Merge pull request #119 from tamiko/bump_petsc

Bump petsc to 3.4.2, include support for scotch and mumps

3 files changed, 256 insertions, 0 deletions

diff --git a/sci-mathematics/petsc/Manifest b/sci-mathematics/petsc/Manifest
index caacbd2ad..c60a5138c 100644
--- a/sci-mathematics/petsc/Manifest
+++ b/sci-mathematics/petsc/Manifest
@@ -1 +1,2 @@
 DIST petsc-3.3-p5.tar.gz 18062672 SHA256 a4a146c469d76a351ca66384e10a65bfe7bcbfc2019dfea69a5340320a9f4591 SHA512 d3347d9bd48d327e27f6e27a9c83e75fcb49ca2874e263292204efafb5d651158012b4644016dcf2b580469bccb92befaaf52123d83d216a20d4182c0788dbea WHIRLPOOL 6c8488f2a13fcb38779e95ab93e3a87737ea8d9858076d41af82fcb26a5df5383cd7a68be3e067e6b119b6c05c556f80377969d618c7cb29a542578e5ccf8eb0
+DIST petsc-3.4.2.tar.gz 18658689 SHA256 f13b0dc978fe0dcc1df032f8142a2fd345217f02b9967936d9aac26ce4b2b52e SHA512 f839e4cfadbee720e53993eb8de74a2d82bfe2a46a418f528b4cdb2e9245b8ecafbc02d6d1718034cfe80d291095187b0946ebe237c8f985e4213c4c35bc345b WHIRLPOOL a00f4340e5dc151c57d9f5e2b764a609a508490756d8337d52bec4712fb26b8c06edf46293ed838f08ff34e1c068549ea9680657b7282cb884df4c1314c58cdb
diff --git a/sci-mathematics/petsc/files/petsc-3.4.2-disable-rpath.patch b/sci-mathematics/petsc/files/petsc-3.4.2-disable-rpath.patch
new file mode 100644
index 000000000..0ccf45ded
--- /dev/null
+++ b/sci-mathematics/petsc/files/petsc-3.4.2-disable-rpath.patch
@@ -0,0 +1,16 @@
+--- config/BuildSystem/config/setCompilers.py	2013-10-08 19:45:00.581513389 +0200
++++ config/BuildSystem/config/setCompilers.py	2013-05-13 23:35:20.000000000 +0200
+@@ -1303,12 +1303,7 @@
+     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/petsc-3.4.2.ebuild b/sci-mathematics/petsc/petsc-3.4.2.ebuild
new file mode 100644
index 000000000..1d8462fd8
--- /dev/null
+++ b/sci-mathematics/petsc/petsc-3.4.2.ebuild
@@ -0,0 +1,239 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+inherit base flag-o-matic fortran-2 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/${MY_P}.tar.gz"
+
+LICENSE="petsc"
+SLOT="0"
+KEYWORDS="~x86 ~amd64"
+IUSE="afterimage complex-scalars cxx debug doc
+	fortran hdf5 hypre mpi mumps scotch sparse superlu threads X"
+# Failed: boost imagemagick metis
+
+# hypre and superlu curretly exclude each other due to missing linking to hypre
+# if both are enabled
+REQUIRED_USE="
+	afterimage? ( X )
+	hdf5? ( mpi )
+	hypre? ( cxx mpi )
+	mumps? ( mpi scotch )
+	scotch? ( mpi )
+	^^ ( hypre superlu )
+"
+#	imagemagick? ( X )
+
+RDEPEND="
+	virtual/blas
+	virtual/lapack
+	afterimage? ( media-libs/libafterimage )
+	hdf5? ( sci-libs/hdf5[mpi?] )
+	hypre? ( >=sci-libs/hypre-2.8.0b[mpi?] )
+	mpi? ( virtual/mpi[cxx?,fortran?] )
+	mumps? ( sci-libs/mumps[mpi?] sci-libs/scalapack )
+	scotch? ( sci-libs/scotch[mpi?] )
+	sparse? ( sci-libs/suitesparse >=sci-libs/cholmod-1.7.0 )
+	superlu? ( sci-libs/superlu )
+	X? ( x11-libs/libX11 )
+"
+#	boost? ( dev-libs/boost )
+#	metis? ( sci-libs/parmetis )
+#	imagemagick? ( media-gfx/imagemagick )
+
+DEPEND="${RDEPEND}
+	virtual/pkgconfig
+	dev-util/cmake
+"
+# cmake is used for parallel building
+# in some configuration setups, legacy build is used (slow)
+
+#
+# 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.
+#
+MAKEOPTS="${MAKEOPTS} -j1"
+
+S="${WORKDIR}/${MY_P}"
+
+PATCHES=(
+	"${FILESDIR}"/${P%_*}-disable-rpath.patch
+)
+
+src_configure() {
+	# 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=$4"
+	}
+
+	local mylang
+	local myopt
+
+	use cxx && mylang="cxx" || mylang="c"
+	use debug && myopt="debug" || myopt="opt"
+
+	# environmental variables expected by petsc during build
+	export PETSC_DIR="${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)
+
+	if use threads; then
+		ewarn "Threads support may be incomplete on $PN-3.3 release and is not officially supported."
+		ewarn "Upstream recommends not to enable threads support for production runs."
+	fi
+
+	# run petsc configure script
+	econf \
+		scrollOutput=1 \
+		CFLAGS="${CFLAGS}" \
+		CXXFLAGS="${CXXFLAGS}" \
+		LDFLAGS="${LDFLAGS}" \
+		--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_enable threads pthread) \
+		$(petsc_enable threads pthreadclasses) \
+		$(petsc_select complex-scalars scalar-type complex real) \
+		--with-windows-graphics=0 \
+		--with-matlab=0 \
+		--with-cmake=cmake \
+		$(petsc_with afterimage afterimage \
+			/usr/include/libAfterImage -lAfterImage) \
+		$(petsc_with hdf5) \
+		$(petsc_with hypre hypre \
+			/usr/include/hypre -lHYPRE) \
+		$(petsc_with sparse cholmod) \
+		$(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 \
+
+# not yet tested:
+#		python bindings, netcdf
+# non-working:
+#		fftw: no mpi-implementaion available in gentoo
+
+# failed dependencies, perhaps fixed in upstream soon:
+#		$(petsc_with metis parmetis) \ # needs metis too (>=5.0.2)
+#		$(petsc_with boost) \
+#		$(petsc_with imagemagick imagemagick \
+#			/usr/include/ImageMagick $($(tc-getPKG_CONFIG) --libs MagickCore)) \
+}
+
+src_install() {
+	# petsc install structure is very different from
+	# installing headers to /usr/include/petsc and lib to /usr/lib
+	# it also installs many unneeded executables and scripts
+	# so manual install is easier than cleanup after "emake install"
+	insinto /usr/include/${PN}
+	doins include/*.h*
+	insinto /usr/include/${PN}/${PETSC_ARCH}/include
+	doins ${PETSC_ARCH}/include/*
+	if use fortran; then
+		insinto /usr/include/${PN}/finclude
+		doins include/finclude/*.h
+	fi
+	if ! use mpi ; then
+		insinto /usr/include/${PN}/mpiuni
+		doins include/mpiuni/*.h
+	fi
+	insinto /usr/include/${PN}/conf
+	doins conf/{variables,rules,test}
+	insinto /usr/include/${PN}/${PETSC_ARCH}/conf
+	doins ${PETSC_ARCH}/conf/{petscrules,petscvariables,RDict.db}
+	insinto /usr/include/${PN}/petsc-private
+	doins include/petsc-private/*.h
+
+	# fix configuration files: replace ${S} by installed location
+	sed -i \
+		-e "s:${S}::g" \
+		"${ED}"/usr/include/${PN}/${PETSC_ARCH}/include/petscconf.h \
+		"${ED}"/usr/include/${PN}/${PETSC_ARCH}/conf/petscvariables || die
+	sed -i \
+		-e "s:usr/lib:usr/$(get_libdir):g" \
+		"${ED}"/usr/include/${PN}/${PETSC_ARCH}/include/petscconf.h || die
+
+	# add information about installation directory and
+	# PETSC_ARCH to environmental variables
+	cat >> 99petsc <<- EOF
+		PETSC_ARCH=${PETSC_ARCH}
+		PETSC_DIR=${EPREFIX}/usr/include/${PN}
+	EOF
+	doenvd 99petsc
+
+	dolib.so ${PETSC_ARCH}/lib/*.so
+
+	if use doc ; then
+		einfo "installing documentation (this could take a while)"
+		dodoc docs/manual.pdf
+		dohtml -r docs/*.html docs/changes docs/manualpages
+	fi
+}
+
+pkg_postinst() {
+	elog "The petsc ebuild is still under development."
+	elog "Help us improve the ebuild in:"
+	elog "http://bugs.gentoo.org/show_bug.cgi?id=53386"
+}