Hi Bob (and others who might be able to help),
I noticed your timings (
http://amber.scripps.edu/amber9.bench2.html)
were on NERSC's new infiniband opteron and power5 machines. I am
starting to run sander and pmemd on these machines. I also noticed
that you did not use the ACML math library on the operton, but did use
the MASSV lib on the power5. Here come the questions: Is there a
reason you (or anyone else) skipped the opteron math library -- is it
no faster? And second, clearly I could test this myself, but I need to
figure out how to get the ACML and MASSV libraries to be used instead
of the built in functions. I have seen this page from Pathscale
regarding amber8 (
http://www.pathscale.com/building_code/amber8.html)
from which I suppose I can put together how to use the math libraries
for sander and pmemd, but I was wondering if there were instructions
out there somewhere. I checked through the Amber9 manual, but didn't
find anything.
Thanks for helping out a new person!
-Nick
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Received on Wed Sep 20 2006 - 06:07:21 PDT
