sci-mathematics/petsc: add 3.21.3

Closes: https://bugs.gentoo.org/929795
Signed-off-by: Matthias Maier <[email protected]>

sci-mathematics/petsc/Manifest

@@ -6,3 +6,4 @@ 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

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:

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

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
+}