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authorMatthias Maier <tamiko@gentoo.org>2019-08-04 23:48:15 -0500
committerMatthias Maier <tamiko@gentoo.org>2019-08-05 01:51:11 -0500
commit44c266fd90ff2510b3d5ee74ed1dcff364eebcb1 (patch)
treea3a9798ce717591c5cc8096ec6e43d437e7c1cdb /sci-mathematics
parentdev-python/jupyter: Drop 1.0.0 (r0) (diff)
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sci-mathematics/petsc: package migration from ::science overlay
After years in ::science it is stable enough to be hosted in ::gentoo. Package-Manager: Portage-2.3.70, Repoman-2.3.16 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-3.7.0-disable-rpath.patch18
-rw-r--r--sci-mathematics/petsc/files/petsc-3.9.0-fix_sandbox_violation.patch17
-rw-r--r--sci-mathematics/petsc/metadata.xml23
-rw-r--r--sci-mathematics/petsc/petsc-3.11.3.ebuild193
5 files changed, 252 insertions, 0 deletions
diff --git a/sci-mathematics/petsc/Manifest b/sci-mathematics/petsc/Manifest
new file mode 100644
index 00000000000..3be30d7421f
--- /dev/null
+++ b/sci-mathematics/petsc/Manifest
@@ -0,0 +1 @@
+DIST petsc-3.11.3.tar.gz 33279017 BLAKE2B 870b8245e5e06d8538ea3ee1d01fa2cebade4a0bd79dfcf17d74e6201f41d21ca021e206744ece28847b434ece142a2789851b5514a8a1e3f82a8551288b695b SHA512 e545f69e87bc72950939ff3cec3e0ba225a5b3e7f1cb93b0fb6123194eb7240ac1d97ba397235d8ab872c653caab1427673124e5e1e706b796c0ae46ec1bcffa
diff --git a/sci-mathematics/petsc/files/petsc-3.7.0-disable-rpath.patch b/sci-mathematics/petsc/files/petsc-3.7.0-disable-rpath.patch
new file mode 100644
index 00000000000..8d0d993309b
--- /dev/null
+++ b/sci-mathematics/petsc/files/petsc-3.7.0-disable-rpath.patch
@@ -0,0 +1,18 @@
+diff --git a/config/BuildSystem/config/setCompilers.py b/config/BuildSystem/config/setCompilers.py
+index 219a35b..ad2ed8c 100644
+--- a/config/BuildSystem/config/setCompilers.py
++++ b/config/BuildSystem/config/setCompilers.py
+@@ -1385,12 +1385,7 @@ class Configure(config.base.Configure):
+ for language in languages:
+ flag = '-L'
+ self.pushLanguage(language)
+- # test '-R' before '-rpath' as sun compilers [c,fortran] don't give proper errors with wrong options.
+- if 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-3.9.0-fix_sandbox_violation.patch b/sci-mathematics/petsc/files/petsc-3.9.0-fix_sandbox_violation.patch
new file mode 100644
index 00000000000..97f8dfed4d7
--- /dev/null
+++ b/sci-mathematics/petsc/files/petsc-3.9.0-fix_sandbox_violation.patch
@@ -0,0 +1,17 @@
+diff --git a/config/PETSc/options/installDir.py b/config/PETSc/options/installDir.py
+index 92f190d..047c85b 100644
+--- a/config/PETSc/options/installDir.py
++++ b/config/PETSc/options/installDir.py
+@@ -41,12 +41,6 @@ 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:
+- self.installSudoMessage = 'You do not have write permissions to the --prefix directory '+self.dir+'\nYou will be prompted for the sudo password for any external package installs'
+- 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/metadata.xml b/sci-mathematics/petsc/metadata.xml
new file mode 100644
index 00000000000..8c9c01d8326
--- /dev/null
+++ b/sci-mathematics/petsc/metadata.xml
@@ -0,0 +1,23 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="person">
+ <email>tamiko@gentoo.org</email>
+ <name>Matthias Maier</name>
+ </maintainer>
+ <maintainer type="project">
+ <email>sci-mathematics@gentoo.org</email>
+ <name>Gentoo Mathematics Project</name>
+ </maintainer>
+ <use>
+ <flag name="afterimage">Use Afterstep image library (media-libs/libafterimage)</flag>
+ <flag name="boost">Use boost (dev-libs/boost)</flag>
+ <flag name="hypre">Use HYPRE (sci-mathematics/hypre) and for preconditioning</flag>
+ <flag name="complex-scalars">Make scalars complex</flag>
+ <flag name="metis">Add support for metis (<pkg>sci-libs/parmetis</pkg>)</flag>
+ <flag name="sparse">Use suitesparse (sci-libs/suitesparse) including cholmod (sci-libs/cholmod) for sparse factorization</flag>
+ <flag name="superlu">Use superlu (sci-libs/superlu) for preconditioning</flag>
+ <flag name="mumps">Add support for mumps (<pkg>sci-libs/mumps</pkg>)</flag>
+ <flag name="scotch">Add support for scotch (<pkg>sci-libs/scotch</pkg>)</flag>
+ </use>
+</pkgmetadata>
diff --git a/sci-mathematics/petsc/petsc-3.11.3.ebuild b/sci-mathematics/petsc/petsc-3.11.3.ebuild
new file mode 100644
index 00000000000..88fb1f58da1
--- /dev/null
+++ b/sci-mathematics/petsc/petsc-3.11.3.ebuild
@@ -0,0 +1,193 @@
+# Copyright 1999-2019 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+PYTHON_COMPAT=( python2_7 )
+
+inherit flag-o-matic fortran-2 python-any-r1 toolchain-funcs
+
+DESCRIPTION="Portable, Extensible Toolkit for Scientific Computation"
+HOMEPAGE="http://www.mcs.anl.gov/petsc/"
+SRC_URI="http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/${P}.tar.gz"
+
+LICENSE="BSD-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="afterimage boost complex-scalars cxx debug doc fftw
+ fortran hdf5 hypre mpi metis mumps scotch sparse superlu threads X"
+
+# hypre and superlu curretly exclude each other due to missing linking to hypre
+# if both are enabled
+REQUIRED_USE="
+ afterimage? ( X )
+ complex-scalars? ( !hypre !superlu )
+ hdf5? ( mpi )
+ hypre? ( cxx mpi !superlu )
+ mumps? ( mpi scotch )
+ scotch? ( mpi )
+ superlu? ( !hypre )
+"
+
+RDEPEND="
+ virtual/blas
+ virtual/lapack
+ afterimage? ( media-libs/libafterimage )
+ boost? ( dev-libs/boost )
+ fftw? ( sci-libs/fftw:3.0[mpi?] )
+ hdf5? ( sci-libs/hdf5[mpi?] )
+ hypre? ( >=sci-libs/hypre-2.8.0b[mpi?] )
+ metis? ( >=sci-libs/parmetis-4 )
+ mpi? ( virtual/mpi[cxx?,fortran?] )
+ mumps? ( sci-libs/mumps[mpi?] sci-libs/scalapack )
+ scotch? ( sci-libs/scotch[mpi?] )
+ sparse? ( sci-libs/suitesparse >=sci-libs/cholmod-1.7.0 )
+ superlu? ( >=sci-libs/superlu-5 )
+ X? ( x11-libs/libX11 )
+"
+
+DEPEND="${RDEPEND}
+ ${PYTHON_DEPS}
+ virtual/pkgconfig
+ dev-util/cmake
+"
+
+PATCHES=(
+ "${FILESDIR}"/${PN}-3.7.0-disable-rpath.patch \
+ "${FILESDIR}"/${PN}-3.9.0-fix_sandbox_violation.patch
+)
+
+src_prepare() {
+ default
+
+ sed -i -e 's%/usr/bin/env python%/usr/bin/env python2%' configure || die
+}
+
+# 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=$4"
+}
+
+src_configure() {
+ # bug 548498
+ # PETSc runs mpi processes during configure that result in a sandbox
+ # violation by trying to open /proc/mtrr rw. This is not easy to
+ # mitigate because it happens in libpciaccess.so called by libhwloc.so,
+ # which is used by libmpi.so.
+ addpredict /proc/mtrr
+ # if mpi is built with knem support it needs /dev/knem too
+ addpredict /dev/knem
+
+ # configureMPITypes with openmpi-2* insists on accessing the scaling
+ # governor rw.
+ addpredict /sys/devices/system/cpu/
+
+ local mylang
+ local myopt
+
+ use cxx && mylang="cxx" || mylang="c"
+ use debug && myopt="debug" || myopt="opt"
+
+ # environmental variables expected by petsc during build
+
+ export PETSC_DIR="${S}"
+ export PETSC_ARCH="linux-gnu-${mylang}-${myopt}"
+
+ if use debug; then
+ strip-flags
+ filter-flags -O*
+ fi
+
+ # 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 \
+ FFLAGS="${FFLAGS} -fPIC" \
+ CFLAGS="${CFLAGS} -fPIC" \
+ CXXFLAGS="${CXXFLAGS} -fPIC" \
+ LDFLAGS="${LDFLAGS}" \
+ --prefix="${EPREFIX}/usr/$(get_libdir)/petsc" \
+ --with-shared-libraries \
+ --with-single-library \
+ --with-clanguage=${mylang} \
+ $(use cxx && ! use complex-scalars && echo "with-c-support=1") \
+ --with-petsc-arch=${PETSC_ARCH} \
+ --with-precision=double \
+ --with-gnu-compilers \
+ --with-blas-lapack-lib="$($(tc-getPKG_CONFIG) --libs blas lapack)" \
+ $(petsc_enable debug debugging) \
+ $(petsc_enable mpi) \
+ $(petsc_select mpi cc mpicc $(tc-getCC)) \
+ $(petsc_select mpi cxx mpicxx $(tc-getCXX)) \
+ $(petsc_enable fortran) \
+ $(use fortran && echo "$(petsc_select mpi fc mpif77 $(tc-getF77))") \
+ $(petsc_enable mpi mpi-compilers) \
+ $(petsc_select complex-scalars scalar-type complex real) \
+ --with-windows-graphics=0 \
+ --with-matlab=0 \
+ --with-cmake:BOOL=1 \
+ $(petsc_enable threads pthread) \
+ $(petsc_with afterimage afterimage \
+ /usr/include/libAfterImage -lAfterImage) \
+ $(petsc_with hdf5) \
+ $(petsc_with hypre hypre \
+ /usr/include/hypre -lHYPRE) \
+ $(petsc_with sparse suitesparse) \
+ $(petsc_with superlu superlu \
+ /usr/include/superlu -lsuperlu) \
+ $(petsc_with X x) \
+ $(petsc_with X x11) \
+ $(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]) \
+ --with-imagemagick=0 \
+ --with-python=0 \
+ $(petsc_with boost) \
+ $(petsc_with fftw)
+}
+
+src_install() {
+ emake DESTDIR="${ED}" install
+
+ # add PETSC_DIR to environmental variables
+ cat >> 99petsc <<- EOF
+ PETSC_DIR=${EPREFIX}/usr/$(get_libdir)/petsc
+ LDPATH=${EPREFIX}/usr/$(get_libdir)/petsc/lib
+ EOF
+ doenvd 99petsc
+
+ if use doc ; then
+ docinto html
+ dodoc -r docs/*.html docs/changes docs/manualpages
+ fi
+}