parallel scaling issues

From: Hyonseok Hwang (
Date: Wed Jul 21 2010 - 09:11:18 CDT

Dear NAMD users,

I set up 6-core Xeon linux cluster (Xeon X5670), which means that each
node has 12 cores. I just downloaded the "NAMD 2.7b3 Linux-x86_64-TCP"
binary code from NAMD website and was running it in the cluster under
CentOS 5.3. Now I have two issues.

The first issue is that when I try to use 12 cores in one node, one
error message saying "poll protocol failure in circuit setup" appears,
and namd2 stops running. Of course, if I use 8 cores, there is no
problem, but if I use more than 8 cores, I have the same error message.
I'm wondering if the maximum number of cores in one node is limited to 8
in NAMD 2.7b3.
The command i issue is "/opt/local/namd27b3/bin/charmrun namd2
++node.list temp.nodelist +p12 configuration file".

The second issue is that when I use 8 cores in one node and look at the
%CPU using "top" command, I can see almost 99% CPU usage in 8 cores.
However, when I use 16 cores in two nodes and look at the same thing, I
can see only 50% CPU usage in 16 cores. As a result, both calculations
are running at the same speed. I don't know why. FYI, the total number
of atoms in my system is 40176, and the number of patches are 2 x 2 x 4.
I'm running the simulation with the PME dimension of 64x64x120.
I use "rsh" for communication and the command I issue is the same above.

Thank you in advance.


Hyonseok Hwang
Assistant Professor
Department of Chemistry
Kangwon National University
192-1 Hyoja-2-dong
Chuncheon, Gangwon-do 200-701, Rep. of Korea
Office:Room 313, Natural Sciences Building #1
Tel:+82-033-250-8497 (office)

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