[ncl-talk] hdf issue with netcdf4 files

[Dave Allured - NOAA Affiliate]

Will,

This is a known bug in netcdf 4.6.2.  It is tagged as fixed in the latest
netcdf version.  Try updating your installed netcdf.

The key message to identify this problem is "Invalid _NCProperties
attribute", which is actually false in this case.

A comment in the original bug report implies that these messages are
harmless and can be ignored:
https://github.com/Unidata/netcdf-c/issues/1207

--Dave


On Mon, Apr 1, 2019 at 6:58 PM Will Hobbs <will.hobbs at utas.edu.au> wrote:

> Hi all
>
>
>
> I recently (like, yesterday) upgraded to v 6.6.2. The install works fine,
> except that when I access any netcdf4 files (either using addfile() or
> ncl_filedump) I get an enormous list of HDF5 error messages (see below). I
> do not get the same errors using ncdump. I have version 1.10.5 of hdf5
> (which I think is up to date)
>
>
>
> The functionality and scripts work just fine, and I can get over this
> using 2>/dev/null, but I wonder if anyone else has had this problem or is
> aware of flag to turn off the the stream of messages.
>
>
>
> I’m happy to send a file across, but this seemas to be happening with a
> lot of my netCDF files
>
>
> Will
>
>
>
> (sample of output from a single file below – the full message is just
> enormous..)
>
>
>
>     NC4_open: path
> ACCESS1-0_historical_r1i1p1_WOD_profiles_watermass_1956-2005.nc mode 4096
> params 0
>
>     HDF5 error messages turned on.
>
>             nc4_open_file: path
> ACCESS1-0_historical_r1i1p1_WOD_profiles_watermass_1956-2005.nc mode 4096
>
>             nc4_grp_list_add: name /
>
>             nc4_rec_read_metadata: grp->hdr.name /
>
>             found dataset pdum
>
>             found dataset mass
>
>             found dataset bounds
>
>             found dataset depth
>
>             found dataset dz
>
>             found dataset lat
>
>             found dataset lon
>
>             found dataset time
>
>             found dataset WODid
>
>             found dataset Sprof
>
>             found dataset Tprof
>
>             found dataset S
>
>             found dataset T
>
>             found dataset Z
>
> ERROR: Invalid _NCProperties attribute
>
>         *** NetCDF-4 Internal Metadata: int_ncid 0x10000 ext_ncid 0x10000
>
>         FILE - path:
> ACCESS1-0_historical_r1i1p1_WOD_profiles_watermass_1956-2005.nc cmode:
> 0x1008 parallel: 0 redef: 0 fill_mode: 0 no_write: 1 next_nc_grpid: 1
>
>         GROUP - / nc_grpid: 0 nvars: 14 natts: 0
>
>         DIMENSION - dimid: 0 name: pdum len: 29985 unlimited: 0
>
>         DIMENSION - dimid: 1 name: mass len: 4 unlimited: 0
>
>         DIMENSION - dimid: 2 name: bounds len: 2 unlimited: 0
>
>         DIMENSION - dimid: 3 name: depth len: 96 unlimited: 0
>
>         VARIABLE - varid: 0 name: pdum ndims: 1 dimscale: 1 dimids: 0
>
>         VARIABLE - varid: 1 name: mass ndims: 1 dimscale: 1 dimids: 1
>
>         VARIABLE - varid: 2 name: bounds ndims: 1 dimscale: 1 dimids: 2
>
>         VARIABLE - varid: 3 name: depth ndims: 1 dimscale: 1 dimids: 3
>
>         VARIABLE - varid: 4 name: dz ndims: 1 dimscale: 0 dimids: 3
>
>         VARIABLE - varid: 5 name: lat ndims: 1 dimscale: 0 dimids: 0
>
>         VARIABLE - varid: 6 name: lon ndims: 1 dimscale: 0 dimids: 0
>
>         VARIABLE - varid: 7 name: time ndims: 1 dimscale: 0 dimids: 0
>
>         VARIABLE - varid: 8 name: WODid ndims: 1 dimscale: 0 dimids: 0
>
>         VARIABLE - varid: 9 name: Sprof ndims: 2 dimscale: 0 dimids: 0 3
>
>         VARIABLE - varid: 10 name: Tprof ndims: 2 dimscale: 0 dimids: 0 3
>
>         VARIABLE - varid: 11 name: S ndims: 2 dimscale: 0 dimids: 0 1
>
>         VARIABLE - varid: 12 name: T ndims: 2 dimscale: 0 dimids: 0 1
>
>         VARIABLE - varid: 13 name: Z ndims: 3 dimscale: 0 dimids: 0 1 2
>
>         NC4_inq: ncid 0x10000
>
>             nc4_att_list_add: name end_year
>
>             nc4_att_list_add: name start_year
>
>             nc4_att_list_add: name member
>
>             nc4_att_list_add: name experiment
>
>             nc4_att_list_add: name model
>
>             nc4_att_list_add: name creation_script
>
>             nc4_att_list_add: name creation_data
>
>             nc4_att_list_add: name description
>
>         nc_inq_attname: ncid 0x10000 varid -1 attnum 0
>
>         nc_inq_attname: ncid 0x10000 varid -1 attnum 0
>
>         NC4_inq_att: ncid 0x10000 varid -1 name end_year
>
>             nc4_get_att: ncid 0x10000 varid -1 name end_year attnum -1
> mem_type 0
>
>         NC4_inq_att: ncid 0x10000 varid -1 name end_year
>
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