Re: [NAMD] Running NAMD in Stampede2

From: Chitrak Gupta (
Date: Sun Oct 01 2017 - 19:21:52 CDT

Hi Sebastian,

I believe you would be able to specify the number of nodes and number of
procs by the "SBATCH -N" and "SBATCH -n" options respectively. So if you
want to use 8 cores and 67 procs per node, you can use the following
options in your submission script

#SBATCH -n 536

And then run the script with the following line:

ibrun namd2 RUN.namd > output.log

I *think* this should work but cannot confirm because I haven't used the
default NAMD on Stampede2.

Hope this helps,

On Fri, Sep 29, 2017 at 3:59 PM, The Cromicus Productions <> wrote:

> Hi everyone,
> I'm trying to run some tests on Stampede2, however I'm really confused
> with using
> "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
> accelerated-applications/namd/
> but I don't have that much experience with parallel computing.
> Thank you very much,
> Sebastian

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