[netCDF #XFB-271301]: netCDF question, char/string attributes, global or variable atts.

Hi Greg,

> I am really struggling with something in netCDF and getting a little
> desperate for help - I've done google search much of the last 2 days,
> checked support/mail archives, stack-overflow, etc.  I'd greatly
> appreciate if you could give me additional guidance on this topic.
> 
> I have a 64-bit offset NC file I created using NCL reading, processing,
> and writing data from an original GRIBv2 file to make the NC file.  Now,
> for further post-processing and deriving new data, I'm reading in that
> NC file (and others), doing some math on the data, and writing a new
> output NC file, using F90 (ifort compiler on Yellowstone).
> 
> I am having a bear of a time with character variables.  And I do
> understand that strings are not stored, but, rather, array of
> characters.  So, when I created my first NC file, I made a global
> attribute called "history" which I can clearly see when I do ncdump -h
> on the file and it looks like this:
>   string :history = "Created Tue Dec 31 11:08:39 MST 2013" ;

It's apparently not a 64-bit offset netCDF file, but a netCDF-4 file
instead.  You can verify this using ncdump -k, assuming you have an
ncdump linked against netCDF version 4.0 or later.

If the file was written using NCL, maybe it's configured for the default
to be writing netCDF-4 files.  NetCDF-4 files use an enhanced data model 
and support additional data types, such as "string", that are not 
accessible to older netCDF-3 libraries or programs linked against them.

For more information on the differences between the netCDF classic data
model and the netCDF-4 enhanced data model, see this FAQ section on
"Formats, Data Models, and Software Releases":

  http://www.unidata.ucar.edu/netcdf/docs/faq.html#formats-and-versions

Evidently, NCL creates netCDF-4 attributes using the netCDF-4 primitive
type "string" instead of an array of chars.

> And, since I'm doing additional computations on data, I want to append
> to that history variable.  So I'm trying to read in this global
> attribute to capture that string, append new text to the end and then
> write to my new NC output file.

To read an attribute of type "string" in netCDF-4, you need to know
about netCDF-4 variable-length types, as the netCDF-4 primitive type 
NF90_STRING is handled like the NF90_VLEN user-defined type, because
a read returns a pointer to allocated space that must later be 
explicitly freed when you're done with it.

I see there are no good examples of using NF90_STRING type data in our
on-line examples, and the documentation for use of that type is poor.
The netCDF Fortran-90 users guide was written before the netCDF-4 APIs
were added, and it looks like the needed rewrite of the docs was not
completed before the developer working on that project left.

I'll try to create a new example that reads and writes NF90_STRING
data using the F90 API, but it may have to wait until after the AMS
meeting.  In the mean time, I recommend seeing if you can make NCL
write either netCDF classic format files or netCDF-4 classic model
files, neither of which use strings for attributes.

> I've read 10s of web pages trying to find anyone who has applied
> NF_GET_ATT function and there's just something I'm missing.
> 
> When I use this:
>                nf_status = nf90_inquire_attribute(ncid, NF90_GLOBAL,
> attname, xtype, leng, j)
> where attname='history', it returns xtype=12 and leng=1.
> The tutorial page (for netcdf) says xtype should be one of NF_BYTE,
> NF_CHAR, ..., which are just consecutively numbered 1 to 6, so I am at a
> loss what 12 indicates.  And, of course, a length of this attribute of 1
> is not helpful.  The string reported by ncdump is clearly longer.

The netCDF-4 documentation for nf90_def_var mentions using NF90_STRING
as a netCDF variable type, but it's not mentioned in the docs as a valid
return type for any of the other netCDF functions!

The source file fortran/netcdf_constants.f90 has all the netCDF-4 type
codes, which should have been documented in the Users Guide:

  ! extra data types:
  integer, parameter, public :: &
       nf90_ubyte = 7, &
       nf90_ushort = 8, &
       nf90_uint = 9, &
       nf90_int64 = 10, &
       nf90_uint64 = 11, &
       nf90_string = 12, &
       nf90_vlen = 13, &
       nf90_opaque = 14, &
       nf90_enum = 15, &
       nf90_compound = 16

> And, then when I attempt just to read in the attribute anyway, of course
> I encounter the error: "NetCDF: Attempt to convert between text &
> numbers" when using:
>    nf_status = nf90_get_att(ncid, NF90_GLOBAL, attname, str_hist)
> where str_hist is a f90 char(len=128).
> 
> I just cannot comprehend how to retrieve textual global attributes of
> netcdf files, nor text attributes of a variable, such as "units" which I
> have clearly set in my variables.  The above inquire_attribute and
> get_att functions do exactly the same thing as my history example.
> 
> Any help would really be appreciated!

I sympathize with your frustration at the incomplete documentation.

I've added a bugtracking issue about this, so it doesn't continue to get
ignored:

  https://bugtracking.unidata.ucar.edu/browse/NCFORTRAN-28

Thanks for reporting the problem!

--Russ

Russ Rew                                         UCAR Unidata Program
address@hidden                      http://www.unidata.ucar.edu



Ticket Details
===================
Ticket ID: XFB-271301
Department: Support netCDF
Priority: Normal
Status: Closed