Changes by eDgar: use test_optdepends, remove patch

4 files changed, 262 insertions, 54 deletions

diff --git a/.SRCINFO b/.SRCINFO
index 5252cad925e8..decc76e75612 100644
--- a/.SRCINFO
+++ b/.SRCINFO
@@ -1,6 +1,6 @@
 pkgbase = petsc-git
-	pkgdesc = Portable, extensible toolkit for scientific computation
-	pkgver = 20191031
+	pkgdesc = Portable, extensible toolkit for scientific computation with MUMPS, Hypre, FFTW, HDF5, Scalapack, Suitesparse, Metis, Scotch, Superlu, OpenBLAS, Eigen, OpenMP, HWloc, CGNS, PNG, MED and trilinos
+	pkgver = 20200512
 	pkgrel = 1
 	url = https://www.mcs.anl.gov/petsc/
 	install = petsc.install
@@ -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 computing
+	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 matrix math
+	optdepends = openmp: Parallel distributed tasks
+	optdepends = hwloc: Portable Hardware Locality (abstraction of hierarchical architectures)
+	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 = fdf016437dd94f33316e734e35858476aeea1ca0f3ab4d0ee36029b016498de7
+	sha256sums = 2c21313b21b7a76ed4d39d040ef60462f8760ae3d4b76ff6aa717ebc43a2275b
 
 pkgname = petsc-git
 
diff --git a/PKGBUILD b/PKGBUILD
index dd088c9c15f8..786ad48c5ba2 100644
--- a/PKGBUILD
+++ b/PKGBUILD
@@ -1,25 +1,76 @@
+# Based on AUR petsc and petsc-git package. Adapted to my
+# MOOSE requirements
+
 # Maintainer: Lucas H. Gabrielli <heitzmann@gmail.com>
 
 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, Hypre, FFTW, HDF5, Scalapack, Suitesparse, Metis, Scotch, Superlu, OpenBLAS, Eigen, OpenMP, HWloc, CGNS, PNG, MED and trilinos"
 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 math"
+            "openmp: Parallel distributed tasks"
+            "hwloc: Portable Hardware Locality (abstraction of hierarchical architectures)"
+            "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
@@ -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/BuildSystem/config/package.py
+
+  sed -i "s/\(raise RuntimeError('--download-openblas libraries cannot be used')\)/#\1/" config/BuildSystem/config/packages/BlasLapack.py
 }
 
 
 build() {
   cd petsc
 
-  CONFOPTS='--with-shared-libraries=1 --COPTFLAGS=-O3 --CXXOPTFLAGS=-O3 --with-cxx-dialect=C++11 --with-mpi=1 --with-fftw=1 --with-hdf5=1 --with-zlib=1'
+  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-debug"
   #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 scalapack suitesparse sundials superlu superlu_dist
-  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} ${CONFOPTS}
-
+  python2 ./configure LDFLAGS="$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}"
@@ -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}/LICENSE
 
   mkdir -p "${pkgdir}/etc/profile.d"
@@ -99,22 +178,5 @@ package() {
   install -dm 755 "${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_dir}/lib/pkgconfig/PETSc.pc"
-  sed -i \
-    -e "s#prefix=.*#prefix=${_install_dir}#" \
-    -e "s#libdir=.*#libdir=\${prefix}/lib#" \
-    -e "s#includedir=.*#includedir=\${prefix}/include#" \
-    "${pkgdir}${_install_dir}/lib/pkgconfig/superlu.pc"
-  sed -i \
-    -e "s#prefix=.*#prefix=${_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}/${_petsc_arch}/lib/pkgconfig/PETSc.pc" "${pkgdir}/usr/share/pkgconfig/PETSc.pc"
+  sed -i "s#-L${_build_dir}/${_petsc_arch}/lib ##" "${pkgdir}${_install_dir}/lib/pkgconfig/PETSc.pc"
 }
diff --git a/patch.diff b/patch.diff
deleted file mode 100644
index 6bad18aa4495..000000000000
--- a/patch.diff
+++ /dev/null
@@ -1,13 +0,0 @@
-diff --git a/config/BuildSystem/config/package.py b/config/BuildSystem/config/package.py
-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 be false positives, SuperLU_DIST when looking for SuperLU
-     self.downloadonWindows      = 0  # 1 means the --download-package works on Microsoft Windows
-     self.requirescxx11          = 0
--    self.publicInstall          = 1  # Installs the package in the --prefix directory if it was given. Packages that are only used
-+    self.publicInstall          = 0  # Installs the package in the --prefix directory if it was given. Packages that are only used
-                                      # during the configuration/installation process such as sowing, make etc should be marked as 0
-     self.parallelMake           = 1  # 1 indicates the package supports make -j np option
- 
diff --git a/test_optdepends.sh b/test_optdepends.sh
new file mode 100644
index 000000000000..ba074436e88a
--- /dev/null
+++ b/test_optdepends.sh
@@ -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 scalapack; do
+# 	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.so,libscotcherr.so"
+	# 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_LIBS} --with-ptscotch-include=${SCOTCH_DIR}"
+fi
+
+# Add superlu support
+SUPERLU_DIR="/usr/include/superlu"
+if [ -d "${SUPERLU_DIR}" ]; then
+	CONFOPTS="${CONFOPTS} --with-superlu=1 --with-superlu-lib=-lsuperlu --with-superlu-include=${SUPERLU_DIR}"
+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=${SUNDIALS_DIR}"
+# fi
+
+# Add openblas support
+if [ -f "/usr/lib/libblas.so" ]; then
+	CONFOPTS="${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/pkgconfig/"
+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/pkgconfig/"
+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=${PASTIX_LIBS} --with-pastix-include=${PASTIX_DIR}"
+# 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}"