From: johan strumpfer (johanstr_at_ks.uiuc.edu)
Date: Tue Sep 20 2011 - 08:46:51 CDT
Hi Joseph,
I see, hmm - I'm out of my depth then. I presume you're using the
Win64-MPI namd build that's available on the website. I wonder if
there's an ibverbs version that can be built for windows, and if this
may be the issue. Maybe Jim or Axel can comment.
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 9:34 AM, Chewning, Joseph
<Joseph.Chewning_at_targacept.com> wrote:
> Johan,
>
> While I would agree, we have an Infiniband 40Gb pipe in between the nodes. That is why I was leaning toward the software side.
>
> Thanks,
> Joseph
>
> -----Original Message-----
> From: johan.ks.uiuc_at_gmail.com [mailto:johan.ks.uiuc_at_gmail.com] On Behalf Of johan strumpfer
> Sent: Tuesday, September 20, 2011 9:31 AM
> To: Chewning, Joseph
> Cc: namd-l_at_ks.uiuc.edu
> Subject: Re: namd-l: NAMD running on windows HPC question
>
> 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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