Re: NAMD on Stampede 2

From: Chitrak Gupta (chgupta_at_mix.wvu.edu)
Date: Fri Oct 06 2017 - 08:32:30 CDT

Hi Giacomo,

Thanks for the response. Yes, I did request 128 cores in the submission
script.

Are you aware whether Jim has compiled versions and/or submission scripts
for Stampede 2?

On Fri, Oct 6, 2017 at 8:50 AM, Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
wrote:

> Please find out how NAMD was compiled there and what part of Stampede
> you're using. Without this information, it's impossible to figure out your
> problem.
>
> If the executable and the related environment module were provided by the
> TACC staff, you should contact them for clarifications.
>
> Understand that the command line you pasted will launch two MPI tasks,
> each of which will spawn 64 threads. So you need 128 available cores on
> the node(s) that you requested.
>
> For more information, look at the files notes.txt that comes with the NAMD
> distribution.
>
> Giacomo
>
>
> On Thu, Oct 5, 2017 at 7:23 PM, Chitrak Gupta <chgupta_at_mix.wvu.edu> wrote:
>
>> Hello,
>>
>> I am trying to run NAMD on Stampede 2 but it is not scaling the way it
>> should. Here is what I have in my submission script
>>
>>
>>
>>
>>
>> *module load intel/16.0.3module load impimodule load namd/2.12mpiexec -np
>> 2 namd2 +ppn 64 filename.conf > logfile.log*
>>
>>
>> I have also tried "ibrun" instead of mpiexec but the problem persists.
>>
>>
>>
>> Best,
>> Chitrak.
>>
>
>
>
> --
> Giacomo Fiorin
> Associate Professor of Research, Temple University, Philadelphia, PA
> Contractor, National Institutes of Health, Bethesda, MD
> http://goo.gl/Q3TBQU
> https://github.com/giacomofiorin
>

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