[ncl-talk] Error in nc_def_var_chunking in file (domain_cfg.nc) for writing

[Dave Allured - NOAA Affiliate]

边晴云, you want to change the value of an existing variable in a netcdf file.

(1)  As Rick indicated, change the *addfile* open mode from "rw" which is
invalid, to just "w".  See documentation for *addfile*.

(2)  Remove this line, it is not needed:

    copy_VarMeta(data,data_v)

(3)  Change this line:

    From:  fin->jperio = data_v
    To:    fin->jperio = (/ data_v /)

This is called "value-only assignment" in the NCL users manual.  This
change will overwrite only the actual data values, and not try to change
any metadata.  I think this will avoid the define error that you are
getting.


On Tue, Oct 27, 2020 at 8:28 AM Rick Brownrigg via ncl-talk <
ncl-talk at mailman.ucar.edu> wrote:

> Hi,
>
> I don't know the issue for certain. However, "rw" is not a valid open mode
> -- its either "r" (read) or "w" (read-write), and I am speculating that the
> code is looking at only the first character and proceeding from there, in
> which case the file would be in read mode. "enddef" refers to ending
> "define mode", which is an esoteric property of NetCDF files whereby one
> must define structural properties (vars, shapes, dims, etc.) before writing
> the actual data. If you read the description of "DefineMode" at the link
> below, it indicates the file would only be in define mode if opened for
> writing.
>
> http://ncl.ucar.edu/Document/Functions/Built-in/setfileoption.shtml
>
> Again, I'm just speculating, but it would be easy to test!
>
> Rick
>
>
> On Tue, Oct 27, 2020 at 1:39 AM 边晴云 via ncl-talk <
> ncl-talk at mailman.ucar.edu> wrote:
>
>>
>> Dear All,
>>
>>
>> I was trying to change the value of an int variable in a netcdf file
>> using NCL. Followed are my code:
>>
>>
>> begin
>>
>> fin = addfile("domain_cfg.nc","rw")
>> data=fin->jperio
>> data_v = new(dimsizes(data),typeof(data),data at _FillValue)
>> data_v = 0
>>
>> copy_VarMeta(data,data_v)
>> fin->jperio = data_v
>>
>> end
>>
>>
>> However, I got the following error message:
>>
>> --------
>>
>> fatal:["NclNetCDF4.c":3073]:NclNetCDF4.c: Error in nc_def_var_chunking in
>> file (domain_cfg.nc) for writing, at line: 3073
>>
>> line 3074 of NclNetCDF4.c: NetCDF: Attempt to define var properties, like
>> deflate, after enddef.
>>
>>
>> I have no idea how to resolve it. Any suggestions?
>>
>> Thank you!
>>
>>
>> Followed are some information about the  netcdf file.
>>
>> ---------
>>
>> netcdf domain_cfg {
>> dimensions:
>>         x = 2710 ;
>>         y = 1542 ;
>>         z = 75 ;
>>         t = UNLIMITED ; // (1 currently)
>> variables:
>>         float nav_lon(y, x) ;
>>                 nav_lon:_Storage = "chunked" ;
>>                 nav_lon:_ChunkSizes = 135, 206 ;
>>                 nav_lon:_Endianness = "little" ;
>>         float nav_lat(y, x) ;
>>                 nav_lat:_Storage = "chunked" ;
>>                 nav_lat:_ChunkSizes = 135, 206 ;
>>                 nav_lat:_Endianness = "little" ;
>>         float nav_lev(z) ;
>>                 nav_lev:_Storage = "chunked" ;
>>                 nav_lev:_ChunkSizes = 1 ;
>>                 nav_lev:_Endianness = "little" ;
>>         double time_counter(t) ;
>>                 time_counter:_Storage = "chunked" ;
>>                 time_counter:_ChunkSizes = 1 ;
>>                 time_counter:_Endianness = "little" ;
>>         int jpiglo ;
>>                 jpiglo:_Endianness = "little" ;
>>         int jpjglo ;
>>                 jpjglo:_Endianness = "little" ;
>>         int jpkglo ;
>>                 jpkglo:_Endianness = "little" ;
>>         int jperio ;
>>                 jperio:_Endianness = "little" ;
>>         double glamt(t, y, x) ;
>>                 glamt:_Storage = "chunked" ;
>>                 glamt:_ChunkSizes = 1, 135, 206 ;
>>                 glamt:_Endianness = "little" ;
>>         double glamu(t, y, x) ;
>>                 glamu:_Storage = "chunked" ;
>>                 glamu:_ChunkSizes = 1, 135, 206 ;
>>                 glamu:_Endianness = "little" ;
>>
>> // global attributes:
>>                 :file_name = "domain_cfg.nc" ;
>>                 :TimeStamp = "24/08/2020 16:38:57 +0800" ;
>>                 :_NCProperties =
>> "version=1|netcdflibversion=4.4.1|hdf5libversion=1.8.13" ;
>>                 :_SuperblockVersion = 0 ;
>>                 :_IsNetcdf4 = 1 ;
>>                 :_Format = "netCDF-4" ;
>>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://mailman.ucar.edu/pipermail/ncl-talk/attachments/20201027/301ac657/attachment.html>