commit: b27eaf57fdd4ac52498914fefa00e54f9c4c67c3 Author: Matthias Maier <tamiko <AT> gentoo <DOT> org> AuthorDate: Wed Jul 3 23:13:48 2024 +0000 Commit: Matthias Maier <tamiko <AT> gentoo <DOT> org> CommitDate: Wed Jul 3 23:28:08 2024 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=b27eaf57
sci-mathematics/petsc: add 3.21.3 Closes: https://bugs.gentoo.org/929795 Signed-off-by: Matthias Maier <tamiko <AT> gentoo.org> sci-mathematics/petsc/Manifest | 1 + .../petsc/files/petsc-3.21.3-disable-rpath.patch | 18 ++ .../files/petsc-3.21.3-fix_sandbox_violation.patch | 17 ++ sci-mathematics/petsc/petsc-3.21.3.ebuild | 240 +++++++++++++++++++++ 4 files changed, 276 insertions(+) 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 +}
