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

[Dave Allured - NOAA Affiliate]

Will,

Find a completely different netcdf-4 file, preferably a very small and
simple one, and retry my simple test to overwrite a single time coordinate
value.  This will help differentiate between a file problem and an NCL
problem.

Also try one other thing.  If by any chance your files are on a file
server, then make local copies on your mac, and repeat the tests.  My work
group has recently experienced compatibility problems with NFS mounted file
servers and netcdf-4 files, accessed from Mac.

--Dave


On Tue, Nov 29, 2016 at 9:16 PM, Will Hobbs <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>
> *Date: *Wednesday, 30 November 2016 at 11:29 AM
> *To: *Will Hobbs <will.hobbs at utas.edu.au>
> *Cc: *"ncl-talk at ucar.edu" <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>
> 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>
> *Date: *Wednesday, 30 November 2016 at 10:38 AM
> *To: *Will Hobbs <will.hobbs at utas.edu.au>
> *Cc: *"ncl-talk at ucar.edu" <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", "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>
> 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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