[gmx-users] Parallel message passing

[Nathan Moore]

>
>> > The PME algorithm uses full all-to-all communication. However in
>> general
>> > you want to reduce communication to a minimum (by using clever
>> > algorithms). What kind of network do you have?
>>
>> A very fast one.  Processors are relatively slow (~700MHz ppc32), nodes
>> are connected on a torus, distributed memory, 256 or 512MB/processor
>> node
>> - no virtual memory.  I compile with xlC, to be practically useful
>> GROMACS
>> has to scale to >=512 processors...
> Blue Gene?

good guess!

How can I enable load-balancing in a parallel job?  I remember seeing
discussion of grompp options "-sort" and "-shuffle" in the manual as
parallel optimizations .  Is a change in performance resulting from this
noted in the log file?

regards,

NT







> --
> David.
> ________________________________________________________________________
> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,          75124 Uppsala, Sweden
> phone:  46 18 471 4205          fax: 46 18 511 755
> spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
>
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
>