[MITgcm-support] "gluemnc grid.t*.nc" omits many variables

[David Wang]

No attachment allowed? All right, check out
http://www.ldeo.columbia.edu/~dwang/mitgcm/gluemnc.m

Haven't used it for a while. Hopefully still working.

D

On 09/27/2010 11:59 AM, David Wang wrote:
> Potentially dangerous attachments were identified and removed from this
> message.
>
> Hi,
>
> If you have Matlab, try gluemnc.m (attached).
>
> David
>
> On 09/27/2010 11:32 AM, Ryan Abernathey wrote:
>> I would say that you definitely identified the problem--old version 
>> of nco.
>>
>> I think that the ncecat -u option is needed for glueing grid files 
>> because they don't have a common record dimension by default. That's 
>> probably why the script worked for the state files but not the grid 
>> files. I think this was one of the hacks I had to do to get the grid 
>> files to glue.
>>
>> You could either update your nco or try to rewrite the script to 
>> avoid using that -u flag.
>>
>> Good luck,
>> Ryan
>>
>> p.s. cc'd to the support list for posterity.
>>
>>
>>
>> On Sep 27, 2010, at 11:20 AM, Maarten Buijsman wrote:
>>
>>> Hi Ryan
>>>
>>> At GFDL we use
>>> (ncecat -r) "NCO netCDF Operators version "3.1.4" last modified 
>>> 2006/06/09 built Dec 11 2006 on hnv by hnv"
>>> which is old and the cause of my trouble.
>>> I am currently checking if they want/can update it..... (cannot mess 
>>> with it myself)
>>>
>>> -u does:
>>>
>>> "A new record dimension is the glue which binds the input file data 
>>> together. The new
>>> record dimension name is, by default, “record”. Its name can be 
>>> specified with the ‘-u
>>> ulm_nm’ short option (or the ‘--ulm_nm’ or ‘rcd_nm’ long options)."
>>>
>>> This functionality is not present in the olde ncecat....:
>>> ncecat [-4] [-A] [-C] [-c] [-D dbg_lvl] [-d ...] [-F] [-H] [-h] [-l 
>>> path] [-n ...] [-O] [-o out.nc] [-p path] [-R] [-r] [-t thr_nbr] [-v 
>>> ...] [-x] in.nc [...] [out.nc]
>>>
>>> -4, --4, --netcdf4 Output file in netCDF4 storage format (HDF5)
>>> -A, --apn, --append Append to existing output file, if any
>>> -c, --crd, --coords Coordinate variables will all be processed
>>> -C, --nocoords Associated coordinate variables should not be processed
>>> -D, --dbg_lvl, --debug-level dbg_lvl Debugging level
>>> -d, --dmn, --dimension dim,[min][,[max]] Dimension's limits in 
>>> hyperslab
>>> -F, --ftn, --fortran Fortran indexing conventions (1-based) for I/O
>>> -H, --fl_lst_in, --file_list Do not create "input_file_list" global 
>>> attribute
>>> -h, --hst, --history Do not append to "history" global attribute
>>> -l, --lcl, --local path Local storage path for remotely-retrieved files
>>> -n, --nintap nbr_files,[nbr_numeric_chars[,increment]] NINTAP-style 
>>> abbreviation of file list
>>> -o, --output, --fl_out fl_out Output file name (or use last 
>>> positional argument)
>>> -O, --ovr, --overwrite Overwrite existing output file, if any
>>> -p, --pth, --path path Path prefix for all input filenames
>>> -R, --rtn, --retain Retain remotely-retrieved files after use
>>> -r, --revision, --vrs, --version Program version and copyright notice
>>> -t, --thr_nbr, --threads, --omp_num_threads thr_nbr Thread number 
>>> for OpenMP
>>> -v, --variable var1[,var2[...]] Variable(s) to process (regular 
>>> expressions supported)
>>> -x, --xcl, --exclude Extract all variables EXCEPT those specified 
>>> with -v
>>> in.nc Input file name(s)
>>> [out.nc] Output file name (or use -o switch)
>>>
>>> so I guess updating is the best ......
>>> although there may be a workaround?
>>>
>>> thanks
>>> Maarten
>>>
>>>
>>> Ryan Abernathey wrote:
>>>> Hi Maarten,
>>>>
>>>> On Sep 27, 2010, at 9:40 AM, Maarten Buijsman wrote:
>>>>
>>>>> ncecat: invalid option -- u
>>>>
>>>>
>>>> This error is telling you that the script is attempting to use an 
>>>> invalid option with the ncecat command. That is probably because 
>>>> you are using a different version of nco from the one I used when I 
>>>> modified the script. Just because it works with the state files 
>>>> doesn't rule out this possibility. (The grid files are actually 
>>>> more complicated because the variables have different sizes, rather 
>>>> than the state files, where the variables are all the same size.)
>>>>
>>>> I will log on to my server this afternoon and tell you which 
>>>> version of nco I used. In the meantime, check out the manual for 
>>>> ncecat and try to figure out how it works.
>>>>
>>>> Cheers,
>>>> Ryan
>>>>
>>>>
>>>
>>> -- 
>>> ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~ ~~
>>> Maarten Buisman (maarten.buijsman at noaa.gov)
>>> Geophysical Fluid Dynamics Laboratory
>>> 201 Forrestal Road
>>> Princeton, NJ 08540-6649
>>> Phone: (609) 452-5305
>>> Fax: (609) 987-5063
>>>
>>
>>
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-- 
Daiwei Wang
Department of Earth and Environmental Sciences and
Lamont-Doherty Earth Observatory
Columbia University

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