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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