vivek sharma wrote:
HI MArtin,
I am using here the infiniband having speed more than 10 gbps..Can you
suggest some option to scale better in this case.
What % imbalance is being reported in the log file? What fraction of the load
is being assigned to PME, from grompp? How many processors are you assigning to
the PME calculation? Are you using dynamic load balancing?
All of these factors affect performance.
-Justin
With Thanks,
Vivek
2008/11/11 Martin Höfling <[EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>>
Am Dienstag 11 November 2008 12:06:06 schrieb vivek sharma:
> I have also tried scaling gromacs for a number of nodes ....but
was not
> able to optimize it beyond 20 processor..on 20 nodes i.e. 1
processor per
As mentioned before, performance strongly depends on the type of
interconnect
you're using between your processes. Shared Memory, Ethernet,
Infiniband,
NumaLink, whatever...
I assume you're using ethernet (100/1000 MBit?), you can tune here
to some
extend as described in:
Kutzner, C.; Spoel, D. V. D.; Fechner, M.; Lindahl, E.; Schmitt, U.
W.; Groot,
B. L. D. & Grubmüller, H. Speeding up parallel GROMACS on high-latency
networks Journal of Computational Chemistry, 2007
...but be aware that principal limitations of ethernet remain. To
come around
this, you might consider to invest in the interconnect. If you can
come out
with <16 cores, shared memory nodes will give you the "biggest bang
for the
buck".
Best
Martin
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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