sci-mathematics/petsc: version bump to 3.13.1

Package-Manager: Portage-2.3.99, Repoman-2.3.22
Signed-off-by: Matthias Maier <tamiko@gentoo.org>

2 files changed, 190 insertions, 0 deletions

diff --git a/sci-mathematics/petsc/Manifest b/sci-mathematics/petsc/Manifest
index c224c7768822..08d519f80c2f 100644
--- a/sci-mathematics/petsc/Manifest
+++ b/sci-mathematics/petsc/Manifest
@@ -1 +1,2 @@
 DIST petsc-3.13.0.tar.gz 35080264 BLAKE2B 0ac58e53751dbc6e053e3591cdf2363194e0cf7a493f252d879031e0135da16fa24e66974dd7bf07ce18558a75f8dd794e87f96590ad9e550d11edfeb462f727 SHA512 0590bb63d9c6dfd6ac03b1b88e5a8c11d42a0fd014084603d4d085060b126aa4341b4ec3a4d2b12146b971da327ccc7ede370e5633282bf44f269465aea32953
+DIST petsc-3.13.1.tar.gz 35097687 BLAKE2B fccf64fd3694deffdd0dc561069ffa7e9342fe279b5c9123edeb011df931874083839d27b7b9a0c63faea6487b104b54fd4ce68a88a074c82de91e8baaf270b0 SHA512 41c3138a6ae6c1f2d9077b464c6aeda96287e5a76849582b8f432e2ee93d2594a78ba2181eac0054a77b6165692be5f1a057049313f2be9743d4246383dfdc77
diff --git a/sci-mathematics/petsc/petsc-3.13.1.ebuild b/sci-mathematics/petsc/petsc-3.13.1.ebuild
new file mode 100644
index 000000000000..961ff927f725
--- /dev/null
+++ b/sci-mathematics/petsc/petsc-3.13.1.ebuild
@@ -0,0 +1,189 @@
+# Copyright 1999-2020 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+PYTHON_COMPAT=( python3_{6,7,8} )
+
+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/${P}.tar.gz"
+
+LICENSE="BSD-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="afterimage boost complex-scalars cxx debug doc fftw
+	fortran hdf5 hypre mpi metis mumps scotch sparse superlu threads X"
+
+# hypre and superlu curretly exclude each other due to missing linking to hypre
+# if both are enabled
+REQUIRED_USE="
+	afterimage? ( X )
+	complex-scalars? ( !hypre !superlu )
+	hdf5? ( mpi )
+	hypre? ( cxx mpi !superlu )
+	mumps? ( mpi scotch )
+	scotch? ( mpi )
+	superlu? ( !hypre )
+"
+
+RDEPEND="
+	virtual/blas
+	virtual/lapack
+	afterimage? ( media-libs/libafterimage )
+	boost? ( dev-libs/boost )
+	fftw? ( sci-libs/fftw:3.0[mpi?] )
+	hdf5? ( sci-libs/hdf5[mpi?] )
+	hypre? ( >=sci-libs/hypre-2.18.0[mpi?] )
+	metis? ( >=sci-libs/parmetis-4 )
+	mpi? ( virtual/mpi[cxx?,fortran?] )
+	mumps? ( sci-libs/mumps[mpi?] sci-libs/scalapack )
+	scotch? ( sci-libs/scotch[mpi?] )
+	sparse? ( sci-libs/suitesparse >=sci-libs/cholmod-1.7.0 )
+	superlu? ( >=sci-libs/superlu-5 )
+	X? ( x11-libs/libX11 )
+"
+
+DEPEND="${RDEPEND}
+	${PYTHON_DEPS}
+	virtual/pkgconfig
+	dev-util/cmake
+"
+
+PATCHES=(
+	"${FILESDIR}"/${PN}-3.7.0-disable-rpath.patch
+	"${FILESDIR}"/${PN}-3.13.0-fix_sandbox_violation.patch
+	"${FILESDIR}"/${PN}-3.13.0-make_hypre_configure.patch
+	"${FILESDIR}"/${PN}-3.13.0-do_not_run_mpiexec.patch
+)
+
+# 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) \
+		$(use_with hdf5) \
+		$(petsc_with hypre hypre \
+			/usr/include/hypre -lHYPRE) \
+		$(use_with sparse suitesparse) \
+		$(petsc_with superlu superlu \
+			/usr/include/superlu -lsuperlu) \
+		$(use_with X x) \
+		$(use_with X x11) \
+		$(petsc_with scotch ptscotch \
+			/usr/include/scotch \
+		[-lptesmumps,-lptscotch,-lptscotcherr,-lscotch,-lscotcherr]) \
+		$(petsc_with mumps scalapack \
+			/usr/include/scalapack -lscalapack) \
+		$(use_with mumps mumps \
+			/usr/include \
+			[-lcmumps,-ldmumps,-lsmumps,-lzmumps,-lmumps_common,-lpord]) \
+		--with-imagemagick=0 \
+		--with-python=0 \
+		$(use_with boost) \
+		$(use_with fftw)
+}
+
+src_install() {
+	emake DESTDIR="${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
+}