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[netCDF #KES-987451]: nccopy fails to generate a netCDF-4 classic file

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  • Subject: [netCDF #KES-987451]: nccopy fails to generate a netCDF-4 classic file
  • Date: Tue, 17 Sep 2013 14:06:52 -0600
Hi Kent,

> Although this issue is confirmed by nccopy, it may be something worth to
> take an action on how to handle the dimension scale inside the netCDF-4
> library.
> 
> netCDF-4 version: netCDF-4.3.0
> 
> 1) The netCDF-3 file:
> 
> ftp://ftp.hdfgroup.uiuc.edu/pub/outgoing/ymuqun/temp/netcdf-4-dim-scale-issue/outfile-n3-GLAH.gz

OK, I got it, thanks.

> 2) nccopy error-message:
> 
> ./nccopy -k 4 -d 1 outfile-n3-GLAH outfile-n4conv-GLAH
> 
> You should see the following error message:
> "NetCDF: HDF error Location: file nccopy.c; line 1437"
> The line is NC_CHECK(nc_enddef(ogrp));

I can't duplicate the error with any of the versions of nccopy I
have built, including 4.3.0, 4.2.1.1, or 4.1.3.  In each case, nccopy
completes with no error message, and the size of the resulting output
file is as expected, for example:

  $ NCDIR=/machine/russ/installs/nc430 ; ${NCDIR}/bin/nccopy -k 4 -d 1 GLAH.nc 
GLAH.nc4 ; ls -l GLAH.nc GLAH.nc4
  -rw-rw-r-- 1 russ ustaff 225935448 Sep 17 13:36 GLAH.nc
  -rw-rw-r-- 1 russ ustaff  36385878 Sep 17 14:00 GLAH.nc4

Is it possible the error message only appears when built with some
non-default configure flag, that the version of nccopy you are
using is older (unfortunately it doesn't have a --version flag), 
or that the error only occurs when built with a newer version of 
HDF5 than 1.8.11?

--Russ

> Curiously, nccopy continues generating a netCDF-4 file. It seems that this
> file is valid.
> 
> 3) Some hints:
> A more detailed log message shows that:
> attach_dimscales: attaching scale for dimid 3 to var BROWSE_Image_00
> ERROR: file nc4hdf.c, line 1994.
> 
> In line nc4hdf.c 1994, it shows that H5DSattach_scale fails.
> 
> A more careful investigation of the variable BROWSE_Image_00 shows that
> it has an attribute CLASS = IMAGE
> 
> If you check the HDF5 dimension scale source code, you will find that
> CLASS = IMAGE is reserved for HDF5 image. H5DSattach_scale will fail if it
> finds this HDF5 dataset is an HDF5 IMAGE.  It doesn't make sense to provide
> a dimension scale for an image.
> 
> In fact, this netcdf-3 file is converted from an HDF5 file that indeed has
> HDF5 IMAGE objects. This can be verified by using HDFView to check the
> original HDF5 file.
> 
> So a possible solution may be not to attach dimension scales if netCDF-4
> finds an attribute CLASS = IMAGE.
> 
> The detailed log message can be found under
> 
> ftp://ftp.hdfgroup.uiuc.edu/pub/outgoing/ymuqun/temp/netcdf-4-dim-scale-issue/n4conv-error-message
> 
> The original HDF5 file can be found under
> ftp://ftp.hdfgroup.uiuc.edu/pub/outgoing/fileout_netcdf/data/GLAH13_633_2103_001_1317_0_01_0001.h5
> 
> Kent
> 
> --
> Kent Yang The HDF Group
> 1800 So. Oak St., Suite 203, Champaign, IL 61820
> 217.531.6107
> http://hdfgroup.org http://hdfeos.org
> 
> 

Russ Rew                                         UCAR Unidata Program
address@hidden                      http://www.unidata.ucar.edu



Ticket Details
===================
Ticket ID: KES-987451
Department: Support netCDF
Priority: Normal
Status: Closed