Bug 299876 – sci-mathematics/octave-3.2.3 segfaults on HDF5 files

• Status: RESOLVED FIXED
• Product: Gentoo Linux

[Description Tolga Dalman 2010-01-06 11:59:52 UTC]

Apparently octave does not handle the datatype H5T_STRING. While Matlab properly
parses the hdf5 file, octave fails with a segfault.

The h5dump of the file is:


HDF5 "file.hdf5" {
GROUP "/" {
   GROUP "MatrixA" {
      DATASET "columnlabels" {
         DATATYPE  H5T_STRING {
               STRSIZE 6;
               STRPAD H5T_STR_NULLTERM;
               CSET H5T_CSET_ASCII;
               CTYPE H5T_C_S1;
            }
         DATASPACE  SIMPLE { ( 1, 3 ) / ( 1, 3 ) }
         DATA {
         (0,0): "col_0", "col_1", "col_2"
         }
      }
      DATASET "data" {
         DATATYPE  H5T_IEEE_F64LE
         DATASPACE  SIMPLE { ( 3, 3 ) / ( 3, 3 ) }
         DATA {
         (0,0): 1, 4, 7,
         (1,0): 2, 5, 8,
         (2,0): 3, 6, 9
         }
      }
      DATASET "rowlabels" {
         DATATYPE  H5T_STRING {
               STRSIZE 6;
               STRPAD H5T_STR_NULLTERM;
               CSET H5T_CSET_ASCII;
               CTYPE H5T_C_S1;
            }
         DATASPACE  SIMPLE { ( 1, 3 ) / ( 1, 3 ) }
         DATA {
         (0,0): "row_0", "row_1", "row_2"
         }
      }
   }
}
}


Reproducible: Always

Steps to Reproduce:
1. run octave
2. load('-hdf5', 'file.hdf5')

[Comment 1 Tolga Dalman 2010-01-06 12:01:23 UTC]

Created attachment 215372 [details]
This HDF5 file crashes octave

[Comment 2 Sébastien Fabbro (RETIRED) 2010-01-07 03:54:06 UTC]

Hi,

It does not seem Gentoo related, I checked octave-3.2.3 on other Linux boxes and it segfaults as well. Could you report your bug upstream?
Thanks.

[Comment 3 Kacper Kowalik (Xarthisius) (RETIRED) 2010-03-02 20:48:29 UTC]

(In reply to comment #2)
> It does not seem Gentoo related, I checked octave-3.2.3 on other Linux boxes
> and it segfaults as well. Could you report your bug upstream?
> Thanks.

There is a response from upstream on twin debian bug ( http://bugs.debian.org/565216 ). In short octave is not supposed to read HDF5 files not created by itself in a first place.

[Comment 4 Tolga Dalman 2010-03-02 22:41:28 UTC]

Thanks for your response. Since nobody from the octave staff seems to care about this apparent bug, I propose to disable the HDF5 flag from octave until this issue is cleared.

[Comment 5 Sébastien Fabbro (RETIRED) 2010-03-09 03:52:09 UTC]

Fixed in 3.2.4-r1.