- 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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