Reading parallel netCDF CDF-5 format data in python

Question

I have a large amount of data generated with parallel netCDF, with enough entries that output could only be generated in CDF-5 format. I have an analysis routine in python I want to pass this data through. However, I have not been able to open the CDF-5 format with any python package (or visit, or read the header files with ncdump, although ncmpidump -h provides the correct header information of course). Does anyone know of either

1) A python package that can read CDF-5 formatted data

2) A utility that can convert parallel netCDF CDF-5 data to something more widely supported, like HDF5, that I could then read in to python?

Option 1 preferable of course.

Thanks

What python modules have You tried exactly? I know the package in scipy.io is different from python-netcdf4 and independent from C library. But if that doesn't work, You probably need to wrap C library to python yourself. — kakk11
– kakk11, Commented Jan 9, 2016 at 9:52
Neither scipy.io nor python-netcdf4 worked. I ended up just writing a little C program using parallel netCDF to convert CDF5 to CDF2, which was relatively painless to do, following included examples. It looks like the parallel netCDF team had committed to including CDF5 support in the standard netCDF distribution, but their postdocs tasked with this keep leaving :) — user2275987
– user2275987, Commented Jan 11, 2016 at 18:07

Charlie Zender · Accepted Answer · 2016-01-15 04:09:44Z

1

The latest NCO pre-release, 4.5.5-alpha02, supports CDF5, and conversion to/from CDF5 with all netCDF types, including netCDF4, e.g.,ncks -4 in_5.nc out_4.nc translates CDF5 files to netCDF4. The requirement is that NCO must be built with netCDF 4.4.0, released a few days ago.

answered Jan 15, 2016 at 4:09

Charlie Zender

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DopplerShift · Accepted Answer · 2016-01-19 20:57:33Z

1

The latest release of netcdf4-python library should be able to make use of the support for CDF-5 added in version 4.4 of the C library. For more details, see here: https://github.com/Unidata/netcdf4-python/pull/482

answered Jan 19, 2016 at 20:57

DopplerShift

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