[gmx-users] OpenMosix and Gromacs

David van der Spoel spoel at xray.bmc.uu.se
Sat Jun 30 13:17:21 CEST 2007

Nicolas Sapay wrote:
> Actually, I have used OpenMosix some time ago in a another life :) All I 
> remember is that NAMD was performing reasonably well as far as you 
> didn't ask it to write coordinates every frames. It was handy to 
> minimize/equilibrate a system or do some small computation like pressure 
> profile. As far as I remember, I was able to compute something like 0.8 
> ns/day on 10 proc for a system of 30~20000 atoms.

there is nothing stopping you from trying. In order for it to be 
efficient you probably need many more processes than processors, and 
IIRC that is how NAMD works. It will definitely not be more efficient 
than the gromacs development code with MPI though.
> Nico
> Sabuj Pattanayek wrote:
>> My 0.02. Based on one of Moshe Bar's OpenMosix papers, Mosix increases
>> the performance of MPI processes by load balancing. However I would have
>> to say that this only works for compute bound processes. If there's
>> going to be lots of I/O between nodes Mosix won't do so well and may
>> very well degrade performance.
>> Did you run any benchmarks of NAMD + its parallel (CHARM?)
>> implementation vs NAMD + CHARM + Mosix? Does it help? Last I checked the
>> Mosix userland tools and some other key functionality still don't work
>> for 2.6 linux kernels.
>> Nicolas Sapay wrote:
>>> Hi everybody,
>>> I wonder if someone has some experience with Gromacs and OpenMosix. Has
>>> someone tried recently to run Gromacs in parallel with an OpenMosix
>>> cluster? I have read some messages about that on the mailing-list but
>>> they have been posted several years ago... Things may have changed now.
>>> Additionally, I have  already used sucessfully NAMD and OpenMosix (but
>>> NAMD uses its own tool for parallel process).
>>> Thanks
>>> Nico
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David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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