Updated to 3.6.1

thanks to getzze

3 files changed, 152 insertions, 36 deletions

diff --git a/.SRCINFO b/.SRCINFO
index 9aed9317d75b..47d502ff75ad 100644
--- a/.SRCINFO
+++ b/.SRCINFO
@@ -1,6 +1,6 @@
 pkgbase = petsc
 	pkgdesc = Portable, extensible toolkit for scientific computation
-	pkgver = 3.6.0
+	pkgver = 3.6.1
 	pkgrel = 1
 	url = http://www.mcs.anl.gov/petsc/petsc-as
 	install = petsc.install
@@ -14,9 +14,19 @@ pkgbase = petsc
 	depends = openmpi
 	depends = boost
 	depends = lapack
+	optdepends = trilinos: support for trilinos
+	optdepends = ptscotch: support for ptscotch parallel graph partitioning library
+	optdepends = parmetis: support for parmetis parallel graph partitioning library
+	optdepends = metis: support for metis graph partitioning library
+	optdepends = pastix: support for the pastix solver
+	optdepends = superlu: support for the superlu sparse solver
+	optdepends = hdf5: support for the parallel version of hdf5
+	optdepends = mumps: support for the mumps sparse solver
 	options = staticlibs
-	source = http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-3.6.0.tar.gz
-	md5sums = f0dcbf25a8dd7f3069c1f094338c5263
+	source = http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-3.6.1.tar.gz
+	source = test_optdepends.sh
+	md5sums = 28f842697159e16e2978732480571147
+	md5sums = 4a82df77c43713f4bc698532db7ae02a
 
 pkgname = petsc
 
diff --git a/PKGBUILD b/PKGBUILD
index 7195e1bccdaf..e304e6f7d5b4 100644
--- a/PKGBUILD
+++ b/PKGBUILD
@@ -1,11 +1,11 @@
 # Maintainer: Myles English <myles at rockhead dot biz>
 pkgname=petsc
-pkgver=3.6.0
+pkgver=3.6.1
 pkgrel=1
-_config=arch-linux2-cxx-opt
+_config=linux-c-opt
 # if --with-debugging=yes is set then PETSC_ARCH is automatically set to
-#"arch-linux2-cxx-debug" for some things, so the _config should be changed too
-#_config=arch-linux2-cxx-debug
+#"linux-c-debug" for some things, so the _config should be changed too
+#_config=linux-c-debug
 pkgdesc="Portable, extensible toolkit for scientific computation"
 arch=('i686' 'x86_64')
 url="http://www.mcs.anl.gov/petsc/petsc-as"
@@ -13,62 +13,85 @@ license=('MIT compatible')
 options=(staticlibs)
 depends=('python2' 'openmpi' 'boost' 'lapack')
 makedepends=('gcc' 'gcc-fortran' 'cmake')
+optdepends=('trilinos: support for trilinos'
+    'ptscotch: support for ptscotch parallel graph partitioning library'
+    'parmetis: support for parmetis parallel graph partitioning library'
+    'metis: support for metis graph partitioning library'
+    'pastix: support for the pastix solver'
+    'superlu: support for the superlu sparse solver'
+    'hdf5: support for the parallel version of hdf5'
+    'mumps: support for the mumps sparse solver'
+    )
 install=petsc.install
-source=(http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/${pkgname}-${pkgver/_/-}.tar.gz)
-md5sums=('f0dcbf25a8dd7f3069c1f094338c5263')
+source=(http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/${pkgname}-${pkgver/_/-}.tar.gz test_optdepends.sh)
+md5sums=('28f842697159e16e2978732480571147'
+    '4a82df77c43713f4bc698532db7ae02a')
 
 _install_dir=/opt/petsc/${_config}
+petsc_arch="arch-${_config}"
 
 # to avoid: "make[2]: *** No rule to make target `libptesmumps.a', needed by `main_esmumps'.  Stop."
 export MAKEFLAGS="-j1"
 
+prepare() {
+	_build_dir="${srcdir}/${pkgname}-${pkgver/_/-}"
+
+	# force using python2
+	find ${srcdir} -name "*" -type f -exec \
+	sed -i 's#\(/usr/bin/env \|/usr/bin/\)python[2-3]*#\1python2#' {} \;
+
+	# install external libraries in _build_dir instead of the prefix
+	sed -i 's/self.publicInstall    = 1/self.publicInstall    = 0/' ${_build_dir}/config/BuildSystem/config/package.py
+}
+
 build() {
 	_build_dir="${srcdir}/${pkgname}-${pkgver/_/-}"
 
 	cd ${_build_dir}
-	#patch -Np1 -i ${startdir}/patch_debug.diff
 
 	unset PETSC_ARCH
 	export PETSC_DIR=${_build_dir}
 
-	find ${srcdir} -name "*" -type f -exec \
-	sed -i 's#\(/usr/bin/env \|/usr/bin/\)python[2-3]*#\1python2#' {} \;
-
-	CONFOPTS="--with-shared-libraries=1 --with-clanguage=C++ --COPTFLAGS=-O2 --CXXOPTFLAGS=-O2"
+	CONFOPTS="--with-shared-libraries=1 --COPTFLAGS=-O3 --CXXOPTFLAGS=-O3"
 
-	# External downloads
-	for external_pkg in ptscotch scalapack metis parmetis superlu mumps pastix hypre suitesparse; do
-		CONFOPTS="${CONFOPTS} --download-${external_pkg}=yes"
-	done
+    # test for the optional dependencies for petsc
+    CONFOPTS="${CONFOPTS} $(sh ${srcdir}/test_optdepends.sh)"
 
-	if [ "${TRILINOS_DIR}" ]; then
-		CONFOPTS="${CONFOPTS} --with-ml=1 --with-ml-lib=${TRILINOS_DIR}/lib/libml.so --with-ml-include=${TRILINOS_DIR}/include"
-	fi
+	# to enable use of type()
+	#CONFOPTS="${CONFOPTS} --with-fortran-datatypes --FOPTFLAGS=-O2"
 
-	# Arch specific
-	CONFOPTS="${CONFOPTS} --with-boost=1 --with-boost-dir=/usr"
+    echo ${CONFOPTS}
+	python2 ./configure \
+		--prefix=${_install_dir} \
+		--PETSC_ARCH=${petsc_arch} \
+		${CONFOPTS}
 
-	# to enable use of type()
-	CONFOPTS="${CONFOPTS} --with-fortran-datatypes --FOPTFLAGS=-O2"
+	make ${MAKEFLAGS} PETSC_DIR=${_build_dir} PETSC_ARCH=${petsc_arch} all
+}
 
-	python2 ./configure --prefix=${_install_dir} ${CONFOPTS}
+check() {
+	_build_dir="${srcdir}/${pkgname}-${pkgver/_/-}"
+	cd ${_build_dir}
 
-	make
+    make test
 }
 
 package() {
 	_build_dir="${srcdir}/${pkgname}-${pkgver/_/-}"
+	_dest_dir="${pkgdir}${_install_dir}"
+
 	cd ${_build_dir}
+	echo "make ${MAKEFLAGS} PETSC_DIR=${_build_dir} DESTDIR=${_dest_dir} install"
 	export PETSC_DIR=${_build_dir}
-	make install DESTDIR=${pkgdir}${_install_dir} # > /dev/null
-
-	sed -i 's#'"${pkgdir}"'##g' "${pkgdir}${_install_dir}/lib/pkgconfig/PETSc.pc"
-	sed -i 's#'"${pkgdir}"'##g' "${pkgdir}${_install_dir}/conf/variables"
-	sed -i 's#'"${pkgdir}"'##g' "${pkgdir}${_install_dir}/conf/petscvariables"
-	sed -i 's#'"${pkgdir}"'##g' "${pkgdir}${_install_dir}/conf/rules"
-	sed -i 's#'"${pkgdir}"'##g' "${pkgdir}${_install_dir}/include/petscconf.h"
-	sed -i 's#'"${pkgdir}"'##g' "${pkgdir}${_install_dir}/include/petscconfiginfo.h"
-	sed -i 's#'"${pkgdir}"'##g' "${pkgdir}${_install_dir}/conf/petscrules"
+	make ${MAKEFLAGS} PETSC_DIR=${_build_dir} DESTDIR=${_dest_dir} install   # > /dev/null
+
+	sed -i 's#'"${_build_dir}"'#'"${_install_dir}"'#g' "${_dest_dir}/lib/pkgconfig/PETSc.pc"
+	sed -i 's#'"${_build_dir}"'#'"${_install_dir}"'#g' "${_dest_dir}/lib/petsc/conf/variables"
+	sed -i 's#'"${_build_dir}"'#'"${_install_dir}"'#g' "${_dest_dir}/lib/petsc/conf/petscvariables"
+	sed -i 's#'"${_build_dir}"'#'"${_install_dir}"'#g' "${_dest_dir}/lib/petsc/conf/rules"
+	sed -i 's#'"${_build_dir}"'#'"${_install_dir}"'#g' "${_dest_dir}/include/petscconf.h"
+	sed -i 's#'"${_build_dir}"'#'"${_install_dir}"'#g' "${_dest_dir}/include/petscconfiginfo.h"
+	sed -i 's#'"${_build_dir}"'#'"${_install_dir}"'#g' "${_dest_dir}/lib/petsc/conf/petscrules"
 
 	export PETSC_DIR=${_install_dir}
 	
diff --git a/test_optdepends.sh b/test_optdepends.sh
new file mode 100644
index 000000000000..6e964dedaa49
--- /dev/null
+++ b/test_optdepends.sh
@@ -0,0 +1,83 @@
+#!/bin/bash
+
+# Test if external packages for PETSC are installed
+
+CONFOPTS=""
+
+## External downloads
+#for external_pkg in hypre; 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 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=${SUPERLU_DIR}"
+fi
+
+# Add pastix support
+PASTIX_CONF=$(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=1"
+	# Add boost support (may be useful for trilinos)
+	#CONFOPTS="${CONFOPTS} --with-boost=1"
+fi
+
+echo "${CONFOPTS}"