[MITgcm-support] run speed unaffected by timestep, 'deltaT'
Jonny Williams
Jonny.Williams at bristol.ac.uk
Wed May 21 06:02:41 EDT 2014
Super, thanks very much for that. I have some more runtime allocation now
so I will be attempting to carry out a fairly detailed benchmarking
exercise.
Jonny
On 20 May 2014 17:53, Menemenlis, Dimitris (329D) <
Dimitris.Menemenlis at jpl.nasa.gov> wrote:
> If you have kept your STDOUT files, there is a lot of useful information
> about timing at the tail end which may help you solve your timing mystery.
>
> On May 20, 2014, at 9:05 AM, "Jonny Williams" <
> Jonny.Williams at bristol.ac.uk> wrote:
>
> Thanks very much for that Jody. Unfortunately I am currently out of
> machine queue time allocation. I will be doing a proper look-up table
> approach to run speed when I have some more allocation. I'll be looking at
> output frequency, number of processors and timestep. Thanks very much for
> your input on this, it's much appreciated.
>
> Jonny
>
>
> On 20 May 2014 17:00, Jody Klymak <jklymak at uvic.ca> wrote:
>
>> Hi Johnny,
>>
>> Many queue programs (PBS etc) give you a "walltime" versus "cpu-time"
>> number. If these are wildly divergent, then you are indeed spending a lot
>> of time on i/o. You may want to check why that's the case. For some runs
>> I am doing now I do a full write every 300 time steps or so, and still most
>> of my walltime is cpu time. Are you writing excessively to STDOUT?
>>
>> Cheers, Jody
>>
>>
>> On May 20, 2014, at 1:36 AM, Jonny Williams <
>> Jonny.Williams at bristol.ac.uk> wrote:
>>
>> Thanks for that Liam
>>
>> I'd already a similar suggestion from others about this. I had reduced
>> my output frequency by a factor of 3 (every 10 days to every 30 days) and
>> have been getting a speed up of about a factor of 10.
>>
>> Thanks again!
>>
>> Jonny
>>
>>
>> On 19 May 2014 17:15, Liam Brannigan <Brannigan at atm.ox.ac.uk> wrote:
>>
>>> 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
>>> ________________________________________
>>> From: mitgcm-support-request at mitgcm.org [
>>> mitgcm-support-request at mitgcm.org]
>>> Sent: 19 May 2014 17:00
>>> To: mitgcm-support at mitgcm.org
>>> Subject: MITgcm-support Digest, Vol 131, Issue 26
>>>
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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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>>>
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>>> MITgcm-support at mitgcm.org
>>> http://mitgcm.org/mailman/listinfo/mitgcm-support
>>>
>>>
>>> End of MITgcm-support Digest, Vol 131, Issue 26
>>> ***********************************************
>>>
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>>
>>
>>
>> --
>> 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
>>
>>
>> --
>> Jody Klymak
>> http://web.uvic.ca/~jklymak/
>>
>>
>>
>>
>>
>>
>> _______________________________________________
>> MITgcm-support mailing list
>> MITgcm-support at mitgcm.org
>> http://mitgcm.org/mailman/listinfo/mitgcm-support
>>
>>
>
>
> --
> 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
>
>
> _______________________________________________
> MITgcm-support mailing list
> MITgcm-support at mitgcm.org
> http://mitgcm.org/mailman/listinfo/mitgcm-support
>
>
--
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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