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<p class="MsoNormal">Hi Dave <o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Thanks for that (and for confirming that I don’t need to worry).
<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Will<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><b><span style="font-size:12.0pt;color:black">From: </span></b><span style="font-size:12.0pt;color:black">Dave Allured - NOAA Affiliate <dave.allured@noaa.gov><br>
<b>Date: </b>Tuesday, 2 April 2019 at 12:23 PM<br>
<b>To: </b>Will Hobbs <will.hobbs@utas.edu.au><br>
<b>Cc: </b>"ncl-talk@ucar.edu" <ncl-talk@ucar.edu><br>
<b>Subject: </b>Re: [ncl-talk] hdf issue with netcdf4 files<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Will, <o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">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.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">The key message to identify this problem is "Invalid _NCProperties attribute", which is actually false in this case.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">A comment in the original bug report implies that these messages are harmless and can be ignored:<o:p></o:p></p>
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<p class="MsoNormal"><a href="https://github.com/Unidata/netcdf-c/issues/1207" target="_blank">https://github.com/Unidata/netcdf-c/issues/1207</a><o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">--Dave<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">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:<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US">Hi all</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US">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)</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US">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. </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US">I’m happy to send a file across, but this seemas to be happening with a lot of my netCDF files</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><o:p> </o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US">Will</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US"> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US">(sample of output from a single file below – the full message is just enormous..)</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US"> </span><o:p></o:p></p>
<p class="gmail-m5483796339017881056p1"><span class="gmail-m5483796339017881056apple-tab-span">
</span><span class="gmail-m5483796339017881056s1">NC4_open: path ACCESS1-0_historical_r1i1p1_WOD_profiles_watermass_1956-2005.nc mode 4096 params 0</span><o:p></o:p></p>
<p class="gmail-m5483796339017881056p1"><span class="gmail-m5483796339017881056apple-tab-span">
</span><span class="gmail-m5483796339017881056s1">HDF5 error messages turned on.</span><o:p></o:p></p>
<p class="gmail-m5483796339017881056p1"><span class="gmail-m5483796339017881056apple-tab-span">
</span><span class="gmail-m5483796339017881056s1">nc4_open_file: path ACCESS1-0_historical_r1i1p1_WOD_profiles_watermass_1956-2005.nc mode 4096</span><o:p></o:p></p>
<p class="gmail-m5483796339017881056p1"><span class="gmail-m5483796339017881056apple-tab-span">
</span><span class="gmail-m5483796339017881056s1">nc4_grp_list_add: name /</span><span class="gmail-m5483796339017881056apple-converted-space"> </span><o:p></o:p></p>
<p class="gmail-m5483796339017881056p1"><span class="gmail-m5483796339017881056apple-tab-span">
</span><span class="gmail-m5483796339017881056s1">nc4_rec_read_metadata: grp-><a href="http://hdr.name" target="_blank">hdr.name</a> /</span><o:p></o:p></p>
<p class="gmail-m5483796339017881056p1"><span class="gmail-m5483796339017881056apple-tab-span">
</span><span class="gmail-m5483796339017881056s1">found dataset pdum</span><o:p></o:p></p>
<p class="gmail-m5483796339017881056p1"><span class="gmail-m5483796339017881056apple-tab-span">
</span><span class="gmail-m5483796339017881056s1">found dataset mass</span><o:p></o:p></p>
<p class="gmail-m5483796339017881056p1"><span class="gmail-m5483796339017881056apple-tab-span">
</span><span class="gmail-m5483796339017881056s1">found dataset bounds</span><o:p></o:p></p>
<p class="gmail-m5483796339017881056p1"><span class="gmail-m5483796339017881056apple-tab-span">
</span><span class="gmail-m5483796339017881056s1">found dataset depth</span><o:p></o:p></p>
<p class="gmail-m5483796339017881056p1"><span class="gmail-m5483796339017881056apple-tab-span">
</span><span class="gmail-m5483796339017881056s1">found dataset dz</span><o:p></o:p></p>
<p class="gmail-m5483796339017881056p1"><span class="gmail-m5483796339017881056apple-tab-span">
</span><span class="gmail-m5483796339017881056s1">found dataset lat</span><o:p></o:p></p>
<p class="gmail-m5483796339017881056p1"><span class="gmail-m5483796339017881056apple-tab-span">
</span><span class="gmail-m5483796339017881056s1">found dataset lon</span><o:p></o:p></p>
<p class="gmail-m5483796339017881056p1"><span class="gmail-m5483796339017881056apple-tab-span">
</span><span class="gmail-m5483796339017881056s1">found dataset time</span><o:p></o:p></p>
<p class="gmail-m5483796339017881056p1"><span class="gmail-m5483796339017881056apple-tab-span">
</span><span class="gmail-m5483796339017881056s1">found dataset WODid</span><o:p></o:p></p>
<p class="gmail-m5483796339017881056p1"><span class="gmail-m5483796339017881056apple-tab-span">
</span><span class="gmail-m5483796339017881056s1">found dataset Sprof</span><o:p></o:p></p>
<p class="gmail-m5483796339017881056p1"><span class="gmail-m5483796339017881056apple-tab-span">
</span><span class="gmail-m5483796339017881056s1">found dataset Tprof</span><o:p></o:p></p>
<p class="gmail-m5483796339017881056p1"><span class="gmail-m5483796339017881056apple-tab-span">
</span><span class="gmail-m5483796339017881056s1">found dataset S</span><o:p></o:p></p>
<p class="gmail-m5483796339017881056p1"><span class="gmail-m5483796339017881056apple-tab-span">
</span><span class="gmail-m5483796339017881056s1">found dataset T</span><o:p></o:p></p>
<p class="gmail-m5483796339017881056p1"><span class="gmail-m5483796339017881056apple-tab-span">
</span><span class="gmail-m5483796339017881056s1">found dataset Z</span><o:p></o:p></p>
<p class="gmail-m5483796339017881056p1"><span class="gmail-m5483796339017881056s1">ERROR: Invalid _NCProperties attribute</span><o:p></o:p></p>
<p class="gmail-m5483796339017881056p1"><span class="gmail-m5483796339017881056apple-tab-span">
</span><span class="gmail-m5483796339017881056s1">*** NetCDF-4 Internal Metadata: int_ncid 0x10000 ext_ncid 0x10000</span><o:p></o:p></p>
<p class="gmail-m5483796339017881056p1"><span class="gmail-m5483796339017881056apple-tab-span">
</span><span class="gmail-m5483796339017881056s1">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><o:p></o:p></p>
<p class="gmail-m5483796339017881056p1"><span class="gmail-m5483796339017881056apple-tab-span">
</span><span class="gmail-m5483796339017881056s1">GROUP - / nc_grpid: 0 nvars: 14 natts: 0</span><o:p></o:p></p>
<p class="gmail-m5483796339017881056p1"><span class="gmail-m5483796339017881056apple-tab-span">
</span><span class="gmail-m5483796339017881056s1">DIMENSION - dimid: 0 name: pdum len: 29985 unlimited: 0</span><o:p></o:p></p>
<p class="gmail-m5483796339017881056p1"><span class="gmail-m5483796339017881056apple-tab-span">
</span><span class="gmail-m5483796339017881056s1">DIMENSION - dimid: 1 name: mass len: 4 unlimited: 0</span><o:p></o:p></p>
<p class="gmail-m5483796339017881056p1"><span class="gmail-m5483796339017881056apple-tab-span">
</span><span class="gmail-m5483796339017881056s1">DIMENSION - dimid: 2 name: bounds len: 2 unlimited: 0</span><o:p></o:p></p>
<p class="gmail-m5483796339017881056p1"><span class="gmail-m5483796339017881056apple-tab-span">
</span><span class="gmail-m5483796339017881056s1">DIMENSION - dimid: 3 name: depth len: 96 unlimited: 0</span><o:p></o:p></p>
<p class="gmail-m5483796339017881056p1"><span class="gmail-m5483796339017881056apple-tab-span">
</span><span class="gmail-m5483796339017881056s1">VARIABLE - varid: 0 name: pdum ndims: 1 dimscale: 1 dimids: 0</span><o:p></o:p></p>
<p class="gmail-m5483796339017881056p1"><span class="gmail-m5483796339017881056apple-tab-span">
</span><span class="gmail-m5483796339017881056s1">VARIABLE - varid: 1 name: mass ndims: 1 dimscale: 1 dimids: 1</span><o:p></o:p></p>
<p class="gmail-m5483796339017881056p1"><span class="gmail-m5483796339017881056apple-tab-span">
</span><span class="gmail-m5483796339017881056s1">VARIABLE - varid: 2 name: bounds ndims: 1 dimscale: 1 dimids: 2</span><o:p></o:p></p>
<p class="gmail-m5483796339017881056p1"><span class="gmail-m5483796339017881056apple-tab-span">
</span><span class="gmail-m5483796339017881056s1">VARIABLE - varid: 3 name: depth ndims: 1 dimscale: 1 dimids: 3</span><o:p></o:p></p>
<p class="gmail-m5483796339017881056p1"><span class="gmail-m5483796339017881056apple-tab-span">
</span><span class="gmail-m5483796339017881056s1">VARIABLE - varid: 4 name: dz ndims: 1 dimscale: 0 dimids: 3</span><o:p></o:p></p>
<p class="gmail-m5483796339017881056p1"><span class="gmail-m5483796339017881056apple-tab-span">
</span><span class="gmail-m5483796339017881056s1">VARIABLE - varid: 5 name: lat ndims: 1 dimscale: 0 dimids: 0</span><o:p></o:p></p>
<p class="gmail-m5483796339017881056p1"><span class="gmail-m5483796339017881056apple-tab-span">
</span><span class="gmail-m5483796339017881056s1">VARIABLE - varid: 6 name: lon ndims: 1 dimscale: 0 dimids: 0</span><o:p></o:p></p>
<p class="gmail-m5483796339017881056p1"><span class="gmail-m5483796339017881056apple-tab-span">
</span><span class="gmail-m5483796339017881056s1">VARIABLE - varid: 7 name: time ndims: 1 dimscale: 0 dimids: 0</span><o:p></o:p></p>
<p class="gmail-m5483796339017881056p1"><span class="gmail-m5483796339017881056apple-tab-span">
</span><span class="gmail-m5483796339017881056s1">VARIABLE - varid: 8 name: WODid ndims: 1 dimscale: 0 dimids: 0</span><o:p></o:p></p>
<p class="gmail-m5483796339017881056p1"><span class="gmail-m5483796339017881056apple-tab-span">
</span><span class="gmail-m5483796339017881056s1">VARIABLE - varid: 9 name: Sprof ndims: 2 dimscale: 0 dimids: 0 3</span><o:p></o:p></p>
<p class="gmail-m5483796339017881056p1"><span class="gmail-m5483796339017881056apple-tab-span">
</span><span class="gmail-m5483796339017881056s1">VARIABLE - varid: 10 name: Tprof ndims: 2 dimscale: 0 dimids: 0 3</span><o:p></o:p></p>
<p class="gmail-m5483796339017881056p1"><span class="gmail-m5483796339017881056apple-tab-span">
</span><span class="gmail-m5483796339017881056s1">VARIABLE - varid: 11 name: S ndims: 2 dimscale: 0 dimids: 0 1</span><o:p></o:p></p>
<p class="gmail-m5483796339017881056p1"><span class="gmail-m5483796339017881056apple-tab-span">
</span><span class="gmail-m5483796339017881056s1">VARIABLE - varid: 12 name: T ndims: 2 dimscale: 0 dimids: 0 1</span><o:p></o:p></p>
<p class="gmail-m5483796339017881056p1"><span class="gmail-m5483796339017881056apple-tab-span">
</span><span class="gmail-m5483796339017881056s1">VARIABLE - varid: 13 name: Z ndims: 3 dimscale: 0 dimids: 0 1 2</span><o:p></o:p></p>
<p class="gmail-m5483796339017881056p1"><span class="gmail-m5483796339017881056apple-tab-span">
</span><span class="gmail-m5483796339017881056s1">NC4_inq: ncid 0x10000</span><o:p></o:p></p>
<p class="gmail-m5483796339017881056p1"><span class="gmail-m5483796339017881056apple-tab-span">
</span><span class="gmail-m5483796339017881056s1">nc4_att_list_add: name end_year</span><span class="gmail-m5483796339017881056apple-converted-space"> </span><o:p></o:p></p>
<p class="gmail-m5483796339017881056p1"><span class="gmail-m5483796339017881056apple-tab-span">
</span><span class="gmail-m5483796339017881056s1">nc4_att_list_add: name start_year</span><span class="gmail-m5483796339017881056apple-converted-space"> </span><o:p></o:p></p>
<p class="gmail-m5483796339017881056p1"><span class="gmail-m5483796339017881056apple-tab-span">
</span><span class="gmail-m5483796339017881056s1">nc4_att_list_add: name member</span><span class="gmail-m5483796339017881056apple-converted-space"> </span><o:p></o:p></p>
<p class="gmail-m5483796339017881056p1"><span class="gmail-m5483796339017881056apple-tab-span">
</span><span class="gmail-m5483796339017881056s1">nc4_att_list_add: name experiment</span><span class="gmail-m5483796339017881056apple-converted-space"> </span><o:p></o:p></p>
<p class="gmail-m5483796339017881056p1"><span class="gmail-m5483796339017881056apple-tab-span">
</span><span class="gmail-m5483796339017881056s1">nc4_att_list_add: name model</span><span class="gmail-m5483796339017881056apple-converted-space"> </span><o:p></o:p></p>
<p class="gmail-m5483796339017881056p1"><span class="gmail-m5483796339017881056apple-tab-span">
</span><span class="gmail-m5483796339017881056s1">nc4_att_list_add: name creation_script</span><span class="gmail-m5483796339017881056apple-converted-space"> </span><o:p></o:p></p>
<p class="gmail-m5483796339017881056p1"><span class="gmail-m5483796339017881056apple-tab-span">
</span><span class="gmail-m5483796339017881056s1">nc4_att_list_add: name creation_data</span><span class="gmail-m5483796339017881056apple-converted-space"> </span><o:p></o:p></p>
<p class="gmail-m5483796339017881056p1"><span class="gmail-m5483796339017881056apple-tab-span">
</span><span class="gmail-m5483796339017881056s1">nc4_att_list_add: name description</span><span class="gmail-m5483796339017881056apple-converted-space"> </span><o:p></o:p></p>
<p class="gmail-m5483796339017881056p1"><span class="gmail-m5483796339017881056apple-tab-span">
</span><span class="gmail-m5483796339017881056s1">nc_inq_attname: ncid 0x10000 varid -1 attnum 0</span><o:p></o:p></p>
<p class="gmail-m5483796339017881056p1"><span class="gmail-m5483796339017881056apple-tab-span">
</span><span class="gmail-m5483796339017881056s1">nc_inq_attname: ncid 0x10000 varid -1 attnum 0</span><o:p></o:p></p>
<p class="gmail-m5483796339017881056p1"><span class="gmail-m5483796339017881056apple-tab-span">
</span><span class="gmail-m5483796339017881056s1">NC4_inq_att: ncid 0x10000 varid -1 name end_year</span><o:p></o:p></p>
<p class="gmail-m5483796339017881056p1"><span class="gmail-m5483796339017881056apple-tab-span">
</span><span class="gmail-m5483796339017881056s1">nc4_get_att: ncid 0x10000 varid -1 name end_year attnum -1 mem_type 0</span><o:p></o:p></p>
<p class="gmail-m5483796339017881056p1"><span class="gmail-m5483796339017881056apple-tab-span">
</span><span class="gmail-m5483796339017881056s1">NC4_inq_att: ncid 0x10000 varid -1 name end_year</span><o:p></o:p></p>
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University of Tasmania Electronic Communications Policy (December, 2014). <br>
This email is confidential, and is for the intended recipient only. Access, disclosure, copying, distribution, or reliance on any of it by anyone outside the intended recipient organisation is prohibited and may be a criminal offence. Please delete if obtained
in error and email confirmation to the sender. The views expressed in this email are not necessarily the views of the University of Tasmania, unless clearly intended otherwise.
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