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

 
 

bug #48375: HDF5 is broken

Submitted by:  None
Submitted on:  Sat 02 Jul 2016 11:11:56 AM UTC  
 
Category: InterpreterSeverity: 3 - Normal
Priority: 5 - NormalItem Group: Incorrect Result
Status: DuplicateAssigned to: None
Originator Name: Claude LacoursiereOriginator Email: -unavailable-
Open/Closed: ClosedRelease: 4.0.2
Operating System: GNU/Linux

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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>
Project 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>
Project Member
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 File(s):
   
   
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

 

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

    Date Changed By Updated Field Previous Value => Replaced By
    Sat 02 Jul 2016 03:47:26 PM UTCmtmillerStatusPatch Submitted=>Duplicate
      Open/ClosedOpen=>Closed
    Sat 02 Jul 2016 02:05:58 PM UTCclaudelAttached File-=>Added octave-gcc6.patch, #37669
    Sat 02 Jul 2016 11:49:38 AM UTClachlanStatusNone=>Patch Submitted
    Sat 02 Jul 2016 11:11:56 AM UTCNoneAttached File-=>Added mm.h5.gz, #37664
      Attached File-=>Added octave-hdf5type.patch, #37665

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