gentoo auto-resync : 20:03:2024 - 13:00:14

8 files changed, 255 insertions, 9 deletions

diff --git a/sci-mathematics/Manifest.gz b/sci-mathematics/Manifest.gz
index 60ba524b06f4..c196faac6932 100644
--- a/sci-mathematics/Manifest.gz
+++ b/sci-mathematics/Manifest.gz
diff --git a/sci-mathematics/petsc/Manifest b/sci-mathematics/petsc/Manifest
index 874cf601da52..3ecf051197f3 100644
--- a/sci-mathematics/petsc/Manifest
+++ b/sci-mathematics/petsc/Manifest
@@ -7,10 +7,12 @@ DIST petsc-3.18.2.tar.gz 18409507 BLAKE2B 999d4fc80dedb5f9ce58333b6052b15ff499e3
 DIST petsc-3.19.1.tar.gz 16659061 BLAKE2B 8c7b22e5f97756261a5d0e8b707670d55db53e209fd1e116a2adb517d42f5e8bd5ecc911c9e967b88a8dc60a2d872c1d7a279539c65064884b4cfbe856434ad3 SHA512 5b9b71599a95e2d82d18d5313c424a08eead0c10f27f40c82159839ef0fa8aeda88ddea693a12d58b8ac29a41c4138e8188a3c91d6af540196ee3a977cf9539d
 DIST petsc-3.19.2.tar.gz 16627765 BLAKE2B 1267db717989c3819f32ac6a62642054af2ac49d9e9276ffd4f0846d73e31ae4a5dcca4ad794b91cdb29463b7ec68040baa4e1cad99aaef8ab910ff7b64d7478 SHA512 f8feeb66fa8bd2406227be0e2cc2946485238362270d40e3f07dc89491177751f6bf680f51b70696bc30b677624c0e525c3fa9784eabdeb2337697ec56f63fc1
 DIST petsc-3.19.4.tar.gz 16630006 BLAKE2B 577655fff12f9f54570393b2023d3386e66c7d4351ef20922f4b8100cbc54eeec0fb6ce249774cb54d2d06062a610c7d755e3b44994a3e053c0c02889810adc8 SHA512 b32b8cf72ea6bf3d976067ce0b722a6fb2ede525bc2293b72daf5693de48c6256e50f3968c0464a5e0d3bb067b936e1d78b66b51626fd27bbef2f57322509564
+DIST petsc-3.20.5.tar.gz 17077395 BLAKE2B e76ff83572f7f0fcfa85b80f36301e0378d240e60726f07ab78a66b87591434bda6a96758037580370965f91c03341d95f60cfb961c2ab6707eeaafd5a7b1e1d SHA512 1e0ebdacbcc9db22dbe3803cbc13f5e0138d0412c328ff49cab024c839527c73b28983717104daf0858d482a8804b931c5c2bf20363c6b801d2be7d27219692f
 EBUILD petsc-3.16.0-r1.ebuild 5423 BLAKE2B f4d1bccdc64f6b1eafe0c88da617f138a3836ef96057d660569c7a010a30d4f12e08127f412290f59386a04896446c8f2202408a3816e9bb8ab9cbfe13fe860b SHA512 61bff72a6c246205bd78b459a5e3357744fa448c9f485474f7e7b56ec0bd96cdb45f0b1e008a509da2bebb52d6b987960defeff21e6b622d8df68ba2d64d9a29
 EBUILD petsc-3.17.1-r1.ebuild 5399 BLAKE2B 75ac3b4b90a9e41f9252a87947396b95fbee6d2ee320d8d5aac4425779021f84d625dbffb2988a2b71e9352ab12710ea85a758081861841afe2f03fce6145567 SHA512 ee28658210f894b5725bc7aeb0e8988124125e9e02ffdf70ded3110140cdcdb803e3cbf1943975c8a75402413c8009d3a769131488e71c026e7d64397d378ca2
-EBUILD petsc-3.18.2.ebuild 7337 BLAKE2B cd39c24ed4bd9c058b14e6e61879d3fbca17baa6ecca3533879336b59e77c6999ee28dce63760d19163ac928ff498f71710a8f896c99388f9313292097c9dfbb SHA512 139bf634581fa61a97873a4058edc8b353eba0ce06c01425d32a16b2f5f2afdadcd32f8f6f4620b5c0e3ce99542973df5b8e4a5a4337b69bae8666a5aed3f0cc
-EBUILD petsc-3.19.1.ebuild 7337 BLAKE2B cd39c24ed4bd9c058b14e6e61879d3fbca17baa6ecca3533879336b59e77c6999ee28dce63760d19163ac928ff498f71710a8f896c99388f9313292097c9dfbb SHA512 139bf634581fa61a97873a4058edc8b353eba0ce06c01425d32a16b2f5f2afdadcd32f8f6f4620b5c0e3ce99542973df5b8e4a5a4337b69bae8666a5aed3f0cc
-EBUILD petsc-3.19.2.ebuild 7337 BLAKE2B cd39c24ed4bd9c058b14e6e61879d3fbca17baa6ecca3533879336b59e77c6999ee28dce63760d19163ac928ff498f71710a8f896c99388f9313292097c9dfbb SHA512 139bf634581fa61a97873a4058edc8b353eba0ce06c01425d32a16b2f5f2afdadcd32f8f6f4620b5c0e3ce99542973df5b8e4a5a4337b69bae8666a5aed3f0cc
-EBUILD petsc-3.19.4.ebuild 7337 BLAKE2B cd39c24ed4bd9c058b14e6e61879d3fbca17baa6ecca3533879336b59e77c6999ee28dce63760d19163ac928ff498f71710a8f896c99388f9313292097c9dfbb SHA512 139bf634581fa61a97873a4058edc8b353eba0ce06c01425d32a16b2f5f2afdadcd32f8f6f4620b5c0e3ce99542973df5b8e4a5a4337b69bae8666a5aed3f0cc
-MISC metadata.xml 1234 BLAKE2B 15951140c7123ce11ae325ab3491822abf4143b053c62e3b47d192785a9fcf8ea3a1e30c68023bdd4eaecafd312aec1b519c2bf4a2a6fc07ae7b88f2266ea4ee SHA512 84fbcacb317baa8fbc71c143d42ae9e4ea00dffbe9fbd1b113065d6d493d52461737c33cdb36e39a558d5aafa58ea3fc7078f3af8605fd7c8733afe6469390e4
+EBUILD petsc-3.18.2.ebuild 7321 BLAKE2B 657741c39700e87eb9f5b72e2ec872897a9ea4dccd4817e546f385eda874113f51e820d068a90a116a3a8a27831690c0066c353491609ffefb3dc682577fa2fc SHA512 6f7f735eb892c3ce8b78d07f45b5974eafb9b34a18af19d7e93ddd2f23697372c025b2fa375d3062aeedff442884420a36445eaba6cf1a490fc14cf17b587279
+EBUILD petsc-3.19.1.ebuild 7321 BLAKE2B 657741c39700e87eb9f5b72e2ec872897a9ea4dccd4817e546f385eda874113f51e820d068a90a116a3a8a27831690c0066c353491609ffefb3dc682577fa2fc SHA512 6f7f735eb892c3ce8b78d07f45b5974eafb9b34a18af19d7e93ddd2f23697372c025b2fa375d3062aeedff442884420a36445eaba6cf1a490fc14cf17b587279
+EBUILD petsc-3.19.2.ebuild 7321 BLAKE2B 657741c39700e87eb9f5b72e2ec872897a9ea4dccd4817e546f385eda874113f51e820d068a90a116a3a8a27831690c0066c353491609ffefb3dc682577fa2fc SHA512 6f7f735eb892c3ce8b78d07f45b5974eafb9b34a18af19d7e93ddd2f23697372c025b2fa375d3062aeedff442884420a36445eaba6cf1a490fc14cf17b587279
+EBUILD petsc-3.19.4.ebuild 7445 BLAKE2B b5abdce667a803e4a3ae5ff056efb61de97e0ebe1efd056d8ef68e986fbc94507cf5fe697830008d56975eb5105a9b74ba09bc19ae38e17f2cad56529cf3bd15 SHA512 87c81ee5e63bf186efa6cddc9b81921b9ba8d137cbc40bae4dc42191254e66328cc4b5e86f94cc237129b524d776362f8fad7a21c5b05ac1b0d6302679fd60b7
+EBUILD petsc-3.20.5.ebuild 7458 BLAKE2B 88b01eb4e9801453dda22fea6768091b523ef2e3c7d6f2fc0dda01693458e2cfd76d8a3860d2aa050b2a1414825d04b0a18e387b6f776e115eb13dede59c6d86 SHA512 e3133fa1ef73a21596bb7e3625ab687e802157b61e31f2e4117be866ed4cc562685e85002202c3c21a68a5ec620ef497887e8fc498e82f17944753a17ed3e867
+MISC metadata.xml 1310 BLAKE2B 04161c348ae88640222ad8d6c3f3471defbfdc0adc223acc6e8d0d21f62090b62f2887caacae5de751cb4b1ddb1e0d4bb4de5ea57d9381c710837262668fc37b SHA512 327aa86d4dba087c0de4ab7e2099bf8df13f2eb04138207802f664c316b74c09b2b15f82e9766b6b713d530f3ee094844f490c4769a1b5719f4912b486156ba9
diff --git a/sci-mathematics/petsc/metadata.xml b/sci-mathematics/petsc/metadata.xml
index 987028fd7636..5d587548e725 100644
--- a/sci-mathematics/petsc/metadata.xml
+++ b/sci-mathematics/petsc/metadata.xml
@@ -21,4 +21,7 @@
 		<flag name="sparse">Use suitesparse (<pkg>sci-libs/suitesparse</pkg>) including cholmod (<pkg>sci-libs/cholmod</pkg>) for sparse factorization</flag>
 		<flag name="superlu">Use superlu (<pkg>sci-libs/superlu</pkg>) for preconditioning</flag>
 	</use>
+	<upstream>
+		<remote-id type="gitlab">petsc/petsc</remote-id>
+	</upstream>
 </pkgmetadata>
diff --git a/sci-mathematics/petsc/petsc-3.18.2.ebuild b/sci-mathematics/petsc/petsc-3.18.2.ebuild
index 27e8a71e87ea..30f4763b16a3 100644
--- a/sci-mathematics/petsc/petsc-3.18.2.ebuild
+++ b/sci-mathematics/petsc/petsc-3.18.2.ebuild
@@ -42,7 +42,6 @@ DEPEND="
 "
 BDEPEND="
 	dev-build/cmake
-	sys-apps/which
 	virtual/pkgconfig
 "
 
diff --git a/sci-mathematics/petsc/petsc-3.19.1.ebuild b/sci-mathematics/petsc/petsc-3.19.1.ebuild
index 27e8a71e87ea..30f4763b16a3 100644
--- a/sci-mathematics/petsc/petsc-3.19.1.ebuild
+++ b/sci-mathematics/petsc/petsc-3.19.1.ebuild
@@ -42,7 +42,6 @@ DEPEND="
 "
 BDEPEND="
 	dev-build/cmake
-	sys-apps/which
 	virtual/pkgconfig
 "
 
diff --git a/sci-mathematics/petsc/petsc-3.19.2.ebuild b/sci-mathematics/petsc/petsc-3.19.2.ebuild
index 27e8a71e87ea..30f4763b16a3 100644
--- a/sci-mathematics/petsc/petsc-3.19.2.ebuild
+++ b/sci-mathematics/petsc/petsc-3.19.2.ebuild
@@ -42,7 +42,6 @@ DEPEND="
 "
 BDEPEND="
 	dev-build/cmake
-	sys-apps/which
 	virtual/pkgconfig
 "
 
diff --git a/sci-mathematics/petsc/petsc-3.19.4.ebuild b/sci-mathematics/petsc/petsc-3.19.4.ebuild
index 27e8a71e87ea..fcd1c43750f1 100644
--- a/sci-mathematics/petsc/petsc-3.19.4.ebuild
+++ b/sci-mathematics/petsc/petsc-3.19.4.ebuild
@@ -42,7 +42,6 @@ DEPEND="
 "
 BDEPEND="
 	dev-build/cmake
-	sys-apps/which
 	virtual/pkgconfig
 "
 
@@ -93,6 +92,11 @@ petsc_select() {
 }
 
 src_configure() {
+	# -Werror=lto-type-mismatch
+	# https://bugs.gentoo.org/863260
+	# https://gitlab.com/petsc/petsc/-/issues/1560
+	filter-lto
+
 	# 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
diff --git a/sci-mathematics/petsc/petsc-3.20.5.ebuild b/sci-mathematics/petsc/petsc-3.20.5.ebuild
new file mode 100644
index 000000000000..ccf9449db9cb
--- /dev/null
+++ b/sci-mathematics/petsc/petsc-3.20.5.ebuild
@@ -0,0 +1,240 @@
+# Copyright 1999-2024 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..11} pypy3 )
+
+inherit flag-o-matic fortran-2 python-any-r1 toolchain-funcs
+
+DESCRIPTION="Portable, Extensible Toolkit for Scientific Computation"
+HOMEPAGE="https://petsc.org/release/"
+SRC_URI="https://web.cels.anl.gov/projects/petsc/download/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}
+	${PYTHON_DEPS}
+"
+BDEPEND="
+	dev-build/cmake
+	virtual/pkgconfig
+"
+
+# hypre and superlu curretly exclude each other due to missing linking to hypre
+# if both are enabled
+REQUIRED_USE="
+	afterimage? ( X )
+	complex-scalars? ( !hypre !superlu )
+	fftw? ( mpi )
+	hdf5? ( mpi )
+	hypre? ( mpi !superlu )
+	mumps? ( mpi scotch )
+	scotch? ( mpi )
+	superlu? ( !hypre )
+"
+PATCHES=(
+	"${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=$4"
+}
+
+src_configure() {
+	# -Werror=lto-type-mismatch
+	# https://bugs.gentoo.org/863260
+	# https://gitlab.com/petsc/petsc/-/issues/1560
+	filter-lto
+
+	# bug 548498
+	# PETSc runs mpi processes during configure that result in a sandbox
+	# violation by trying to open /proc/mtrr rw. This is not easy to
+	# mitigate because it happens in libpciaccess.so called by libhwloc.so,
+	# which is used by libmpi.so.
+	addpredict /proc/mtrr
+	# if mpi is built with knem support it needs /dev/knem too
+	addpredict /dev/knem
+
+	# configureMPITypes with openmpi-2* insists on accessing the scaling
+	# governor rw.
+	addpredict /sys/devices/system/cpu/
+
+	# bug 771711
+	# configureMPIEXEC and  configureMPITypes access /dev/nvidiactl
+	addpredict /dev/nvidiactl
+
+	# bug 810841
+	addpredict /dev/kfd
+
+	local myopt
+
+	use debug && myopt="debug" || myopt="opt"
+
+	# environmental variables expected by petsc during build
+
+	export PETSC_DIR="${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
+}