[ncl-talk] Editing a netcdf4 file

[David Brown]

Hi Gerry,
I have been able to duplicate this seg fault and I am looking into it now.
 -dave

On Mon, Jun 22, 2015 at 4:14 PM, Gerry Creager - NOAA Affiliate
<gerry.creager at noaa.gov> wrote:
> 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)