<div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr">Will,<div><br></div><div><div>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.</div><div><br></div><div>The key message to identify this problem is "Invalid _NCProperties attribute", which is actually false in this case.</div><div><br></div><div>A comment in the original bug report implies that these messages are harmless and can be ignored:</div><div><a href="https://github.com/Unidata/netcdf-c/issues/1207" target="_blank">https://github.com/Unidata/netcdf-c/issues/1207</a></div><div><br></div><div>--Dave</div></div></div><div><br></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Mon, Apr 1, 2019 at 6:58 PM Will Hobbs <<a href="mailto:will.hobbs@utas.edu.au">will.hobbs@utas.edu.au</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-style:solid;border-left-color:rgb(204,204,204);padding-left:1ex">
<div lang="EN-AU">
<div class="gmail-m_5483796339017881056WordSection1">
<p class="MsoNormal"><span lang="EN-US" style="font-size:11pt">Hi all<u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11pt"><u></u> <u></u></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11pt">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)<u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11pt"><u></u> <u></u></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11pt">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.
<u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11pt"><u></u> <u></u></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11pt">I’m happy to send a file across, but this seemas to be happening with a lot of my netCDF files<u></u><u></u></span></p>
<p class="MsoNormal"><br></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11pt">Will<u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11pt"><u></u> <u></u></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11pt">(sample of output from a single file below – the full message is just enormous..)<u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11pt"><u></u> <u></u></span></p>
<p class="gmail-m_5483796339017881056p1"><span class="gmail-m_5483796339017881056apple-tab-span"> </span><span class="gmail-m_5483796339017881056s1">NC4_open: path ACCESS1-0_historical_r1i1p1_WOD_profiles_watermass_1956-2005.nc mode 4096 params 0</span><u></u><u></u></p>
<p class="gmail-m_5483796339017881056p1"><span class="gmail-m_5483796339017881056apple-tab-span"> </span><span class="gmail-m_5483796339017881056s1">HDF5 error messages turned on.</span><u></u><u></u></p>
<p class="gmail-m_5483796339017881056p1"><span class="gmail-m_5483796339017881056apple-tab-span"> </span><span class="gmail-m_5483796339017881056s1">nc4_open_file: path ACCESS1-0_historical_r1i1p1_WOD_profiles_watermass_1956-2005.nc mode 4096</span><u></u><u></u></p>
<p class="gmail-m_5483796339017881056p1"><span class="gmail-m_5483796339017881056apple-tab-span"> </span><span class="gmail-m_5483796339017881056s1">nc4_grp_list_add: name /</span><span class="gmail-m_5483796339017881056apple-converted-space"> </span><u></u><u></u></p>
<p class="gmail-m_5483796339017881056p1"><span class="gmail-m_5483796339017881056apple-tab-span"> </span><span class="gmail-m_5483796339017881056s1">nc4_rec_read_metadata: grp-><a href="http://hdr.name" target="_blank">hdr.name</a> /</span><u></u><u></u></p>
<p class="gmail-m_5483796339017881056p1"><span class="gmail-m_5483796339017881056apple-tab-span"> </span><span class="gmail-m_5483796339017881056s1">found dataset pdum</span><u></u><u></u></p>
<p class="gmail-m_5483796339017881056p1"><span class="gmail-m_5483796339017881056apple-tab-span"> </span><span class="gmail-m_5483796339017881056s1">found dataset mass</span><u></u><u></u></p>
<p class="gmail-m_5483796339017881056p1"><span class="gmail-m_5483796339017881056apple-tab-span"> </span><span class="gmail-m_5483796339017881056s1">found dataset bounds</span><u></u><u></u></p>
<p class="gmail-m_5483796339017881056p1"><span class="gmail-m_5483796339017881056apple-tab-span"> </span><span class="gmail-m_5483796339017881056s1">found dataset depth</span><u></u><u></u></p>
<p class="gmail-m_5483796339017881056p1"><span class="gmail-m_5483796339017881056apple-tab-span"> </span><span class="gmail-m_5483796339017881056s1">found dataset dz</span><u></u><u></u></p>
<p class="gmail-m_5483796339017881056p1"><span class="gmail-m_5483796339017881056apple-tab-span"> </span><span class="gmail-m_5483796339017881056s1">found dataset lat</span><u></u><u></u></p>
<p class="gmail-m_5483796339017881056p1"><span class="gmail-m_5483796339017881056apple-tab-span"> </span><span class="gmail-m_5483796339017881056s1">found dataset lon</span><u></u><u></u></p>
<p class="gmail-m_5483796339017881056p1"><span class="gmail-m_5483796339017881056apple-tab-span"> </span><span class="gmail-m_5483796339017881056s1">found dataset time</span><u></u><u></u></p>
<p class="gmail-m_5483796339017881056p1"><span class="gmail-m_5483796339017881056apple-tab-span"> </span><span class="gmail-m_5483796339017881056s1">found dataset WODid</span><u></u><u></u></p>
<p class="gmail-m_5483796339017881056p1"><span class="gmail-m_5483796339017881056apple-tab-span"> </span><span class="gmail-m_5483796339017881056s1">found dataset Sprof</span><u></u><u></u></p>
<p class="gmail-m_5483796339017881056p1"><span class="gmail-m_5483796339017881056apple-tab-span"> </span><span class="gmail-m_5483796339017881056s1">found dataset Tprof</span><u></u><u></u></p>
<p class="gmail-m_5483796339017881056p1"><span class="gmail-m_5483796339017881056apple-tab-span"> </span><span class="gmail-m_5483796339017881056s1">found dataset S</span><u></u><u></u></p>
<p class="gmail-m_5483796339017881056p1"><span class="gmail-m_5483796339017881056apple-tab-span"> </span><span class="gmail-m_5483796339017881056s1">found dataset T</span><u></u><u></u></p>
<p class="gmail-m_5483796339017881056p1"><span class="gmail-m_5483796339017881056apple-tab-span"> </span><span class="gmail-m_5483796339017881056s1">found dataset Z</span><u></u><u></u></p>
<p class="gmail-m_5483796339017881056p1"><span class="gmail-m_5483796339017881056s1">ERROR: Invalid _NCProperties attribute</span><u></u><u></u></p>
<p class="gmail-m_5483796339017881056p1"><span class="gmail-m_5483796339017881056apple-tab-span"> </span><span class="gmail-m_5483796339017881056s1">*** NetCDF-4 Internal Metadata: int_ncid 0x10000 ext_ncid 0x10000</span><u></u><u></u></p>
<p class="gmail-m_5483796339017881056p1"><span class="gmail-m_5483796339017881056apple-tab-span"> </span><span class="gmail-m_5483796339017881056s1">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</span><u></u><u></u></p>
<p class="gmail-m_5483796339017881056p1"><span class="gmail-m_5483796339017881056apple-tab-span"> </span><span class="gmail-m_5483796339017881056s1">GROUP - / nc_grpid: 0 nvars: 14 natts: 0</span><u></u><u></u></p>
<p class="gmail-m_5483796339017881056p1"><span class="gmail-m_5483796339017881056apple-tab-span"> </span><span class="gmail-m_5483796339017881056s1">DIMENSION - dimid: 0 name: pdum len: 29985 unlimited: 0</span><u></u><u></u></p>
<p class="gmail-m_5483796339017881056p1"><span class="gmail-m_5483796339017881056apple-tab-span"> </span><span class="gmail-m_5483796339017881056s1">DIMENSION - dimid: 1 name: mass len: 4 unlimited: 0</span><u></u><u></u></p>
<p class="gmail-m_5483796339017881056p1"><span class="gmail-m_5483796339017881056apple-tab-span"> </span><span class="gmail-m_5483796339017881056s1">DIMENSION - dimid: 2 name: bounds len: 2 unlimited: 0</span><u></u><u></u></p>
<p class="gmail-m_5483796339017881056p1"><span class="gmail-m_5483796339017881056apple-tab-span"> </span><span class="gmail-m_5483796339017881056s1">DIMENSION - dimid: 3 name: depth len: 96 unlimited: 0</span><u></u><u></u></p>
<p class="gmail-m_5483796339017881056p1"><span class="gmail-m_5483796339017881056apple-tab-span"> </span><span class="gmail-m_5483796339017881056s1">VARIABLE - varid: 0 name: pdum ndims: 1 dimscale: 1 dimids: 0</span><u></u><u></u></p>
<p class="gmail-m_5483796339017881056p1"><span class="gmail-m_5483796339017881056apple-tab-span"> </span><span class="gmail-m_5483796339017881056s1">VARIABLE - varid: 1 name: mass ndims: 1 dimscale: 1 dimids: 1</span><u></u><u></u></p>
<p class="gmail-m_5483796339017881056p1"><span class="gmail-m_5483796339017881056apple-tab-span"> </span><span class="gmail-m_5483796339017881056s1">VARIABLE - varid: 2 name: bounds ndims: 1 dimscale: 1 dimids: 2</span><u></u><u></u></p>
<p class="gmail-m_5483796339017881056p1"><span class="gmail-m_5483796339017881056apple-tab-span"> </span><span class="gmail-m_5483796339017881056s1">VARIABLE - varid: 3 name: depth ndims: 1 dimscale: 1 dimids: 3</span><u></u><u></u></p>
<p class="gmail-m_5483796339017881056p1"><span class="gmail-m_5483796339017881056apple-tab-span"> </span><span class="gmail-m_5483796339017881056s1">VARIABLE - varid: 4 name: dz ndims: 1 dimscale: 0 dimids: 3</span><u></u><u></u></p>
<p class="gmail-m_5483796339017881056p1"><span class="gmail-m_5483796339017881056apple-tab-span"> </span><span class="gmail-m_5483796339017881056s1">VARIABLE - varid: 5 name: lat ndims: 1 dimscale: 0 dimids: 0</span><u></u><u></u></p>
<p class="gmail-m_5483796339017881056p1"><span class="gmail-m_5483796339017881056apple-tab-span"> </span><span class="gmail-m_5483796339017881056s1">VARIABLE - varid: 6 name: lon ndims: 1 dimscale: 0 dimids: 0</span><u></u><u></u></p>
<p class="gmail-m_5483796339017881056p1"><span class="gmail-m_5483796339017881056apple-tab-span"> </span><span class="gmail-m_5483796339017881056s1">VARIABLE - varid: 7 name: time ndims: 1 dimscale: 0 dimids: 0</span><u></u><u></u></p>
<p class="gmail-m_5483796339017881056p1"><span class="gmail-m_5483796339017881056apple-tab-span"> </span><span class="gmail-m_5483796339017881056s1">VARIABLE - varid: 8 name: WODid ndims: 1 dimscale: 0 dimids: 0</span><u></u><u></u></p>
<p class="gmail-m_5483796339017881056p1"><span class="gmail-m_5483796339017881056apple-tab-span"> </span><span class="gmail-m_5483796339017881056s1">VARIABLE - varid: 9 name: Sprof ndims: 2 dimscale: 0 dimids: 0 3</span><u></u><u></u></p>
<p class="gmail-m_5483796339017881056p1"><span class="gmail-m_5483796339017881056apple-tab-span"> </span><span class="gmail-m_5483796339017881056s1">VARIABLE - varid: 10 name: Tprof ndims: 2 dimscale: 0 dimids: 0 3</span><u></u><u></u></p>
<p class="gmail-m_5483796339017881056p1"><span class="gmail-m_5483796339017881056apple-tab-span"> </span><span class="gmail-m_5483796339017881056s1">VARIABLE - varid: 11 name: S ndims: 2 dimscale: 0 dimids: 0 1</span><u></u><u></u></p>
<p class="gmail-m_5483796339017881056p1"><span class="gmail-m_5483796339017881056apple-tab-span"> </span><span class="gmail-m_5483796339017881056s1">VARIABLE - varid: 12 name: T ndims: 2 dimscale: 0 dimids: 0 1</span><u></u><u></u></p>
<p class="gmail-m_5483796339017881056p1"><span class="gmail-m_5483796339017881056apple-tab-span"> </span><span class="gmail-m_5483796339017881056s1">VARIABLE - varid: 13 name: Z ndims: 3 dimscale: 0 dimids: 0 1 2</span><u></u><u></u></p>
<p class="gmail-m_5483796339017881056p1"><span class="gmail-m_5483796339017881056apple-tab-span"> </span><span class="gmail-m_5483796339017881056s1">NC4_inq: ncid 0x10000</span><u></u><u></u></p>
<p class="gmail-m_5483796339017881056p1"><span class="gmail-m_5483796339017881056apple-tab-span"> </span><span class="gmail-m_5483796339017881056s1">nc4_att_list_add: name end_year</span><span class="gmail-m_5483796339017881056apple-converted-space"> </span><u></u><u></u></p>
<p class="gmail-m_5483796339017881056p1"><span class="gmail-m_5483796339017881056apple-tab-span"> </span><span class="gmail-m_5483796339017881056s1">nc4_att_list_add: name start_year</span><span class="gmail-m_5483796339017881056apple-converted-space"> </span><u></u><u></u></p>
<p class="gmail-m_5483796339017881056p1"><span class="gmail-m_5483796339017881056apple-tab-span"> </span><span class="gmail-m_5483796339017881056s1">nc4_att_list_add: name member</span><span class="gmail-m_5483796339017881056apple-converted-space"> </span><u></u><u></u></p>
<p class="gmail-m_5483796339017881056p1"><span class="gmail-m_5483796339017881056apple-tab-span"> </span><span class="gmail-m_5483796339017881056s1">nc4_att_list_add: name experiment</span><span class="gmail-m_5483796339017881056apple-converted-space"> </span><u></u><u></u></p>
<p class="gmail-m_5483796339017881056p1"><span class="gmail-m_5483796339017881056apple-tab-span"> </span><span class="gmail-m_5483796339017881056s1">nc4_att_list_add: name model</span><span class="gmail-m_5483796339017881056apple-converted-space"> </span><u></u><u></u></p>
<p class="gmail-m_5483796339017881056p1"><span class="gmail-m_5483796339017881056apple-tab-span"> </span><span class="gmail-m_5483796339017881056s1">nc4_att_list_add: name creation_script</span><span class="gmail-m_5483796339017881056apple-converted-space"> </span><u></u><u></u></p>
<p class="gmail-m_5483796339017881056p1"><span class="gmail-m_5483796339017881056apple-tab-span"> </span><span class="gmail-m_5483796339017881056s1">nc4_att_list_add: name creation_data</span><span class="gmail-m_5483796339017881056apple-converted-space"> </span><u></u><u></u></p>
<p class="gmail-m_5483796339017881056p1"><span class="gmail-m_5483796339017881056apple-tab-span"> </span><span class="gmail-m_5483796339017881056s1">nc4_att_list_add: name description</span><span class="gmail-m_5483796339017881056apple-converted-space"> </span><u></u><u></u></p>
<p class="gmail-m_5483796339017881056p1"><span class="gmail-m_5483796339017881056apple-tab-span"> </span><span class="gmail-m_5483796339017881056s1">nc_inq_attname: ncid 0x10000 varid -1 attnum 0</span><u></u><u></u></p>
<p class="gmail-m_5483796339017881056p1"><span class="gmail-m_5483796339017881056apple-tab-span"> </span><span class="gmail-m_5483796339017881056s1">nc_inq_attname: ncid 0x10000 varid -1 attnum 0</span><u></u><u></u></p>
<p class="gmail-m_5483796339017881056p1"><span class="gmail-m_5483796339017881056apple-tab-span"> </span><span class="gmail-m_5483796339017881056s1">NC4_inq_att: ncid 0x10000 varid -1 name end_year</span><u></u><u></u></p>
<p class="gmail-m_5483796339017881056p1"><span class="gmail-m_5483796339017881056apple-tab-span"> </span><span class="gmail-m_5483796339017881056s1">nc4_get_att: ncid 0x10000 varid -1 name end_year attnum -1 mem_type 0</span><u></u><u></u></p>
<p class="gmail-m_5483796339017881056p1"><span class="gmail-m_5483796339017881056apple-tab-span"> </span><span class="gmail-m_5483796339017881056s1">NC4_inq_att: ncid 0x10000 varid -1 name end_year</span></p></div></div>
</blockquote></div></div></div></div>