Please sync gromacs 4.0.3-1 (universe) from Debian unstable (main).

[Stefan Lesicnik]

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Please sync gromacs 4.0.3-1 (universe) from Debian unstable (main).

Explanation of the Ubuntu delta and why it can be dropped:
Ubuntu changes by James Westby to use autoreconf has been incorporated by Debian. There are no outstanding Ubuntu changes.

Changelog since current jaunty version 4.0.2-1ubuntu1:

gromacs (4.0.3-1) unstable; urgency=low

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

 -- Nicholas Breen <email address hidden> Mon, 19 Jan 2009 13:35:23 -0800

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.

 -- Nicholas Breen <email address hidden> Mon, 19 Jan 2009 10:42:26 -0800

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[Morten Kjeldgaard (mok0)]

ACKed, subscribing archive-admin.

[Sebastien Bacher (seb128)]

[Updating] gromacs (4.0.2-1ubuntu1 [Ubuntu] < 4.0.3-1 [Debian])
 * Trying to add gromacs...
  - <gromacs_4.0.3-1.diff.gz: downloading from http://ftp.debian.org/debian/>
  - <gromacs_4.0.3-1.dsc: downloading from http://ftp.debian.org/debian/>
  - <gromacs_4.0.3.orig.tar.gz: downloading from http://ftp.debian.org/debian/>
I: gromacs [universe] -> gromacs_4.0.2-1ubuntu1 [universe].
I: gromacs [universe] -> gromacs-data_4.0.2-1ubuntu1 [universe].
I: gromacs [universe] -> gromacs-dev_4.0.2-1ubuntu1 [universe].
I: gromacs [universe] -> gromacs-mpich_4.0.2-1ubuntu1 [universe].
I: gromacs [universe] -> gromacs-lam_4.0.2-1ubuntu1 [universe].
I: gromacs [universe] -> gromacs-openmpi_4.0.2-1ubuntu1 [universe].