Hi,

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 same.

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?

Mark

Attachment: scaling.pdf
Description: application/applefile

_______________________________________________
gmx-users mailing list    gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

Reply via email to