- To: netcdfgroup@xxxxxxxxxxxxxxxx
- Subject: [netcdfgroup] Problem using h5repack with netcdf-4 files
- From: "Gregory Sjaardema" <gdsjaar@xxxxxxxxxx>
- Date: Tue, 20 Mar 2012 09:59:09 -0600
I am trying to use the h5repack utility with netcdf-4 files and it
doesn't seem to work. The data below shows this on a small datafile
included in ncdump/small2.nc. Basically:
* Convert the netcdf-3 format small2.nc to netcdf-4 format using nccopy -k 4 * Use h5repack on that file to create a third file. * ncdump can access the original and nccopy'd file * ncdump give HDF error when accessing the h5repack'd file * A diff of the h5dump output shows that h5repack seems to replace DATASET with GROUP...Are there options to h5repack that can be used to produce a valid netcdf file?
--Greg s927819> nccopy -k 4 small2.nc small2.nc4 s927819> h5repack small2.nc4 small2.nc4.rep s927819> ./ncdump small2.nc4 netcdf small2 { dimensions: t = UNLIMITED ; // (1 currently) m = 5 ; variables: byte b(t, m) ; data: b = 1, 2, 3, 4, 5 ; } s927819> ./ncdump small2.nc4.rep /Users/gdsjaar/src/SEACAS/TPL/netcdf/netcdf-4.2/ncdump/.libs/ncdump: small2.nc4.rep: NetCDF: HDF error s927819> h5dump small2.nc4>good.out s927819> h5dump small2.nc4.rep>bad.out s927819> diff -c good.out bad.out *** good.out 2012-03-20 09:52:47.000000000 -0600 --- bad.out 2012-03-20 09:52:53.000000000 -0600 *************** *** 1,4 **** ! HDF5 "small2.nc4" { GROUP "/" { ATTRIBUTE "_nc3_strict" { DATATYPE H5T_STD_I32LE --- 1,4 ---- ! HDF5 "small2.nc4.rep" { GROUP "/" { ATTRIBUTE "_nc3_strict" { DATATYPE H5T_STD_I32LE *************** *** 17,23 **** DATATYPE H5T_VLEN { H5T_REFERENCE { H5T_STD_REF_OBJECT }} DATASPACE SIMPLE { ( 2 ) / ( 2 ) } DATA { ! (0): (DATASET 255 /t ), (DATASET 547 /m ) } } } --- 17,23 ---- DATATYPE H5T_VLEN { H5T_REFERENCE { H5T_STD_REF_OBJECT }} DATASPACE SIMPLE { ( 2 ) / ( 2 ) } DATA { ! (0): (GROUP 0), (GROUP 0) } } } *************** *** 59,65 **** DATASPACE SIMPLE { ( 1 ) / ( 1 ) } DATA { (0): { ! DATASET 969 /b , 1 } } --- 59,65 ---- DATASPACE SIMPLE { ( 1 ) / ( 1 ) } DATA { (0): { ! GROUP 140734799797120, 1 } } *************** *** 102,108 **** DATASPACE SIMPLE { ( 1 ) / ( 1 ) } DATA { (0): { ! DATASET 969 /b , 0 } } --- 102,108 ---- DATASPACE SIMPLE { ( 1 ) / ( 1 ) } DATA { (0): { ! GROUP 140734799797120, 0 } }
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- Re: [netcdfgroup] Problem using h5repack with netcdf-4 files