Hi to all,
We are using a cluster with AMD opteron 6278 (16 core, 2.4 Ghz, 16 ML 3
cache) on 2 nodes (4 processors on each node, total 128 cores) and 64GB RAM
on each node to run AMBER 11. Parallel environment was created by
installing mvapich2.
While running PMEMD simulations for a system with 150k atoms on 64 cores,
the performance starts with 1.4 ns / day. After continuing for 2-3 ns, the
performance reduces to 1.0 ns / day or 0.8 in longer run time. The
performance reduces more rapidly when additional jobs are run
simultaneously on the remaining cores.
We are new to parallel computing environment. Is this to be expected? If
not why does the performance get affected?
Any help regarding this issue is appreciated.
--
Thank you,
With regards,
B. Sangeetha
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Aug 20 2013 - 23:00:02 PDT
