[gpfsug-discuss] Singularity + GPFS

Thu Apr 26 16:25:54 BST 2018

Happy to share on the list in case anyone else finds it useful:

We use GPFS for home/scratch on our HPC clusters, supporting engineering
applications, so 95+% of our jobs are multi-node MPI.   We have had some
questions/concerns about GPFS+Singularity+MPI-IO, as we've had issues with
GPFS+MPI-IO in the past that was solved by building the applications
against GPFS.   If users start using Singularity containers, we then can't
guarantee how the contained applications have been built.

I've got a small test system (2 nsd nodes, 6 compute nodes) to see if we
can break it, before we deploy onto our production systems.   Everything
seems to be ok under synthetic benchmarks, but I've handed over to one of
my chaos monkey users to let him do his worst.

On 26 April 2018 at 15:53, Yugendra Guvvala <yguvvala at cambridgecomputer.com>
wrote:

> I am interested to learn this too. So please add me sending a direct mail.
>
> Thanks,
> Yugi
>
> On Apr 26, 2018, at 10:51 AM, Oesterlin, Robert <
> Robert.Oesterlin at nuance.com> wrote:
>
> Hi Lohit, Nathan
>
>
>
> Would you be willing to share some more details about your setup? We are
> just getting started here and I would like to hear about what your
> configuration looks like. Direct email to me is fine, thanks.
>
>
>
> Bob Oesterlin
>
> Sr Principal Storage Engineer, Nuance
>
>
>
>
>
> *From: *<gpfsug-discuss-bounces at spectrumscale.org> on behalf of "
> valleru at cbio.mskcc.org" <valleru at cbio.mskcc.org>
> *Reply-To: *gpfsug main discussion list <gpfsug-discuss at spectrumscale.org>
> *Date: *Thursday, April 26, 2018 at 9:45 AM
> *To: *gpfsug main discussion list <gpfsug-discuss at spectrumscale.org>
> *Subject: *[EXTERNAL] Re: [gpfsug-discuss] Singularity + GPFS
>
>
>
> We do run Singularity + GPFS, on our production HPC clusters.
>
> Most of the time things are fine without any issues.
>
>
>
> However, i do see a significant performance loss when running some
> applications on singularity containers with GPFS.
>
>
>
> As of now, the applications that have severe performance issues with
> singularity on GPFS - seem to be because of “mmap io”. (Deep learning
> applications)
>
> When i run the same application on bare metal, they seem to have a huge
> difference in GPFS IO when compared to running on singularity containers.
>
> I am yet to raise a PMR about this with IBM.
>
> I have not seen performance degradation for any other kind of IO, but i am
> not sure.
>
>
> Regards,
> Lohit
>
>
> On Apr 26, 2018, 10:35 AM -0400, Nathan Harper <nathan.harper at cfms.org.uk>,
> wrote:
>
> We are running on a test system at the moment, and haven't run into any
> issues yet, but so far it's only been 'hello world' and running FIO.
>
>
>
> I'm interested to hear about experience with MPI-IO within Singularity.
>
>
>
> On 26 April 2018 at 15:20, Oesterlin, Robert <Robert.Oesterlin at nuance.com>
> wrote:
>
> Anyone (including IBM) doing any work in this area? I would appreciate
> hearing from you.
>
>
>
> Bob Oesterlin
>
> Sr Principal Storage Engineer, Nuance
>
>
>
>
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>
> --
>
> *Nathan* *Harper* // IT Systems Lead
>
>
>
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-- 
*Nathan Harper* // IT Systems Lead

<https://cfms.org.uk/news-events/events/2018/july/farnborough-international-airshow-2018/>

*e: *nathan.harper at cfms.org.uk   *t*: 0117 906 1104  *m*:  0787 551 0891
*w: *www.cfms.org.uk
CFMS Services Ltd // Bristol & Bath Science Park // Dirac Crescent // Emersons
Green // Bristol // BS16 7FR

CFMS Services Ltd is registered in England and Wales No 05742022 - a
subsidiary of CFMS Ltd
CFMS Services Ltd registered office // 43 Queens Square // Bristol // BS1
4QP
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