math/libmesh: Update 1.4.1 -> 1.6.0-rc3

5 files changed, 69 insertions, 38 deletions

diff --git a/math/libmesh/Makefile b/math/libmesh/Makefile
index 6a1fad5fa13b..49f290fc76ae 100644
--- a/math/libmesh/Makefile
+++ b/math/libmesh/Makefile
@@ -3,8 +3,7 @@
 
 PORTNAME=	libmesh
 DISTVERSIONPREFIX=	v
-DISTVERSION=	1.4.1
-PORTREVISION=	3
+DISTVERSION=	1.6.0-rc3
 CATEGORIES=	math
 
 MAINTAINER=	yuri@FreeBSD.org
@@ -15,10 +14,8 @@ LICENSE_FILE=	${WRKSRC}/COPYING
 
 LIB_DEPENDS=	libboost_system.so:devel/boost-libs
 
-USES=		autoreconf compiler:c++11-lang eigen:3 gmake libtool
+USES=		compiler:c++11-lang eigen:3 gmake libtool perl5
 GNU_CONFIGURE=	yes
-USE_GITHUB=	yes
-GH_ACCOUNT=	libMesh
 CONFIGURE_ARGS=	--disable-static \
 		--with-methods=opt \
 		--with-thread-model=pthread \
@@ -30,9 +27,18 @@ CONFIGURE_ARGS=	--disable-static \
 		--with-boost=${LOCALBASE} \
 		--with-eigen-include=${LOCALBASE}/include/eigen3 \
 		--disable-netcdf --disable-netcdf-4 # https://github.com/libMesh/libmesh/issues/1542
+CONFIGURE_ARGS+=	--disable-metaphysicl # enabling this causes libmesh to install a bundled metaphysicl that would conflict with the metaphysicl package
 MAKE_ARGS=	LDFLAGS="-pthread -lexecinfo"
 USE_LDCONFIG=	yes
 
+INSTALL_TARGET=	install-strip
+
+USE_GITHUB=	yes
+GH_ACCOUNT=	libMesh
+GH_TUPLE=	\
+		libMesh:TIMPI:7fbe63d:TIMPI/contrib/timpi \
+		libMesh:autoconf-submodule:9bb972f:autoconf_submodule/m4/autoconf-submodule
+
 OPTIONS_DEFINE=			GLPK HDF5 MPI EXAMPLES
 OPTIONS_DEFAULT=		MPI
 GLPK_DESC=			Glpk linear programming solver library
diff --git a/math/libmesh/distinfo b/math/libmesh/distinfo
index 116c32a70733..6fa3ed352fb2 100644
--- a/math/libmesh/distinfo
+++ b/math/libmesh/distinfo
@@ -1,3 +1,7 @@
-TIMESTAMP = 1556957959
-SHA256 (libMesh-libmesh-v1.4.1_GH0.tar.gz) = 2123c77900b93cc9cc80a1d4a350cc90667a5e04fb7770d70d6d164a613d2032
-SIZE (libMesh-libmesh-v1.4.1_GH0.tar.gz) = 31433372
+TIMESTAMP = 1602651092
+SHA256 (libMesh-libmesh-v1.6.0-rc3_GH0.tar.gz) = 3e62b8c676ae3ffa72a48790446dc9617b135d9b14347c47c768e51d2012acff
+SIZE (libMesh-libmesh-v1.6.0-rc3_GH0.tar.gz) = 32267256
+SHA256 (libMesh-TIMPI-7fbe63d_GH0.tar.gz) = 5e24d2ba25944a2b8402b37b4e7f92c5e75d426e249e9a00bb223b69bd075927
+SIZE (libMesh-TIMPI-7fbe63d_GH0.tar.gz) = 502232
+SHA256 (libMesh-autoconf-submodule-9bb972f_GH0.tar.gz) = abaa9c68f3838d8739328741a94743ba4954a5d61505aae3c77d937f93428083
+SIZE (libMesh-autoconf-submodule-9bb972f_GH0.tar.gz) = 10557
diff --git a/math/libmesh/files/patch-Makefile.am b/math/libmesh/files/patch-Makefile.am
deleted file mode 100644
index 7973069df9f2..000000000000
--- a/math/libmesh/files/patch-Makefile.am
+++ /dev/null
@@ -1,14 +0,0 @@
---- Makefile.am.orig	2017-07-25 16:33:31 UTC
-+++ Makefile.am
-@@ -102,9 +102,8 @@ install-data-hook:
-         fi
- 	cd $(DESTDIR)$(prefix) && rm -f Make.common && $(LN_S) -f etc/libmesh/Make.common Make.common
- 	cat $(DESTDIR)$(libmesh_configdir)/libmesh-config | $(SED) "s/has_been_installed=no/has_been_installed=yes/g" > $(DESTDIR)$(libmesh_configdir)/libmesh-config.installed
--	mv $(DESTDIR)$(libmesh_configdir)/libmesh-config.installed $(DESTDIR)$(libmesh_configdir)/libmesh-config && chmod +x $(DESTDIR)$(libmesh_configdir)/libmesh-config
--	cat $(DESTDIR)$(prefix)/contrib/bin/libtool | $(SED) "s/-l //g" > $(DESTDIR)$(prefix)/contrib/bin/libtool.fixed
--	mv $(DESTDIR)$(prefix)/contrib/bin/libtool.fixed $(DESTDIR)$(prefix)/contrib/bin/libtool && chmod +x $(DESTDIR)$(prefix)/contrib/bin/libtool
-+	install -c $(DESTDIR)$(libmesh_configdir)/libmesh-config.installed $(DESTDIR)$(libmesh_configdir)/libmesh-config
-+	rm $(DESTDIR)$(libmesh_configdir)/libmesh-config.installed
- 
- 
- # this rule invokes emacs on each source file to remove trailing whitespace.
diff --git a/math/libmesh/files/patch-contrib_netcdf_4.4.1.1_configure.ac b/math/libmesh/files/patch-contrib_netcdf_4.4.1.1_configure.ac
deleted file mode 100644
index 1babc46b7a02..000000000000
--- a/math/libmesh/files/patch-contrib_netcdf_4.4.1.1_configure.ac
+++ /dev/null
@@ -1,11 +0,0 @@
---- contrib/netcdf/4.4.1.1/configure.ac.orig	2017-07-25 16:33:31 UTC
-+++ contrib/netcdf/4.4.1.1/configure.ac
-@@ -926,7 +926,7 @@ if test "x$enable_netcdf_4" = xyes; then
-       if test "x$nc_dlfcn_h_missing" = xyes; then
-       	      AC_MSG_ERROR([Cannot find dlfcn.h, yet --enable-dynamic-loading was used.])
-       fi
--      AC_CHECK_LIB([dl],[dlopen], [], [AC_MSG_ERROR([Can't find or link against libdf. See config.log for errors.])])
-+      #AC_CHECK_LIB([dl],[dlopen], [], [AC_MSG_ERROR([Can't find or link against libdf. See config.log for errors.])])
-       AC_DEFINE([USE_LIBDL],[1], [if true, enable dynamic loading support])
-    fi
- 
diff --git a/math/libmesh/pkg-plist b/math/libmesh/pkg-plist
index 1cd16f2567fa..ecaafb482771 100644
--- a/math/libmesh/pkg-plist
+++ b/math/libmesh/pkg-plist
@@ -15,6 +15,8 @@ bin/output_libmesh_version-opt
 bin/projection-opt
 bin/solution_components-opt
 bin/splitter-opt
+bin/timpi-config
+bin/timpi_version-opt
 include/gzstream.h
 include/libmesh/abaqus_io.h
 include/libmesh/adaptive_time_solver.h
@@ -67,12 +69,14 @@ include/libmesh/data_type.h
 include/libmesh/default_coupling.h
 include/libmesh/dense_matrix.h
 include/libmesh/dense_matrix_base.h
+include/libmesh/dense_matrix_base_impl.h
 include/libmesh/dense_matrix_impl.h
 include/libmesh/dense_submatrix.h
 include/libmesh/dense_subvector.h
 include/libmesh/dense_vector.h
 include/libmesh/dense_vector_base.h
 include/libmesh/dg_fem_context.h
+include/libmesh/diagonal_matrix.h
 include/libmesh/diff_context.h
 include/libmesh/diff_physics.h
 include/libmesh/diff_qoi.h
@@ -88,6 +92,7 @@ include/libmesh/dof_object.h
 include/libmesh/dtk_adapter.h
 include/libmesh/dtk_evaluator.h
 include/libmesh/dtk_solution_transfer.h
+include/libmesh/dyna_io.h
 include/libmesh/edge.h
 include/libmesh/edge_edge2.h
 include/libmesh/edge_edge3.h
@@ -126,6 +131,7 @@ include/libmesh/enum_quadrature_type.h
 include/libmesh/enum_solver_package.h
 include/libmesh/enum_solver_type.h
 include/libmesh/enum_subset_solve_mode.h
+include/libmesh/enum_to_string.h
 include/libmesh/enum_xdr_mode.h
 include/libmesh/equation_systems.h
 include/libmesh/error_estimator.h
@@ -136,6 +142,7 @@ include/libmesh/exact_error_estimator.h
 include/libmesh/exact_solution.h
 include/libmesh/exodusII_io.h
 include/libmesh/exodusII_io_helper.h
+include/libmesh/exodus_header_info.h
 include/libmesh/explicit_system.h
 include/libmesh/face.h
 include/libmesh/face_inf_quad.h
@@ -158,6 +165,8 @@ include/libmesh/fe_abstract.h
 include/libmesh/fe_base.h
 include/libmesh/fe_compute_data.h
 include/libmesh/fe_interface.h
+include/libmesh/fe_interface_macros.h
+include/libmesh/fe_lagrange_shape_1D.h
 include/libmesh/fe_macro.h
 include/libmesh/fe_map.h
 include/libmesh/fe_transformation_base.h
@@ -167,7 +176,9 @@ include/libmesh/fem_context.h
 include/libmesh/fem_function_base.h
 include/libmesh/fem_physics.h
 include/libmesh/fem_system.h
+include/libmesh/file_solution_history.h
 include/libmesh/first_order_unsteady_solver.h
+include/libmesh/float128_shims.h
 include/libmesh/fourth_error_estimators.h
 include/libmesh/fparser.hh
 include/libmesh/fparser_ad.hh
@@ -182,6 +193,7 @@ include/libmesh/gmsh_io.h
 include/libmesh/gmv_io.h
 include/libmesh/gnuplot_io.h
 include/libmesh/h1_fe_transformation.h
+include/libmesh/hashing.h
 include/libmesh/hashword.h
 include/libmesh/hcurl_fe_transformation.h
 include/libmesh/hilbert_sfc_partitioner.h
@@ -197,11 +209,12 @@ include/libmesh/inf_fe_instantiate_1D.h
 include/libmesh/inf_fe_instantiate_2D.h
 include/libmesh/inf_fe_instantiate_3D.h
 include/libmesh/inf_fe_macro.h
+include/libmesh/inf_fe_map.h
 include/libmesh/int_range.h
+include/libmesh/jacobi_polynomials.h
 include/libmesh/jump_error_estimator.h
 include/libmesh/kelly_error_estimator.h
 include/libmesh/libmesh.h
-include/libmesh/libmesh_C_isnan.h
 include/libmesh/libmesh_base.h
 include/libmesh/libmesh_call_mpi.h
 include/libmesh/libmesh_common.h
@@ -313,6 +326,7 @@ include/libmesh/petsc_macro.h
 include/libmesh/petsc_matrix.h
 include/libmesh/petsc_nonlinear_solver.h
 include/libmesh/petsc_preconditioner.h
+include/libmesh/petsc_shell_matrix.h
 include/libmesh/petsc_solver_exception.h
 include/libmesh/petsc_vector.h
 include/libmesh/petscdmlibmesh.h
@@ -345,6 +359,7 @@ include/libmesh/quadrature_gm.h
 include/libmesh/quadrature_grid.h
 include/libmesh/quadrature_jacobi.h
 include/libmesh/quadrature_monomial.h
+include/libmesh/quadrature_nodal.h
 include/libmesh/quadrature_simpson.h
 include/libmesh/quadrature_trap.h
 include/libmesh/radial_basis_functions.h
@@ -460,15 +475,46 @@ include/libmesh/wrapped_functor.h
 include/libmesh/xdr_cxx.h
 include/libmesh/xdr_io.h
 include/libmesh/zero_function.h
+include/metis.h
+include/timpi/attributes.h
+include/timpi/communicator.h
+include/timpi/data_type.h
+include/timpi/ignore_warnings.h
+include/timpi/message_tag.h
+include/timpi/op_function.h
+include/timpi/packing.h
+include/timpi/packing_forward.h
+include/timpi/parallel_communicator_specializations
+include/timpi/parallel_implementation.h
+include/timpi/parallel_sync.h
+include/timpi/post_wait_copy_buffer.h
+include/timpi/post_wait_delete_buffer.h
+include/timpi/post_wait_dereference_shared_ptr.h
+include/timpi/post_wait_dereference_tag.h
+include/timpi/post_wait_free_buffer.h
+include/timpi/post_wait_unpack_buffer.h
+include/timpi/post_wait_unpack_nested_buffer.h
+include/timpi/post_wait_work.h
+include/timpi/request.h
+include/timpi/restore_warnings.h
+include/timpi/serial_implementation.h
+include/timpi/standard_type.h
+include/timpi/status.h
+include/timpi/timpi.h
+include/timpi/timpi_assert.h
+include/timpi/timpi_call_mpi.h
+include/timpi/timpi_config.h
+include/timpi/timpi_init.h
+include/timpi/timpi_version.h
 lib/libmesh_opt.so
 lib/libmesh_opt.so.0
 lib/libmesh_opt.so.0.0.0
-libdata/pkgconfig/libmesh-dbg.pc
-libdata/pkgconfig/libmesh-devel.pc
-libdata/pkgconfig/libmesh-oprof.pc
+lib/libtimpi_opt.so
+lib/libtimpi_opt.so.2
+lib/libtimpi_opt.so.2.0.0
 libdata/pkgconfig/libmesh-opt.pc
-libdata/pkgconfig/libmesh-prof.pc
 libdata/pkgconfig/libmesh.pc
+libdata/pkgconfig/timpi.pc
 %%DATADIR%%/Make.common
 %%DATADIR%%/reference_elements/2D/one_quad.xda
 %%DATADIR%%/reference_elements/2D/one_quad8.xda