[MITgcm-support] run speed unaffected by timestep, 'deltaT'
Menemenlis, Dimitris (329D)
Dimitris.Menemenlis at jpl.nasa.gov
Tue May 20 12:53:17 EDT 2014
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<mailto: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<mailto: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<mailto: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<mailto: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
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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<mailto:Martin.Losch at awi.de>>
To: MITgcm Support <mitgcm-support at mitgcm.org<mailto:mitgcm-support at mitgcm.org>>
Subject: Re: [MITgcm-support] Problems
Message-ID: <EEA0E79F-01B2-4528-A369-4CD21C874C3E at awi.de<mailto: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<http://nco.sourceforge.net/>)
M.
On May 18, 2014, at 12:40 AM, Michael Schaferkotter <schaferk at bellsouth.net<mailto: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<mailto: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
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>
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------------------------------
Message: 2
Date: Mon, 19 May 2014 12:17:18 +0100
From: Jonny Williams <Jonny.Williams at bristol.ac.uk<mailto:Jonny.Williams at bristol.ac.uk>>
To: MITgcm Support <mitgcm-support at mitgcm.org<mailto: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<mailto:nveeD6PvNafKZp5YkFzUAQ at mail.gmail.com>>
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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<tel:%2B44%20%280%29117%203318352>
jonny.williams at bristol.ac.uk<mailto:jonny.williams at bristol.ac.uk>
bit.ly/jonnywilliams<http://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<mailto:schaferk at bellsouth.net>>
To: "mitgcm-support at mitgcm.org<mailto:mitgcm-support at mitgcm.org>" <mitgcm-support at mitgcm.org<mailto: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<mailto:5A22E78C-06EF-4A8F-A3FE-58EB9EB8C393 at bellsouth.net>>
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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<mailto: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<tel:%2B44%20%280%29117%203318352>
> jonny.williams at bristol.ac.uk<mailto:jonny.williams at bristol.ac.uk>
> bit.ly/jonnywilliams<http://bit.ly/jonnywilliams>
> _______________________________________________
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Message: 4
Date: Mon, 19 May 2014 12:30:32 +0100
From: Jonny Williams <Jonny.Williams at bristol.ac.uk<mailto:Jonny.Williams at bristol.ac.uk>>
To: MITgcm Support <mitgcm-support at mitgcm.org<mailto:mitgcm-support at mitgcm.org>>
Subject: Re: [MITgcm-support] run speed unaffected by timestep,
'deltaT', in?
Message-ID:
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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<mailto: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<tel:%2B44%20%280%29117%203318352>
> jonny.williams at bristol.ac.uk<mailto:jonny.williams at bristol.ac.uk>
> bit.ly/jonnywilliams<http://bit.ly/jonnywilliams>
>
--
Dr Jonny Williams
School of Geographical Sciences
University of Bristol
University Road
BS8 1SS
+44 (0)117 3318352<tel:%2B44%20%280%29117%203318352>
jonny.williams at bristol.ac.uk<mailto:jonny.williams at bristol.ac.uk>
bit.ly/jonnywilliams<http://bit.ly/jonnywilliams>
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Dr Jonny Williams
School of Geographical Sciences
University of Bristol
University Road
BS8 1SS
+44 (0)117 3318352<tel:%2B44%20%280%29117%203318352>
jonny.williams at bristol.ac.uk<mailto:jonny.williams at bristol.ac.uk>
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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<mailto:jonny.williams at bristol.ac.uk>
bit.ly/jonnywilliams<http://bit.ly/jonnywilliams>
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