Hi Andrew,
You've run across a limitation in the number of simultaneously open groups
permitted in netCDF-4. The groups documentation
<http://www.unidata.ucar.edu/netcdf/docs/group__groups.html> says
... Encoding both the open file id and group id in a single integer
currently limits the number of groups per netCDF-4 file to no more than
32767. Similarly, the number of simultaneously open netCDF-4 files in one
program context is limited to 32767.
I think both those limits should actually be 65535 (== 2**16 - 1), but in
any case, your HDF5 file has 119254 groups, which is too many for netCDF-4
to handle.
The only workaround I can think of would be to close some groups if you
don't need to have them all open simultaneously.
--Russ
On Mon, Nov 17, 2014 at 8:14 AM, Andrew Dowsey <
andrew.dowsey@xxxxxxxxxxxxxxxx> wrote:
> Hi,
>
> I’m trying to create HDF5 files that can be read by NetCDF4 and I’ve run
> into a problem in that nc_inq_grps seems to report some bad ids. ncdump
> bails with this error too. h5dump works fine. The problem is deterministic
> but I haven’t been able to figure out what causes it because slightly
> different HDF5 files work fine. I have created a test file that has this
> problem, which contains nothing but groups. It can be downloaded from
> http://personalpages.manchester.ac.uk/staff/andrew.dowsey/test.h5
>
> I am creating a new format for a type of instrument data we use, and for
> flexibility I would like it to be writeable/readable both by HDF5 and
> netCDF4 libraries.
>
> Any insight would be greatly appreciated!
>
> Kind regards,
> Andy
>
>
> *Andrew Dowsey PhD*
> *Lecturer and CADET Bioinformatics Research Lead*
> Institute of Human Development, The University of Manchester
>
> t: +44 161 701 0244
> f: +44 161 701 0242
> http://www.manchester.ac.uk/research/andrew.dowsey
>
> Centre for Advanced Discovery and Experimental Therapeutics (CADET)
> Central Manchester University Hospitals NHS Foundation Trust
> Oxford Road
> Manchester M13 9WL
> UK
>
>
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