[netcdfgroup] nccopy -c does not rechunk properly (4.3.1.1)

• To: netcdfgroup@xxxxxxxxxxxxxxxx
• Subject: [netcdfgroup] nccopy -c does not rechunk properly (4.3.1.1)
• From: Simon Stähler <staehler@xxxxxxxxxxxxxxxxxxxxxxxxx>
• Date: Wed, 26 Feb 2014 17:35:24 +0100

Dear all,

I want to use the nccopy script to change the chunking of a large 2D
dataset (first dimension time ("snapshots"), second point index
("gllpoints_all")). The original file has the structure:

$ ncdump -sch original.nc
netcdf original {
dimensions:
        snapshots = 820 ;
        gllpoints_all = 249984 ;
variables:

// global attributes:
                :npoints = 249984 ;

group: Snapshots {
  variables:
        float strain_dsus(snapshots, gllpoints_all) ;
                strain_dsus:_Storage = "chunked" ;
                strain_dsus:_ChunkSizes = 1, 249984 ;
  } // group Snapshots


For further processing of the file, I want to change the chunks so that
each contains all the time steps at one point.
I do this with

$ nccopy -c "snapshots/820,gllpoints_all/1" original.nc new.nc

However, the resulting chunk sizes are somewhat weird:
{55, 17856} instead of {820, 1}:

$ ncdump -sch new.nc
netcdf axisem_output_3 {
dimensions:
        snapshots = 820 ;
        gllpoints_all = 249984 ;

// global attributes:
                :npoints = 249984 ;

group: Snapshots {
  variables:
        float strain_dsus(snapshots, gllpoints_all) ;
                strain_dsus:_Storage = "chunked" ;
                strain_dsus:_ChunkSizes = 55, 17856 ;
  } // group Snapshots

Is there an obvious mistake on my side or might there be a problem with
variables in groups?

I am using netcdf library version 4.3.1.1 of Feb 26 2014 12:06:45

cheers,

Simon Stähler

-- 
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|  Simon Stähler                         PhD student   |
|                                                      |
|  Geophysik, Ludwig-Maximilians-Universität München   |
|  Theresienstrasse 41    80333 München      Germany   |
|  Tel.  : +49 (0)89 2180 4143                         |
|  www.geophysik.uni-muenchen.de/members/staehler      |
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  • Re: [netcdfgroup] nccopy -c does not rechunk properly (4.3.1.1)
    • From: Russ Rew