Re: Problems writing NetCDF4 file

Thanks, Dave. Adding "fout->time = new_t" before writing the variable to
the file worked, though I'm getting "warning:Right hand side has no
coordinate variable can not delete coordinate variable of a file, use (/ ..
/) to avoid this message." Also, the "delete(new_t@bounds)" call does not
appear to be working since the attribute is still writing to the file. Not
sure what's going on there...

-Bridget

On Wed, Mar 7, 2012 at 1:31 PM, David Brown <dbrown@ucar.edu> wrote:

> Hi Bridget,
>
> Unlike NetCDF3, NetCDF4 requires that the _FillValue attribute be written
> prior to any data for any particular variable and also it cannot be changed
> after it is created. This created a problem for NCL's simple style of
> writing variables because originally when a variable was assigned to a file
> using the simple method (f->var = var), the data was written before the
> attributes. So in 2009 I modified the code so that the attributes were
> written first. However, it is possible something is written in the wrong
> order in your case. It looks like you are not explicitly writing the 'time'
> variable to the file, but that, because it is a coordinate of your data
> variable, it is being implicitly written. I didn't think this would be a
> problem, but perhaps there is a pathway that I have not considered.
>
> As a work-around you could try explicitly assigning the 'time' variable to
> the file (fout->time = time) before writing the 'new_agggcm' variable. Let
> us know whether or not this works.
> In any case, it would be good if you can send us enough code and data to
> duplicate the problem. See the 'report bugs' page if you need a refresher
> on uploading to the ftp site.
> -dave
>
>
>
>
> On Mar 7, 2012, at 2:03 PM, Bridget Thrasher wrote:
>
> I am getting an error that I don't understand and cannot seem to get
> around when trying to write out a file with a NetCDF4 format. Can anyone
> explain this to me? Here is my output with the error followed by the
> pertinent code snippets:
>
> Copyright (C) 1995-2011 - All Rights Reserved
> University Corporation for Atmospheric Research
> NCAR Command Language Version 6.0.0
> The use of this software is governed by a License Agreement.
> See http://www.ncl.ucar.edu/ for more details.
>
> Variable: new_t
> Type: double
> Total Size: 29216 bytes
> 3652 values
> Number of Dimensions: 1
> Dimensions and sizes: [time | 3652]
> Coordinates:
> Number Of Attributes: 6
> standard_name : time
> long_name : time
> axis : T
> calendar : gregorian
> units : days since 1850-01-01
> _FillValue : 9.969209968386869e+36
>
> (0) writing file
> ncattput: ncid 131072: NetCDF: Attempt to define fill value when data
> already exists.
> fatal:Attempt to delete undefined attribute from variable
> warning:FileWriteVarVar: Could not write attribute (_FillValue) to
> variable (time) in file
> (regridded_2deg_tasmin_day_bcc-csm1-1_historical_r1i1p1_19500101-19591231),
> continuing anyway
> ncendef: ncid 131072: NetCDF: Can't open HDF5 attribute
> ncendef: ncid 131072: NetCDF: Can't open HDF5 attribute
> (0) file written
>
>
>
> setfileoption("nc","Format","NetCDF4Classic")
> setfileoption("nc","CompressionLevel",5) ; 0 through 9 possible
>
> t = fin->time
> ut = ut_calendar(t,-5)
> ii = ind(isleapyear(ut(:,0)).and.ut(:,1).eq.2.and.ut(:,2).eq.28)
> n = dimsizes(ii)
> dims = dimsizes(agggcm)
> new_agggcm = new((/dims(0)+n,dims(1),dims(2)/),float,fill)
> new_ut = new((/dimsizes(t)+n,6/),typeof(ut))
> new_t = new((/dimsizes(t)+n/),typeof(t))
> new_agggcm(:ii(0),:,:) = agggcm(:ii(0),:,:)
> new_ut(:ii(0),:) = ut(:ii(0),:)
> do i = 0,n-1
> new_agggcm(ii(i)+1+i,:,:) = (agggcm(ii(i),:,:) + agggcm(ii(i)+1,:,:))/2.
> new_ut(ii(i)+1+i,:) =
> (/ut(ii(i)+i,0),2,29,ut(ii(i)+i,3),ut(ii(i)+i,4),ut(ii(i)+i,5)/)
> if (i.lt.n-1) then
> new_agggcm(ii(i)+2+i:ii(i+1)+1+i,:,:) = agggcm(ii(i)+1:ii(i+1),:,:)
> new_ut(ii(i)+2+i:ii(i+1)+1+i,:) = ut(ii(i)+1:ii(i+1),:)
> end if
> end do
> new_agggcm((ii(n-1)+n+1):,:,:) = agggcm(ii(n-1)+1:,:,:)
> new_ut((ii(n-1)+n+1):,:) = ut(ii(n-1)+1:,:)
> new_t =
> ut_inv_calendar(new_ut(:,0),new_ut(:,1),new_ut(:,2),new_ut(:,3),new_ut(:,4),new_ut(:,5),t@units
> ,0)
> new_agggcm!0 = "time"
> new_agggcm!1 = "lat"
> new_agggcm!2 = "lon"
> new_t!0 = "time"
> copy_VarAtts(t,new_t)
> new_t@calendar = "gregorian"
> if (isatt(new_t,"bounds")) then delete(new_t@bounds) end if
> printVarSummary(new_t)
> copy_VarAtts(agggcm,new_agggcm)
> new_agggcm&time = new_t
> print("writing file")
> fout->$var$ = new_agggcm
> print("file written")
>
>
>
>
> --
> Bridget Thrasher, PhD
> Independent Contractor, Research Scientist
>
>
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>
>

-- 
Bridget Thrasher, PhD
Independent Contractor, Research Scientist

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Received on Wed Mar 7 11:54:29 2012