[gmx-users] Announcement: Large biomolecule benchmark report

David van der Spoel spoel at xray.bmc.uu.se
Thu Mar 15 22:02:21 CET 2012

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

David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se

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