[MITgcm-support] Converting mdsio output to netcdf, or reading mdsio in python

[Ryan Abernathey]

Hi Andrea,
This is something that was only implemented very recently (like last  
week). I am working on writing some documentation for it, but there is  
nothing yet.
-Ryan

On Oct 26, 2012, at 1:23 AM, cimatori wrote:

> For completeness, does anybody have any feedback on layers output  
> through the diagnostic package?
> Thanks,
>
> Andrea Cimatoribus
> Royal Netherlands Meteorological Institute
> www.knmi.nl/~cimatori
>
> On 10/25/2012 11:40 PM, Oliver Jahn wrote:
>> Hi Andrea,
>>
>> there is one now, in MITgcm/utils/python/MITgcmutils
>>
>> Either install it by running
>>
>>  python setup.py install --user
>>
>> (or wherever you like), or just put the directory on your PYTHONPATH.
>> Either way, you should be able to
>>
>>  from MITgcmutils import rdmds
>>
>> and start reading mds files using rdmds.  It has a (hopefully  
>> reasonably useful) doc string.
>>
>> There is also a script scripts/gluemncbig for gluing netcdf files,  
>> in case you go the other way.  It depends only on python and numpy.
>>
>> Cheers,
>> Oliver
>>
>>
>> On 2012-10-25 12:13, cimatori wrote:
>>> If there is a MITgcm python package, I will gladly shift to mds  
>>> output
>>> (which seems a lot faster).
>>>
>>> Andrea Cimatoribus
>>> Royal Netherlands Meteorological Institute
>>> www.knmi.nl/~cimatori
>>>
>>> On 10/25/2012 04:07 PM, Ryan Abernathey wrote:
>>>> Hi Andrea,
>>>>
>>>> You have 3 options:
>>>> - Simply read the mds files into python using np.fromfile (they are
>>>> just raw binary data)
>>>> - Use Oliver Jahn's MITgcm python utils package, which contains a
>>>> python mdsio and many other useful scripts (Oliver, is this  
>>>> publicly
>>>> available yet?)
>>>> - Upgrade your code to the latest version of layers, which now does
>>>> output via the diagnostics package and therefore should support  
>>>> netcdf
>>>> format. (Disclaimer: I have not tested netcdf output, but maybe  
>>>> Gael
>>>> has?)
>>>>
>>>> Personally, I actually prefer mds output. The main reason is that
>>>> netcdf does not support singleCPUio and consequently produces a
>>>> ridiculous amount of output files that then have to be glued  
>>>> together
>>>> in a separate step.
>>>>
>>>> Best,
>>>> Ryan
>>>>
>>>>
>>>> On Oct 25, 2012, at 6:26 AM, cimatori wrote:
>>>>
>>>>> Hi everybody,
>>>>> I have a technical issue which is probably rather common. I am  
>>>>> using
>>>>> layers package to compute the stream function in density, but  
>>>>> layers
>>>>> package can produce output only in the meta/data format.
>>>>> Unfortunately, I have no matlab available, and all my scripts are
>>>>> based on netcdf format. Is there a way convert meta/data to  
>>>>> netcdf?
>>>>> Is there an easy way to read meta/data files in python?
>>>>> I do have access to octave (an open source version of matlab) if  
>>>>> that
>>>>> can help.
>>>>> Many thanks,
>>>>>
>>>>> -- 
>>>>>
>>>>> Andrea Cimatoribus
>>>>> Royal Netherlands Meteorological Institute
>>>>> www.knmi.nl/~cimatori
>>>>>
>>>>>
>>>>> _______________________________________________
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>>>>> MITgcm-support at mitgcm.org
>>>>> http://mitgcm.org/mailman/listinfo/mitgcm-support
>>>>
>>>>
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