Fix dependencies, download external

3 files changed, 80 insertions, 211 deletions

diff --git a/.SRCINFO b/.SRCINFO
index decc76e75612..70707d3cda86 100644
--- a/.SRCINFO
+++ b/.SRCINFO
@@ -1,6 +1,6 @@
 pkgbase = petsc-git
-	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
+	pkgdesc = Portable, extensible toolkit for scientific computation (external downloads enabled)
+	pkgver = 20200520
 	pkgrel = 1
 	url = https://www.mcs.anl.gov/petsc/
 	install = petsc.install
@@ -11,37 +11,23 @@ pkgbase = petsc-git
 	makedepends = gcc-fortran
 	makedepends = cmake
 	makedepends = sowing
-	depends = python2
+	makedepends = 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
+	depends = suitesparse
 	optdepends = opencl: GPU computing
+	optdepends = hwloc: hardware locality
+	optdepends = cgns: CFD data support
+	optdepends = libpng: PNG support
+	optdepends = libyaml: YAML configuration support
+	optdepends = libx11: GUI tools
+	optdepends = python: Tools, examples, tutorials
 	provides = petsc
 	conflicts = petsc
 	source = petsc::git+https://gitlab.com/petsc/petsc.git#branch=maint
-	source = test_optdepends.sh
 	sha256sums = SKIP
-	sha256sums = 2c21313b21b7a76ed4d39d040ef60462f8760ae3d4b76ff6aa717ebc43a2275b
 
 pkgname = petsc-git
 
diff --git a/PKGBUILD b/PKGBUILD
index 786ad48c5ba2..101d855ce405 100644
--- a/PKGBUILD
+++ b/PKGBUILD
@@ -1,44 +1,27 @@
-# Based on AUR petsc and petsc-git package. Adapted to my
-# MOOSE requirements
-
 # Maintainer: Lucas H. Gabrielli <heitzmann@gmail.com>
 
 pkgname=petsc-git
-pkgver=20200512
+pkgver=20200520
 pkgrel=1
 _config=linux-c-opt
-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"
+pkgdesc="Portable, extensible toolkit for scientific computation (external downloads enabled)"
 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' '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")
+depends=('openmpi' 'lapack' 'fftw' 'hdf5' 'suitesparse')
+makedepends=('gcc' 'gcc-fortran' 'cmake' 'sowing' 'python2')
+optdepends=("opencl: GPU computing"
+            "hwloc: hardware locality"
+            "cgns: CFD data support"
+            "libpng: PNG support"
+            "libyaml: YAML configuration support"
+            "libx11: GUI tools"
+            "python: Tools, examples, tutorials")
 install=petsc.install
-source=(petsc::git+https://gitlab.com/petsc/petsc.git#branch=maint
-        test_optdepends.sh)
-sha256sums=('SKIP'
-            '2c21313b21b7a76ed4d39d040ef60462f8760ae3d4b76ff6aa717ebc43a2275b')
+source=(petsc::git+https://gitlab.com/petsc/petsc.git#branch=maint)
+sha256sums=('SKIP')
 
 _petsc_arch="arch-${_config}"
 
@@ -60,16 +43,16 @@ _petsc_arch="arch-${_config}"
 generic_flags="-fPIC -fopenmp -O3 -march=x86-64 -mtune=generic"
 # generic_flags="-fPIC -fopenmp -O3 -march=amdfam10 -mtune=generic"
 
-export   COPTFLAGS=-O3
+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="$generic_flags"
+export FOPTFLAGS=-O3
+export CPPFLAGS="$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() {
@@ -86,9 +69,7 @@ prepare() {
   done < <( find ${srcdir} -name "*" -type f -exec grep -le "$MATCH" \{\} + )
 
   cd "${srcdir}/petsc"
-  # 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
 }
 
@@ -96,11 +77,11 @@ prepare() {
 build() {
   cd petsc
 
-  declare -a CONFOPTS
   # Run python2 ./configure --help for the meaning of this
+  declare -a CONFOPTS
   CONFOPTS=(
     --COPTFLAGS="$COPTFLAGS"
-    --CXXOPTFLAGS="CXXOPTFLAGS"
+    --CXXOPTFLAGS="$CXXOPTFLAGS"
     --CPPFLAGS="$CPPFLAGS"
     --CFLAGS="$CFLAGS"
     --CXXFLAGS="$CXXFLAGS"
@@ -115,18 +96,59 @@ build() {
     --with-shared-libraries=1
     --with-zlib=1
 
+    --with-fftw=1
+    --with-hdf5=1
+    --with-suitesparse=1
+
     --with-scalar-type=complex
-    # Add this to test_optdepends.sh
-    --with-opencl=1
-    --with-yaml=1
+
+    --download-amd=1
+    --download-eigen=1
+    --download-hypre=1
+    --download-metis=1
+    --download-mumps=1
+    --download-parmetis=1
+    #--download-party=1  # not working
+    --download-ptscotch=1
+    --download-scalapack=1
+    #--download-suitesparse=1  # not working
+    #--download-sundials=1  # incompatible with complex
+    --download-superlu=1
+    --download-superlu_dist=1
   )
 
+  CONFOPTS=( "${CONFOPTS[@]}" )
+
+  # Add OpenCL support
+  OPENCL_DIR="/usr/include/CL/"
+  if [ -f "${OPENCL_DIR}/cl.h" ]; then
+    CONFOPTS="${CONFOPTS} --with-opencl=1"
+  fi
+
+  # Add hwloc support
+  if [ -f "/usr/lib/libhwloc.so" ]; then
+    CONFOPTS="${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 YAML support
+  if [ -f "/usr/lib/libyaml.so" ]; then
+    CONFOPTS="${CONFOPTS} --with-yaml=1 --with-yaml-pkg-config=/usr/lib/pkgconfig/"
+  fi
+
   # if --with-debugging=1 is set then PETSC_ARCH is automatically set to
   # "linux-c-debug" for some things, so _config should be changed to "linux-c-debug"
   #CONFOPTS="${CONFOPTS} --with-debugging=1"
 
-  CONFOPTS=( "${CONFOPTS[@]}" $(sh "${srcdir}"/test_optdepends.sh) )
-
   dirpkg=${srcdir}/petsc/${_petsc_arch}/externalpackages/
 
   export PETSC_DIR="${srcdir}/petsc"
diff --git a/test_optdepends.sh b/test_optdepends.sh
deleted file mode 100644
index ba074436e88a..000000000000
--- a/test_optdepends.sh
+++ /dev/null
@@ -1,139 +0,0 @@
-#!/bin/bash
-
-# Test if external packages for PETSC are installed
-
-# CONFOPTS=""
-
-# # External downloads
-# for external_pkg in hypre fblaslapack metis parmetis superlu_dist mumps scalapack; do
-# 	CONFOPTS="${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}"