Re: [netcdfgroup] NetCDF4 problem

• To: netCDF Mail List <netcdfgroup@xxxxxxxxxxxxxxxx>, Antonio Rodriges <antonio.rrz@xxxxxxxxx>
• Subject: Re: [netcdfgroup] NetCDF4 problem
• From: Charlie Zender <zender@xxxxxxx>
• Date: Tue, 28 Oct 2014 14:29:32 -0700

Dear Antonio,

Forgive the delayed response. We prefer that NCO issues be posted on
Sourceforge forum as described on nco.sf.net. Thank you for doing so
later and for providing the test file. The issue you first raised on
the netCDF group list occurs not only with NCO on Windows, but also
with NCO and with nccopy on all OSs attempted. The output file
produced by the chunking allows simple reads (e.g., with ncks), but
produces an exotic menagerie of error when read by more sophisticated
applications (e.g., Java or ncwa). Since NCO and nccopy are completely
independent implementations of chunking that rely on the same library,
it's a good bet that there is a problem with the library. The
information below will help Unidata investigate this and hopefully
produce a fix that works with both NCO and nccopy.

Best,
Charlie

These two commands produce files that crash when ingested by ncwa
(all OSs) and, according to the OP, lib Java on Windows.

ncks -4 --cnk_dmn latitude,4 --cnk_dmn longitude,4 \
           --cnk_dmn time,512 ~/2014.nc ~/2014_ch.nc
nccopy -c time/512,latitude/4,longitude/4 ~/2014.nc \
           ~/2014_ch_nccopy.nc

zender@roulee:~$ ncwa -O ~/2014_ch.nc ~/foo.nc
Bus error

zender@roulee:~$ ncwa -O ~/2014_ch_nccopy.nc ~/foo.nc
*** Error in `HDF5-DIAG: Error detected in HDF5 (1.8.13) thread 0:
  #000: H5Dio.c line 149 in H5Sselect_hyperslab(): not a data space
HDF5-DIAG: Error detected in HDF5 (1.8.13) Aborted

Input file is available at

http://glace.ess.uci.edu/tmp/2014.nc

> Message: 1
> Date: Sun, 19 Oct 2014 22:48:50 +0300
> From: Antonio Rodriges <antonio.rrz@xxxxxxxxx>
> To: netcdfgroup@xxxxxxxxxxxxxxxx
> Subject: [netcdfgroup] NetCDF4 problem
> Message-ID:
>    <CAPrLoNci5pbm26yCG4qjuMthTe4PAnWzQ2KD4606y2amKwB=yw@xxxxxxxxxxxxxx>
> Content-Type: text/plain; charset=UTF-8
>
> Hello,
>
>   I have file 2014.nc of NetCDF version 3.

>
>   The new file 2014_ch.nc can be read by WCT, for example.
>   However, java code yields
>   [ucar.nc2.NetcdfFile] DEBUG Using IOSP ucar.nc2.iosp.hdf5.H5iosp
>   [ucar.nc2.iosp.hdf5.H5header] ERROR bad version 72 at filePos 22386
> and throws exception
>
> The code is
> import ucar.nc2.NetcdfFile;
> NetcdfFile nativeNetCDFFile = NetcdfFile.open(fullPath);
>
> I use the latest NetCDF4.5
> http://www.unidata.ucar.edu/downloads/netcdf/netcdf-java-4/index.jsp
>
> What is wrong?

--
Charlie Zender, Earth System Sci. & Computer Sci.
University of California, Irvine 949-891-2429 )'(

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