sci-mathematics/petsc: add 3.18.2

Closes: https://bugs.gentoo.org/722612
Closes: https://bugs.gentoo.org/846428
Closes: https://bugs.gentoo.org/846425
Closes: https://bugs.gentoo.org/846422
Closes: https://bugs.gentoo.org/846431
Signed-off-by: Matthias Maier <tamiko@gentoo.org>

2 files changed, 237 insertions, 0 deletions

diff --git a/sci-mathematics/petsc/Manifest b/sci-mathematics/petsc/Manifest
index 8a1dcafa8362..1d6310cc9c0a 100644
--- a/sci-mathematics/petsc/Manifest
+++ b/sci-mathematics/petsc/Manifest
@@ -1,3 +1,4 @@
 DIST petsc-3.16.0-fftw-without-mpi.patch.bz2 5824 BLAKE2B 59615b1bbaf8ca1da92d7d193a45a2dd434f762cd741d711d4f408183a201a276ac3c968a3e7d740d19212120271701bce52bb7b0f4e311268f40915c81f9dcb SHA512 8e07dfe56a9150ce9a3a5ab8012657875ef84e6e7daa60560bbdd9062078c876a826057f3f3eaf1697ce046a82756ee6eb6a8b819eb51245367c9d5c8a72ee8e
 DIST petsc-3.16.0.tar.gz 16748960 BLAKE2B 87f9fdb79a9c44e5f476fa4746ad0cbe72f3eda9f6039f2e4743105626701d7c8d6c010fdb9d89becf8619288d0b7a60c8bc4e2fc0793eac5b39030b02c04fd9 SHA512 5280032fb4ec4d058733788bb0ae674e7400565e204133bd10ed88a2965230ec7adeaca2d498267ce661377ca7e6f9d948992206b1d679587606cb422c004655
 DIST petsc-3.17.1.tar.gz 17082265 BLAKE2B de1bfe45f93e18e32181499e59912df9225c8e24d75f52e641e552fd43e4d5be48d549d284365b173aa93e51603f5b7740eaac0557ff8c7c96b370f4683257f6 SHA512 8c81cc148b1a899a55e54a013d61519ec7b44f98f7ae30c3f8d0e83ba285b23f4b4d9e2cd483c531d337bc41887e4079b727ba73676b1b653910140291e93575
+DIST petsc-3.18.2.tar.gz 18409507 BLAKE2B 999d4fc80dedb5f9ce58333b6052b15ff499e3d5e4fee3e37639f5e3d2c5e86b514290d01e75b71795467436254d2cb8b05dac3d6252c80db898010bbed95544 SHA512 a8e9757144a20d61c004f54615821df7f9dbd920af71fea4674eb0fd1bf9f0b50dbc5c89aae285fef35a23daf67ba9647e479a6e92dbcd26e53fd8302735a47b
diff --git a/sci-mathematics/petsc/petsc-3.18.2.ebuild b/sci-mathematics/petsc/petsc-3.18.2.ebuild
new file mode 100644
index 000000000000..b011f88b5043
--- /dev/null
+++ b/sci-mathematics/petsc/petsc-3.18.2.ebuild
@@ -0,0 +1,236 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{8..11} pypy3 )
+
+inherit flag-o-matic fortran-2 python-any-r1 toolchain-funcs
+
+DESCRIPTION="Portable, Extensible Toolkit for Scientific Computation"
+HOMEPAGE="https://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 debug +examples fftw
+fortran hdf5 hypre int64 mpi metis mumps scotch superlu threads X"
+
+# readd sparse when suitesparse-5.6.0 is in tree
+# sparse? ( >=sci-libs/suitesparse-5.6.0 >=sci-libs/cholmod-1.7.0 )
+# $(use_with sparse suitesparse) \
+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[int64?,mpi?] )
+	metis? ( >=sci-libs/parmetis-4 )
+	mpi? ( virtual/mpi[fortran?] )
+	mumps? ( sci-libs/mumps[mpi?] sci-libs/scalapack )
+	scotch? ( sci-libs/scotch[int64?,mpi?] )
+	superlu? ( >=sci-libs/superlu-5 )
+	X? ( x11-libs/libX11 )
+"
+DEPEND="
+	${RDEPEND}
+	${PYTHON_DEPS}
+"
+BDEPEND="
+	dev-util/cmake
+	sys-apps/which
+	virtual/pkgconfig
+"
+
+# hypre and superlu curretly exclude each other due to missing linking to hypre
+# if both are enabled
+REQUIRED_USE="
+	afterimage? ( X )
+	complex-scalars? ( !hypre !superlu )
+	fftw? ( mpi )
+	hdf5? ( mpi )
+	hypre? ( mpi !superlu )
+	mumps? ( mpi scotch )
+	scotch? ( mpi )
+	superlu? ( !hypre )
+"
+PATCHES=(
+	"${FILESDIR}/${PN}-3.7.0-disable-rpath.patch"
+	"${FILESDIR}"/${PN}-3.16.0-fix_sandbox_violation.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=$4"
+}
+
+src_configure() {
+	# bug 548498
+	# PETSc runs mpi processes during configure that result in a sandbox
+	# violation by trying to open /proc/mtrr rw. This is not easy to
+	# mitigate because it happens in libpciaccess.so called by libhwloc.so,
+	# which is used by libmpi.so.
+	addpredict /proc/mtrr
+	# if mpi is built with knem support it needs /dev/knem too
+	addpredict /dev/knem
+
+	# configureMPITypes with openmpi-2* insists on accessing the scaling
+	# governor rw.
+	addpredict /sys/devices/system/cpu/
+
+	# bug 771711
+	# configureMPIEXEC and  configureMPITypes access /dev/nvidiactl
+	addpredict /dev/nvidiactl
+
+	# bug 810841
+	addpredict /dev/kfd
+
+	local myopt
+
+	use debug && myopt="debug" || myopt="opt"
+
+	# environmental variables expected by petsc during build
+
+	export PETSC_DIR="${S}"
+	export PETSC_ARCH="linux-gnu-c-${myopt}"
+
+	if use debug; then
+		strip-flags
+		filter-flags -O*
+	fi
+
+	tc-export AR RANLIB
+
+	# C Support on CXX builds is enabled if possible i.e. when not using
+	# complex scalars (no complex type for both available at the same time)
+
+	econf \
+		scrollOutput=1 \
+		AR="${AR}" \
+		CFLAGS="${CFLAGS} -fPIC" \
+		CPPFLAGS="${CPPFLAGS}" \
+		CXXFLAGS="${CXXFLAGS} -fPIC" \
+		CXXOPTFLAGS="${CXXFLAGS} -fPIC" \
+		FCFLAGS="${FCFLAGS} -fPIC" \
+		FFLAGS="${FFLAGS} -fPIC" \
+		LDFLAGS="${LDFLAGS}" \
+		MAKEFLAGS="${MAKEFLAGS}" \
+		RANLIB="${RANLIB}" \
+		--prefix="${EPREFIX}/usr/$(get_libdir)/petscdir/" \
+		--with-blas-lapack-lib="$($(tc-getPKG_CONFIG) --libs blas lapack)" \
+		--with-cmake:BOOL=1 \
+		--with-gnu-compilers \
+		--with-imagemagick=0 \
+		--with-petsc-arch="${PETSC_ARCH}" \
+		--with-precision=double \
+		--with-python=0 \
+		--with-shared-libraries \
+		--with-single-library \
+		--with-windows-graphics=0 \
+		$(petsc_enable debug debugging) \
+		$(petsc_enable fortran) \
+		$(petsc_enable mpi) \
+		$(petsc_enable mpi mpi-compilers) \
+		$(petsc_enable threads pthread) \
+		$(petsc_select complex-scalars scalar-type complex real) \
+		$(petsc_select mpi cc mpicc $(tc-getCC)) \
+		$(petsc_select mpi cxx mpicxx $(tc-getCXX)) \
+		$(petsc_with afterimage afterimage /usr/include/libAfterImage -lAfterImage) \
+		$(petsc_with hypre hypre /usr/include/hypre -lHYPRE) \
+		$(petsc_with superlu superlu /usr/include/superlu -lsuperlu) \
+		$(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]) \
+		$(use fortran && echo "$(petsc_select mpi fc mpif77 $(tc-getF77))") \
+		$(use int64 && echo "--with-index-size=64") \
+		$(use_with boost) \
+		$(use_with fftw) \
+		$(use_with hdf5) \
+		$(use_with X x) \
+		$(use_with X x11)
+}
+
+src_install() {
+	emake DESTDIR="${ED}" install
+
+	#
+	# Clean up the mess:
+	#
+
+	# put all include directories under a proper subdirectory
+	mkdir "${ED}"/usr/include || die "mkdir failed (include)"
+	mv "${ED}"/usr/{$(get_libdir)/petscdir/include,include/petsc} || die "mv failed (include)"
+
+	# put libraries and pkconfig file into proper place
+	mv "${ED}"/usr/$(get_libdir)/petscdir/lib/{libpetsc*,pkgconfig} \
+		"${ED}/usr/$(get_libdir)" || die "mv failed (lib)"
+
+	# move share to proper location
+	mv "${ED}"/usr/{$(get_libdir)/petscdir/share,share} || die "mv failed (share)"
+
+	# fix pc files:
+	sed -i \
+		-e 's#include$#include/petsc#' \
+		-e "s#lib\$#$(get_libdir)#" \
+		-e "s#^prefix=.*petscdir\$#prefix=${EPREFIX}/usr#" \
+		"${ED}"/usr/$(get_libdir)/pkgconfig/*.pc || die "sed failed (pkgconfig)"
+
+	# recreate a "valid" petscdir:
+	for i in "${ED}"/usr/$(get_libdir)/*; do
+		[ $(basename $i) = petscdir ] && continue
+		ln -s "${EPREFIX}/usr/$(get_libdir)/$(basename $i)" \
+			"${ED}/usr/$(get_libdir)/petscdir/lib/$(basename $i)" || die "ln failed (petscdir)"
+	done
+	ln -s "${EPREFIX}"/usr/include/petsc/ \
+		"${ED}/usr/$(get_libdir)/petscdir/include" || die "ln failed (petscdir)"
+	mkdir "${ED}/usr/$(get_libdir)/petscdir/share" || die "mkdir fialed (petscdir)"
+	ln -s "${EPREFIX}"/usr/share/petsc/ \
+		"${ED}/usr/$(get_libdir)/petscdir/share/petsc" || die "ln failed (petscdir)"
+
+	# automatically symlink petsc matlab modules:
+	mkdir -p "${ED}"/usr/share/octave/site/m/
+	ln -s "${EPREFIX}"/usr/share/petsc/matlab "${ED}"/usr/share/octave/site/m/petsc || die "ln failed (matlab)"
+
+	if use examples; then
+		mkdir -p "${ED}"/usr/share/doc/${PF} || die "mkdir failed (examples)"
+		mv "${ED}"/usr/share/petsc/examples "${ED}"/usr/share/doc/${PF} || die "mv failed (examples)"
+		ln -s "${EPREFIX}"/usr/share/doc/${PF}/examples "${ED}"/usr/share/petsc/examples || die "ln failed (examples)"
+		docompress -x /usr/share/doc/${PF}/examples
+	else
+		rm -r "${ED}"/usr/share/petsc/examples || die "rm failed (examples)"
+	fi
+
+	# add PETSC_DIR to environmental variables
+	cat >> 99petsc <<- EOF
+		PETSC_DIR=${EPREFIX}/usr/$(get_libdir)/petscdir
+	EOF
+	doenvd 99petsc
+}