EPD NetCDF4 Dataset gives 'Can't add HDF5 file metadata' when creating new netCDF files, but only sometimes

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EPD NetCDF4 Dataset gives 'Can't add HDF5 file metadata' when creating new netCDF files, but only sometimes #141

Closed GoogleCodeExporter closed 8 years ago

GoogleCodeExporter commented 8 years ago

What steps will reproduce the problem?
1. In iPython, import netCDF4 as nc
2. output = nc.Dataset('StartField_glb100x100_tropo25_2007010100.nc4','w')

*Note that if I shorten the name, there is no error - is there a netCDF name 
length limit?*

What is the expected output? What do you see instead?

I don't expect any output, since the creation of a new Dataset object doesn't 
usually return any. Instead, I get

RuntimeError: Can't add HDF5 file metadata

What version of the product are you using? On what operating system?

Printing out nc.__netcdf4libversion__ returns '4.1.1', and 
nc.__hdf5libversion__ returns '1.8.5-patch1'.  

Please provide any additional information below.

Original issue reported on code.google.com by sean.m.c...@gmail.com on 14 Sep 2012 at 2:25

GoogleCodeExporter commented 8 years ago

Sorry, I'm running on OS X 10.7 on a Mac Pro.

Original comment by sean.m.c...@gmail.com on 14 Sep 2012 at 2:26

GoogleCodeExporter commented 8 years ago

Sounds like a bug in the C lib that has been fixed.  Please try upgrading 
netcdf (now at version 4.2.1) and hdf5 (now at 1.8.9)

Original comment by whitaker.jeffrey@gmail.com on 19 Sep 2012 at 8:07

GoogleCodeExporter commented 8 years ago

Sorry - I see you have EPD, which means that will not be easy to do.  I see 
that EPD 7.3 has netcdf version 4.2 and hdf5 1.8.9.  Can you upgrade to EPD 7.3?

Original comment by whitaker.jeffrey@gmail.com on 19 Sep 2012 at 8:09

GoogleCodeExporter commented 8 years ago

Until recently, the C lib gave the error "Can't add HDF5 file metadata" from 
the HDF5 layer when trying to create a netCDF-4 file in a directory in which 
the user lacked write permissions.  The current netCDF-4.3.0 release candidate 
fixes this bug to give the system error "Permission denied" instead of the 
HDF5-specific error.

Original comment by Russ...@gmail.com on 8 Apr 2013 at 8:22

GoogleCodeExporter commented 8 years ago

This error occurs (tested with netcdf library version 4.1.1 and version 4.2.1.1 
(+hdf5 1.8.10))
when creating the netCDF file was interrupted by an error (during writing and 
not before writing) and one wants to try to create it a second time.
(I don't know how to reproduce that error in python but with the R-netCDF 
interface it works: The function which creates a netCDF file needs the 
definition of at least one variable. If this variable definition is incorrect, 
a new netCDF file is created on the disc, data is written to the file and an 
errors is thrown regarding the incorrect varibale definition.)
The file already exists but it is locked for further netCDF operations. This 
also explains why files with shorter files names (see "What steps will 
reproduce the problem?") work fine.

Original comment by neumann....@googlemail.com on 7 Aug 2013 at 3:23

GoogleCodeExporter commented 8 years ago

Original comment by whitaker.jeffrey@gmail.com on 26 Feb 2014 at 2:04

Changed state: Fixed