# ChangeLog for sci-chemistry/gromacs # Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2 # $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v 1.108 2012/05/04 07:02:33 jdhore Exp $ 04 May 2012; Jeff Horelick gromacs-4.5.5-r1.ebuild: dev-util/pkgconfig -> virtual/pkgconfig 09 Mar 2012; Christoph Junghans -gromacs-4.5.4-r1.ebuild, metadata.xml: remove old (fixes bug #392121) 08 Mar 2012; Brent Baude gromacs-4.5.5-r1.ebuild: Marking gromacs-4.5.5-r1 ppc64 for bug 391147 06 Feb 2012; Christoph Junghans gromacs-4.5.4-r1.ebuild, gromacs-4.5.5-r1.ebuild: fix bug #402339 05 Feb 2012; Raúl Porcel gromacs-4.5.4-r1.ebuild, gromacs-4.5.5-r1.ebuild: Drop alpha/sparc keywords 06 Jan 2012; Christoph Junghans -gromacs-4.5.4-r2.ebuild, -gromacs-4.5.5.ebuild: remove obsolete 06 Jan 2012; Christoph Junghans gromacs-4.5.5-r1.ebuild: keyword ~x86-macos 26 Dec 2011; Markus Meier gromacs-4.5.5-r1.ebuild: x86 stable, bug #391147 20 Dec 2011; Agostino Sarubbo gromacs-4.5.5-r1.ebuild: Stable for AMD64, wrt bug #391147 *gromacs-4.5.5-r1 (19 Dec 2011) 19 Dec 2011; Christoph Junghans +gromacs-4.5.5-r1.ebuild, +files/gromacs-4.5.5-cmake-cpp-asm.patch, +files/gromacs-4.5.5-enable-see.patch: bring back sse2 kernels 14 Dec 2011; Agostino Sarubbo gromacs-4.5.5.ebuild: Stable for AMD64, wrt bug #391147 11 Dec 2011; Pawel Hajdan jr gromacs-4.5.5.ebuild: x86 stable wrt bug #391147 28 Sep 2011; Christoph Junghans gromacs-4.5.5.ebuild: cmake variable LIB was renamed to GMXLIB *gromacs-4.5.5 (27 Sep 2011) 27 Sep 2011; Alexey Shvetsov +gromacs-4.5.5.ebuild: Version bump 10 Sep 2011; Christoph Junghans gromacs-4.5.4-r1.ebuild, gromacs-4.5.4-r2.ebuild: Migrate to the bash-completion-r1 eclass 18 Jul 2011; Christoph Junghans gromacs-4.5.4-r2.ebuild: fix for external blas/lapack (bug #373559) 17 Jul 2011; Christoph Junghans gromacs-4.5.4-r2.ebuild: corrected libdir (bug #375473) 26 Jun 2011; Justin Lecher gromacs-4.5.4-r1.ebuild, gromacs-4.5.4-r2.ebuild, metadata.xml: migrate from 'git' to 'git-2' 23 Jun 2011; Christoph Junghans gromacs-4.5.4-r1.ebuild, gromacs-4.5.4-r2.ebuild: only USE=fkernels needs fortran 21 Jun 2011; Justin Lecher gromacs-4.5.4-r1.ebuild, gromacs-4.5.4-r2.ebuild: Add dependency on virtual/fortran 21 Jun 2011; Justin Lecher gromacs-4.5.4-r1.ebuild, gromacs-4.5.4-r2.ebuild: Added fortran-2.eclass support 21 Jun 2011; Justin Lecher gromacs-4.5.4-r1.ebuild: Use append-libs *gromacs-4.5.4-r2 (08 Jun 2011) 08 Jun 2011; Christoph Junghans +gromacs-4.5.4-r2.ebuild: build with cmake to decrease build time 01 May 2011; Kacper Kowalik -gromacs-4.5.3-r4.ebuild, -gromacs-4.5.4.ebuild, gromacs-4.5.4-r1.ebuild: ppc64 stable wrt #357017. Drop old. 11 Apr 2011; Christoph Mende gromacs-4.5.4-r1.ebuild: Stable on amd64 wrt bug #357017 10 Apr 2011; Raúl Porcel gromacs-4.5.4-r1.ebuild: alpha/sparc stable wrt #357017 10 Apr 2011; Christoph Junghans -gromacs-4.0.7-r4.ebuild, -files/gromacs-4.0.9999-docdir.patch: remove 4.0.* (EOM) 10 Apr 2011; Thomas Kahle gromacs-4.5.4-r1.ebuild: x86 stable per bug 357017 *gromacs-4.5.4-r1 (04 Apr 2011) 04 Apr 2011; Alexey Shvetsov +gromacs-4.5.4-r1.ebuild: Fix QA execstack bug #361687 04 Apr 2011; Christoph Junghans -gromacs-4.0.7-r5.ebuild, -gromacs-4.5.3.ebuild, -gromacs-4.5.3-r3.ebuild: Removed old 04 Apr 2011; Christoph Junghans gromacs-4.5.4.ebuild: Removed sse use flag (fixed bug #361933) 02 Apr 2011; Raúl Porcel gromacs-4.5.3-r4.ebuild: alpha/sparc stable wrt #357017 02 Apr 2011; Kacper Kowalik gromacs-4.5.4.ebuild: Bump to EAPI=4 for REQUIRED_USE on fkernels and threads wrt #361687. Mark ppc64 stable wrt #357017 02 Apr 2011; Samuli Suominen gromacs-4.5.4.ebuild: Remove illegal QA_EXECSTACK for source based package. 02 Apr 2011; Kacper Kowalik gromacs-4.5.4.ebuild: Revert to ~ppc64 25 Mar 2011; Kacper Kowalik gromacs-4.5.4.ebuild: ppc64 stable wrt #357017 22 Mar 2011; Christoph Junghans gromacs-4.5.4.ebuild: New manual, added back pkg-config to DEPEND *gromacs-4.5.4 (21 Mar 2011) 21 Mar 2011; Alexey Shvetsov +gromacs-4.5.4.ebuild: Version bump 17 Mar 2011; Alexey Shvetsov gromacs-4.5.3-r4.ebuild: Clean up ebuild a bit 09 Mar 2011; Thomas Kahle gromacs-4.5.3-r4.ebuild: x86 stable per bug 357017 08 Mar 2011; Markos Chandras gromacs-4.5.3-r4.ebuild: Stable on amd64 wrt bug #357017 *gromacs-4.5.3-r4 (05 Mar 2011) 05 Mar 2011; Alexey Shvetsov +gromacs-4.5.3-r4.ebuild: Rework using of external blas & lapack. Also fix issues with prefix and mpi build 02 Mar 2011; Justin Lecher gromacs-4.0.7-r4.ebuild, gromacs-4.0.7-r5.ebuild, gromacs-4.5.3.ebuild, gromacs-4.5.3-r3.ebuild: Correct Slots for gtk 3 introduction to tree *gromacs-4.5.3-r3 (19 Feb 2011) 19 Feb 2011; Christoph Junghans +gromacs-4.5.3-r3.ebuild: Version bump (fixes bug #339837) 04 Jan 2011; Jeremy Olexa metadata.xml: QA: Remove redundant local use flag description 16 Dec 2010; Justin Lecher gromacs-4.0.7-r4.ebuild, gromacs-4.0.7-r5.ebuild, gromacs-4.5.3.ebuild: Removal of fortran.eclass, #348851 *gromacs-4.5.3 (25 Nov 2010) *gromacs-4.0.7-r5 (25 Nov 2010) 25 Nov 2010; Alexey Shvetsov -gromacs-4.0.4.ebuild, -files/gromacs-4.0.4-configure-gfortran.patch, -files/gromacs-4.0.4-sparc-cyclecounter.patch, -gromacs-4.0.5.ebuild, gromacs-4.0.7-r4.ebuild, +gromacs-4.0.7-r5.ebuild, -files/gromacs-4.0.9999-ccache.patch, -files/gromacs-4.0.9999-configure-gfortran.patch, -gromacs-4.5.1.ebuild, +gromacs-4.5.3.ebuild: Version bump. Clean up old versions. Thanks to Christoph Junghans 25 Oct 2010; Samuli Suominen gromacs-4.0.7-r4.ebuild: ppc64 stable wrt #326151 12 Oct 2010; Raúl Porcel gromacs-4.0.7-r4.ebuild: sparc stable wrt #326151 *gromacs-4.5.1 (14 Sep 2010) 14 Sep 2010; Alexey Shvetsov -gromacs-4.0.7-r3.ebuild, +gromacs-4.5.1.ebuild: Version bump. Now it can use ffambber. And threads. Many thanks to Christoph Junghans 11 Sep 2010; Tobias Klausmann gromacs-4.0.7-r4.ebuild: Stable on alpha, bug #326151 17 Jul 2010; Kacper Kowalik gromacs-4.0.7-r3.ebuild, gromacs-4.0.7-r4.ebuild, -files/gromacs-4.0.7_upstream2010-06-08.patch.gz: Move gromacs-4.0.7_upstream2010-06-08.patch.gz to gentoo mirrors. Fixes bug 328659. Thanks to Samuli for the report 10 Jul 2010; Christian Faulhammer gromacs-4.0.7-r4.ebuild: stable x86, bug 326151 09 Jul 2010; Pacho Ramos gromacs-4.0.7-r4.ebuild: amd64 stable, bug 326151 08 Jul 2010; Alexey Shvetsov gromacs-4.0.7-r4.ebuild: Fix typo in ebuild for prefix setup *gromacs-4.0.7-r4 (04 Jul 2010) 04 Jul 2010; Alexey Shvetsov +gromacs-4.0.7-r4.ebuild: Fix bug #326331. thanks to Christoph Junghans 05 Jul 2010; Alexey Shvetsov -gromacs-3.3.1-r1.ebuild, -gromacs-3.3.3.ebuild: Gromacs 3.x moved to sci overlay since its unmaintained and no longer supported *gromacs-4.0.7-r3 (27 Jun 2010) 27 Jun 2010; Alexey Shvetsov -gromacs-4.0.7.ebuild, -gromacs-4.0.7-r1.ebuild, +gromacs-4.0.7-r3.ebuild, -files/gromacs-4.0.7-docdir.patch, +files/gromacs-4.0.7_upstream2010-06-08.patch: Added patches from upstream stable branch. Added ffamber ports. Also fixed bugs #301854 and #284431. Big thank to Christoph Junghans 24 Jun 2010; Justin Lecher gromacs-3.3.1-r1.ebuild, gromacs-3.3.3.ebuild: Blocking sci-mathematics/num-utils, #257566 *gromacs-4.0.7-r1 (24 Jan 2010) 24 Jan 2010; Alexey Shvetsov +gromacs-4.0.7-r1.ebuild, +files/gromacs-4.0.9999-ccache.patch, +files/gromacs-4.0.9999-configure-gfortran.patch, +files/gromacs-4.0.9999-docdir.patch: Fix bug #302048. thanks to Christoph Junghans 18 Jan 2010; Raúl Porcel gromacs-4.0.5.ebuild: alpha stable 08 Dec 2009; Alexey Shvetsov +files/gromacs-4.0.7-docdir.patch: Add missing patch. thanks to rei4dan *gromacs-4.0.7 (07 Dec 2009) 07 Dec 2009; Alexey Shvetsov +gromacs-4.0.7.ebuild: Version bump 31 Oct 2009; Raúl Porcel gromacs-4.0.5.ebuild: sparc stable wrt #260995 30 Oct 2009; Markus Meier gromacs-4.0.5.ebuild: amd64/x86 stable, bug #260995 26 Sep 2009; Brent Baude gromacs-4.0.4.ebuild: Marking gromacs-4.0.4 ppc64 for bug 260995 28 Aug 2009; William Hubbs metadata.xml: new global use flag "zsh-completion" 15 May 2009; Markus Meier gromacs-4.0.4.ebuild: amd64 stable, bug #260995 14 May 2009; Alexey Shvetsov -gromacs-4.0.3.ebuild, +gromacs-4.0.5.ebuild: Drop old version; Fix keywords for 4.0.5. Sorry =) *gromacs-4.0.5 (14 May 2009) 14 May 2009; Alexey Shvetsov +gromacs-4.0.5.ebuild: Bump new version with bugfixes. Bug #269754 14 May 2009; Christian Faulhammer gromacs-4.0.4.ebuild: stable x86, bug 260995 13 May 2009; Tobias Klausmann gromacs-4.0.4.ebuild: Stable on alpha, bug #260995 10 May 2009; Ferris McCormick gromacs-4.0.4.ebuild: Sparc stable, Bug #260995, which see for discussion. 10 May 2009; Alexey Shvetsov gromacs-4.0.4.ebuild, +files/gromacs-4.0.4-sparc-cyclecounter.patch: Add upstream fix for sparc bug #260995 *gromacs-4.0.4 (20 Apr 2009) 20 Apr 2009; Alexey Shvetsov +files/gromacs-4.0.4-configure-gfortran.patch, metadata.xml, -gromacs-4.0.ebuild, -gromacs-4.0.2.ebuild, +gromacs-4.0.4.ebuild: Add new gromacs 4.0.4 08 Mar 2009; Markus Meier gromacs-4.0.3.ebuild: amd64/x86 stable, bug #260995 22 Jan 2009; Jeff Gardner +gromacs-4.0.3.ebuild: Latest version. *gromacs-4.0.2 (04 Jan 2009) 04 Jan 2009; Jeff Gardner +gromacs-4.0.2.ebuild: Latest version, thanks to Alexxy for the prod :) *gromacs-4.0 (12 Oct 2008) 12 Oct 2008; Jeff Gardner +gromacs-4.0.ebuild: Latest version, closing bug #241474 thanks to Alexey Shvetsov 06 Oct 2008; Jeff Gardner ChangeLog, Manifest: Fixing changelog to reflect addition of gromacs-3.3.3.ebuild *gromacs-3.3.3 (06 Oct 2008) 06 Oct 2008; Jeff Gardner +gromacs-3.3.3.ebuild: Latest stable version, thanks to Alexey Shvetsov, closing bug #193532 06 Aug 2008; Ulrich Mueller metadata.xml: Add USE flag description to metadata wrt GLEP 56. 27 Jun 2008; Ulrich Mueller gromacs-3.3.1-r1.ebuild: Change dependency from virtual/motif to x11-libs/openmotif, bug 224749. 23 Jun 2008; Jeff Gardner -files/gromacs-alpha-axp_asm.patch, -files/gromacs-ppc64-altivec.patch, -gromacs-3.2.1-r1.ebuild, gromacs-3.3.1-r1.ebuild: Moving disco manpage to g_disco, fixing bug 210083. 03 Jun 2008; Jeff Gardner gromacs-3.3.1-r1.ebuild: No altivec patching with this gromacs version. Thanks to Maik Nijhuis in bug #224773. 13 Jun 2007; Raúl Porcel gromacs-3.3.1-r1.ebuild: Modify the ebuild so it compiles on alpha and mark stable wrt #168182 17 Mar 2007; Steve Dibb gromacs-3.3.1-r1.ebuild: amd64 stable, bug 168182 11 Mar 2007; Sven Wegener gromacs-3.3.1-r1.ebuild: Properly indent src_compile, thanks to ferringb. 08 Mar 2007; Jason Wever gromacs-3.3.1-r1.ebuild: Stable on SPARC wrt bug #168182. 07 Mar 2007; Jeff Gardner gromacs-3.3.1-r1.ebuild: Fix up the demo script so the xterms stay open. 24 Feb 2007; Raúl Porcel gromacs-3.3.1-r1.ebuild: x86 stable wrt bug 168182 23 Feb 2007; Markus Rothe gromacs-3.3.1-r1.ebuild: Stable on ppc64; bug #168182 07 Jan 2007; Danny van Dyk -gromacs-3.2.1.ebuild, -gromacs-3.3.ebuild, -gromacs-3.3.1.ebuild: QA: Removed unused versions. 20 Dec 2006; Jeff Gardner gromacs-3.3.1-r1.ebuild: Small fix of DEPEND 20 Dec 2006; Jeff Gardner ChangeLog: Many thanks to Rene Meier, Shvetsov Alexey Mathias Weigt, dawe, and Mike Hlavac for their contributions to gromacs-3.3.1-r1. *gromacs-3.3.1-r1 (17 Dec 2006) 17 Dec 2006; Jeff Gardner +gromacs-3.3.1-r1.ebuild: Fixup to address bugs 135146 118421 and 147614. 20 Sep 2006; Donnie Berkholz ; metadata.xml: (#148281) Change herd to sci-chemistry from sci. *gromacs-3.3.1 (08 Aug 2006) 08 Aug 2006; Markus Dittrich +gromacs-3.3.1.ebuild: Version bump. Ebuild now inherits the fortran.eclass and forces the use of g77 since gfortran is presently missing some of the fortran intrinsics needed by gromacs. See bug #141672. 05 Aug 2006; Donnie Berkholz ; metadata.xml: Remove myself as maintainer, anyone feel free to work on this, although I'll continue to do so as well. 07 Jul 2006; Donnie Berkholz ; metadata.xml: Update to my new email address. 25 Jun 2006; Donnie Berkholz ; gromacs-3.2.1.ebuild, gromacs-3.2.1-r1.ebuild, gromacs-3.3.ebuild: (#116346) Change xml2 USE flag to xml. 07 May 2006; Markus Rothe gromacs-3.2.1-r1.ebuild: Stable on ppc64; bug #89969 *gromacs-3.3 (14 Oct 2005) 14 Oct 2005; Donnie Berkholz ; +gromacs-3.3.ebuild: (#109184) Bump. Main change in ebuild is adding a check for fftw built w/ mpi if trying to build w/ mpi. One of the more interesting upstream changes is the addition of x86-64 and ia64 assembly. 05 Aug 2005; +files/gromacs-ppc64-altivec.patch, gromacs-3.2.1-r1.ebuild: Added patch back as binary due to metatags. Made sure patch only applies when ppc64 && altivec *gromacs-3.2.1-r1 (04 Aug 2005) 04 Aug 2005; +files/gromacs-ppc64-altivec.patch, +gromacs-3.2.1-r1.ebuild: Added ppc64 support and altivec support 24 Dec 2004; Olivier Fisette +metadata.xml, +gromacs-3.2.1.ebuild: Moved from app-sci/gromacs to sci-chemistry/gromacs. 06 Jun 2004; Danny van Dyk gromacs-3.2.1.ebuild: Marked stable on amd64. 22 Apr 2004; Donnie Berkholz ; -files/gromacs-3.2-all-static-fix.patch, -gromacs-3.1.4-r1.ebuild, -gromacs-3.1.4-r2.ebuild, gromacs-3.2.1.ebuild, -gromacs-3.2.ebuild: Mark 3.2.1 stable on x86. Remove old versions. 22 Apr 2004; Donnie Berkholz ; gromacs-3.1.4-r1.ebuild, gromacs-3.2.1.ebuild: Add app-shells/tcsh to dependencies (#48691). 22 Apr 2004; Danny van Dyk gromacs-3.2.1.ebuild: marked ~amd64 *gromacs-3.2.1 (02 Apr 2004) 02 Apr 2004; Donnie Berkholz ; gromacs-3.2.1.ebuild: Version bump, closes #44377. *gromacs-3.2 (29 Feb 2004) 29 Feb 2004; Donnie Berkholz ; gromacs-3.2.ebuild, files/gromacs-3.2-all-static-fix.patch: Version bump. New xml2 USE flag. *gromacs-3.1.4-r2 (28 Feb 2004) 28 Feb 2004; Donnie Berkholz ; gromacs-3.1.4-r2.ebuild: Closing bug #42989 by installing binaries to /usr/bin. Also discovered libs needed to be installed to /usr/lib. Enabled assembly for Alphas too, if any Alpha user ever tries this. 04 Oct 2003; Donnie Berkholz ; gromacs-3.1.3.ebuild, gromacs-3.1.4.ebuild: Pulling old versions. 04 Oct 2003; Donnie Berkholz ; gromacs-3.1.4-r1.ebuild: Fixing fftw dep. Won't compile against fftw-3 yet, in part because it looks for fftw3.h instead of fftw.h, and in part because MPI doesn't work in fftw-3 yet. *gromacs-3.1.4-r1 (23 Mar 2003) 23 Mar 2003; George Shapovalov gromacs-3.1.4-r1.ebuild : added mpi support, lam-mpi is the only working implementation at the moment. !IMPORTANT!: Since portage cannot at present check whether optional dependencies of dependencies were turned on, please check yourself that gromacs and fftw have identical mpi setting. Generally USE="mpi" emerge gromacs should work fine if you did not install fftw previously (with different mpi off for example). *gromacs-3.1.4 (08 Nov 2002) 08 Nov 2002; George Shapovalov gromacs-3.1.4.ebuild, files/digest-gromacs-3.1.4 : new version. !!!IMPORTANT!!! I changed --prefix to point to /usr for FHS compliance. Now the binaries and the libs are getting installed into /usr/i686-pc-linux-gnu/{bin,lib} correspondingly and the data into /usr/share/gromacs-${PV} This seems to fit well in the existing direcory structure and does not conflict with gcc. *gromacs-3.1.3 (27 Apr 2002) 27 Apr 2002; George Shapovalov all_files : initial release.