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[netCDF #RRZ-677956]: nccopy terminates with "NetCDF: HDF error"

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  • Subject: [netCDF #RRZ-677956]: nccopy terminates with "NetCDF: HDF error"
  • Date: Thu, 22 Oct 2015 10:35:15 -0600
Hello Günther,

> Dear Unidata support engineer,

As an aside, due to resource constraints, we don't have support engineers; we 
(the software engineers) must provide the support :).

I have read your question, but do not have an immediate answer for you.  
Instead, I have the following questions:
 
1. When you say your fortran program is able to read the file, is it using the 
netcdf-fortran library? Or is it completely separate from the netcdf technology 
stack?
2. As you can use nccopy on larger files, I suspect that the issue is slightly 
different than the one you referenced, in that you are not having memory 
errors.  Are the larger files the same format, e.g. NetCDF4-classic model?
3. What version of libhdf5 are you using? I wonder if the problem is an 
incompatibility with the data file and an older version of hdf5.
4. Have you tried with the latest version of netcdf, 4.3.3.1?  We have had 
multiple bug fixes between 4.3. and 4.3.3.1.
5. What happens if you use ncdump to create a cdl version of the file? This is 
probably not practical, since it would take a very long time and require a lot 
of disk space.  Although redirecting the output to /dev/null, I wonder if you 
would receive the same error.

The ncdump file you provided does not reveal any obvious problems, so we must 
look elsewhere.  If you can provide answers to some of the questions above, I 
will try to figure out what is possibly happening. 

Thank you,

-Ward


> we have problems to apply nccopy (version netcdf4.3.0) for one of our files .
> 
> In case we execute
> 
> nccopy in.nc out.nc
> 
> nccopy ends after some time with a
> 
> NetCDF: HDF error
> Location: file nccopy.c; line 1036
> 
> error message.
> 
> Some additional remarks:
> 
> 1.) The file in.nc is rather large (400 GB);
> 2.) We were able to apply (the very same) nccopy successfully to even larger
> files (900 GB);
> 3.) Our Fortran based programs are able to read file in.nc without problems;
> 4.) Attached you can find ncdump -h -s in.nc > in.ncdump.txt.
> 
> We have found a support message in your archives which seems to reference
> the very same problem, but we failed to find a clear answer to it.
> --> 
> https://www.unidata.ucar.edu/support/help/MailArchives/netcdf/msg12314.html
> 
> Also the error message itself is unfortunately very unspecific in this case .
> 
> Please let me know your suggestions how to proceed.
> 
> Günther Lang
> Bundesanstalt für Wasserbau - Dienststelle Hamburg
> Referat Ästuarsysteme II
> Wedeler Landstraße 157
> 22559 Hamburg
> Telefon +49 (0) 40 81908 360
> E-Mail address@hidden
> WWW http://www.baw.de/EN/Home/home_node.html
> 

Ticket Details
===================
Ticket ID: RRZ-677956
Department: Support netCDF
Priority: Normal
Status: Closed