Re: NAMD on Stampede 2

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Fri Oct 06 2017 - 09:08:35 CDT

I don't have an account there. Since you're using it, you should check.

Not sure whether which username he goes by there (TACC uses their own
system), but it may be possible to use:

getent passwd | grep Phillips

Giacomo

On Fri, Oct 6, 2017 at 9:32 AM, Chitrak Gupta <chgupta_at_mix.wvu.edu> wrote:

> 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
>>
>
>

-- 
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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