[netcdfgroup] Problem using h5repack with netcdf-4 files

• 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

 * 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...

--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
              }
           }

• Follow-Ups:
  • Re: [netcdfgroup] Problem using h5repack with netcdf-4 files
    • From: Russ Rew