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Subject: Re: [OMPI devel] Open-MPI build of NAMD launched from srun over 20% slowed than with mpirun
From: Ralph Castain (rhc_at_[hidden])
Date: 2013-09-04 09:15:01


This is 1.7.3 - there is no comm thread in ORTE in that version.

On Sep 4, 2013, at 1:33 AM, George Bosilca <bosilca_at_[hidden]> wrote:

> You can confirm that the slowdown happen during the MPI initialization stages by profiling the application (especially the MPI_Init call).
>
> Another possible cause of slowdown might be the communication thread in the ORTE. If it remains active outside the initialization it will definitively disturb the application, by taking away critical resources.
>
> George.
>
> On Sep 4, 2013, at 05:59 , Christopher Samuel <samuel_at_[hidden]> wrote:
>
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>> On 04/09/13 11:29, Ralph Castain wrote:
>>
>>> Your code is obviously doing something much more than just
>>> launching and wiring up, so it is difficult to assess the
>>> difference in speed between 1.6.5 and 1.7.3 - my guess is that it
>>> has to do with changes in the MPI transport layer and nothing to do
>>> with PMI or not.
>>
>> I'm testing with what would be our most used application in aggregate
>> across our systems, the NAMD molecular dynamics code from here:
>>
>> http://www.ks.uiuc.edu/Research/namd/
>>
>> so yes, you're quite right, it's doing a lot more than that and has a
>> reputation for being a *very* chatty MPI code.
>>
>> For comparison whilst users see GROMACS also suffer with srun under
>> 1.6.5 they don't see anything like the slow down that NAMD gets.
>>
>> All the best,
>> Chris
>> - --
>> Christopher Samuel Senior Systems Administrator
>> VLSCI - Victorian Life Sciences Computation Initiative
>> Email: samuel_at_[hidden] Phone: +61 (0)3 903 55545
>> http://www.vlsci.org.au/ http://twitter.com/vlsci
>>
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