[ncl-talk] Editing a netcdf4 file

Mon Jun 22 16:14:12 MDT 2015

David

Looks like it may not have been fixed quite yet. Mary sent me a version and
I finally fooled the system into working today, when testing began. The
short script included, inline below, can be run against the netcdf (wrfout)
I uploaded recently (advise if I need to upload it again), results in a seg
fault.

;=============
load "$NCARG_ROOT/lib/ncarg/nclscripts/csm/gsn_code.ncl"
load "$NCARG_ROOT/lib/ncarg/nclscripts/csm/gsn_csm.ncl"
load "$NCARG_ROOT/lib/ncarg/nclscripts/csm/contributed.ncl"
load "$NCARG_ROOT/lib/ncarg/nclscripts/wrf/WRFUserARW.ncl"
;=============
begin

dimx = 225
dimy = 225
dimz = 55

a = addfile("wrfinput_d02.nc", "w")
var_orig=a->QRAIN
var_mod = new((/1,dimz,dimy,dimx/),"float")
var_mod = 5.

print(dimsizes(var_orig))
print(dimsizes(var_mod))

a->QRAIN = (/var_mod/)

end

On Mon, Jun 8, 2015 at 9:00 PM, David Brown <dbrown at ucar.edu> wrote:

> Dustan and Gerry,
> This issue relating to writing a variable with chunking in an existing
> NetCDF4 file has been fixed. Also a secondary issue involving
> re-writing existing variable attributes has been addressed as well.
> Let us know if you need a version with these fixes and we will try to
> accommodate you as soon as possible.
> Thanks for letting us know of this problem.
>  -dave
>
>
> On Wed, Jun 3, 2015 at 8:50 AM, David Brown <dbrown at ucar.edu> wrote:
> > Hi Dustin and Gerry,
> > I have confirmed there is a problem. It has been partially but not
> > completely fixed in the development version of the code. I am looking
> > into the remaining issue and will let you know when it has been fixed.
> >  -dave
> >
> > On Tue, Jun 2, 2015 at 10:34 AM, Gerry Creager - NOAA Affiliate
> > <gerry.creager at noaa.gov> wrote:
> >> Additional information: If we do an addfile("<filename>","r"), we can
> open
> >> and read the file. If we use "w", well, we can open the file but
> assigning
> >> an existing variable to an internal variable fails on the assign (var =
> >> a->QRAIN). Of course, because it fails there, we can't see if it'd also
> fail
> >> on write.
> >>
> >> Thanks
> >> Gerry
> >>
> >> On Mon, Jun 1, 2015 at 7:15 PM, Gerry Creager - NOAA Affiliate
> >> <gerry.creager at noaa.gov> wrote:
> >>>
> >>> I've started looking at this with Dusty. Appreciate any thought you
> might
> >>> have as to why we're failing.
> >>>
> >>> I've uploaded the input file (wrfinput_d02) to the FTP incoming site.
> I'm
> >>> testing with the script:
> >>>
> >>> var = "QRAIN"
> >>> print(var)
> >>> a=addfile("wrfinput_d02.nc", "w")
> >>> var_orig=a->QRAIN
> >>> print(var_orig)
> >>>
> >>>
> >>> The result looks like:gerry at loki:~/NEWSe/NCL> ncl test.ncl
> >>>  Copyright (C) 1995-2015 - All Rights Reserved
> >>>  University Corporation for Atmospheric Research
> >>>  NCAR Command Language Version 6.3.0
> >>>  The use of this software is governed by a License Agreement.
> >>>  See http://www.ncl.ucar.edu/ for more details.
> >>>
> >>>
> >>> Variable: var
> >>> Type: string
> >>> Total Size: 8 bytes
> >>>             1 values
> >>> Number of Dimensions: 1
> >>> Dimensions and sizes: [1]
> >>> Coordinates:
> >>> (0) QRAIN
> >>> fatal:["NclNetCDF4.c":3073]:NclNetCDF4.c: Error in nc_def_var_chunking
> in
> >>> file (wrfinput_d02.nc) for writing, at line: 3073
> >>>
> >>> line 3074 of NclNetCDF4.c: NetCDF: Attempt to define var properties,
> like
> >>> deflate, after enddef.
> >>>
> >>>
> >>> On Fri, May 29, 2015 at 8:54 PM, Dustan Wheatley - NOAA Affiliate
> >>> <dustan.wheatley at noaa.gov> wrote:
> >>>>
> >>>> I am trying to overwrite a netcdf4 file analogous to what is shown at
> >>>> http://www.ncl.ucar.edu/Applications/change_netCDF.shtml.  In the
> attached
> >>>> ncl script, I open the file to be modified at line 35 and attempt the
> >>>> modification at line 73 (with a lot of calculations in between).
> While I
> >>>> have double-checked that the modified field (var_mod) has the same
> >>>> dimensionality as the original variable (QRAIN), I am still get a
> >>>> segmentation fault/core dump.  Never had this problem when I tried to
> >>>> manipulate netcdf3 files.  Could it possibly be related to the netcdf4
> >>>> compression?  It’s possible I may be trying to do something that’s no
> longer
> >>>> possible.
> >>>>
> >>>> Thanks in advance for any suggestions.
> >>>>
> >>>> -Dusty Wheatley
> >>>>
> >>>> _______________________________________________
> >>>> ncl-talk mailing list
> >>>> ncl-talk at ucar.edu
> >>>> List instructions, subscriber options, unsubscribe:
> >>>> http://mailman.ucar.edu/mailman/listinfo/ncl-talk
> >>>>
> >>>
> >>>
> >>>
> >>> --
> >>> Gerry Creager
> >>> NSSL/CIMMS
> >>> 405.325.6371
> >>> ++++++++++++++++++++++
> >>> “Big whorls have little whorls,
> >>> That feed on their velocity;
> >>> And little whorls have lesser whorls,
> >>> And so on to viscosity.”
> >>> Lewis Fry Richardson (1881-1953)
> >>
> >>
> >>
> >>
> >> --
> >> Gerry Creager
> >> NSSL/CIMMS
> >> 405.325.6371
> >> ++++++++++++++++++++++
> >> “Big whorls have little whorls,
> >> That feed on their velocity;
> >> And little whorls have lesser whorls,
> >> And so on to viscosity.”
> >> Lewis Fry Richardson (1881-1953)
> >>
> >> _______________________________________________
> >> ncl-talk mailing list
> >> ncl-talk at ucar.edu
> >> List instructions, subscriber options, unsubscribe:
> >> http://mailman.ucar.edu/mailman/listinfo/ncl-talk
> >>
>

-- 
Gerry Creager
NSSL/CIMMS
405.325.6371
++++++++++++++++++++++
“Big whorls have little whorls,
That feed on their velocity;
And little whorls have lesser whorls,
And so on to viscosity.”
Lewis Fry Richardson (1881-1953)
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