Problem installing/using Sfepy
Hello,
I am trying to use sfepy instead of comsol, and I have some issues with the installation. The sfepy website recommend to post the output of the failed test ran in debug mode here, so that's what I'm trying to do.
I am using a mac OS 10.13.4, with Python 3.6.4. A lot of tests are failing, the first one is assembling, so when I run:
python3 run_tests.py --debug tests/test_assembling.py
Here is the output:
<<< directory: tests, test files: 1 <<< [1] tests/test_assembling.py [1] sfepy: left over: ['__name__', '__doc__', '__package__', '__loader__', '__spec__', '__file__', '__cached__', '__builtins__', 'absolute_import', 'nm', 'sps', 'TestCommon', 'verbose', '_filename']
test instance prepared (4 test(s)) <class 'ModuleNotFoundError'>
ModuleNotFoundError Traceback (most recent call last) ~/sfepy/run_tests.py in <module>() 232 233 if __name__ == '__main__': --> 234 sys.exit(main()) global sys.exit = <built-in function exit> global main = <function main at 0x10a41fea0>
~/sfepy/run_tests.py in main() 221 for test_filename in options.test_filename: 222 dirname, filename = op.split(test_filename) --> 223 run_tests(stats, dirname, [filename]) run_tests = <function wrap_run_tests.<locals>.run_tests at 0x10996aea0> stats = [0, 0, 0, 0.0] dirname = 'tests' filename = 'test_assembling.py' 224 else: 225 for dirpath, dirnames, filenames in os.walk(options.test_dir):
~/sfepy/run_tests.py in run_tests(stats=[0, 0, 0, 0.0], dir_name='tests', filenames=['test_assembling.py']) 142 143 n_fail, n_total, test_time = run_test(conf_name, options, --> 144 stats[0] + 1) stats = [0, 0, 0, 0.0] 145 146 stats[0] += 1
~/sfepy/run_tests.py in run_test(conf_name='tests/test_assembling.py', options=Namespace(debug=True, filter_less=False, filter_...sts', test_filename=['tests/test_assembling.py']), ifile=1) 106 output.set_output_prefix(orig_prefix) 107 ok, n_fail, n_total = test.run(debug=options.raise_on_error, --> 108 ifile=ifile) ifile = 1 109 output.set_output_prefix('[%d] %s' % (ifile, orig_prefix)) 110 test_time = time.clock() - tt
~/sfepy/sfepy/base/testing.py in run(self=Test, debug=True, ifile=1) 65 66 try: ---> 67 ret = test_method() ret = undefined test_method = <bound method Test.test_assemble_matrix of Test> 68 except: 69 if debug:
~/sfepy/tests/test_assembling.py in test_assemble_matrix(self=Test) 62 63 def test_assemble_matrix(self): ---> 64 from sfepy.discrete.common.extmods.assemble import assemble_matrix global sfepy.discrete.common.extmods.assemble = undefined assemble_matrix = undefined 65 66 mtx = sps.csr_matrix(nm.ones((self.num, self.num),
~/sfepy/sfepy/discrete/__init__.py in <module>() 7 from .functions import Functions, Function 8 from .conditions import Conditions ----> 9 from .variables import Variables, Variable, FieldVariable, create_adof_conns global variables = undefined global Variables = undefined global Variable = undefined global FieldVariable = undefined global create_adof_conns = undefined 10 from .materials import Materials, Material 11 from .equations import Equations, Equation
~/sfepy/sfepy/discrete/variables.py in <module>() 12 output, OneTypeList, Container, Struct, basestr, 13 iter_dict_of_lists) ---> 14 import sfepy.linalg as la global sfepy.linalg = undefined global la = undefined 15 from sfepy.discrete.functions import Function 16 from sfepy.discrete.conditions import get_condition_value
~/sfepy/sfepy/linalg/__init__.py in <module>() 1 from __future__ import absolute_import ----> 2 from .extmods.crcm import rcm, permute_in_place global extmods.crcm = undefined global rcm = undefined global permute_in_place = undefined 3 from .sparse import * 4 from .utils import * 5 from .geometry import *
ModuleNotFoundError: No module named 'sfepy.linalg.extmods.crcm'
/Users/jeff/sfepy/sfepy/linalg/__init__.py(2)<module>() 1 from __future__ import absolute_import ----> 2 from .extmods.crcm import rcm, permute_in_place 3 from .sparse import * 4 from .utils import * 5 from .geometry import *
ipdb>
Thank you in advance for any help provided.
Hi Jean-François,
it seems that the extension modules of sfepy are not compiled - did you run "python setup.py build_ext --inplace" in the source directory?
r.
On 04/13/2018 01:52 PM, jeanfrancois.louf@gmail.com wrote:
Hello,
I am trying to use sfepy instead of comsol, and I have some issues with the installation. The sfepy website recommend to post the output of the failed test ran in debug mode here, so that's what I'm trying to do.
I am using a mac OS 10.13.4, with Python 3.6.4. A lot of tests are failing, the first one is assembling, so when I run:
python3 run_tests.py --debug tests/test_assembling.py
Here is the output:
<<< directory: tests, test files: 1 <<< [1] tests/test_assembling.py [1] sfepy: left over: ['__name__', '__doc__', '__package__', '__loader__', '__spec__', '__file__', '__cached__', '__builtins__', 'absolute_import', 'nm', 'sps', 'TestCommon', 'verbose', '_filename']
test instance prepared (4 test(s)) <class 'ModuleNotFoundError'>
ModuleNotFoundError Traceback (most recent call last) ~/sfepy/run_tests.py in <module>() 232 233 if __name__ == '__main__': --> 234 sys.exit(main()) global sys.exit = <built-in function exit> global main = <function main at 0x10a41fea0>
~/sfepy/run_tests.py in main() 221 for test_filename in options.test_filename: 222 dirname, filename = op.split(test_filename) --> 223 run_tests(stats, dirname, [filename]) run_tests = <function wrap_run_tests.<locals>.run_tests at 0x10996aea0> stats = [0, 0, 0, 0.0] dirname = 'tests' filename = 'test_assembling.py' 224 else: 225 for dirpath, dirnames, filenames in os.walk(options.test_dir):
~/sfepy/run_tests.py in run_tests(stats=[0, 0, 0, 0.0], dir_name='tests', filenames=['test_assembling.py']) 142 143 n_fail, n_total, test_time = run_test(conf_name, options, --> 144 stats[0] + 1) stats = [0, 0, 0, 0.0] 145 146 stats[0] += 1
~/sfepy/run_tests.py in run_test(conf_name='tests/test_assembling.py', options=Namespace(debug=True, filter_less=False, filter_...sts', test_filename=['tests/test_assembling.py']), ifile=1) 106 output.set_output_prefix(orig_prefix) 107 ok, n_fail, n_total = test.run(debug=options.raise_on_error, --> 108 ifile=ifile) ifile = 1 109 output.set_output_prefix('[%d] %s' % (ifile, orig_prefix)) 110 test_time = time.clock() - tt
~/sfepy/sfepy/base/testing.py in run(self=Test, debug=True, ifile=1) 65 66 try: ---> 67 ret = test_method() ret = undefined test_method = <bound method Test.test_assemble_matrix of Test> 68 except: 69 if debug:
~/sfepy/tests/test_assembling.py in test_assemble_matrix(self=Test) 62 63 def test_assemble_matrix(self): ---> 64 from sfepy.discrete.common.extmods.assemble import assemble_matrix global sfepy.discrete.common.extmods.assemble = undefined assemble_matrix = undefined 65 66 mtx = sps.csr_matrix(nm.ones((self.num, self.num),
~/sfepy/sfepy/discrete/__init__.py in <module>() 7 from .functions import Functions, Function 8 from .conditions import Conditions ----> 9 from .variables import Variables, Variable, FieldVariable, create_adof_conns global variables = undefined global Variables = undefined global Variable = undefined global FieldVariable = undefined global create_adof_conns = undefined 10 from .materials import Materials, Material 11 from .equations import Equations, Equation
~/sfepy/sfepy/discrete/variables.py in <module>() 12 output, OneTypeList, Container, Struct, basestr, 13 iter_dict_of_lists) ---> 14 import sfepy.linalg as la global sfepy.linalg = undefined global la = undefined 15 from sfepy.discrete.functions import Function 16 from sfepy.discrete.conditions import get_condition_value
~/sfepy/sfepy/linalg/__init__.py in <module>() 1 from __future__ import absolute_import ----> 2 from .extmods.crcm import rcm, permute_in_place global extmods.crcm = undefined global rcm = undefined global permute_in_place = undefined 3 from .sparse import * 4 from .utils import * 5 from .geometry import *
ModuleNotFoundError: No module named 'sfepy.linalg.extmods.crcm'
/Users/jeff/sfepy/sfepy/linalg/__init__.py(2)<module>() 1 from __future__ import absolute_import ----> 2 from .extmods.crcm import rcm, permute_in_place 3 from .sparse import * 4 from .utils import * 5 from .geometry import *
ipdb>
Thank you in advance for any help provided.
SfePy mailing list sfepy@python.org https://mail.python.org/mm3/mailman3/lists/sfepy.python.org/
Hi Robert,
Thank you very much, that was indeed the issue.
Now when I run:
python3 run_tests.py
I have 2 things happening:
1- After the 13th test, everytime I have a window popping up, telling me that python quit unexpectedly.
2- I have 2 tests that are failing (I copy/paste the report), but in debug mode, they both are fine. So I don't really understand what is the issue...
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
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
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
SfePy mailing list sfepy@python.org https://mail.python.org/mm3/mailman3/lists/sfepy.python.org/
Hi Robert,
Thank you very much for your quick answer. It seems it does. Here is the output:
python3 run_tests.py --debug tests/test_refine_hanging.py <<< directory: tests, test files: 1 <<< [1] tests/test_refine_hanging.py [1] sfepy: left over: ['__name__', '__doc__', '__package__', '__loader__', '__spec__', '__file__', '__cached__', '__builtins__', 'absolute_import', 'op', 'nm', 'TestCommon', 'assert_', 'Struct', 'eval_fun', '_gen_lines_2_4', '_gen_grid_3_8', '_build_filenames', 'verbose', '_filename']
test instance prepared (2 test(s)) [1/1] sfepy: generating 9 vertices... [1/1] sfepy: ...done [1/1] sfepy: generating 4 cells... [1/1] sfepy: ...done ... geometry: 2_4, order: 1, permutation: 0: [0 1 2 3] [1/1] sfepy: updating variables... [1/1] sfepy: ...done [1/1] sfepy: setting up dof connectivities... [1/1] sfepy: ...done in 0.00 s [1/1] sfepy: matrix shape: (20, 20) [1/1] sfepy: assembling matrix graph... [1/1] sfepy: ...done in 0.00 s [1/1] sfepy: matrix structural nonzeros: 132 (3.30e-01% fill) [1/1] sfepy: updating variables... [1/1] sfepy: ...done [1/1] sfepy: updating materials... [1/1] sfepy: m [1/1] sfepy: ...done in 0.00 s [1/1] sfepy: nls: iter: 0, residual: 4.625153e-01 (rel: 1.000000e+00) [1/1] sfepy: residual: 0.17 [s] [1/1] sfepy: matrix: 0.00 [s] [1/1] sfepy: solve: 0.00 [s] [1/1] sfepy: nls: iter: 1, residual: 7.050749e-17 (rel: 1.524436e-16) [1/1] sfepy: solved in 1 steps in 0.18 seconds ... geometry: 2_4, order: 1, permutation: 1: [1 2 3 0] [1/1] sfepy: updating variables... [1/1] sfepy: ...done [1/1] sfepy: setting up dof connectivities... [1/1] sfepy: ...done in 0.00 s [1/1] sfepy: matrix shape: (20, 20) [1/1] sfepy: assembling matrix graph... [1/1] sfepy: ...done in 0.00 s [1/1] sfepy: matrix structural nonzeros: 132 (3.30e-01% fill) [1/1] sfepy: updating variables... [1/1] sfepy: ...done [1/1] sfepy: updating materials... [1/1] sfepy: m [1/1] sfepy: ...done in 0.00 s [1/1] sfepy: nls: iter: 0, residual: 4.625153e-01 (rel: 1.000000e+00) [1/1] sfepy: residual: 0.00 [s] [1/1] sfepy: matrix: 0.00 [s] [1/1] sfepy: solve: 0.00 [s] [1/1] sfepy: nls: iter: 1, residual: 6.091325e-17 (rel: 1.317000e-16) [1/1] sfepy: solved in 1 steps in 0.00 seconds ... geometry: 2_4, order: 1, permutation: 2: [2 3 0 1] [1/1] sfepy: updating variables... [1/1] sfepy: ...done [1/1] sfepy: setting up dof connectivities... [1/1] sfepy: ...done in 0.00 s [1/1] sfepy: matrix shape: (20, 20) [1/1] sfepy: assembling matrix graph... [1/1] sfepy: ...done in 0.00 s [1/1] sfepy: matrix structural nonzeros: 132 (3.30e-01% fill) [1/1] sfepy: updating variables... [1/1] sfepy: ...done [1/1] sfepy: updating materials... [1/1] sfepy: m [1/1] sfepy: ...done in 0.00 s [1/1] sfepy: nls: iter: 0, residual: 4.625153e-01 (rel: 1.000000e+00) [1/1] sfepy: residual: 0.00 [s] [1/1] sfepy: matrix: 0.00 [s] [1/1] sfepy: solve: 0.00 [s] [1/1] sfepy: nls: iter: 1, residual: 7.519581e-17 (rel: 1.625801e-16) [1/1] sfepy: solved in 1 steps in 0.01 seconds ... geometry: 2_4, order: 1, permutation: 3: [3 0 1 2] [1/1] sfepy: updating variables... [1/1] sfepy: ...done [1/1] sfepy: setting up dof connectivities... [1/1] sfepy: ...done in 0.00 s [1/1] sfepy: matrix shape: (20, 20) [1/1] sfepy: assembling matrix graph... [1/1] sfepy: ...done in 0.00 s [1/1] sfepy: matrix structural nonzeros: 132 (3.30e-01% fill) [1/1] sfepy: updating variables... [1/1] sfepy: ...done [1/1] sfepy: updating materials... [1/1] sfepy: m [1/1] sfepy: ...done in 0.00 s [1/1] sfepy: nls: iter: 0, residual: 4.625153e-01 (rel: 1.000000e+00) [1/1] sfepy: residual: 0.00 [s] [1/1] sfepy: matrix: 0.00 [s] [1/1] sfepy: solve: 0.00 [s] [1/1] sfepy: nls: iter: 1, residual: 9.897050e-17 (rel: 2.139832e-16) [1/1] sfepy: solved in 1 steps in 0.01 seconds [1/1] sfepy: generating 9 vertices... [1/1] sfepy: ...done [1/1] sfepy: generating 4 cells... [1/1] sfepy: ...done ... geometry: 2_4, order: 2, permutation: 0: [0 1 2 3] [1/1] sfepy: updating variables... [1/1] sfepy: ...done [1/1] sfepy: setting up dof connectivities... [1/1] sfepy: ...done in 0.00 s [1/1] sfepy: matrix shape: (65, 65) [1/1] sfepy: assembling matrix graph... [1/1] sfepy: ...done in 0.00 s [1/1] sfepy: matrix structural nonzeros: 865 (2.05e-01% fill) [1/1] sfepy: updating variables... [1/1] sfepy: ...done [1/1] sfepy: updating materials... [1/1] sfepy: m [1/1] sfepy: ...done in 0.00 s [1/1] sfepy: nls: iter: 0, residual: 3.522174e-01 (rel: 1.000000e+00) [1/1] sfepy: residual: 0.00 [s] [1/1] sfepy: matrix: 0.00 [s] [1/1] sfepy: solve: 0.00 [s] [1/1] sfepy: nls: iter: 1, residual: 7.280935e-17 (rel: 2.067171e-16) [1/1] sfepy: solved in 1 steps in 0.01 seconds ... geometry: 2_4, order: 2, permutation: 1: [1 2 3 0] [1/1] sfepy: updating variables... [1/1] sfepy: ...done [1/1] sfepy: setting up dof connectivities... [1/1] sfepy: ...done in 0.00 s [1/1] sfepy: matrix shape: (65, 65) [1/1] sfepy: assembling matrix graph... [1/1] sfepy: ...done in 0.00 s [1/1] sfepy: matrix structural nonzeros: 865 (2.05e-01% fill) [1/1] sfepy: updating variables... [1/1] sfepy: ...done [1/1] sfepy: updating materials... [1/1] sfepy: m [1/1] sfepy: ...done in 0.00 s [1/1] sfepy: nls: iter: 0, residual: 3.522174e-01 (rel: 1.000000e+00) [1/1] sfepy: residual: 0.00 [s] [1/1] sfepy: matrix: 0.00 [s] [1/1] sfepy: solve: 0.00 [s] [1/1] sfepy: nls: iter: 1, residual: 6.239283e-17 (rel: 1.771429e-16) [1/1] sfepy: solved in 1 steps in 0.01 seconds ... geometry: 2_4, order: 2, permutation: 2: [2 3 0 1] [1/1] sfepy: updating variables... [1/1] sfepy: ...done [1/1] sfepy: setting up dof connectivities... [1/1] sfepy: ...done in 0.00 s [1/1] sfepy: matrix shape: (65, 65) [1/1] sfepy: assembling matrix graph... [1/1] sfepy: ...done in 0.00 s [1/1] sfepy: matrix structural nonzeros: 865 (2.05e-01% fill) [1/1] sfepy: updating variables... [1/1] sfepy: ...done [1/1] sfepy: updating materials... [1/1] sfepy: m [1/1] sfepy: ...done in 0.00 s [1/1] sfepy: nls: iter: 0, residual: 3.522174e-01 (rel: 1.000000e+00) [1/1] sfepy: residual: 0.00 [s] [1/1] sfepy: matrix: 0.00 [s] [1/1] sfepy: solve: 0.00 [s] [1/1] sfepy: nls: iter: 1, residual: 6.381378e-17 (rel: 1.811772e-16) [1/1] sfepy: solved in 1 steps in 0.01 seconds ... geometry: 2_4, order: 2, permutation: 3: [3 0 1 2] [1/1] sfepy: updating variables... [1/1] sfepy: ...done [1/1] sfepy: setting up dof connectivities... [1/1] sfepy: ...done in 0.00 s [1/1] sfepy: matrix shape: (65, 65) [1/1] sfepy: assembling matrix graph... [1/1] sfepy: ...done in 0.00 s [1/1] sfepy: matrix structural nonzeros: 865 (2.05e-01% fill) [1/1] sfepy: updating variables... [1/1] sfepy: ...done [1/1] sfepy: updating materials... [1/1] sfepy: m [1/1] sfepy: ...done in 0.00 s [1/1] sfepy: nls: iter: 0, residual: 3.522174e-01 (rel: 1.000000e+00) [1/1] sfepy: residual: 0.00 [s] [1/1] sfepy: matrix: 0.00 [s] [1/1] sfepy: solve: 0.00 [s] [1/1] sfepy: nls: iter: 1, residual: 7.128679e-17 (rel: 2.023943e-16) [1/1] sfepy: solved in 1 steps in 0.01 seconds [1/1] sfepy: generating 9 vertices... [1/1] sfepy: ...done [1/1] sfepy: generating 4 cells... [1/1] sfepy: ...done ... geometry: 2_4, order: 3, permutation: 0: [0 1 2 3] [1/1] sfepy: updating variables... [1/1] sfepy: ...done [1/1] sfepy: setting up dof connectivities... [1/1] sfepy: ...done in 0.00 s [1/1] sfepy: matrix shape: (136, 136) [1/1] sfepy: assembling matrix graph... [1/1] sfepy: ...done in 0.00 s [1/1] sfepy: matrix structural nonzeros: 2980 (1.61e-01% fill) [1/1] sfepy: updating variables... [1/1] sfepy: ...done [1/1] sfepy: updating materials... [1/1] sfepy: m [1/1] sfepy: ...done in 0.00 s [1/1] sfepy: nls: iter: 0, residual: 2.451436e-01 (rel: 1.000000e+00) [1/1] sfepy: residual: 0.00 [s] [1/1] sfepy: matrix: 0.00 [s] [1/1] sfepy: solve: 0.00 [s] [1/1] sfepy: nls: iter: 1, residual: 5.570534e-17 (rel: 2.272355e-16) [1/1] sfepy: solved in 1 steps in 0.01 seconds ... geometry: 2_4, order: 3, permutation: 1: [1 2 3 0] [1/1] sfepy: updating variables... [1/1] sfepy: ...done [1/1] sfepy: setting up dof connectivities... [1/1] sfepy: ...done in 0.00 s [1/1] sfepy: matrix shape: (136, 136) [1/1] sfepy: assembling matrix graph... [1/1] sfepy: ...done in 0.00 s [1/1] sfepy: matrix structural nonzeros: 2980 (1.61e-01% fill) [1/1] sfepy: updating variables... [1/1] sfepy: ...done [1/1] sfepy: updating materials... [1/1] sfepy: m [1/1] sfepy: ...done in 0.00 s [1/1] sfepy: nls: iter: 0, residual: 2.451436e-01 (rel: 1.000000e+00) [1/1] sfepy: residual: 0.00 [s] [1/1] sfepy: matrix: 0.00 [s] [1/1] sfepy: solve: 0.00 [s] [1/1] sfepy: nls: iter: 1, residual: 4.668504e-17 (rel: 1.904396e-16) [1/1] sfepy: solved in 1 steps in 0.01 seconds ... geometry: 2_4, order: 3, permutation: 2: [2 3 0 1] [1/1] sfepy: updating variables... [1/1] sfepy: ...done [1/1] sfepy: setting up dof connectivities... [1/1] sfepy: ...done in 0.00 s [1/1] sfepy: matrix shape: (136, 136) [1/1] sfepy: assembling matrix graph... [1/1] sfepy: ...done in 0.00 s [1/1] sfepy: matrix structural nonzeros: 2980 (1.61e-01% fill) [1/1] sfepy: updating variables... [1/1] sfepy: ...done [1/1] sfepy: updating materials... [1/1] sfepy: m [1/1] sfepy: ...done in 0.00 s [1/1] sfepy: nls: iter: 0, residual: 2.451436e-01 (rel: 1.000000e+00) [1/1] sfepy: residual: 0.00 [s] [1/1] sfepy: matrix: 0.00 [s] [1/1] sfepy: solve: 0.00 [s] [1/1] sfepy: nls: iter: 1, residual: 6.186562e-17 (rel: 2.523648e-16) [1/1] sfepy: solved in 1 steps in 0.01 seconds ... geometry: 2_4, order: 3, permutation: 3: [3 0 1 2] [1/1] sfepy: updating variables... [1/1] sfepy: ...done [1/1] sfepy: setting up dof connectivities... [1/1] sfepy: ...done in 0.00 s [1/1] sfepy: matrix shape: (136, 136) [1/1] sfepy: assembling matrix graph... [1/1] sfepy: ...done in 0.00 s [1/1] sfepy: matrix structural nonzeros: 2980 (1.61e-01% fill) [1/1] sfepy: updating variables... [1/1] sfepy: ...done [1/1] sfepy: updating materials... [1/1] sfepy: m [1/1] sfepy: ...done in 0.00 s [1/1] sfepy: nls: iter: 0, residual: 2.451436e-01 (rel: 1.000000e+00) [1/1] sfepy: residual: 0.00 [s] [1/1] sfepy: matrix: 0.00 [s] [1/1] sfepy: solve: 0.00 [s] [1/1] sfepy: nls: iter: 1, residual: 5.613388e-17 (rel: 2.289837e-16) [1/1] sfepy: solved in 1 steps in 0.01 seconds [1/1] sfepy: generating 27 vertices... [1/1] sfepy: ...done [1/1] sfepy: generating 8 cells... [1/1] sfepy: ...done ... geometry: 3_8, order: 1, permutation: 0: [0 1 2 3 4 5 6 7] [1/1] sfepy: updating variables... [1/1] sfepy: ...done [1/1] sfepy: setting up dof connectivities... [1/1] sfepy: ...done in 0.00 s [1/1] sfepy: matrix shape: (106, 106) [1/1] sfepy: assembling matrix graph... [1/1] sfepy: ...done in 0.00 s [1/1] sfepy: matrix structural nonzeros: 1834 (1.63e-01% fill) [1/1] sfepy: updating variables... [1/1] sfepy: ...done [1/1] sfepy: updating materials... [1/1] sfepy: m [1/1] sfepy: ...done in 0.00 s [1/1] sfepy: nls: iter: 0, residual: 3.007920e-01 (rel: 1.000000e+00) [1/1] sfepy: residual: 0.00 [s] [1/1] sfepy: matrix: 0.00 [s] [1/1] sfepy: solve: 0.00 [s] [1/1] sfepy: nls: iter: 1, residual: 6.773414e-17 (rel: 2.251859e-16) [1/1] sfepy: solved in 1 steps in 0.01 seconds ... geometry: 3_8, order: 1, permutation: 1: [1 2 3 0 5 6 7 4] [1/1] sfepy: updating variables... [1/1] sfepy: ...done [1/1] sfepy: setting up dof connectivities... [1/1] sfepy: ...done in 0.00 s [1/1] sfepy: matrix shape: (106, 106) [1/1] sfepy: assembling matrix graph... [1/1] sfepy: ...done in 0.00 s [1/1] sfepy: matrix structural nonzeros: 1834 (1.63e-01% fill) [1/1] sfepy: updating variables... [1/1] sfepy: ...done [1/1] sfepy: updating materials... [1/1] sfepy: m [1/1] sfepy: ...done in 0.00 s [1/1] sfepy: nls: iter: 0, residual: 3.007920e-01 (rel: 1.000000e+00) [1/1] sfepy: residual: 0.00 [s] [1/1] sfepy: matrix: 0.00 [s] [1/1] sfepy: solve: 0.00 [s] [1/1] sfepy: nls: iter: 1, residual: 6.175505e-17 (rel: 2.053081e-16) [1/1] sfepy: solved in 1 steps in 0.01 seconds ... geometry: 3_8, order: 1, permutation: 2: [2 3 0 1 6 7 4 5] [1/1] sfepy: updating variables... [1/1] sfepy: ...done [1/1] sfepy: setting up dof connectivities... [1/1] sfepy: ...done in 0.00 s [1/1] sfepy: matrix shape: (106, 106) [1/1] sfepy: assembling matrix graph... [1/1] sfepy: ...done in 0.00 s [1/1] sfepy: matrix structural nonzeros: 1834 (1.63e-01% fill) [1/1] sfepy: updating variables... [1/1] sfepy: ...done [1/1] sfepy: updating materials... [1/1] sfepy: m [1/1] sfepy: ...done in 0.00 s [1/1] sfepy: nls: iter: 0, residual: 3.007920e-01 (rel: 1.000000e+00) [1/1] sfepy: residual: 0.00 [s] [1/1] sfepy: matrix: 0.00 [s] [1/1] sfepy: solve: 0.00 [s] [1/1] sfepy: nls: iter: 1, residual: 8.010373e-17 (rel: 2.663093e-16) [1/1] sfepy: solved in 1 steps in 0.01 seconds ... geometry: 3_8, order: 1, permutation: 3: [3 0 1 2 7 4 5 6] [1/1] sfepy: updating variables... [1/1] sfepy: ...done [1/1] sfepy: setting up dof connectivities... [1/1] sfepy: ...done in 0.00 s [1/1] sfepy: matrix shape: (106, 106) [1/1] sfepy: assembling matrix graph... [1/1] sfepy: ...done in 0.00 s [1/1] sfepy: matrix structural nonzeros: 1834 (1.63e-01% fill) [1/1] sfepy: updating variables... [1/1] sfepy: ...done [1/1] sfepy: updating materials... [1/1] sfepy: m [1/1] sfepy: ...done in 0.00 s [1/1] sfepy: nls: iter: 0, residual: 3.007920e-01 (rel: 1.000000e+00) [1/1] sfepy: residual: 0.00 [s] [1/1] sfepy: matrix: 0.00 [s] [1/1] sfepy: solve: 0.00 [s] [1/1] sfepy: nls: iter: 1, residual: 8.931224e-17 (rel: 2.969235e-16) [1/1] sfepy: solved in 1 steps in 0.01 seconds ... geometry: 3_8, order: 1, permutation: 4: [3 2 6 7 0 1 5 4] [1/1] sfepy: updating variables... [1/1] sfepy: ...done [1/1] sfepy: setting up dof connectivities... [1/1] sfepy: ...done in 0.00 s [1/1] sfepy: matrix shape: (106, 106) [1/1] sfepy: assembling matrix graph... [1/1] sfepy: ...done in 0.00 s [1/1] sfepy: matrix structural nonzeros: 1834 (1.63e-01% fill) [1/1] sfepy: updating variables... [1/1] sfepy: ...done [1/1] sfepy: updating materials... [1/1] sfepy: m [1/1] sfepy: ...done in 0.00 s [1/1] sfepy: nls: iter: 0, residual: 3.007920e-01 (rel: 1.000000e+00) [1/1] sfepy: residual: 0.00 [s] [1/1] sfepy: matrix: 0.00 [s] [1/1] sfepy: solve: 0.00 [s] [1/1] sfepy: nls: iter: 1, residual: 6.297008e-17 (rel: 2.093476e-16) [1/1] sfepy: solved in 1 steps in 0.01 seconds ... geometry: 3_8, order: 1, permutation: 5: [7 6 5 4 3 2 1 0] [1/1] sfepy: updating variables... [1/1] sfepy: ...done [1/1] sfepy: setting up dof connectivities... [1/1] sfepy: ...done in 0.00 s [1/1] sfepy: matrix shape: (106, 106) [1/1] sfepy: assembling matrix graph... [1/1] sfepy: ...done in 0.00 s [1/1] sfepy: matrix structural nonzeros: 1834 (1.63e-01% fill) [1/1] sfepy: updating variables... [1/1] sfepy: ...done [1/1] sfepy: updating materials... [1/1] sfepy: m [1/1] sfepy: ...done in 0.00 s [1/1] sfepy: nls: iter: 0, residual: 3.007920e-01 (rel: 1.000000e+00) [1/1] sfepy: residual: 0.00 [s] [1/1] sfepy: matrix: 0.00 [s] [1/1] sfepy: solve: 0.00 [s] [1/1] sfepy: nls: iter: 1, residual: 8.473112e-17 (rel: 2.816933e-16) [1/1] sfepy: solved in 1 steps in 0.01 seconds ... geometry: 3_8, order: 1, permutation: 6: [4 5 1 0 7 6 2 3] [1/1] sfepy: updating variables... [1/1] sfepy: ...done [1/1] sfepy: setting up dof connectivities... [1/1] sfepy: ...done in 0.00 s [1/1] sfepy: matrix shape: (106, 106) [1/1] sfepy: assembling matrix graph... [1/1] sfepy: ...done in 0.00 s [1/1] sfepy: matrix structural nonzeros: 1834 (1.63e-01% fill) [1/1] sfepy: updating variables... [1/1] sfepy: ...done [1/1] sfepy: updating materials... [1/1] sfepy: m [1/1] sfepy: ...done in 0.00 s [1/1] sfepy: nls: iter: 0, residual: 3.007920e-01 (rel: 1.000000e+00) [1/1] sfepy: residual: 0.00 [s] [1/1] sfepy: matrix: 0.00 [s] [1/1] sfepy: solve: 0.00 [s] [1/1] sfepy: nls: iter: 1, residual: 1.065369e-16 (rel: 3.541879e-16) [1/1] sfepy: solved in 1 steps in 0.01 seconds ... geometry: 3_8, order: 1, permutation: 7: [1 5 6 2 0 4 7 3] [1/1] sfepy: updating variables... [1/1] sfepy: ...done [1/1] sfepy: setting up dof connectivities... [1/1] sfepy: ...done in 0.00 s [1/1] sfepy: matrix shape: (106, 106) [1/1] sfepy: assembling matrix graph... [1/1] sfepy: ...done in 0.00 s [1/1] sfepy: matrix structural nonzeros: 1834 (1.63e-01% fill) [1/1] sfepy: updating variables... [1/1] sfepy: ...done [1/1] sfepy: updating materials... [1/1] sfepy: m [1/1] sfepy: ...done in 0.00 s [1/1] sfepy: nls: iter: 0, residual: 3.007920e-01 (rel: 1.000000e+00) [1/1] sfepy: residual: 0.00 [s] [1/1] sfepy: matrix: 0.00 [s] [1/1] sfepy: solve: 0.00 [s] [1/1] sfepy: nls: iter: 1, residual: 1.053300e-16 (rel: 3.501756e-16) [1/1] sfepy: solved in 1 steps in 0.01 seconds ... geometry: 3_8, order: 1, permutation: 8: [5 4 7 6 1 0 3 2] [1/1] sfepy: updating variables... [1/1] sfepy: ...done [1/1] sfepy: setting up dof connectivities... [1/1] sfepy: ...done in 0.00 s [1/1] sfepy: matrix shape: (106, 106) [1/1] sfepy: assembling matrix graph... [1/1] sfepy: ...done in 0.00 s [1/1] sfepy: matrix structural nonzeros: 1834 (1.63e-01% fill) [1/1] sfepy: updating variables... [1/1] sfepy: ...done [1/1] sfepy: updating materials... [1/1] sfepy: m [1/1] sfepy: ...done in 0.00 s [1/1] sfepy: nls: iter: 0, residual: 3.007920e-01 (rel: 1.000000e+00) [1/1] sfepy: residual: 0.00 [s] [1/1] sfepy: matrix: 0.00 [s] [1/1] sfepy: solve: 0.00 [s] [1/1] sfepy: nls: iter: 1, residual: 6.390952e-17 (rel: 2.124708e-16) [1/1] sfepy: solved in 1 steps in 0.01 seconds ... geometry: 3_8, order: 1, permutation: 9: [4 0 3 7 5 1 2 6] [1/1] sfepy: updating variables... [1/1] sfepy: ...done [1/1] sfepy: setting up dof connectivities... [1/1] sfepy: ...done in 0.00 s [1/1] sfepy: matrix shape: (106, 106) [1/1] sfepy: assembling matrix graph... [1/1] sfepy: ...done in 0.00 s [1/1] sfepy: matrix structural nonzeros: 1834 (1.63e-01% fill) [1/1] sfepy: updating variables... [1/1] sfepy: ...done [1/1] sfepy: updating materials... [1/1] sfepy: m [1/1] sfepy: ...done in 0.00 s [1/1] sfepy: nls: iter: 0, residual: 3.007920e-01 (rel: 1.000000e+00) [1/1] sfepy: residual: 0.00 [s] [1/1] sfepy: matrix: 0.00 [s] [1/1] sfepy: solve: 0.00 [s] [1/1] sfepy: nls: iter: 1, residual: 6.434249e-17 (rel: 2.139102e-16) [1/1] sfepy: solved in 1 steps in 0.01 seconds [1/1] sfepy: generating 27 vertices... [1/1] sfepy: ...done [1/1] sfepy: generating 8 cells... [1/1] sfepy: ...done ... geometry: 3_8, order: 2, permutation: 0: [0 1 2 3 4 5 6 7] [1/1] sfepy: updating variables... [1/1] sfepy: ...done [1/1] sfepy: setting up dof connectivities... [1/1] sfepy: ...done in 0.00 s [1/1] sfepy: matrix shape: (631, 631) [1/1] sfepy: assembling matrix graph... [1/1] sfepy: ...done in 0.00 s [1/1] sfepy: matrix structural nonzeros: 30937 (7.77e-02% fill) [1/1] sfepy: updating variables... [1/1] sfepy: ...done [1/1] sfepy: updating materials... [1/1] sfepy: m [1/1] sfepy: ...done in 0.00 s [1/1] sfepy: nls: iter: 0, residual: 1.780860e-01 (rel: 1.000000e+00) [1/1] sfepy: residual: 0.01 [s] [1/1] sfepy: matrix: 0.01 [s] [1/1] sfepy: solve: 0.01 [s] [1/1] sfepy: nls: iter: 1, residual: 5.837067e-17 (rel: 3.277668e-16) [1/1] sfepy: solved in 1 steps in 0.03 seconds ... geometry: 3_8, order: 2, permutation: 1: [1 2 3 0 5 6 7 4] [1/1] sfepy: updating variables... [1/1] sfepy: ...done [1/1] sfepy: setting up dof connectivities... [1/1] sfepy: ...done in 0.00 s [1/1] sfepy: matrix shape: (631, 631) [1/1] sfepy: assembling matrix graph... [1/1] sfepy: ...done in 0.00 s [1/1] sfepy: matrix structural nonzeros: 30937 (7.77e-02% fill) [1/1] sfepy: updating variables... [1/1] sfepy: ...done [1/1] sfepy: updating materials... [1/1] sfepy: m [1/1] sfepy: ...done in 0.00 s [1/1] sfepy: nls: iter: 0, residual: 1.780860e-01 (rel: 1.000000e+00) [1/1] sfepy: residual: 0.01 [s] [1/1] sfepy: matrix: 0.01 [s] [1/1] sfepy: solve: 0.01 [s] [1/1] sfepy: nls: iter: 1, residual: 7.285727e-17 (rel: 4.091129e-16) [1/1] sfepy: solved in 1 steps in 0.03 seconds ... geometry: 3_8, order: 2, permutation: 2: [2 3 0 1 6 7 4 5] [1/1] sfepy: updating variables... [1/1] sfepy: ...done [1/1] sfepy: setting up dof connectivities... [1/1] sfepy: ...done in 0.00 s [1/1] sfepy: matrix shape: (631, 631) [1/1] sfepy: assembling matrix graph... [1/1] sfepy: ...done in 0.00 s [1/1] sfepy: matrix structural nonzeros: 30937 (7.77e-02% fill) [1/1] sfepy: updating variables... [1/1] sfepy: ...done [1/1] sfepy: updating materials... [1/1] sfepy: m [1/1] sfepy: ...done in 0.00 s [1/1] sfepy: nls: iter: 0, residual: 1.780860e-01 (rel: 1.000000e+00) [1/1] sfepy: residual: 0.01 [s] [1/1] sfepy: matrix: 0.01 [s] [1/1] sfepy: solve: 0.01 [s] [1/1] sfepy: nls: iter: 1, residual: 6.720750e-17 (rel: 3.773880e-16) [1/1] sfepy: solved in 1 steps in 0.03 seconds ... geometry: 3_8, order: 2, permutation: 3: [3 0 1 2 7 4 5 6] [1/1] sfepy: updating variables... [1/1] sfepy: ...done [1/1] sfepy: setting up dof connectivities... [1/1] sfepy: ...done in 0.00 s [1/1] sfepy: matrix shape: (631, 631) [1/1] sfepy: assembling matrix graph... [1/1] sfepy: ...done in 0.00 s [1/1] sfepy: matrix structural nonzeros: 30937 (7.77e-02% fill) [1/1] sfepy: updating variables... [1/1] sfepy: ...done [1/1] sfepy: updating materials... [1/1] sfepy: m [1/1] sfepy: ...done in 0.00 s [1/1] sfepy: nls: iter: 0, residual: 1.780860e-01 (rel: 1.000000e+00) [1/1] sfepy: residual: 0.01 [s] [1/1] sfepy: matrix: 0.01 [s] [1/1] sfepy: solve: 0.01 [s] [1/1] sfepy: nls: iter: 1, residual: 6.579303e-17 (rel: 3.694453e-16) [1/1] sfepy: solved in 1 steps in 0.03 seconds ... geometry: 3_8, order: 2, permutation: 4: [3 2 6 7 0 1 5 4] [1/1] sfepy: updating variables... [1/1] sfepy: ...done [1/1] sfepy: setting up dof connectivities... [1/1] sfepy: ...done in 0.00 s [1/1] sfepy: matrix shape: (631, 631) [1/1] sfepy: assembling matrix graph... [1/1] sfepy: ...done in 0.00 s [1/1] sfepy: matrix structural nonzeros: 30937 (7.77e-02% fill) [1/1] sfepy: updating variables... [1/1] sfepy: ...done [1/1] sfepy: updating materials... [1/1] sfepy: m [1/1] sfepy: ...done in 0.00 s [1/1] sfepy: nls: iter: 0, residual: 1.780860e-01 (rel: 1.000000e+00) [1/1] sfepy: residual: 0.01 [s] [1/1] sfepy: matrix: 0.01 [s] [1/1] sfepy: solve: 0.01 [s] [1/1] sfepy: nls: iter: 1, residual: 6.120915e-17 (rel: 3.437056e-16) [1/1] sfepy: solved in 1 steps in 0.03 seconds ... geometry: 3_8, order: 2, permutation: 5: [7 6 5 4 3 2 1 0] [1/1] sfepy: updating variables... [1/1] sfepy: ...done [1/1] sfepy: setting up dof connectivities... [1/1] sfepy: ...done in 0.00 s [1/1] sfepy: matrix shape: (631, 631) [1/1] sfepy: assembling matrix graph... [1/1] sfepy: ...done in 0.00 s [1/1] sfepy: matrix structural nonzeros: 30937 (7.77e-02% fill) [1/1] sfepy: updating variables... [1/1] sfepy: ...done [1/1] sfepy: updating materials... [1/1] sfepy: m [1/1] sfepy: ...done in 0.00 s [1/1] sfepy: nls: iter: 0, residual: 1.780860e-01 (rel: 1.000000e+00) [1/1] sfepy: residual: 0.01 [s] [1/1] sfepy: matrix: 0.01 [s] [1/1] sfepy: solve: 0.01 [s] [1/1] sfepy: nls: iter: 1, residual: 6.689915e-17 (rel: 3.756565e-16) [1/1] sfepy: solved in 1 steps in 0.04 seconds ... geometry: 3_8, order: 2, permutation: 6: [4 5 1 0 7 6 2 3] [1/1] sfepy: updating variables... [1/1] sfepy: ...done [1/1] sfepy: setting up dof connectivities... [1/1] sfepy: ...done in 0.00 s [1/1] sfepy: matrix shape: (631, 631) [1/1] sfepy: assembling matrix graph... [1/1] sfepy: ...done in 0.00 s [1/1] sfepy: matrix structural nonzeros: 30937 (7.77e-02% fill) [1/1] sfepy: updating variables... [1/1] sfepy: ...done [1/1] sfepy: updating materials... [1/1] sfepy: m [1/1] sfepy: ...done in 0.00 s [1/1] sfepy: nls: iter: 0, residual: 1.780860e-01 (rel: 1.000000e+00) [1/1] sfepy: residual: 0.01 [s] [1/1] sfepy: matrix: 0.01 [s] [1/1] sfepy: solve: 0.01 [s] [1/1] sfepy: nls: iter: 1, residual: 5.286647e-17 (rel: 2.968593e-16) [1/1] sfepy: solved in 1 steps in 0.03 seconds ... geometry: 3_8, order: 2, permutation: 7: [1 5 6 2 0 4 7 3] [1/1] sfepy: updating variables... [1/1] sfepy: ...done [1/1] sfepy: setting up dof connectivities... [1/1] sfepy: ...done in 0.00 s [1/1] sfepy: matrix shape: (631, 631) [1/1] sfepy: assembling matrix graph... [1/1] sfepy: ...done in 0.00 s [1/1] sfepy: matrix structural nonzeros: 30937 (7.77e-02% fill) [1/1] sfepy: updating variables... [1/1] sfepy: ...done [1/1] sfepy: updating materials... [1/1] sfepy: m [1/1] sfepy: ...done in 0.00 s [1/1] sfepy: nls: iter: 0, residual: 1.780860e-01 (rel: 1.000000e+00) [1/1] sfepy: residual: 0.01 [s] [1/1] sfepy: matrix: 0.01 [s] [1/1] sfepy: solve: 0.01 [s] [1/1] sfepy: nls: iter: 1, residual: 6.217194e-17 (rel: 3.491120e-16) [1/1] sfepy: solved in 1 steps in 0.03 seconds ... geometry: 3_8, order: 2, permutation: 8: [5 4 7 6 1 0 3 2] [1/1] sfepy: updating variables... [1/1] sfepy: ...done [1/1] sfepy: setting up dof connectivities... [1/1] sfepy: ...done in 0.00 s [1/1] sfepy: matrix shape: (631, 631) [1/1] sfepy: assembling matrix graph... [1/1] sfepy: ...done in 0.00 s [1/1] sfepy: matrix structural nonzeros: 30937 (7.77e-02% fill) [1/1] sfepy: updating variables... [1/1] sfepy: ...done [1/1] sfepy: updating materials... [1/1] sfepy: m [1/1] sfepy: ...done in 0.00 s [1/1] sfepy: nls: iter: 0, residual: 1.780860e-01 (rel: 1.000000e+00) [1/1] sfepy: residual: 0.01 [s] [1/1] sfepy: matrix: 0.01 [s] [1/1] sfepy: solve: 0.01 [s] [1/1] sfepy: nls: iter: 1, residual: 7.391497e-17 (rel: 4.150522e-16) [1/1] sfepy: solved in 1 steps in 0.03 seconds ... geometry: 3_8, order: 2, permutation: 9: [4 0 3 7 5 1 2 6] [1/1] sfepy: updating variables... [1/1] sfepy: ...done [1/1] sfepy: setting up dof connectivities... [1/1] sfepy: ...done in 0.00 s [1/1] sfepy: matrix shape: (631, 631) [1/1] sfepy: assembling matrix graph... [1/1] sfepy: ...done in 0.00 s [1/1] sfepy: matrix structural nonzeros: 30937 (7.77e-02% fill) [1/1] sfepy: updating variables... [1/1] sfepy: ...done [1/1] sfepy: updating materials... [1/1] sfepy: m [1/1] sfepy: ...done in 0.00 s [1/1] sfepy: nls: iter: 0, residual: 1.780860e-01 (rel: 1.000000e+00) [1/1] sfepy: residual: 0.01 [s] [1/1] sfepy: matrix: 0.01 [s] [1/1] sfepy: solve: 0.01 [s] [1/1] sfepy: nls: iter: 1, residual: 7.527482e-17 (rel: 4.226881e-16) [1/1] sfepy: solved in 1 steps in 0.03 seconds [1/1] sfepy: generating 27 vertices... [1/1] sfepy: ...done [1/1] sfepy: generating 8 cells... [1/1] sfepy: ...done ... geometry: 3_8, order: 3, permutation: 0: [0 1 2 3 4 5 6 7] [1/1] sfepy: updating variables... [1/1] sfepy: ...done [1/1] sfepy: setting up dof connectivities... [1/1] sfepy: ...done in 0.00 s [1/1] sfepy: matrix shape: (1918, 1918) [1/1] sfepy: assembling matrix graph... [1/1] sfepy: ...done in 0.02 s [1/1] sfepy: matrix structural nonzeros: 197938 (5.38e-02% fill) [1/1] sfepy: updating variables... [1/1] sfepy: ...done [1/1] sfepy: updating materials... [1/1] sfepy: m [1/1] sfepy: ...done in 0.00 s [1/1] sfepy: nls: iter: 0, residual: 1.008581e-01 (rel: 1.000000e+00) [1/1] sfepy: residual: 0.06 [s] [1/1] sfepy: matrix: 0.12 [s] [1/1] sfepy: solve: 0.05 [s] [1/1] sfepy: nls: iter: 1, residual: 5.033037e-17 (rel: 4.990215e-16) [1/1] sfepy: solved in 1 steps in 0.24 seconds ... geometry: 3_8, order: 3, permutation: 1: [1 2 3 0 5 6 7 4] [1/1] sfepy: updating variables... [1/1] sfepy: ...done [1/1] sfepy: setting up dof connectivities... [1/1] sfepy: ...done in 0.00 s [1/1] sfepy: matrix shape: (1918, 1918) [1/1] sfepy: assembling matrix graph... [1/1] sfepy: ...done in 0.02 s [1/1] sfepy: matrix structural nonzeros: 197938 (5.38e-02% fill) [1/1] sfepy: updating variables... [1/1] sfepy: ...done [1/1] sfepy: updating materials... [1/1] sfepy: m [1/1] sfepy: ...done in 0.00 s [1/1] sfepy: nls: iter: 0, residual: 1.008581e-01 (rel: 1.000000e+00) [1/1] sfepy: residual: 0.06 [s] [1/1] sfepy: matrix: 0.12 [s] [1/1] sfepy: solve: 0.05 [s] [1/1] sfepy: nls: iter: 1, residual: 4.882531e-17 (rel: 4.840989e-16) [1/1] sfepy: solved in 1 steps in 0.23 seconds ... geometry: 3_8, order: 3, permutation: 2: [2 3 0 1 6 7 4 5] [1/1] sfepy: updating variables... [1/1] sfepy: ...done [1/1] sfepy: setting up dof connectivities... [1/1] sfepy: ...done in 0.00 s [1/1] sfepy: matrix shape: (1918, 1918) [1/1] sfepy: assembling matrix graph... [1/1] sfepy: ...done in 0.02 s [1/1] sfepy: matrix structural nonzeros: 197938 (5.38e-02% fill) [1/1] sfepy: updating variables... [1/1] sfepy: ...done [1/1] sfepy: updating materials... [1/1] sfepy: m [1/1] sfepy: ...done in 0.00 s [1/1] sfepy: nls: iter: 0, residual: 1.008581e-01 (rel: 1.000000e+00) [1/1] sfepy: residual: 0.07 [s] [1/1] sfepy: matrix: 0.13 [s] [1/1] sfepy: solve: 0.08 [s] [1/1] sfepy: nls: iter: 1, residual: 4.634362e-17 (rel: 4.594931e-16) [1/1] sfepy: solved in 1 steps in 0.29 seconds ... geometry: 3_8, order: 3, permutation: 3: [3 0 1 2 7 4 5 6] [1/1] sfepy: updating variables... [1/1] sfepy: ...done [1/1] sfepy: setting up dof connectivities... [1/1] sfepy: ...done in 0.00 s [1/1] sfepy: matrix shape: (1918, 1918) [1/1] sfepy: assembling matrix graph... [1/1] sfepy: ...done in 0.02 s [1/1] sfepy: matrix structural nonzeros: 197938 (5.38e-02% fill) [1/1] sfepy: updating variables... [1/1] sfepy: ...done [1/1] sfepy: updating materials... [1/1] sfepy: m [1/1] sfepy: ...done in 0.00 s [1/1] sfepy: nls: iter: 0, residual: 1.008581e-01 (rel: 1.000000e+00) [1/1] sfepy: residual: 0.07 [s] [1/1] sfepy: matrix: 0.12 [s] [1/1] sfepy: solve: 0.05 [s] [1/1] sfepy: nls: iter: 1, residual: 4.825050e-17 (rel: 4.783997e-16) [1/1] sfepy: solved in 1 steps in 0.25 seconds ... geometry: 3_8, order: 3, permutation: 4: [3 2 6 7 0 1 5 4] [1/1] sfepy: updating variables... [1/1] sfepy: ...done [1/1] sfepy: setting up dof connectivities... [1/1] sfepy: ...done in 0.00 s [1/1] sfepy: matrix shape: (1918, 1918) [1/1] sfepy: assembling matrix graph... [1/1] sfepy: ...done in 0.02 s [1/1] sfepy: matrix structural nonzeros: 197938 (5.38e-02% fill) [1/1] sfepy: updating variables... [1/1] sfepy: ...done [1/1] sfepy: updating materials... [1/1] sfepy: m [1/1] sfepy: ...done in 0.00 s [1/1] sfepy: nls: iter: 0, residual: 1.008581e-01 (rel: 1.000000e+00) [1/1] sfepy: residual: 0.06 [s] [1/1] sfepy: matrix: 0.11 [s] [1/1] sfepy: solve: 0.05 [s] [1/1] sfepy: nls: iter: 1, residual: 4.788403e-17 (rel: 4.747662e-16) [1/1] sfepy: solved in 1 steps in 0.22 seconds ... geometry: 3_8, order: 3, permutation: 5: [7 6 5 4 3 2 1 0] [1/1] sfepy: updating variables... [1/1] sfepy: ...done [1/1] sfepy: setting up dof connectivities... [1/1] sfepy: ...done in 0.00 s [1/1] sfepy: matrix shape: (1918, 1918) [1/1] sfepy: assembling matrix graph... [1/1] sfepy: ...done in 0.02 s [1/1] sfepy: matrix structural nonzeros: 197938 (5.38e-02% fill) [1/1] sfepy: updating variables... [1/1] sfepy: ...done [1/1] sfepy: updating materials... [1/1] sfepy: m [1/1] sfepy: ...done in 0.00 s [1/1] sfepy: nls: iter: 0, residual: 1.008581e-01 (rel: 1.000000e+00) [1/1] sfepy: residual: 0.06 [s] [1/1] sfepy: matrix: 0.11 [s] [1/1] sfepy: solve: 0.05 [s] [1/1] sfepy: nls: iter: 1, residual: 4.619485e-17 (rel: 4.580181e-16) [1/1] sfepy: solved in 1 steps in 0.22 seconds ... geometry: 3_8, order: 3, permutation: 6: [4 5 1 0 7 6 2 3] [1/1] sfepy: updating variables... [1/1] sfepy: ...done [1/1] sfepy: setting up dof connectivities... [1/1] sfepy: ...done in 0.00 s [1/1] sfepy: matrix shape: (1918, 1918) [1/1] sfepy: assembling matrix graph... [1/1] sfepy: ...done in 0.02 s [1/1] sfepy: matrix structural nonzeros: 197938 (5.38e-02% fill) [1/1] sfepy: updating variables... [1/1] sfepy: ...done [1/1] sfepy: updating materials... [1/1] sfepy: m [1/1] sfepy: ...done in 0.00 s [1/1] sfepy: nls: iter: 0, residual: 1.008581e-01 (rel: 1.000000e+00) [1/1] sfepy: residual: 0.06 [s] [1/1] sfepy: matrix: 0.10 [s] [1/1] sfepy: solve: 0.05 [s] [1/1] sfepy: nls: iter: 1, residual: 5.154120e-17 (rel: 5.110268e-16) [1/1] sfepy: solved in 1 steps in 0.21 seconds ... geometry: 3_8, order: 3, permutation: 7: [1 5 6 2 0 4 7 3] [1/1] sfepy: updating variables... [1/1] sfepy: ...done [1/1] sfepy: setting up dof connectivities... [1/1] sfepy: ...done in 0.00 s [1/1] sfepy: matrix shape: (1918, 1918) [1/1] sfepy: assembling matrix graph... [1/1] sfepy: ...done in 0.02 s [1/1] sfepy: matrix structural nonzeros: 197938 (5.38e-02% fill) [1/1] sfepy: updating variables... [1/1] sfepy: ...done [1/1] sfepy: updating materials... [1/1] sfepy: m [1/1] sfepy: ...done in 0.00 s [1/1] sfepy: nls: iter: 0, residual: 1.008581e-01 (rel: 1.000000e+00) [1/1] sfepy: residual: 0.06 [s] [1/1] sfepy: matrix: 0.12 [s] [1/1] sfepy: solve: 0.05 [s] [1/1] sfepy: nls: iter: 1, residual: 5.041088e-17 (rel: 4.998197e-16) [1/1] sfepy: solved in 1 steps in 0.23 seconds ... geometry: 3_8, order: 3, permutation: 8: [5 4 7 6 1 0 3 2] [1/1] sfepy: updating variables... [1/1] sfepy: ...done [1/1] sfepy: setting up dof connectivities... [1/1] sfepy: ...done in 0.00 s [1/1] sfepy: matrix shape: (1918, 1918) [1/1] sfepy: assembling matrix graph... [1/1] sfepy: ...done in 0.02 s [1/1] sfepy: matrix structural nonzeros: 197938 (5.38e-02% fill) [1/1] sfepy: updating variables... [1/1] sfepy: ...done [1/1] sfepy: updating materials... [1/1] sfepy: m [1/1] sfepy: ...done in 0.00 s [1/1] sfepy: nls: iter: 0, residual: 1.008581e-01 (rel: 1.000000e+00) [1/1] sfepy: residual: 0.06 [s] [1/1] sfepy: matrix: 0.11 [s] [1/1] sfepy: solve: 0.05 [s] [1/1] sfepy: nls: iter: 1, residual: 4.637736e-17 (rel: 4.598277e-16) [1/1] sfepy: solved in 1 steps in 0.22 seconds ... geometry: 3_8, order: 3, permutation: 9: [4 0 3 7 5 1 2 6] [1/1] sfepy: updating variables... [1/1] sfepy: ...done [1/1] sfepy: setting up dof connectivities... [1/1] sfepy: ...done in 0.00 s [1/1] sfepy: matrix shape: (1918, 1918) [1/1] sfepy: assembling matrix graph... [1/1] sfepy: ...done in 0.02 s [1/1] sfepy: matrix structural nonzeros: 197938 (5.38e-02% fill) [1/1] sfepy: updating variables... [1/1] sfepy: ...done [1/1] sfepy: updating materials... [1/1] sfepy: m [1/1] sfepy: ...done in 0.00 s [1/1] sfepy: nls: iter: 0, residual: 1.008581e-01 (rel: 1.000000e+00) [1/1] sfepy: residual: 0.06 [s] [1/1] sfepy: matrix: 0.10 [s] [1/1] sfepy: solve: 0.05 [s] [1/1] sfepy: nls: iter: 1, residual: 4.789867e-17 (rel: 4.749114e-16) [1/1] sfepy: solved in 1 steps in 0.21 seconds +++ test_continuity: ok [1/2] sfepy: generating 121 vertices... [1/2] sfepy: ...done [1/2] sfepy: generating 100 cells... [1/2] sfepy: ...done ... coarse cells positions preserved: True ... coarse cells cell groups preserved: True ... coarse cells vertex groups preserved: True ... refined cells cell groups preserved: True +++ test_preserve_coarse_entities: ok all passed in 27.74 s 1 test file(s) executed in 27.74 s, 0 failure(s) of 2 test(s)
Best, JF
In that case I would ignore the errors for the moment (a ghost in the machine? :)) - I am not able to reproduce the problems anyway.
r.
On 04/18/2018 11:17 AM, Jean-François Louf wrote:
Hi Robert,
Thank you very much for your quick answer. It seems it does. Here is the output:
python3 run_tests.py --debug tests/test_refine_hanging.py
<snip>
all passed in 27.74 s 1 test file(s) executed in 27.74 s, 0 failure(s) of 2 test(s)
Best, JF
SfePy mailing list sfepy@python.org https://mail.python.org/mm3/mailman3/lists/sfepy.python.org/
Thank you very much for all the help, Robert.
So I tried to run a script from the sfepy website called its2D_1.py (but I renamed it tuto_sfepy.py). I put it in the sfepy folder, and here is the output I get:
Jean-Francoiss-MacBook-Air:sfepy jeff$ ./simple.py tuto_sfepy.py Traceback (most recent call last): File "./simple.py", line 19, in <module> from sfepy.base.base import output File "/Users/jeff/sfepy/sfepy/base/base.py", line 10, in <module> import numpy as nm ImportError: No module named numpy
IIRC you used python3 to run the tests - does "python3 ./simple.py tuto_sfepy.py" help?
r.
On 04/19/2018 11:04 AM, Jean-François Louf wrote:
Thank you very much for all the help, Robert.
So I tried to run a script from the sfepy website called its2D_1.py (but I renamed it tuto_sfepy.py). I put it in the sfepy folder, and here is the output I get:
Jean-Francoiss-MacBook-Air:sfepy jeff$ ./simple.py tuto_sfepy.py Traceback (most recent call last): File "./simple.py", line 19, in <module> from sfepy.base.base import output File "/Users/jeff/sfepy/sfepy/base/base.py", line 10, in <module> import numpy as nm ImportError: No module named numpy
SfePy mailing list sfepy@python.org https://mail.python.org/mm3/mailman3/lists/sfepy.python.org/
participants (3)
-
Jean-François Louf -
jeanfrancois.louf＠gmail.com
-
Robert Cimrman