[MITgcm-support] problem running MITgcm/verification//tutorial_global_oce_latlon/
Renske Gelderloos
Renske.Gelderloos at earth.ox.ac.uk
Thu Oct 10 05:42:50 EDT 2013
Hi Jonny,
Your model has indeed run succesfully. Unfortunately, the standard in
the MIT model is binary output (all .data files are binary files), but
the model has the option of choosing NetCDF output (which I would
suggest :-) ). To enable NetCDF output, you need to do a number of things:
1) at compile time, add 'mnc' to the list of packages to compile in the
'packages.conf' file in your 'code' directory. This compiles the
optional package that enables the usage of NetCDF.
2) at runtime, add
2a) 'useMNC=.TRUE.,' to the 'data.pkg' file
2b) a file data.mnc which you can copy from from any of the verification
experiments that use NetCDF output
3) on Hector, netcdf is not automatically enabled so you need to type
'module load netcdf' before you run genmake.
I think that is all. Good luck!
Renske
On 10/10/13 10:33, Jonny Williams wrote:
> Thanks for your suggestions.
>
> In the ~/MITgcm/verification/tutorial_global_oce_latlon/ example, I
> hadn't copied the contents of the input directory to my run directory.
> Having now done this I get many .meta and .data files in my run
> directory and the contents of the testing1.e1727853 output file reads...
>
> Warning: ieee_inexact is signaling
> Warning: ieee_inexact is signaling
> NORMAL END
> NORMAL END
>
>
> ... which I assume means that the job has terminated normally? I can't
> see any actual model output however.
>
> Assuming I am correct (a big assumption!) would anyone be able to
> suggest a different experiment for me to try running a model with some
> (ideally) NetCDF output?
>
> Many thanks again
>
> Jonny
>
>
> On 9 October 2013 21:32, Menemenlis, Dimitris (3248)
> <Dimitris.Menemenlis at jpl.nasa.gov
> <mailto:Dimitris.Menemenlis at jpl.nasa.gov>> wrote:
>
> I agree with Jody's assessment.
> It looks like your build options file is missing a few links
> to libraries, include files, compilers, etc.
>
> Dimitris Menemenlis
>
> On Oct 9, 2013, at 7:47 AM, Jonny Williams wrote:
>
>> Thanks, I've attached the command line output from running this
>> command as you suggested...
>>
>> Jonny
>>
>>
>> On 9 October 2013 15:38, Menemenlis, Dimitris (3248)
>> <Dimitris.Menemenlis at jpl.nasa.gov
>> <mailto:Dimitris.Menemenlis at jpl.nasa.gov>> wrote:
>>
>> Looks like you are missing other parameter files too.
>>
>> In verification try: ./testreport -mpi -t global_ovean.cs32x15
>>
>> Dimitris Menemenlis
>> 818-625-6498 <tel:818-625-6498>
>>
>> On Oct 9, 2013, at 7:32 AM, "Jonny Williams"
>> <Jonny.Williams at bristol.ac.uk
>> <mailto:Jonny.Williams at bristol.ac.uk>> wrote:
>>
>>> I have now found a file which I think is along the lines of
>>> what I need (eedata). Its contents is as follows...
>>>
>>> START
>>>
>>> # Example "eedata" file
>>> # Lines beginning "#" are comments
>>> # nTx - No. threads per process in X
>>> # nTy - No. threads per process in Y
>>> &EEPARMS
>>> nTx=1,nTy=1
>>> /
>>> # Note: Some systems use & as the
>>> # namelist terminator. Other systems
>>> # use a / character (as shown here).
>>>
>>> END
>>>
>>> I am now getting a different error, which is as follows...
>>>
>>> START
>>>
>>> Warning: ieee_inexact is signaling
>>> Warning: ieee_inexact is signaling
>>> ABNORMAL END: S/R OPEN_COPY_DATA_FILE
>>> ABNORMAL END: S/R OPEN_COPY_DATA_FILE
>>> [NID 02345] 2013-10-09 14:27:15 Apid 5947911: initiated
>>> application termination
>>>
>>> END
>>>
>>> Thanks again
>>>
>>> Jonny
>>>
>>>
>>> On 9 October 2013 15:01, Menemenlis, Dimitris (3248)
>>> <Dimitris.Menemenlis at jpl.nasa.gov
>>> <mailto:Dimitris.Menemenlis at jpl.nasa.gov>> wrote:
>>>
>>> Do you have a file called "eedata" in your run directory?
>>>
>>> Dimitris Menemenlis
>>> 818-625-6498 <tel:818-625-6498>
>>>
>>> On Oct 9, 2013, at 6:57 AM, "Jonny Williams"
>>> <Jonny.Williams at bristol.ac.uk
>>> <mailto:Jonny.Williams at bristol.ac.uk>> wrote:
>>>
>>>> Hi there
>>>>
>>>> I am trying to run
>>>> the MITgcm/verification//tutorial_global_oce_latlon/
>>>> example which was pre-loaded when I downloaded the
>>>> MITgcm code using CVS a couple of days ago.
>>>>
>>>> I plan to run parallelised codes in the future and so I
>>>> am using the SIZE.h file which was originally called
>>>> SIZE.h_mpi in the default installation.
>>>>
>>>> The code compiled successfully as far as I can tell.
>>>>
>>>> When I attempt to run the script I get the following
>>>> error message in a file called testing1.e1726317 (my
>>>> job is called testing1)...
>>>>
>>>> START
>>>>
>>>> gPGFIO-F-209/formatted read/unit=13/'OLD' specified for
>>>> file which does not exist.
>>>> In source file eeset_parms.f, at line number 1778
>>>> [NID 02545] 2013-10-09 13:28:18 Apid 5947459: initiated
>>>> application termination
>>>>
>>>> END
>>>>
>>>> The offending line (line 1778 of eeset_parms.f) reads
>>>> as follows...
>>>>
>>>> START
>>>>
>>>> READ(eeDataUnit,FMT='(A)',END=1001) RECORD
>>>>
>>>> END
>>>>
>>>> Is anyone able to shed any light on this?
>>>>
>>>> For your information I am running on the HECToR
>>>> supercomputer cluster in the UK using scripts which
>>>> were given to me by a collaborator who is already
>>>> successfully using the MITgcm model on the same machine.
>>>>
>>>> Many thanks!
>>>>
>>>> Jonny Williams
>>>>
>>>>
>>>> --
>>>> 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
>>>> <https://mail.google.com/mail/?view=cm&fs=1&tf=1&to=jonny.williams@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>
>>> 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>
>> 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
> jonny.williams at bristol.ac.uk <mailto:jonny.williams at bristol.ac.uk>
> bit.ly/jonnywilliams <http://bit.ly/jonnywilliams>
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