Hi Jean-François,
there are some multiprocessing-related issues on some platforms that occur with homogenization examples - you can ignore those if you do not need that functionality. But the last problem with the test [92] is a new one for me - does it also disappear with --debug?
r.
On 04/17/2018 02:26 PM, Jean-François Louf wrote:
Hi Robert,
Thank you for the response, it was indeed the issue.
Now, when I run python3 run_tests.py everything is fine, except for 2 things that are happening:
1- After the 13th test, a window pops-up telling me that python quit unexpectedly.
2- Two tests are failing, but when I run then in debug mode they are fine, so I don't understand what is the issue? I copy/paste the output:
Jean-Francoiss-MacBook-Air:sfepy jeff$ python3 run_tests.py <<< directory: tests, test files: 101 [1] tests/test_assembling.py +++ test_assemble_matrix: ok +++ test_assemble_matrix_complex: ok +++ test_assemble_vector: ok +++ test_assemble_vector_complex: ok [2] tests/test_base.py +++ test_container_add: ok +++ test_parse_conf: ok +++ test_resolve_deps: ok +++ test_struct_add: ok +++ test_struct_i_add: ok +++ test_verbose_output: ok [3] tests/test_cmesh.py +++ test_cmesh_counts: ok +++ test_entity_volumes: ok [4] tests/test_conditions.py +++ test_ebcs: ok +++ test_epbcs: ok +++ test_ics: ok +++ test_save_ebc: ok [5] tests/test_domain.py +++ test_facets: ok +++ test_refine_2_3: ok +++ test_refine_2_4: ok +++ test_refine_3_4: ok +++ test_refine_3_8: ok +++ test_refine_hexa: ok +++ test_refine_tetra: ok [6] tests/test_eigenvalue_solvers.py +++ test_eigenvalue_solvers: ok [7] tests/test_elasticity_small_strain.py +++ test_get_solution: ok +++ test_linear_terms: ok [8] tests/test_fem.py +++ test_base_functions_delta: ok +++ test_base_functions_values: ok [9] tests/test_functions.py +++ test_ebc_functions: ok +++ test_material_functions: ok +++ test_region_functions: ok [10] tests/test_high_level.py +++ test_solving: ok +++ test_term_arithmetics: ok +++ test_term_evaluation: ok +++ test_variables: ok [11] tests/test_homogenization_engine.py +++ test_chunk_micro: ok +++ test_dependencies: ok [12] tests/test_homogenization_perfusion.py --- test_solution: failed! [13] tests/test_hyperelastic_tlul.py +++ test_solution: ok [14] tests/test_input_acoustics.py +++ test_input: ok [15] tests/test_input_acoustics3d.py +++ test_input: ok [16] tests/test_input_active_fibres.py +++ test_input: ok [17] tests/test_input_balloon.py warp violation -8.131380e-01 at (iel: 9, iqp: 0)! warp violation -8.131380e-01 at (iel: 9, iqp: 1)! warp violation -8.131380e-01 at (iel: 9, iqp: 2)! warp violation -8.131380e-01 at (iel: 9, iqp: 3)! warp violation -5.266340e-01 at (iel: 330, iqp: 0)! warp violation -5.266340e-01 at (iel: 330, iqp: 1)! warp violation -5.266340e-01 at (iel: 330, iqp: 2)! warp violation -5.266340e-01 at (iel: 330, iqp: 3)! warp violation -4.581797e-01 at (iel: 11, iqp: 0)! warp violation -4.581797e-01 at (iel: 11, iqp: 1)! warp violation -4.581797e-01 at (iel: 11, iqp: 2)! warp violation -4.581797e-01 at (iel: 11, iqp: 3)! warp violation -8.029812e-02 at (iel: 104, iqp: 0)! warp violation -8.029812e-02 at (iel: 104, iqp: 1)! warp violation -8.029812e-02 at (iel: 104, iqp: 2)! warp violation -8.029812e-02 at (iel: 104, iqp: 3)! warp violation -2.155647e+00 at (iel: 196, iqp: 0)! warp violation -2.155647e+00 at (iel: 196, iqp: 1)! warp violation -2.155647e+00 at (iel: 196, iqp: 2)! warp violation -2.155647e+00 at (iel: 196, iqp: 3)! warp violation -1.038675e+00 at (iel: 196, iqp: 0)! warp violation -1.038675e+00 at (iel: 196, iqp: 1)! warp violation -1.038675e+00 at (iel: 196, iqp: 2)! warp violation -1.038675e+00 at (iel: 196, iqp: 3)! +++ test_input: ok [18] tests/test_input_biot.py +++ test_input: ok [19] tests/test_input_biot_npbc.py +++ test_input: ok [20] tests/test_input_biot_npbc_lagrange.py +++ test_input: ok [21] tests/test_input_biot_short_syntax.py +++ test_input: ok [22] tests/test_input_cube.py +++ test_input: ok [23] tests/test_input_darcy_flow_multicomp.py +++ test_input: ok [24] tests/test_input_elastic_contact_planes.py +++ test_input: ok [25] tests/test_input_elastic_contact_sphere.py +++ test_input: ok [26] tests/test_input_elastic_shifted_periodic.py +++ test_input: ok [27] tests/test_input_elastodynamic.py +++ test_input: ok [28] tests/test_input_its2D_2.py +++ test_input: ok [29] tests/test_input_laplace_1d.py +++ test_input: ok [30] tests/test_input_laplace_coupling_lcbcs.py +++ test_input: ok [31] tests/test_input_laplace_time_ebcs.py +++ test_input: ok [32] tests/test_input_linear_elastic.py +++ test_input: ok [33] tests/test_input_linear_elastic_damping.py +++ test_input: ok [34] tests/test_input_linear_elastic_iga.py +++ test_input: ok [35] tests/test_input_linear_elastic_mM.py Process Process-6: Process Process-7: Process Process-8: Traceback (most recent call last): Traceback (most recent call last): File "/usr/local/Cellar/python/3.6.4_4/Frameworks/Python.framework/Versions/3.6/lib/python3.6/multiprocessing/process.py", line 258, in _bootstrap self.run() File "/usr/local/Cellar/python/3.6.4_4/Frameworks/Python.framework/Versions/3.6/lib/python3.6/multiprocessing/process.py", line 93, in run self._target(*self._args, **self._kwargs) File "/Users/jeff/sfepy/sfepy/homogenization/engine.py", line 421, in calculate_req_multi dependencies, micro_coors, time_tag, chunk_tab, proc_id) File "/Users/jeff/sfepy/sfepy/homogenization/engine.py", line 280, in calculate_req rargs = req_info[name] KeyError: 'corrs_gamma_B_2' File "/usr/local/Cellar/python/3.6.4_4/Frameworks/Python.framework/Versions/3.6/lib/python3.6/multiprocessing/process.py", line 258, in _bootstrap self.run() File "/usr/local/Cellar/python/3.6.4_4/Frameworks/Python.framework/Versions/3.6/lib/python3.6/multiprocessing/process.py", line 93, in run self._target(*self._args, **self._kwargs) File "/Users/jeff/sfepy/sfepy/homogenization/engine.py", line 421, in calculate_req_multi dependencies, micro_coors, time_tag, chunk_tab, proc_id) File "/Users/jeff/sfepy/sfepy/homogenization/engine.py", line 280, in calculate_req rargs = req_info[name] KeyError: 'corrs_gamma_B_3' Traceback (most recent call last): File "/usr/local/Cellar/python/3.6.4_4/Frameworks/Python.framework/Versions/3.6/lib/python3.6/multiprocessing/process.py", line 258, in _bootstrap self.run() File "/usr/local/Cellar/python/3.6.4_4/Frameworks/Python.framework/Versions/3.6/lib/python3.6/multiprocessing/process.py", line 93, in run self._target(*self._args, **self._kwargs) File "/Users/jeff/sfepy/sfepy/homogenization/engine.py", line 421, in calculate_req_multi dependencies, micro_coors, time_tag, chunk_tab, proc_id) File "/Users/jeff/sfepy/sfepy/homogenization/engine.py", line 280, in calculate_req rargs = req_info[name] KeyError: 'corrs_gamma_A_2' Process Process-9: Traceback (most recent call last): File "/usr/local/Cellar/python/3.6.4_4/Frameworks/Python.framework/Versions/3.6/lib/python3.6/multiprocessing/process.py", line 258, in _bootstrap self.run() File "/usr/local/Cellar/python/3.6.4_4/Frameworks/Python.framework/Versions/3.6/lib/python3.6/multiprocessing/process.py", line 93, in run self._target(*self._args, **self._kwargs) File "/Users/jeff/sfepy/sfepy/homogenization/engine.py", line 421, in calculate_req_multi dependencies, micro_coors, time_tag, chunk_tab, proc_id) File "/Users/jeff/sfepy/sfepy/homogenization/engine.py", line 280, in calculate_req rargs = req_info[name] KeyError: 'corrs_piB' --- test_input: failed! [36] tests/test_input_linear_elastic_probes.py +++ test_input: ok [37] tests/test_input_linear_elastic_tractions.py +++ test_input: ok [38] tests/test_input_linear_elastic_up.py +++ test_input: ok [39] tests/test_input_linear_viscoelastic.py +++ test_input: ok [40] tests/test_input_material_nonlinearity.py +++ test_input: ok [41] tests/test_input_navier_stokes.py +++ test_input: ok [42] tests/test_input_navier_stokes2d.py +++ test_input: ok [43] tests/test_input_navier_stokes2d_iga.py +++ test_input: ok [44] tests/test_input_nodal_lcbcs.py +++ test_input: ok [45] tests/test_input_perfusion_tl.py +++ test_input: ok [46] tests/test_input_piezo_elasticity.py +++ test_ebc: ok +++ test_input: ok [47] tests/test_input_poisson.py +++ test_input: ok [48] tests/test_input_poisson_field_dependent_material.py +++ test_input: ok [49] tests/test_input_poisson_functions.py +++ test_input: ok [50] tests/test_input_poisson_iga.py +++ test_input: ok [51] tests/test_input_poisson_neumann.py +++ test_input: ok [52] tests/test_input_poisson_periodic_boundary_condition.py +++ test_input: ok [53] tests/test_input_prestress_fibres.py +++ test_input: ok [54] tests/test_input_shell10x_cantilever.py +++ test_input: ok [55] tests/test_input_sinbc.py +++ test_input: ok [56] tests/test_input_stabilized_navier_stokes.py +++ test_input: ok [57] tests/test_input_stokes.py +++ test_input: ok [58] tests/test_input_stokes_slip_bc.py +++ test_input: ok [59] tests/test_input_stokes_slip_bc_penalty.py +++ test_input: ok [60] tests/test_input_thermo_elasticity.py +++ test_input: ok [61] tests/test_input_thermo_elasticity_ess.py +++ test_input: ok [62] tests/test_input_time_advection_diffusion.py +++ test_input: ok [63] tests/test_input_time_poisson.py +++ test_input: ok [64] tests/test_input_two_bodies_contact.py +++ test_input: ok [65] tests/test_input_vibro_acoustic3d.py +++ test_input: ok [66] tests/test_io.py +++ test_recursive_dict_hdf5: ok +++ test_sparse_matrix_hdf5: ok [67] tests/test_laplace_unit_disk.py +++ test_boundary_fluxes: ok [68] tests/test_laplace_unit_square.py +++ test_boundary_fluxes: ok +++ test_solution: ok [69] tests/test_lcbc_2d.py +++ test_linear_rigid_body_bc: ok [70] tests/test_lcbc_3d.py +++ test_linear_rigid_body_bc: ok [71] tests/test_lcbcs.py +++ test_laplace_shifted_periodic: ok +++ test_stokes_slip_bc: ok [72] tests/test_linalg.py +++ test_assemble1d: ok +++ test_geometry: ok +++ test_tensors: ok +++ test_unique_rows: ok [73] tests/test_linear_solvers.py +++ test_ls_reuse: ok +++ test_solvers: ok [74] tests/test_linearization.py +++ test_linearization: ok [75] tests/test_matcoefs.py +++ test_conversion_functions: ok +++ test_elastic_constants: ok +++ test_stiffness_tensors: ok [76] tests/test_mesh_expand.py +++ test_mesh_expand: ok [77] tests/test_mesh_generators.py +++ test_gen_block_mesh: ok +++ test_gen_cylinder_mesh: ok +++ test_gen_extended_block_mesh: ok +++ test_gen_mesh_from_geom: ok +++ test_gen_mesh_from_voxels: ok +++ test_gen_tiled_mesh: ok [78] tests/test_mesh_interp.py +++ test_evaluate_at: ok +++ test_field_gradient: ok +++ test_interpolation: ok +++ test_interpolation_two_meshes: ok +++ test_invariance: ok +++ test_invariance_qp: ok [79] tests/test_mesh_smoothing.py +++ test_mesh_smoothing: ok [80] tests/test_meshio.py +++ test_read_meshes: ok +++ test_compare_same_meshes: ok +++ test_read_dimension: ok +++ test_write_read_meshes: ok +++ test_hdf5_meshio: ok [81] tests/test_msm_laplace.py +++ test_msm_laplace: ok [82] tests/test_msm_symbolic.py +++ test_msm_symbolic_diffusion: ok +++ test_msm_symbolic_laplace: ok [83] tests/test_normals.py +++ test_normals: ok [84] tests/test_parsing.py +++ test_parse_equations: ok +++ test_parse_regions: ok [85] tests/test_periodic_bc_2d.py +++ test_pbc: ok [86] tests/test_periodic_bc_3d.py +++ test_pbc: ok [87] tests/test_permutations.py +++ test_rcm: ok [88] tests/test_poly_spaces.py +++ test_continuity: ok +++ test_gradients: ok +++ test_hessians: ok [89] tests/test_projections.py +++ test_mass_matrix: ok +++ test_project_tensors: ok +++ test_projection_iga_fem: ok +++ test_projection_tri_quad: ok [90] tests/test_quadratures.py +++ test_quadratures: ok +++ test_weight_consistency: ok [91] tests/test_ref_coors.py +++ test_ref_coors_fem: ok +++ test_ref_coors_iga: ok [92] tests/test_refine_hanging.py [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger [0]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind [0]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS X to find memory corruption errors [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run [0]PETSC ERROR: to get more information on the crash. application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0 [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=59 : system msg for write_line failure : Bad file descriptor
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