OpenMosix indeed provides a second model for clustering besides beuwolf
model, which uses MPI, PVM-based communication. You may run thousands of
processes and get good scaling.
I tried it with normal network, 100M Ethernet, two processes, quite bad
efficiency, 1.1-1.3x speed-up. To get OpenMosix running for high
performance, a good networking is necessary. IMHO, I don't think
OpenMosix will help in the context of gromacs or any MPI-based parallel
program because it adds another level of control over inter-process
communication which can be more directly managed by MPI library itself.
Plus, without OpenMosix, processes are fixed to be run on certain nodes
without concerns whether to migrate or not. Unless you don't have a
dedicated cluster for Gromacs, you may consider.
OpenMosix is more fit to be used for
1) building a computing farm with minimal client installation.
2) dynamic environment. The computing farm can withstand dynamic
addition and withdrawn. Nodes can be loaded to run other jobs.
3) Combing coLinux and OpenMosix and running background on Windows-based
computer
4) huge amount of processes, each of them is running for sufficient
amount of time for OpenMosix to migrate.
5) Next-generation software to come out...
Regards,
Yang Ye
On 6/30/2007 7:17 PM, David van der Spoel wrote:
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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