From e937ca8df21d3186f65edc11c872706c80eb8a61 Mon Sep 17 00:00:00 2001 From: V3n3RiX Date: Wed, 20 Mar 2024 13:00:15 +0000 Subject: gentoo auto-resync : 20:03:2024 - 13:00:14 --- sci-mathematics/Manifest.gz | Bin 19317 -> 19321 bytes sci-mathematics/petsc/Manifest | 12 +- sci-mathematics/petsc/metadata.xml | 3 + sci-mathematics/petsc/petsc-3.18.2.ebuild | 1 - sci-mathematics/petsc/petsc-3.19.1.ebuild | 1 - sci-mathematics/petsc/petsc-3.19.2.ebuild | 1 - sci-mathematics/petsc/petsc-3.19.4.ebuild | 6 +- sci-mathematics/petsc/petsc-3.20.5.ebuild | 240 ++++++++++++++++++++++++++++++ 8 files changed, 255 insertions(+), 9 deletions(-) create mode 100644 sci-mathematics/petsc/petsc-3.20.5.ebuild (limited to 'sci-mathematics') diff --git a/sci-mathematics/Manifest.gz b/sci-mathematics/Manifest.gz index 60ba524b06f4..c196faac6932 100644 Binary files a/sci-mathematics/Manifest.gz and b/sci-mathematics/Manifest.gz differ 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 @@ Use suitesparse (sci-libs/suitesparse) including cholmod (sci-libs/cholmod) for sparse factorization Use superlu (sci-libs/superlu) for preconditioning + + petsc/petsc + 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 +} -- cgit v1.2.3