[MITgcm-support] run speed unaffected by timestep, 'deltaT'

Liam Brannigan Brannigan at atm.ox.ac.uk
Mon May 19 12:15:09 EDT 2014


Hi Jonny - are you writing to disk in both runs?  When you increase the time step you may be producing outputs much more frequently.  If writing to disk is a bottleneck on your system then this could greatly reduce the efficiency gain from the larger timestep.

Liam
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Today's Topics:

   1. Re: Problems (Martin Losch)
   2. run speed unaffected by timestep, 'deltaT', in? (Jonny Williams)
   3. Re: run speed unaffected by timestep, 'deltaT', in?
      (Michael Schaferkotter)
   4. Re: run speed unaffected by timestep, 'deltaT', in?
      (Jonny Williams)


----------------------------------------------------------------------

Message: 1
Date: Mon, 19 May 2014 09:46:31 +0200
From: Martin Losch <Martin.Losch at awi.de>
To: MITgcm Support <mitgcm-support at mitgcm.org>
Subject: Re: [MITgcm-support] Problems
Message-ID: <EEA0E79F-01B2-4528-A369-4CD21C874C3E at awi.de>
Content-Type: text/plain; charset="windows-1252"

Hi Mehrdad,

Michael?s (very good) suggestions with the singleCPUio/globalFile flags unfortunately works only for mds output (the *.meta/data pairs), but for netcdf (i.e., mnc), the singleCPUio/globalFile flags have no effect (not implemented).

The current workaround is to use post-processing tools. I find the python script utils/python/MITgcmutils/scripts/gluemncbig most useful (requrires a working python installation).
Alternatively there is the script pair gluemnc xplodemnc in utils/scripts (require the nco operators: nco.sourceforge.net)

M.

On May 18, 2014, at 12:40 AM, Michael Schaferkotter <schaferk at bellsouth.net> wrote:

> For density in output files
>
> 1) In ./code sub directory you might have to modify DIAGNOSTICS_SIZE.h, depending on size of domain and how much data you write out.
>
> 2) in ./run sub directory
>
> a) data.pkg
>
>  useDiagnostics=.TRUE.
>
>  b) data.diagnostics
>
>   &diagnostics_list
>
>
>   frequency(k)=-3600.,                          (For hourly dump)
>   timePhase(k)=0.,
>   fields(1,k)='RHOAnoma',
>    filename(k)='Rhoanoma',
>
> Where k is the kth variable in the list.
>
>
>
>  For combining data into single files,
>
> In ./run/data
>
> globalFiles=.FALSE.
> useSingleCpuIO=.TRUE.
>
> Also you/ll need to properly configure the mnc package similarly to the diagnostics package and compile with compiler compatible netCDF libraries.
>
>
> Sent from an iOS device.
>
>> On May 17, 2014, at 14:48, meh tab <meryzoon at gmail.com> wrote:
>>
>> Dear sir/Madam,
>> I have started using MITgcm software, recently for modeling internal
>> wave. I have faced some problems and I could not understand the user's
>> manual guidelines related to these problems. My problems are:
>> 1- How can we add density variable to nc output file?
>> 2- When using multiple CPU cores, the results are broken into several
>> different files. How can I gather the results into one unique file?
>> Beforehand, I appreciate your kindness for kind attention to my email.
>> Sincerely Yours,
>> Mehrdad Tabatabaei
>>
>> _______________________________________________
>> MITgcm-support mailing list
>> MITgcm-support at mitgcm.org
>> http://mitgcm.org/mailman/listinfo/mitgcm-support
>
> _______________________________________________
> MITgcm-support mailing list
> MITgcm-support at mitgcm.org
> http://mitgcm.org/mailman/listinfo/mitgcm-support




------------------------------

Message: 2
Date: Mon, 19 May 2014 12:17:18 +0100
From: Jonny Williams <Jonny.Williams at bristol.ac.uk>
To: MITgcm Support <mitgcm-support at mitgcm.org>
Subject: [MITgcm-support] run speed unaffected by timestep, 'deltaT',
        in?
Message-ID:
        <CAA-NaP5GrO+HqD+n90Zob+M3gUM=nveeD6PvNafKZp5YkFzUAQ at mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

Hi there

I am currently running a regional version of the MIgcm with OBCS and EXF
forcing packages turned on. For the initial few years of the run I am
running with a very short timestep of 24s and then after that I am running
with a much linger timestep, 2400s.

I was expecting a significant increased in run speed but this has not
happened. I am recompiling in between these run steps.

Is there something that I've missed?

Many thanks!

Jonny

--
Dr Jonny Williams
School of Geographical Sciences
University of Bristol
University Road
BS8 1SS

+44 (0)117 3318352
jonny.williams at bristol.ac.uk
bit.ly/jonnywilliams
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Message: 3
Date: Mon, 19 May 2014 06:28:59 -0500
From: Michael Schaferkotter <schaferk at bellsouth.net>
To: "mitgcm-support at mitgcm.org" <mitgcm-support at mitgcm.org>
Subject: Re: [MITgcm-support] run speed unaffected by timestep,
        'deltaT', in?
Message-ID: <5A22E78C-06EF-4A8F-A3FE-58EB9EB8C393 at bellsouth.net>
Content-Type: text/plain; charset="us-ascii"

Since deltaT is a run time parameter, recompiling is unnecessary, though that does not answer your question.

Sent from an iOS device.

> On May 19, 2014, at 6:17, Jonny Williams <Jonny.Williams at bristol.ac.uk> wrote:
>
> Hi there
>
> I am currently running a regional version of the MIgcm with OBCS and EXF forcing packages turned on. For the initial few years of the run I am running with a very short timestep of 24s and then after that I am running with a much linger timestep, 2400s.
>
> I was expecting a significant increased in run speed but this has not happened. I am recompiling in between these run steps.
>
> Is there something that I've missed?
>
> Many thanks!
>
> Jonny
>
> --
> Dr Jonny Williams
> School of Geographical Sciences
> University of Bristol
> University Road
> BS8 1SS
>
> +44 (0)117 3318352
> jonny.williams at bristol.ac.uk
> bit.ly/jonnywilliams
> _______________________________________________
> MITgcm-support mailing list
> MITgcm-support at mitgcm.org
> http://mitgcm.org/mailman/listinfo/mitgcm-support
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Message: 4
Date: Mon, 19 May 2014 12:30:32 +0100
From: Jonny Williams <Jonny.Williams at bristol.ac.uk>
To: MITgcm Support <mitgcm-support at mitgcm.org>
Subject: Re: [MITgcm-support] run speed unaffected by timestep,
        'deltaT', in?
Message-ID:
        <CAA-NaP4QA83X8BkdxxU6tixh-97ob-nsFFj3+UrEsfiBKP0hxQ at mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

Hi again

Regarding this, it seems that I do actually get a speed up of approximately
10 times from a factor of 100 difference in the timestep. Is this roughly
what people would expect?

Thanks again and sorry for the initial confusion!

Jonny


On 19 May 2014 12:17, Jonny Williams <Jonny.Williams at bristol.ac.uk> wrote:

> Hi there
>
> I am currently running a regional version of the MIgcm with OBCS and EXF
> forcing packages turned on. For the initial few years of the run I am
> running with a very short timestep of 24s and then after that I am running
> with a much linger timestep, 2400s.
>
> I was expecting a significant increased in run speed but this has not
> happened. I am recompiling in between these run steps.
>
> Is there something that I've missed?
>
> Many thanks!
>
> Jonny
>
> --
> Dr Jonny Williams
> School of Geographical Sciences
> University of Bristol
> University Road
> BS8 1SS
>
> +44 (0)117 3318352
> jonny.williams at bristol.ac.uk
> bit.ly/jonnywilliams
>



--
Dr Jonny Williams
School of Geographical Sciences
University of Bristol
University Road
BS8 1SS

+44 (0)117 3318352
jonny.williams at bristol.ac.uk
bit.ly/jonnywilliams
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