bugGNU Octave - Bugs: bug #48375, HDF5 is broken

 
 

bug #48375: HDF5 is broken

Submitter:  None
Submitted:  Sat 02 Jul 2016 11:11:56 AM UTC
   
 
Category:  Interpreter Severity:  3 - Normal
Priority:  5 - Normal Item Group:  Incorrect Result
Status:  Duplicate Assigned to:  None
Originator Name:  Claude Lacoursiere Originator Email:  -email is unavailable-
Open/Closed:  * Closed Release:  * 4.0.2
Operating System:  * GNU/Linux Fixed Release:  None
Planned Release:  None
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Sat 02 Jul 2016 03:24:22 PM UTC, comment #3: 

We won't be fixing the problem with the HDF5 hid_t type for the 4.0.x release series.

See also bug #47858, where there is a fix for the development version of Octave.

Also, we won't be fixing Octave 4.0.x to build with GCC 6.x.  You'll have to either use GCC 5.x to build Octave 4.0.x, or use the development version of Octave if you want to use GCC 6.x and later.

John W. Eaton <jwe>
Group administrator
Sat 02 Jul 2016 02:05:58 PM UTC, comment #2: 

I'm using

gcc 6.1.1
glibc 2.23
hdf5  1.10

I work with arch  so I also applied the patch related to problems with cmath, math.h, etc.   I attached this as well now.

But I think these are orthogonal changes.

(file #37669)

Claude Lacoursiere <claudel>
Sat 02 Jul 2016 11:49:38 AM UTC, comment #1: 

Thanks, Claude.

What versions of the libraries and compiler are you using?

Lachlan Andrew <lachlan>
Sat 02 Jul 2016 11:11:56 AM UTC, original submission:  

It appears that the new definition of  octave_hdf5_id is wrong since loading any file results in

warning: the size of octave_hdf5_id is smaller than the size of HDF5 hid_t

This is followed by segfault upon exit.



The problem appears to be in oct-hdf5-id.h  where
 
typedef int octave_hdf5_id;

this is then compared in length with hid_t    which is a 64 bit signed integers. 

Attached is a patch file to redefine octave_hdf5_id  which is working for me, as well as a small hdf5 file containing one array illustrating the problem. 


Anonymous

 

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Attach Files:
   
   
Comment:
   

Attached Files
file #37669:  octave-gcc6.patch added by claudel (2KiB - text/x-patch - patch to build with gcc 6.1.1)
file #37664:  mm.h5.gz added by None (1KiB - application/gzip)
file #37665:  octave-hdf5type.patch added by None (496B - text/x-patch)

 

Depends on the following items: None found

Items that depend on this one: None found

 

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  • -email is unavailable- added by mtmiller (Updated the item)
  • -email is unavailable- added by jwe (Posted a comment)
  • -email is unavailable- added by claudel (Updated the item)
  • -email is unavailable- added by lachlan (Posted a comment)
  • -email is unavailable- added by None (Submitted the item)
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    Follow 6 latest changes.

    Date Changed by Updated Field Previous Value => Replaced by
    2016-07-02 mtmiller StatusPatch Submitted Duplicate
        Open/ClosedOpen Closed
    2016-07-02 claudel Attached File- Added octave-gcc6.patch, #37669
    2016-07-02 lachlan StatusNone Patch Submitted
    2016-07-02 None Attached File- Added mm.h5.gz, #37664
        Attached File- Added octave-hdf5type.patch, #37665

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