Re: NAMD running on windows HPC question

From: johan strumpfer (johanstr_at_ks.uiuc.edu)
Date: Tue Sep 20 2011 - 08:30:51 CDT

Hi Joseph,

It sounds like you have a slow network that is hampering your
calculation. Although you can crunch more numbers with more
processors, NAMD needs to communicate between all nodes. The faster
you process, the faster your network needs to be.

Cheers,
Johan

------------------------------------------------------------------------------------------------------
Johan Strumpfer:         johanstr_at_ks.uiuc.edu        www.ks.uiuc.edu/~johanstr
Theoretical and Computational Biophysics Group
3115 Beckman Institute
University of Illinois at Urbana-Champaign
405 N. Mathews
Urbana, IL 61801, USA
------------------------------------------------------------------------------------------------------

On Tue, Sep 20, 2011 at 8:58 AM, Chewning, Joseph
<Joseph.Chewning_at_targacept.com> wrote:
> Hi All,
>
>
>
> I am running into a problem on our new Microsoft HPC system running NAMD. We
> have two computer nodes with 32 processors each. If we run the job on one
> node the bench marks look fine but if we run the job on both nodes it takes
> a lot longer. I am using the following command to run the job:
>
>
>
> mpiexec -cores 64 \\HPC-PROD\NAMD\2.8\NAMD2.exe
> \\HPC-Prod\Jobs\Test_Job\ch25.conf >
> \\hpc-prod\Jobs\Test_Job\test_joe\namd.log
>
>
>
> Is the CUDA code ready for testing yet?
>
>
>
> Thanks,
>
>
>
> Joseph
>
>
>
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