summaryrefslogtreecommitdiff
diff options
context:
space:
mode:
authorAlexey Shvetsov <alexxy@gentoo.org>2014-12-22 16:07:19 +0300
committerAlexey Shvetsov <alexxy@gentoo.org>2014-12-22 16:07:19 +0300
commit888044fa6cbc97c1cf12f89d0a70ddd87c6117f2 (patch)
tree1894cabddd31644aa180ff8297a081d1cf7534fd
parentAdd einspline (diff)
downloadalexxy-888044fa6cbc97c1cf12f89d0a70ddd87c6117f2.zip
alexxy-888044fa6cbc97c1cf12f89d0a70ddd87c6117f2.tar.gz
alexxy-888044fa6cbc97c1cf12f89d0a70ddd87c6117f2.tar.bz2
Add experimental python bindings
Package-Manager: portage-2.2.15
-rw-r--r--sci-chemistry/gromacs/ChangeLog532
-rw-r--r--sci-chemistry/gromacs/gromacs-9999.ebuild279
-rw-r--r--sci-chemistry/gromacs/metadata.xml27
3 files changed, 838 insertions, 0 deletions
diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
new file mode 100644
index 0000000..da2baae
--- /dev/null
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -0,0 +1,532 @@
+# ChangeLog for sci-chemistry/gromacs
+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+ 21 Dec 2014; Christoph Junghans <ottxor@gentoo.org> gromacs-5.0.9999.ebuild:
+ sync with gx86
+
+ 25 Nov 2014; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild,
+ gromacs-5.0.9999.ebuild, gromacs-9999.ebuild:
+ fixed a typo preventing AVX2 support (bug #530454)
+
+ 09 Oct 2014; Alexey Shvetsov <alexxy@gentoo.org> gromacs-9999.ebuild:
+ Fix doc install
+
+ 07 Sep 2014; Christoph Junghans <ottxor@gentoo.org> gromacs-5.0.9999.ebuild:
+ fix completion install
+
+ 06 Sep 2014; Christoph Junghans <ottxor@gentoo.org> gromacs-5.0.9999.ebuild:
+ sync with gx86
+
+ 04 Sep 2014; Christoph Junghans <ottxor@gentoo.org> gromacs-5.0.9999.ebuild:
+ sync with gx86
+
+ 03 Sep 2014; Christoph Junghans <ottxor@gentoo.org> -Manifest,
+ -gromacs-5.0_rc1.ebuild:
+ drop old
+
+ 03 Sep 2014; Christoph Junghans <ottxor@gentoo.org> gromacs-5.0.9999.ebuild:
+ live update
+
+ 07 Jul 2014; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild,
+ gromacs-5.0.9999.ebuild:
+ sync with gx86, fix FEATURES=test
+
+ 26 Jun 2014; Christoph Junghans <ottxor@gentoo.org> gromacs-5.0.9999.ebuild:
+ live ebuild update
+
+ 14 Apr 2014; Christoph Junghans <ottxor@gentoo.org> gromacs-5.0.9999.ebuild,
+ gromacs-5.0_rc1.ebuild, gromacs-9999.ebuild, metadata.xml:
+ added make-symlinks use flag, multilib-strict fix
+
+*gromacs-5.0.9999 (08 Apr 2014)
+*gromacs-5.0_rc1 (08 Apr 2014)
+
+ 08 Apr 2014; Alexey Shvetsov <alexxy@gentoo.org> +gromacs-5.0.9999.ebuild,
+ +gromacs-5.0_rc1.ebuild, -gromacs-5.0_beta1.ebuild, gromacs-9999.ebuild,
+ metadata.xml:
+ [sci-chemistry/gromacs] New ebuilds
+
+ 05 Mar 2014; Christoph Junghans <ottxor@gentoo.org> gromacs-9999.ebuild:
+ fix multilib-strict
+
+ 20 Feb 2014; Alexey Shvetsov <alexxy@gentoo.org> gromacs-9999.ebuild:
+ Update gromacs 5.0
+
+ 16 Feb 2014; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild:
+ git-r3 too smart, migrate back to git-2
+
+ 05 Feb 2014; Alexey Shvetsov <alexxy@gentoo.org> gromacs-9999.ebuild:
+ Bash completion changes are comming =D
+
+ 05 Feb 2014; Alexey Shvetsov <alexxy@gentoo.org> gromacs-9999.ebuild:
+ Revert back to git-2 since git-r2 gives problems
+
+ 25 Jan 2014; Justin Lecher <jlec@gentoo.org> gromacs-4.6.9999.ebuild,
+ gromacs-5.0_beta1.ebuild, gromacs-9999.ebuild:
+ Add missing dep for USE=doc
+
+ 06 Jan 2014; Justin Lecher <jlec@gentoo.org> gromacs-4.6.9999.ebuild,
+ gromacs-5.0_beta1.ebuild, gromacs-9999.ebuild:
+ Switch from git-2 to git-r3
+
+ 06 Jan 2014; Justin Lecher <jlec@gentoo.org> gromacs-4.6.9999.ebuild,
+ gromacs-5.0_beta1.ebuild, gromacs-9999.ebuild:
+ Switch from git-2 to git-r3
+
+ 07 Dec 2013; Justin Lecher <jlec@gentoo.org> gromacs-5.0_beta1.ebuild,
+ metadata.xml:
+ Fix multilib-strict problems
+
+*gromacs-5.0_beta1 (06 Dec 2013)
+
+ 06 Dec 2013; Alexey Shvetsov <alexxy@gentoo.org> +gromacs-5.0_beta1.ebuild,
+ gromacs-9999.ebuild:
+ Add 5.0-beta1 release
+
+ 05 Dec 2013; Alexey Shvetsov <alexxy@gentoo.org> gromacs-9999.ebuild:
+ Make gromacs 9999 build manual again
+
+ 05 Dec 2013; Alexey Shvetsov <alexxy@gentoo.org> -Manifest,
+ -gromacs-4.5.9999.ebuild, metadata.xml:
+ Drop 4.5
+
+ 05 Dec 2013; Alexey Shvetsov <alexxy@gentoo.org> gromacs-9999.ebuild:
+ Update live ebuild to current state
+
+ 03 Dec 2013; Alexey Shvetsov <alexxy@gentoo.org> gromacs-9999.ebuild:
+ make mdrun target work for gmx live
+
+ 03 Dec 2013; Alexey Shvetsov <alexxy@gentoo.org> gromacs-9999.ebuild:
+ More updates #2 to gmx live
+
+ 03 Dec 2013; Alexey Shvetsov <alexxy@gentoo.org> gromacs-9999.ebuild:
+ More updates to gmx live
+
+ 03 Dec 2013; Alexey Shvetsov <alexxy@gentoo.org> gromacs-9999.ebuild:
+ Slightly update live ebuild for master branch
+
+ 01 Jun 2013; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild:
+ sync with gx86
+
+ 05 May 2013; Christoph Junghans <ottxor@gentoo.org> gromacs-4.5.9999.ebuild:
+ sync with gx86
+
+*gromacs-4.5.9999 (03 May 2013)
+
+ 03 May 2013; Christoph Junghans <ottxor@gentoo.org>
+ +files/gromacs-4.5.7-cmake-cpp-asm.patch, +gromacs-4.5.9999.ebuild,
+ metadata.xml:
+ added recent 4.5.x version from gx86 (bug #468454)
+
+ 15 Mar 2013; Alexey Shvetsov <alexxy@gentoo.org> gromacs-4.6.9999.ebuild:
+ nvcc flags dont needed anymore here
+
+ 15 Mar 2013; Alexey Shvetsov <alexxy@gentoo.org> gromacs-4.6.9999.ebuild,
+ gromacs-9999.ebuild:
+ Fix build with cuda enabled
+
+ 10 Mar 2013; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild:
+ added cuda build fix from gx86
+
+ 09 Mar 2013; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild:
+ fixed deps + doc build on darwin
+
+ 06 Mar 2013; Christoph Junghans <ottxor@gentoo.org> -Manifest,
+ -gromacs-4.5.9999.ebuild, gromacs-4.6.9999.ebuild, gromacs-9999.ebuild,
+ metadata.xml:
+ sync with gx86 + clean up
+
+ 12 Feb 2013; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild,
+ gromacs-9999.ebuild, metadata.xml:
+ sse41 -> sse4_1 (bug #456886) + ninja has missing keywords
+
+ 30 Jan 2013; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild,
+ gromacs-9999.ebuild:
+ added subslot, removed gromacs-manual blocker
+
+ 30 Jan 2013; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild:
+ clean up
+
+ 28 Jan 2013; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild:
+ added app-doc/gromacs-manual in here
+
+ 21 Jan 2013; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild:
+ sci-chemistry/gromacs: use cuda.eclass
+
+ 21 Jan 2013; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild:
+ fixed sci-chemistry/gromacs[test]
+
+ 21 Jan 2013; Alexey Shvetsov <alexxy@gentoo.org> gromacs-4.6.9999.ebuild:
+ [sci-chemistry/gromacs] Drop restrict test for 4.6
+
+ 21 Jan 2013; Alexey Shvetsov <alexxy@gentoo.org> gromacs-4.6.9999.ebuild:
+ [sci-chemistry/gromacs] Update 4.6 series ebuild
+
+ 18 Jan 2013; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild:
+ yet another update for git
+
+ 18 Jan 2013; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild:
+ live ebuild update
+
+ 30 Dec 2012; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild:
+ further clean up
+
+ 29 Dec 2012; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild:
+ fixed build with newer mkl
+
+ 27 Dec 2012; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild:
+ sci-chemistry/gromacs: clean up
+
+ 26 Dec 2012; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild:
+ fixed openmm suffix
+
+ 26 Dec 2012; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild:
+ fixed another typo
+
+ 26 Dec 2012; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild:
+ fixed typo
+
+ 26 Dec 2012; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild,
+ metadata.xml:
+ Added mkl support
+
+ 22 Dec 2012; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild,
+ gromacs-9999.ebuild, metadata.xml:
+ sync with gx86
+
+ 20 Dec 2012; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild:
+ fortran is gone
+
+ 08 Dec 2012; Christoph Junghans <ottxor@gentoo.org> gromacs-4.5.9999.ebuild,
+ gromacs-4.6.9999.ebuild, gromacs-9999.ebuild:
+ CMAKE_BUILD_DIR -> BUILD_DIR
+
+ 30 Nov 2012; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild:
+ sync with gx86
+
+ 27 Nov 2012; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild,
+ metadata.xml:
+ added openmm support
+
+ 19 Nov 2012; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild:
+ live ebuild update
+
+ 04 Oct 2012; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild,
+ gromacs-9999.ebuild:
+ live ebuild update
+
+ 03 Oct 2012; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild,
+ metadata.xml:
+ hybrid stuff got merged
+
+ 09 Aug 2012; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild:
+ use ninja if available
+
+ 25 Jul 2012; Christoph Junghans <ottxor@gentoo.org> gromacs-4.5.9999.ebuild,
+ gromacs-4.6.9999.ebuild, gromacs-9999.ebuild:
+ added ~x86-macos
+
+ 19 Jun 2012; Alexey Shvetsov <alexxy@gentoo.org> gromacs-4.6.9999.ebuild,
+ gromacs-9999.ebuild, metadata.xml:
+ [sci-chemistry/gromacs] Add new acceleration use flags for gromacs
+
+ 11 Jun 2012; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild,
+ metadata.xml:
+ add support for new hybrid kernels
+
+ 28 Apr 2012; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild:
+ [sci-chemistry/gromacs] add more mirrors
+
+ 19 Apr 2012; Alexey Shvetsov <alexxy@gentoo.org> gromacs-4.5.9999.ebuild,
+ gromacs-4.6.9999.ebuild, gromacs-9999.ebuild:
+ [sci-chemistry/gromacs] Also add http mirror git uri
+
+ 04 Mar 2012; Christoph Junghans <ottxor@gentoo.org> gromacs-4.5.9999.ebuild,
+ gromacs-9999.ebuild:
+ removed obsolete call to env-update
+
+ 04 Mar 2012; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild:
+ reworked fortran and openmp support
+
+ 12 Feb 2012; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild:
+ sci-chemistry/gromacs: clean up
+
+ 12 Feb 2012; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild:
+ fixed threads and mpi
+
+ 05 Feb 2012; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild:
+ handle new vmd detection
+
+ 05 Feb 2012; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild:
+ added openmp support
+
+*gromacs-4.6.9999 (28 Sep 2011)
+
+ 28 Sep 2011; Christoph Junghans <ottxor@gentoo.org> +gromacs-4.6.9999.ebuild:
+ Added gromacs-4.6 live version
+
+ 10 Sep 2011; Christoph Junghans <ottxor@gentoo.org> gromacs-4.5.9999.ebuild,
+ gromacs-9999.ebuild:
+ Migrate to the bash-completion-r1 eclass
+
+ 18 Jul 2011; Christoph Junghans <ottxor@gentoo.org> gromacs-4.5.9999.ebuild,
+ gromacs-9999.ebuild:
+ sync with tree
+
+ 25 Jun 2011; Christoph Junghans <ottxor@gentoo.org> gromacs-4.5.9999.ebuild,
+ gromacs-9999.ebuild:
+ migrate to git-2
+
+ 25 Jun 2011; Justin Lecher <jlec@gentoo.org> gromacs-4.5.9999.ebuild,
+ gromacs-9999.ebuild, metadata.xml:
+ migrate from 'git' to 'git-2'
+
+ 21 Jun 2011; Christoph Junghans <ottxor@gentoo.org> gromacs-4.5.9999.ebuild,
+ gromacs-9999.ebuild:
+ only USE=fkernels needs fortran
+
+ 21 Jun 2011; Justin Lecher <jlec@gentoo.org> gromacs-4.5.9999.ebuild,
+ gromacs-9999.ebuild:
+ Added fortran-2.eclass support
+
+ 19 Jun 2011; Christoph Junghans <ottxor@gentoo.org> gromacs-4.5.9999.ebuild,
+ metadata.xml:
+ autotools is broken
+
+ 10 Apr 2011; Christoph Junghans <ottxor@gentoo.org> -gromacs-4.0.9999.ebuild:
+ remove 4.0.* (EOM)
+
+ 08 Mar 2011; Christoph Junghans <ottxor@gentoo.org> gromacs-4.5.9999.ebuild,
+ gromacs-9999.ebuild:
+ added fixes from 4.5.3-r4
+
+ 07 Mar 2011; Justin Lecher <jlec@gentoo.org> gromacs-4.0.9999.ebuild,
+ gromacs-4.5.9999.ebuild, gromacs-9999.ebuild:
+ Correct Slots for gtk 3 introduction to tree
+
+ 19 Feb 2011; Christoph Junghans <ottxor@gentoo.org> -gromacs-4.5.3-r3.ebuild:
+ InCVS
+
+*gromacs-4.5.3-r3 (17 Feb 2011)
+
+ 17 Feb 2011; Christoph Junghans <ottxor@gentoo.org> -gromacs-4.5.3-r2.ebuild,
+ +gromacs-4.5.3-r3.ebuild:
+ version bump
+
+*gromacs-4.5.3-r2 (14 Feb 2011)
+
+ 14 Feb 2011; Christoph Junghans <ottxor@gentoo.org> -gromacs-4.5.3-r1.ebuild,
+ +gromacs-4.5.3-r2.ebuild, gromacs-4.5.9999.ebuild, gromacs-9999.ebuild:
+ bring back sse/sse2 useflag (bug #339837)
+
+ 20 Jan 2011; Christoph Junghans <kleiner_otti@gmx.de> gromacs-9999.ebuild:
+ add back live manual
+
+ 17 Jan 2011; Christoph Junghans <kleiner_otti@gmx.de> gromacs-9999.ebuild:
+ QA fixes
+
+ 16 Dec 2010; Justin Lecher <jlec@gentoo.org> gromacs-4.0.9999.ebuild,
+ gromacs-4.5.9999.ebuild, gromacs-9999.ebuild:
+ Removal of fortran.eclass, #348851
+
+ 25 Nov 2010; Alexey Shvetsov <alexxy@gentoo.org> -gromacs-4.0.7-r5.ebuild,
+ -files/gromacs-4.0.7_missing_distfiles.patch.gz,
+ -files/gromacs-4.0.7_upstream2010-09-15.patch.gz, -gromacs-4.5.2.ebuild,
+ -gromacs-4.5.3.ebuild:
+ Moved to tree
+
+*gromacs-4.5.3 (23 Nov 2010)
+
+ 23 Nov 2010; Christoph Junghans <kleiner_otti@gmx.de>
+ +gromacs-4.5.3.ebuild:
+ version bump
+
+*gromacs-4.5.2 (30 Oct 2010)
+
+ 30 Oct 2010; Christoph Junghans <kleiner_otti@gmx.de>
+ +gromacs-4.5.2.ebuild:
+ Version bump
+
+ 25 Oct 2010; Christoph Junghans <kleiner_otti@gmx.de>
+ gromacs-4.5.9999.ebuild, gromacs-9999.ebuild, metadata.xml:
+ added natural vmd support (bug #340651#c8)
+
+ 21 Oct 2010; Christoph Junghans <kleiner_otti@gmx.de>
+ gromacs-4.5.9999.ebuild, metadata.xml:
+ added vmd use flag
+
+ 17 Oct 2010; Christoph Junghans <kleiner_otti@gmx.de>
+ gromacs-4.0.7-r5.ebuild, gromacs-4.0.9999.ebuild:
+ rename manual in distfiles
+
+ 16 Oct 2010; Christoph Junghans <kleiner_otti@gmx.de>
+ gromacs-4.0.9999.ebuild, gromacs-4.5.9999.ebuild, gromacs-9999.ebuild:
+ Live ebuild updates
+
+*gromacs-4.0.7-r5 (16 Oct 2010)
+
+ 16 Oct 2010; Christoph Junghans <kleiner_otti@gmx.de>
+ +gromacs-4.0.7-r5.ebuild, +files/gromacs-4.0.7_missing_distfiles.patch.gz,
+ +files/gromacs-4.0.7_upstream2010-09-15.patch.gz:
+ Version bump
+
+*gromacs-4.5.1 (02 Sep 2010)
+
+ 02 Sep 2010; Christoph Junghans <kleiner_otti@gmx.de>
+ -gromacs-4.5_beta3.ebuild, +gromacs-4.5.1.ebuild:
+ version bump
+
+*gromacs-4.5_beta3 (11 Aug 2010)
+
+ 11 Aug 2010; Alexey Shvetsov <alexxy@gentoo.org> gromacs-4.0.9999.ebuild,
+ -gromacs-4.5_beta2.ebuild, +gromacs-4.5_beta3.ebuild,
+ gromacs-4.5.9999.ebuild, gromacs-9999.ebuild:
+ Add epatch_user
+
+*gromacs-4.5_beta2 (02 Aug 2010)
+
+ 02 Aug 2010; Christoph Junghans <kleiner_otti@gmx.de>
+ -gromacs-4.5_beta1.ebuild, +gromacs-4.5_beta2.ebuild,
+ gromacs-4.5.9999.ebuild, gromacs-9999.ebuild:
+ Version bump + new manual
+
+*gromacs-4.5.9999 (31 Jul 2010)
+*gromacs-4.5_beta1 (31 Jul 2010)
+
+ 31 Jul 2010; Christoph Junghans <kleiner_otti@gmx.de>
+ +gromacs-4.5_beta1.ebuild, +gromacs-4.5.9999.ebuild, gromacs-9999.ebuild:
+ Version bump
+
+ 24 Jul 2010; Alexey Shvetsov <alexxy@gentoo.org> gromacs-9999.ebuild:
+ ffamber officialy shipped with gromacs from now on
+
+ 08 Jul 2010; Christoph Junghans <kleiner_otti@gmx.de>
+ gromacs-4.0.9999.ebuild, gromacs-9999.ebuild:
+ fix for bug #301854
+
+ 04 Jul 2010; Christoph Junghans <kleiner_otti@gmx.de>
+ gromacs-4.0.9999.ebuild, -files/gromacs-4.0.9999-ccache.patch,
+ -files/gromacs-4.0.9999-configure-gfortran.patch, gromacs-9999.ebuild:
+ make it compile without fortran again
+
+ 04 Jul 2010; Christoph Junghans <kleiner_otti@gmx.de>
+ gromacs-4.0.9999.ebuild, gromacs-9999.ebuild:
+ Fixes for Bug #326331
+
+ 28 Jun 2010; Christoph Junghans <kleiner_otti@gmx.de>
+ gromacs-4.0.9999.ebuild, +files/gromacs-4.0.9999-docdir.patch:
+ docdir patch is still not in 4.0 branch
+
+*gromacs-4.0.7-r3 (22 Jun 2010)
+
+ 22 Jun 2010; Christoph Junghans <kleiner_otti@gmx.de>
+ +gromacs-4.0.7-r3.ebuild, +files/gromacs-4.0.7to2010-06-08.patch.gz:
+ added patches from stable branch
+
+*gromacs-4.0.7-r2 (26 Feb 2010)
+
+ 26 Feb 2010; Alexey Shvetsov <alexxy@gentoo.org> +gromacs-4.0.7-r2.ebuild:
+ Add ffamber port to gromacs
+
+ 18 Feb 2010; Alexey Shvetsov <alexxy@gentoo.org> gromacs-9999.ebuild,
+ -files/gromacs-9999-dirent.patch:
+ Dropped unneded patches. They all were applied to git master
+
+ 18 Feb 2010; Alexey Shvetsov <alexxy@gentoo.org> gromacs-9999.ebuild,
+ -files/gromacs-9999-as-needed.patch,
+ -files/gromacs-9999-install-mdrun.patch:
+ Dropped unneded patches. They all were applied to git master
+
+ 09 Feb 2010; Christoph Junghans <kleiner_otti@gmx.de> gromacs-9999.ebuild,
+ +files/gromacs-9999-as-needed.patch:
+ added as-needed fix
+
+ 06 Feb 2010; Christoph Junghans <kleiner_otti@gmx.de>
+ -gromacs-4.0.7-r1.ebuild, -files/gromacs-4.0.9999-docdir.patch:
+ InCvs
+
+ 06 Feb 2010; Christoph Junghans <kleiner_otti@gmx.de>
+ gromacs-4.0.9999.ebuild, gromacs-9999.ebuild:
+ docdir patch went upstream
+
+ 01 Feb 2010; Christoph Junghans <kleiner_otti@gmx.de> gromacs-9999.ebuild,
+ +files/gromacs-9999-install-mdrun.patch:
+ update live ebuild
+
+*gromacs-4.0.7-r1 (24 Jan 2010)
+
+ 24 Jan 2010; Christoph Junghans <kleiner_otti@gmx.de>
+ -files/gromacs-4.0.4-configure-gfortran.patch, +gromacs-4.0.7-r1.ebuild,
+ gromacs-4.0.9999.ebuild, +files/gromacs-4.0.9999-ccache.patch,
+ +files/gromacs-4.0.9999-configure-gfortran.patch, gromacs-9999.ebuild:
+ Fixes bug #302048
+
+ 23 Jan 2010; Christoph Junghans <kleiner_otti@gmx.de>
+ gromacs-4.0.9999.ebuild, gromacs-9999.ebuild:
+ fixed --as-needed confusion
+
+ 21 Jan 2010; Christoph Junghans <kleiner_otti@gmx.de>
+ -gromacs-3.3.9999.ebuild, -gromacs-4.0.4.ebuild,
+ -files/gromacs-4.0.4-sparc-cyclecounter.patch, -gromacs-4.0.5-r1.ebuild,
+ -files/gromacs-4.0.5-docdir.patch,
+ -files/gromacs-4.0.5-path-overflow.patch, gromacs-4.0.9999.ebuild,
+ +files/gromacs-4.0.9999-docdir.patch, gromacs-9999.ebuild:
+ sync with tree and removed old ebuilds
+
+ 30 Nov 2009; Christoph Junghans <kleiner_otti@gmx.de>
+ files/gromacs-4.0.5-docdir.patch:
+ docdir -> htmldir
+
+ 30 Nov 2009; Christoph Junghans <kleiner_otti@gmx.de>
+ gromacs-4.0.5-r1.ebuild, +files/gromacs-4.0.5-docdir.patch:
+ htmldoc was installed in the wrong path
+
+ 22 Nov 2009; Christoph Junghans <kleiner_otti@gmx.de>
+ gromacs-4.0.5-r1.ebuild:
+ build mpi and non-mpi libs, enable gsl by default
+
+*gromacs-4.0.5-r1 (14 Nov 2009)
+
+ 14 Nov 2009; Christoph Junghans <kleiner_otti@gmx.de>
+ +files/gromacs-4.0.4-sparc-cyclecounter.patch, +gromacs-4.0.5-r1.ebuild,
+ +files/gromacs-4.0.5-path-overflow.patch:
+ fixes bug #284431
+
+*gromacs-9999 (21 Jun 2009)
+*gromacs-4.0.9999 (21 Jun 2009)
+*gromacs-3.3.9999 (21 Jun 2009)
+
+ 21 Jun 2009; Christoph Junghans <kleiner_otti@gmx.de>
+ +gromacs-3.3.9999.ebuild, +files/gromacs-4.0.4-configure-gfortran.patch,
+ +gromacs-4.0.9999.ebuild, +gromacs-9999.ebuild, metadata.xml:
+ added live ebuilds for old, stable, experimental branch
+
+ 21 Jun 2009; Christoph Junghans <kleiner_otti@gmx.de>
+ gromacs-4.0.4.ebuild:
+ Fixed some repoman errors
+
+ 22 Feb 2009; Jeff Gardner <je_fro@gentoo.org>
+ gromacs-4.0.4.ebuild:
+ Add 'append-ldflags' to facilitate building for users with --as-needed.
+
+*gromacs-4.0.4 (20 Feb 2009)
+
+ 20 Feb 2009; Alexey Shvetsov <alexxy@gentoo.org> -gromacs-4.0.3-r1.ebuild,
+ +gromacs-4.0.4.ebuild:
+ Version bump\!
+
+ 20 Feb 2009; Alexey Shvetsov <alexxy@gentoo.org> gromacs-4.0.3-r1.ebuild:
+ Fix typo
+
+*gromacs-4.0.3-r1 (20 Feb 2009)
+
+ 20 Feb 2009; Alexey Shvetsov <alexxy@gentoo.org> +gromacs-4.0.3-r1.ebuild,
+ -gromacs-4.0.3.ebuild:
+ Add support for qm/mm with mopac7 for gromacs
+
+*gromacs-4.0.3 (20 Jan 2009)
+
+ 20 Jan 2009; Alexey Shvetsov <alexxy@gentoo.org> -gromacs-3.3.3.ebuild,
+ +gromacs-4.0.3.ebuild:
+ Version bump
diff --git a/sci-chemistry/gromacs/gromacs-9999.ebuild b/sci-chemistry/gromacs/gromacs-9999.ebuild
new file mode 100644
index 0000000..d26c345
--- /dev/null
+++ b/sci-chemistry/gromacs/gromacs-9999.ebuild
@@ -0,0 +1,279 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+TEST_PV="5.0-rc1"
+
+CMAKE_MAKEFILE_GENERATOR="ninja"
+
+PYTHON_COMPAT=( python{3_2,3_3,3_4} )
+
+inherit bash-completion-r1 cmake-utils cuda eutils multilib python-single-r1 readme.gentoo toolchain-funcs
+
+if [[ $PV = *9999* ]]; then
+ if use python; then
+ EGIT_REPO_URI="git://biod.pnpi.spb.ru/alexxy/gromacs.git"
+ EGIT_BRANCH="pygromacs"
+ else
+ EGIT_REPO_URI="git://git.gromacs.org/gromacs.git
+ https://gerrit.gromacs.org/gromacs.git
+ git://github.com/gromacs/gromacs.git
+ http://repo.or.cz/r/gromacs.git"
+ EGIT_BRANCH="master"
+ fi
+ inherit git-r3
+else
+ SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz
+ test? ( http://gerrit.gromacs.org/download/regressiontests-${TEST_PV}.tar.gz )"
+fi
+
+ACCE_IUSE="sse2 sse4_1 avx_128_fma avx_256 avx2_256"
+
+DESCRIPTION="The ultimate molecular dynamics simulation package"
+HOMEPAGE="http://www.gromacs.org/"
+
+# see COPYING for details
+# http://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING
+# base, vmd plugins, fftpack from numpy, blas/lapck from netlib, memtestG80 library, mpi_thread lib
+LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )"
+SLOT="0/${PV}"
+KEYWORDS=""
+IUSE="X blas boost cuda +doc -double-precision +fftw lapack +make-symlinks mkl mpi +offensive openmp python +single-precision test +threads +tng ${ACCE_IUSE}"
+
+CDEPEND="
+ X? (
+ x11-libs/libX11
+ x11-libs/libSM
+ x11-libs/libICE
+ )
+ blas? ( virtual/blas )
+ boost? ( >=dev-libs/boost-1.55 )
+ cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 )
+ fftw? ( sci-libs/fftw:3.0 )
+ lapack? ( virtual/lapack )
+ mkl? ( sci-libs/mkl )
+ mpi? ( virtual/mpi )
+ python? (
+ dev-python/numpy
+ dev-python/sip
+ )
+ "
+DEPEND="${CDEPEND}
+ virtual/pkgconfig
+ doc? (
+ app-doc/doxygen
+ dev-texlive/texlive-latex
+ dev-texlive/texlive-latexextra
+ media-gfx/imagemagick
+ )"
+RDEPEND="${CDEPEND}"
+
+REQUIRED_USE="
+ || ( single-precision double-precision )
+ cuda? ( single-precision )
+ mkl? ( !blas !fftw !lapack )
+ python? ( ${PYTHON_REQUIRED_USE} )"
+
+DOCS=( AUTHORS README )
+
+if [[ ${PV} != *9999 ]]; then
+ S="${WORKDIR}/${PN}-${PV/_/-}"
+fi
+
+pkg_pretend() {
+ [[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs"
+ use openmp && ! tc-has-openmp && \
+ die "Please switch to an openmp compatible compiler"
+}
+
+pkg_setup() {
+ use python && python-single-r1_pkg_setup
+}
+
+src_unpack() {
+ if [[ ${PV} != *9999 ]]; then
+ default
+ else
+ git-r3_src_unpack
+ if use test; then
+ EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \
+ EGIT_BRANCH="master" EGIT_NOUNPACK="yes" EGIT_COMMIT="master" \
+ EGIT_SOURCEDIR="${WORKDIR}/regressiontests"\
+ git-r3_src_unpack
+ fi
+ fi
+}
+
+src_prepare() {
+ #notes/todos
+ # -on apple: there is framework support
+
+ cmake-utils_src_prepare
+
+ use cuda && cuda_src_prepare
+
+ GMX_DIRS=""
+ use single-precision && GMX_DIRS+=" float"
+ use double-precision && GMX_DIRS+=" double"
+
+ if use test; then
+ for x in ${GMX_DIRS}; do
+ mkdir -p "${WORKDIR}/${P}_${x}" || die
+ cp -al "${WORKDIR}/regressiontests"* "${WORKDIR}/${P}_${x}/tests" || die
+ done
+ fi
+
+ DOC_CONTENTS="Gromacs can use sci-chemistry/vmd to read additional file formats"
+}
+
+src_configure() {
+ local mycmakeargs_pre=( ) extra fft_opts=( )
+
+ #go from slowest to fastest acceleration
+ local acce="None"
+ use sse2 && acce="SSE2"
+ use sse4_1 && acce="SSE4.1"
+ use avx_128_fma && acce="AVX_128_FMA"
+ use avx_256 && acce="AVX_256"
+ use avx2_256 && acce="AVX2_256"
+
+ #to create man pages, build tree binaries are executed (bug #398437)
+ [[ ${CHOST} = *-darwin* ]] && \
+ extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF"
+
+ if use fftw; then
+ fft_opts=( -DGMX_FFT_LIBRARY=fftw3 )
+ elif use mkl && has_version "=sci-libs/mkl-10*"; then
+ fft_opts=( -DGMX_FFT_LIBRARY=mkl
+ -DMKL_INCLUDE_DIR="${MKLROOT}/include"
+ -DMKL_LIBRARIES="$(echo /opt/intel/mkl/10.0.5.025/lib/*/libmkl.so);$(echo /opt/intel/mkl/10.0.5.025/lib/*/libiomp*.so)"
+ )
+ elif use mkl; then
+ local bits=$(get_libdir)
+ fft_opts=( -DGMX_FFT_LIBRARY=mkl
+ -DMKL_INCLUDE_DIR="$(echo /opt/intel/*/mkl/include)"
+ -DMKL_LIBRARIES="$(echo /opt/intel/*/mkl/lib/*${bits/lib}/libmkl_rt.so)"
+ )
+ else
+ fft_opts=( -DGMX_FFT_LIBRARY=fftpack )
+ fi
+
+ mycmakeargs_pre+=(
+ "${fft_opts[@]}"
+ $(cmake-utils_use X GMX_X11)
+ $(cmake-utils_use blas GMX_EXTERNAL_BLAS)
+ $(cmake-utils_use lapack GMX_EXTERNAL_LAPACK)
+ $(cmake-utils_use openmp GMX_OPENMP)
+ $(cmake-utils_use offensive GMX_COOL_QUOTES)
+ $(cmake-utils_use boost GMX_EXTERNAL_BOOST)
+ $(cmake-utils_use tng GMX_USE_TNG)
+ $(cmake-utils_use doc GMX_BUILD_MANUAL)
+ $(cmake-utils_use make-symlinks GMX_SYMLINK_OLD_BINARY_NAMES)
+ $(cmake-utils_use python GMX_PYTHON_BINDINGS)
+ -DGMX_DEFAULT_SUFFIX=off
+ -DGMX_SIMD="$acce"
+ -DGMX_LIB_INSTALL_DIR="$(get_libdir)"
+ -DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/"
+ -DGMX_X86_AVX_GCC_MASKLOAD_BUG=OFF
+ -DGMX_USE_GCC44_BUG_WORKAROUND=OFF
+ -DBUILD_TESTING=OFF
+ -DGMX_BUILD_UNITTESTS=OFF
+ ${extra}
+ )
+
+ for x in ${GMX_DIRS}; do
+ einfo "Configuring for ${x} precision"
+ local suffix=""
+ #if we build single and double - double is suffixed
+ use double-precision && use single-precision && \
+ [[ ${x} = "double" ]] && suffix="_d"
+ local p
+ [[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF"
+ local cuda=( "-DGMX_GPU=OFF" )
+ [[ ${x} = "float" ]] && use cuda && \
+ cuda=( -DGMX_GPU=ON )
+ mycmakeargs=(
+ ${mycmakeargs_pre[@]} ${p}
+ -DGMX_MPI=OFF
+ $(cmake-utils_use threads GMX_THREAD_MPI)
+ "${cuda[@]}"
+ -DGMX_OPENMM=OFF
+ "$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")"
+ -DGMX_BINARY_SUFFIX="${suffix}"
+ -DGMX_LIBS_SUFFIX="${suffix}"
+ )
+ BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure
+ use mpi || continue
+ einfo "Configuring for ${x} precision with mpi"
+ mycmakeargs=(
+ ${mycmakeargs_pre[@]} ${p}
+ -DGMX_THREAD_MPI=OFF
+ -DGMX_MPI=ON ${cuda}
+ -DGMX_OPENMM=OFF
+ -DGMX_BUILD_MDRUN_ONLY=ON
+ -DBUILD_SHARED_LIBS=OFF
+ -DGMX_BUILD_MANUAL=OFF
+ -DGMX_BINARY_SUFFIX="_mpi${suffix}"
+ -DGMX_LIBS_SUFFIX="_mpi${suffix}"
+ )
+ BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake-utils_src_configure
+ done
+}
+
+src_compile() {
+ for x in ${GMX_DIRS}; do
+ einfo "Compiling for ${x} precision"
+ BUILD_DIR="${WORKDIR}/${P}_${x}"\
+ cmake-utils_src_compile
+ # generate bash completion
+ BUILD_DIR="${WORKDIR}/${P}_${x}"\
+ cmake-utils_src_compile completion
+ if use doc; then
+ BUILD_DIR="${WORKDIR}/${P}_${x}"\
+ cmake-utils_src_compile manual
+ fi
+ use mpi || continue
+ einfo "Compiling for ${x} precision with mpi"
+ BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\
+ cmake-utils_src_compile
+ done
+}
+
+src_test() {
+ for x in ${GMX_DIRS}; do
+ BUILD_DIR="${WORKDIR}/${P}_${x}"\
+ cmake-utils_src_make check
+ done
+}
+
+src_install() {
+ for x in ${GMX_DIRS}; do
+ BUILD_DIR="${WORKDIR}/${P}_${x}" \
+ cmake-utils_src_install
+ if use doc; then
+ newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf"
+ fi
+ newbashcomp "${WORKDIR}/${P}_${x}"/src/programs/completion/gmx-completion.bash gromacs
+ use mpi || continue
+ BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \
+ cmake-utils_src_install
+ done
+ # drop unneeded stuff
+ rm -f "${ED}"usr/bin/gmx-completion*
+ rm -f "${ED}"usr/bin/g_options*
+ rm -f "${ED}"usr/bin/GMXRC*
+ rm -f "${ED}"usr/lib*/libtng*.a
+
+ readme.gentoo_create_doc
+}
+
+pkg_postinst() {
+ einfo
+ einfo "Please read and cite:"
+ einfo "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). "
+ einfo "http://dx.doi.org/10.1021/ct700301q"
+ einfo
+ readme.gentoo_print_elog
+}
diff --git a/sci-chemistry/gromacs/metadata.xml b/sci-chemistry/gromacs/metadata.xml
new file mode 100644
index 0000000..87e0f0a
--- /dev/null
+++ b/sci-chemistry/gromacs/metadata.xml
@@ -0,0 +1,27 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-chemistry</herd>
+ <maintainer>
+ <email>ottxor@gentoo.org</email>
+ <name>Christoph Junghans</name>
+ </maintainer>
+ <use>
+ <flag name="cuda">Enable cuda non-bonded kernels</flag>
+ <flag name="double-precision">More precise calculations at the expense of speed</flag>
+ <flag name="single-precision">Single precision version of gromacs (default)</flag>
+ <flag name="boost">Enable external boost library</flag>
+ <flag name="tng">Enable new trajectory format - tng</flag>
+ <flag name="make-symlinks">Create symbolic links for pre-5.0 binary names</flag>
+ <!-- acceleration optimization flags -->
+ <flag name="sse4_1">Enable sse4.1 acceleration</flag>
+ <flag name="avx128fma">Enable 128bit avx with fma (e.g. AMD BullDozer)</flag>
+ <flag name="avx_128_fma">Enable 128bit avx with fma (e.g. AMD BullDozer)</flag>
+ <flag name="avx256">Enable 256bit avx (e.g. Intel Sandy Bridge)</flag>
+ <flag name="avx_256">Enable 256bit avx (e.g. Intel Sandy Bridge)</flag>
+ <flag name="avx2_256">Enable 256bit avx2 (e.g. Intel Haswell)</flag>
+ <flag name="offensive">Enable gromacs partly offensive quotes</flag>
+ <flag name="openmm">Add acceleration through <pkg>sci-libs/openmm</pkg></flag>
+ <flag name="mkl">Use <pkg>sci-libs/mkl</pkg> for fft, blas, lapack routines</flag>
+ </use>
+</pkgmetadata>