On 11/06/2012 3:06 PM, delara aghaie wrote:
Dear Gromacs users
I have checked something today and it seems starnge to me. Doing the
Justin lyzozyme tutorial, I checked the performance of our parallel
system. Subimitting the job on 8 processors of one node, I get0.86
ns/daywhich seems to be very weak performance. Do you have any idea
about the ns/day performance of 8 processors for the same lyzozyme system?
When starting a new discussion, please do not reply to an existing
email. This confuses the mailing list archive.
Parallel algorithms are not magic - they are engineered to provide
benefits under a range of conditions. Simply observing the rate on one
system at a number processors can give no real idea whether you are
getting value for running in parallel. This will depend on the size of
your simulation system and the attributes of your hardware. There is
lots of output in the .log file about how the parallel calculation is
running, and you will need to have read and understood a fair bit of
chapter 3 of the manual (particularly the last sections) for that to
make sense.
Mark
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