From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from lists.gentoo.org (pigeon.gentoo.org [208.92.234.80]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (No client certificate requested) by finch.gentoo.org (Postfix) with ESMTPS id 258E4138337 for ; Fri, 31 Aug 2018 15:39:37 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id 5B575E087B; Fri, 31 Aug 2018 15:39:36 +0000 (UTC) Received: from smtp.gentoo.org (smtp.gentoo.org [140.211.166.183]) (using TLSv1.2 with cipher ECDHE-RSA-AES128-GCM-SHA256 (128/128 bits)) (No client certificate requested) by pigeon.gentoo.org (Postfix) with ESMTPS id 251CFE087B for ; Fri, 31 Aug 2018 15:39:36 +0000 (UTC) Received: from oystercatcher.gentoo.org (unknown [IPv6:2a01:4f8:202:4333:225:90ff:fed9:fc84]) (using TLSv1.2 with cipher ECDHE-RSA-AES128-GCM-SHA256 (128/128 bits)) (No client certificate requested) by smtp.gentoo.org (Postfix) with ESMTPS id C8F6A335CE9 for ; Fri, 31 Aug 2018 15:39:33 +0000 (UTC) Received: from localhost.localdomain (localhost [IPv6:::1]) by oystercatcher.gentoo.org (Postfix) with ESMTP id 910523BB for ; Fri, 31 Aug 2018 15:39:31 +0000 (UTC) From: "Matthias Maier" To: gentoo-commits@lists.gentoo.org Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=UTF-8 Reply-To: gentoo-dev@lists.gentoo.org, "Matthias Maier" Message-ID: <1535685926.7942c05fe297d82b7f4a1e81282aaa9b3bfb406a.tamiko@gentoo> Subject: [gentoo-commits] proj/sci:master commit in: sci-mathematics/petsc/files/, sci-mathematics/petsc/ X-VCS-Repository: proj/sci X-VCS-Files: sci-mathematics/petsc/files/petsc-3.5.3-disable-rpath.patch sci-mathematics/petsc/files/petsc-3.6.0-disable-rpath.patch sci-mathematics/petsc/files/petsc-3.6.0-fix_sandbox_violation.patch sci-mathematics/petsc/files/petsc-3.7.0-fix_sandbox_violation.patch sci-mathematics/petsc/petsc-3.7.7-r1.ebuild X-VCS-Directories: sci-mathematics/petsc/ sci-mathematics/petsc/files/ X-VCS-Committer: tamiko X-VCS-Committer-Name: Matthias Maier X-VCS-Revision: 7942c05fe297d82b7f4a1e81282aaa9b3bfb406a X-VCS-Branch: master Date: Fri, 31 Aug 2018 15:39:31 +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: 04ee4a4b-9cb1-469b-88c3-38fb162d03bd X-Archives-Hash: 853f51b3e749f2b7bd983ae90193c35b commit: 7942c05fe297d82b7f4a1e81282aaa9b3bfb406a Author: Matthias Maier gentoo org> AuthorDate: Fri Aug 31 03:25:26 2018 +0000 Commit: Matthias Maier gentoo org> CommitDate: Fri Aug 31 03:25:26 2018 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=7942c05f sci-mathematics/petsc: remove obsolete patches Package-Manager: Portage-2.3.48, Repoman-2.3.10 .../petsc/files/petsc-3.5.3-disable-rpath.patch | 18 -- .../petsc/files/petsc-3.6.0-disable-rpath.patch | 17 -- .../files/petsc-3.6.0-fix_sandbox_violation.patch | 15 -- .../files/petsc-3.7.0-fix_sandbox_violation.patch | 17 -- sci-mathematics/petsc/petsc-3.7.7-r1.ebuild | 205 --------------------- 5 files changed, 272 deletions(-) diff --git a/sci-mathematics/petsc/files/petsc-3.5.3-disable-rpath.patch b/sci-mathematics/petsc/files/petsc-3.5.3-disable-rpath.patch deleted file mode 100644 index 7fe3760c9..000000000 --- a/sci-mathematics/petsc/files/petsc-3.5.3-disable-rpath.patch +++ /dev/null @@ -1,18 +0,0 @@ -diff --git a/config/BuildSystem/config/setCompilers.py b/config/BuildSystem/config/setCompilers.py -index 8e0d2ee..ce53ad0 100644 ---- a/config/BuildSystem/config/setCompilers.py -+++ b/config/BuildSystem/config/setCompilers.py -@@ -1326,12 +1326,7 @@ class Configure(config.base.Configure): - for language in languages: - flag = '-L' - self.pushLanguage(language) -- # test '-R' before '-rpath' as sun compilers [c,fortran] don't give proper errors with wrong options. -- if not Configure.isDarwin(): -- testFlags = ['-Wl,-rpath,', '-R','-rpath ' , '-Wl,-R,'] -- else: -- testFlags = [] -- # test '-R' before '-Wl,-rpath' for SUN compilers [as cc on linux accepts -Wl,-rpath, but f90 & CC do not. -+ testFlags = [] - if self.isSun(self.framework.getCompiler()): - testFlags.insert(0,'-R') - for testFlag in testFlags: diff --git a/sci-mathematics/petsc/files/petsc-3.6.0-disable-rpath.patch b/sci-mathematics/petsc/files/petsc-3.6.0-disable-rpath.patch deleted file mode 100644 index 88a7db565..000000000 --- a/sci-mathematics/petsc/files/petsc-3.6.0-disable-rpath.patch +++ /dev/null @@ -1,17 +0,0 @@ -diff --git a/config/BuildSystem/config/setCompilers.py b/config/BuildSystem/config/setCompilers.py ---- a/config/BuildSystem/config/setCompilers.py -+++ b/config/BuildSystem/config/setCompilers.py -@@ -1326,12 +1326,7 @@ class Configure(config.base.Configure): - for language in languages: - flag = '-L' - self.pushLanguage(language) -- # test '-R' before '-rpath' as sun compilers [c,fortran] don't give proper errors with wrong options. -- if not Configure.isDarwin(): -- testFlags = ['-Wl,-rpath,', '-R','-rpath ' , '-Wl,-R,'] -- else: -- testFlags = ['-Wl,-rpath,'] -- # test '-R' before '-Wl,-rpath' for SUN compilers [as cc on linux accepts -Wl,-rpath, but f90 & CC do not. -+ testFlags = [] - if self.isSun(self.framework.getCompiler()): - testFlags.insert(0,'-R') - for testFlag in testFlags: diff --git a/sci-mathematics/petsc/files/petsc-3.6.0-fix_sandbox_violation.patch b/sci-mathematics/petsc/files/petsc-3.6.0-fix_sandbox_violation.patch deleted file mode 100644 index 7510631a1..000000000 --- a/sci-mathematics/petsc/files/petsc-3.6.0-fix_sandbox_violation.patch +++ /dev/null @@ -1,15 +0,0 @@ ---- config/PETSc/options/installDir.py.orig 2015-06-23 18:11:25.054911894 +0200 -+++ config/PETSc/options/installDir.py 2015-06-23 18:11:44.100289841 +0200 -@@ -38,12 +38,6 @@ - self.installSudoMessage = '' - if self.framework.argDB['prefix']: - self.dir = self.framework.argDB['prefix'] -- try: -- os.makedirs(os.path.join(self.dir,'PETScTestDirectory')) -- os.rmdir(os.path.join(self.dir,'PETScTestDirectory')) -- except: -- self.installSudoMessage = 'You do not have write permissions to the --prefix directory '+self.dir+'\nYou will be prompted for the sudo password for any external package installs' -- self.installSudo = 'sudo ' - else: - self.dir = os.path.abspath(os.path.join(self.petscdir.dir, self.arch.arch)) - self.confDir = os.path.abspath(os.path.join(self.petscdir.dir, self.arch.arch)) diff --git a/sci-mathematics/petsc/files/petsc-3.7.0-fix_sandbox_violation.patch b/sci-mathematics/petsc/files/petsc-3.7.0-fix_sandbox_violation.patch deleted file mode 100644 index 191ca18c4..000000000 --- a/sci-mathematics/petsc/files/petsc-3.7.0-fix_sandbox_violation.patch +++ /dev/null @@ -1,17 +0,0 @@ -diff --git a/config/PETSc/options/installDir.py b/config/PETSc/options/installDir.py -index 0e2567c..bf782b5 100644 ---- a/config/PETSc/options/installDir.py -+++ b/config/PETSc/options/installDir.py -@@ -38,12 +38,6 @@ class Configure(config.base.Configure): - self.installSudoMessage = '' - if self.framework.argDB['prefix']: - self.dir = os.path.abspath(os.path.expanduser(self.framework.argDB['prefix'])) -- try: -- os.makedirs(os.path.join(self.dir,'PETScTestDirectory')) -- os.rmdir(os.path.join(self.dir,'PETScTestDirectory')) -- except: -- self.installSudoMessage = 'You do not have write permissions to the --prefix directory '+self.dir+'\nYou will be prompted for the sudo password for any external package installs' -- self.installSudo = 'sudo ' - else: - self.dir = os.path.abspath(os.path.join(self.petscdir.dir, self.arch.arch)) - self.confDir = os.path.abspath(os.path.join(self.petscdir.dir, self.arch.arch)) diff --git a/sci-mathematics/petsc/petsc-3.7.7-r1.ebuild b/sci-mathematics/petsc/petsc-3.7.7-r1.ebuild deleted file mode 100644 index ddd6202e0..000000000 --- a/sci-mathematics/petsc/petsc-3.7.7-r1.ebuild +++ /dev/null @@ -1,205 +0,0 @@ -# Copyright 1999-2018 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -PYTHON_COMPAT=( python2_7 ) - -inherit eutils flag-o-matic fortran-2 python-any-r1 toolchain-funcs versionator - -MY_P="${PN}-$(replace_version_separator _ -)" - -DESCRIPTION="Portable, Extensible Toolkit for Scientific Computation" -HOMEPAGE="http://www.mcs.anl.gov/petsc/" -SRC_URI="http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/${MY_P}.tar.gz" - -LICENSE="BSD-2" -SLOT="0" -KEYWORDS="~x86 ~amd64" -IUSE="afterimage boost complex-scalars cxx debug doc fftw - fortran hdf5 hypre mpi metis mumps scotch sparse superlu threads X" - -# hypre and superlu curretly exclude each other due to missing linking to hypre -# if both are enabled -REQUIRED_USE=" - afterimage? ( X ) - complex-scalars? ( !hypre !superlu ) - hdf5? ( mpi ) - hypre? ( cxx mpi !superlu ) - mumps? ( mpi scotch ) - scotch? ( mpi ) - superlu? ( !hypre ) -" - -RDEPEND=" - virtual/blas - virtual/lapack - afterimage? ( media-libs/libafterimage ) - boost? ( dev-libs/boost ) - fftw? ( sci-libs/fftw:3.0[mpi?] ) - hdf5? ( sci-libs/hdf5[mpi?] ) - hypre? ( >=sci-libs/hypre-2.8.0b[mpi?] ) - metis? ( >=sci-libs/parmetis-4 ) - mpi? ( virtual/mpi[cxx?,fortran?] ) - mumps? ( sci-libs/mumps[mpi?] sci-libs/scalapack ) - scotch? ( sci-libs/scotch[mpi?] ) - sparse? ( sci-libs/suitesparse >=sci-libs/cholmod-1.7.0 ) - superlu? ( >=sci-libs/superlu-5 ) - X? ( x11-libs/libX11 ) -" - -DEPEND="${RDEPEND} - ${PYTHON_DEPS} - virtual/pkgconfig - dev-util/cmake -" - -# -# PETSc does not want its Makefiles to be invoked with anything higher than -# -j1. The underlying build system does automatically invoke a parallel -# build. This might not be what you want, but *hey* not your choice. -# -# V=1 enables verbose output with full compiler and linker invocation -# -MAKEOPTS="${MAKEOPTS} -j1 V=1" - -S="${WORKDIR}/${MY_P}" - -PATCHES=( - "${FILESDIR}"/${PN}-3.7.0-disable-rpath.patch \ - "${FILESDIR}"/${PN}-3.7.0-fix_sandbox_violation.patch -) - -src_prepare() { - default - - sed -i -e 's%/usr/bin/env python%/usr/bin/env python2%' configure || die -} - -# petsc uses --with-blah=1 and --with-blah=0 to en/disable options -petsc_enable() { - use "$1" && echo "--with-${2:-$1}=1" || echo "--with-${2:-$1}=0" -} -# add external library: -# petsc_with use_flag libname libdir -# petsc_with use_flag libname include linking_libs -petsc_with() { - local myuse p=${2:-${1}} - if use ${1}; then - myuse="--with-${p}=1" - if [[ $# -ge 4 ]]; then - myuse="${myuse} --with-${p}-include=${EPREFIX}${3}" - shift 3 - myuse="${myuse} --with-${p}-lib=$@" - else - myuse="${myuse} --with-${p}-dir=${EPREFIX}${3:-/usr}" - fi - else - myuse="--with-${p}=0" - fi - echo ${myuse} -} - -# select between configure options depending on use flag -petsc_select() { - use "$1" && echo "--with-$2=$3" || echo "--with-$2=$4" -} - -src_configure() { - # bug 548498 - # PETSc runs mpi processes during configure that result in a sandbox - # violation by trying to open /proc/mtrr rw. This is not easy to - # mitigate because it happens in libpciaccess.so called by libhwloc.so, - # which is used by libmpi.so. - addpredict /proc/mtrr - # if mpi is built with knem support it needs /dev/knem too - addpredict /dev/knem - - # configureMPITypes with openmpi-2* insists on accessing the scaling - # governor rw. - addpredict /sys/devices/system/cpu/ - - local mylang - local myopt - - use cxx && mylang="cxx" || mylang="c" - use debug && myopt="debug" || myopt="opt" - - # environmental variables expected by petsc during build - - export PETSC_DIR="${S}" - export PETSC_ARCH="linux-gnu-${mylang}-${myopt}" - - if use debug; then - strip-flags - filter-flags -O* - fi - - # C Support on CXX builds is enabled if possible i.e. when not using - # complex scalars (no complex type for both available at the same time) - - econf \ - scrollOutput=1 \ - FFLAGS="${FFLAGS} -fPIC" \ - CFLAGS="${CFLAGS} -fPIC" \ - CXXFLAGS="${CXXFLAGS} -fPIC" \ - LDFLAGS="${LDFLAGS}" \ - --prefix="${EPREFIX}/usr/$(get_libdir)/petsc" \ - --with-shared-libraries \ - --with-single-library \ - --with-clanguage=${mylang} \ - $(use cxx && ! use complex-scalars && echo "with-c-support=1") \ - --with-petsc-arch=${PETSC_ARCH} \ - --with-precision=double \ - --with-gnu-compilers \ - --with-blas-lapack-lib="$($(tc-getPKG_CONFIG) --libs lapack)" \ - $(petsc_enable debug debugging) \ - $(petsc_enable mpi) \ - $(petsc_select mpi cc mpicc $(tc-getCC)) \ - $(petsc_select mpi cxx mpicxx $(tc-getCXX)) \ - $(petsc_enable fortran) \ - $(use fortran && echo "$(petsc_select mpi fc mpif77 $(tc-getF77))") \ - $(petsc_enable mpi mpi-compilers) \ - $(petsc_select complex-scalars scalar-type complex real) \ - --with-windows-graphics=0 \ - --with-matlab=0 \ - --with-cmake=cmake \ - $(petsc_enable threads pthread) \ - $(petsc_with afterimage afterimage \ - /usr/include/libAfterImage -lAfterImage) \ - $(petsc_with hdf5) \ - $(petsc_with hypre hypre \ - /usr/include/hypre -lHYPRE) \ - $(petsc_with sparse suitesparse) \ - $(petsc_with superlu superlu \ - /usr/include/superlu -lsuperlu) \ - $(petsc_with X x) \ - $(petsc_with X x11) \ - $(petsc_with scotch ptscotch \ - /usr/include/scotch \ - [-lptesmumps,-lptscotch,-lptscotcherr,-lscotch,-lscotcherr]) \ - $(petsc_with mumps scalapack \ - /usr/include/scalapack -lscalapack) \ - $(petsc_with mumps mumps \ - /usr/include \ - [-lcmumps,-ldmumps,-lsmumps,-lzmumps,-lmumps_common,-lpord]) \ - --with-imagemagick=0 \ - --with-python=0 \ - $(petsc_with boost) \ - $(petsc_with fftw) -} - -src_install() { - emake DESTDIR="${D}/usr/$(get_libdir)/petsc" install - - # add PETSC_DIR to environmental variables - cat >> 99petsc <<- EOF - PETSC_DIR=${EPREFIX}/usr/$(get_libdir)/petsc - EOF - doenvd 99petsc - - if use doc ; then - dodoc docs/developers.pdf docs/manual.pdf - dohtml -r docs/*.html docs/changes docs/manualpages - fi -}