[gmx-developers] Gromacs on Mare Nostrum (Barcelona Supercomputing Centre)

[Tsjerk Wassenaar]

Hi Xavier,

I have not yet started a project on Marenostrum. I have been given
time on DEISA and will do some tests as to what serves my (errm, our
projects ;)) purposes best. I would be very interested to hear from
your endeavours in Barcelona :)

Cheers,

Tsjerk

On 4/16/07, Xavier Periole <X.Periole at rug.nl> wrote:
>
> Hi Tsjerk,
>
> I also saw this report, which seemed to me a bit strange as they
> recently reported extensive simulations using GROMAS (Rueda M,
> Ferrer-Costa C, Meyer T, Perez A, Camps J, Hospital A, Gelpi JL,
> Orozco M. A consensus view of protein dynamics. PNAS. 2007;104(3):796-801.)
> Note however that they used a serial version of GROMACS in the paper.
>
> I do not think that this report means much. They explain very
> little about their setup and protocole, which might explain the
> deviation from the exp structure.
>
> I am in contact with somebody using the Mare Nostrum, that would be
> useful to get a working version on it! Did you install one?
>
> Best,
> XAvier
>
> > Actually, these were my sentiments too. It's a bit cheap to suggest
> > that gmx just does weird, without further investigation and without
> > trying to contact you guys. Of course, I won't suggest that there are
> > _no_ bugs in gmx :p But unfolding like that...
> >
> > Tsjerk
> >
> > On 4/16/07, Erik Lindahl <lindahl at cbr.su.se> wrote:
> >> Hi Tsjerk,
> >>
> >> We'll get in touch with them, but considering we've run tons of
> >> protein in parallel without unfolding even with v 3.2.1, I think it's
> >> more probably that this is an error with the compiler/setup/user.
> >>
> >> We can't rule out a bug of course (in particular since PPC970 + IBM
> >> compilers isn't such a common combination), but we're a bit irritated
> >> that they don't even seem to have bothered getting in touch with is
> >> to get help before claiming it's a bug...
> >>
> >> Cheers,
> >>
> >> Erik
> >>
> >> On Apr 16, 2007, at 9:43 AM, Tsjerk Wassenaar wrote:
> >>
> >> > Dear developers,
> >> >
> >> > Here is a link to a technical report comparing three different MD
> >> > suites, including Gromacs (3.2.1/ffG43a1/PME), on the Barcelona
> >> > supercomputer. I'd appreciate if one of you could give it a glance and
> >> > a reaction. They mention consistent unfolding of proteins when using
> >> > multiple processors.
> >> >
> >> > http://www.bsc.es/media/809.pdf
> >> >
> >> > In the report they mention additional data on-site, but I haven't
> >> > found it yet.
> >> >
> >> > I'll put in a request to check 3.3, but would like some additional
> >> > input. There may also be added value in contact between the Gromacs
> >> > crew and the Mare Nostrum one, but that may be considered later. Note
> >> > that these efforts are done within the framework of DEISA and that the
> >> > outcomes may be of some significance for the use of Gromacs.
> >> >
> >> > Cheers,
> >> >
> >> > Tsjerk
> >> >
> >> > --
> >> > Tsjerk A. Wassenaar, Ph.D.
> >> > Junior UD (post-doc)
> >> > Biomolecular NMR, Bijvoet Center
> >> > Utrecht University
> >> > Padualaan 8
> >> > 3584 CH Utrecht
> >> > The Netherlands
> >> > P: +31-30-2539931
> >> > F: +31-30-2537623
> >> > _______________________________________________
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> >> > gmx-developers at gromacs.org
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> >>
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> >>
> >
> >
> > --
> > Tsjerk A. Wassenaar, Ph.D.
> > Junior UD (post-doc)
> > Biomolecular NMR, Bijvoet Center
> > Utrecht University
> > Padualaan 8
> > 3584 CH Utrecht
> > The Netherlands
> > P: +31-30-2539931
> >F: +31-30-2537623
> > _______________________________________________
> > gmx-developers mailing list
> > gmx-developers at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-developers
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> >or send it to gmx-developers-request at gromacs.org.
>
> -----------------------------------------------------
> XAvier Periole - PhD
>
> 1- Institute of Molecular Assemblies
>       City University of New York - USA
> 2- Molecular Dynamics-Group
>       University of Groningen - The Netherlands
> http://md.chem.rug.nl/~periole
> -----------------------------------------------------
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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623