Dear Charlie,
Thank you for the detailed response. I suppose it is worth noting at
http://www.unidata.ucar.edu/support/index.html#mailinglists
about forwarding questions to Sourceforge.
Before the bug would be fixed, is there another way to rechunk the
2014.nc? Maybe there is an example code of rechunking using Java
NetCDF libarary?
Kind regards,
Antonio
2014-10-28 23:29 GMT+02:00 Charlie Zender <zender@xxxxxxx>:
> 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.
>> I used the latest ncks for Windows (released 1 Oct 2014) to rechunk my
>> file
>> ncks -4 --cnk_dmn lat,4 --cnk_dmn lon,4 --cnk_dmn time,512 2014.nc
>> 2014_ch.nc
>>
>> 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 )'(
