2009
gromacs (4.0.5-4) unstable; urgency=low
* patches/21_makefile_dups.dpatch: Eliminate duplicated files in the
installation list of include/Makefile.am. Automake 1.11 now passes
multiple files to `install' at once, causing failures when one name
is given twice. (Closes: #543059)
* control: Increment S-V to 3.8.3. No changes required.
* rules: Remove obsolete --disable-nice option from *_CONFIG_PARAMS.
* man/gromacs.7: Update macros for lintian cleanliness.
-- Nicholas Breen <nbreen@ofb.net> Tue, 25 Aug 2009 12:30:15 -0700
gromacs (4.0.5-3) unstable; urgency=low
* patches/20_altivec_kernel.dpatch: Extend patch to cover
nb_kernel_ppc_altivec.c, which does not include the same headers.
* control: Increment Standards-Version to 3.8.2. No packaging changes
required.
-- Nicholas Breen <nbreen@ofb.net> Wed, 24 Jun 2009 17:21:26 -0700
gromacs (4.0.5-2) unstable; urgency=low
* patches/20_altivec_kernel.dpatch: Resolve FTBFS on AltiVec-enabled
PPC builds caused by use of "restrict" keyword, which GCC does not
normally accept unless in C99 mode. Reported upstream at
http://bugzilla.gromacs.org/show_bug.cgi?id=324
-- Nicholas Breen <nbreen@ofb.net> Sun, 17 May 2009 15:52:53 -0700
gromacs (4.0.5-1) unstable; urgency=low
* New upstream release.
* debian/control: Bump Standards-Version to 3.8.1. No packaging
changes required.
* debian/control: Replace svn+ssh:// URI with svn:// .
* debian/copyright: Replace "(C)" with "Copyright", update dates.
* debian/rules: #452047 rears its ugly head again! Add LDFLAGS to -lam
and -openmpi builds with -L arguments to their respective library
directories, exclusive of update-alternatives trickery, in order to
prevent accidental cross-linking. Thanks again to Manuel Prinz.
(Closes: #526266)
-- Nicholas Breen <nbreen@ofb.net> Mon, 11 May 2009 18:15:11 -0700
gromacs (4.0.4-1) unstable; urgency=low
* New upstream release.
* patches/05_lt_init.dpatch: Add LT_INIT to configure.ac so that the
libtool script can find its version. Necessary for current Ubuntu
build environment. Patch courtesy of James Westby.
-- Nicholas Breen <nbreen@ofb.net> Sat, 28 Feb 2009 16:45:25 -0800
gromacs (4.0.3-1) unstable; urgency=low
* New upstream release. * Remove obsoleted patches 40, 41, 50, 51, 52.
-- Nicholas Breen <nbreen@ofb.net> 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 <nbreen@ofb.net> Mon, 19 Jan 2009 10:42:26 -0800
2008
gromacs (4.0.2-1) unstable; urgency=low
* New upstream release.
- Remove obsoleted debian/patches/50_confio.dpatch (fixed),
10_manpages.dpatch (merged upstream).
* debian/gromacs.README.Debian: suggest OpenMPI for new installations.
-- Nicholas Breen <nbreen@ofb.net> Mon, 10 Nov 2008 12:36:15 -0800
gromacs (4.0-1) unstable; urgency=low
* New upstream release.
- debian/man: Remove g_nmtraj.1, g_sdf.1, g_spatial.1 (incorporated
upstream). Remove average.1 (no longer shipped). Update gromacs.7
with changed commands and reference to new J. Chem. Theory Comput.
paper. Update mdrun_mpi.*.1 based on upstream mdrun.1. Write new
man pages xplor2gmx.1 and demux.1.
- debian/lintian-overrides.gromacs: Update against new list of man
pages.
- debian/patches: Remove 05_autoconf_gsl.dpatch (fixed upstream) and
40_missing_cpp.dpatch (preprocessor functionality now built in).
Resynchronize 10_manpages.dpatch. Add GROMACS 4 reference to
11_readme.dpatch.
- debian/rules: Remove g_ffscan renaming (no longer shipped).
* debian/control: Drop versioned dependency on base-files. Add Build-
Depends on libtool.
* debian/rules: Don't link MPI binaries to GSL, eliminating a spurious
dependency.
* patches/50_confio.dpatch: Avoid segfault when using make_ndx on .tpr
files. (cf.
http://www.gromacs.org/pipermail/gmx-developers/2008-October/002775.html)
-- Nicholas Breen <nbreen@ofb.net> Wed, 29 Oct 2008 15:44:28 -0700
gromacs (3.3.3-3) unstable; urgency=low
[ Daniel Leidert ]
* debian/gromacs-data.doc-base (Section): Fixed accordingly to latest
doc-base policy 0.8.10.
[ Nicholas Breen ]
* debian/README.source: add reference to dpatch system, as required by
latest policy (sec. 4.14). Having done so:
* debian/control: Update Standards-Version to 3.8.0.
* debian/rules: Remove obsolete and now-inaccurate comment about
parallel builds. Remove duplicated dh_installdeb call.
* debian/man/g_kinetics.1: Update documentation.
* debian/patches/05_autoconf_gsl.dpatch: libgsl was not properly
detected by autoconf when the test didn't also link libgslcblas,
rendering the g_kinetics program unusable. This changes the test
to pass along LIBS appropriately.
-- Nicholas Breen <nbreen@ofb.net> Wed, 20 Aug 2008 11:55:39 -0700
gromacs (3.3.3-2) unstable; urgency=low
* debian/control: Eliminate unneeded Build-Depends on libxml-dev.
Spotted by Pierre Habouzit. (Closes: #470000)
* debian/rules: Force --with-gsl in configuration.
-- Nicholas Breen <nbreen@ofb.net> Sat, 08 Mar 2008 12:34:36 -0800
gromacs (3.3.3-1) unstable; urgency=low
[ Nicholas Breen ]
* New upstream release.
* debian/rules, debian/control: Reconfigure gromacs-doc as gromacs-data.
This moves all architecture independent files into a single package,
including many topology files formerly shipped in gromacs instead.
- Rename debian/gromacs-doc to debian/gromacs-data .
- debian/gromacs-doc.preinst: no longer necessary, removed.
* Remove PDF manual for the time being, as modifiable sources are not
currently available.
- debian/gromacs.README.Debian, debian/man/gromacs.7: Provide pointers
to its location online instead.
- debian/control: Drop build dependency on sharutils, which was used
only to provide the manual.
- debian/gromacs-data.doc-base: Remove reference to PDF.
* debian/control: Add Build-Depends on libgsl0-dev to support addition
of /usr/bin/g_kinetics.
* debian/gromacs.README.Debian: Update suggested MPI implementations.
* debian/man: write preliminary man pages for undocumented new commands,
g_kinetics.1 g_spatial.1 g_sdf.1
* debian/patches/10_manpages: Update with ROFF fixes to 18 files; fix a
few minor typos; resync patch against upstream CVS.
* debian/man/mdrun_mpi.{mpich,lam,openmpi}.1: Propagate those fixes.
* debian/lintian-overrides.gromacs: Drop binary-without-manpage override.
* debian/linda-overrides.gromacs, debian/rules: Remove linda override.
[ Daniel Leidert ]
* debian/man/average.1: Minor ROFF improvements, hyphen/minus and typo
fixes.
* debian/man/g_nmtraj.1: Ditto.
* debian/man/luck.1: Ditto.
-- Nicholas Breen <nbreen@ofb.net> Mon, 03 Mar 2008 21:23:01 -0800
gromacs (3.3.3~pre1-1) unstable; urgency=low
[ Nicholas Breen ]
* New upstream release.
- Remove obsolete patches now incorporated upstream:
50_xtcio_double_range_checking, 51_180_degree_angle,
52_pme_spline, 53_pbc_compiler.
* debian/rules:
- Clean up patch syntax to prevent double compilations.
- Add .NOTPARALLEL target to prevent the various MPI builds from
compiling on the same source tree simultaneously, while still
allowing -j options to be passed to sublevel targets.
- Improve DEB_BUILD_OPTIONS=parallel=X handling, now in line with
the example proposed for policy.
- Disable FORTRAN inner loops for gromacs-openmpi on alpha. This
is a temporary workaround to avoid lingering linking problems
regarding libmpi.so and the update-alternatives system.
- Add support for DEB_BUILD_OPTIONS=noopt.
- Additional rewrite work (see below): use new format for build
commands, but split for individual MPI implementations.
- Run autotools between patch and configuration steps.
- New format for MPI library suffix configuration.
* debian/control:
- Add versioned Build-Depends on libmpich1.0-dev for its
g77 -> gfortran transition.
- Add Build-Depends on autoconf and automake, and Build-Conflicts
on autoconf2.13, to support updated mpisuffix patch.
- Downgrade gromacs-doc Depends: on gromacs to a Recommends:, as -doc
now ships its own copyright file.
* debian/patches/04_autoconf_mpisuffix.dpatch: Apply dleidert's improved
patch to allow arbitrary overrides of LIBSUFFIX; reduce patch to only
the directly changed code in configure.ac, and add an invocation of
autotools during the build process rather than patching configure
itself directly.
* debian/gromacs-{doc,dev}.preinst: Remove symlinks for package doc
directories on upgrade, in order to replace them with actual directories.
[ Daniel Leidert ]
* debian/control (Suggests): Fixed a debcheck issue - gromacs-openmpi should
only be suggested on supported architectures.
* debian/copyright: Added copyright information to satisfy lintian.
* debian/gromacs-doc.doc-base (Section): Fixed accordingly to menu policy.
(Format): Fixed path to HTML files.
* debian/rules: Major rewrite. Changes/improvements include:
- drop dpatch target definitions in favour of dpatch.make
- put all configure flags to the top of the file
- moved all configure related commands into configure-stamp
- moved all build related commands into build-stamp
- moved all install related commands into separate install targets
- configure and build in sub-directories to avoid $(MAKE) clean calls
- clean target removes build/ instead to run clean/distclean
- replaced ln with dh_link and gzip with dh_installman
- adjusted target requirements for binary* and install*
- install a /usr/share/doc/$package directory for gromacs-doc and -dev
too; put the HTML into the -doc documentation directory; add links to
the HTML directory for the gromacs and the -dev package pointing to the
-doc directory
- fixed .PHONY target for above
* debian/watch: Added pre-release version handling.
-- Nicholas Breen <nbreen@ofb.net> Wed, 13 Feb 2008 15:01:50 -0800
2007
gromacs (3.3.2-3) unstable; urgency=low
* Package transferred to Debichem team maintenance.
* debian/control:
- Switched Maintainer to Debichem Team, moved myself to
Uploaders. Added Vcs-Browser, Vcs-Svn fields.
- Increase Standards-Version to 3.7.3. No changes required.
- Build-Depend on libopenmpi-dev >= 1.2.4-5 (Closes: #456860).
* debian/rules: include kfreebsd-* variants explicitly in OPENMPI_ARCH.
* debian/patches/11_readme.dpatch: change edited README to an explicit
patch, rather than modifying it directly in the .diff.gz.
* Multiple bugfixes from upstream CVS:
- 51_180_degree_angle.dpatch: apply upstream patches to avoid crashes
crashes when operating on precisely linear 2-bond pairs.
(cf. http://bugzilla.gromacs.org/show_bug.cgi?id=172,
http://bugzilla.gromacs.org/show_bug.cgi?id=177)
- 52_pme_spline.dpatch: calculate mesh contribution when charges
are 0 in A state, but non-zero in B state.
(cf. http://bugzilla.gromacs.org/show_bug.cgi?id=175)
- 53_pbc_compiler: Solve regression in gmxlib/pbc.c introduced by a
previous compiler workaround.
(cf. http://bugzilla.gromacs.org/show_bug.cgi?id=179)
* debian/gromacs-doc.doc-base: remove extraneous spaces.
-- Nicholas Breen <nbreen@ofb.net> Wed, 26 Dec 2007 12:26:09 -0800
gromacs (3.3.2-2) unstable; urgency=low
* Add support for OpenMPI with new "gromacs-openmpi" binary package.
Thanks to Manuel Prinz for assistance. (Closes: #448635)
* Build binaries for double-precision floating point operations, in
addition to the existing single-precision binaries. Double precision
commands are denoted by a "_d" suffix.
* debian/control: Update feature summary URL in package description,
and add Homepage field.
* Reformat all man page headers to work with whatis(1), apropos(1), and
similar tools.
-- Nicholas Breen <nbreen@ofb.net> Tue, 13 Nov 2007 13:03:22 -0800
gromacs (3.3.2-1) unstable; urgency=low
* New upstream release. (Closes: #446760) - Incorporates fix for amd64 double-precision builds. (Closes: #442886) - Remove obsolete patches 50_gmx_order, 51_libxdrf_trajectory, 52_genion_compiler_workaround, 60_amd64_double. * Add a Recommends: cpp to gromacs binary package, and improve the error message given by grompp when no preprocessor is installed to clarify the "-pp" option. (Closes: #442139) * Update Build-Depends to reflect fftw3-dev -> libfftw3-dev renaming. * Conflict with radiance (<= 3R8+20070924.dfsg-1) due to overlapping /usr/bin/genbox. Related to #446726, which will be closed by a future upload of radiance. * src/gmxlib/xtcio.c: import upstream fix for range checking failures when running both parallel and double-precision simulations. (cf. http://www.gromacs.org/pipermail/gmx-users/2007-October/029990.html)
-- Nicholas Breen <nbreen@ofb.net> Mon, 15 Oct 2007 14:39:30 -0700
gromacs (3.3.1-7) unstable; urgency=low
* debian/rules: correct typo that broke alpha builds.
-- Nicholas Breen <nbreen@ofb.net> Tue, 11 Sep 2007 12:23:52 -0700
gromacs (3.3.1-6) unstable; urgency=low
* Update alpha Build-Depends from g77 to gfortran, and set F77 variable
in debian/rules accordingly.
* Increase update-alternatives priority of mdrun_mpi.lam to 20.
* src/tools/gmx_xpm2ps.c: explicitly initialize 'ninp' to 0 to work
around a peculiar compiler/shared-library/i386 bug. (Closes: #428795)
* debian/copyright: clarify license as GPL v2 or later. Add Depends: on
base-files (>=4.0.1) until the next release to ensure that the GPL v3
license text is installed as well. (Closes: #435208)
* When building from source, two DEB_BUILD_OPTIONS are available:
- "parallel" adds -j4 to the make flags.
- "double" will compile binaries for both single-precision (the
default) and double-precision (with _d suffix) floating point
operations.
* Minor packaging cleanups: set debhelper compatibility level to 5,
clarify versioned dependencies for -doc and -dev packages, improve
"make clean" error handling, clean up lintian overrides.
-- Nicholas Breen <nbreen@ofb.net> Mon, 10 Sep 2007 17:29:10 -0700
gromacs (3.3.1-5) unstable; urgency=low
* Workaround for compiler problems on some platforms that could cause
genion to hang in an infinite loop when using cubic boxes.
(cf. http://bugzilla.gromacs.org/show_bug.cgi?id=108)
* Eliminate spurious mdrun warnings when using triclinic boxes.
(cf. http://bugzilla.gromacs.org/show_bug.cgi?id=121)
-- Nicholas Breen <nbreen@ofb.net> Tue, 10 Apr 2007 17:08:02 -0700
2006
gromacs (3.3.1-4) unstable; urgency=medium
* Rename /usr/bin/ffscan to g_ffscan, resolving a filename conflict with
the 'forutil' package. (Closes: #403879)
-- Nicholas Breen <nbreen@ofb.net> Sat, 23 Dec 2006 11:24:59 -0800
gromacs (3.3.1-3) unstable; urgency=low
* Update URL to features list in package description. (Closes: #393750) * Correct deuterium order parameter generation in src/tools/g_order.c. (cf. http://bugzilla.gromacs.org/show_bug.cgi?id=84) * Patch src/gmxlib/libxdrf.c to eliminate errors when the specified time for a search inside a trajectory falls on a frame boundary. (cf. http://bugzilla.gromacs.org/show_bug.cgi?id=106)
-- Nicholas Breen <nbreen@ofb.net> Wed, 6 Dec 2006 11:04:01 -0800
gromacs (3.3.1-2) unstable; urgency=low
* _Really_ register gromacs-doc with doc-base. (The previous attempt
contained an error.) Thanks again to Drew Parsons.
(Closes: #359999)
* Update Standards-Version to 3.7.2. No packaging changes required.
-- Nicholas Breen <nbreen@ofb.net> Tue, 26 Sep 2006 15:21:48 -0700
gromacs (3.3.1-1) unstable; urgency=low
* New upstream release. * Updated PDF manual to 3.3 release. * disco(1) is no longer shipped, so it no longer needs renaming.
-- Nicholas Breen <nbreen@ofb.net> Thu, 13 Apr 2006 15:53:29 -0700
gromacs (3.3-2) unstable; urgency=low
* Adding Build-Depends on g77 for alpha only. (No other architectures
use FORTRAN inner loops by default.) (Closes: #360486)
* Recategorizing to different parts of archive: gromacs-doc to 'doc',
gromacs-dev to 'devel'.
* Correct implicit pointer size declaration in src/mdlib/ghat.c, which
could lead to segfaults on 64-bit architectures. Thanks to Dann
Frazier for catching it. (Closes: #360002)
* Registered gromacs-doc with doc-base. Patch courtesy of Drew Parsons.
(Closes: #359999)
* Renaming /usr/bin/disco to g_disco, to avoid filename conflict with
mono-mcs. (Closes: #360374)
-- Nicholas Breen <nbreen@ofb.net> Mon, 3 Apr 2006 09:50:44 -0700
gromacs (3.3-1) unstable; urgency=low
* Initial Debian release. (Closes: #228319, #252101)
-- Nicholas Breen <nbreen@ofb.net> Thu, 16 Mar 2006 23:00:13 -0800