector
> > > Extensions
> > > * (AVX)) that can make float calculation in Intel CPU faster two times
> > > compared with the old instruction set. I want to know if the Gromacs
> > > developers have a plan to make GMX support AVX. if the GMX can support
> > GMX,
> > > I think maybe two times speed-up in GMX will be gotten immediately.
> > >
> > Yes AVX is supported. But you won't see a 2x speedup.
> >
> > Roland
> >
> >
> > >
> > >   Best
> > >
> > > Yukun Wang
> > > PhD candidate
> > > Institute of Natural Sciences && College of Life Science, Shanghai Jiao
> > > Tong University
> > > Cell phone: 13621806236.
> > > China Shanghai
> > >
> > >
> > > 2012/12/7 Mark Abraham <mark.j.abraham at gmail.com>
> > >
> > > > Hi all,
> > > >
> > > > We've updated the GROMACS beta version to fix some bugs both you and
> we
> > > > found. We've also added the Adaptive resolution scheme (adResS) to
> our
> > > list
> > > > of new features (though we still have yet to publish a complete list
> of
> > > > those!). adResS couples two systems with different resolutions by a
> > force
> > > > interpolation, which can be used to speed-up atomistic simulations.
> The
> > > new
> > > > source package can be found at
> > > > ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6-beta2.tar.gz.
> > Installation
> > > > instructions still here
> > > > http://www.gromacs.org/Documentation/Installation_Instructions
> > > >
> > > > Please try it out, particularly if you haven't done so already! Also,
> > if
> > > > everything is smooth sailing, please drop us a line on gmx-users just
> > to
> > > > say that. We can't tell whether silence is "worked great, nothing to
> > say"
> > > > or "haven't tried it yet". That will help us judge when things are
> > stable
> > > > enough to make a real release!
> > > >
> > > > Speaking of that, we are keen to make that final release soon. While
> we
> > > > can't pick a date yet, we promise that if you give us feedback by
> > > December
> > > > 21, then we will make a sincere effort to incorporate the results of
> > that
> > > > feedback in the final release. In particular, if it's an issue on our
> > > > Redmine bug report database http://redmine.gromacs.org, then it will
> > be
> > > > sure to get our attention and consideration. You'll need to register
> an
> > > > account to make a bug report (so that we can get back to you), but
> > that's
> > > > free and easy.
> > > >
> > > > We hope to release a current version of our regression test suite
> next
> > > > week, and a benchmark set soon.
> > > >
> > > > Cheers,
> > > >
> > > > Mark Abraham
> > > > GROMACS development manager
> > > > --
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> > >
> > >
> > >
> > > --
> > > Yukun Wang
> > > PhD candidate
> > > Institute of Natural Sciences && College of Life Science, Shanghai Jiao
> > > Tong University
> > > Cell phone: 13621806236.
> > > China Shanghai
> > > --
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> >
> >
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>
> --
> Yukun Wang
> PhD candidate
> Institute of Natural Sciences && College of Life Science, Shanghai Jiao
> Tong University
> Cell phone: 13621806236.
> China Shanghai
> --
> gmx-users mailing list    gmx-users at gromacs.org
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