From: Chitrak Gupta (chgupta_at_mix.wvu.edu)
Date: Fri Oct 06 2017 - 11:04:16 CDT
Hi Josh,
Thanks for pointing that out.
Now I have one confusion. Is it possible to use 65 CPUs in a single core
and run 5 processes? In other words, is this a valid thing to do?
*#SBATCH -N 1*
*#SBATCH -n 65*
*.*
*.*
*.*
*ibrun -np 5 namd2 +ppn 13 filename.conf > logfile.log*
On Fri, Oct 6, 2017 at 11:43 AM, Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov>
wrote:
> Take a look at /home1/00288/tg455591/NAMD_scripts/runbatch_latest_knl.
> NAMD scales quite poorly if you use the default 64-68 processes per node.
> 13 (for whatever reason), behaves pretty well.
>
> -Josh
>
> On 10/06/2017 08:13 AM, Giacomo Fiorin wrote:
> 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<mailto:
> 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<
> mailto: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<mailto:
> 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/16.0.3
> module load impi
> module load namd/2.12
>
> mpiexec -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
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>
> --
> Giacomo Fiorin
> Associate Professor of Research, Temple University, Philadelphia, PA
> Contractor, National Institutes of Health, Bethesda, MD
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