Re: [thredds] TDS NCSS: issue with netCDF4 files as input and netCDF4 requested as output

• To: Jolibois Tony <tjolibois@xxxxxx>
• Subject: Re: [thredds] TDS NCSS: issue with netCDF4 files as input and netCDF4 requested as output
• From: Christian Ward-Garrison <cwardgar@xxxxxxxx>
• Date: Thu, 10 Dec 2015 09:40:17 -0700

Hi Tony,

Can you provide an example of the NetCDF-4 input file so that we can
recreate the problem locally?

Thanks,
Christian

On Thu, Dec 10, 2015 at 8:29 AM, Jolibois Tony <tjolibois@xxxxxx> wrote:

> Hi Thredds team,
>
>
>
> We’re currently testing TDS netCDF Subset Service, its performance,
> robustness.. These tests include different netCDF format, to study the
> impact on performance and robustness with different compression levels.
>
> To study this impact, we run 4 scenarios for input/output data files for
> TDS NCSS.
>
> Input netCDF3 => output netCDF3
>
> Input netCDF4 => output netCDF3
>
> Input netCDF3 => output netCDF4
>
> Input netCDF4 => output netCDF4
>
> We’re facing an error only with the 4th scenario, netCDF4 => netCDF4 (NCSS
> REST parameter &accept=netcdf4).
>
>
>
> java.io.IOException: -101: *NetCDF: HDF error*
>
>         at ucar.nc2.jni.netcdf.Nc4Iosp.writeData(Nc4Iosp.java:2821) ~[
> netcdf4-4.6.3.jar:4.6.3]
>
>         at ucar.nc2.jni.netcdf.Nc4Iosp.writeData(Nc4Iosp.java:2729) ~[
> netcdf4-4.6.3.jar:4.6.3]
>
>         at ucar.nc2.NetcdfFileWriter.write(NetcdfFileWriter.java:953)
> ~[cdm-4.6.3.jar:4.6.3]
>
>         at ucar.nc2.NetcdfFileWriter.write(NetcdfFileWriter.java:937)
> ~[cdm-4.6.3.jar:4.6.3]
>
>         at ucar.nc2.FileWriter2.copyAll(FileWriter2.java:427)
> ~[cdm-4.6.3.jar:4.6.3]
>
>         at ucar.nc2.FileWriter2.copyVarData(FileWriter2.java:380)
> ~[cdm-4.6.3.jar:4.6.3]
>
>         at
> ucar.nc2.dt.grid.CFGridWriter2.writeOrTestSize(CFGridWriter2.java:244)
> ~[cdm-4.6.3.jar:4.6.3]
>
>         at
> ucar.nc2.dt.grid.CFGridWriter2.writeFile(CFGridWriter2.java:112)
> ~[cdm-4.6.3.jar:4.6.3]
>
>         at
> thredds.server.ncss.controller.GridResponder.writeGridFile(GridResponder.java:250)
> ~[classes/:4.6.3]
>
>         at
> thredds.server.ncss.controller.GridResponder.writeLatLonSubset(GridResponder.java:166)
> ~[classes/:4.6.3]
>
>         at
> thredds.server.ncss.controller.GridResponder.getResponseFile(GridResponder.java:97)
> ~[classes/:4.6.3]
>
>         at
> thredds.server.ncss.controller.NcssController.handleRequestGrid(NcssController.java:175)
> ~[classes/:4.6.3]
>
>         at
> thredds.server.ncss.controller.NcssController.handleRequest(NcssController.java:140)
> ~[classes/:4.6.3]
>
>         at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
> ~[?:1.8.0_65]
>
>         at
> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
> ~[?:1.8.0_65]
>
>         at
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
> ~[?:1.8.0_65]
>
>         at java.lang.reflect.Method.invoke(Method.java:497) ~[?:1.8.0_65]
>
>
>
> The error comes from netcdf4 java library used inside TDS version 4.6.3
> (latest stable version).
>
> The error appears only if we have a geographical subset (works with no
> subset or temporal aggregation).
>
> Different NetCDF-4 input files have been tested:
>
> ·         original Netcdf3 files converted with the command nccopy –k4
> –d3 input.nc output.nc4
>
> ·         original Netcdf4 generated with python library
>
> For information on software versions:
>
> misgw-qt-new:/home/misgw# ls -ltr
>
> total 246300
>
> -rw-r--r-- 1 root  root    9130958 oct  7 21:09 apache-tomcat-8.0.28.tar.gz
>
> -rw-rw-r-- 1 misgw misgw 181260798 nov  9 10:48 jdk-8u65-linux-x64.gz
>
> -rw-r--r-- 1 root  root   61808104 nov  9 11:03 thredds_4.6.3.war
>
>
>
> Thanks for the support.
>
> Tony Jolibois
>
>
>
> *-*
>
> *Tony Jolibois*
>
> *Product Dissemination Services *
>
> Space Oceanography
>
> +33 5 61 39 37 97
>
>
>
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>
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>
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>
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• References:
  • [thredds] TDS NCSS: issue with netCDF4 files as input and netCDF4 requested as output
    • From: Jolibois Tony