From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from lists.gentoo.org (pigeon.gentoo.org [208.92.234.80]) by finch.gentoo.org (Postfix) with ESMTP id A06F11381F3 for ; Sat, 22 Dec 2012 19:46:24 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id 5420C21C020; Sat, 22 Dec 2012 19:46:14 +0000 (UTC) Received: from smtp.gentoo.org (smtp.gentoo.org [140.211.166.183]) (using TLSv1 with cipher AECDH-AES256-SHA (256/256 bits)) (No client certificate requested) by pigeon.gentoo.org (Postfix) with ESMTPS id B725821C020 for ; Sat, 22 Dec 2012 19:46:13 +0000 (UTC) Received: from hornbill.gentoo.org (hornbill.gentoo.org [94.100.119.163]) (using TLSv1 with cipher AECDH-AES256-SHA (256/256 bits)) (No client certificate requested) by smtp.gentoo.org (Postfix) with ESMTPS id 8DD4833D81A for ; Sat, 22 Dec 2012 19:46:12 +0000 (UTC) Received: from localhost.localdomain (localhost [127.0.0.1]) by hornbill.gentoo.org (Postfix) with ESMTP id 269F0E543C for ; Sat, 22 Dec 2012 19:46:11 +0000 (UTC) From: "Christoph Junghans" To: gentoo-commits@lists.gentoo.org Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=UTF-8 Reply-To: gentoo-dev@lists.gentoo.org, "Christoph Junghans" Message-ID: <1356205456.085cbb1fbc4d10a7005d7bfee2617b7cd117dec1.kleiner_otti@gentoo> Subject: [gentoo-commits] proj/sci:master commit in: sci-chemistry/gromacs/ X-VCS-Repository: proj/sci X-VCS-Files: sci-chemistry/gromacs/ChangeLog sci-chemistry/gromacs/gromacs-4.6.9999.ebuild sci-chemistry/gromacs/gromacs-9999.ebuild sci-chemistry/gromacs/metadata.xml X-VCS-Directories: sci-chemistry/gromacs/ X-VCS-Committer: kleiner_otti X-VCS-Committer-Name: Christoph Junghans X-VCS-Revision: 085cbb1fbc4d10a7005d7bfee2617b7cd117dec1 X-VCS-Branch: master Date: Sat, 22 Dec 2012 19:46:11 +0000 (UTC) Precedence: bulk List-Post: List-Help: List-Unsubscribe: List-Subscribe: List-Id: Gentoo Linux mail X-BeenThere: gentoo-commits@lists.gentoo.org X-Archives-Salt: 65545111-4810-4af2-8d06-dc47d8112675 X-Archives-Hash: df0c37cff3a934644fda53e10fd46f8e commit: 085cbb1fbc4d10a7005d7bfee2617b7cd117dec1 Author: Christoph Junghans gentoo org> AuthorDate: Sat Dec 22 19:44:16 2012 +0000 Commit: Christoph Junghans gmx de> CommitDate: Sat Dec 22 19:44:16 2012 +0000 URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=085cbb1f sync with gx86 Package-Manager: portage-2.2.0_alpha149 --- sci-chemistry/gromacs/ChangeLog | 4 ++++ sci-chemistry/gromacs/gromacs-4.6.9999.ebuild | 19 ++++++++++--------- sci-chemistry/gromacs/gromacs-9999.ebuild | 18 ++---------------- sci-chemistry/gromacs/metadata.xml | 2 +- 4 files changed, 17 insertions(+), 26 deletions(-) diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog index 2f10b59..92c7232 100644 --- a/sci-chemistry/gromacs/ChangeLog +++ b/sci-chemistry/gromacs/ChangeLog @@ -2,6 +2,10 @@ # Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 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 diff --git a/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild b/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild index 69a3d46..a41494e 100644 --- a/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild +++ b/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild @@ -23,11 +23,11 @@ if [[ $PV = *9999* ]]; then http://repo.or.cz/r/gromacs.git" EGIT_BRANCH="release-4-6" inherit git-2 - PDEPEND="doc? ( ~app-doc/gromacs-manual-${PV} )" + PDEPEND="doc? ( ~app-doc/${PN}-manual-${PV} )" else S="${WORKDIR}/${P//_/-}" SRC_URI="${SRC_URI} ftp://ftp.gromacs.org/pub/${PN}/${P//_/-}.tar.gz - doc? ( ftp://ftp.gromacs.org/pub/manual/gromacs-manual-${MANUAL_PV}.pdf )" + doc? ( ftp://ftp.gromacs.org/pub/manual/${PN}-manual-${MANUAL_PV}.pdf )" fi ACCE_IUSE="sse2 sse41 avx128fma avx256" @@ -38,8 +38,7 @@ HOMEPAGE="http://www.gromacs.org/" LICENSE="GPL-2" SLOT="0" KEYWORDS="~alpha ~amd64 ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~x86-macos" -IUSE="X blas cuda doc -double-precision +fftw gsl lapack -mpi openmm openmp +single-precision test +threads zsh-completion ${ACCE_IUSE}" +IUSE="X blas cuda doc -double-precision +fftw gsl lapack mpi +offensive openmm openmp +single-precision test +threads zsh-completion ${ACCE_IUSE}" CDEPEND=" X? ( @@ -94,7 +93,6 @@ src_configure() { #go from slowest to fastest acceleration local acce="None" - use power6 && acce="Power6" use sse2 && acce="SSE2" use sse41 && acce="SSE4.1" use avx128fma && acce="AVX_128_FMA" @@ -111,6 +109,7 @@ src_configure() { $(cmake-utils_use gsl GMX_GSL) $(cmake-utils_use lapack GMX_EXTERNAL_LAPACK) $(cmake-utils_use openmp GMX_OPENMP) + $(cmake-utils_use !offensive GMX_NO_QUOTES) -DGMX_DEFAULT_SUFFIX=off -DGMX_ACCELERATION="$acce" -DGMXLIB="$(get_libdir)" @@ -208,7 +207,7 @@ src_install() { ls -1 "${ED}"/usr/bin | sed -e '/_d$/d' > "${T}"/programs.list doins "${T}"/programs.list else - dodoc "${DISTDIR}/gromacs-manual-${MANUAL_PV}.pdf" + dodoc "${DISTDIR}/${PN}-manual-${MANUAL_PV}.pdf" fi fi rm -rf "${ED}usr/share/gromacs/html/" @@ -219,9 +218,11 @@ pkg_postinst() { einfo "Please read and cite:" einfo "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). " einfo "http://dx.doi.org/10.1021/ct700301q" - einfo - einfo $(g_luck) - einfo "For more Gromacs cool quotes (gcq) add g_luck to your .bashrc" + if use offensive; then + einfo + einfo $(g_luck) + einfo "For more Gromacs cool quotes (gcq) add g_luck to your .bashrc" + fi einfo elog "Gromacs can use sci-chemistry/vmd to read additional file formats" } diff --git a/sci-chemistry/gromacs/gromacs-9999.ebuild b/sci-chemistry/gromacs/gromacs-9999.ebuild index 55770d0..56187b0 100644 --- a/sci-chemistry/gromacs/gromacs-9999.ebuild +++ b/sci-chemistry/gromacs/gromacs-9999.ebuild @@ -9,12 +9,12 @@ TEST_PV="4.0.4" EGIT_REPO_URI="git://git.gromacs.org/gromacs http://repo.or.cz/r/gromacs.git" EGIT_BRANCH="master" -ACCE_IUSE="fkernels power6 sse2 sse41 avx128fma avx256" +ACCE_IUSE="sse2 sse41 avx128fma avx256" #to find external blas/lapack CMAKE_MIN_VERSION="2.8.5-r2" -inherit bash-completion-r1 cmake-utils eutils fortran-2 git-2 multilib toolchain-funcs +inherit bash-completion-r1 cmake-utils eutils git-2 multilib toolchain-funcs DESCRIPTION="The ultimate molecular dynamics simulation package" HOMEPAGE="http://www.gromacs.org/" @@ -25,7 +25,6 @@ SLOT="0" KEYWORDS="~alpha ~amd64 ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux" IUSE="X blas doc -double-precision +fftw gsl lapack mpi +single-precision test +threads xml zsh-completion ${ACCE_IUSE}" -REQUIRED_USE="fkernels? ( !threads )" CDEPEND=" X? ( @@ -35,7 +34,6 @@ CDEPEND=" ) blas? ( virtual/blas ) fftw? ( sci-libs/fftw:3.0 ) - fkernels? ( virtual/fortran ) gsl? ( sci-libs/gsl ) lapack? ( virtual/lapack ) mpi? ( virtual/mpi ) @@ -47,10 +45,6 @@ PDEPEND="doc? ( ~app-doc/gromacs-manual-${PV} )" RESTRICT="test" -pkg_setup() { - use fkernels && fortran-2_pkg_setup -} - src_prepare() { #add user patches from /etc/portage/patches/sci-chemistry/gromacs epatch_user @@ -95,12 +89,6 @@ src_configure() { #note for gentoo-PREFIX on apple: use --enable-apple-64bit - #note for gentoo-PREFIX on aix, fortran (xlf) is still much faster - if use fkernels; then - ewarn "Fortran kernels are usually not faster than C kernels and assembly" - ewarn "I hope, you know what are you doing..." - fi - if use double-precision ; then #from gromacs manual elog @@ -124,8 +112,6 @@ src_configure() { #go from slowest to fasterest acceleration local acce="None" - use fkernels && use !threads && acce="Fortran" - use power6 && acce="Power6" use sse2 && acce="SSE2" use sse41 && acce="SSE4.1" use avx128fma && acce="AVX_128_FMA" diff --git a/sci-chemistry/gromacs/metadata.xml b/sci-chemistry/gromacs/metadata.xml index 41931c0..24ddf42 100644 --- a/sci-chemistry/gromacs/metadata.xml +++ b/sci-chemistry/gromacs/metadata.xml @@ -15,7 +15,7 @@ Enable sse4.1 acceleration Enable 128bit avx with fma (e.g. AMD BullDozer) Enable 256bit avx (e.g. Intel Sandy Bridge) + Enable gromacs partly offensive quotes Add acceleration through sci-libs/openmm - Enable Power6 optimizations