[gmx-users] Announcement: Large biomolecule benchmark report

Hannes Loeffler Hannes.Loeffler at stfc.ac.uk
Fri Mar 16 12:16:17 CET 2012

Thanks a a lot to you and also to Szilárd for your feedback and
encouragement.  I am very happy to see that this work is indeed useful
especially to developers.

We have no plans to make this into a 'proper' publication.  I am not
sure how much interested the simulation community would be because, to
be honest, I have no overview what has been done in this area (besides
the few benchmarks studies I have cited).

Thanks again,

On Thu, 15 Mar 2012 22:02:21 +0100
David van der Spoel <spoel at xray.bmc.uu.se> wrote:

> On 2012-03-15 14:37, Hannes Loeffler wrote:
> > Dear all,
> >
> > we proudly announce our third benchmarking report on (large)
> > biomolecular systems carried out on various HPC platforms.  We have
> > expanded our repertoire to five MD codes (AMBER, CHARMM, GROMACS,
> > LAMMPS and NAMD) and to five protein and protein-membrane systems
> > ranging from 20 thousand to 3 million atoms.
> >
> > Please find the report on
> > http://www.stfc.ac.uk/CSE/randd/cbg/Benchmark/25241.aspx
> > where we also offer the raw runtime data.  We also plan to release
> > the complete joint benchmark suite at a later date (as soon as we
> > have access to a web server with sufficient storage space).
> >
> > We are open to any questions or comments related to our reports.
> >
> It looks very interesting, and having benchmarks done by independent 
> researchers is the best way to avoid bias. The differences are quite 
> revealing, but it's also good that you point to problems compiling 
> gromacs. Is this going to be submitted for publication somewhere too?
> Thanks for doing this, it must have been quite a job!
> >
> > Kind regards,
> > Hannes Loeffler
> > STFC Daresbury

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