[gentoo-commits] repo/gentoo:master commit in: sci-mathematics/petsc/, sci-mathematics/petsc/files/

["Matthias Maier" <tamiko@gentoo.org>]

commit:     44c266fd90ff2510b3d5ee74ed1dcff364eebcb1
Author:     Matthias Maier <tamiko <AT> gentoo <DOT> org>
AuthorDate: Mon Aug  5 04:48:15 2019 +0000
Commit:     Matthias Maier <tamiko <AT> gentoo <DOT> org>
CommitDate: Mon Aug  5 06:51:11 2019 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=44c266fd

sci-mathematics/petsc: package migration from ::science overlay

After years in ::science it is stable enough to be hosted in ::gentoo.

Package-Manager: Portage-2.3.70, Repoman-2.3.16
Signed-off-by: Matthias Maier <tamiko <AT> gentoo.org>

 sci-mathematics/petsc/Manifest                     |   1 +
 .../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, 252 insertions(+)

diff --git a/sci-mathematics/petsc/Manifest b/sci-mathematics/petsc/Manifest
new file mode 100644
index 00000000000..3be30d7421f
--- /dev/null
+++ b/sci-mathematics/petsc/Manifest
@@ -0,0 +1 @@
+DIST petsc-3.11.3.tar.gz 33279017 BLAKE2B 870b8245e5e06d8538ea3ee1d01fa2cebade4a0bd79dfcf17d74e6201f41d21ca021e206744ece28847b434ece142a2789851b5514a8a1e3f82a8551288b695b SHA512 e545f69e87bc72950939ff3cec3e0ba225a5b3e7f1cb93b0fb6123194eb7240ac1d97ba397235d8ab872c653caab1427673124e5e1e706b796c0ae46ec1bcffa

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 00000000000..8d0d993309b
--- /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 00000000000..97f8dfed4d7
--- /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 00000000000..8c9c01d8326
--- /dev/null
+++ b/sci-mathematics/petsc/metadata.xml
@@ -0,0 +1,23 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="person">
+		<email>tamiko@gentoo.org</email>
+		<name>Matthias Maier</name>
+	</maintainer>
+	<maintainer type="project">
+		<email>sci-mathematics@gentoo.org</email>
+		<name>Gentoo Mathematics Project</name>
+	</maintainer>
+	<use>
+		<flag name="afterimage">Use Afterstep image library (media-libs/libafterimage)</flag>
+		<flag name="boost">Use boost (dev-libs/boost)</flag>
+		<flag name="hypre">Use HYPRE (sci-mathematics/hypre) and for preconditioning</flag>
+		<flag name="complex-scalars">Make scalars complex</flag>
+		<flag name="metis">Add support for metis (<pkg>sci-libs/parmetis</pkg>)</flag>
+		<flag name="sparse">Use suitesparse (sci-libs/suitesparse) including cholmod (sci-libs/cholmod) for sparse factorization</flag>
+		<flag name="superlu">Use superlu (sci-libs/superlu) for preconditioning</flag>
+		<flag name="mumps">Add support for mumps (<pkg>sci-libs/mumps</pkg>)</flag>
+		<flag name="scotch">Add support for scotch (<pkg>sci-libs/scotch</pkg>)</flag>
+	</use>
+</pkgmetadata>

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 00000000000..88fb1f58da1
--- /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
+}