[gmx-users] GROMACS 4.6-beta2 released

[Yorquant Wang]

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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> >
> >
> >
> >
>
>
> --
> ORNL/UT Center for Molecular Biophysics cmb.ornl.gov
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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