[MITgcm-support] problem running MITgcm/verification//tutorial_global_oce_latlon/

Thu Oct 10 06:16:28 EDT 2013

Thanks very much Renske

Indeed the 'useMNC=.TRUE. line in the data.pkg line was absent and I have
loaded the netcdf module. I am now getting the following error at compile
time however...

/usr/bin/ld: cannot find -lnetcdf
make[1]: *** [mitgcmuv] Error 2
make[1]: Leaving directory
`/nfs01/n02/n02/ggjhtw/MITgcm/verification/tutorial_global_oce_latlon/build'
make: *** [fwd_exe_target] Error 2

Should there be a NetCDF config file in /usr/bin/?

Sorry for all the emails!

Jonny

On 10 October 2013 10:42, Renske Gelderloos <
Renske.Gelderloos at earth.ox.ac.uk> wrote:

>  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> 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> wrote:
>>
>>>  Looks like you are missing other parameter files too.
>>>
>>>  In verification try: ./testreport -mpi -t global_ovean.cs32x15
>>>
>>> Dimitris Menemenlis
>>> 818-625-6498
>>>
>>> On Oct 9, 2013, at 7:32 AM, "Jonny Williams" <
>>> 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> wrote:
>>>
>>>>  Do you have a file called "eedata" in your run directory?
>>>>
>>>> Dimitris Menemenlis
>>>> 818-625-6498
>>>>
>>>> On Oct 9, 2013, at 6:57 AM, "Jonny Williams" <
>>>> 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 <%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
>>>>
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>>>>
>>>
>>>
>>>  --
>>>  Dr Jonny Williams
>>> School of Geographical Sciences
>>> University of Bristol
>>> University Road
>>> BS8 1SS
>>>
>>>  +44 (0)117 3318352 <%2B44%20%280%29117%203318352>
>>> jonny.williams at bristol.ac.uk
>>> 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 <%2B44%20%280%29117%203318352>
>> jonny.williams at bristol.ac.uk
>> bit.ly/jonnywilliams
>>   <out.txt>_______________________________________________
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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
>
>
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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
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