commit: 888044fa6cbc97c1cf12f89d0a70ddd87c6117f2 Author: Alexey Shvetsov <alexxy <AT> gentoo <DOT> org> AuthorDate: Mon Dec 22 13:07:19 2014 +0000 Commit: Alexey Shvetsov <alexxy <AT> gentoo <DOT> org> CommitDate: Mon Dec 22 13:07:19 2014 +0000 URL: http://sources.gentoo.org/gitweb/?p=dev/alexxy.git;a=commit;h=888044fa
Add experimental python bindings Package-Manager: portage-2.2.15 --- sci-chemistry/gromacs/ChangeLog | 532 ++++++++++++++++++++++++++++++ sci-chemistry/gromacs/gromacs-9999.ebuild | 279 ++++++++++++++++ sci-chemistry/gromacs/metadata.xml | 27 ++ 3 files changed, 838 insertions(+) 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 <[email protected]> gromacs-5.0.9999.ebuild: + sync with gx86 + + 25 Nov 2014; Christoph Junghans <[email protected]> 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 <[email protected]> gromacs-9999.ebuild: + Fix doc install + + 07 Sep 2014; Christoph Junghans <[email protected]> gromacs-5.0.9999.ebuild: + fix completion install + + 06 Sep 2014; Christoph Junghans <[email protected]> gromacs-5.0.9999.ebuild: + sync with gx86 + + 04 Sep 2014; Christoph Junghans <[email protected]> gromacs-5.0.9999.ebuild: + sync with gx86 + + 03 Sep 2014; Christoph Junghans <[email protected]> -Manifest, + -gromacs-5.0_rc1.ebuild: + drop old + + 03 Sep 2014; Christoph Junghans <[email protected]> gromacs-5.0.9999.ebuild: + live update + + 07 Jul 2014; Christoph Junghans <[email protected]> gromacs-4.6.9999.ebuild, + gromacs-5.0.9999.ebuild: + sync with gx86, fix FEATURES=test + + 26 Jun 2014; Christoph Junghans <[email protected]> gromacs-5.0.9999.ebuild: + live ebuild update + + 14 Apr 2014; Christoph Junghans <[email protected]> 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 <[email protected]> +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 <[email protected]> gromacs-9999.ebuild: + fix multilib-strict + + 20 Feb 2014; Alexey Shvetsov <[email protected]> gromacs-9999.ebuild: + Update gromacs 5.0 + + 16 Feb 2014; Christoph Junghans <[email protected]> gromacs-4.6.9999.ebuild: + git-r3 too smart, migrate back to git-2 + + 05 Feb 2014; Alexey Shvetsov <[email protected]> gromacs-9999.ebuild: + Bash completion changes are comming =D + + 05 Feb 2014; Alexey Shvetsov <[email protected]> gromacs-9999.ebuild: + Revert back to git-2 since git-r2 gives problems + + 25 Jan 2014; Justin Lecher <[email protected]> gromacs-4.6.9999.ebuild, + gromacs-5.0_beta1.ebuild, gromacs-9999.ebuild: + Add missing dep for USE=doc + + 06 Jan 2014; Justin Lecher <[email protected]> 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 <[email protected]> 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 <[email protected]> gromacs-5.0_beta1.ebuild, + metadata.xml: + Fix multilib-strict problems + +*gromacs-5.0_beta1 (06 Dec 2013) + + 06 Dec 2013; Alexey Shvetsov <[email protected]> +gromacs-5.0_beta1.ebuild, + gromacs-9999.ebuild: + Add 5.0-beta1 release + + 05 Dec 2013; Alexey Shvetsov <[email protected]> gromacs-9999.ebuild: + Make gromacs 9999 build manual again + + 05 Dec 2013; Alexey Shvetsov <[email protected]> -Manifest, + -gromacs-4.5.9999.ebuild, metadata.xml: + Drop 4.5 + + 05 Dec 2013; Alexey Shvetsov <[email protected]> gromacs-9999.ebuild: + Update live ebuild to current state + + 03 Dec 2013; Alexey Shvetsov <[email protected]> gromacs-9999.ebuild: + make mdrun target work for gmx live + + 03 Dec 2013; Alexey Shvetsov <[email protected]> gromacs-9999.ebuild: + More updates #2 to gmx live + + 03 Dec 2013; Alexey Shvetsov <[email protected]> gromacs-9999.ebuild: + More updates to gmx live + + 03 Dec 2013; Alexey Shvetsov <[email protected]> gromacs-9999.ebuild: + Slightly update live ebuild for master branch + + 01 Jun 2013; Christoph Junghans <[email protected]> gromacs-4.6.9999.ebuild: + sync with gx86 + + 05 May 2013; Christoph Junghans <[email protected]> gromacs-4.5.9999.ebuild: + sync with gx86 + +*gromacs-4.5.9999 (03 May 2013) + + 03 May 2013; Christoph Junghans <[email protected]> + +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 <[email protected]> gromacs-4.6.9999.ebuild: + nvcc flags dont needed anymore here + + 15 Mar 2013; Alexey Shvetsov <[email protected]> gromacs-4.6.9999.ebuild, + gromacs-9999.ebuild: + Fix build with cuda enabled + + 10 Mar 2013; Christoph Junghans <[email protected]> gromacs-4.6.9999.ebuild: + added cuda build fix from gx86 + + 09 Mar 2013; Christoph Junghans <[email protected]> gromacs-4.6.9999.ebuild: + fixed deps + doc build on darwin + + 06 Mar 2013; Christoph Junghans <[email protected]> -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 <[email protected]> gromacs-4.6.9999.ebuild, + gromacs-9999.ebuild, metadata.xml: + sse41 -> sse4_1 (bug #456886) + ninja has missing keywords + + 30 Jan 2013; Christoph Junghans <[email protected]> gromacs-4.6.9999.ebuild, + gromacs-9999.ebuild: + added subslot, removed gromacs-manual blocker + + 30 Jan 2013; Christoph Junghans <[email protected]> gromacs-4.6.9999.ebuild: + clean up + + 28 Jan 2013; Christoph Junghans <[email protected]> gromacs-4.6.9999.ebuild: + added app-doc/gromacs-manual in here + + 21 Jan 2013; Christoph Junghans <[email protected]> gromacs-4.6.9999.ebuild: + sci-chemistry/gromacs: use cuda.eclass + + 21 Jan 2013; Christoph Junghans <[email protected]> gromacs-4.6.9999.ebuild: + fixed sci-chemistry/gromacs[test] + + 21 Jan 2013; Alexey Shvetsov <[email protected]> gromacs-4.6.9999.ebuild: + [sci-chemistry/gromacs] Drop restrict test for 4.6 + + 21 Jan 2013; Alexey Shvetsov <[email protected]> gromacs-4.6.9999.ebuild: + [sci-chemistry/gromacs] Update 4.6 series ebuild + + 18 Jan 2013; Christoph Junghans <[email protected]> gromacs-4.6.9999.ebuild: + yet another update for git + + 18 Jan 2013; Christoph Junghans <[email protected]> gromacs-4.6.9999.ebuild: + live ebuild update + + 30 Dec 2012; Christoph Junghans <[email protected]> gromacs-4.6.9999.ebuild: + further clean up + + 29 Dec 2012; Christoph Junghans <[email protected]> gromacs-4.6.9999.ebuild: + fixed build with newer mkl + + 27 Dec 2012; Christoph Junghans <[email protected]> gromacs-4.6.9999.ebuild: + sci-chemistry/gromacs: clean up + + 26 Dec 2012; Christoph Junghans <[email protected]> gromacs-4.6.9999.ebuild: + fixed openmm suffix + + 26 Dec 2012; Christoph Junghans <[email protected]> gromacs-4.6.9999.ebuild: + fixed another typo + + 26 Dec 2012; Christoph Junghans <[email protected]> gromacs-4.6.9999.ebuild: + fixed typo + + 26 Dec 2012; Christoph Junghans <[email protected]> gromacs-4.6.9999.ebuild, + metadata.xml: + Added mkl support + + 22 Dec 2012; Christoph Junghans <[email protected]> gromacs-4.6.9999.ebuild, + gromacs-9999.ebuild, metadata.xml: + sync with gx86 + + 20 Dec 2012; Christoph Junghans <[email protected]> gromacs-4.6.9999.ebuild: + fortran is gone + + 08 Dec 2012; Christoph Junghans <[email protected]> gromacs-4.5.9999.ebuild, + gromacs-4.6.9999.ebuild, gromacs-9999.ebuild: + CMAKE_BUILD_DIR -> BUILD_DIR + + 30 Nov 2012; Christoph Junghans <[email protected]> gromacs-4.6.9999.ebuild: + sync with gx86 + + 27 Nov 2012; Christoph Junghans <[email protected]> gromacs-4.6.9999.ebuild, + metadata.xml: + added openmm support + + 19 Nov 2012; Christoph Junghans <[email protected]> gromacs-4.6.9999.ebuild: + live ebuild update + + 04 Oct 2012; Christoph Junghans <[email protected]> gromacs-4.6.9999.ebuild, + gromacs-9999.ebuild: + live ebuild update + + 03 Oct 2012; Christoph Junghans <[email protected]> gromacs-4.6.9999.ebuild, + metadata.xml: + hybrid stuff got merged + + 09 Aug 2012; Christoph Junghans <[email protected]> gromacs-4.6.9999.ebuild: + use ninja if available + + 25 Jul 2012; Christoph Junghans <[email protected]> gromacs-4.5.9999.ebuild, + gromacs-4.6.9999.ebuild, gromacs-9999.ebuild: + added ~x86-macos + + 19 Jun 2012; Alexey Shvetsov <[email protected]> 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 <[email protected]> gromacs-4.6.9999.ebuild, + metadata.xml: + add support for new hybrid kernels + + 28 Apr 2012; Christoph Junghans <[email protected]> gromacs-4.6.9999.ebuild: + [sci-chemistry/gromacs] add more mirrors + + 19 Apr 2012; Alexey Shvetsov <[email protected]> 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 <[email protected]> gromacs-4.5.9999.ebuild, + gromacs-9999.ebuild: + removed obsolete call to env-update + + 04 Mar 2012; Christoph Junghans <[email protected]> gromacs-4.6.9999.ebuild: + reworked fortran and openmp support + + 12 Feb 2012; Christoph Junghans <[email protected]> gromacs-4.6.9999.ebuild: + sci-chemistry/gromacs: clean up + + 12 Feb 2012; Christoph Junghans <[email protected]> gromacs-4.6.9999.ebuild: + fixed threads and mpi + + 05 Feb 2012; Christoph Junghans <[email protected]> gromacs-4.6.9999.ebuild: + handle new vmd detection + + 05 Feb 2012; Christoph Junghans <[email protected]> gromacs-4.6.9999.ebuild: + added openmp support + +*gromacs-4.6.9999 (28 Sep 2011) + + 28 Sep 2011; Christoph Junghans <[email protected]> +gromacs-4.6.9999.ebuild: + Added gromacs-4.6 live version + + 10 Sep 2011; Christoph Junghans <[email protected]> gromacs-4.5.9999.ebuild, + gromacs-9999.ebuild: + Migrate to the bash-completion-r1 eclass + + 18 Jul 2011; Christoph Junghans <[email protected]> gromacs-4.5.9999.ebuild, + gromacs-9999.ebuild: + sync with tree + + 25 Jun 2011; Christoph Junghans <[email protected]> gromacs-4.5.9999.ebuild, + gromacs-9999.ebuild: + migrate to git-2 + + 25 Jun 2011; Justin Lecher <[email protected]> gromacs-4.5.9999.ebuild, + gromacs-9999.ebuild, metadata.xml: + migrate from 'git' to 'git-2' + + 21 Jun 2011; Christoph Junghans <[email protected]> gromacs-4.5.9999.ebuild, + gromacs-9999.ebuild: + only USE=fkernels needs fortran + + 21 Jun 2011; Justin Lecher <[email protected]> gromacs-4.5.9999.ebuild, + gromacs-9999.ebuild: + Added fortran-2.eclass support + + 19 Jun 2011; Christoph Junghans <[email protected]> gromacs-4.5.9999.ebuild, + metadata.xml: + autotools is broken + + 10 Apr 2011; Christoph Junghans <[email protected]> -gromacs-4.0.9999.ebuild: + remove 4.0.* (EOM) + + 08 Mar 2011; Christoph Junghans <[email protected]> gromacs-4.5.9999.ebuild, + gromacs-9999.ebuild: + added fixes from 4.5.3-r4 + + 07 Mar 2011; Justin Lecher <[email protected]> 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 <[email protected]> -gromacs-4.5.3-r3.ebuild: + InCVS + +*gromacs-4.5.3-r3 (17 Feb 2011) + + 17 Feb 2011; Christoph Junghans <[email protected]> -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 <[email protected]> -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 <[email protected]> gromacs-9999.ebuild: + add back live manual + + 17 Jan 2011; Christoph Junghans <[email protected]> gromacs-9999.ebuild: + QA fixes + + 16 Dec 2010; Justin Lecher <[email protected]> gromacs-4.0.9999.ebuild, + gromacs-4.5.9999.ebuild, gromacs-9999.ebuild: + Removal of fortran.eclass, #348851 + + 25 Nov 2010; Alexey Shvetsov <[email protected]> -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 <[email protected]> + +gromacs-4.5.3.ebuild: + version bump + +*gromacs-4.5.2 (30 Oct 2010) + + 30 Oct 2010; Christoph Junghans <[email protected]> + +gromacs-4.5.2.ebuild: + Version bump + + 25 Oct 2010; Christoph Junghans <[email protected]> + gromacs-4.5.9999.ebuild, gromacs-9999.ebuild, metadata.xml: + added natural vmd support (bug #340651#c8) + + 21 Oct 2010; Christoph Junghans <[email protected]> + gromacs-4.5.9999.ebuild, metadata.xml: + added vmd use flag + + 17 Oct 2010; Christoph Junghans <[email protected]> + gromacs-4.0.7-r5.ebuild, gromacs-4.0.9999.ebuild: + rename manual in distfiles + + 16 Oct 2010; Christoph Junghans <[email protected]> + 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 <[email protected]> + +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 <[email protected]> + -gromacs-4.5_beta3.ebuild, +gromacs-4.5.1.ebuild: + version bump + +*gromacs-4.5_beta3 (11 Aug 2010) + + 11 Aug 2010; Alexey Shvetsov <[email protected]> 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 <[email protected]> + -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 <[email protected]> + +gromacs-4.5_beta1.ebuild, +gromacs-4.5.9999.ebuild, gromacs-9999.ebuild: + Version bump + + 24 Jul 2010; Alexey Shvetsov <[email protected]> gromacs-9999.ebuild: + ffamber officialy shipped with gromacs from now on + + 08 Jul 2010; Christoph Junghans <[email protected]> + gromacs-4.0.9999.ebuild, gromacs-9999.ebuild: + fix for bug #301854 + + 04 Jul 2010; Christoph Junghans <[email protected]> + 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 <[email protected]> + gromacs-4.0.9999.ebuild, gromacs-9999.ebuild: + Fixes for Bug #326331 + + 28 Jun 2010; Christoph Junghans <[email protected]> + 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 <[email protected]> + +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 <[email protected]> +gromacs-4.0.7-r2.ebuild: + Add ffamber port to gromacs + + 18 Feb 2010; Alexey Shvetsov <[email protected]> gromacs-9999.ebuild, + -files/gromacs-9999-dirent.patch: + Dropped unneded patches. They all were applied to git master + + 18 Feb 2010; Alexey Shvetsov <[email protected]> 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 <[email protected]> gromacs-9999.ebuild, + +files/gromacs-9999-as-needed.patch: + added as-needed fix + + 06 Feb 2010; Christoph Junghans <[email protected]> + -gromacs-4.0.7-r1.ebuild, -files/gromacs-4.0.9999-docdir.patch: + InCvs + + 06 Feb 2010; Christoph Junghans <[email protected]> + gromacs-4.0.9999.ebuild, gromacs-9999.ebuild: + docdir patch went upstream + + 01 Feb 2010; Christoph Junghans <[email protected]> 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 <[email protected]> + -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 <[email protected]> + gromacs-4.0.9999.ebuild, gromacs-9999.ebuild: + fixed --as-needed confusion + + 21 Jan 2010; Christoph Junghans <[email protected]> + -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 <[email protected]> + files/gromacs-4.0.5-docdir.patch: + docdir -> htmldir + + 30 Nov 2009; Christoph Junghans <[email protected]> + 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 <[email protected]> + 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 <[email protected]> + +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 <[email protected]> + +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 <[email protected]> + gromacs-4.0.4.ebuild: + Fixed some repoman errors + + 22 Feb 2009; Jeff Gardner <[email protected]> + 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 <[email protected]> -gromacs-4.0.3-r1.ebuild, + +gromacs-4.0.4.ebuild: + Version bump\! + + 20 Feb 2009; Alexey Shvetsov <[email protected]> gromacs-4.0.3-r1.ebuild: + Fix typo + +*gromacs-4.0.3-r1 (20 Feb 2009) + + 20 Feb 2009; Alexey Shvetsov <[email protected]> +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 <[email protected]> -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>[email protected]</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>
