[gmx-users] OpenMosix and Gromacs
nsapay at ucalgary.ca
Wed Jul 4 18:55:21 CEST 2007
Thanks for your comments (and sorry for the late answer)
Actually, I was not primarily thinking about using OpenMosix to run
simulation (that would be stupid considering the size of our cluster).
But it could be valuable to have a tool like OpenMosix when you quickly
want to setup a system (i.e. run severla minimization) and don't want to
be bored by the file transfer and the queuing system. If you say that
Gromacs can run successfully with OpenMosix, it's enough for me. I just
didn't want to spend hours to setup the software and realize after that
it can't run.
Yang Ye wrote:
> 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 addition and withdrawn.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...
> 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.
>>> 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
>>>> 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
>>>>> Additionally, I have already used sucessfully NAMD and OpenMosix
>>>>> NAMD uses its own tool for parallel process).
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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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