[MITgcm-support] glue netcdf files efficiently

[何映晖]

Hi all,

I have some problems in gluing the netcdf tile files. I have tried *
scripts/gluemnc*, *matlab/gluemnc.m* and *
/python/MITgcmutils/scripts/gluemncbig*, but none of them is done.

I'm using system CentOS 6.3 and nco version 4.0.5. First, I use the *
scripts/gluemnc* command "gluemnc state.0000000000.t*", but an error is
occurred in running the *ncrcat* command.

XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
Combining X tile 1
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
Found these variables to combine: Eta S Temp U V W
YYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYY
Combining Eta files in Y
YYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYYY
/home/Phoenix/MITgcm_c64b/utils/scripts/gluemnc: line 288: 10082
Aborted                 (core dumped) ncrcat $DEBUG
i$countxx.$somevar.$somepre.*.nc $somevar.$somepre.gloy.$countxx.nc >
$LOGFILE
Just combined 1001.Eta
ncdump: Eta.state.0000000000.gloy.1001.nc: No such file or directory
Changing T to record variable in Eta.state.0000000000.gloy.1001.nc
ncpdq: ERROR Eta.state.0000000000.gloy.1001.nc neither exists locally nor
matches remote filename patterns

Then I try to use the matlab/gluemnc.m in Matlab 2011b. After I download
the file ncload.m in the forum, it is still not work with error:

>>foo=gluemnc('state','0000000000');
Undefined function 'netcdf' for input arguments of type 'char'.

Error in mnc_assembly (line 112)
  fnc = netcdf(fnm, 'nowrite');

Error in gluemnc (line 33)
[nt,nf] = mnc_assembly(nc_in, vars, nc_out);

I try to down the mexcdf53, but it seems that the mexcdf53 is not
compatible with MATLAB 2011b, and the new version of mexcdf didn't contain *
netcdf.m* function.

Finally, I try to use the python script *gluemncbig*. Since I don't know
the python at all, it also doesn't work.

$ gluemncbig -o state.glob.nc state.0000000000.t00*
Tiled dimensions: Yp1 Y X Xp1
Record dimension: T
Writing non-record variables
Traceback (most recent call last):
  File
"/home/Phoenix/MITgcm_c64b/utils/python/MITgcmutils/scripts/gluemncbig",
line 1336, in <module>
    if progress and not verbose: sys.stderr.write('Writing {} records:
'.format(nrec))
ValueError: zero length field name in format

Any ideas why I get those errors? Considering the files which I want to
combine are so large (about 50G), which method is more efficient?

Thanks,

Yinghui He
LTO, SCSIO
Chinese Academy of Sciences
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