From bcd6bd1f63ce2e5ffdf99579dfa101b60f73256f Mon Sep 17 00:00:00 2001 From: Alexey Shvetsov Date: Tue, 14 Jan 2020 14:40:46 +0300 Subject: [sci-chemistry/gromacs] drop old version Package-Manager: Portage-2.3.64, Repoman-2.3.12 Signed-off-by: Alexey Shvetsov --- sci-chemistry/gromacs/ChangeLog | 532 ------------------------------ sci-chemistry/gromacs/gromacs-9999.ebuild | 285 ---------------- sci-chemistry/gromacs/metadata.xml | 22 -- 3 files changed, 839 deletions(-) delete mode 100644 sci-chemistry/gromacs/ChangeLog delete mode 100644 sci-chemistry/gromacs/gromacs-9999.ebuild delete mode 100644 sci-chemistry/gromacs/metadata.xml diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog deleted file mode 100644 index da2baae..0000000 --- a/sci-chemistry/gromacs/ChangeLog +++ /dev/null @@ -1,532 +0,0 @@ -# ChangeLog for sci-chemistry/gromacs -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 -# $Header: $ - - 21 Dec 2014; Christoph Junghans gromacs-5.0.9999.ebuild: - sync with gx86 - - 25 Nov 2014; Christoph Junghans 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 gromacs-9999.ebuild: - Fix doc install - - 07 Sep 2014; Christoph Junghans gromacs-5.0.9999.ebuild: - fix completion install - - 06 Sep 2014; Christoph Junghans gromacs-5.0.9999.ebuild: - sync with gx86 - - 04 Sep 2014; Christoph Junghans gromacs-5.0.9999.ebuild: - sync with gx86 - - 03 Sep 2014; Christoph Junghans -Manifest, - -gromacs-5.0_rc1.ebuild: - drop old - - 03 Sep 2014; Christoph Junghans gromacs-5.0.9999.ebuild: - live update - - 07 Jul 2014; Christoph Junghans gromacs-4.6.9999.ebuild, - gromacs-5.0.9999.ebuild: - sync with gx86, fix FEATURES=test - - 26 Jun 2014; Christoph Junghans gromacs-5.0.9999.ebuild: - live ebuild update - - 14 Apr 2014; Christoph Junghans 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 +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 gromacs-9999.ebuild: - fix multilib-strict - - 20 Feb 2014; Alexey Shvetsov gromacs-9999.ebuild: - Update gromacs 5.0 - - 16 Feb 2014; Christoph Junghans gromacs-4.6.9999.ebuild: - git-r3 too smart, migrate back to git-2 - - 05 Feb 2014; Alexey Shvetsov gromacs-9999.ebuild: - Bash completion changes are comming =D - - 05 Feb 2014; Alexey Shvetsov gromacs-9999.ebuild: - Revert back to git-2 since git-r2 gives problems - - 25 Jan 2014; Justin Lecher gromacs-4.6.9999.ebuild, - gromacs-5.0_beta1.ebuild, gromacs-9999.ebuild: - Add missing dep for USE=doc - - 06 Jan 2014; Justin Lecher 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 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 gromacs-5.0_beta1.ebuild, - metadata.xml: - Fix multilib-strict problems - -*gromacs-5.0_beta1 (06 Dec 2013) - - 06 Dec 2013; Alexey Shvetsov +gromacs-5.0_beta1.ebuild, - gromacs-9999.ebuild: - Add 5.0-beta1 release - - 05 Dec 2013; Alexey Shvetsov gromacs-9999.ebuild: - Make gromacs 9999 build manual again - - 05 Dec 2013; Alexey Shvetsov -Manifest, - -gromacs-4.5.9999.ebuild, metadata.xml: - Drop 4.5 - - 05 Dec 2013; Alexey Shvetsov gromacs-9999.ebuild: - Update live ebuild to current state - - 03 Dec 2013; Alexey Shvetsov gromacs-9999.ebuild: - make mdrun target work for gmx live - - 03 Dec 2013; Alexey Shvetsov gromacs-9999.ebuild: - More updates #2 to gmx live - - 03 Dec 2013; Alexey Shvetsov gromacs-9999.ebuild: - More updates to gmx live - - 03 Dec 2013; Alexey Shvetsov gromacs-9999.ebuild: - Slightly update live ebuild for master branch - - 01 Jun 2013; Christoph Junghans gromacs-4.6.9999.ebuild: - sync with gx86 - - 05 May 2013; Christoph Junghans gromacs-4.5.9999.ebuild: - sync with gx86 - -*gromacs-4.5.9999 (03 May 2013) - - 03 May 2013; Christoph Junghans - +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 gromacs-4.6.9999.ebuild: - nvcc flags dont needed anymore here - - 15 Mar 2013; Alexey Shvetsov gromacs-4.6.9999.ebuild, - gromacs-9999.ebuild: - Fix build with cuda enabled - - 10 Mar 2013; Christoph Junghans gromacs-4.6.9999.ebuild: - added cuda build fix from gx86 - - 09 Mar 2013; Christoph Junghans gromacs-4.6.9999.ebuild: - fixed deps + doc build on darwin - - 06 Mar 2013; Christoph Junghans -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 gromacs-4.6.9999.ebuild, - gromacs-9999.ebuild, metadata.xml: - sse41 -> sse4_1 (bug #456886) + ninja has missing keywords - - 30 Jan 2013; Christoph Junghans gromacs-4.6.9999.ebuild, - gromacs-9999.ebuild: - added subslot, removed gromacs-manual blocker - - 30 Jan 2013; Christoph Junghans gromacs-4.6.9999.ebuild: - clean up - - 28 Jan 2013; Christoph Junghans gromacs-4.6.9999.ebuild: - added app-doc/gromacs-manual in here - - 21 Jan 2013; Christoph Junghans gromacs-4.6.9999.ebuild: - sci-chemistry/gromacs: use cuda.eclass - - 21 Jan 2013; Christoph Junghans gromacs-4.6.9999.ebuild: - fixed sci-chemistry/gromacs[test] - - 21 Jan 2013; Alexey Shvetsov gromacs-4.6.9999.ebuild: - [sci-chemistry/gromacs] Drop restrict test for 4.6 - - 21 Jan 2013; Alexey Shvetsov gromacs-4.6.9999.ebuild: - [sci-chemistry/gromacs] Update 4.6 series ebuild - - 18 Jan 2013; Christoph Junghans gromacs-4.6.9999.ebuild: - yet another update for git - - 18 Jan 2013; Christoph Junghans gromacs-4.6.9999.ebuild: - live ebuild update - - 30 Dec 2012; Christoph Junghans gromacs-4.6.9999.ebuild: - further clean up - - 29 Dec 2012; Christoph Junghans gromacs-4.6.9999.ebuild: - fixed build with newer mkl - - 27 Dec 2012; Christoph Junghans gromacs-4.6.9999.ebuild: - sci-chemistry/gromacs: clean up - - 26 Dec 2012; Christoph Junghans gromacs-4.6.9999.ebuild: - fixed openmm suffix - - 26 Dec 2012; Christoph Junghans gromacs-4.6.9999.ebuild: - fixed another typo - - 26 Dec 2012; Christoph Junghans gromacs-4.6.9999.ebuild: - fixed typo - - 26 Dec 2012; Christoph Junghans gromacs-4.6.9999.ebuild, - metadata.xml: - Added mkl support - - 22 Dec 2012; Christoph Junghans gromacs-4.6.9999.ebuild, - gromacs-9999.ebuild, metadata.xml: - sync with gx86 - - 20 Dec 2012; Christoph Junghans gromacs-4.6.9999.ebuild: - fortran is gone - - 08 Dec 2012; Christoph Junghans gromacs-4.5.9999.ebuild, - gromacs-4.6.9999.ebuild, gromacs-9999.ebuild: - CMAKE_BUILD_DIR -> BUILD_DIR - - 30 Nov 2012; Christoph Junghans gromacs-4.6.9999.ebuild: - sync with gx86 - - 27 Nov 2012; Christoph Junghans gromacs-4.6.9999.ebuild, - metadata.xml: - added openmm support - - 19 Nov 2012; Christoph Junghans gromacs-4.6.9999.ebuild: - live ebuild update - - 04 Oct 2012; Christoph Junghans gromacs-4.6.9999.ebuild, - gromacs-9999.ebuild: - live ebuild update - - 03 Oct 2012; Christoph Junghans gromacs-4.6.9999.ebuild, - metadata.xml: - hybrid stuff got merged - - 09 Aug 2012; Christoph Junghans gromacs-4.6.9999.ebuild: - use ninja if available - - 25 Jul 2012; Christoph Junghans gromacs-4.5.9999.ebuild, - gromacs-4.6.9999.ebuild, gromacs-9999.ebuild: - added ~x86-macos - - 19 Jun 2012; Alexey Shvetsov 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 gromacs-4.6.9999.ebuild, - metadata.xml: - add support for new hybrid kernels - - 28 Apr 2012; Christoph Junghans gromacs-4.6.9999.ebuild: - [sci-chemistry/gromacs] add more mirrors - - 19 Apr 2012; Alexey Shvetsov 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 gromacs-4.5.9999.ebuild, - gromacs-9999.ebuild: - removed obsolete call to env-update - - 04 Mar 2012; Christoph Junghans gromacs-4.6.9999.ebuild: - reworked fortran and openmp support - - 12 Feb 2012; Christoph Junghans gromacs-4.6.9999.ebuild: - sci-chemistry/gromacs: clean up - - 12 Feb 2012; Christoph Junghans gromacs-4.6.9999.ebuild: - fixed threads and mpi - - 05 Feb 2012; Christoph Junghans gromacs-4.6.9999.ebuild: - handle new vmd detection - - 05 Feb 2012; Christoph Junghans gromacs-4.6.9999.ebuild: - added openmp support - -*gromacs-4.6.9999 (28 Sep 2011) - - 28 Sep 2011; Christoph Junghans +gromacs-4.6.9999.ebuild: - Added gromacs-4.6 live version - - 10 Sep 2011; Christoph Junghans gromacs-4.5.9999.ebuild, - gromacs-9999.ebuild: - Migrate to the bash-completion-r1 eclass - - 18 Jul 2011; Christoph Junghans gromacs-4.5.9999.ebuild, - gromacs-9999.ebuild: - sync with tree - - 25 Jun 2011; Christoph Junghans gromacs-4.5.9999.ebuild, - gromacs-9999.ebuild: - migrate to git-2 - - 25 Jun 2011; Justin Lecher gromacs-4.5.9999.ebuild, - gromacs-9999.ebuild, metadata.xml: - migrate from 'git' to 'git-2' - - 21 Jun 2011; Christoph Junghans gromacs-4.5.9999.ebuild, - gromacs-9999.ebuild: - only USE=fkernels needs fortran - - 21 Jun 2011; Justin Lecher gromacs-4.5.9999.ebuild, - gromacs-9999.ebuild: - Added fortran-2.eclass support - - 19 Jun 2011; Christoph Junghans gromacs-4.5.9999.ebuild, - metadata.xml: - autotools is broken - - 10 Apr 2011; Christoph Junghans -gromacs-4.0.9999.ebuild: - remove 4.0.* (EOM) - - 08 Mar 2011; Christoph Junghans gromacs-4.5.9999.ebuild, - gromacs-9999.ebuild: - added fixes from 4.5.3-r4 - - 07 Mar 2011; Justin Lecher 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 -gromacs-4.5.3-r3.ebuild: - InCVS - -*gromacs-4.5.3-r3 (17 Feb 2011) - - 17 Feb 2011; Christoph Junghans -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 -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 gromacs-9999.ebuild: - add back live manual - - 17 Jan 2011; Christoph Junghans gromacs-9999.ebuild: - QA fixes - - 16 Dec 2010; Justin Lecher gromacs-4.0.9999.ebuild, - gromacs-4.5.9999.ebuild, gromacs-9999.ebuild: - Removal of fortran.eclass, #348851 - - 25 Nov 2010; Alexey Shvetsov -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 - +gromacs-4.5.3.ebuild: - version bump - -*gromacs-4.5.2 (30 Oct 2010) - - 30 Oct 2010; Christoph Junghans - +gromacs-4.5.2.ebuild: - Version bump - - 25 Oct 2010; Christoph Junghans - gromacs-4.5.9999.ebuild, gromacs-9999.ebuild, metadata.xml: - added natural vmd support (bug #340651#c8) - - 21 Oct 2010; Christoph Junghans - gromacs-4.5.9999.ebuild, metadata.xml: - added vmd use flag - - 17 Oct 2010; Christoph Junghans - gromacs-4.0.7-r5.ebuild, gromacs-4.0.9999.ebuild: - rename manual in distfiles - - 16 Oct 2010; Christoph Junghans - 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 - +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 - -gromacs-4.5_beta3.ebuild, +gromacs-4.5.1.ebuild: - version bump - -*gromacs-4.5_beta3 (11 Aug 2010) - - 11 Aug 2010; Alexey Shvetsov 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 - -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 - +gromacs-4.5_beta1.ebuild, +gromacs-4.5.9999.ebuild, gromacs-9999.ebuild: - Version bump - - 24 Jul 2010; Alexey Shvetsov gromacs-9999.ebuild: - ffamber officialy shipped with gromacs from now on - - 08 Jul 2010; Christoph Junghans - gromacs-4.0.9999.ebuild, gromacs-9999.ebuild: - fix for bug #301854 - - 04 Jul 2010; Christoph Junghans - 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 - gromacs-4.0.9999.ebuild, gromacs-9999.ebuild: - Fixes for Bug #326331 - - 28 Jun 2010; Christoph Junghans - 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 - +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 +gromacs-4.0.7-r2.ebuild: - Add ffamber port to gromacs - - 18 Feb 2010; Alexey Shvetsov gromacs-9999.ebuild, - -files/gromacs-9999-dirent.patch: - Dropped unneded patches. They all were applied to git master - - 18 Feb 2010; Alexey Shvetsov 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 gromacs-9999.ebuild, - +files/gromacs-9999-as-needed.patch: - added as-needed fix - - 06 Feb 2010; Christoph Junghans - -gromacs-4.0.7-r1.ebuild, -files/gromacs-4.0.9999-docdir.patch: - InCvs - - 06 Feb 2010; Christoph Junghans - gromacs-4.0.9999.ebuild, gromacs-9999.ebuild: - docdir patch went upstream - - 01 Feb 2010; Christoph Junghans 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 - -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 - gromacs-4.0.9999.ebuild, gromacs-9999.ebuild: - fixed --as-needed confusion - - 21 Jan 2010; Christoph Junghans - -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 - files/gromacs-4.0.5-docdir.patch: - docdir -> htmldir - - 30 Nov 2009; Christoph Junghans - 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 - 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 - +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 - +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 - gromacs-4.0.4.ebuild: - Fixed some repoman errors - - 22 Feb 2009; Jeff Gardner - 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 -gromacs-4.0.3-r1.ebuild, - +gromacs-4.0.4.ebuild: - Version bump\! - - 20 Feb 2009; Alexey Shvetsov gromacs-4.0.3-r1.ebuild: - Fix typo - -*gromacs-4.0.3-r1 (20 Feb 2009) - - 20 Feb 2009; Alexey Shvetsov +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 -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 deleted file mode 100644 index acf329d..0000000 --- a/sci-chemistry/gromacs/gromacs-9999.ebuild +++ /dev/null @@ -1,285 +0,0 @@ -# Copyright 1999-2018 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -CMAKE_MAKEFILE_GENERATOR="ninja" - -PYTHON_COMPAT=( python{3_2,3_3,3_4,3_5} ) - -inherit bash-completion-r1 cmake-utils cuda eutils multilib python-single-r1 readme.gentoo-r1 toolchain-funcs - -if [[ $PV = *9999* ]]; then - 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" - [[ $PV = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="release-${PV:0:1}-${PV:2:1}" - inherit git-r3 - KEYWORDS="" -else - SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz - test? ( http://gerrit.gromacs.org/download/regressiontests-${PV}.tar.gz )" - KEYWORDS="~alpha ~amd64 ~arm ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos" -fi - -ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2" - -DESCRIPTION="The ultimate molecular dynamics simulation package" -HOMEPAGE="http://www.gromacs.org/" - -# see COPYING for details -# http://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING -# base, vmd plugins, fftpack from numpy, blas/lapck from netlib, memtestG80 library, mpi_thread lib -LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )" -SLOT="0/${PV}" -IUSE="X blas boost cuda +doc -double-precision +fftw lapack mkl mpi +offensive openmp python +single-precision test +threads +tng ${ACCE_IUSE}" - -CDEPEND=" - X? ( - x11-libs/libX11 - x11-libs/libSM - x11-libs/libICE - ) - blas? ( virtual/blas ) - boost? ( >=dev-libs/boost-1.55 ) - cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 ) - fftw? ( sci-libs/fftw:3.0 ) - lapack? ( virtual/lapack ) - mkl? ( sci-libs/mkl ) - mpi? ( virtual/mpi ) - python? ( - dev-python/numpy[${PYTHON_USEDEP}] - dev-python/sip[${PYTHON_USEDEP}] - ) - " -DEPEND="${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 [[ ${PV} != *9999 ]]; then - default - else - if use python; then - EGIT_REPO_URI="git://biod.pnpi.spb.ru/alexxy/gromacs.git" - EGIT_BRANCH="pygromacs_v2" - fi - git-r3_src_unpack - if use test; then - EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \ - EGIT_BRANCH="${EGIT_BRANCH}" \ - EGIT_CHECKOUT_DIR="${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 cpu_flags_x86_sse2 && acce="SSE2" - use cpu_flags_x86_sse4_1 && acce="SSE4.1" - use cpu_flags_x86_fma4 && acce="AVX_128_FMA" - use cpu_flags_x86_avx && acce="AVX_256" - use cpu_flags_x86_avx2 && 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 python GMX_PYTHON_BINDINGS) - $(cmake-utils_use tng GMX_USE_TNG) - $(cmake-utils_use doc GMX_BUILD_MANUAL) - -DGMX_DEFAULT_SUFFIX=off - -DGMX_SIMD="$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 - [[ ${CHOST} != *-darwin* ]] || \ - sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die - 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 - [[ ${CHOST} != *-darwin* ]] || \ - sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}_mpi/gentoo_rules.cmake" || die - done -} - -src_compile() { - for x in ${GMX_DIRS}; do - einfo "Compiling for ${x} precision" - BUILD_DIR="${WORKDIR}/${P}_${x}"\ - cmake-utils_src_compile - # not 100% necessary for rel ebuilds as available from website - 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-${PV}.pdf" - fi - use mpi || continue - BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \ - cmake-utils_src_install - done - - if use tng; then - insinto /usr/include/tng - doins src/external/tng_io/include/tng/*h - fi - # drop unneeded stuff - rm "${ED}"usr/bin/GMXRC* || die - for x in "${ED}"usr/bin/gmx-completion-*.bash ; do - local n=${x##*/gmx-completion-} - n="${n%.bash}" - cat "${ED}"usr/bin/gmx-completion.bash "$x" > "${T}/${n}" || die - newbashcomp "${T}"/"${n}" "${n}" - done - rm "${ED}"usr/bin/gmx-completion*.bash || die - 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 deleted file mode 100644 index 753027d..0000000 --- a/sci-chemistry/gromacs/metadata.xml +++ /dev/null @@ -1,22 +0,0 @@ - - - - - ottxor@gentoo.org - Christoph Junghans - - - sci-chemistry@gentoo.org - Gentoo Chemistry Project - - - Enable cuda non-bonded kernels - More precise calculations at the expense of speed - Single precision version of gromacs (default) - Enable external boost library - Enable new trajectory format - tng - - Enable gromacs partly offensive quotes - Use sci-libs/mkl for fft, blas, lapack routines - - -- cgit v1.2.3-65-gdbad