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On 21/02/2012 8:11 AM, Floris Buelens wrote:
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<div><span>Poor scaling with MPI on many-core machines can also
be due uneven job distributions across cores or jobs being
wastefully swapped between cores. You might be able to fix
this with some esoteric configuration options of mpirun
(--bind-to-core worked for me with openMPI), but the surest
option is to switch to gromacs 4.5 and run using
thread-level parallelisation, bypassing MPI entirely.</span></div>
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<br>
That can avoid problems arising from MPI performance, but not those
arising from PP-vs-PME load balance, or intra-PP load balance. The
end of the .log files will suggest if these latter effects are
strong contributors. Carsten's suggested solution is one good one.<br>
<br>
Mark<br>
<br>
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<hr size="1"> <b><span style="font-weight:bold;">From:</span></b>
Sara Campos <a class="moz-txt-link-rfc2396E" href="mailto:srrcampos@gmail.com"><srrcampos@gmail.com></a><br>
<b><span style="font-weight: bold;">To:</span></b>
<a class="moz-txt-link-abbreviated" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a> <br>
<b><span style="font-weight: bold;">Sent:</span></b>
Monday, 20 February 2012, 17:12<br>
<b><span style="font-weight: bold;">Subject:</span></b>
[gmx-users] Scaling/performance on Gromacs 4<br>
</font> </div>
<br>
<div id="yiv704499279"><span style="font-family: 'courier
new', monospace; ">Dear GROMACS users</span><br>
<br style="font-family: 'courier new', monospace; ">
<span style="font-family: 'courier new', monospace; ">My
group has had access to a quad processor, 64 core
machine (4 x Opteron 6274 @ 2.2 GHz with 16 cores)<br>
and I made some</span>
<span style="font-family: 'courier new', monospace; ">performance
tests, using the following specifications:</span><br
style="font-family: 'courier new', monospace; ">
<br style="font-family: 'courier new', monospace; ">
<span style="font-family: 'courier new', monospace; ">System
size: 299787 atoms</span><br style="font-family:
'courier new', monospace; ">
<span style="font-family: 'courier new', monospace; ">Number
of MD steps: 1500</span><br style="font-family: 'courier
new', monospace; ">
<span style="font-family: 'courier new', monospace; ">Electrostatics
treatment: PME</span><br style="font-family: 'courier
new', monospace; ">
<span style="font-family: 'courier new', monospace; ">Gromacs
version: 4.0.4</span><br style="font-family: 'courier
new', monospace; ">
<span style="font-family: 'courier new', monospace; ">MPI:
LAM</span><br style="font-family: 'courier new',
monospace; ">
<span style="font-family: 'courier new', monospace; ">Command
ran: mpirun -ssi rpi tcp C mdrun_mpi ...</span><br
style="font-family: 'courier new', monospace; ">
<br style="font-family: 'courier new', monospace; ">
<span style="font-family: 'courier new', monospace; ">#CPUS
Time (s) Steps/s</span><br
style="font-family: 'courier new', monospace; ">
<span style="font-family: 'courier new', monospace; ">64
195.000 7.69</span><br style="font-family:
'courier new', monospace; ">
<span style="font-family: 'courier new', monospace; ">32
192.000 7.81</span><br style="font-family:
'courier new', monospace; ">
<span style="font-family: 'courier new', monospace; ">16
275.000 5.45</span><br style="font-family:
'courier new', monospace; ">
<span style="font-family: 'courier new', monospace; ">8
381.000 3.94</span><br
style="font-family: 'courier new', monospace; ">
<span style="font-family: 'courier new', monospace; ">4
751.000 2.00</span><br
style="font-family: 'courier new', monospace; ">
<span style="font-family: 'courier new', monospace; ">2
1001.000 1.50</span><br
style="font-family: 'courier new', monospace; ">
<span style="font-family: 'courier new', monospace; ">1
2352.000 0.64</span><br
style="font-family: 'courier new', monospace; ">
<br style="font-family: 'courier new', monospace; ">
<span style="font-family: 'courier new', monospace; ">The
scaling is not good. But the weirdest is the 64
processors performing</span><br style="font-family:
'courier new', monospace; ">
<span style="font-family: 'courier new', monospace; ">the
same as 32. I see the plots from Dr. Hess on the GROMACS
4 paper on JCTC</span><br style="font-family: 'courier
new', monospace; ">
<span style="font-family: 'courier new', monospace; ">and
I do not understand why this is happening. Can anyone
help?</span><br style="font-family: 'courier new',
monospace; ">
<br style="font-family: 'courier new', monospace; ">
<span style="font-family: 'courier new', monospace; ">Thanks
in advance,</span><br style="font-family: 'courier new',
monospace; ">
<span style="font-family: 'courier new', monospace; ">Sara</span><br>
</div>
<br>
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