From fc637fb28da700da71ec2064d65ca5a7a31b9c6c Mon Sep 17 00:00:00 2001 From: V3n3RiX Date: Sun, 18 Aug 2019 18:16:17 +0100 Subject: gentoo resync : 18.08.2019 --- sci-mathematics/petsc/Manifest | 5 + .../petsc/files/petsc-3.7.0-disable-rpath.patch | 18 ++ .../files/petsc-3.9.0-fix_sandbox_violation.patch | 17 ++ sci-mathematics/petsc/metadata.xml | 23 +++ sci-mathematics/petsc/petsc-3.11.3.ebuild | 193 +++++++++++++++++++++ 5 files changed, 256 insertions(+) create mode 100644 sci-mathematics/petsc/Manifest create mode 100644 sci-mathematics/petsc/files/petsc-3.7.0-disable-rpath.patch create mode 100644 sci-mathematics/petsc/files/petsc-3.9.0-fix_sandbox_violation.patch create mode 100644 sci-mathematics/petsc/metadata.xml create mode 100644 sci-mathematics/petsc/petsc-3.11.3.ebuild (limited to 'sci-mathematics/petsc') diff --git a/sci-mathematics/petsc/Manifest b/sci-mathematics/petsc/Manifest new file mode 100644 index 000000000000..a44ec7dfeb4e --- /dev/null +++ b/sci-mathematics/petsc/Manifest @@ -0,0 +1,5 @@ +AUX petsc-3.7.0-disable-rpath.patch 909 BLAKE2B b9b6064886d6c10b382982778398cb7fa254242e5ed0dfb86dd4cd6c094dc51eecfd625f6de5c2779bfc5b3beda351ac44145c69ac246d814a728d7565da8086 SHA512 8241c593d903615feb175bfe8213792ace739a18ac5f4c1d1890155ccea7de30b5ef5d97e2fa3b043e9a1e520e022abedeb038d0b4db671f89045e04edc65a68 +AUX petsc-3.9.0-fix_sandbox_violation.patch 916 BLAKE2B f58ba79c3082d253c9a95b0c9ce0bcc6373fa91b4155fac5a6d4688c21805d938f5c04a939ab9d8b810732e79699e7156bd4916717b9ab0217ab257ca64bb92e SHA512 cde22a54f0f6c73cfa326ea0c0026878b3099381ec703154bb8d2746a502ffc9ae82e65082f63579abce5b3d3f89bccf0cbc7db7d031e642c5c02ca8281e616c +DIST petsc-3.11.3.tar.gz 33279017 BLAKE2B 870b8245e5e06d8538ea3ee1d01fa2cebade4a0bd79dfcf17d74e6201f41d21ca021e206744ece28847b434ece142a2789851b5514a8a1e3f82a8551288b695b SHA512 e545f69e87bc72950939ff3cec3e0ba225a5b3e7f1cb93b0fb6123194eb7240ac1d97ba397235d8ab872c653caab1427673124e5e1e706b796c0ae46ec1bcffa +EBUILD petsc-3.11.3.ebuild 5339 BLAKE2B e864ef1479ee6bfc878e8ea5ba294d7987b0a810555d51ef2cfa3aa96fa07e3de4b2acbbea80c2bd80d0aaf2618636d18f916e2ccb990adb05a0f68bb7968039 SHA512 1e1ceacac2c4c03f1cb634f7695180832eb7042e21089df0f76a0fee2ae3a4c8935ed9286497f2ea8268a5d4b4179a9e535fadd4b61ab4982d8104843d3f2037 +MISC metadata.xml 1131 BLAKE2B db15101bb24374026158a0b45bab1b4b38ab6869bb13fc1df48eef96ca003cea0a8b9118033a3d53c735cefd5ca7563e074d458aee32e038a39e68a6a91b7364 SHA512 19cf1bcddd8bc1378bf85c47b090dd684474f29896c1877bfbeb53a24b1112ed4bb6e823cbc830ee40c886727c6c90d0852081488b1df63f8b4f071d3d453630 diff --git a/sci-mathematics/petsc/files/petsc-3.7.0-disable-rpath.patch b/sci-mathematics/petsc/files/petsc-3.7.0-disable-rpath.patch new file mode 100644 index 000000000000..8d0d993309bc --- /dev/null +++ b/sci-mathematics/petsc/files/petsc-3.7.0-disable-rpath.patch @@ -0,0 +1,18 @@ +diff --git a/config/BuildSystem/config/setCompilers.py b/config/BuildSystem/config/setCompilers.py +index 219a35b..ad2ed8c 100644 +--- a/config/BuildSystem/config/setCompilers.py ++++ b/config/BuildSystem/config/setCompilers.py +@@ -1385,12 +1385,7 @@ 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(self.log): +- 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(), self.log): + testFlags.insert(0,'-R') + for testFlag in testFlags: diff --git a/sci-mathematics/petsc/files/petsc-3.9.0-fix_sandbox_violation.patch b/sci-mathematics/petsc/files/petsc-3.9.0-fix_sandbox_violation.patch new file mode 100644 index 000000000000..97f8dfed4d71 --- /dev/null +++ b/sci-mathematics/petsc/files/petsc-3.9.0-fix_sandbox_violation.patch @@ -0,0 +1,17 @@ +diff --git a/config/PETSc/options/installDir.py b/config/PETSc/options/installDir.py +index 92f190d..047c85b 100644 +--- a/config/PETSc/options/installDir.py ++++ b/config/PETSc/options/installDir.py +@@ -41,12 +41,6 @@ class Configure(config.base.Configure): + self.dir = os.path.abspath(os.path.expanduser(self.framework.argDB['prefix'])) + self.petscDir = self.dir + self.petscArch = '' +- 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.petscDir = self.petscdir.dir diff --git a/sci-mathematics/petsc/metadata.xml b/sci-mathematics/petsc/metadata.xml new file mode 100644 index 000000000000..8c9c01d83268 --- /dev/null +++ b/sci-mathematics/petsc/metadata.xml @@ -0,0 +1,23 @@ + + + + + tamiko@gentoo.org + Matthias Maier + + + sci-mathematics@gentoo.org + Gentoo Mathematics Project + + + Use Afterstep image library (media-libs/libafterimage) + Use boost (dev-libs/boost) + Use HYPRE (sci-mathematics/hypre) and for preconditioning + Make scalars complex + Add support for metis (sci-libs/parmetis) + Use suitesparse (sci-libs/suitesparse) including cholmod (sci-libs/cholmod) for sparse factorization + Use superlu (sci-libs/superlu) for preconditioning + Add support for mumps (sci-libs/mumps) + Add support for scotch (sci-libs/scotch) + + diff --git a/sci-mathematics/petsc/petsc-3.11.3.ebuild b/sci-mathematics/petsc/petsc-3.11.3.ebuild new file mode 100644 index 000000000000..88fb1f58da1c --- /dev/null +++ b/sci-mathematics/petsc/petsc-3.11.3.ebuild @@ -0,0 +1,193 @@ +# Copyright 1999-2019 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=7 + +PYTHON_COMPAT=( python2_7 ) + +inherit flag-o-matic fortran-2 python-any-r1 toolchain-funcs + +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/${P}.tar.gz" + +LICENSE="BSD-2" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="afterimage boost complex-scalars cxx debug doc fftw + fortran hdf5 hypre mpi metis mumps scotch sparse superlu threads X" + +# hypre and superlu curretly exclude each other due to missing linking to hypre +# if both are enabled +REQUIRED_USE=" + afterimage? ( X ) + complex-scalars? ( !hypre !superlu ) + hdf5? ( mpi ) + hypre? ( cxx mpi !superlu ) + mumps? ( mpi scotch ) + scotch? ( mpi ) + superlu? ( !hypre ) +" + +RDEPEND=" + virtual/blas + virtual/lapack + afterimage? ( media-libs/libafterimage ) + boost? ( dev-libs/boost ) + fftw? ( sci-libs/fftw:3.0[mpi?] ) + hdf5? ( sci-libs/hdf5[mpi?] ) + hypre? ( >=sci-libs/hypre-2.8.0b[mpi?] ) + metis? ( >=sci-libs/parmetis-4 ) + mpi? ( virtual/mpi[cxx?,fortran?] ) + mumps? ( sci-libs/mumps[mpi?] sci-libs/scalapack ) + scotch? ( sci-libs/scotch[mpi?] ) + sparse? ( sci-libs/suitesparse >=sci-libs/cholmod-1.7.0 ) + superlu? ( >=sci-libs/superlu-5 ) + X? ( x11-libs/libX11 ) +" + +DEPEND="${RDEPEND} + ${PYTHON_DEPS} + virtual/pkgconfig + dev-util/cmake +" + +PATCHES=( + "${FILESDIR}"/${PN}-3.7.0-disable-rpath.patch \ + "${FILESDIR}"/${PN}-3.9.0-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 blas 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:BOOL=1 \ + $(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) \ + $(petsc_with fftw) +} + +src_install() { + emake DESTDIR="${ED}" install + + # add PETSC_DIR to environmental variables + cat >> 99petsc <<- EOF + PETSC_DIR=${EPREFIX}/usr/$(get_libdir)/petsc + LDPATH=${EPREFIX}/usr/$(get_libdir)/petsc/lib + EOF + doenvd 99petsc + + if use doc ; then + docinto html + dodoc -r docs/*.html docs/changes docs/manualpages + fi +} -- cgit v1.2.3