namd2 erratic performance over 104 procs

From: Zailo Leite (
Date: Fri Dec 05 2008 - 12:52:36 CST

We're running it on a 64-node cluster, 8 cores per node, infiniband
Using the ApoA1 benchmark, thing go pretty well until we go over 104
cores, then not only it degrades signifcantly but the scaling becomes
very chaotic. Any suggestions? something relating to the matrix
decomposition perhaps?


Zailo Leite
Sysadmin, IMSS -
     Academic Unix Solutions /
     High Performance Computing Group
California Institute of Technology
Phone (626)395-3507 - Cell (626)394-6989

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:50:12 CST