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	tChanges by eDgar: use test_optdepends, remove patch - petsc-git-PKGBUILD - bui…
	git clone git://src.adamsgaard.dk/petsc-git-PKGBUILD
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	---
	commit acf8ee6afcc1b738e1337c2901eeb948346c64d6
	parent b3de4b154ef9aa84493368218f6a96e13df17ed7
	Author: Lucas Heitzmann Gabrielli <[email protected]>
	Date: Tue, 12 May 2020 12:13:21 -0300

	Changes by eDgar: use test_optdepends, remove patch

	Diffstat:
	M .SRCINFO \| 30 +++++++++++++++++++++++++-----
	M PKGBUILD \| 134 ++++++++++++++++++++++-------…
	D patch.diff \| 13 -------------
	A test_optdepends.sh \| 139 ++++++++++++++++++++++++++++++

	4 files changed, 262 insertions(+), 54 deletions(-)
	---
	diff --git a/.SRCINFO b/.SRCINFO
	t@@ -1,6 +1,6 @@
	pkgbase = petsc-git
	- pkgdesc = Portable, extensible toolkit for scientific computation
	- pkgver = 20191031
	+ pkgdesc = Portable, extensible toolkit for scientific computation with…
	+ pkgver = 20200512
	pkgrel = 1
	url = https://www.mcs.anl.gov/petsc/
	install = petsc.install
	t@@ -10,18 +10,38 @@ pkgbase = petsc-git
	makedepends = gcc
	makedepends = gcc-fortran
	makedepends = cmake
	+ makedepends = sowing
	depends = python2
	depends = openmpi
	depends = boost
	depends = lapack
	depends = fftw
	depends = hdf5
	+ optdepends = hdf5: large files
	+ optdepends = fftw: Fast-Fourier Transform
	+ optdepends = openblas: Linear algebra libraries
	+ optdepends = scalapack: Parallel memory linear algebra
	+ optdepends = mumps: Sparse solver library
	+ optdepends = hypre: Large and sparse linear with massive parallel comp…
	+ optdepends = suitesparse: Sparse matrix library
	+ optdepends = metis: Partitioning library (for meshes)
	+ optdepends = scotch: Partitioning with sparse matrices
	+ optdepends = superlu: Subroutines for sparsse linear systems
	+ optdepends = eigen: Lightweight C++ template library for vector and ma…
	+ optdepends = openmp: Parallel distributed tasks
	+ optdepends = hwloc: Portable Hardware Locality (abstraction of hierarc…
	+ optdepends = cgns: Recording and recovering computer data
	+ optdepends = png
	+ optdepends = med>=4.0: Data Modelization and Exchanges (meshes)
	+ optdepends = boost: Free peer-reviewed portable C++ source libraries
	+ optdepends = yaml: configuration files
	+ optdepends = opencl: GPU computing
	provides = petsc
	conflicts = petsc
	- source = petsc::git+https://gitlab.com/petsc/petsc#branch=maint
	- source = patch.diff
	+ source = petsc::git+https://gitlab.com/petsc/petsc.git#branch=maint
	+ source = test_optdepends.sh
	sha256sums = SKIP
	- sha256sums = fdf016437dd94f33316e734e35858476aeea1ca0f3ab4d0ee36029b01…
	+ sha256sums = 2c21313b21b7a76ed4d39d040ef60462f8760ae3d4b76ff6aa717ebc4…

	pkgname = petsc-git

	diff --git a/PKGBUILD b/PKGBUILD
	t@@ -1,25 +1,76 @@
	+# Based on AUR petsc and petsc-git package. Adapted to my
	+# MOOSE requirements
	+
	# Maintainer: Lucas H. Gabrielli <[email protected]>

	pkgname=petsc-git
	-pkgver=20191031
	+pkgver=20200512
	pkgrel=1
	_config=linux-c-opt
	-pkgdesc="Portable, extensible toolkit for scientific computation"
	+pkgdesc="Portable, extensible toolkit for scientific computation with MUMPS, H…
	provides=(petsc)
	conflicts=(petsc)
	arch=('i686' 'x86_64')
	url="https://www.mcs.anl.gov/petsc/"
	license=('BSD')
	depends=('python2' 'openmpi' 'boost' 'lapack' 'fftw' 'hdf5')
	-makedepends=('gcc' 'gcc-fortran' 'cmake')
	+makedepends=('gcc' 'gcc-fortran' 'cmake' 'sowing')
	+optdepends=("hdf5: large files"
	+ "fftw: Fast-Fourier Transform"
	+ "openblas: Linear algebra libraries"
	+ "scalapack: Parallel memory linear algebra"
	+ "mumps: Sparse solver library"
	+ "hypre: Large and sparse linear with massive parallel computing"
	+ "suitesparse: Sparse matrix library"
	+ "metis: Partitioning library (for meshes)"
	+ "scotch: Partitioning with sparse matrices"
	+ "superlu: Subroutines for sparsse linear systems"
	+ "eigen: Lightweight C++ template library for vector and matrix mat…
	+ "openmp: Parallel distributed tasks"
	+ "hwloc: Portable Hardware Locality (abstraction of hierarchical ar…
	+ "cgns: Recording and recovering computer data"
	+ "png"
	+ "med>=4.0: Data Modelization and Exchanges (meshes)"
	+ "boost: Free peer-reviewed portable C++ source libraries"
	+ "yaml: configuration files"
	+ "opencl: GPU computing")
	install=petsc.install
	-source=(petsc::git+https://gitlab.com/petsc/petsc#branch=maint
	- patch.diff)
	+source=(petsc::git+https://gitlab.com/petsc/petsc.git#branch=maint
	+ test_optdepends.sh)
	sha256sums=('SKIP'
	- 'fdf016437dd94f33316e734e35858476aeea1ca0f3ab4d0ee36029b016498de7')
	+ '2c21313b21b7a76ed4d39d040ef60462f8760ae3d4b76ff6aa717ebc43a2275b')

	_petsc_arch="arch-${_config}"

	+#####################################################################
	+# From UPC: Building And Using Static And Shared "C" Libraries.html #
	+# #+begin_QUOTE #
	+# we need that all jump calls ("goto", in assembly speak) #
	+# and subroutine calls will use relative addresses, and not #
	+# absolute addresses. Thus, we need to use ... ~-fPIC~ or #
	+# ~-fpic~ #
	+# #+end_QUOTE #
	+#####################################################################
	+###############################################################################
	+# From makepkg.conf #
	+# -march (or -mcpu) builds exclusively for an architecture #
	+# -mtune optimizes for an architecture, but builds for whole processor family #
	+###############################################################################
	+# -O3 optimises
	+generic_flags="-fPIC -fopenmp -O3 -march=x86-64 -mtune=generic"
	+# generic_flags="-fPIC -fopenmp -O3 -march=amdfam10 -mtune=generic"
	+
	+export COPTFLAGS=-O3
	+export CXXOPTFLAGS=-O3
	+export FOPTFLAGS=-O3
	+export CPPFLAGS="$generic_flags -O2 -D-FORTIFY-SOURCE=2"
	+export CFLAGS="$generic_flags"
	+export CXXFLAGS="$generic_flags"
	+export FFLAGS="$generic_flags"
	+export FCFLAGS="$generic_flags"
	+export F90FLAGS="$generic_flags"
	+export F77FLAGS="$generic_flags"
	+

	pkgver() {
	cd petsc
	t@@ -35,39 +86,67 @@ prepare() {
	done < <( find ${srcdir} -name "*" -type f -exec grep -le "$MATCH" \{\} + )

	cd "${srcdir}/petsc"
	- patch -p1 < ../patch.diff
	+ # patch -p1 < ../patch.diff
	+ sed -i 's-$self.publicInstall[^=]=[[:space:]]$[^#]-\10 -g' config/BuildS…
	+
	+ sed -i "s/\(raise RuntimeError('--download-openblas libraries cannot be used…
	}


	build() {
	cd petsc

	- CONFOPTS='--with-shared-libraries=1 --COPTFLAGS=-O3 --CXXOPTFLAGS=-O3 --with…
	+ declare -a CONFOPTS
	+ # Run python2 ./configure --help for the meaning of this
	+ CONFOPTS=(
	+ --COPTFLAGS="$COPTFLAGS"
	+ --CXXOPTFLAGS="CXXOPTFLAGS"
	+ --CPPFLAGS="$CPPFLAGS"
	+ --CFLAGS="$CFLAGS"
	+ --CXXFLAGS="$CXXFLAGS"
	+ --FFLAGS="$FFLAGS"
	+ --FCFLAGS="$FCFLAGS"
	+ --F90FLAGS="$F90FLAGS"
	+ --F77FLAGS="$F77FLAGS"
	+
	+ --with-cxx-dialect=C++11
	+ --with-mpi=1
	+ --with-pic=1
	+ --with-shared-libraries=1
	+ --with-zlib=1
	+
	+ --with-scalar-type=complex
	+ # Add this to test_optdepends.sh
	+ --with-opencl=1
	+ --with-yaml=1
	+ )

	# if --with-debugging=1 is set then PETSC_ARCH is automatically set to
	# "linux-c-debug" for some things, so _config should be changed to "linux-c-…
	#CONFOPTS="${CONFOPTS} --with-debugging=1"

	- # Removed pastix due to incompatibility with current MPI (2019-10-31)
	- for external_pkg in amd eigen hypre metis mumps parmetis party ptscotch scal…
	- do
	- CONFOPTS="${CONFOPTS} --download-${external_pkg}=1"
	- done
	+ CONFOPTS=( "${CONFOPTS[@]}" $(sh "${srcdir}"/test_optdepends.sh) )
	+
	+ dirpkg=${srcdir}/petsc/${_petsc_arch}/externalpackages/

	export PETSC_DIR="${srcdir}/petsc"
	export PETSC_ARCH="${_petsc_arch}"

	- python2 ./configure LDFLAGS="$LDFLAGS" --prefix=/opt/petsc/${_config} ${CONF…
	-
	+ python2 ./configure LDFLAGS="$LDFLAGS" \
	+ --prefix=/usr/petsc/${_config} \
	+ --MAKEFLAGS="$MAKEFLAGS" \
	+ $(for (( i=1; i<=${#CONFOPTS[@]}; i++)); do
	+ echo "${CONFOPTS[$i]}";
	+ done)
	+ make clean
	make all
	}

	-
	package() {
	cd petsc

	_build_dir="${srcdir}/petsc"
	- _install_dir=/opt/petsc/${_config}
	+ _install_dir=/usr/petsc/${_config}

	export PETSC_DIR=${_build_dir}
	export PETSC_ARCH="${_petsc_arch}"
	t@@ -88,7 +167,7 @@ package() {
	#mkdir -p ${pkgdir}/usr/share/doc/petsc/include
	#cp -r ${_build_dir}/include/*.html ${pkgdir}/usr/share/doc/petsc/include/

	- # install licence (even though there is no such word as licenses)
	+ # install license (even though there is no such word as licenses)
	install -Dm 644 ${_build_dir}/LICENSE ${pkgdir}/usr/share/licenses/${pkgname…

	mkdir -p "${pkgdir}/etc/profile.d"
	t@@ -99,22 +178,5 @@ package() {
	install -dm 755 "${pkgdir}/etc/ld.so.conf.d/"
	echo "${_install_dir}/lib" > "${pkgdir}/etc/ld.so.conf.d/petsc.conf"

	- sed -i "s#-L${_build_dir}/${_petsc_arch}/lib ##" "${pkgdir}${_install_…
	- sed -i \
	- -e "s#prefix=.*#prefix=${_install_dir}#" \
	- -e "s#libdir=.*#libdir=\${prefix}/lib#" \
	- -e "s#includedir=.*#includedir=\${prefix}/include#" \
	- "${pkgdir}${_install_dir}/lib/pkgconfig/superlu.pc"
	- sed -i \
	- -e "s#prefix=.*#prefix=${_install_dir}#" \
	- -e "s#libdir=.*#libdir=\${prefix}/lib#" \
	- -e "s#includedir=.*#includedir=\${prefix}/include#" \
	- "${pkgdir}${_install_dir}/lib/pkgconfig/superlu_dist.pc"
	- sed -i \
	- -e "s#prefix=.*#prefix=${_install_dir};#" \
	- -e "s#libdir=.*#libdir=\${prefix}/lib;#" \
	- "${pkgdir}${_install_dir}/lib/petsc/bin/sundials-config"
	-
	- # install pkgconfig settings
	- #install -Dm 644 "${_build_dir}/${_petsc_arch}/lib/pkgconfig/PETSc.pc" "${pk…
	+ sed -i "s#-L${_build_dir}/${_petsc_arch}/lib ##" "${pkgdir}${_install_dir}/l…
	}
	diff --git a/patch.diff b/patch.diff
	t@@ -1,13 +0,0 @@
	-diff --git a/config/BuildSystem/config/package.py b/config/BuildSystem/config/…
	-index d7777d623b..9dfcf66cee 100644
	---- a/config/BuildSystem/config/package.py
	-+++ b/config/BuildSystem/config/package.py
	-@@ -60,7 +60,7 @@ class Package(config.base.Configure):
	- self.excludedDirs = [] # list of directory names that could b…
	- self.downloadonWindows = 0 # 1 means the --download-package works o…
	- self.requirescxx11 = 0
	-- self.publicInstall = 1 # Installs the package in the --prefix d…
	-+ self.publicInstall = 0 # Installs the package in the --prefix d…
	- # during the configuration/installation …
	- self.parallelMake = 1 # 1 indicates the package supports make …
	-
	diff --git a/test_optdepends.sh b/test_optdepends.sh
	t@@ -0,0 +1,139 @@
	+#!/bin/bash
	+
	+# Test if external packages for PETSC are installed
	+
	+# CONFOPTS=""
	+
	+# # External downloads
	+# for external_pkg in hypre fblaslapack metis parmetis superlu_dist mumps scal…
	+# CONFOPTS="${CONFOPTS} --download-${external_pkg}=1"
	+# done
	+
	+# Add hypre support
	+if [ -f "/usr/lib/libHYPRE.so" ]; then
	+ CONFOPTS="${CONFOPTS} --with-hypre=1"
	+fi
	+
	+# Add mumps support
	+if [ -f "/usr/lib/libmumps_common.so" ]; then
	+ CONFOPTS="${CONFOPTS} --with-mumps=1"
	+fi
	+
	+# Add fftw support
	+if [ -f "/usr/lib/libfftw3_mpi.so" ]; then
	+ CONFOPTS="${CONFOPTS} --with-fftw=1"
	+fi
	+
	+# Add hdf5 support
	+if [[ "$(h5stat -V)" ]]; then
	+ CONFOPTS="${CONFOPTS} --with-hdf5=1"
	+fi
	+
	+# Add scalapack support
	+if [ -f "/usr/lib/pkgconfig/scalapack.pc" ]; then
	+ CONFOPTS="${CONFOPTS} --with-scalapack=1"
	+fi
	+
	+# Add suitesparse support
	+if [ -f "/usr/include/SuiteSparse_config.h" ]; then
	+ CONFOPTS="${CONFOPTS} --with-suitesparse=1"
	+fi
	+
	+# Add metis support
	+if [ -f "/usr/include/metis.h" ]; then
	+ CONFOPTS="${CONFOPTS} --with-metis=1"
	+ # Add parmetis support
	+ if [ -f "/usr/include/parmetis.h" ]; then
	+ CONFOPTS="${CONFOPTS} --with-parmetis=1"
	+ fi
	+fi
	+
	+# Add scotch support
	+SCOTCH_DIR="/usr/include/scotch"
	+if [ -d "${SCOTCH_DIR}" ]; then
	+ SCOTCH_LIBS="libesmumps.so,libptscotch.so,libptscotcherr.so,libscotch.…
	+ # Include bzip2 if scotch was build with bzip2 support
	+ if [ -f /usr/include/bzlib.h ];then
	+ SCOTCH_LIBS="${SCOTCH_LIBS},libbz2.so"
	+ fi
	+ SCOTCH_LIBS="[${SCOTCH_LIBS}]"
	+ CONFOPTS="${CONFOPTS} --with-ptscotch=1 --with-ptscotch-lib=${SCOTCH_L…
	+fi
	+
	+# Add superlu support
	+SUPERLU_DIR="/usr/include/superlu"
	+if [ -d "${SUPERLU_DIR}" ]; then
	+ CONFOPTS="${CONFOPTS} --with-superlu=1 --with-superlu-lib=-lsuperlu --…
	+fi
	+
	+# Incompatible with complex
	+# # Add sundials support
	+# SUNDIALS_DIR="/usr/include/sundials/"
	+# if [ -d "${SUNDIALS_DIR}" ]; then
	+# CONFOPTS="${CONFOPTS} --with-sundials=1 --with-sundials-include=${SU…
	+# fi
	+
	+# Add openblas support
	+if [ -f "/usr/lib/libblas.so" ]; then
	+ CONFOPTS="${CONFOPTS} --with-openblas=1"
	+fi
	+
	+# Add OpenCL support
	+OPENCL_DIR="/usr/include/CL/"
	+if [ -f "${OPENCL_DIR}/cl.h" ]; then
	+ CONFOPTS="${CONFOPTS} --with-opencl=1"
	+else
	+ CONFOPTS="${CONFOPTS} --with-opencl=0"
	+fi
	+
	+# Add eigen support
	+EIGEN_DIR="/usr/include/eigen3"
	+if [ -d "${EIGEN_DIR}" ]; then
	+ CONFOPTS="${CONFOPTS} --with-eigen=1 --with-eigen-include=${EIGEN_DIR}"
	+fi
	+
	+# Add OpenMP support
	+if [ -f "/usr/lib/libomp.so" ]; then
	+ CONFOPTS="${CONFOPTS} --with-openmp=1"
	+fi
	+
	+# Add hwloc support
	+if [ -f "/usr/lib/libhwloc.so" ]; then
	+ CONFOPTS="${CONFOPTS} --with-hwloc=1 --with-hwloc-pkg-config=/usr/lib/…
	+fi
	+
	+# Add CGNS support
	+if [ -f "/usr/lib/libcgns.so" ]; then
	+ CONFOPTS="${CONFOPTS} --with-cgns=1"
	+fi
	+
	+# Add PNG support
	+if [ -f "/usr/lib/libpng.so" ]; then
	+ CONFOPTS="${CONFOPTS} --with-png=1 --with-png-pkg-config=/usr/lib/pkgc…
	+fi
	+
	+# Add MED support
	+if [ -f "/usr/lib/libmed.so" ]; then
	+ CONFOPTS="${CONFOPTS} --with-med=1"
	+fi
	+
	+# # Add pastix support
	+# PASTIX_CONF=$(which pastix-conf)
	+# if [ -f "${PASTIX_CONF}" ]; then
	+# PASTIX_DIR="$($PASTIX_CONF --incs \| sed 's/-I//')"
	+# if [ ! -d ${PASTIX_DIR} ]; then
	+# PASTIX_DIR="[]"
	+# fi
	+# #PASTIX_LIBS="$($PASTIX_CONF --libs)"
	+# PASTIX_LIBS="[libpastix.a,librt.so,libhwloc.so,libpthread.a]"
	+# CONFOPTS="${CONFOPTS} --with-pastix=1 --with-pastix-lib=${PASTIX_LIB…
	+# fi
	+
	+# Add trilinos support
	+if [ "${TRILINOS_DIR}" ]; then
	+ CONFOPTS="${CONFOPTS} --with-ml-dir=${TRILINOS_DIR}"
	+ # Add boost support (may be useful for trilinos)
	+ CONFOPTS="${CONFOPTS} --with-boost=1"
	+fi
	+
	+echo "${CONFOPTS}"