running multicore version on a 2-CPU node

From: Gianluca Interlandi (
Date: Sat Jul 04 2015 - 15:33:25 CDT

Dear NAMD list,

I am a bit puzzled about the documentation (file "notes.txt" included in
the source of NAMD 2.9 and 2.10). It says that:

"These multicore builds lack a network layer, so they can only be used on
a single machine. ... For other multiprocessor workstations the included
charmrun program is needed to run multiple namd2 processes."

I wonder whether this is still correct for versions >= 2.9. I have
compiled the multicore version myself on which has two CPUs
with 12 cores each. I was able to run it using "namd2 +p24" and I believe
that it used all 24 cores of the node (2 x 12). I tried running with
"namd2 +p12" and it ran 50% slower (half the cores). Also, in the
multicore version "charmrun" is a short script that simply passes a few
arguments to "namd2". It seems to be provided just for backwards
compatibility. Also, the option "++local" is no longer recognized by the
multicore version of charmrun. Maybe, the file "notes.txt" needs to be
updated at lines 122-126?


Gianluca Interlandi, PhD
                     +1 (206) 685 4435

Research Assistant Professor at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.

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