Sourish,
You are getting this confusing error because the underlying HDF5 layer
supporting netcdf4 format is currently limited to only pass/fail return
codes. A fail status is returned simply as "HDF error", regardless of the
details. This means that when some program such as ncap2 tries to
initially open a netcdf4 file, it can't tell the difference between file
not found, and some other format problem, without adding messy and
redundant error analysis code. I wish this situation could be improved.
Since your file actually exists, try some other methods to see what HDF5
and netcdf might not like. First see if ncdump works. You can check the
file signature in the first 8 bytes with the "file" command or the simple
"od" command. Then try HDF tools such as h5dump and h5debug. Make sure
your HDF5 tools are relatively recent. It would be quite helpful to get
the HDF5 error stack to print under ncap2. If you figure out how to do
that, please let the rest of us know.
Here are several more probable causes of HDF error on open, with an
existing file.
* The file is network mounted, and you did not disable HDF5 file locking.
* The file was created with a later version of HDF5, without the proper
backward compatibility setting.
* The file or path is read protected.
* On Mac OS, the file is in a pseudo locked state due to a recent program
crash.
* Oh yeah, triple check the file name and path. This happens more often
than we like to admit.
It is possible that you really have a broken netcdf4 file. In my
experience, such reports are usually one of these other things in
disguise. HTH.
--Dave
On Sun, Mar 24, 2019 at 4:40 PM Sourish Basu <Sourish.Basu@xxxxxxxxxxxx>
wrote:
> Hello all,
>
> I am trying to add two variables and put the result in a third one with
> ncap2, and I have this strange error:
>
> $ ncap2 -L 6 -4 -h -A -s
> 'co2_flux_natural=bio_flux_opt+fire_flux_imp+ocn_flux_opt' guineapig.nc
> ERROR: nco__open() unable to open file "guineapig.nc"
> nco_err_exit(): ERROR Short NCO-generated message (usually name of
> function that triggered error): nco__open()
> nco_err_exit(): ERROR Error code is -101. Translation into English with
> nc_strerror(-101) is "NetCDF: HDF error"
> nco_err_exit(): ERROR NCO will now exit with system call exit(EXIT_FAILURE)
>
> Which is extremely strange, because the file guineapig.nc *does* exist
> in the current folder:
>
> $ ls -l guineapig.nc
> -rw-r--r-- 1 i i 4862322 Mar 24 16:28 guineapig.nc
>
> What is more, I can use ncap2 to perform the exact same operation on
> some other files without a problem. Which leaves me very confused as to
> why ncap2 fails and tells me that this file does not exist, when it
> clearly does and is writable. The guineapig is attached. Anyone has any
> idea?
>
> Thanks,
>
> Sourish
>
