[hdf-forum] Assertion when running h5repack.

[Quincey Koziol]

Hi Richard,

On Jun 4, 2009, at 4:35 AM, Richard Corden wrote:

> 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.

	Sounds reasonable to me - could you contact the HDF helpdesk (help at hdfgroup.org 
) with a test program that shows the error and we'll verify it and try  
to get it fixed.

	Thanks,
		Quincey

>
>
>
> 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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