[hdf-forum] Assertion when running h5repack.

[Richard Corden]

Hi,

After reading this post: "HDF5 Deleting Datasets AND Recovering Space", 
I thought I'd run h5repack over some of my datasets to see what the 
affect would be.

However, when I run it over one "test" dataset I get the following 
assertion:

h5repack: H5Dscatgath.c:501: H5D_scatgath_read: Assertion 
`(H5S_select_iter_nelmts(&file_iter)) == (nelmts - smine_start)' failed.
Aborted

What's interesting is that this only happens if before I close the 
dataset I call "H5Dset_extent" to the exact number of elements in my 
dataset.  So, for example, if I don't call this function, or if I set 
the dataset extent to the "size +1", then h5repack runs without an error.

My main concern is that I'm not "misusing" the HDF5 format and this 
problem is only shows (at the moment) by using h5repack.


The command I'm using:

    h5repack -v -f GZIP=1 file1.qa  file2.qa

And the output of the run is:

    Objects to modify layout are...
    Objects to apply filter are...
     All with GZIP, parameter 1
    Making file <file2.qa>...
    -----------------------------------------
     Type     Filter (Compression)     Name
    -----------------------------------------
     group                       /
     group                       /analysis
     group                       /analysis/filenames
     dset                        /analysis/filenames/filenames
     group                       /analysis/locations
    h5repack: H5Dscatgath.c:501: H5D_scatgath_read: Assertion
    `(H5S_select_iter_nelmts(&file_iter)) == (nelmts - smine_start)' failed.
    Aborted


Here's the contents of '/analysis/locations/locations' which at least 
from the output above, appears to be where the problem occurs:


      GROUP "locations" {
         DATASET "locations" {
            DATATYPE  H5T_COMPOUND {
               H5T_STD_U64LE "filename";
               H5T_STD_I32LE "line";
               H5T_STD_I32LE "column";
               H5T_STD_U64LE "incl_from";
               H5T_STD_I32LE "hash_line_file";
               H5T_STD_I32LE "hash_line_line";
               H5T_REFERENCE "properties";
            }
            DATASPACE  SIMPLE { ( 1 ) / ( H5S_UNLIMITED ) }
            DATA {
            (0): {
                  0,
                  184,
                  183,
                  18446744073709551615,
                  -1,
                  -1,
                  NULL
               }
            }
         }
      }

Thanks for your help.

Regards,

Richard

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