[ubuntu/jaunty] gromacs 4.0.3-1 (Accepted)

[Ubuntu Installer]

gromacs (4.0.3-1) unstable; urgency=low

  * New upstream release.
  * Remove obsoleted patches 40, 41, 50, 51, 52.

gromacs (4.0.2-2) unstable; urgency=low

  * debian/*.postinst: Resort update-alternatives priorities for the MPI
    packages to follow the newly proposed priorities of the individual
    MPI implementations themselves, OpenMPI > MPICH > LAM.
  * New patches:
    - 40_hppa_asm.dpatch: Attempt to correct FTBFS on HPPA
      inline ASM code by replacing an undefined variable.
      (cf. http://bugzilla.gromacs.org/show_bug.cgi?id=260)
    - 41_sprintf.dpatch: Replace sprintf calls relying on undefined
      behavior with proper, portable code.  Problem identified by Kees
      Cook: http://lists.debian.org/debian-devel/2008/12/msg01079.html
    - 50_type2bonds.dpatch: Fix grompp freeze when using type 2 bonds
      (G96) and all-angle constraints.
      (cf. http://bugzilla.gromacs.org/show_bug.cgi?id=261)
    - 51_mshift.dpatch: When running mdrun on multiple processors, it
      will crash under certain circumstances when an error is generated
      but there is no log file attached to that specific process.  This
      was triggered by some incorrect "inconsistent shift" warning
      messages.  Both problems are corrected by this patch.
      (cf. http://bugzilla.gromacs.org/show_bug.cgi?id=267)
    - 52_ia64_single_pointer.dpatch: Test for non-zero pointer in IA64
      single-precision kernel when writing to log file.  Pointer is
      zero on non-master MPI processes, and would previously segfault.
      (cf. http://bugzilla.gromacs.org/show_bug.cgi?id=262)
  * debian/rules: Use autoreconf in lieu of automake&&autoconf&&... to
    avoid version skew.  Thanks to James Westby for the patch.

Date: Mon,  09 Feb 2009 08:48:17 +0000
Changed-By: Stefan Lesicnik <stefan at lsd.co.za>
Maintainer: Debichem Team <debichem-devel at lists.alioth.debian.org>
Origin: Debian/unstable
https://launchpad.net/ubuntu/jaunty/+source/gromacs/4.0.3-1
-------------- next part --------------
Origin: Debian/unstable
Format: 1.7
Date: Mon,  09 Feb 2009 08:48:17 +0000
Source: gromacs
Binary: gromacs, gromacs-data, gromacs-dev, gromacs-mpich, gromacs-lam, gromacs-openmpi
Architecture: source
Version: 4.0.3-1
Distribution: jaunty
Urgency: low
Maintainer: Debichem Team <debichem-devel at lists.alioth.debian.org>
Changed-By: Stefan Lesicnik <stefan at lsd.co.za>
Description: 
 gromacs    - Molecular dynamics simulator, with building and analysis tools
Changes: 
 gromacs (4.0.3-1) unstable; urgency=low
 .
   * New upstream release.
   * Remove obsoleted patches 40, 41, 50, 51, 52.
 .
 gromacs (4.0.2-2) unstable; urgency=low
 .
   * debian/*.postinst: Resort update-alternatives priorities for the MPI
     packages to follow the newly proposed priorities of the individual
     MPI implementations themselves, OpenMPI > MPICH > LAM.
   * New patches:
     - 40_hppa_asm.dpatch: Attempt to correct FTBFS on HPPA
       inline ASM code by replacing an undefined variable.
       (cf. http://bugzilla.gromacs.org/show_bug.cgi?id=260)
     - 41_sprintf.dpatch: Replace sprintf calls relying on undefined
       behavior with proper, portable code.  Problem identified by Kees
       Cook: http://lists.debian.org/debian-devel/2008/12/msg01079.html
     - 50_type2bonds.dpatch: Fix grompp freeze when using type 2 bonds
       (G96) and all-angle constraints.
       (cf. http://bugzilla.gromacs.org/show_bug.cgi?id=261)
     - 51_mshift.dpatch: When running mdrun on multiple processors, it
       will crash under certain circumstances when an error is generated
       but there is no log file attached to that specific process.  This
       was triggered by some incorrect "inconsistent shift" warning
       messages.  Both problems are corrected by this patch.
       (cf. http://bugzilla.gromacs.org/show_bug.cgi?id=267)
     - 52_ia64_single_pointer.dpatch: Test for non-zero pointer in IA64
       single-precision kernel when writing to log file.  Pointer is
       zero on non-master MPI processes, and would previously segfault.
       (cf. http://bugzilla.gromacs.org/show_bug.cgi?id=262)
   * debian/rules: Use autoreconf in lieu of automake&&autoconf&&... to
     avoid version skew.  Thanks to James Westby for the patch.
Files: 
 0a8bdc7557390ad655230fda009f787e 35903 science extra gromacs_4.0.3-1.diff.gz
 72e8f9b513f4792ab8674460919052ea 1619 science extra gromacs_4.0.3-1.dsc
 2902403671a0f9b0934ddf3ca586b7ec 8420556 science extra gromacs_4.0.3.orig.tar.gz