AMBER Archive (2006)

Subject: AMBER: CPU utilization with Parallel Sander

From: Jingyuan Luke (jyluke_at_mimos.my)
Date: Thu Mar 09 2006 - 06:14:01 CST

Dear all,

I recently compiled sander with LAM/MPI (version 7.1.1) with Pathscale
2.3.1 running on a cluster with CentOS 4.2 and noticed some unusual CPU
utilization.

I did a lamboot on my cluster on 5 nodes (headnode with no-schedule=1,
each node with 4 CPUs) and decided to run the benchmark with 16 CPUs.
disturbing thing I saw is that each sander running on each CPU was only
utilizing less than 50% of each CPU cycle. This was not an issue when I
had an older cluster with an older Pathscale (version 2) as well as
older kernel version.

So are there anybody out there that have similar issues and found
solutions to this matter? Thanks in advance.

Regards,
Luke
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