[MITgcm-support] Problem with gluemnc.m / mnc_assembly.m

[Oliver Jahn]

Hi Ryan,

have you tried putting the netcdf toolbox at the beginning of your path?
I have the lines

addpath('/opt/matlab/toolbox/netcdf/')
addpath('/opt/matlab/toolbox/netcdf/nctype')
addpath('/opt/matlab/toolbox/netcdf/ncutility')
addpath('/opt/matlab/toolbox/mexnc/')

in my $HOME/matlab/startup.m (will depend on where your toolbox is, of 
course).  Using this, I got rdmnc to work with matlab 2009a.

Oliver


On Thu, 9 Jul 2009, Ryan Abernathey wrote:

> Apparently it does work in MATLAB R2007a but not in R2008a. I believe that 
> R2008a includes a built-in netcdf library. I guess it is incompatible with 
> the mnc_assembly.m code.
>
> On Jul 8, 2009, at 4:45 PM, Ryan Abernathey wrote:
>
>> Dear GCM People,
>> 
>> I am trying to use gluemnc.m to glue together my output netcdf files. The 
>> script runs with no errors, but the resulting output file is an empty 
>> netcdf file. This is very frustrating because I can't look at the output of 
>> my model in one piece. Does anyone have any idea what could be wrong?
>> 
>> I have confirmed that the problem is inside mnc_assembly.m by just running 
>> the commands of gluemnc.m manually from the command line. I am using MATLAB 
>> 7.6.0.324 (R2008a).
>> 
>> Many thanks for the help,
>> Ryan
>> 
>>>> gluemnc('state','0000000000');
>> 
>> theResult =
>> 
>> Columns 1 through 9
>>
>>   'T'    'iter'    'Xp1'    'Y'    'Z'    'U'    'X'    'Yp1'    'V'
>> 
>> Columns 10 through 14
>>
>>   'Temp'    'S'    'Eta'    'Zl'    'W'
>> 
>> Found 4 files matching the pattern:  "state.0000000000.t%03d.nc"
>> Looking for variable:   T
>> Looking for variable:   iter
>> Looking for variable:   Xp1
>> Looking for variable:   Y
>> Looking for variable:   Z
>> Looking for variable:   U
>> Looking for variable:   X
>> Looking for variable:   Yp1
>> Looking for variable:   V
>> Looking for variable:   Temp
>> Looking for variable:   S
>> Looking for variable:   Eta
>> Looking for variable:   Zl
>> Looking for variable:   W
>> Warning: FINITE is obsolete and will be removed in future versions.
>> Use ISFINITE instead.
>>> In ncdim.ncdim at 70
>> In netcdf.subsasgn at 91
>> In mnc_assembly at 337
>> In gluemnc at 33
>> Warning: FINITE is obsolete and will be removed in future versions.
>> Use ISFINITE instead.
>>> In ncdim.ncdim at 70
>> In netcdf.subsasgn at 91
>> In mnc_assembly at 337
>> In gluemnc at 33
>> Warning: FINITE is obsolete and will be removed in future versions.
>> Use ISFINITE instead.
>>> In ncdim.ncdim at 70
>> In netcdf.subsasgn at 91
>> In mnc_assembly at 337
>> In gluemnc at 33
>> Warning: FINITE is obsolete and will be removed in future versions.
>> Use ISFINITE instead.
>>> In ncdim.ncdim at 70
>> In netcdf.subsasgn at 91
>> In mnc_assembly at 337
>> In gluemnc at 33
>> Warning: FINITE is obsolete and will be removed in future versions.
>> Use ISFINITE instead.
>>> In ncdim.ncdim at 70
>> In netcdf.subsasgn at 91
>> In mnc_assembly at 337
>> In gluemnc at 33
>> Warning: FINITE is obsolete and will be removed in future versions.
>> Use ISFINITE instead.
>>> In ncdim.ncdim at 70
>> In netcdf.subsasgn at 91
>> In mnc_assembly at 337
>> In gluemnc at 33
>> Warning: FINITE is obsolete and will be removed in future versions.
>> Use ISFINITE instead.
>>> In ncdim.ncdim at 70
>> In netcdf.subsasgn at 91
>> In mnc_assembly at 337
>> In gluemnc at 33
>> Copying variable:   T
>> Copying variable:   iter
>> Copying variable:   Xp1
>> Copying variable:   Y
>> Copying variable:   Z
>> Copying variable:   U
>> Copying variable:   X
>> Copying variable:   Yp1
>> Copying variable:   V
>> Copying variable:   Temp
>> Copying variable:   S
>> Copying variable:   Eta
>> Copying variable:   Zl
>> Copying variable:   W
>> delete the original tiled files? [y/n] n
>>>> ls -l
>> total 1704
>> -rw-------  1 rpa  rpa   14204 Jul  8 15:40 monitor.0000000000.t001.nc
>> -rw-------  1 rpa  rpa  209024 Jul  8 15:23 state.0000000000.t001.nc
>> -rw-------  1 rpa  rpa  209024 Jul  8 15:23 state.0000000000.t002.nc
>> -rw-------  1 rpa  rpa  209024 Jul  8 15:23 state.0000000000.t003.nc
>> -rw-------  1 rpa  rpa  209024 Jul  8 15:23 state.0000000000.t004.nc
>> -rw-r--r--  1 rpa  rpa    4096 Jul  8 16:32 state_0000000000.nc
>> 
>> 
>> _______________________________________________
>> MITgcm-support mailing list
>> MITgcm-support at mitgcm.org
>> http://mitgcm.org/mailman/listinfo/mitgcm-support
>
> _______________________________________________
> MITgcm-support mailing list
> MITgcm-support at mitgcm.org
> http://mitgcm.org/mailman/listinfo/mitgcm-support