[ncl-talk] Writing data to the existing record dimension of a netCDF

[Will Hobbs]

Dennis

I’m using NCl v 6.3.0, on OS 10.11.6

Will

From: Dennis Shea <shea at ucar.edu>
Date: Wednesday, 30 November 2016 at 4:32 PM
To: Will Hobbs <will.hobbs at utas.edu.au>
Subject: Re: [ncl-talk] Writing data to the existing record dimension of a netCDF

The file is netCDF-4
What version of NCL are you using?
What system?
%> ncl -V
%> uname -a



On Tue, Nov 29, 2016 at 9:16 PM, Will Hobbs <will.hobbs at utas.edu.au<mailto:will.hobbs at utas.edu.au>> wrote:
Hi Dave

I tried your test but I still get the same segmentation fault, so I guess the problem is with the files.

Thanks anyway

From: Dave Allured - NOAA Affiliate <dave.allured at noaa.gov<mailto:dave.allured at noaa.gov>>
Date: Wednesday, 30 November 2016 at 11:29 AM

To: Will Hobbs <will.hobbs at utas.edu.au<mailto:will.hobbs at utas.edu.au>>
Cc: "ncl-talk at ucar.edu<mailto:ncl-talk at ucar.edu>" <ncl-talk at ucar.edu<mailto:ncl-talk at ucar.edu>>
Subject: Re: [ncl-talk] Writing data to the existing record dimension of a netCDF

Will,

Please keep messages on the discussion list.  To debug your seg fault, try this simple test to overwrite a single junk time coordinate value:

    fi = addfile (fil, "w")
    fi->time(0) = (/ 1.0d /)
    print ("Single value written")
    exit
If this test works, the problem is probably in your code.  If this fails, there is probably something wrong with the file or with NCL, or else your time dimension is named something other than "time".

On your side question, t3 would still be a record variable because it shares the dimension name "time" with your old time coordinate variable, which is also a record variable.  I assumed that your actual time dimension name is "time".  If the time dimension has a different name, please change "time" in these examples to the actual name of the time dimension.

--Dave


On Tue, Nov 29, 2016 at 5:03 PM, Will Hobbs <will.hobbs at utas.edu.au<mailto:will.hobbs at utas.edu.au>> wrote:
Hi Dave

I had a go trying what you suggested, (i.e. write a new time variable) and I still get the segmentation fault, so it’s possible there’s a problem with my file.

As an aside, in your code snippet would the new file variables, t3, still be a record dimension? I presume not. This would become an issue with post-processing using CDO, NCO etc.

Thanks

Will

From: Dave Allured - NOAA Affiliate <dave.allured at noaa.gov<mailto:dave.allured at noaa.gov>>
Date: Wednesday, 30 November 2016 at 10:38 AM
To: Will Hobbs <will.hobbs at utas.edu.au<mailto:will.hobbs at utas.edu.au>>
Cc: "ncl-talk at ucar.edu<mailto:ncl-talk at ucar.edu>" <ncl-talk at ucar.edu<mailto:ncl-talk at ucar.edu>>
Subject: Re: [ncl-talk] Writing data to the existing record dimension of a netCDF

Will,

If the junk time array has the correct variable name and dimension name (probably both "time"), and a data type with sufficient precision, then the simplest method is to just overwrite the junk time coordinate values with correct time coordinates that you calculate in NCL.  I have found that trying to swap a new coordinate variable in place of an old one is very troublesome.

As a side note, I just ran very simple tests on NCL 6.3.0 on Mac.  The following program easily added a new 1-D variable, to both netcdf-3 and netcdf-4 test files with unlimited time dimension.  In short, I do not see why your program crashed.

    f = addfile ("test.nc<http://test.nc>", "w")
    t3 = f->time      ; note both time and t3 are double in this case
    f->t3 = t3          ; both have single dimension "time"
    exit

--Dave

On Tue, Nov 29, 2016 at 3:45 PM, Will Hobbs <will.hobbs at utas.edu.au<mailto:will.hobbs at utas.edu.au>> wrote:
Hi all

I am working with some model output monthly files (one year for each file, with filename t.<year>.nc), which have a junk time array, and which I am trying to fix. I was hoping to create a new time array, add the values to each file’s time array, and update the variable attributes using NCO:

>Begin

yrst = 1979
yren=2014
vNam = “t”


;create new time array

ydum = new(12, integer)
mdum = ispan(1,12,1)
  ddum = conform_dims(12,15,-1)
 tdum = conform_dims(12,0,-1)

  opt          = 1
  opt at calendar = "standard"
  tunits        = "days after 1-1-1"


;loop through each year
  do yy = yrst, yren

    ;create time array
    ydum = yy
    ntime = cd_inv_calendar(ydum,mdum,ddum,tdum,tdum,tdum,tunits,opt)


    ;add time to file
    fil   =systemfunc("ls "+vNam+"."+yy+".nc")
    fi = addfile(fil,"w")

    fi->time = (/ntime/)

;update attributes
  CMD = “ncatted –a time,units,o,c,”+tunits+” “+fil
system(CMD)

end do


Unfortunately when I try and write the data to file (i.e.    fi->time = (/ntime/) ) I get a segmentation fault:

Segmentation fault: 11

I’ve checked the file permissions and it doesn’t seem to be that. I ‘speculate’ that netCDF won’t allow me to update the record dimension – is this the case? If so, presumably I will need rewrite each file from scratch with new time arrays.

Many thanks,

Will


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