[ncl-talk] Bug: _FillValue attribute erases previous data

[Rick Brownrigg]

Hi Dave,

I will look into this and likely file a bug report. At one point, there was
an issue whereby if _FillValue (or any attribute) was added to a variable,
it caused all the other attributes to be dropped (but the data was
preserved). This was traced to a bug in the underlying NetCDF library,
which was fixed in version 4.4.1 around summer 2016.  The NetCDF library
was going to a lot of effort to make it possible to rewrite a preexisting
variable, so I would think the correct response is for it to "just work",
rather than error out and do nothing?

Rick

On Tue, Mar 28, 2017 at 2:59 PM, Dave Allured - NOAA Affiliate <
dave.allured at noaa.gov> wrote:

> NCL team,
>
> Under some conditions, adding a _FillValue attribute to an existing
> Netcdf-4 file erases previous data.  I find this behavior with both NCL
> 6.3.0 and 6.4.0 on Mac OS 10.11 (El Capitan).  I get the same behavior with
> both netcdf4-classic and full netcdf4 formats.
>
> mac56:~/ncl/bugs/fillvalue1 2> ncdump -s test3.nc
> netcdf test3 {
> dimensions:
> dim = 10 ;
> variables:
> int var(dim) ;
> var:_Storage = "contiguous" ;
> var:_Endianness = "little" ;
>
> // global attributes:
> :_NCProperties = "version=1|netcdflibversion=4.4.1|hdf5libversion=1.8.17"
> ;
> :_SuperblockVersion = 0 ;
> :_IsNetcdf4 = 1 ;
> :_Format = "netCDF-4 classic model" ;
> data:
>
>  var = 11, 22, 33, 44, 55, _, _, _, _, _ ;
> }
>
> mac56:~/ncl/bugs/fillvalue1 3> ncl
>  Copyright (C) 1995-2017 - All Rights Reserved
>  University Corporation for Atmospheric Research
>  NCAR Command Language Version 6.4.0
>  The use of this software is governed by a License Agreement.
>  See http://www.ncl.ucar.edu/ for more details.
> ncl 0> f=addfile("test3.nc","w")
> ncl 1> f->var at _FillValue = 99
> ncl 2> exit
>
> mac56:~/ncl/bugs/fillvalue1 4> ncdump -s test3.nc
> netcdf test3 {
> dimensions:
> dim = 10 ;
> variables:
> int var(dim) ;
> var:_FillValue = 99 ;
> var:_Storage = "contiguous" ;
> var:_Endianness = "little" ;
>
> // global attributes:
> :_NCProperties = "version=1|netcdflibversion=4.4.1|hdf5libversion=1.8.17"
> ;
> :_SuperblockVersion = 0 ;
> :_IsNetcdf4 = 1 ;
> :_Format = "netCDF-4 classic model" ;
> data:
>
>  var = _, _, _, _, _, _, _, _, _, _ ;
> }
>
> In my opinion, the correct response for netcdf-4 formats should be an
> error, something like "Can not change _FillValue after data is written in
> netcdf-4", and the file is unchanged.  In any case, previous data should
> not be silently erased.  If you agree, please fix this for the next
> release.  Thanks.
>
> --Dave
>
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