Upgrade to PETSc 2.3.3.

Changelog at
<http://www-unix.mcs.anl.gov/petsc/petsc-as/documentation/changes/233.html>

3 files changed, 61 insertions, 35 deletions

diff --git a/math/petsc/Makefile b/math/petsc/Makefile
index 936da70b9165..1cb0f38add26 100644
--- a/math/petsc/Makefile
+++ b/math/petsc/Makefile
@@ -6,8 +6,7 @@
 #
 
 PORTNAME=	petsc
-DISTVERSION=	2.3.2-p8
-PORTREVISION=	1
+DISTVERSION=	2.3.3-p0
 PORTEPOCH=	1
 CATEGORIES=	math parallel
 MASTER_SITES=	ftp://ftp.mcs.anl.gov/pub/petsc/release-snapshots/
@@ -15,18 +14,20 @@ MASTER_SITES=	ftp://ftp.mcs.anl.gov/pub/petsc/release-snapshots/
 MAINTAINER=	ports@FreeBSD.org
 COMMENT=	Portable, Extensible Toolkit for Scientific computation
 
-RUN_DEPENDS=	ksh:${PORTSDIR}/shells/pdksh
+RUN_DEPENDS=	ksh:${PORTSDIR}/shells/pdksh	\
+		qsub:${PORTSDIR}/sysutils/torque
+
+SLAVEDIRS=	math/petsc-mpich
 
 HAS_CONFIGURE=		yes
 USE_PYTHON=		yes
-USE_LDCONFIG=		yes
 CONFIGURE_SCRIPT=	config/configure.py
 CONFIGURE_LOG=		configure.log
 CONFIGURE_ENV=		PETSC_ARCH=${TARGET}	\
 			PETSC_DIR=${WRKSRC}
 CONFIGURE_ARGS=		--prefix=${PREFIX}/${PFX} --COPTFLAGS="${CFLAGS}"	\
 			--CXXOPTFLAGS="${CXXFLAGS}" --FOPTFLAGS="${FFLAGS}"	\
-			--with-shared=1 --with-cc=${CC} --with-fc=${F77}	\
+			--with-shared=1 --with-cc=${CC} --with-fc=${FC}	\
 			--CPPFLAGS="-I${LOCALBASE}/include"
 ALL_TARGET=		all
 MAKEFILE=		makefile
@@ -43,9 +44,9 @@ CONFIGURE_ARGS+=	--with-x-include=${X11BASE}/include	\
 .endif
 
 WANT_FORTRAN=yes #dummy but future use
-BUILD_DEPENDS+= gfortran42:${PORTSDIR}/lang/gcc42
-FC=	gfortran42
-F77=	gfortran42
+BUILD_DEPENDS+=	gfortran42:${PORTSDIR}/lang/gcc42
+FC=		gfortran42
+F77=		gfortran42
 FFLAGS+=	-O2
 PFX=		${PORTNAME}
 TARGET=		${OPSYS:L}
@@ -144,20 +145,22 @@ CONFIGURE_ARGS+=	--with-blocksolve95-include=${LOCALBASE}/mpich2/include	\
 			--with-blocksolve95-lib=${LOCALBASE}/lib/libBS95.a
 .endif
 
-.if defined(WITHOUT_PARMETIS)
+.if defined(WITHOUT_PARMETIS) || exists(${LOCALBASE}/lib/libmetis.so)
+# parmetis cannot be built with suitesparse
 CONFIGURE_ARGS+=	--with-parmetis=0
 .else
 BUILD_DEPENDS+=	${LOCALBASE}/lib/parmetis/libparmetis.a:${PORTSDIR}/math/parmetis
 CONFIGURE_ARGS+=	--with-parmetis=1					\
 			--with-parmetis-include=${LOCALBASE}/include/parmetis	\
 			--with-parmetis-lib=[${LOCALBASE}/lib/parmetis/libparmetis.a,${LOCALBASE}/lib/parmetis/libmetis.a]
+CONFLICTS+=		metis-4*
 .endif
 
 .if exists(${LIBBLACS})
 WITH_BLACS=	yes
 .endif
 .if defined(WITH_BLACS) && defined(WITH_MPI)
-BUILD_DEPENDS+=	${LIBBLACS}:${PORTSDIR}/math/blacs
+LIB_DEPENDS+=		blacs.1:${PORTSDIR}/math/blacs
 CONFIGURE_ARGS+=	--with_blacs=1	\
 			--with-blacs-include=${LOCALBASE}/include	\
 			--with-blacs-lib=[${LOCALBASE}/lib/libblacsc.a,${LOCALBASE}/lib/libblacsf77.a,${LOCALBASE}/lib/libblacs.a]
@@ -165,7 +168,7 @@ CONFIGURE_ARGS+=	--with_blacs=1	\
 WITH_SCALAPACK=	yes
 . endif
 . if defined(WITH_SCALAPACK)
-BUILD_DEPENDS+=	${LIBSCALAPACK}:${PORTSDIR}/math/scalapack
+LIB_DEPENDS+=		scalapack.1:${PORTSDIR}/math/scalapack
 CONFIGURE_ARGS+=	--with-scalapack=1	\
 			--with-scalapack-dir=${LOCALBASE}
 . endif
@@ -183,7 +186,7 @@ CONFIGURE_ARGS+=	--with-scalapack=1	\
 WITH_NETCDF=	yes
 .endif
 .if defined(WITH_NETCDF)
-LIB_DEPENDS+=	netcdf.1:${PORTSDIR}/science/netcdf
+LIB_DEPENDS+=	netcdf.4:${PORTSDIR}/science/netcdf
 CONFIGURE_ENV+=	PNETCDF_INCLUDE=${LOCALBASE}/include	\
 		PNETCDF_LIB=${LOCALBASE}/lib
 .endif
@@ -251,18 +254,18 @@ pre-everything::
 
 pre-configure:
 	@${RM} ${WRKSRC}/bmake/common/rules.shared.basic.orig
-	@${REINPLACE_CMD} -e "s|AMD/Include|include/AMD|"	\
+	${REINPLACE_CMD} -e "s|AMD/Include|include/AMD|"	\
 			-e "s|AMD/Lib|${LOCALBASE}/lib|"	\
 		${WRKSRC}/python/PETSc/packages/UMFPACK.py
-	@${REINPLACE_CMD} -e "s|/bin/ksh|${LOCALBASE}/bin/ksh|"	\
+	${REINPLACE_CMD} -e "s|/bin/ksh|${LOCALBASE}/bin/ksh|"	\
 		${WRKSRC}/bin/popup
 	@${RM} ${WRKSRC}/bin/popup.bak
 .if defined(PACKAGE_BUILDING)
-	@${REINPLACE_CMD} -e "s|%%PACKAGE%%exit 1; ||"		\
+	${REINPLACE_CMD} -e "s|%%PACKAGE%%exit 1; ||"		\
 		-e "s|%%PACKAGE%%sys.exit(3)||"			\
 		${WRKSRC}/makefile ${WRKSRC}/config/configure.py
 .else
-	@${REINPLACE_CMD} -e "s|%%PACKAGE%%||"			\
+	${REINPLACE_CMD} -e "s|%%PACKAGE%%||"			\
 		${WRKSRC}/makefile ${WRKSRC}/config/configure.py
 .endif
 
@@ -272,7 +275,7 @@ post-install:
 	${PYTHON_CMD} ${PYTHON_LIBDIR}/compileall.py ${PREFIX}/${PFX}/bmake
 	${PYTHON_CMD} -O ${PYTHON_LIBDIR}/compileall.py ${PREFIX}/${PFX}/bmake
 .if !defined(NOPORTDOCS)
-	@(cd ${BUILD_WRKSRC}; ${SETENV} ${MAKE_ENV} ${MAKE} ${MAKE_FLAGS}	\
+	(cd ${BUILD_WRKSRC}; ${SETENV} ${MAKE_ENV} ${MAKE} ${MAKE_FLAGS}	\
 		${MAKEFILE} ${MAKE_ARGS} install_docs)
 .endif
 	@${ECHO_MSG}
@@ -289,7 +292,7 @@ regression-test:
 .  endif
 	${LOCALBASE}/mpich2/bin/mpd &
 . endif
-	@(cd ${BUILD_WRKSRC};	\
+	(cd ${BUILD_WRKSRC};	\
 	${SETENV} ${MAKE_ENV} ${MAKE} ${MAKE_FLAGS} ${MAKEFILE} ${MAKE_ARGS} test)
 . if defined (WITH_MPI) && !defined(WITH_OPENMPI)
 	${LOCALBASE}/mpich2/bin/mpdallexit
diff --git a/math/petsc/distinfo b/math/petsc/distinfo
index 0ff7253001cb..ad43bfbfed01 100644
--- a/math/petsc/distinfo
+++ b/math/petsc/distinfo
@@ -1,3 +1,3 @@
-MD5 (petsc-2.3.2-p8.tar.gz) = 6eb51facb8ef2a3dc1cceb5d1b60162e
-SHA256 (petsc-2.3.2-p8.tar.gz) = 9a5bf4b9d77ca200fdecce9fd093bc2b37410e974a85b7cb13102e9b94bbc103
-SIZE (petsc-2.3.2-p8.tar.gz) = 10836578
+MD5 (petsc-2.3.3-p0.tar.gz) = 040475e8e7bacc126053537e3b3cdbc3
+SHA256 (petsc-2.3.3-p0.tar.gz) = a08d0f2022349321a26ae6c63f0ad5b069d37f48028377c549b81cc3e7b97ddf
+SIZE (petsc-2.3.3-p0.tar.gz) = 10966078
diff --git a/math/petsc/pkg-plist b/math/petsc/pkg-plist
index 5affadf53e8d..8b803a9670a2 100644
--- a/math/petsc/pkg-plist
+++ b/math/petsc/pkg-plist
@@ -19,28 +19,35 @@
 %%PFX%%/bin/config/install-sh
 %%PFX%%/bin/configarch
 %%PFX%%/bin/hostnames.chiba
+%%PFX%%/bin/matlab/@freader/close.m
+%%PFX%%/bin/matlab/@freader/freader.m
+%%PFX%%/bin/matlab/@freader/read.m
+%%PFX%%/bin/matlab/@sreader/close.m
+%%PFX%%/bin/matlab/@sreader/read.m
+%%PFX%%/bin/matlab/@sreader/sreader.m
 %%PFX%%/bin/matlab/PetscBagRead.m
 %%PFX%%/bin/matlab/PetscBinaryRead.m
 %%PFX%%/bin/matlab/PetscBinaryWrite.m
 %%PFX%%/bin/matlab/PetscReadBinaryMatlab.m
-%%PFX%%/bin/matlab/closeport.m
 %%PFX%%/bin/matlab/launch.m
-%%PFX%%/bin/matlab/openport.m
-%%PFX%%/bin/matlab/receive.m
+%%PFX%%/bin/mpiexec.chiba
+%%PFX%%/bin/mpiexec.gmalloc
+%%PFX%%/bin/mpiexec.lam
+%%PFX%%/bin/mpiexec.llrun
+%%PFX%%/bin/mpiexec.poe
+%%PFX%%/bin/mpiexec.prun
+%%PFX%%/bin/mpiexec.sshsync
+%%PFX%%/bin/mpiexec.uni
 %%PFX%%/bin/mpiexec.valgrind
-%%PFX%%/bin/mpirun.chiba
-%%PFX%%/bin/mpirun.gmalloc
-%%PFX%%/bin/mpirun.lam
-%%PFX%%/bin/mpirun.llrun
-%%PFX%%/bin/mpirun.poe
-%%PFX%%/bin/mpirun.prun
-%%PFX%%/bin/mpirun.uni
 %%PFX%%/bin/parseargs.py
 %%PFX%%/bin/parseargs.pyc
 %%PFX%%/bin/parseargs.pyo
 %%PFX%%/bin/petsc_libtool
-%%PFX%%/bin/petscmpirun
+%%PFX%%/bin/petscmpiexec
 %%PFX%%/bin/popup
+%%PFX%%/bin/portabilitycheck.py
+%%PFX%%/bin/portabilitycheck.pyc
+%%PFX%%/bin/portabilitycheck.pyo
 %%PFX%%/bin/processSummary.py
 %%PFX%%/bin/processSummary.pyc
 %%PFX%%/bin/processSummary.pyo
@@ -61,9 +68,6 @@
 %%PFX%%/bmake/adicmfb.init
 %%PFX%%/bmake/common/base
 %%PFX%%/bmake/common/rules
-%%PFX%%/bmake/common/rules.fortran.cpp
-%%PFX%%/bmake/common/rules.fortran.nocpp
-%%PFX%%/bmake/common/rules.fortran.none
 %%PFX%%/bmake/common/rules.shared.basic
 %%PFX%%/bmake/common/test
 %%PFX%%/bmake/common/variables
@@ -108,8 +112,11 @@
 %%PFX%%/include/finclude/moddeps
 %%PFX%%/include/finclude/petsc.h
 %%PFX%%/include/finclude/petsc.h.html
+%%PFX%%/include/finclude/petscall.h
+%%PFX%%/include/finclude/petscall.h90
 %%PFX%%/include/finclude/petscao.h
 %%PFX%%/include/finclude/petscao.h.html
+%%PFX%%/include/finclude/petscbag.h
 %%PFX%%/include/finclude/petscda.h
 %%PFX%%/include/finclude/petscda.h.html
 %%PFX%%/include/finclude/petscda.h90
@@ -131,6 +138,8 @@
 %%PFX%%/include/finclude/petscmat.h.html
 %%PFX%%/include/finclude/petscmat.h90
 %%PFX%%/include/finclude/petscmat.h90.html
+%%PFX%%/include/finclude/petscmesh.h
+%%PFX%%/include/finclude/petscmesh.h90
 %%PFX%%/include/finclude/petscmg.h
 %%PFX%%/include/finclude/petscmg.h.html
 %%PFX%%/include/finclude/petscpc.h
@@ -147,6 +156,7 @@
 %%PFX%%/include/finclude/petscvec.h90.html
 %%PFX%%/include/finclude/petscviewer.h
 %%PFX%%/include/finclude/petscviewer.h.html
+%%PFX%%/include/finclude/petscviewer.h90
 %%PFX%%/include/index.html
 %%PFX%%/include/makefile
 %%PFX%%/include/makefile.html
@@ -216,10 +226,21 @@
 %%PFX%%/include/petscversion.h.html
 %%PFX%%/include/petscviewer.h
 %%PFX%%/include/petscviewer.h.html
+%%PFX%%/include/private/isimpl.h
+%%PFX%%/include/private/isimpl.h.html
+%%PFX%%/include/private/kspimpl.h
+%%PFX%%/include/private/kspimpl.h.html
+%%PFX%%/include/private/matimpl.h
+%%PFX%%/include/private/matimpl.h.html
+%%PFX%%/include/private/meshimpl.h
 %%PFX%%/include/private/pcimpl.h
 %%PFX%%/include/private/pcimpl.h.html
 %%PFX%%/include/private/petscimpl.h
 %%PFX%%/include/private/petscimpl.h.html
+%%PFX%%/include/private/snesimpl.h
+%%PFX%%/include/private/snesimpl.h.html
+%%PFX%%/include/private/tsimpl.h
+%%PFX%%/include/private/tsimpl.h.html
 %%PFX%%/include/private/vecimpl.h
 %%PFX%%/include/private/vecimpl.h.html
 %%PFX%%/include/zpetsc.h
@@ -253,6 +274,8 @@
 @dirrm %%PFX%%/bmake/common
 @dirrm %%PFX%%/bmake
 @dirrm %%PFX%%/bin/win32fe
+@dirrm %%PFX%%/bin/matlab/@sreader
+@dirrm %%PFX%%/bin/matlab/@freader
 @dirrm %%PFX%%/bin/matlab
 @dirrm %%PFX%%/bin/config
 @dirrm %%PFX%%/bin