[netcdfgroup] [netCDF #AYG-518147]: nf_copy_var

• To: netcdfgroup@xxxxxxxxxxxxxxxx
• Subject: [netcdfgroup] [netCDF #AYG-518147]: nf_copy_var
• From: "Unidata netCDF Support" <support-netcdf@xxxxxxxxxxxxxxxx>
• Date: Thu, 06 Dec 2012 14:58:48 -0700

Hi Simon,

> we have quite big output files from a seismic wavefield simulation and
> want to fourier transform them for further use.
> 
> The idea would be that the output file is opened, the wavefields are
> read and transformed and copied into a new file.
> However, there are a lot of smaller variables in the file, which should
> be copied to the new file as well. I do not want to declare temporary
> arrays for all of them and so I gave NF_COPY_VAR a try.
> 
> 
> The questions:
> 
> 1. NetCDF-C has the routine nc_copy_var, which seems to be perfectly
> suited. Can you call it from a Fortran90 code?

The only portable way (that would work with different Fortran compilers) is if 
you 
use the Fortran-2003 C interoperability feature that provides a standard way to
call C functions from Fortran.  Otherwise you have to either customize your 
solution
to the Fortran compiler you have, adapting to it's non-standard way of 
referring to 
a C function and character string arguments, or learn to use a more general 
solution
such as the cfortran.h macros that come with the netCDF Fortran software.

We are providing a beta-release of netcdf-fortran software that implements
use of the Fortran-2003 solution for calling C functions from Fortran, including
nf_copy_var, as well as a more recent daily snapshot of that software that has
additional bug fixes:

  ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-fortran-4.4-beta1.tar.gz
  ftp://ftp.unidata.ucar.edu/pub/netcdf/snapshot/netcdf-fortran-4.4-daily.tar.gz

> 2. There is the undocumented NF_COPY_VAR. However, using this like
> 
> status = nf_copy_var(ncin_grpid, varid, ncout_id)
> print *, nf_strerror(status), status
> 
> Results in
> 
> NetCDF: Invalid dimension ID or name -46
> 
> even though nf90_get_var can read perfectly from this variable with the
> same group and variable id. Also, the error does not seem to make much
> sense, since neither dimensions or names are even involved.

Note that nc_copy_var (and nf_copy_var that calls it) both depend on the
dimensions that the variable uses having already been defined in the
output file.  If you try to copy a variable with a dimension not yet
defined, you will get that error.

That assumption seems to have been omitted from the documentation.  We'll 
fix that.

> 3. Is there any reliable documentation for NF_COPY_VAR or a Fortran90
> version of it?

No, the Fortran documentation doesn't appear to include that function.  We'll
fix that too.
  
> Since the code is to be distributed, we would not like it to rely on NCO
> or similar external routines and do everything with the normal Fortran
> interface.
> 
> Any ideas?

Keep in mind that using nc_copy_var or nf_copy_var can be very inefficient if
the target is a large netCDF-3 (classic or 64-bit offset format) file, as 
described by this paragraph from the documentation:

  For large netCDF-3 files, this can be a very inefficient way to copy
  data from one file to another, because adding a new variable to the
  target file may require more space in the header and thus result in
  moving data for other variables in the target file.  This is not a problem
  for netCDF-4 files, which support efficient addition of variables
  without moving data for other variables.

--Russ

Russ Rew                                         UCAR Unidata Program
russ@xxxxxxxxxxxxxxxx                      http://www.unidata.ucar.edu



Ticket Details
===================
Ticket ID: AYG-518147
Department: Support netCDF
Priority: Normal
Status: Closed