gentoo auto-resync : 04:07:2024 - 08:06:07

4 files changed, 279 insertions, 0 deletions

diff --git a/sci-mathematics/petsc/Manifest b/sci-mathematics/petsc/Manifest
index 9e6237acb008..02e227302149 100644
--- a/sci-mathematics/petsc/Manifest
+++ b/sci-mathematics/petsc/Manifest
@@ -1,4 +1,6 @@
 AUX petsc-3.16.0-fix_sandbox_violation.patch 717 BLAKE2B 9bef08265c058433cf903cc33739e9a1a2dc19f6ee77d92f2884c8a3fbdabe6585e9afa663a2a9ecf622d2e5c688ee0e931249e2e053213e3f0991070a0dd352 SHA512 3c8b490f8f6f0a4ceff8dbafdcc835174549cfe397753a7855995543c51dc5629c576b3af76c0ef527a62b2475dd5e6f059036048619f4ca83146879682835b9
+AUX petsc-3.21.3-disable-rpath.patch 955 BLAKE2B aa129ea846f424982cb7b8e3bc4f62bddb699bad2f8421cc186f90562b169b20cb64f36732cd305bcd45d224776a6cdb60f1c475a20ce853a791ea7dc2a88390 SHA512 a9fc9fdb94b03dbd543a3247b1469598f2d3d0521d136bf2e1995f0b1c4e12f688c06ac4c62aa03ad102d4f49546c1157641738dec413304f50f51e6b3ffd6a5
+AUX petsc-3.21.3-fix_sandbox_violation.patch 829 BLAKE2B 4a1cdeffbb2cfa3dd423334fd61806f760cf32dcaee76160509e567fc9d1f34d5f01eeb93f6df0c714e58d7d362daf8b531b8b3962188c1009f499da3161dcad SHA512 445867c6ecd55b4a85fcbb4ac18225a817c214f2fa32d98ffba32017e5b49252d46112d293d661e5eb2963376fec6bce9909a8206185992da7246fe08e0ecc2c
 AUX petsc-3.7.0-disable-rpath.patch 909 BLAKE2B b9b6064886d6c10b382982778398cb7fa254242e5ed0dfb86dd4cd6c094dc51eecfd625f6de5c2779bfc5b3beda351ac44145c69ac246d814a728d7565da8086 SHA512 8241c593d903615feb175bfe8213792ace739a18ac5f4c1d1890155ccea7de30b5ef5d97e2fa3b043e9a1e520e022abedeb038d0b4db671f89045e04edc65a68
 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
@@ -8,6 +10,7 @@ DIST petsc-3.19.1.tar.gz 16659061 BLAKE2B 8c7b22e5f97756261a5d0e8b707670d55db53e
 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
+DIST petsc-3.21.3.tar.gz 17334266 BLAKE2B 6a34ae9f57b6f6c9ece4d411da8374d0b5675539f4041b8aa872c639084c7d38b7ddcf27889e7b835df453a8725869d04b4515615dba5998fb00fe28074043ec SHA512 699bbf3ddfc8fe8ebd4a1cb51a04108c10cafb65d30e7a74a9bf1b1ddd0f4350f0b893b256ea8a835e076e0a2f982189902bff30a9e301b3e04b539d2d2b6f99
 EBUILD petsc-3.16.0-r2.ebuild 5425 BLAKE2B a38f36283aa2a802f886565daebfd57681c8bf81a56ba8fde8f82247216cdb21548fc4bf5088d76f0e4ea56afc29f8891ac20986cbfb1cd05c3408e85977a636 SHA512 ed7e01fef273d5c6acbb39dfcf94df854555cd5c27173a5b6e4acdc2f542a3cfc126c361cb0193c7a8fa266478182634a97615a9c72bbe2b98e6cce5ba7d0cd9
 EBUILD petsc-3.17.1-r2.ebuild 5401 BLAKE2B 0e77a30b419b34758ac36ece7f3a210c1ca8a878bf2cf381039def0ef354d497b5e5d5172e5c663a61e54d256c43bd623fd299839f73db8d9cd9885c1d1cab2a SHA512 c9820edc2ae6218ccffcb4fc8213431c33e9e0dc2d1b7c4e79a70f79485ee0dbd6ecacdc2630732b2b65fc98044914d25b8a6c5fbee35908bef4e4d41f6a6d63
 EBUILD petsc-3.18.2-r1.ebuild 7323 BLAKE2B d42ef6d5dea72728bca65edbd783ad38ed809ed9ab312cd5f21e9039d560166beca6a44859094346a52f33ea5810b429cd61db4812ef8747966778d77636d233 SHA512 540bbc5210587b45df3fd5038b0671eafbe330683198661fdacd1eda10a08c4f89d7dbed6966b69154dd54a98fc5238c615bc27cff2ddee270d32fb170d2d7ef
@@ -15,4 +18,5 @@ EBUILD petsc-3.19.1-r1.ebuild 7323 BLAKE2B d42ef6d5dea72728bca65edbd783ad38ed809
 EBUILD petsc-3.19.2-r1.ebuild 7323 BLAKE2B d42ef6d5dea72728bca65edbd783ad38ed809ed9ab312cd5f21e9039d560166beca6a44859094346a52f33ea5810b429cd61db4812ef8747966778d77636d233 SHA512 540bbc5210587b45df3fd5038b0671eafbe330683198661fdacd1eda10a08c4f89d7dbed6966b69154dd54a98fc5238c615bc27cff2ddee270d32fb170d2d7ef
 EBUILD petsc-3.19.4-r1.ebuild 7447 BLAKE2B 25b7431319effec19012133dd480cc76309206f3de7789262fc09d2724cde19dcdc9ae86a40432fa40dc6b927c49e445d5e67c010e5e47eee1c27aa8db8510b2 SHA512 835ef674e227720e47e86165143b3b55d79694c9424b666f94a9191d70d2f435acd5d4f0aada1765520194eb97126e064b49c71a2efaf90775a867eec9a49acd
 EBUILD petsc-3.20.5-r1.ebuild 7460 BLAKE2B ba8adc670eb453336766c670caa28fd1130f10eb222bc1aafa3e69e616288059908ff845d3a290f71f65d6011f82f0d94c4ba87d79a298b80f17035575ead102 SHA512 89db7fbeda8e15bac7194b84f07a0a12f85d2916be9ba45d5ae64e389fd9dd39233611bab424b8916be2a55569409afd08bd8efb830b422bd18347d16e9cc428
+EBUILD petsc-3.21.3.ebuild 7445 BLAKE2B caa8f098a17253540ffd738a251d630f1478e62321b3cb4b68dd8e332c1c23f1b7ffeda2932e2dd85914dcd89b1bc5dfd4e281d9d8b5a60891a44d1f154ecc27 SHA512 2908d9f0e4fd7432e65134d7559ad95b3c9bc88d35dbd6215debecf487ca08502821bd22e6d501ae1e7649dee3ca0a90ab9cf7fbcc622dad99eb68638af33dab
 MISC metadata.xml 1310 BLAKE2B 04161c348ae88640222ad8d6c3f3471defbfdc0adc223acc6e8d0d21f62090b62f2887caacae5de751cb4b1ddb1e0d4bb4de5ea57d9381c710837262668fc37b SHA512 327aa86d4dba087c0de4ab7e2099bf8df13f2eb04138207802f664c316b74c09b2b15f82e9766b6b713d530f3ee094844f490c4769a1b5719f4912b486156ba9
diff --git a/sci-mathematics/petsc/files/petsc-3.21.3-disable-rpath.patch b/sci-mathematics/petsc/files/petsc-3.21.3-disable-rpath.patch
new file mode 100644
index 000000000000..3035a963786e
--- /dev/null
+++ b/sci-mathematics/petsc/files/petsc-3.21.3-disable-rpath.patch
@@ -0,0 +1,18 @@
+diff --git a/config/BuildSystem/config/setCompilers.py b/config/BuildSystem/config/setCompilers.py
+index bcf0181..a56bf8a 100644
+--- a/config/BuildSystem/config/setCompilers.py
++++ b/config/BuildSystem/config/setCompilers.py
+@@ -2543,12 +2543,7 @@ class Configure(config.base.Configure):
+       if Configure.isCygwin(self.log):
+         self.logPrint('Cygwin detected! disabling -rpath test.')
+         testFlags = []
+-      # test '-R' before '-rpath' as sun compilers [c,fortran] don't give proper errors with wrong options.
+-      elif 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-3.21.3-fix_sandbox_violation.patch b/sci-mathematics/petsc/files/petsc-3.21.3-fix_sandbox_violation.patch
new file mode 100644
index 000000000000..1b38a88c343b
--- /dev/null
+++ b/sci-mathematics/petsc/files/petsc-3.21.3-fix_sandbox_violation.patch
@@ -0,0 +1,17 @@
+diff --git a/config/PETSc/options/installDir.py b/config/PETSc/options/installDir.py
+index 0ef7ecd..be21ec8 100755
+--- a/config/PETSc/options/installDir.py
++++ b/config/PETSc/options/installDir.py
+@@ -36,12 +36,6 @@ 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 Exception as e:
+-        self.logPrint('Error trying to test write permissions on directory '+str(e))
+-        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/petsc-3.21.3.ebuild b/sci-mathematics/petsc/petsc-3.21.3.ebuild
new file mode 100644
index 000000000000..34622426cdb2
--- /dev/null
+++ b/sci-mathematics/petsc/petsc-3.21.3.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..12} 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}/${P}-disable-rpath.patch"
+	"${FILESDIR}"/${P}-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
+}