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[netCDF #PFU-753378]: Error in closing netCDF file (due to presence of user-defined type)

Lynton,

The Jira ticket for this bug, with two C example programs, is now available 
here:

  https://bugtracking.unidata.ucar.edu/browse/NCF-217

in case you want to follow the progress.

--Russ

> Lynton,
> 
> > Thanks for the reply. In fact the "feature" you picked up was a genuine
> > mistake of mine
> > when translating from the C++ API to the C API. The real problem was
> > somewhat different
> > as I will explain. The programme I attach is the same as before but with
> > the user-type error corrected
> > and some data assigned to the variable "weightDDXXYY"
> >
> > I can compile the code fine and run it fine.
> >
> > However, when I run ncdump I get problems. In this case the output is
> > wrong, but in other cases ncdump can actually crash.
> > The error appears to be associated with assigning values to the variable
> > "ironBoundaries" on line 44 of efit++.cpp.
> > This causes the dimensioning of weightDDXXYY to be screwed up, at least
> > according to ncdump.
> > However h5dump appears not to have the same problem suggesting that
> > there is a problem in ncdump !!
> >
> > To see this for yourself, compare the files efitOut.txt (ncdump output)
> > and efitOut.hdf5.txt (h5Dump output).
> > You will see that the dimensioning of weightDDXXYY is apparently different.
> >
> > Note as I said before, this is using netCDF version 4.2
> 
> OK, now I can reproduce the bug.  It appears to be an example of the bug that 
> depends
> on the order in which netCDF functions are called, but the results should not 
> depend on
> the order.
> 
> I'm attaching a version of your program that works when I reorder the 
> function calls to
> appear in the following groups of calls:
> 
> create file and groups
> define types
> define dimensions
> define variables
> write data
> 
> and it works as expected.  I don't know if there's a simpler permutation of 
> statement orders
> that would also work.
> 
> The fact that it doesn't work in the order you used is definitely a major bug.
> I'm also creating a Jira ticket for this and will consider it a priority to 
> try
> to diagnose the underlying problem and fix it.
> 
> --Russ
> 
> > On 01/24/2013 01:46 PM, Unidata netCDF Support wrote:
> > > Hi Lynton,
> > >
> > >> I have a short programme that throws up an HDF5 error: NC_EHDFERR  when 
> > >> closing. It appears to be connected with defining a user-defined type:
> > >> Have  you got any idea what the problem is?
> > >>
> > >>
> > >> The output of the code is:
> > >> 0 1
> > >> 0 2
> > >> 0 3
> > >> 0 4
> > >> 0 5
> > >> 0 6
> > >> 0 7
> > >> 0 9
> > >> 0 10
> > >> -101 11
> > > It looks to me as if you started to define a netCDF user-defined type
> > > named "ironBoundaryType", but didn't finish that definition.  Then you
> > > tried to define netCDF variables of the incompletely defined type.
> > > It's a bug that the netCDF API lets you do this without returning an
> > > error until you close the file.  I'm not sure whether there's also a
> > > corresponding bug in HDF5 that allows this.
> > >
> > > To complete the definition of the user-defined type, you need to fill
> > > out the type with repeated calls to nc_insert_compound(). Call the
> > > nc_insert_compound function once for each field (member) you wish to
> > > insert into the compound type.  Don't define variables using a type
> > > until you finish defining the type.
> > >
> > > I'll enter a Jira ticket for this later and try to determine where the bug
> > > is, but it may have to wait until after we get the 4.3 release for the C
> > > library out ...
> > >
> > > --Russ
> 
> Russ Rew                                         UCAR Unidata Program
> address@hidden                      http://www.unidata.ucar.edu
> 
> 
Russ Rew                                         UCAR Unidata Program
address@hidden                      http://www.unidata.ucar.edu



Ticket Details
===================
Ticket ID: PFU-753378
Department: Support netCDF
Priority: Normal
Status: Closed