gromacs (2019.1-1) unstable; urgency=medium * New upstream bugfix release. * On x32 only, set openmpi tests to non-failing. They pass, but as of openmpi >= 3.1.3~rc1, timeout on teardown. 3.1.2 works cleanly. -- Nicholas Breen Sun, 17 Feb 2019 09:22:14 -0800 gromacs (2019-2) unstable; urgency=medium * Fix error in update-alternatives call for bash completion. -- Nicholas Breen Fri, 01 Feb 2019 21:26:58 -0800 gromacs (2019-1) unstable; urgency=medium * New upstream final release - return uploads to unstable. * Install bash completion files. Add completion files for the MPI variants to the update-alternatives group. * Remove unused GMXRC* files and the /usr/share/gromacs/shell-specific directory, as they are unneeded with binaries in the standard locations. * Bump Standards-Version to 4.3.0, no changes required. * Drop B-D on libtinyxml-dev, as a specific version of libtinyxml2 is used instead only for testing, not in shipped binaries. -- Nicholas Breen Tue, 01 Jan 2019 20:03:55 -0800 gromacs (2019~rc1-1) experimental; urgency=medium * New upstream release candidate. * Set debhelper compat 11. * Re-enable several previously disabled OpenMPI tests that now work again, but set hurd-i386 tests to non-fatal as their failures all seem to be from outside sources. * control: Point Vcs-Git URL at debian-experimental branch specifically. -- Nicholas Breen Sun, 16 Dec 2018 09:56:11 -0800 gromacs (2019~beta3-1) experimental; urgency=medium * New upstream beta release. * Move libgromacs3.lintian-overrides to libgromacs4.lintian-overrides. -- Nicholas Breen Sun, 25 Nov 2018 09:17:37 -0800 gromacs (2018.4-1) unstable; urgency=medium * New upstream release. * Bump Standards-Version to 4.2.1, no changes required. -- Nicholas Breen Wed, 21 Nov 2018 16:01:14 -0800 gromacs (2019~beta2-1) experimental; urgency=medium * New upstream beta release, upload to experimental. - patches/reproducible-builds.patch and sphinx-version-detect.patch removed, equivalent functionality integrated upstream. - Other patches rebased. * Rename libgromacs3 to libgromacs4 for SONAME increment. * CMAKE_SKIP_RPATH causes build failures at the moment, so replace it with chrpath after the build. * Depend on, and build documentation against, local copy of libjs-mathjax. -- Nicholas Breen Thu, 08 Nov 2018 22:06:20 -0800 gromacs (2018.3-1) unstable; urgency=medium * New upstream release. * Bump Standards-Version to 4.2.0, no changes required. -- Nicholas Breen Thu, 23 Aug 2018 08:55:48 -0700 gromacs (2018.2-2) unstable; urgency=medium * Disable tests on armhf for mpich build; it seems to have a sensitivity to where mpich itself was built. -- Nicholas Breen Sun, 17 Jun 2018 16:43:08 -0700 gromacs (2018.2-1) unstable; urgency=medium [ Steffen Möller ] * Updated RRID in debian/upstream/metadata. [ Nicholas Breen ] * New upstream release. -- Nicholas Breen Sat, 16 Jun 2018 10:24:50 -0700 gromacs (2018.1-4) unstable; urgency=medium * Additionally exclude MdrunUtilityMpiUnitTests on OpenMPI builds only, which fail erratically. * Set Rules-Requires-Root: no. * patches/sphinx-version-detect.patch: permit identification of newer versions of python-sphinx, which changed their --version output. -- Nicholas Breen Sat, 28 Apr 2018 08:25:15 -0700 gromacs (2018.1-3) unstable; urgency=medium * Exchange patch from 2018.1-2 for a GTEST_FILTER exclusion in rules. (Closes: #896194) * Bump Standards-Version to 4.1.4. -- Nicholas Breen Tue, 24 Apr 2018 20:01:16 -0700 gromacs (2018.1-2) unstable; urgency=medium * patches/openmpi-disable-gputest.patch: bypass one test on OpenMPI builds only, ChangingPinningPolicyRequiresCuda hangs and times out. (Closes: #896194) -- Nicholas Breen Sun, 22 Apr 2018 14:34:48 -0700 gromacs (2018.1-1) unstable; urgency=medium * New upstream release. * Remove gtest-death-test.patch, incorporated upstream. * Moved VCS from alioth to salsa (thanks to Andreas Tille). -- Nicholas Breen Sat, 31 Mar 2018 10:12:46 -0700 gromacs (2018-2) unstable; urgency=medium * Extend gtest-death-test.patch to exclude x32. This addresses #887340 but is not a complete fix. Thanks to Aaron Ucko for testing assistance. * Increase CTest verbosity level. -- Nicholas Breen Sat, 20 Jan 2018 11:31:44 -0800 gromacs (2018-1) unstable; urgency=low * New upstream release. - Remove test_GMX_ALIGNED.patch, incorporated. - Update debian/man/*mdrun* man pages. * Bump Standards-Version to 4.1.3. -- Nicholas Breen Wed, 10 Jan 2018 22:23:18 -0800 gromacs (2018~rc1-3) experimental; urgency=medium * patches/gtest-death-test.patch: disable EXPECT_DEATH tests if unavailable on that platform. * patches/mdrun-test-timeout.patch: increase timeout for integration test (using mdrun) from 120 to 600 seconds, to help prevent termination on slower buildds. -- Nicholas Breen Wed, 03 Jan 2018 20:58:25 -0800 gromacs (2018~rc1-2) experimental; urgency=medium * Apply upstream patch to address BasedefinitionsTest.GmxAlignedDeclaresAlignedVariable failures on non- Intel architectures. -- Nicholas Breen Wed, 27 Dec 2017 12:56:20 -0800 gromacs (2018~rc1-1) experimental; urgency=medium * New upstream release candidate. -- Nicholas Breen Tue, 26 Dec 2017 23:10:55 -0800 gromacs (2018~beta3-1) experimental; urgency=medium [ Andreas Tille ] * New upstream version (beta2) * Moved packaging from SVN to Git [ Nicholas Breen ] * New upstream release (beta3). * Explicitly set MPIEXEC for the two different MPI implementations, to prevent mismatches via the alternatives system. Also B-D on mpich, providing /usr/bin/mpiexec.mpich for tests. * Update Standards-Version to 4.1.2. * Remove obsolete zero byte file lintian overrides. * SONAME bump: rename libgromacs2 to libgromacs3. * Set GMX_EXTERNAL_ZLIB=ON to prevent it from opportunistically linking statically. -- Nicholas Breen Sun, 24 Dec 2017 10:35:12 -0800 gromacs (2016.4-1) unstable; urgency=medium * New upstream release. * Bump Standards-Version to 4.1.0. Set Priority to optional. * Drop Multi-Arch: same for libgromacs-dev, it seems to have some per-arch conflicts from autogenerated files. * Depend on sse2-support [any-i386] | neon-support [armhf], for the minimum useful levels of SIMD support on those architectures. Also enable NEON for arm64. * Set hardening options BINDNOW and PIE. -- Nicholas Breen Sun, 17 Sep 2017 10:29:19 -0700 gromacs (2016.3-2) unstable; urgency=medium * Upload to unstable after the stretch release. * Remove the old gromacs-dev metapackage, now that it's passed one stable release with libgromacs-dev available. Also remove some old Breaks: from well before oldstable. * Set Multi-Arch: foreign for gromacs-data, M-A: same for gromacs-dev and libgromacs2. -- Nicholas Breen Sun, 18 Jun 2017 13:32:39 -0700 gromacs (2016.3-1) experimental; urgency=medium * New upstream release. -- Nicholas Breen Wed, 15 Mar 2017 21:18:12 -0700 gromacs (2016.2-1) experimental; urgency=medium * New upstream release. Uploaded to experimental during freeze. * Remove dh_shlibdeps workaround introduced in 2016~rc1-3, which is fixed via the MPI implementations now. * Remove old .NOTPARALLEL restriction when building. * Use chrpath to remove RUNPATH on OpenMPI binaries -- see . -- Nicholas Breen Wed, 08 Feb 2017 17:58:11 -0800 gromacs (2016.1-2) unstable; urgency=medium * Disable OpenMPI tests on hurd-i386/kfreebsd-*. This appears related to . * Move to debhelper compat version 10, requiring no changes. * Drop some obsolete lintian overrides, and add a pair for zero-length documentation files not yet shipped. * Update debian/copyright. -- Nicholas Breen Sun, 30 Oct 2016 17:12:11 -0700 gromacs (2016.1-1) unstable; urgency=medium * New upstream release. * rules: Build without SIMD on ppc64. -- Nicholas Breen Sun, 30 Oct 2016 08:44:09 -0700 gromacs (2016-3) unstable; urgency=medium * rules: Adjust SIMD detection logic to set GMX_SIMD=None by default, and enable it case-by-case only on those architectures where it's safe to do so. (Closes: #834991) * Work around OpenMPI 2 test failures: (Closes: #837061) - control: Add openmpi-bin to Build-Depends. - rules: Apply the OMPI_MCA_plm_rsh_agent workaround from #494046. -- Nicholas Breen Thu, 08 Sep 2016 19:38:53 -0700 gromacs (2016-2) unstable; urgency=medium * Accept DEB_BUILD_OPTIONS=nocheck for the "build-openmpi" target, which was missing and causing m68k build failures. (Closes: #834786) * patches/hurd-disable-numa-test.patch: On hurd-i386 only, this test fails for what seem to be detection limitations rather than an actual problem, so disable the test conditionally on that architecture. -- Nicholas Breen Fri, 19 Aug 2016 08:52:08 +0200 gromacs (2016-1) unstable; urgency=low * New upstream release, upload to unstable. - Remove patches/gmxManageSimd.patch, incorporated upstream. -- Nicholas Breen Tue, 09 Aug 2016 06:06:12 -0700 gromacs (2016~rc1-3) experimental; urgency=medium * Workaround for #831442: manually prepend /usr/lib/ to search path for dh_shlibdeps -pgromacs-mpich. * Set SIMD extensions to VSX on ppc64el, already the minimum requirement for that architecture. Disable SIMD on ppc64 due to lower CPU baseline requirements and the lack of double-precision support in basic VMX. -- Nicholas Breen Sat, 16 Jul 2016 10:17:07 -0700 gromacs (2016~rc1-2) experimental; urgency=medium * OpenMPI now supported on all relevant architectures, so gromacs-openmpi changed to "Architecture: any" and arch-specific handling removed. * Revive part of the test patch from beta2-2 as disable-cpuinfotest.patch, as the issue is not fully resolved upstream. * For SSE settings, use DEB_HOST_ARCH_CPU instead of DEB_HOST_ARCH. * patches/gmxManageSimd.patch: Correctly pass -msse2 to compiler flags. -- Nicholas Breen Fri, 15 Jul 2016 17:44:18 -0700 gromacs (2016~rc1-1) experimental; urgency=medium * First upstream release candidate. - Drop patches from beta2-2, incorporated or fixed upstream. * Switch from building with libxml2 to libtinyxml. * rules: Convert deprecated debhelper -s flags to -a. -- Nicholas Breen Mon, 11 Jul 2016 18:28:25 -0700 gromacs (2016~beta2-2) experimental; urgency=medium * Two patches to address test suits failures: - numerically-unstable-gaussian-test.patch: Backport a fix from git master branch to address Gaussian test failures on all i386 platforms. (http://redmine.gromacs.org/issues/1986) - disable-hardware-topology-tests.patch: Two CPU info tests cause hard failures that should probably just be warnings, so disable those tests for now. (http://redmine.gromacs.org/issues/1987) -- Nicholas Breen Fri, 17 Jun 2016 06:40:18 -0700 gromacs (2016~beta2-1) experimental; urgency=low * Beta for major new upstream release. New date-based versioning system. - SONAME bump: package rename, libgromacs1 -> libgromacs2 - spelling and empty-man7-directory patches incorporated upstream. - Refresh other patches. - Versioned Depends: on python-sphinx (>= 1.4) for new imgmath extension. * Update Standards-Version to 3.9.8, no changes required. -- Nicholas Breen Tue, 07 Jun 2016 14:20:10 -0700 gromacs (5.1.2-3) experimental; urgency=medium * Add LD_LIBRARY_PATH overrides to unit tests. -- Nicholas Breen Thu, 21 Apr 2016 17:35:41 -0700 gromacs (5.1.2-2) experimental; urgency=medium * Run upstream unit tests. Supports DEB_BUILD_OPTIONS=nocheck bypass. * Use rdfind/symlinks to reduce internal duplication in doxygen output. * Only build process changes in this upload - uploading to experimental as a safety. -- Nicholas Breen Mon, 18 Apr 2016 21:04:31 -0700 gromacs (5.1.2-1) unstable; urgency=medium * New upstream release. * Add hppa, s390x, x32 to list of architectures for gromacs-openmpi. In turn, increase required version of libopenmpi-dev to >= 1.10.2-7. * Add new patches/reproducible-builds.patch for... reproducible builds. This is preliminary work and may not be complete. * doxygen.patch: work around FTBFS with doxygen >= 1.8.11 (no problems with previous 1.8.9). (Closes: #815678) * spelling.patch: Additional fixes. * Update Standards-Version to 3.9.7, no changes required. -- Nicholas Breen Sun, 28 Feb 2016 13:31:21 -0800 gromacs (5.1.1-2) unstable; urgency=medium * Replace compiler calls to "mpic++" with "mpicxx". MPICH >= 3.2 no longer ships mpic++ links. (Closes: #808659) * Remove obsolete build dependency on libgsl0-dev. -- Nicholas Breen Tue, 22 Dec 2015 17:18:40 -0800 gromacs (5.1.1-1) unstable; urgency=medium * New upstream release. -- Nicholas Breen Mon, 09 Nov 2015 17:24:02 -0800 gromacs (5.1-1) unstable; urgency=low * New upstream release. This release completes the transition to "gmx" as the sole binary to replace all the former g_* commands, and the compatibility symlinks have been removed. Standalone mdrun_mpi programs in gromacs-mpich and gromacs-openmpi are unaffected. - gmx anadock no longer crashes on invalid input. (Closes: #715934) * Some package reshuffling: gromacs-dev becomes libgromacs-dev, and the shared library gets split out into libgromacs1. (Closes: #797744) Upload priority set to "low" due to the unusually extensive restructure. * Remove gromacs-dev.preinst, only needed for upgrades from well before the version in squeeze. * Lots more documentation! PDF manual is built once again, and doxygen output for developer use is included. Several Build-Depends-Indep entries added to support this. - patches/manpage-hyphenation.patch removed, no longer needed. - mdrun_mpi.{mpich,openmpi}.1 updated. * debian/control: apply wrap-and-sort. -- Nicholas Breen Thu, 01 Oct 2015 17:38:08 -0700 gromacs (5.0.6-1) unstable; urgency=medium * New upstream release. -- Nicholas Breen Sun, 26 Jul 2015 13:58:11 -0700 gromacs (5.0.5-1) unstable; urgency=medium * New upstream release. -- Nicholas Breen Sat, 16 May 2015 11:30:11 -0700 gromacs (5.0.4-2) unstable; urgency=medium * Post-Jessie upload to unstable, no other changes. -- Nicholas Breen Mon, 27 Apr 2015 10:00:09 -0700 gromacs (5.0.4-1) experimental; urgency=medium * New upstream release. Uploaded to experimental during the freeze. Minor patch rebasing only. -- Nicholas Breen Sun, 21 Dec 2014 12:54:35 -0800 gromacs (5.0.2-1) unstable; urgency=medium * New upstream release. * Update Standards-Version to 3.9.6, no changes required. * Update rules to build GPU-accelerated packages, with thanks to Steffen Möller. -- Nicholas Breen Sun, 05 Oct 2014 10:29:34 -0700 gromacs (5.0.1-1) unstable; urgency=medium * New upstream release. * Rebase patches involving man pages (moved from share/man to doc/man in tarball), drop 20_random123_platforms.patch (incorporated upstream), and remove the leading numbers from all patch filenames (a leftover from dpatch). * man/mdrun_mpi.*: Update .TH line. * rules: Set CMAKE_RULE_MESSAGES=OFF to work around blhc false positives for "W-compiler-flags-hidden". * Move debian/upstream to debian/upstream/metadata. -- Nicholas Breen Sat, 06 Sep 2014 11:20:17 -0700 gromacs (5.0-3) unstable; urgency=medium * Upload to unstable. -- Nicholas Breen Sun, 24 Aug 2014 20:02:24 -0700 gromacs (5.0-2) experimental; urgency=low * Add 20_random123_platforms.patch to disable architecture check from external Random123 code. * Drop discussion of shared libraries from README.Debian for gromacs-{mpich,openmpi}. -- Nicholas Breen Wed, 02 Jul 2014 20:13:01 -0700 gromacs (5.0-1) experimental; urgency=low * New upstream release, experimental upload. - g_sigeps / gmx sigeps command line handling no longer crashes on invalid input (Closes: #715935). * Rebase existing patches. Add new patches: - 31_manpage_hyphenation.patch: Some parts of the man page generation get the hyphen/dash separation right, some don't. A temporary fix pending significant overhaul of the man page system. - 32_spelling.patch: Correction of minor spelling errors. * man/g_{dos,kinetics,luck}.1: Incorporated upstream, removed. * man/gmx.1: Rudimentary man page written and added. * man/mdrun_mpi.*.1: Updated with text from upstream gmx-mpich.1. * rules: Updates for MPI builds and assorted upstream changes. * gromacs-data.lintian-overrides, source/lintian-overrides: Removed. * Add Build-Depends on external libboost-dev. * Switch away from hardening-wrapper in favor of dpkg-buildflags. * Update copyright file. -- Nicholas Breen Wed, 02 Jul 2014 17:35:18 -0700 gromacs (4.6.5-2) unstable; urgency=medium * Update list of OpenMPI architectures to include mips*, arm64. * patches/21_hurd.patch: Cherry-pick upstream commit 2c81d3ab to build shared libraries on GNU/Hurd. * watch: Extend regex to detect -beta, -pre, _pre, *and* -rc suffixes. * Remove chrpath workaround, no longer needed as of mpich 3.0.4-6. -- Nicholas Breen Mon, 16 Jun 2014 18:48:37 -0700 gromacs (4.6.5-1) unstable; urgency=low * New upstream release. * rules: Override autodetection of CPU extensions on amd64 and i386; force to SSE2 only, and provide new DEB_BUILD_OPTIONS=cpuopt flag to re-enable autodetection for local builds. (Closes: #725013) * rules: Fix misplaced COPYING symlink in gromacs-data. * source/lintian-overrides: Add overrides for outstanding lintian bugs #729096 (newer policy version), #724866 (libmpich-dev not virtual). * patches/20_manpages.patch: Fix formatting errors in the NAME line of several man pages. * gromacs-data.doc-base: Change root to getting_started.html. The shipped HTML documentation is slowly being eliminated in favor of a wiki on gromacs.org. -- Nicholas Breen Mon, 09 Dec 2013 10:40:36 -0800 gromacs (4.6.3-4) unstable; urgency=low * control: Add versioned Build-Depends on libmpich-dev (>= 3), to prevent build failures on architectures where that still represents the old MPICH version 1. * rules: More mpich2 -> mpich replacements. -- Nicholas Breen Sun, 29 Sep 2013 21:39:46 -0700 gromacs (4.6.3-3) unstable; urgency=low * control: - Move Replaces/Breaks to MPI packages instead. (Closes: #718001) - Move all mpich2 dependencies to new mpich (v3) package names. * control, rules: - Add ppc64 to list of supported architectures for gromacs-openmpi. - Temporarily add use of "chrpath -d" on gromacs-mpich binaries, due to mpicc.mpich setting RPATH unconditionally (see #724864). -- Nicholas Breen Sun, 29 Sep 2013 16:30:43 -0700 gromacs (4.6.3-2) unstable; urgency=low * control: - Add B-Ds for external BLAS/LAPACK libraries. - Have -dev Replaces/Breaks earlier versions of -openmpi/-mpich to handle file move. (Closes: #718001) - For gromacs, remove Conflicts with a long-obsolete (before squeeze) version of radiance, and add Suggests on pymol for visualization. * rules: Specify verbose output from CMake. -- Nicholas Breen Sun, 11 Aug 2013 13:05:19 -0700 gromacs (4.6.3-1) unstable; urgency=low * New upstream release; post-freeze, uploading to unstable. * rules, control: Remove special provisions for FORTRAN on Alpha. * rules: Update configuration parameters. * rules, patches/12_copyright-file.patch: Avoid duplication of copyright information into two files, but provide a link to keep both filenames. * control: Drop obsolete B-D on lesstif2-dev. (Closes: #714753) * rules: Move .so symlinks for MPI libraries from -dev to their respective packages, to ensure that they can't be installed without their targets. * control: Update SCM links. -- Nicholas Breen Fri, 05 Jul 2013 13:57:44 -0700 gromacs (4.6-1) experimental; urgency=low * New upstream release, targeted at experimental during freeze. - Remove patches/10_release-4-5-patches.patch (obsolete), 31_manpages.patch (incorporated upstream). - Update lintian overrides. -- Nicholas Breen Mon, 25 Feb 2013 10:47:14 -0800 gromacs (4.5.5-2) unstable; urgency=low [ Andreas Tille ] * debian/upstream: - copied citations from tasks/bio to debian/upstream - make last citation conform to BibTeX syntax [ Nicholas Breen ] * Update to current release-4.5-patches git (f361fa9c) via addition of patches/10_release-4.5-patches.patch. * source/format: Move to 3.0 (quilt). Adjust patches accordingly. * control: Remove specific listing of MPI packages from description of gromacs-dev. (Closes: #644820) Update maintainer address and drop DMUA stanza. Drop Build-Depends on dpatch, add on hardening-wrapper. Update to S-V 3.9.3, no packaging changes required. * rules, README.source: Remove dpatch cruft. * rules: Apply compiler hardening flags with hardening-wrapper. * patches/*: Tidy up with DEP-3 headers. * control, rules: Update list of architectures for gromacs-openmpi, adding armel, armhf, powerpcspe, and sparc64. -- Nicholas Breen Sat, 09 Jun 2012 11:42:56 -0700 gromacs (4.5.5-1) unstable; urgency=low * New upstream release. - Remove patches/30_git_release-4.5-patches.dpatch. - man/g_dos.1: Create man page for new binary. * rules: Add build-arch/build-indep targets. Add preliminary support for building GPU-accelerated binaries: set DEB_BUILD_OPTIONS=gpu to try it. * patches/31_manpages.dpatch: Update. -- Nicholas Breen Wed, 21 Sep 2011 19:10:08 -0700 gromacs (4.5.4-2) unstable; urgency=low * control: remove obsolete Build-Depends and Suggests on libice-dev, libsm-dev, libxext-dev, libxp-dev, libxt-dev. Update Standards-Version to 3.9.2. * patches/30_git_release-4.5-patches.dpatch: Routine update from upstream git, to commit 873563ef of 22 April 2011. * patches/31_manpages.dpatch: Various minor spelling and header fixes. * lintian-overrides.gromacs: Remove checks no longer needed, per #120323. * rules: Switch to using dh_lintian. -- Nicholas Breen Mon, 25 Apr 2011 13:47:00 -0700 gromacs (4.5.4-1) unstable; urgency=low * New upstream release. * Remove gromacs-lam transitional package. * man/g_options.1: Create man page for new binary. * lintian-overrides.gromacs-data: Override script-not-executable for demo scripts not in $PATH. -- Nicholas Breen Mon, 21 Mar 2011 19:59:54 -0700 gromacs (4.5.3-1) unstable; urgency=low * New upstream release. * Force -DGMX_X11=ON to build ngmx. (Closes: #603327) -- Nicholas Breen Sat, 13 Nov 2010 12:02:17 -0800 gromacs (4.5.2-1) unstable; urgency=low * Major new upstream release. * All patches incorporated upstream and removed, except the Debian- specific bug reporting portion of 11_readme.dpatch. * man/gromacs.7: incorporated upstream, removed from Debian patch. * man/luck.1: Rename to g_luck.1 and edit to reflect new name. * man/mdrun_mpi.*.1: Resynchronize with upstream mdrun.1. * watch: Update to recognize -betaX tarballs and ignore -GPU builds. * rules: Convert from autotools to new CMake build system. * control: - Add Build-Depends on libxml2-dev. - Update Standards-Version to 3.9.1. - Replace Conflicts: with Breaks:. -- Nicholas Breen Wed, 03 Nov 2010 17:39:52 -0700 gromacs (4.0.7-3) unstable; urgency=low * New patch 03_autoconf_bashisms.dpatch: Eliminate two bashisms (test == instead of =) in configure.ac, permitting use with dash instead. * patches/30_git_release-4.0-patches.dpatch: Update to commit 36df279783944c11d1ba43936ea820f8e6003ffd. -- Nicholas Breen Tue, 25 May 2010 19:30:48 -0700 gromacs (4.0.7-2) unstable; urgency=low * rules: - Drop chrpath workaround, underlying bug solved with mpich2 1.2.1.1-2. - Add sparc to list of architectures for -openmpi. * control: - Per above. - Set DM-Upload-Allowed: yes. - Update Standards-Version to 3.8.4. - Add ${misc:Depends} for Lintian, except for -data and -lam which receive overrides instead. * gromacs-parallel.README.Debian.in: Remove reference to LAM-MPI. * patches/30_git_release-4.0-patches.dpatch: Update to commit 444432a51f87f003fc6e7098f9e07a2a2d142c64. * source/format: Create and set explicitly to 1.0. * source/lintian-overrides: Override debhelper-but-no-misc-depends for gromacs-data and gromacs-lam. -- Nicholas Breen Tue, 13 Apr 2010 23:33:27 -0700 gromacs (4.0.7-1) unstable; urgency=low * New upstream release. * patches/30_git_release-4.0-patches.dpatch: Empty out, replace with fresh pull starting at the 4.0.7 release; current to git commit 665dce86638df8ac1062b0b022d7827ea0f11788. -- Nicholas Breen Thu, 31 Dec 2009 16:43:03 -0800 gromacs (4.0.5-5) unstable; urgency=low * Transition to only the two supported MPI implementations: - gromacs-mpich now builds against MPICH2, not MPICH1. - gromacs-lam replaced with a dummy package installing gromacs- openmpi on all supported architectures, -mpich on the holdouts. - Update documentation accordingly. * patches/30_git_release-4.0-patches.dpatch: Pull from upstream git repository, release-4.0-patches branch. Current to git commit 37a4dd35fec7579ca7faca25c62c71cf1d8e1621, 29 Nov. 2009. * patches/21_makefile_dups.dpatch: Delete, incorporated above (commit c93db8511af09c144fe4b2b8f57b14a5ad1e6cc7). * compat: Update to debhelper v7 mode. - rules: Replace dh_clean -k with dh_prep. - control: Adjust Build-Depends to debhelper (>= 7.0.0). * copyright: Increment year. * rules: Use chrpath to eliminate RPATH from MPICH2-compiled binaries. This is a workaround for a libmpich2-dev bug, #558960. - control: Add chrpath to Build-Depends. * rules: Add -Wl,--as-needed to LDFLAGS. -- Nicholas Breen Mon, 30 Nov 2009 16:18:34 -0800 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 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 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 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 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 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 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 Mon, 19 Jan 2009 10:42:26 -0800 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 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 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 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 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 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 Wed, 13 Feb 2008 15:01:50 -0800 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 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 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 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 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 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 Tue, 10 Apr 2007 17:08:02 -0700 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 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 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 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 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 Mon, 3 Apr 2006 09:50:44 -0700 gromacs (3.3-1) unstable; urgency=low * Initial Debian release. (Closes: #228319, #252101) -- Nicholas Breen Thu, 16 Mar 2006 23:00:13 -0800