[gmx-users] OpenMosix and Gromacs

Nicolas Sapay nsapay at ucalgary.ca
Sat Jun 30 01:22:27 CEST 2007

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.


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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[ Nicolas SAPAY, Ph.D. ]
University of Calgary, Dept. of Biological Sciences
2500 University drive NW, Calgary AB, T2N 1N4, Canada
Tel: (403) 220-6869
Fax: (403) 289-9311

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