Metis problem after PETSc maint commit 53980de

[torquil]

After PETSc commit 53980de on the maint branch, I'm getting the following build error for libmesh:

mv -f src/apps/.deps/meshplot_opt-meshplot.Tpo src/apps/.deps/meshplot_opt-meshplot.Po mv -f src/apps/.deps/solution_components_opt-solution_components.Tpo src/apps/.deps/solution_components_opt-solution_components.Po mv -f src/apps/.deps/projection_opt-projection.Tpo src/apps/.deps/projection_opt-projection.Po libtool: link: mpicxx -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-linux-gnu/5/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/5/crtbeginS.o src/base/.libs/libmesh_opt_la-dof_map.o src/base/.libs/libmesh_opt_la-dof_map_constraints.o src/base/.libs/libmesh_opt_la-dof_object.o src/base/.libs/libmesh_opt_la-libmesh.o src/base/.libs/libmesh_opt_la-libmesh_common.o src/base/.libs/libmesh_opt_la-libmesh_isnan.o src/base/.libs/libmesh_opt_la-libmesh_singleton.o src/base/.libs/libmesh_opt_la-periodic_boundaries.o src/base/.libs/libmesh_opt_la-periodic_boundary.o src/base/.libs/libmesh_opt_la-periodic_boundary_base.o src/base/.libs/libmesh_opt_la-print_trace.o src/base/.libs/libmesh_opt_la-reference_counted_object.o src/base/.libs/libmesh_opt_la-reference_counter.o src/base/.libs/libmesh_opt_la-sparsity_pattern.o src/error_estimation/.libs/libmesh_opt_la-adjoint_refinement_estimator.o src/error_estimation/.libs/libmesh_opt_la-adjoint_residual_error_estimator.o src/error_estimation/.libs/libmesh_opt_la-discontinuity_measure.o src/error_estimation/.libs/libmesh_opt_la-error_estimator.o src/error_estimation/.libs/libmesh_opt_la-exact_error_estimator.o src/error_estimation/.libs/libmesh_opt_la-exact_solution.o src/error_estimation/.libs/libmesh_opt_la-fourth_error_estimators.o src/error_estimation/.libs/libmesh_opt_la-hp_coarsentest.o src/error_estimation/.libs/libmesh_opt_la-hp_selector.o src/error_estimation/.libs/libmesh_opt_la-hp_singular.o src/error_estimation/.libs/libmesh_opt_la-jump_error_estimator.o src/error_estimation/.libs/libmesh_opt_la-kelly_error_estimator.o src/error_estimation/.libs/libmesh_opt_la-patch_recovery_error_estimator.o src/error_estimation/.libs/libmesh_opt_la-uniform_refinement_estimator.o src/error_estimation/.libs/libmesh_opt_la-weighted_patch_recovery_estimator.o src/fe/.libs/libmesh_opt_la-fe.o src/fe/.libs/libmesh_opt_la-fe_abstract.o src/fe/.libs/libmesh_opt_la-fe_base.o src/fe/.libs/libmesh_opt_la-fe_bernstein.o src/fe/.libs/libmesh_opt_la-fe_bernstein_shape_0D.o src/fe/.libs/libmesh_opt_la-fe_bernstein_shape_1D.o src/fe/.libs/libmesh_opt_la-fe_bernstein_shape_2D.o src/fe/.libs/libmesh_opt_la-fe_bernstein_shape_3D.o src/fe/.libs/libmesh_opt_la-fe_boundary.o src/fe/.libs/libmesh_opt_la-fe_clough.o src/fe/.libs/libmesh_opt_la-fe_clough_shape_0D.o src/fe/.libs/libmesh_opt_la-fe_clough_shape_1D.o src/fe/.libs/libmesh_opt_la-fe_clough_shape_2D.o src/fe/.libs/libmesh_opt_la-fe_clough_shape_3D.o src/fe/.libs/libmesh_opt_la-fe_compute_data.o src/fe/.libs/libmesh_opt_la-fe_hermite.o src/fe/.libs/libmesh_opt_la-fe_hermite_shape_0D.o src/fe/.libs/libmesh_opt_la-fe_hermite_shape_1D.o src/fe/.libs/libmesh_opt_la-fe_hermite_shape_2D.o src/fe/.libs/libmesh_opt_la-fe_hermite_shape_3D.o src/fe/.libs/libmesh_opt_la-fe_hierarchic.o src/fe/.libs/libmesh_opt_la-fe_hierarchic_shape_0D.o src/fe/.libs/libmesh_opt_la-fe_hierarchic_shape_1D.o src/fe/.libs/libmesh_opt_la-fe_hierarchic_shape_2D.o src/fe/.libs/libmesh_opt_la-fe_hierarchic_shape_3D.o src/fe/.libs/libmesh_opt_la-fe_interface.o src/fe/.libs/libmesh_opt_la-fe_interface_inf_fe.o src/fe/.libs/libmesh_opt_la-fe_l2_hierarchic.o src/fe/.libs/libmesh_opt_la-fe_l2_hierarchic_shape_0D.o src/fe/.libs/libmesh_opt_la-fe_l2_hierarchic_shape_1D.o src/fe/.libs/libmesh_opt_la-fe_l2_hierarchic_shape_2D.o src/fe/.libs/libmesh_opt_la-fe_l2_hierarchic_shape_3D.o src/fe/.libs/libmesh_opt_la-fe_l2_lagrange.o src/fe/.libs/libmesh_opt_la-fe_l2_lagrange_shape_0D.o src/fe/.libs/libmesh_opt_la-fe_l2_lagrange_shape_1D.o src/fe/.libs/libmesh_opt_la-fe_l2_lagrange_shape_2D.o src/fe/.libs/libmesh_opt_la-fe_l2_lagrange_shape_3D.o src/fe/.libs/libmesh_opt_la-fe_lagrange.o src/fe/.libs/libmesh_opt_la-fe_lagrange_shape_0D.o src/fe/.libs/libmesh_opt_la-fe_lagrange_shape_1D.o src/fe/.libs/libmesh_opt_la-fe_lagrange_shape_2D.o src/fe/.libs/libmesh_opt_la-fe_lagrange_shape_3D.o src/fe/.libs/libmesh_opt_la-fe_lagrange_vec.o src/fe/.libs/libmesh_opt_la-fe_map.o src/fe/.libs/libmesh_opt_la-fe_monomial.o src/fe/.libs/libmesh_opt_la-fe_monomial_shape_0D.o src/fe/.libs/libmesh_opt_la-fe_monomial_shape_1D.o src/fe/.libs/libmesh_opt_la-fe_monomial_shape_2D.o src/fe/.libs/libmesh_opt_la-fe_monomial_shape_3D.o src/fe/.libs/libmesh_opt_la-fe_nedelec_one.o src/fe/.libs/libmesh_opt_la-fe_nedelec_one_shape_2D.o src/fe/.libs/libmesh_opt_la-fe_nedelec_one_shape_3D.o src/fe/.libs/libmesh_opt_la-fe_scalar.o src/fe/.libs/libmesh_opt_la-fe_scalar_shape_0D.o src/fe/.libs/libmesh_opt_la-fe_scalar_shape_1D.o src/fe/.libs/libmesh_opt_la-fe_scalar_shape_2D.o src/fe/.libs/libmesh_opt_la-fe_scalar_shape_3D.o src/fe/.libs/libmesh_opt_la-fe_subdivision_2D.o src/fe/.libs/libmesh_opt_la-fe_szabab.o src/fe/.libs/libmesh_opt_la-fe_szabab_shape_0D.o src/fe/.libs/libmesh_opt_la-fe_szabab_shape_1D.o src/fe/.libs/libmesh_opt_la-fe_szabab_shape_2D.o src/fe/.libs/libmesh_opt_la-fe_szabab_shape_3D.o src/fe/.libs/libmesh_opt_la-fe_transformation_base.o src/fe/.libs/libmesh_opt_la-fe_type.o src/fe/.libs/libmesh_opt_la-fe_xyz.o src/fe/.libs/libmesh_opt_la-fe_xyz_boundary.o src/fe/.libs/libmesh_opt_la-fe_xyz_map.o src/fe/.libs/libmesh_opt_la-fe_xyz_shape_0D.o src/fe/.libs/libmesh_opt_la-fe_xyz_shape_1D.o src/fe/.libs/libmesh_opt_la-fe_xyz_shape_2D.o src/fe/.libs/libmesh_opt_la-fe_xyz_shape_3D.o src/fe/.libs/libmesh_opt_la-h1_fe_transformation.o src/fe/.libs/libmesh_opt_la-hcurl_fe_transformation.o src/fe/.libs/libmesh_opt_la-inf_fe.o src/fe/.libs/libmesh_opt_la-inf_fe_base_radial.o src/fe/.libs/libmesh_opt_la-inf_fe_boundary.o src/fe/.libs/libmesh_opt_la-inf_fe_jacobi_20_00_eval.o src/fe/.libs/libmesh_opt_la-inf_fe_jacobi_30_00_eval.o src/fe/.libs/libmesh_opt_la-inf_fe_lagrange_eval.o src/fe/.libs/libmesh_opt_la-inf_fe_legendre_eval.o src/fe/.libs/libmesh_opt_la-inf_fe_map.o src/fe/.libs/libmesh_opt_la-inf_fe_map_eval.o src/fe/.libs/libmesh_opt_la-inf_fe_static.o src/geom/.libs/libmesh_opt_la-cell.o src/geom/.libs/libmesh_opt_la-cell_hex.o src/geom/.libs/libmesh_opt_la-cell_hex20.o src/geom/.libs/libmesh_opt_la-cell_hex27.o src/geom/.libs/libmesh_opt_la-cell_hex8.o src/geom/.libs/libmesh_opt_la-cell_inf.o src/geom/.libs/libmesh_opt_la-cell_inf_hex.o src/geom/.libs/libmesh_opt_la-cell_inf_hex16.o src/geom/.libs/libmesh_opt_la-cell_inf_hex18.o src/geom/.libs/libmesh_opt_la-cell_inf_hex8.o src/geom/.libs/libmesh_opt_la-cell_inf_prism.o src/geom/.libs/libmesh_opt_la-cell_inf_prism12.o src/geom/.libs/libmesh_opt_la-cell_inf_prism6.o src/geom/.libs/libmesh_opt_la-cell_prism.o src/geom/.libs/libmesh_opt_la-cell_prism15.o src/geom/.libs/libmesh_opt_la-cell_prism18.o src/geom/.libs/libmesh_opt_la-cell_prism6.o src/geom/.libs/libmesh_opt_la-cell_pyramid.o src/geom/.libs/libmesh_opt_la-cell_pyramid13.o src/geom/.libs/libmesh_opt_la-cell_pyramid14.o src/geom/.libs/libmesh_opt_la-cell_pyramid5.o src/geom/.libs/libmesh_opt_la-cell_tet.o src/geom/.libs/libmesh_opt_la-cell_tet10.o src/geom/.libs/libmesh_opt_la-cell_tet4.o src/geom/.libs/libmesh_opt_la-edge.o src/geom/.libs/libmesh_opt_la-edge_edge2.o src/geom/.libs/libmesh_opt_la-edge_edge3.o src/geom/.libs/libmesh_opt_la-edge_edge4.o src/geom/.libs/libmesh_opt_la-edge_inf_edge2.o src/geom/.libs/libmesh_opt_la-elem.o src/geom/.libs/libmesh_opt_la-elem_cutter.o src/geom/.libs/libmesh_opt_la-elem_quality.o src/geom/.libs/libmesh_opt_la-elem_refinement.o src/geom/.libs/libmesh_opt_la-face.o src/geom/.libs/libmesh_opt_la-face_inf_quad.o src/geom/.libs/libmesh_opt_la-face_inf_quad4.o src/geom/.libs/libmesh_opt_la-face_inf_quad6.o src/geom/.libs/libmesh_opt_la-face_quad.o src/geom/.libs/libmesh_opt_la-face_quad4.o src/geom/.libs/libmesh_opt_la-face_quad8.o src/geom/.libs/libmesh_opt_la-face_quad9.o src/geom/.libs/libmesh_opt_la-face_tri.o src/geom/.libs/libmesh_opt_la-face_tri3.o src/geom/.libs/libmesh_opt_la-face_tri3_subdivision.o src/geom/.libs/libmesh_opt_la-face_tri6.o src/geom/.libs/libmesh_opt_la-node.o src/geom/.libs/libmesh_opt_la-node_elem.o src/geom/.libs/libmesh_opt_la-plane.o src/geom/.libs/libmesh_opt_la-point.o src/geom/.libs/libmesh_opt_la-reference_elem.o src/geom/.libs/libmesh_opt_la-remote_elem.o src/geom/.libs/libmesh_opt_la-sphere.o src/geom/.libs/libmesh_opt_la-surface.o src/mesh/.libs/libmesh_opt_la-abaqus_io.o src/mesh/.libs/libmesh_opt_la-boundary_info.o src/mesh/.libs/libmesh_opt_la-boundary_mesh.o src/mesh/.libs/libmesh_opt_la-checkpoint_io.o src/mesh/.libs/libmesh_opt_la-diva_io.o src/mesh/.libs/libmesh_opt_la-ensight_io.o src/mesh/.libs/libmesh_opt_la-exodusII_io.o src/mesh/.libs/libmesh_opt_la-exodusII_io_helper.o src/mesh/.libs/libmesh_opt_la-fro_io.o src/mesh/.libs/libmesh_opt_la-gmsh_io.o src/mesh/.libs/libmesh_opt_la-gmv_io.o src/mesh/.libs/libmesh_opt_la-gnuplot_io.o src/mesh/.libs/libmesh_opt_la-inf_elem_builder.o src/mesh/.libs/libmesh_opt_la-legacy_xdr_io.o src/mesh/.libs/libmesh_opt_la-matlab_io.o src/mesh/.libs/libmesh_opt_la-medit_io.o src/mesh/.libs/libmesh_opt_la-mesh_base.o src/mesh/.libs/libmesh_opt_la-mesh_communication.o src/mesh/.libs/libmesh_opt_la-mesh_communication_global_indices.o src/mesh/.libs/libmesh_opt_la-mesh_data.o src/mesh/.libs/libmesh_opt_la-mesh_data_tetgen_support.o src/mesh/.libs/libmesh_opt_la-mesh_data_unv_support.o src/mesh/.libs/libmesh_opt_la-mesh_data_xdr_support.o src/mesh/.libs/libmesh_opt_la-mesh_function.o src/mesh/.libs/libmesh_opt_la-mesh_generation.o src/mesh/.libs/libmesh_opt_la-mesh_iterators.o src/mesh/.libs/libmesh_opt_la-mesh_modification.o src/mesh/.libs/libmesh_opt_la-mesh_output.o src/mesh/.libs/libmesh_opt_la-mesh_refinement.o src/mesh/.libs/libmesh_opt_la-mesh_refinement_flagging.o src/mesh/.libs/libmesh_opt_la-mesh_refinement_smoothing.o src/mesh/.libs/libmesh_opt_la-mesh_serializer.o src/mesh/.libs/libmesh_opt_la-mesh_smoother.o src/mesh/.libs/libmesh_opt_la-mesh_smoother_laplace.o src/mesh/.libs/libmesh_opt_la-mesh_smoother_vsmoother.o src/mesh/.libs/libmesh_opt_la-mesh_subdivision_support.o src/mesh/.libs/libmesh_opt_la-mesh_tetgen_interface.o src/mesh/.libs/libmesh_opt_la-mesh_tetgen_wrapper.o src/mesh/.libs/libmesh_opt_la-mesh_tools.o src/mesh/.libs/libmesh_opt_la-mesh_triangle_holes.o src/mesh/.libs/libmesh_opt_la-mesh_triangle_interface.o src/mesh/.libs/libmesh_opt_la-mesh_triangle_wrapper.o src/mesh/.libs/libmesh_opt_la-namebased_io.o src/mesh/.libs/libmesh_opt_la-nemesis_io.o src/mesh/.libs/libmesh_opt_la-nemesis_io_helper.o src/mesh/.libs/libmesh_opt_la-off_io.o src/mesh/.libs/libmesh_opt_la-parallel_mesh.o src/mesh/.libs/libmesh_opt_la-patch.o src/mesh/.libs/libmesh_opt_la-postscript_io.o src/mesh/.libs/libmesh_opt_la-serial_mesh.o src/mesh/.libs/libmesh_opt_la-tecplot_io.o src/mesh/.libs/libmesh_opt_la-tetgen_io.o src/mesh/.libs/libmesh_opt_la-ucd_io.o src/mesh/.libs/libmesh_opt_la-unstructured_mesh.o src/mesh/.libs/libmesh_opt_la-unv_io.o src/mesh/.libs/libmesh_opt_la-vtk_io.o src/mesh/.libs/libmesh_opt_la-xdr_head.o src/mesh/.libs/libmesh_opt_la-xdr_io.o src/mesh/.libs/libmesh_opt_la-xdr_mesh.o src/mesh/.libs/libmesh_opt_la-xdr_mgf.o src/mesh/.libs/libmesh_opt_la-xdr_soln.o src/numerics/.libs/libmesh_opt_la-analytic_function.o src/numerics/.libs/libmesh_opt_la-coupling_matrix.o src/numerics/.libs/libmesh_opt_la-dense_matrix.o src/numerics/.libs/libmesh_opt_la-dense_matrix_base.o src/numerics/.libs/libmesh_opt_la-dense_matrix_blas_lapack.o src/numerics/.libs/libmesh_opt_la-dense_submatrix.o src/numerics/.libs/libmesh_opt_la-dense_subvector.o src/numerics/.libs/libmesh_opt_la-dense_vector.o src/numerics/.libs/libmesh_opt_la-dense_vector_base.o src/numerics/.libs/libmesh_opt_la-distributed_vector.o src/numerics/.libs/libmesh_opt_la-eigen_preconditioner.o src/numerics/.libs/libmesh_opt_la-eigen_sparse_matrix.o src/numerics/.libs/libmesh_opt_la-eigen_sparse_vector.o src/numerics/.libs/libmesh_opt_la-function_base.o src/numerics/.libs/libmesh_opt_la-laspack_matrix.o src/numerics/.libs/libmesh_opt_la-laspack_vector.o src/numerics/.libs/libmesh_opt_la-numeric_vector.o src/numerics/.libs/libmesh_opt_la-petsc_matrix.o src/numerics/.libs/libmesh_opt_la-petsc_preconditioner.o src/numerics/.libs/libmesh_opt_la-petsc_vector.o src/numerics/.libs/libmesh_opt_la-preconditioner.o src/numerics/.libs/libmesh_opt_la-sparse_matrix.o src/numerics/.libs/libmesh_opt_la-sparse_shell_matrix.o src/numerics/.libs/libmesh_opt_la-sum_shell_matrix.o src/numerics/.libs/libmesh_opt_la-tensor_shell_matrix.o src/numerics/.libs/libmesh_opt_la-tensor_tools.o src/numerics/.libs/libmesh_opt_la-trilinos_epetra_matrix.o src/numerics/.libs/libmesh_opt_la-trilinos_epetra_vector.o src/numerics/.libs/libmesh_opt_la-trilinos_preconditioner.o src/numerics/.libs/libmesh_opt_la-type_tensor.o src/numerics/.libs/libmesh_opt_la-type_vector.o src/parallel/.libs/libmesh_opt_la-parallel_bin_sorter.o src/parallel/.libs/libmesh_opt_la-parallel_elem.o src/parallel/.libs/libmesh_opt_la-parallel_ghost_sync.o src/parallel/.libs/libmesh_opt_la-parallel_histogram.o src/parallel/.libs/libmesh_opt_la-parallel_node.o src/parallel/.libs/libmesh_opt_la-parallel_sort.o src/parallel/.libs/libmesh_opt_la-threads.o src/partitioning/.libs/libmesh_opt_la-centroid_partitioner.o src/partitioning/.libs/libmesh_opt_la-linear_partitioner.o src/partitioning/.libs/libmesh_opt_la-metis_partitioner.o src/partitioning/.libs/libmesh_opt_la-parmetis_partitioner.o src/partitioning/.libs/libmesh_opt_la-partitioner.o src/partitioning/.libs/libmesh_opt_la-partitioner_factory.o src/partitioning/.libs/libmesh_opt_la-sfc_partitioner.o src/physics/.libs/libmesh_opt_la-diff_physics.o src/physics/.libs/libmesh_opt_la-diff_qoi.o src/physics/.libs/libmesh_opt_la-fem_physics.o src/quadrature/.libs/libmesh_opt_la-quadrature.o src/quadrature/.libs/libmesh_opt_la-quadrature_build.o src/quadrature/.libs/libmesh_opt_la-quadrature_clough.o src/quadrature/.libs/libmesh_opt_la-quadrature_clough_1D.o src/quadrature/.libs/libmesh_opt_la-quadrature_clough_2D.o src/quadrature/.libs/libmesh_opt_la-quadrature_clough_3D.o src/quadrature/.libs/libmesh_opt_la-quadrature_composite.o src/quadrature/.libs/libmesh_opt_la-quadrature_conical.o src/quadrature/.libs/libmesh_opt_la-quadrature_conical_2D.o src/quadrature/.libs/libmesh_opt_la-quadrature_conical_3D.o src/quadrature/.libs/libmesh_opt_la-quadrature_gauss.o src/quadrature/.libs/libmesh_opt_la-quadrature_gauss_1D.o src/quadrature/.libs/libmesh_opt_la-quadrature_gauss_2D.o src/quadrature/.libs/libmesh_opt_la-quadrature_gauss_3D.o src/quadrature/.libs/libmesh_opt_la-quadrature_gauss_lobatto.o src/quadrature/.libs/libmesh_opt_la-quadrature_gauss_lobatto_1D.o src/quadrature/.libs/libmesh_opt_la-quadrature_gauss_lobatto_2D.o src/quadrature/.libs/libmesh_opt_la-quadrature_gauss_lobatto_3D.o src/quadrature/.libs/libmesh_opt_la-quadrature_gm.o src/quadrature/.libs/libmesh_opt_la-quadrature_gm_2D.o src/quadrature/.libs/libmesh_opt_la-quadrature_gm_3D.o src/quadrature/.libs/libmesh_opt_la-quadrature_grid.o src/quadrature/.libs/libmesh_opt_la-quadrature_grid_1D.o src/quadrature/.libs/libmesh_opt_la-quadrature_grid_2D.o src/quadrature/.libs/libmesh_opt_la-quadrature_grid_3D.o src/quadrature/.libs/libmesh_opt_la-quadrature_jacobi.o src/quadrature/.libs/libmesh_opt_la-quadrature_jacobi_1D.o src/quadrature/.libs/libmesh_opt_la-quadrature_monomial.o src/quadrature/.libs/libmesh_opt_la-quadrature_monomial_1D.o src/quadrature/.libs/libmesh_opt_la-quadrature_monomial_2D.o src/quadrature/.libs/libmesh_opt_la-quadrature_monomial_3D.o src/quadrature/.libs/libmesh_opt_la-quadrature_simpson.o src/quadrature/.libs/libmesh_opt_la-quadrature_simpson_1D.o src/quadrature/.libs/libmesh_opt_la-quadrature_simpson_2D.o src/quadrature/.libs/libmesh_opt_la-quadrature_simpson_3D.o src/quadrature/.libs/libmesh_opt_la-quadrature_trap.o src/quadrature/.libs/libmesh_opt_la-quadrature_trap_1D.o src/quadrature/.libs/libmesh_opt_la-quadrature_trap_2D.o src/quadrature/.libs/libmesh_opt_la-quadrature_trap_3D.o src/reduced_basis/.libs/libmesh_opt_la-rb_assembly_expansion.o src/reduced_basis/.libs/libmesh_opt_la-rb_construction.o src/reduced_basis/.libs/libmesh_opt_la-rb_construction_base.o src/reduced_basis/.libs/libmesh_opt_la-rb_data_deserialization.o src/reduced_basis/.libs/libmesh_opt_la-rb_data_serialization.o src/reduced_basis/.libs/libmesh_opt_la-rb_eim_assembly.o src/reduced_basis/.libs/libmesh_opt_la-rb_eim_construction.o src/reduced_basis/.libs/libmesh_opt_la-rb_eim_evaluation.o src/reduced_basis/.libs/libmesh_opt_la-rb_eim_theta.o src/reduced_basis/.libs/libmesh_opt_la-rb_evaluation.o src/reduced_basis/.libs/libmesh_opt_la-rb_parameters.o src/reduced_basis/.libs/libmesh_opt_la-rb_parametrized.o src/reduced_basis/.libs/libmesh_opt_la-rb_scm_construction.o src/reduced_basis/.libs/libmesh_opt_la-rb_scm_evaluation.o src/reduced_basis/.libs/libmesh_opt_la-rb_temporal_discretization.o src/reduced_basis/.libs/libmesh_opt_la-rb_theta_expansion.o src/reduced_basis/.libs/libmesh_opt_la-transient_rb_assembly_expansion.o src/reduced_basis/.libs/libmesh_opt_la-transient_rb_construction.o src/reduced_basis/.libs/libmesh_opt_la-transient_rb_evaluation.o src/reduced_basis/.libs/libmesh_opt_la-transient_rb_theta_expansion.o src/solution_transfer/.libs/libmesh_opt_la-direct_solution_transfer.o src/solution_transfer/.libs/libmesh_opt_la-dtk_adapter.o src/solution_transfer/.libs/libmesh_opt_la-dtk_evaluator.o src/solution_transfer/.libs/libmesh_opt_la-dtk_solution_transfer.o src/solution_transfer/.libs/libmesh_opt_la-meshfree_interpolation.o src/solution_transfer/.libs/libmesh_opt_la-meshfree_solution_transfer.o src/solution_transfer/.libs/libmesh_opt_la-meshfunction_solution_transfer.o src/solution_transfer/.libs/libmesh_opt_la-radial_basis_interpolation.o src/solution_transfer/.libs/libmesh_opt_la-solution_transfer.o src/solvers/.libs/libmesh_opt_la-adaptive_time_solver.o src/solvers/.libs/libmesh_opt_la-diff_solver.o src/solvers/.libs/libmesh_opt_la-eigen_solver.o src/solvers/.libs/libmesh_opt_la-eigen_sparse_linear_solver.o src/solvers/.libs/libmesh_opt_la-eigen_time_solver.o src/solvers/.libs/libmesh_opt_la-euler2_solver.o src/solvers/.libs/libmesh_opt_la-euler_solver.o src/solvers/.libs/libmesh_opt_la-laspack_linear_solver.o src/solvers/.libs/libmesh_opt_la-linear_solver.o src/solvers/.libs/libmesh_opt_la-memory_solution_history.o src/solvers/.libs/libmesh_opt_la-newmark_solver.o src/solvers/.libs/libmesh_opt_la-newton_solver.o src/solvers/.libs/libmesh_opt_la-nlopt_optimization_solver.o src/solvers/.libs/libmesh_opt_la-no_solution_history.o src/solvers/.libs/libmesh_opt_la-nonlinear_solver.o src/solvers/.libs/libmesh_opt_la-optimization_solver.o src/solvers/.libs/libmesh_opt_la-petsc_auto_fieldsplit.o src/solvers/.libs/libmesh_opt_la-petsc_diff_solver.o src/solvers/.libs/libmesh_opt_la-petsc_linear_solver.o src/solvers/.libs/libmesh_opt_la-petsc_nonlinear_solver.o src/solvers/.libs/libmesh_opt_la-petscdmlibmesh.o src/solvers/.libs/libmesh_opt_la-petscdmlibmeshimpl.o src/solvers/.libs/libmesh_opt_la-second_order_unsteady_solver.o src/solvers/.libs/libmesh_opt_la-slepc_eigen_solver.o src/solvers/.libs/libmesh_opt_la-steady_solver.o src/solvers/.libs/libmesh_opt_la-tao_optimization_solver.o src/solvers/.libs/libmesh_opt_la-time_solver.o src/solvers/.libs/libmesh_opt_la-trilinos_aztec_linear_solver.o src/solvers/.libs/libmesh_opt_la-trilinos_nox_nonlinear_solver.o src/solvers/.libs/libmesh_opt_la-twostep_time_solver.o src/solvers/.libs/libmesh_opt_la-unsteady_solver.o src/systems/.libs/libmesh_opt_la-condensed_eigen_system.o src/systems/.libs/libmesh_opt_la-continuation_system.o src/systems/.libs/libmesh_opt_la-dg_fem_context.o src/systems/.libs/libmesh_opt_la-diff_context.o src/systems/.libs/libmesh_opt_la-diff_system.o src/systems/.libs/libmesh_opt_la-eigen_system.o src/systems/.libs/libmesh_opt_la-equation_systems.o src/systems/.libs/libmesh_opt_la-equation_systems_io.o src/systems/.libs/libmesh_opt_la-explicit_system.o src/systems/.libs/libmesh_opt_la-fem_context.o src/systems/.libs/libmesh_opt_la-fem_system.o src/systems/.libs/libmesh_opt_la-frequency_system.o src/systems/.libs/libmesh_opt_la-implicit_system.o src/systems/.libs/libmesh_opt_la-linear_implicit_system.o src/systems/.libs/libmesh_opt_la-newmark_system.o src/systems/.libs/libmesh_opt_la-nonlinear_implicit_system.o src/systems/.libs/libmesh_opt_la-optimization_system.o src/systems/.libs/libmesh_opt_la-parameter_vector.o src/systems/.libs/libmesh_opt_la-qoi_set.o src/systems/.libs/libmesh_opt_la-steady_system.o src/systems/.libs/libmesh_opt_la-system.o src/systems/.libs/libmesh_opt_la-system_io.o src/systems/.libs/libmesh_opt_la-system_projection.o src/systems/.libs/libmesh_opt_la-system_subset.o src/systems/.libs/libmesh_opt_la-system_subset_by_subdomain.o src/systems/.libs/libmesh_opt_la-transient_system.o src/utils/.libs/libmesh_opt_la-error_vector.o src/utils/.libs/libmesh_opt_la-hashword.o src/utils/.libs/libmesh_opt_la-libmesh_version.o src/utils/.libs/libmesh_opt_la-location_maps.o src/utils/.libs/libmesh_opt_la-number_lookups.o src/utils/.libs/libmesh_opt_la-perf_log.o src/utils/.libs/libmesh_opt_la-plt_loader.o src/utils/.libs/libmesh_opt_la-plt_loader_read.o src/utils/.libs/libmesh_opt_la-plt_loader_write.o src/utils/.libs/libmesh_opt_la-point_locator_base.o src/utils/.libs/libmesh_opt_la-point_locator_list.o src/utils/.libs/libmesh_opt_la-point_locator_tree.o src/utils/.libs/libmesh_opt_la-statistics.o src/utils/.libs/libmesh_opt_la-string_to_enum.o src/utils/.libs/libmesh_opt_la-timestamp.o src/utils/.libs/libmesh_opt_la-topology_map.o src/utils/.libs/libmesh_opt_la-tree.o src/utils/.libs/libmesh_opt_la-tree_node.o src/utils/.libs/libmesh_opt_la-utility.o src/utils/.libs/libmesh_opt_la-xdr_cxx.o -Wl,--whole-archive contrib/.libs/libcontrib_opt.a -Wl,--no-whole-archive -Wl,-rpath -Wl,/home/tmac/src/upstream/libmesh/contrib/netcdf/v4/liblib/.libs -Wl,-rpath -Wl,/home/tmac/usr/stow/libmesh/lib /home/tmac/src/upstream/libmesh/contrib/netcdf/v4/liblib/.libs/libnetcdf.so -L/usr/lib/x86_64-linux-gnu /usr/lib/x86_64-linux-gnu/libcurl-gnutls.so -L/home/tmac/usr/slepc_maint/arch-linux2-c-complex-opt/lib -L/home/tmac/usr/petsc_maint/arch-linux2-c-complex-opt/lib -L/lib/x86_64-linux-gnu -L/usr/lib -L/usr/lib/openmpi/lib -L/usr/lib/gcc/x86_64-linux-gnu/5 -lglpk -lvtkIOCore-6.2 -lvtkCommonCore-6.2 -lvtkCommonDataModel-6.2 -lvtkFiltersCore-6.2 -lvtkIOXML-6.2 -lvtkImagingCore-6.2 -lvtkIOImage-6.2 -lvtkImagingMath-6.2 -lvtkIOParallelXML-6.2 -ltbb -ltbbmalloc -lslepc -lpetsc -lsuperlu_4.3 -lflapack -lfblas -lparmetis -lmetis -lptesmumps -lptscotch -lptscotcherr -lscotch -lscotcherr -lX11 -lhwloc -lssl -lcrypto -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh -lgfortran -lquadmath -lrt -lz -ldl -L/usr/lib/gcc/x86_64-linux-gnu/5/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/5/../../../../lib -L/lib/../lib -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/5/../../.. -lmpi_cxx -lmpi -lstdc++ -lm -lpthread -lc -lgcc_s /usr/lib/gcc/x86_64-linux-gnu/5/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/5/../../../x86_64-linux-gnu/crtn.o -O2 -fopenmp -Wl,-rpath -Wl,/lib/x86_64-linux-gnu -Wl,-rpath -Wl,/usr/lib -Wl,-rpath -Wl,/home/tmac/usr/slepc_maint/arch-linux2-c-complex-opt/lib -Wl,-rpath -Wl,/home/tmac/usr/petsc_maint/arch-linux2-c-complex-opt/lib -Wl,-rpath -Wl,/usr/lib/gcc/x86_64-linux-gnu/5 -Wl,-rpath -Wl,/usr/lib/x86_64-linux-gnu -Wl,-rpath -Wl,/usr/lib/openmpi/lib -Wl,-rpath -Wl,/lib/x86_64-linux-gnu -Wl,-rpath -Wl,/usr/lib -Wl,-rpath -Wl,/home/tmac/usr/slepc_maint/arch-linux2-c-complex-opt/lib -Wl,-rpath -Wl,/home/tmac/usr/petsc_maint/arch-linux2-c-complex-opt/lib -Wl,-rpath -Wl,/usr/lib/gcc/x86_64-linux-gnu/5 -Wl,-rpath -Wl,/usr/lib/x86_64-linux-gnu -Wl,-rpath -Wl,/usr/lib/openmpi/lib -fopenmp -pthread -Wl,-soname -Wl,libmesh_opt.so.0 -o .libs/libmesh_opt.so.0.0.0 /usr/bin/ld: gk_cur_jbufs: TLS definition in contrib/.libs/libcontrib_opt.a(libopt_la-error.o) section .tdata mismatches non-TLS definition in /home/tmac/usr/petsc_maint/arch-linux2-c-complex-opt/lib/libmetis.so section .data /home/tmac/usr/petsc_maint/arch-linux2-c-complex-opt/lib/libmetis.so: error adding symbols: Bad value collect2: error: ld returned 1 exit status Makefile:9679: recipe for target 'libmesh_opt.la' failed make[1]: * [libmesh_opt.la] Error 1 make[1]: Leaving directory '/home/tmac/src/upstream/libmesh' Makefile:28783: recipe for target 'install-recursive' failed make: * [install-recursive] Error 1

This happended on two different Linux systems, Debian Sid and Red Hat Enterprise Linux Server release 6.7, the latter updated to gcc (GCC) 5.3.1 20160322. PETSc and SLEPc were the updated maint branches, and libmesh the newest GIT version.

Downgrading PETSc maint to the commit before 53980de fixes the problem. I also tried to configure libmesh with --with-metis=internal, but it had no effect. As far as I could see, it still tried to link against the Metis installed by PETSc.

Here is a link to the PETSc commit:

https://bitbucket.org/petsc/petsc/commits/53980de7c74b5380ebc1ba49244aaa94dd3e32b2?at=maint

[roystgnr]

On Wed, 30 Mar 2016, torquil wrote:

After PETSc commit 53980de on the maint branch, I'm getting the following build error for libmesh:

/usr/bin/ld: gk_cur_jbufs: TLS definition in contrib/.libs/libcontrib_opt.a(libopt_la-error.o) section .tdata mismatches non-TLS definition in /home/tmac/usr/petsc_maint/arch-linux2-c-complex-opt/lib/libmetis.so section .data

Downgrading PETSc maint to the commit before 53980de fixes the problem. I also tried to configure libmesh with --with-metis=internal, but it had no effect. As far as I could see, it still tried to link against the Metis installed by PETSc.

There's no way to avoid linking against the Metis installed by PETSc, if you link against PETSc, since linking is transitive.

What you should need to do is link against only the Metis installed by PETSc; i.e. configure with --with-metis=PETSc

This should disable the libMesh-Metis (and ParMetis) builds in contrib, so there won't be any symbols from it to conflict with the PETsc-Metis installation.

Use a new build dir just to make sure that there aren't any

libMesh-Metis objects left around from the previous build.

Roy

[jwpeterson]

On Wed, Mar 30, 2016 at 7:10 AM, roystgnr notifications@github.com wrote:

On Wed, 30 Mar 2016, torquil wrote:

After PETSc commit 53980de on the maint branch, I'm getting the following build error for libmesh:

/usr/bin/ld: gk_cur_jbufs: TLS definition in contrib/.libs/libcontrib_opt.a(libopt_la-error.o) section .tdata mismatches non-TLS definition in /home/tmac/usr/petsc_maint/arch-linux2-c-complex-opt/lib/libmetis.so section .data

Downgrading PETSc maint to the commit before 53980de fixes the problem. I also tried to configure libmesh with --with-metis=internal, but it had no effect. As far as I could see, it still tried to link against the Metis installed by PETSc.

There's no way to avoid linking against the Metis installed by PETSc, if you link against PETSc, since linking is transitive.

What you should need to do is link against only the Metis installed by PETSc; i.e. configure with --with-metis=PETSc

This should disable the libMesh-Metis (and ParMetis) builds in contrib, so there won't be any symbols from it to conflict with the PETsc-Metis installation.

Use a new build dir just to make sure that there aren't any libMesh-Metis objects left around from the previous build.

Since 53980de7c just bumps the version of METIS downloaded by PETSc, I'd strongly suggest a dirty/invalid build is the culprit on the libmesh end. I'm just not sure how it was ever working for you without "--with-metis=PETSc" in the first place, unless you changed your PETSc configure flags slightly between builds and enabled an option that caused PETSc to start building it.

BTW, this commit looks like it also might be relevant to an issue the MOOSE developers are dealing with related to the recent Xcode 7.3 update, so thanks for pointing it out!

commit 53980de7c74b5380ebc1ba49244aaa94dd3e32b2 (upstream/maint, upstream/balay/update-metis-xcode-fix-to-maint) Author: Satish Balay balay@mcs.anl.gov Date: Tue Mar 22 22:02:48 2016

metis: update with fix for Xcode 7.3 thread issue
ld: section __DATA/__thread_bss extends beyond end of file, file 'CMakeFiles/metis.dir/__/GKlib/error.c.o' for architecture x86_64

Reported-by: Peter Lichtner <peter.lichtner@gmail.com>
Reported-by: Bastien Chaudet <bastien.chaudet.1@ulaval.ca>

[jwpeterson]

BTW, this commit looks like it also might be relevant to an issue the MOOSE developers are dealing with related to the recent Xcode 7.3 update

Hmm... looks like all they did was disable TLS in Metis entirely, regardless of the architecture.

diff --git a/GKlib/GKlibSystem.cmake b/GKlib/GKlibSystem.cmake
index 219277d..2b78fea 100644
--- a/GKlib/GKlibSystem.cmake
+++ b/GKlib/GKlibSystem.cmake
@@ -100,16 +100,16 @@ endif(HAVE_GETLINE)

 set(GKlib_TLS "")
 # Custom check for TLS.
-foreach(tls_name "__thread" "__declspec(thread)")
-  check_c_source_runs("${tls_name} int x; int main() {x=0; return x;}" HAVE${tls_name})
-  if(HAVE${tls_name})
-    set(GKlib_TLS "${tls_name}")
-    message(STATUS "checking for ${tls_name} thread-local storage - found")
-    break()
-  else()
-    message(STATUS "checking for ${tls_name} thread-local storage - not found")
-  endif(HAVE${tls_name})
-endforeach()
+#foreach(tls_name "__thread" "__declspec(thread)")
+#  check_c_source_runs("${tls_name} int x; int main() {x=0; return x;}" HAVE${tls_name})
+#  if(HAVE${tls_name})
+#    set(GKlib_TLS "${tls_name}")
+#    message(STATUS "checking for ${tls_name} thread-local storage - found")
+#    break()
+#  else()
+#    message(STATUS "checking for ${tls_name} thread-local storage - not found")
+#  endif(HAVE${tls_name})
+#endforeach()

Seems a little bit heavy-handed, but then again maybe the TLS stuff in Metis is only relevant if you call METIS functions from multiple threads... We're currently using __thread for the LIBMESH_TLS that we use in our own Metis fork -- I can check if disabling that fixes the Xcode 7.3 issues for us as well.

[jwpeterson]

I can check if disabling that fixes the Xcode 7.3 issues for us as well.

I confirmed that undefining LIBMESH_TLS does indeed allow libmesh to build properly under Xcode command line tools 7.3. I suppose we'll just have to keep an eye on the situation going forward... this feels like a huge bug in Xcode that they will fix in the next release, but just in case it isn't, the current workaround would be to not use LIBMESH_TLS in Metis any more.

[friedmud]

Do you need METIS in PETSc? I would just configure PETSc without it...

Derek

On Wed, Mar 30, 2016 at 4:05 AM torquil notifications@github.com wrote:

After PETSc commit 53980de on the maint branch, I'm getting the following build error for libmesh:

mv -f src/apps/.deps/meshplot_opt-meshplot.Tpo src/apps/.deps/meshplot_opt-meshplot.Po mv -f src/apps/.deps/solution_components_opt-solution_components.Tpo src/apps/.deps/solution_components_opt-solution_components.Po mv -f src/apps/.deps/projection_opt-projection.Tpo src/apps/.deps/projection_opt-projection.Po libtool: link: mpicxx -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/x86_64-linux-gnu/5/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/5/crtbeginS.o src/base/.libs/libmesh_opt_la-dof_map.o src/base/.libs/libmesh_opt_la-dof_map_constraints.o src/base/.libs/libmesh_opt_la-dof_object.o src/base/.libs/libmesh_opt_la-libmesh.o src/base/.libs/libmesh_opt_la-libmesh_common.o src/base/.libs/libmesh_opt_la-libmesh_isnan.o src/base/.libs/libmesh_opt_la-libmesh_singleton.o src/base/.libs/libmesh_opt_la-periodic_boundaries.o src/base/.libs/libmesh_opt_la-periodic_boundary.o src/base/.libs/libmesh_opt_la-periodic_boundary_base.o src/base/.libs/libmesh_opt_la-print_trace.o src/base/.libs/libmesh_opt_la-reference_counted_object.o src/base/.libs/libmesh_opt_la-reference_counter.o src/base/.libs/libmesh_opt_la-sparsity_pattern.o src/error_estimation/.libs/libmesh_opt_la-adjoint_refinement_estimator.o src/error_estimation/.libs/libmesh_opt_la-adjoint_residual_errorestimator.o src/error estimation/.libs/libmesh_opt_la-discontinuity_measure.o src/error_estimation/.libs/libmesh_opt_la-error_estimator.o src/error_estimation/.libs/libmesh_opt_la-exact_error_estimator.o src/error_estimation/.libs/libmesh_opt_la-exact_solution.o src/error_estimation/.libs/libmesh_opt_la-fourth_error_estimators.o src/error_estimation/.libs/libmesh_opt_la-hp_coarsentest.o src/error_estimation/.libs/libmesh_opt_la-hp_selector.o src/error_estimation/.libs/libmesh_opt_la-hp_singular.o src/error_estimation/.libs/libmesh_opt_la-jump_error_estimator.o src/error_estimation/.libs/libmesh_opt_la-kelly_error_estimator.o src/error_estimation/.libs/libmesh_opt_la-patch_recovery_error_estimator.o src/error_estimation/.libs/libmesh_opt_la-uniform_refinement_estimator.o src/error_estimation/.libs/libmesh_opt_la-weighted_patch_recovery_estimator.o src/fe/.libs/libmesh_opt_la-fe.o src/fe/.libs/libmesh_opt_la-fe_abstract.o src/fe/.libs/libmesh_opt_la-fe_base.o src/fe/.libs/libmesh_opt_la-fe_bernstein.o src/ fe/.libs/libmesh_opt_la-fe_bernstein_shape_0D.o src/fe/.libs/libmesh_opt_la-fe_bernstein_shape_1D.o src/fe/.libs/libmesh_opt_la-fe_bernstein_shape_2D.o src/fe/.libs/libmesh_opt_la-fe_bernstein_shape_3D.o src/fe/.libs/libmesh_opt_la-fe_boundary.o src/fe/.libs/libmesh_opt_la-fe_clough.o src/fe/.libs/libmesh_opt_la-fe_clough_shape_0D.o src/fe/.libs/libmesh_opt_la-fe_clough_shape_1D.o src/fe/.libs/libmesh_opt_la-fe_clough_shape_2D.o src/fe/.libs/libmesh_opt_la-fe_clough_shape_3D.o src/fe/.libs/libmesh_opt_la-fe_compute_data.o src/fe/.libs/libmesh_opt_la-fe_hermite.o src/fe/.libs/libmesh_opt_la-fe_hermite_shape_0D.o src/fe/.libs/libmesh_opt_la-fe_hermite_shape_1D.o src/fe/.libs/libmesh_opt_la-fe_hermite_shape_2D.o src/fe/.libs/libmesh_opt_la-fe_hermite_shape_3D.o src/fe/.libs/libmesh_opt_la-fe_hierarchic.o src/fe/.libs/libmesh_opt_la-fe_hierarchic_shape_0D.o src/fe/.libs/libmesh_opt_la-fe_hierarchic_shape_1D.o src/fe/.libs/libmesh_opt_la-fe_hierarchic_shape_2D.o src/fe/.libs/libmeshopt la-fe_hierarchic_shape_3D.o src/fe/.libs/libmesh_opt_la-fe_interface.o src/fe/.libs/libmesh_opt_la-fe_interface_inf_fe.o src/fe/.libs/libmesh_opt_la-fe_l2_hierarchic.o src/fe/.libs/libmesh_opt_la-fe_l2_hierarchic_shape_0D.o src/fe/.libs/libmesh_opt_la-fe_l2_hierarchic_shape_1D.o src/fe/.libs/libmesh_opt_la-fe_l2_hierarchic_shape_2D.o src/fe/.libs/libmesh_opt_la-fe_l2_hierarchic_shape_3D.o src/fe/.libs/libmesh_opt_la-fe_l2_lagrange.o src/fe/.libs/libmesh_opt_la-fe_l2_lagrange_shape_0D.o src/fe/.libs/libmesh_opt_la-fe_l2_lagrange_shape_1D.o src/fe/.libs/libmesh_opt_la-fe_l2_lagrange_shape_2D.o src/fe/.libs/libmesh_opt_la-fe_l2_lagrange_shape_3D.o src/fe/.libs/libmesh_opt_la-fe_lagrange.o src/fe/.libs/libmesh_opt_la-fe_lagrange_shape_0D.o src/fe/.libs/libmesh_opt_la-fe_lagrange_shape_1D.o src/fe/.libs/libmesh_opt_la-fe_lagrange_shape_2D.o src/fe/.libs/libmesh_opt_la-fe_lagrange_shape_3D.o src/fe/.libs/libmesh_opt_la-fe_lagrange_vec.o src/fe/.libs/libmesh_opt_la-fe_map.o src/fe/.libs/li bmesh_opt_la-fe_monomial.o src/fe/.libs/libmesh_opt_la-fe_monomial_shape_0D.o src/fe/.libs/libmesh_opt_la-fe_monomial_shape_1D.o src/fe/.libs/libmesh_opt_la-fe_monomial_shape_2D.o src/fe/.libs/libmesh_opt_la-fe_monomial_shape_3D.o src/fe/.libs/libmesh_opt_la-fe_nedelec_one.o src/fe/.libs/libmesh_opt_la-fe_nedelec_one_shape_2D.o src/fe/.libs/libmesh_opt_la-fe_nedelec_one_shape_3D.o src/fe/.libs/libmesh_opt_la-fe_scalar.o src/fe/.libs/libmesh_opt_la-fe_scalar_shape_0D.o src/fe/.libs/libmesh_opt_la-fe_scalar_shape_1D.o src/fe/.libs/libmesh_opt_la-fe_scalar_shape_2D.o src/fe/.libs/libmesh_opt_la-fe_scalar_shape_3D.o src/fe/.libs/libmesh_opt_la-fe_subdivision_2D.o src/fe/.libs/libmesh_opt_la-fe_szabab.o src/fe/.libs/libmesh_opt_la-fe_szabab_shape_0D.o src/fe/.libs/libmesh_opt_la-fe_szabab_shape_1D.o src/fe/.libs/libmesh_opt_la-fe_szabab_shape_2D.o src/fe/.libs/libmesh_opt_la-fe_szabab_shape_3D.o src/fe/.libs/libmesh_opt_la-fe_transformation_base.o src/fe/.libs/libmesh_opt_la-fe_type.o sr c/fe/.libs/libmesh_opt_la-fe_xyz.o src/fe/.libs/libmesh_opt_la-fe_xyz_boundary.o src/fe/.libs/libmesh_opt_la-fe_xyz_map.o src/fe/.libs/libmesh_opt_la-fe_xyz_shape_0D.o src/fe/.libs/libmesh_opt_la-fe_xyz_shape_1D.o src/fe/.libs/libmesh_opt_la-fe_xyz_shape_2D.o src/fe/.libs/libmesh_opt_la-fe_xyz_shape_3D.o src/fe/.libs/libmesh_opt_la-h1_fe_transformation.o src/fe/.libs/libmesh_opt_la-hcurl_fe_transformation.o src/fe/.libs/libmesh_opt_la-inf_fe.o src/fe/.libs/libmesh_opt_la-inf_fe_base_radial.o src/fe/.libs/libmesh_opt_la-inf_fe_boundary.o src/fe/.libs/libmesh_opt_la-inf_fe_jacobi_20_00_eval.o 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src/systems/.libs/libmesh_opt_la-optimization_system.o src/systems/.libs/libmesh_opt_la-parameter_vector.o src/systems/.libs/libmesh_opt_la-qoi_set.o src/systems/.libs/libmesh_opt_la-steady_system.o src/systems/.libs/libmesh_opt_la-system.o src/systems/.libs/libmesh_opt_la-system_io.o src/systems/.libs/libmesh_opt_la-system_projection.o src/systems/.libs/libmesh_opt_la-system_subset.o src/systems/.libs/libmesh_opt_la-system_subset_by_subdomain.o src/systems/.libs/libmesh_opt_la-transient_system.o src/utils/.libs/libmesh_opt_la-error_vector.o src/utils/.libs/libmesh_opt_la-hashword.o src/utils/.libs/libmesh_opt_la-libmesh_version.o src/utils/.libs/libmesh_opt_la-location_maps.o src/utils/.libs/libmesh_opt_la-number_lookups.o src/utils/.libs/lib mesh_opt_la-perf_log.o src/utils/.libs/libmesh_opt_la-plt_loader.o src/utils/.libs/libmesh_opt_la-plt_loader_read.o src/utils/.libs/libmesh_opt_la-plt_loader_write.o src/utils/.libs/libmesh_opt_la-point_locator_base.o src/utils/.libs/libmesh_opt_la-point_locator_list.o src/utils/.libs/libmesh_opt_la-point_locator_tree.o src/utils/.libs/libmesh_opt_la-statistics.o src/utils/.libs/libmesh_opt_la-string_to_enum.o src/utils/.libs/libmesh_opt_la-timestamp.o src/utils/.libs/libmesh_opt_la-topology_map.o src/utils/.libs/libmesh_opt_la-tree.o src/utils/.libs/libmesh_opt_la-tree_node.o src/utils/.libs/libmesh_opt_la-utility.o src/utils/.libs/libmesh_opt_la-xdr_cxx.o -Wl,--whole-archive contrib/.libs/libcontrib_opt.a -Wl,--no-whole-archive -Wl,-rpath -Wl,/home/tmac/src/upstream/libmesh/contrib/netcdf/v4/liblib/.libs -Wl,-rpath -Wl,/home/tmac/usr/stow/libmesh/lib /home/tmac/src/upstream/libmesh/contrib/netcdf/v4/liblib/.libs/libnetcdf.so -L/usr/lib/x86_64-linux-gnu /usr/lib/x86_64-linux-gnu/ libcurl-gnutls.so -L/home/tmac/usr/slepc_maint/arch-linux2-c-complex-opt/lib -L/home/tmac/usr/petsc_maint/arch-linux2-c-complex-opt/lib -L/lib/x86_64-linux-gnu -L/usr/lib -L/usr/lib/openmpi/lib -L/usr/lib/gcc/x86_64-linux-gnu/5 -lglpk -lvtkIOCore-6.2 -lvtkCommonCore-6.2 -lvtkCommonDataModel-6.2 -lvtkFiltersCore-6.2 -lvtkIOXML-6.2 -lvtkImagingCore-6.2 -lvtkIOImage-6.2 -lvtkImagingMath-6.2 -lvtkIOParallelXML-6.2 -ltbb -ltbbmalloc -lslepc -lpetsc -lsuperlu_4.3 -lflapack -lfblas -lparmetis -lmetis -lptesmumps -lptscotch -lptscotcherr -lscotch -lscotcherr -lX11 -lhwloc -lssl -lcrypto -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh -lgfortran -lquadmath -lrt -lz -ldl -L/usr/lib/gcc/x86_64-linux-gnu/5/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/5/../../../../lib -L/lib/../lib -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/5/../../.. -lmpi_cxx -lmpi -lstdc++ -lm -lpthread -lc -lgcc_s /usr/lib/gcc/x86_64-linux-gnu/5/crtendS.o /usr/lib/gcc/x8664-linux-gnu/5/../../../x86 64-linux-gnu/crtn.o -O2 -fopenmp -Wl,-rpath -Wl,/lib/x86_64-linux-gnu -Wl,-rpath -Wl,/usr/lib -Wl,-rpath -Wl,/home/tmac/usr/slepc_maint/arch-linux2-c-complex-opt/lib -Wl,-rpath -Wl,/home/tmac/usr/petsc_maint/arch-linux2-c-complex-opt/lib -Wl,-rpath -Wl,/usr/lib/gcc/x86_64-linux-gnu/5 -Wl,-rpath -Wl,/usr/lib/x86_64-linux-gnu -Wl,-rpath -Wl,/usr/lib/openmpi/lib -Wl,-rpath -Wl,/lib/x86_64-linux-gnu -Wl,-rpath -Wl,/usr/lib -Wl,-rpath -Wl,/home/tmac/usr/slepc_maint/arch-linux2-c-complex-opt/lib -Wl,-rpath -Wl,/home/tmac/usr/petsc_maint/arch-linux2-c-complex-opt/lib -Wl,-rpath -Wl,/usr/lib/gcc/x86_64-linux-gnu/5 -Wl,-rpath -Wl,/usr/lib/x86_64-linux-gnu -Wl,-rpath -Wl,/usr/lib/openmpi/lib -fopenmp -pthread -Wl,-soname -Wl,libmesh_opt.so.0 -o .libs/libmesh_opt.so.0.0.0 /usr/bin/ld: gk_cur_jbufs: TLS definition in contrib/.libs/libcontrib_opt.a(libopt_la-error.o) section .tdata mismatches non-TLS definition in /home/tmac/usr/petsc_maint/arch-linux2-c-complex-opt/lib/libmetis.so section .data /home/tmac/usr/petsc_maint/arch-linux2-c-complex-opt/lib/libmetis.so: error adding symbols: Bad value collect2: error: ld returned 1 exit status Makefile:9679: recipe for target 'libmesh_opt.la' failed make[1]: * [libmesh_opt.la] Error 1 make[1]: Leaving directory '/home/tmac/src/upstream/libmesh' Makefile:28783: recipe for target 'install-recursive' failed make: * [install-recursive] Error 1

This happended on two different Linux systems, Debian Sid and Red Hat Enterprise Linux Server release 6.7, the latter updated to gcc (GCC) 5.3.1

20160322. PETSc and SLEPc were the updated maint branches, and libmesh the newest GIT version.

Downgrading PETSc maint to the commit before 53980de fixes the problem. I also tried to configure libmesh with --with-metis=internal, but it had no effect. As far as I could see, it still tried to link against the Metis installed by PETSc.

Here is a link to the PETSc commit:

https://bitbucket.org/petsc/petsc/commits/53980de7c74b5380ebc1ba49244aaa94dd3e32b2?at=maint http://url

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[torquil]

Using the configure flag --with-metis=PETSc fixes the problem, so I will be doing that. I did not change any PETSc configure when the problem appeared. Thanks!

[jwpeterson]

Glad it worked, I'll close this but may still comment if I find out any more about the TLS issue.