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authorMatthias Maier <tamiko@gentoo.org>2024-07-03 18:13:48 -0500
committerMatthias Maier <tamiko@gentoo.org>2024-07-03 18:28:08 -0500
commitb27eaf57fdd4ac52498914fefa00e54f9c4c67c3 (patch)
tree32e71b7ff10012b1969cb8d75ca9b1befee36d32 /sci-mathematics
parentprofiles: arm64/riscv: Drop obsolete qt6 package.use.mask entries (diff)
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sci-mathematics/petsc: add 3.21.3
Closes: https://bugs.gentoo.org/929795 Signed-off-by: Matthias Maier <tamiko@gentoo.org>
Diffstat (limited to 'sci-mathematics')
-rw-r--r--sci-mathematics/petsc/Manifest1
-rw-r--r--sci-mathematics/petsc/files/petsc-3.21.3-disable-rpath.patch18
-rw-r--r--sci-mathematics/petsc/files/petsc-3.21.3-fix_sandbox_violation.patch17
-rw-r--r--sci-mathematics/petsc/petsc-3.21.3.ebuild240
4 files changed, 276 insertions, 0 deletions
diff --git a/sci-mathematics/petsc/Manifest b/sci-mathematics/petsc/Manifest
index d2cf6223e721..01fcfa003c56 100644
--- a/sci-mathematics/petsc/Manifest
+++ b/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
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
+}