[ncl-talk] hdf issue with netcdf4 files

[Will Hobbs]

Hi Dave

Thanks for that (and for confirming that I don’t need to worry).

Will



From: Dave Allured - NOAA Affiliate <dave.allured at noaa.gov>
Date: Tuesday, 2 April 2019 at 12:23 PM
To: Will Hobbs <will.hobbs at utas.edu.au>
Cc: "ncl-talk at ucar.edu" <ncl-talk at ucar.edu>
Subject: Re: [ncl-talk] hdf issue with netcdf4 files

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<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<mailto: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<http://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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