[gmx-users] GROMACS scaling at 64 cpus
gmx3 at hotmail.com
Fri Oct 16 21:22:56 CEST 2009
This of course depends very much on all your settings.
Up to now I have found that a 3:1 ratio is optimal for rectangular boxes,
whereas 2:1 is optimal for rhombic dodecahedra.
64 cores was the limit for the benchmark system on that hardware,
so I had to increase the number of PME beyond the 1/3 to get optimal performance.
I recently got a nice Sun X6275 blade system
http://nf.nci.org.au/facilities/vayu/hardware.php (ok, not just for me!)
whose hardware ought to be better, but very comparable to that used in
the GROMACS 4 paper (http://pubs.acs.org/doi/abs/10.1021/ct700301q).
Figure 5 there demonstrates good scaling out to 38 cpus, but it drops
away from linearity by 64. On the same test system on this hardware (pdf
attached; blue arrow is ideal linearity) the drop-off is still about the
For 64 cpus, that paper reports using 28 PME nodes, which is an
appreciably lower ratio than the 2:1 for the rest of the tests. On my
hardware I found that that choice cost about 30% performance, compared
with a more reasonable use of 19 PME nodes (64 vs 86 ns/day, pdf
attached). Is that 28 a typo for 18?
What can you do with the new Windows Live? Find out
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