[NAMD] Running NAMD in Stampede2

From: The Cromicus Productions (thecromicusproductions_at_gmail.com)
Date: Fri Sep 29 2017 - 14:59:34 CDT

Hi everyone,

I'm trying to run some tests on Stampede2, however I'm really confused with
"ibrun" (I usually just use mpirun). Does anyone have experience on this?
For example,
if I want to use 8 nodes and 68 cores per node (total 544 cores), I'm trying

ibrun -np 544 namd2 ++p 544 ++ppn 67 RUN.namd > output.log

But run into errors such as
"CmiStartThreads: Resource temporarily unavailable(11)".

I tried other combinations and in the best case scenario I managed to do a
VERY slow
run. How can I fix this to use A nodes and B cores per node, in general?
Found some information at
but I don't have that much experience with parallel computing.

Thank you very much,


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