Installation test failed
Hi,
I tried to install SfePy on my openSUSE 13.2 64bit machine. I had a hard time installing PyTables, but I could handle this by installing it using /usr/bin/pip2.7 install tables
...after installing python-pip, hdf5-devel, python-devel and python-numpy-devel.
Everything else went smooth and SfePy compiled successfully. But most tests failed and importing in python did not work.
*Importing in Python:*
Python 2.7.8 (default, Sep 30 2014, 15:34:38) [GCC] on linux2 Type "help", "copyright", "credits" or "license" for more information.
from sfepy.base.base import * Traceback (most recent call last): File "<stdin>", line 1, in <module> ImportError: No module named sfepy.base.base
*Test:*
useraccount@linux:~/Programmes/sfepy> ./run_tests.py <<< directory: tests, test files: 82 tests/test_assembling.py --- test_assemble_matrix: failed! --- test_assemble_matrix_complex: failed! --- test_assemble_vector: failed! --- test_assemble_vector_complex: failed! tests/test_base.py +++ test_resolve_deps: ok +++ test_struct_add: ok +++ test_struct_i_add: ok +++ test_verbose_output: ok tests/test_cmesh.py --- test_cmesh_counts: failed! tests/test_domain.py --- test instance creation failed tests/test_ebcs.py --- test instance creation failed tests/test_elasticity_small_strain.py --- test_get_solution: failed! --- test_linear_terms: failed! tests/test_fem.py --- test instance creation failed tests/test_functions.py --- test instance creation failed tests/test_high_level.py --- test instance creation failed tests/test_homogenization_perfusion.py --- test_solution: failed! tests/test_hyperelastic_tlul.py --- test_solution: failed! tests/test_input_acoustics.py --- test instance creation failed tests/test_input_acoustics3d.py --- test instance creation failed tests/test_input_active_fibres.py --- test instance creation failed tests/test_input_biot.py --- test instance creation failed tests/test_input_biot_npbc.py --- test instance creation failed tests/test_input_biot_npbc_lagrange.py --- test instance creation failed tests/test_input_cube.py --- test instance creation failed tests/test_input_elastic_contact_planes.py --- test instance creation failed tests/test_input_elastic_contact_sphere.py --- test instance creation failed tests/test_input_elastic_shifted_periodic.py --- test instance creation failed tests/test_input_its2D_2.py --- test instance creation failed tests/test_input_laplace_coupling_lcbcs.py --- test instance creation failed tests/test_input_laplace_time_ebcs.py --- test instance creation failed tests/test_input_linear_elastic.py --- test instance creation failed tests/test_input_linear_elastic_damping.py --- test instance creation failed tests/test_input_linear_elastic_mM.py --- test instance creation failed tests/test_input_linear_elastic_probes.py --- test instance creation failed tests/test_input_linear_elastic_tractions.py --- test instance creation failed tests/test_input_linear_elastic_up.py --- test instance creation failed tests/test_input_linear_viscoelastic.py --- test instance creation failed tests/test_input_material_nonlinearity.py --- test instance creation failed tests/test_input_navier_stokes.py --- test instance creation failed tests/test_input_navier_stokes2d.py --- test instance creation failed tests/test_input_perfusion_tl.py --- test instance creation failed tests/test_input_piezo.py --- test instance creation failed tests/test_input_poisson.py --- test instance creation failed tests/test_input_poisson_field_dependent_material.py --- test instance creation failed tests/test_input_poisson_functions.py --- test instance creation failed tests/test_input_poisson_neumann.py --- test instance creation failed tests/test_input_poisson_periodic_boundary_condition.py --- test instance creation failed tests/test_input_prestress_fibres.py --- test instance creation failed tests/test_input_sinbc.py --- test instance creation failed tests/test_input_stabilized_navier_stokes.py --- test instance creation failed tests/test_input_stokes.py --- test instance creation failed tests/test_input_stokes_slip_bc.py --- test instance creation failed tests/test_input_thermo_elasticity.py --- test instance creation failed tests/test_input_thermo_elasticity_ess.py --- test instance creation failed tests/test_input_time_poisson.py --- test instance creation failed tests/test_input_vibro_acoustic3d.py --- test instance creation failed tests/test_io.py +++ test_recursive_dict_hdf5: ok +++ test_sparse_matrix_hdf5: ok tests/test_laplace_unit_disk.py --- test instance creation failed tests/test_laplace_unit_square.py --- test instance creation failed tests/test_lcbc_2d.py --- test_linear_rigid_body_bc: failed! tests/test_lcbc_3d.py --- test_linear_rigid_body_bc: failed! tests/test_lcbcs.py --- test_laplace_shifted_periodic: failed! tests/test_linalg.py --- test_assemble1d: failed! --- test_geometry: failed! --- test_tensors: failed! --- test_unique_rows: failed! tests/test_linear_solvers.py --- test instance creation failed tests/test_linearization.py --- test_linearization: failed! tests/test_matcoefs.py +++ test_conversion_functions: ok +++ test_elastic_constants: ok +++ test_stiffness_tensors: ok tests/test_mesh_generators.py --- test_gen_block_mesh: failed! --- test_gen_cylinder_mesh: failed! --- test_gen_extended_block_mesh: failed! tests/test_mesh_interp.py --- test_interpolation: failed! --- test_interpolation_two_meshes: failed! --- test_invariance: failed! --- test_invariance_qp: failed! tests/test_mesh_smoothing.py --- test_mesh_smoothing: failed! tests/test_meshio.py --- test instance creation failed tests/test_msm_laplace.py --- test instance creation failed tests/test_msm_symbolic.py --- test instance creation failed tests/test_normals.py --- test_normals: failed! tests/test_parsing.py --- test_parse_equations: failed! --- test_parse_regions: failed! tests/test_periodic_bc_2d.py --- test instance creation failed tests/test_periodic_bc_3d.py --- test instance creation failed tests/test_permutations.py --- test_rcm: failed! tests/test_poly_spaces.py --- test instance creation failed tests/test_projections.py --- test instance creation failed tests/test_quadratures.py --- test_quadratures: failed! --- test_weight_consistency: failed! tests/test_regions.py --- test instance creation failed tests/test_semismooth_newton.py --- test_semismooth_newton: failed! tests/test_sparse.py --- test_compose_sparse: failed! tests/test_tensors.py --- test_stress_transform: failed! --- test_tensors: failed! --- test_transform_data: failed! --- test_transform_data4: failed! tests/test_term_call_modes.py --- test instance creation failed tests/test_term_consistency.py --- test instance creation failed tests/test_units.py +++ test_consistent_sets: ok +++ test_units: ok tests/test_volume.py --- test instance creation failed 82 test file(s) executed in 0.46 s, 95 failure(s) of 106 test(s)
*Test debug for test_term_consistency.py:*
useraccount@linux:~/Programmes/sfepy> python run_tests.py --debug tests/test_term_consistency.py <<< directory: tests, test files: 1 <<< tests/test_term_consistency.py sfepy: left over: ['verbose', '__builtins__', '_integrate', 'test_terms', '__doc__', '__name__', 'get_pars', 'TestCommon', 'dim', 'data_dir', 'nm', '__package__', '_filename', '__file__'] --- test instance creation failed Traceback (most recent call last): File "run_tests.py", line 206, in <module> main() File "run_tests.py", line 197, in main run_tests(stats, dirname, [filename]) File "run_tests.py", line 131, in run_tests n_fail, n_total, test_time = run_test(conf_name, options) File "run_tests.py", line 83, in run_test test = conf.funmod.Test.from_conf(conf, options) File "/home/sergeetienne/Programmes/sfepy/tests/test_term_consistency.py", line 94, in from_conf from sfepy.discrete import Problem File "/home/sergeetienne/Programmes/sfepy/sfepy/discrete/__init__.py", line 8, in <module> from variables import Variables, Variable, FieldVariable, create_adof_conns File "/home/sergeetienne/Programmes/sfepy/sfepy/discrete/variables.py", line 12, in <module> import sfepy.linalg as la File "/home/sergeetienne/Programmes/sfepy/sfepy/linalg/__init__.py", line 1, in <module> from extmods.crcm import rcm, permute_in_place ImportError: No module named crcm
Hi Serge-Étienne,
how did you compiled sfepy? We have recently fixed the documentation [1] w.r.t. the testing - you need to compile for the in-place build to run the tests in the sfepy directory.
r. [1] http://sfepy.org/doc-devel/installation.html#testing
On 11/12/2014 08:04 PM, Serge-Étienne Parent wrote:
Hi,
I tried to install SfePy on my openSUSE 13.2 64bit machine. I had a hard time installing PyTables, but I could handle this by installing it using /usr/bin/pip2.7 install tables
...after installing python-pip, hdf5-devel, python-devel and python-numpy-devel.
Everything else went smooth and SfePy compiled successfully. But most tests failed and importing in python did not work.
*Importing in Python:*
Python 2.7.8 (default, Sep 30 2014, 15:34:38) [GCC] on linux2 Type "help", "copyright", "credits" or "license" for more information.
from sfepy.base.base import * Traceback (most recent call last): File "<stdin>", line 1, in <module> ImportError: No module named sfepy.base.base
*Test:*
useraccount@linux:~/Programmes/sfepy> ./run_tests.py <<< directory: tests, test files: 82 tests/test_assembling.py --- test_assemble_matrix: failed! --- test_assemble_matrix_complex: failed! --- test_assemble_vector: failed! --- test_assemble_vector_complex: failed! tests/test_base.py +++ test_resolve_deps: ok +++ test_struct_add: ok +++ test_struct_i_add: ok +++ test_verbose_output: ok tests/test_cmesh.py --- test_cmesh_counts: failed! tests/test_domain.py --- test instance creation failed tests/test_ebcs.py --- test instance creation failed tests/test_elasticity_small_strain.py --- test_get_solution: failed! --- test_linear_terms: failed! tests/test_fem.py --- test instance creation failed tests/test_functions.py --- test instance creation failed tests/test_high_level.py --- test instance creation failed tests/test_homogenization_perfusion.py --- test_solution: failed! tests/test_hyperelastic_tlul.py --- test_solution: failed! tests/test_input_acoustics.py --- test instance creation failed tests/test_input_acoustics3d.py --- test instance creation failed tests/test_input_active_fibres.py --- test instance creation failed tests/test_input_biot.py --- test instance creation failed tests/test_input_biot_npbc.py --- test instance creation failed tests/test_input_biot_npbc_lagrange.py --- test instance creation failed tests/test_input_cube.py --- test instance creation failed tests/test_input_elastic_contact_planes.py --- test instance creation failed tests/test_input_elastic_contact_sphere.py --- test instance creation failed tests/test_input_elastic_shifted_periodic.py --- test instance creation failed tests/test_input_its2D_2.py --- test instance creation failed tests/test_input_laplace_coupling_lcbcs.py --- test instance creation failed tests/test_input_laplace_time_ebcs.py --- test instance creation failed tests/test_input_linear_elastic.py --- test instance creation failed tests/test_input_linear_elastic_damping.py --- test instance creation failed tests/test_input_linear_elastic_mM.py --- test instance creation failed tests/test_input_linear_elastic_probes.py --- test instance creation failed tests/test_input_linear_elastic_tractions.py --- test instance creation failed tests/test_input_linear_elastic_up.py --- test instance creation failed tests/test_input_linear_viscoelastic.py --- test instance creation failed tests/test_input_material_nonlinearity.py --- test instance creation failed tests/test_input_navier_stokes.py --- test instance creation failed tests/test_input_navier_stokes2d.py --- test instance creation failed tests/test_input_perfusion_tl.py --- test instance creation failed tests/test_input_piezo.py --- test instance creation failed tests/test_input_poisson.py --- test instance creation failed tests/test_input_poisson_field_dependent_material.py --- test instance creation failed tests/test_input_poisson_functions.py --- test instance creation failed tests/test_input_poisson_neumann.py --- test instance creation failed tests/test_input_poisson_periodic_boundary_condition.py --- test instance creation failed tests/test_input_prestress_fibres.py --- test instance creation failed tests/test_input_sinbc.py --- test instance creation failed tests/test_input_stabilized_navier_stokes.py --- test instance creation failed tests/test_input_stokes.py --- test instance creation failed tests/test_input_stokes_slip_bc.py --- test instance creation failed tests/test_input_thermo_elasticity.py --- test instance creation failed tests/test_input_thermo_elasticity_ess.py --- test instance creation failed tests/test_input_time_poisson.py --- test instance creation failed tests/test_input_vibro_acoustic3d.py --- test instance creation failed tests/test_io.py +++ test_recursive_dict_hdf5: ok +++ test_sparse_matrix_hdf5: ok tests/test_laplace_unit_disk.py --- test instance creation failed tests/test_laplace_unit_square.py --- test instance creation failed tests/test_lcbc_2d.py --- test_linear_rigid_body_bc: failed! tests/test_lcbc_3d.py --- test_linear_rigid_body_bc: failed! tests/test_lcbcs.py --- test_laplace_shifted_periodic: failed! tests/test_linalg.py --- test_assemble1d: failed! --- test_geometry: failed! --- test_tensors: failed! --- test_unique_rows: failed! tests/test_linear_solvers.py --- test instance creation failed tests/test_linearization.py --- test_linearization: failed! tests/test_matcoefs.py +++ test_conversion_functions: ok +++ test_elastic_constants: ok +++ test_stiffness_tensors: ok tests/test_mesh_generators.py --- test_gen_block_mesh: failed! --- test_gen_cylinder_mesh: failed! --- test_gen_extended_block_mesh: failed! tests/test_mesh_interp.py --- test_interpolation: failed! --- test_interpolation_two_meshes: failed! --- test_invariance: failed! --- test_invariance_qp: failed! tests/test_mesh_smoothing.py --- test_mesh_smoothing: failed! tests/test_meshio.py --- test instance creation failed tests/test_msm_laplace.py --- test instance creation failed tests/test_msm_symbolic.py --- test instance creation failed tests/test_normals.py --- test_normals: failed! tests/test_parsing.py --- test_parse_equations: failed! --- test_parse_regions: failed! tests/test_periodic_bc_2d.py --- test instance creation failed tests/test_periodic_bc_3d.py --- test instance creation failed tests/test_permutations.py --- test_rcm: failed! tests/test_poly_spaces.py --- test instance creation failed tests/test_projections.py --- test instance creation failed tests/test_quadratures.py --- test_quadratures: failed! --- test_weight_consistency: failed! tests/test_regions.py --- test instance creation failed tests/test_semismooth_newton.py --- test_semismooth_newton: failed! tests/test_sparse.py --- test_compose_sparse: failed! tests/test_tensors.py --- test_stress_transform: failed! --- test_tensors: failed! --- test_transform_data: failed! --- test_transform_data4: failed! tests/test_term_call_modes.py --- test instance creation failed tests/test_term_consistency.py --- test instance creation failed tests/test_units.py +++ test_consistent_sets: ok +++ test_units: ok tests/test_volume.py --- test instance creation failed 82 test file(s) executed in 0.46 s, 95 failure(s) of 106 test(s)
*Test debug for test_term_consistency.py:*
useraccount@linux:~/Programmes/sfepy> python run_tests.py --debug tests/test_term_consistency.py <<< directory: tests, test files: 1 <<< tests/test_term_consistency.py sfepy: left over: ['verbose', '__builtins__', '_integrate', 'test_terms', '__doc__', '__name__', 'get_pars', 'TestCommon', 'dim', 'data_dir', 'nm', '__package__', '_filename', '__file__'] --- test instance creation failed Traceback (most recent call last): File "run_tests.py", line 206, in <module> main() File "run_tests.py", line 197, in main run_tests(stats, dirname, [filename]) File "run_tests.py", line 131, in run_tests n_fail, n_total, test_time = run_test(conf_name, options) File "run_tests.py", line 83, in run_test test = conf.funmod.Test.from_conf(conf, options) File "/home/sergeetienne/Programmes/sfepy/tests/test_term_consistency.py", line 94, in from_conf from sfepy.discrete import Problem File "/home/sergeetienne/Programmes/sfepy/sfepy/discrete/__init__.py", line 8, in <module> from variables import Variables, Variable, FieldVariable, create_adof_conns File "/home/sergeetienne/Programmes/sfepy/sfepy/discrete/variables.py", line 12, in <module> import sfepy.linalg as la File "/home/sergeetienne/Programmes/sfepy/sfepy/linalg/__init__.py", line 1, in <module> from extmods.crcm import rcm, permute_in_place ImportError: No module named crcm
Hi Robert,
I compiled everything from the beginning. The test failed for tests/test_elasticity_small_strain.py and stops by a segmentation fault at tests/test_input_stokes_slip_bc.py, but the import return no error! Please find the debug info below.
Many**2 thanks!
Essi Parent Universite Laval, Quebec, Canada
*test_input_stokes_slip_bc.py*
test instance prepared (1 test(s)) ... solving ../examples/linear_elasticity/linear_elastic_probes.py... sfepy: reading mesh [line2, tri3, quad4, tetra4, hexa8] (/home/useraccount/Programmes/sfepy/meshes/3d/cylinder.mesh)... sfepy: ...done in 0.00 s sfepy: creating regions... sfepy: SomewhereTop sfepy: Right sfepy: Omega sfepy: Left sfepy: ...done in 0.02 s sfepy: equation "balance_of_forces": sfepy: dw_lin_elastic_iso.i.Omega(solid.lam, solid.mu, v, u) = 0 sfepy: using solvers: ts: no ts nls: newton ls: ls sfepy: updating variables... sfepy: ...done sfepy: setting up dof connectivities... sfepy: ...done in 0.00 s sfepy: matrix shape: (886, 886) sfepy: assembling matrix graph... sfepy: ...done in 0.01 s sfepy: matrix structural nonzeros: 31052 (3.96e-02% fill) sfepy: updating materials... sfepy: solid sfepy: ...done in 0.00 s sfepy: nls: iter: 0, residual: 4.778054e-03 (rel: 1.000000e+00) sfepy: rezidual: 0.00 [s] sfepy: solve: 0.01 [s] sfepy: matrix: 0.01 [s] sfepy: nls: iter: 1, residual: 7.452809e-18 (rel: 1.559800e-15) sfepy: equation "tmp": sfepy: ev_cauchy_strain.i.Omega( u ) sfepy: updating materials... sfepy: ...done in 0.00 s sfepy: equation "tmp": sfepy: ev_cauchy_stress.i.Omega( solid.D, u ) sfepy: updating materials... sfepy: solid sfepy: ...done in 0.00 s <type 'exceptions.AttributeError'> Traceback (most recent call last): File "run_tests.py", line 206, in <module> main() File "run_tests.py", line 197, in main run_tests(stats, dirname, [filename]) File "run_tests.py", line 131, in run_tests n_fail, n_total, test_time = run_test(conf_name, options) File "run_tests.py", line 99, in run_test ok, n_fail, n_total = test.run(options.debug) File "/home/useraccount/Programmes/sfepy/sfepy/base/testing.py", line 58, in run ret = test_method() File "/home/useraccount/Programmes/sfepy/tests/tests_basic.py", line 73, in test_input post_process_hook_final=self.post_process_hook_final) File "/home/useraccount/Programmes/sfepy/sfepy/applications/pde_solver_app.py",
useraccount@linux:~/Programmes/sfepy> python run_tests.py --debug tests/test_elasticity_small_strain.pypython run_tests.py --debug tests/test_input_linear_elastic_probes.py <<< directory: tests, test files: 0 <<< directory: , test files: 0 <<< directory: tests, test files: 1 <<< tests/test_input_linear_elastic_probes.py sfepy: left over: ['verbose', '__builtins__', '_filename', '__file__', '__package__', 'TestInput', 'input_name', '__name__', 'output_name', '__doc__'] sfepy: left over: ['lam', 'plt', 'Struct', '__builtins__', '__file__', 'deepcopy', 'fm', 'verbose', 'par_fun', 'mu', 'data_dir', 'nm', 'solid', '__name__', 'Probe', '__package__', 'stiffness_from_lame', '_filename', 'post_process', 'os', '__doc__'] line 55, in solve_pde return app(nls_status=nls_status) File "/home/useraccount/Programmes/sfepy/sfepy/applications/application.py", line 29, in call_basic return self.call(**kwargs) File "/home/useraccount/Programmes/sfepy/sfepy/applications/pde_solver_app.py", line 220, in call nls_status=nls_status) File "/home/useraccount/Programmes/sfepy/sfepy/solvers/ts_solvers.py", line 37, in __call__ file_per_var=None) File "/home/useraccount/Programmes/sfepy/sfepy/discrete/problem.py", line 725, in save_state out = post_process_hook(out, self, state, extend=extend) File "/home/useraccount/Programmes/sfepy/examples/linear_elasticity/linear_elastic_probes.py", line 99, in post_process probe = Probe(out, mesh) File "/home/useraccount/Programmes/sfepy/sfepy/postprocess/probes_vtk.py", line 34, in __init__ self.vtkprobe.SetSource(self.vtkdata) AttributeError: SetSource
*test_input_linear_elastic_probes.py*
useraccount@linux:~/Programmes/sfepy> python run_tests.py --debug tests/test_input_stokes_slip_bc.py <<< directory: tests, test files: 1 <<< tests/test_input_stokes_slip_bc.py sfepy: left over: ['verbose', '__builtins__', '_filename', '__file__', '__package__', 'TestInput', 'input_name', '__name__', 'output_name', '__doc__'] sfepy: left over: ['verbose', '__builtins__', 'dims', 'shape', '__file__', '__name__', 'nm', 'UserMeshIO', 'define_box_regions', 'gen_block_mesh', '__package__', 'get_u_d', '_filename', '__doc__', 'mesh_hook']
test instance prepared (1 test(s)) ... solving ../examples/navier_stokes/stokes_slip_bc.py... sfepy: reading mesh [user] (function:mesh_hook)... sfepy: ...done in 0.00 s sfepy: creating regions... sfepy: Right sfepy: Bottom sfepy: Far sfepy: Corners sfepy: Top sfepy: Omega sfepy: Near sfepy: Left sfepy: Gamma1_f sfepy: Edges_v sfepy: Gamma2_f sfepy: Gamma_f sfepy: Gamma_v sfepy: Inlet_f sfepy: ...done in 0.06 s sfepy: equation "balance": sfepy: dw_div_grad.5.Omega(m.nu, v, u) - dw_stokes.5.Omega(v, p) + dw_surface_dot.5.Gamma1_f(m.beta, v, u) + dw_surface_dot.5.Gamma2_f(m.beta, v, u) = + dw_surface_dot.5.Gamma1_f(m.beta, v, u_d) sfepy: equation "incompressibility": sfepy: dw_laplace.5.Omega(m.mu, q, p) + dw_stokes.5.Omega(u, q) = 0 sfepy: using solvers: ts: no ts nls: newton ls: ls_d sfepy: updating variables... sfepy: data of u_d set by get_u_d() sfepy: ...done sfepy: setting up dof connectivities... sfepy: ...done in 0.01 s sfepy: lcbc: walls sfepy: lcbc: edges Erreur de segmentation
Le mercredi 12 novembre 2014 15:14:41 UTC-5, Robert Cimrman a écrit :
Hi Serge-Étienne,
how did you compiled sfepy? We have recently fixed the documentation [1] w.r.t. the testing - you need to compile for the in-place build to run the tests in the sfepy directory.
r. [1] http://sfepy.org/doc-devel/installation.html#testing
Hi,
I tried to install SfePy on my openSUSE 13.2 64bit machine. I had a hard time installing PyTables, but I could handle this by installing it using /usr/bin/pip2.7 install tables
...after installing python-pip, hdf5-devel, python-devel and python-numpy-devel.
Everything else went smooth and SfePy compiled successfully. But most tests failed and importing in python did not work.
*Importing in Python:*
Python 2.7.8 (default, Sep 30 2014, 15:34:38) [GCC] on linux2 Type "help", "copyright", "credits" or "license" for more information.
from sfepy.base.base import * Traceback (most recent call last): File "<stdin>", line 1, in <module> ImportError: No module named sfepy.base.base
*Test:*
useraccount@linux:~/Programmes/sfepy> ./run_tests.py <<< directory: tests, test files: 82 tests/test_assembling.py --- test_assemble_matrix: failed! --- test_assemble_matrix_complex: failed! --- test_assemble_vector: failed! --- test_assemble_vector_complex: failed! tests/test_base.py +++ test_resolve_deps: ok +++ test_struct_add: ok +++ test_struct_i_add: ok +++ test_verbose_output: ok tests/test_cmesh.py --- test_cmesh_counts: failed! tests/test_domain.py --- test instance creation failed tests/test_ebcs.py --- test instance creation failed tests/test_elasticity_small_strain.py --- test_get_solution: failed! --- test_linear_terms: failed! tests/test_fem.py --- test instance creation failed tests/test_functions.py --- test instance creation failed tests/test_high_level.py --- test instance creation failed tests/test_homogenization_perfusion.py --- test_solution: failed! tests/test_hyperelastic_tlul.py --- test_solution: failed! tests/test_input_acoustics.py --- test instance creation failed tests/test_input_acoustics3d.py --- test instance creation failed tests/test_input_active_fibres.py --- test instance creation failed tests/test_input_biot.py --- test instance creation failed tests/test_input_biot_npbc.py --- test instance creation failed tests/test_input_biot_npbc_lagrange.py --- test instance creation failed tests/test_input_cube.py --- test instance creation failed tests/test_input_elastic_contact_planes.py --- test instance creation failed tests/test_input_elastic_contact_sphere.py --- test instance creation failed tests/test_input_elastic_shifted_periodic.py --- test instance creation failed tests/test_input_its2D_2.py --- test instance creation failed tests/test_input_laplace_coupling_lcbcs.py --- test instance creation failed tests/test_input_laplace_time_ebcs.py --- test instance creation failed tests/test_input_linear_elastic.py --- test instance creation failed tests/test_input_linear_elastic_damping.py --- test instance creation failed tests/test_input_linear_elastic_mM.py --- test instance creation failed tests/test_input_linear_elastic_probes.py --- test instance creation failed tests/test_input_linear_elastic_tractions.py --- test instance creation failed tests/test_input_linear_elastic_up.py --- test instance creation failed tests/test_input_linear_viscoelastic.py --- test instance creation failed tests/test_input_material_nonlinearity.py --- test instance creation failed tests/test_input_navier_stokes.py --- test instance creation failed tests/test_input_navier_stokes2d.py --- test instance creation failed tests/test_input_perfusion_tl.py --- test instance creation failed tests/test_input_piezo.py --- test instance creation failed tests/test_input_poisson.py --- test instance creation failed tests/test_input_poisson_field_dependent_material.py --- test instance creation failed tests/test_input_poisson_functions.py --- test instance creation failed tests/test_input_poisson_neumann.py --- test instance creation failed tests/test_input_poisson_periodic_boundary_condition.py --- test instance creation failed tests/test_input_prestress_fibres.py --- test instance creation failed tests/test_input_sinbc.py --- test instance creation failed tests/test_input_stabilized_navier_stokes.py --- test instance creation failed tests/test_input_stokes.py --- test instance creation failed tests/test_input_stokes_slip_bc.py --- test instance creation failed tests/test_input_thermo_elasticity.py --- test instance creation failed tests/test_input_thermo_elasticity_ess.py --- test instance creation failed tests/test_input_time_poisson.py --- test instance creation failed tests/test_input_vibro_acoustic3d.py --- test instance creation failed tests/test_io.py +++ test_recursive_dict_hdf5: ok +++ test_sparse_matrix_hdf5: ok tests/test_laplace_unit_disk.py --- test instance creation failed tests/test_laplace_unit_square.py --- test instance creation failed tests/test_lcbc_2d.py --- test_linear_rigid_body_bc: failed! tests/test_lcbc_3d.py --- test_linear_rigid_body_bc: failed! tests/test_lcbcs.py --- test_laplace_shifted_periodic: failed! tests/test_linalg.py --- test_assemble1d: failed! --- test_geometry: failed! --- test_tensors: failed! --- test_unique_rows: failed! tests/test_linear_solvers.py --- test instance creation failed tests/test_linearization.py --- test_linearization: failed! tests/test_matcoefs.py +++ test_conversion_functions: ok +++ test_elastic_constants: ok +++ test_stiffness_tensors: ok tests/test_mesh_generators.py --- test_gen_block_mesh: failed! --- test_gen_cylinder_mesh: failed! --- test_gen_extended_block_mesh: failed! tests/test_mesh_interp.py --- test_interpolation: failed! --- test_interpolation_two_meshes: failed! --- test_invariance: failed! --- test_invariance_qp: failed! tests/test_mesh_smoothing.py --- test_mesh_smoothing: failed! tests/test_meshio.py --- test instance creation failed tests/test_msm_laplace.py --- test instance creation failed tests/test_msm_symbolic.py --- test instance creation failed tests/test_normals.py --- test_normals: failed! tests/test_parsing.py --- test_parse_equations: failed! --- test_parse_regions: failed! tests/test_periodic_bc_2d.py --- test instance creation failed tests/test_periodic_bc_3d.py --- test instance creation failed tests/test_permutations.py --- test_rcm: failed! tests/test_poly_spaces.py --- test instance creation failed tests/test_projections.py --- test instance creation failed tests/test_quadratures.py --- test_quadratures: failed! --- test_weight_consistency: failed! tests/test_regions.py --- test instance creation failed tests/test_semismooth_newton.py --- test_semismooth_newton: failed! tests/test_sparse.py --- test_compose_sparse: failed! tests/test_tensors.py --- test_stress_transform: failed! --- test_tensors: failed! --- test_transform_data: failed! --- test_transform_data4: failed! tests/test_term_call_modes.py --- test instance creation failed tests/test_term_consistency.py --- test instance creation failed tests/test_units.py +++ test_consistent_sets: ok +++ test_units: ok tests/test_volume.py --- test instance creation failed 82 test file(s) executed in 0.46 s, 95 failure(s) of 106 test(s)
*Test debug for test_term_consistency.py:*
useraccount@linux:~/Programmes/sfepy> python run_tests.py --debug tests/test_term_consistency.py <<< directory: tests, test files: 1 <<< tests/test_term_consistency.py sfepy: left over: ['verbose', '__builtins__', '_integrate', 'test_terms', '__doc__', '__name__', 'get_pars', 'TestCommon', 'dim', 'data_dir', 'nm', '__package__', '_filename', '__file__'] --- test instance creation failed Traceback (most recent call last): File "run_tests.py", line 206, in <module> main() File "run_tests.py", line 197, in main run_tests(stats, dirname, [filename]) File "run_tests.py", line 131, in run_tests n_fail, n_total, test_time = run_test(conf_name, options) File "run_tests.py", line 83, in run_test test = conf.funmod.Test.from_conf(conf, options) File "/home/sergeetienne/Programmes/sfepy/tests/test_term_consistency.py",
94, in from_conf from sfepy.discrete import Problem File "/home/sergeetienne/Programmes/sfepy/sfepy/discrete/__init__.py", line 8, in <module> from variables import Variables, Variable, FieldVariable, create_adof_conns File "/home/sergeetienne/Programmes/sfepy/sfepy/discrete/variables.py", line 12, in <module> import sfepy.linalg as la File "/home/sergeetienne/Programmes/sfepy/sfepy/linalg/__init__.py",
On 11/12/2014 08:04 PM, Serge-Étienne Parent wrote: line line
1, in <module> from extmods.crcm import rcm, permute_in_place ImportError: No module named crcm
On 11/12/2014 10:25 PM, Serge-Étienne Parent wrote:
Hi Robert,
I compiled everything from the beginning. The test failed for tests/test_elasticity_small_strain.py and stops by a segmentation fault at tests/test_input_stokes_slip_bc.py, but the import return no error! Please find the debug info below.
So the other tests pass, right? The first example that fails uses a new feature (vtk probes) that is based on pyvtk. There might be some incompatibility or version problem - could you report the versions you use?
The other fails because of a problem in some versions of scipy.sparse [1].
r.
[1] https://code.google.com/p/pythonxy/issues/detail?id=747
Many**2 thanks!
Essi Parent Universite Laval, Quebec, Canada
*test_input_stokes_slip_bc.py*
test instance prepared (1 test(s)) ... solving ../examples/linear_elasticity/linear_elastic_probes.py... sfepy: reading mesh [line2, tri3, quad4, tetra4, hexa8] (/home/useraccount/Programmes/sfepy/meshes/3d/cylinder.mesh)... sfepy: ...done in 0.00 s sfepy: creating regions... sfepy: SomewhereTop sfepy: Right sfepy: Omega sfepy: Left sfepy: ...done in 0.02 s sfepy: equation "balance_of_forces": sfepy: dw_lin_elastic_iso.i.Omega(solid.lam, solid.mu, v, u) = 0 sfepy: using solvers: ts: no ts nls: newton ls: ls sfepy: updating variables... sfepy: ...done sfepy: setting up dof connectivities... sfepy: ...done in 0.00 s sfepy: matrix shape: (886, 886) sfepy: assembling matrix graph... sfepy: ...done in 0.01 s sfepy: matrix structural nonzeros: 31052 (3.96e-02% fill) sfepy: updating materials... sfepy: solid sfepy: ...done in 0.00 s sfepy: nls: iter: 0, residual: 4.778054e-03 (rel: 1.000000e+00) sfepy: rezidual: 0.00 [s] sfepy: solve: 0.01 [s] sfepy: matrix: 0.01 [s] sfepy: nls: iter: 1, residual: 7.452809e-18 (rel: 1.559800e-15) sfepy: equation "tmp": sfepy: ev_cauchy_strain.i.Omega( u ) sfepy: updating materials... sfepy: ...done in 0.00 s sfepy: equation "tmp": sfepy: ev_cauchy_stress.i.Omega( solid.D, u ) sfepy: updating materials... sfepy: solid sfepy: ...done in 0.00 s <type 'exceptions.AttributeError'> Traceback (most recent call last): File "run_tests.py", line 206, in <module> main() File "run_tests.py", line 197, in main run_tests(stats, dirname, [filename]) File "run_tests.py", line 131, in run_tests n_fail, n_total, test_time = run_test(conf_name, options) File "run_tests.py", line 99, in run_test ok, n_fail, n_total = test.run(options.debug) File "/home/useraccount/Programmes/sfepy/sfepy/base/testing.py", line 58, in run ret = test_method() File "/home/useraccount/Programmes/sfepy/tests/tests_basic.py", line 73, in test_input post_process_hook_final=self.post_process_hook_final) File "/home/useraccount/Programmes/sfepy/sfepy/applications/pde_solver_app.py",
useraccount@linux:~/Programmes/sfepy> python run_tests.py --debug tests/test_elasticity_small_strain.pypython run_tests.py --debug tests/test_input_linear_elastic_probes.py <<< directory: tests, test files: 0 <<< directory: , test files: 0 <<< directory: tests, test files: 1 <<< tests/test_input_linear_elastic_probes.py sfepy: left over: ['verbose', '__builtins__', '_filename', '__file__', '__package__', 'TestInput', 'input_name', '__name__', 'output_name', '__doc__'] sfepy: left over: ['lam', 'plt', 'Struct', '__builtins__', '__file__', 'deepcopy', 'fm', 'verbose', 'par_fun', 'mu', 'data_dir', 'nm', 'solid', '__name__', 'Probe', '__package__', 'stiffness_from_lame', '_filename', 'post_process', 'os', '__doc__'] line 55, in solve_pde return app(nls_status=nls_status) File "/home/useraccount/Programmes/sfepy/sfepy/applications/application.py", line 29, in call_basic return self.call(**kwargs) File "/home/useraccount/Programmes/sfepy/sfepy/applications/pde_solver_app.py", line 220, in call nls_status=nls_status) File "/home/useraccount/Programmes/sfepy/sfepy/solvers/ts_solvers.py", line 37, in __call__ file_per_var=None) File "/home/useraccount/Programmes/sfepy/sfepy/discrete/problem.py", line 725, in save_state out = post_process_hook(out, self, state, extend=extend) File "/home/useraccount/Programmes/sfepy/examples/linear_elasticity/linear_elastic_probes.py", line 99, in post_process probe = Probe(out, mesh) File "/home/useraccount/Programmes/sfepy/sfepy/postprocess/probes_vtk.py", line 34, in __init__ self.vtkprobe.SetSource(self.vtkdata) AttributeError: SetSource
*test_input_linear_elastic_probes.py*
useraccount@linux:~/Programmes/sfepy> python run_tests.py --debug tests/test_input_stokes_slip_bc.py <<< directory: tests, test files: 1 <<< tests/test_input_stokes_slip_bc.py sfepy: left over: ['verbose', '__builtins__', '_filename', '__file__', '__package__', 'TestInput', 'input_name', '__name__', 'output_name', '__doc__'] sfepy: left over: ['verbose', '__builtins__', 'dims', 'shape', '__file__', '__name__', 'nm', 'UserMeshIO', 'define_box_regions', 'gen_block_mesh', '__package__', 'get_u_d', '_filename', '__doc__', 'mesh_hook']
test instance prepared (1 test(s)) ... solving ../examples/navier_stokes/stokes_slip_bc.py... sfepy: reading mesh [user] (function:mesh_hook)... sfepy: ...done in 0.00 s sfepy: creating regions... sfepy: Right sfepy: Bottom sfepy: Far sfepy: Corners sfepy: Top sfepy: Omega sfepy: Near sfepy: Left sfepy: Gamma1_f sfepy: Edges_v sfepy: Gamma2_f sfepy: Gamma_f sfepy: Gamma_v sfepy: Inlet_f sfepy: ...done in 0.06 s sfepy: equation "balance": sfepy: dw_div_grad.5.Omega(m.nu, v, u) - dw_stokes.5.Omega(v, p) + dw_surface_dot.5.Gamma1_f(m.beta, v, u) + dw_surface_dot.5.Gamma2_f(m.beta, v, u) = + dw_surface_dot.5.Gamma1_f(m.beta, v, u_d) sfepy: equation "incompressibility": sfepy: dw_laplace.5.Omega(m.mu, q, p) + dw_stokes.5.Omega(u, q) = 0 sfepy: using solvers: ts: no ts nls: newton ls: ls_d sfepy: updating variables... sfepy: data of u_d set by get_u_d() sfepy: ...done sfepy: setting up dof connectivities... sfepy: ...done in 0.01 s sfepy: lcbc: walls sfepy: lcbc: edges Erreur de segmentation
Le mercredi 12 novembre 2014 15:14:41 UTC-5, Robert Cimrman a écrit :
Hi Serge-Étienne,
how did you compiled sfepy? We have recently fixed the documentation [1] w.r.t. the testing - you need to compile for the in-place build to run the tests in the sfepy directory.
r. [1] http://sfepy.org/doc-devel/installation.html#testing
On 11/12/2014 08:04 PM, Serge-Étienne Parent wrote:
Hi,
I tried to install SfePy on my openSUSE 13.2 64bit machine. I had a hard time installing PyTables, but I could handle this by installing it using /usr/bin/pip2.7 install tables
...after installing python-pip, hdf5-devel, python-devel and python-numpy-devel.
Everything else went smooth and SfePy compiled successfully. But most tests failed and importing in python did not work.
I installed the very last versions of python-vtk and scipy available for my system. python-vtk version 6.1.0-4.3 scipy version 0.14.0-47.6
test_input_linear_elastic_probes.py is now all good. All tests passed until the seg fault appears with test_input_stokes_slip_bc.py, but this is not a big issue. Now that Sfepy is installed, the fun begins.
Thanks a lot!
Essi
Le jeudi 13 novembre 2014 04:44:32 UTC-5, Robert Cimrman a écrit :
On 11/12/2014 10:25 PM, Serge-Étienne Parent wrote:
Hi Robert,
I compiled everything from the beginning. The test failed for tests/test_elasticity_small_strain.py and stops by a segmentation fault at tests/test_input_stokes_slip_bc.py, but the import return no error! Please find the debug info below.
So the other tests pass, right? The first example that fails uses a new feature (vtk probes) that is based on pyvtk. There might be some incompatibility or version problem - could you report the versions you use?
The other fails because of a problem in some versions of scipy.sparse [1].
r.
[1] https://code.google.com/p/pythonxy/issues/detail?id=747
Many**2 thanks!
Essi Parent Universite Laval, Quebec, Canada
*test_input_stokes_slip_bc.py*
useraccount@linux:~/Programmes/sfepy> python run_tests.py --debug tests/test_elasticity_small_strain.pypython run_tests.py --debug tests/test_input_linear_elastic_probes.py <<< directory: tests, test files: 0 <<< directory: , test files: 0 <<< directory: tests, test files: 1 <<< tests/test_input_linear_elastic_probes.py sfepy: left over: ['verbose', '__builtins__', '_filename', '__file__', '__package__', 'TestInput', 'input_name', '__name__', 'output_name', '__doc__'] sfepy: left over: ['lam', 'plt', 'Struct', '__builtins__', '__file__', 'deepcopy', 'fm', 'verbose', 'par_fun', 'mu', 'data_dir', 'nm', 'solid', '__name__', 'Probe', '__package__', 'stiffness_from_lame', '_filename', 'post_process', 'os', '__doc__']
test instance prepared (1 test(s)) ... solving ../examples/linear_elasticity/linear_elastic_probes.py... sfepy: reading mesh [line2, tri3, quad4, tetra4, hexa8] (/home/useraccount/Programmes/sfepy/meshes/3d/cylinder.mesh)... sfepy: ...done in 0.00 s sfepy: creating regions... sfepy: SomewhereTop sfepy: Right sfepy: Omega sfepy: Left sfepy: ...done in 0.02 s sfepy: equation "balance_of_forces": sfepy: dw_lin_elastic_iso.i.Omega(solid.lam, solid.mu, v, u) = 0 sfepy: using solvers: ts: no ts nls: newton ls: ls sfepy: updating variables... sfepy: ...done sfepy: setting up dof connectivities... sfepy: ...done in 0.00 s sfepy: matrix shape: (886, 886) sfepy: assembling matrix graph... sfepy: ...done in 0.01 s sfepy: matrix structural nonzeros: 31052 (3.96e-02% fill) sfepy: updating materials... sfepy: solid sfepy: ...done in 0.00 s sfepy: nls: iter: 0, residual: 4.778054e-03 (rel: 1.000000e+00) sfepy: rezidual: 0.00 [s] sfepy: solve: 0.01 [s] sfepy: matrix: 0.01 [s] sfepy: nls: iter: 1, residual: 7.452809e-18 (rel: 1.559800e-15) sfepy: equation "tmp": sfepy: ev_cauchy_strain.i.Omega( u ) sfepy: updating materials... sfepy: ...done in 0.00 s sfepy: equation "tmp": sfepy: ev_cauchy_stress.i.Omega( solid.D, u ) sfepy: updating materials... sfepy: solid sfepy: ...done in 0.00 s <type 'exceptions.AttributeError'> Traceback (most recent call last): File "run_tests.py", line 206, in <module> main() File "run_tests.py", line 197, in main run_tests(stats, dirname, [filename]) File "run_tests.py", line 131, in run_tests n_fail, n_total, test_time = run_test(conf_name, options) File "run_tests.py", line 99, in run_test ok, n_fail, n_total = test.run(options.debug) File "/home/useraccount/Programmes/sfepy/sfepy/base/testing.py", line 58, in run ret = test_method() File "/home/useraccount/Programmes/sfepy/tests/tests_basic.py", line 73, in test_input post_process_hook_final=self.post_process_hook_final) File
"/home/useraccount/Programmes/sfepy/sfepy/applications/pde_solver_app.py",
line 55, in solve_pde return app(nls_status=nls_status) File "/home/useraccount/Programmes/sfepy/sfepy/applications/application.py", line 29, in call_basic return self.call(**kwargs) File
line 220, in call nls_status=nls_status) File "/home/useraccount/Programmes/sfepy/sfepy/solvers/ts_solvers.py", line 37, in __call__ file_per_var=None) File "/home/useraccount/Programmes/sfepy/sfepy/discrete/problem.py",
"/home/useraccount/Programmes/sfepy/sfepy/applications/pde_solver_app.py", line
725, in save_state out = post_process_hook(out, self, state, extend=extend) File
"/home/useraccount/Programmes/sfepy/examples/linear_elasticity/linear_elastic_probes.py",
line 99, in post_process probe = Probe(out, mesh) File "/home/useraccount/Programmes/sfepy/sfepy/postprocess/probes_vtk.py", line 34, in __init__ self.vtkprobe.SetSource(self.vtkdata) AttributeError: SetSource
*test_input_linear_elastic_probes.py*
useraccount@linux:~/Programmes/sfepy> python run_tests.py --debug tests/test_input_stokes_slip_bc.py <<< directory: tests, test files: 1 <<< tests/test_input_stokes_slip_bc.py sfepy: left over: ['verbose', '__builtins__', '_filename', '__file__', '__package__', 'TestInput', 'input_name', '__name__', 'output_name', '__doc__'] sfepy: left over: ['verbose', '__builtins__', 'dims', 'shape', '__file__', '__name__', 'nm', 'UserMeshIO', 'define_box_regions', 'gen_block_mesh', '__package__', 'get_u_d', '_filename', '__doc__', 'mesh_hook']
test instance prepared (1 test(s)) ... solving ../examples/navier_stokes/stokes_slip_bc.py... sfepy: reading mesh [user] (function:mesh_hook)... sfepy: ...done in 0.00 s sfepy: creating regions... sfepy: Right sfepy: Bottom sfepy: Far sfepy: Corners sfepy: Top sfepy: Omega sfepy: Near sfepy: Left sfepy: Gamma1_f sfepy: Edges_v sfepy: Gamma2_f sfepy: Gamma_f sfepy: Gamma_v sfepy: Inlet_f sfepy: ...done in 0.06 s sfepy: equation "balance": sfepy: dw_div_grad.5.Omega(m.nu, v, u) - dw_stokes.5.Omega(v, p) + dw_surface_dot.5.Gamma1_f(m.beta, v, u) + dw_surface_dot.5.Gamma2_f(m.beta, v, u) = + dw_surface_dot.5.Gamma1_f(m.beta, v, u_d) sfepy: equation "incompressibility": sfepy: dw_laplace.5.Omega(m.mu, q, p) + dw_stokes.5.Omega(u, q) = 0 sfepy: using solvers: ts: no ts nls: newton ls: ls_d sfepy: updating variables... sfepy: data of u_d set by get_u_d() sfepy: ...done sfepy: setting up dof connectivities... sfepy: ...done in 0.01 s sfepy: lcbc: walls sfepy: lcbc: edges Erreur de segmentation
Le mercredi 12 novembre 2014 15:14:41 UTC-5, Robert Cimrman a écrit :
Hi Serge-Étienne,
how did you compiled sfepy? We have recently fixed the documentation
[1]
w.r.t. the testing - you need to compile for the in-place build to run the tests in the sfepy directory.
r. [1] http://sfepy.org/doc-devel/installation.html#testing
On 11/12/2014 08:04 PM, Serge-Étienne Parent wrote:
Hi,
I tried to install SfePy on my openSUSE 13.2 64bit machine. I had a hard time installing PyTables, but I could handle this by installing it using /usr/bin/pip2.7 install tables
...after installing python-pip, hdf5-devel, python-devel and python-numpy-devel.
Everything else went smooth and SfePy compiled successfully. But most tests failed and importing in python did not work.
Hi Essi,
there are some changes in VTK6. I have fixed the version issue related to SetInput() method, see [1].
Regards Vladimir
[1] https://github.com/sfepy/sfepy/pull/277
On 11/13/2014 03:12 PM, Serge-Étienne Parent wrote:
I installed the very last versions of python-vtk and scipy available for my system. python-vtk version 6.1.0-4.3 scipy version 0.14.0-47.6
test_input_linear_elastic_probes.py is now all good. All tests passed until the seg fault appears with test_input_stokes_slip_bc.py, but this is not a big issue. Now that Sfepy is installed, the fun begins.
Thanks a lot!
Essi
Le jeudi 13 novembre 2014 04:44:32 UTC-5, Robert Cimrman a écrit :
On 11/12/2014 10:25 PM, Serge-Étienne Parent wrote: > Hi Robert, > > I compiled everything from the beginning. The test failed for > tests/test_elasticity_small_strain.py and stops by a segmentation fault at > tests/test_input_stokes_slip_bc.py, but the import return no error! Please > find the debug info below. So the other tests pass, right? The first example that fails uses a new feature (vtk probes) that is based on pyvtk. There might be some incompatibility or version problem - could you report the versions you use? The other fails because of a problem in some versions of scipy.sparse [1]. r. [1] https://code.google.com/p/pythonxy/issues/detail?id=747 <https://code.google.com/p/pythonxy/issues/detail?id=747> > Many**2 thanks! > > Essi Parent > Universite Laval, > Quebec, Canada > > > *test_input_stokes_slip_bc.py* > > useraccount@linux:~/Programmes/sfepy> python run_tests.py --debug > tests/test_elasticity_small_strain.pypython run_tests.py --debug > tests/test_input_linear_elastic_probes.py > <<< directory: tests, test files: 0 > <<< directory: , test files: 0 > <<< directory: tests, test files: 1 > <<< tests/test_input_linear_elastic_probes.py > sfepy: left over: ['verbose', '__builtins__', '_filename', '__file__', > '__package__', 'TestInput', 'input_name', '__name__', 'output_name', > '__doc__'] > sfepy: left over: ['lam', 'plt', 'Struct', '__builtins__', '__file__', > 'deepcopy', 'fm', 'verbose', 'par_fun', 'mu', 'data_dir', 'nm', 'solid', > '__name__', 'Probe', '__package__', 'stiffness_from_lame', '_filename', > 'post_process', 'os', '__doc__'] >>>> test instance prepared (1 test(s)) > ... solving ../examples/linear_elasticity/linear_elastic_probes.py... > sfepy: reading mesh [line2, tri3, quad4, tetra4, hexa8] > (/home/useraccount/Programmes/sfepy/meshes/3d/cylinder.mesh)... > sfepy: ...done in 0.00 s > sfepy: creating regions... > sfepy: SomewhereTop > sfepy: Right > sfepy: Omega > sfepy: Left > sfepy: ...done in 0.02 s > sfepy: equation "balance_of_forces": > sfepy: dw_lin_elastic_iso.i.Omega(solid.lam, solid.mu <http://solid.mu>, v, u) = 0 > sfepy: using solvers: > ts: no ts > nls: newton > ls: ls > sfepy: updating variables... > sfepy: ...done > sfepy: setting up dof connectivities... > sfepy: ...done in 0.00 s > sfepy: matrix shape: (886, 886) > sfepy: assembling matrix graph... > sfepy: ...done in 0.01 s > sfepy: matrix structural nonzeros: 31052 (3.96e-02% fill) > sfepy: updating materials... > sfepy: solid > sfepy: ...done in 0.00 s > sfepy: nls: iter: 0, residual: 4.778054e-03 (rel: 1.000000e+00) > sfepy: rezidual: 0.00 [s] > sfepy: solve: 0.01 [s] > sfepy: matrix: 0.01 [s] > sfepy: nls: iter: 1, residual: 7.452809e-18 (rel: 1.559800e-15) > sfepy: equation "tmp": > sfepy: ev_cauchy_strain.i.Omega( u ) > sfepy: updating materials... > sfepy: ...done in 0.00 s > sfepy: equation "tmp": > sfepy: ev_cauchy_stress.i.Omega( solid.D, u ) > sfepy: updating materials... > sfepy: solid > sfepy: ...done in 0.00 s >>>> <type 'exceptions.AttributeError'> > Traceback (most recent call last): > File "run_tests.py", line 206, in <module> > main() > File "run_tests.py", line 197, in main > run_tests(stats, dirname, [filename]) > File "run_tests.py", line 131, in run_tests > n_fail, n_total, test_time = run_test(conf_name, options) > File "run_tests.py", line 99, in run_test > ok, n_fail, n_total = test.run(options.debug) > File "/home/useraccount/Programmes/sfepy/sfepy/base/testing.py", line 58, > in run > ret = test_method() > File "/home/useraccount/Programmes/sfepy/tests/tests_basic.py", line 73, > in test_input > post_process_hook_final=self.post_process_hook_final) > File > "/home/useraccount/Programmes/sfepy/sfepy/applications/pde_solver_app.py", > line 55, in solve_pde > return app(nls_status=nls_status) > File > "/home/useraccount/Programmes/sfepy/sfepy/applications/application.py", > line 29, in call_basic > return self.call(**kwargs) > File > "/home/useraccount/Programmes/sfepy/sfepy/applications/pde_solver_app.py", > line 220, in call > nls_status=nls_status) > File "/home/useraccount/Programmes/sfepy/sfepy/solvers/ts_solvers.py", > line 37, in __call__ > file_per_var=None) > File "/home/useraccount/Programmes/sfepy/sfepy/discrete/problem.py", line > 725, in save_state > out = post_process_hook(out, self, state, extend=extend) > File > "/home/useraccount/Programmes/sfepy/examples/linear_elasticity/linear_elastic_probes.py", > line 99, in post_process > probe = Probe(out, mesh) > File > "/home/useraccount/Programmes/sfepy/sfepy/postprocess/probes_vtk.py", line > 34, in __init__ > self.vtkprobe.SetSource(self.vtkdata) > AttributeError: SetSource > > > *test_input_linear_elastic_probes.py* > > useraccount@linux:~/Programmes/sfepy> python run_tests.py --debug > tests/test_input_stokes_slip_bc.py > <<< directory: tests, test files: 1 > <<< tests/test_input_stokes_slip_bc.py > sfepy: left over: ['verbose', '__builtins__', '_filename', '__file__', > '__package__', 'TestInput', 'input_name', '__name__', 'output_name', > '__doc__'] > sfepy: left over: ['verbose', '__builtins__', 'dims', 'shape', '__file__', > '__name__', 'nm', 'UserMeshIO', 'define_box_regions', 'gen_block_mesh', > '__package__', 'get_u_d', '_filename', '__doc__', 'mesh_hook'] >>>> test instance prepared (1 test(s)) > ... solving ../examples/navier_stokes/stokes_slip_bc.py... > sfepy: reading mesh [user] (function:mesh_hook)... > sfepy: ...done in 0.00 s > sfepy: creating regions... > sfepy: Right > sfepy: Bottom > sfepy: Far > sfepy: Corners > sfepy: Top > sfepy: Omega > sfepy: Near > sfepy: Left > sfepy: Gamma1_f > sfepy: Edges_v > sfepy: Gamma2_f > sfepy: Gamma_f > sfepy: Gamma_v > sfepy: Inlet_f > sfepy: ...done in 0.06 s > sfepy: equation "balance": > sfepy: dw_div_grad.5.Omega(m.nu <http://m.nu>, v, u) > - dw_stokes.5.Omega(v, p) > + dw_surface_dot.5.Gamma1_f(m.beta, v, u) > + dw_surface_dot.5.Gamma2_f(m.beta, v, u) > = > + dw_surface_dot.5.Gamma1_f(m.beta, v, u_d) > sfepy: equation "incompressibility": > sfepy: dw_laplace.5.Omega(m.mu <http://m.mu>, q, p) > + dw_stokes.5.Omega(u, q) = 0 > sfepy: using solvers: > ts: no ts > nls: newton > ls: ls_d > sfepy: updating variables... > sfepy: data of u_d set by get_u_d() > sfepy: ...done > sfepy: setting up dof connectivities... > sfepy: ...done in 0.01 s > sfepy: lcbc: walls > sfepy: lcbc: edges > Erreur de segmentation > > > > > > Le mercredi 12 novembre 2014 15:14:41 UTC-5, Robert Cimrman a écrit : >> >> Hi Serge-Étienne, >> >> how did you compiled sfepy? We have recently fixed the documentation [1] >> w.r.t. >> the testing - you need to compile for the in-place build to run the tests >> in >> the sfepy directory. >> >> r. >> [1] http://sfepy.org/doc-devel/installation.html#testing <http://sfepy.org/doc-devel/installation.html#testing> >> >> On 11/12/2014 08:04 PM, Serge-Étienne Parent wrote: >>> Hi, >>> >>> I tried to install SfePy on my openSUSE 13.2 64bit machine. I had a hard >>> time installing PyTables, but I could handle this by installing it using >>> /usr/bin/pip2.7 install tables >>> >>> ...after installing python-pip, hdf5-devel, python-devel and >>> python-numpy-devel. >>> >>> Everything else went smooth and SfePy compiled successfully. But most >> tests >>> failed and importing in python did not work. >>>-- You received this message because you are subscribed to the Google Groups "sfepy-devel" group. 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On 11/13/2014 03:12 PM, Serge-Étienne Parent wrote:
I installed the very last versions of python-vtk and scipy available for my system. python-vtk version 6.1.0-4.3 scipy version 0.14.0-47.6
test_input_linear_elastic_probes.py is now all good. All tests passed until the seg fault appears with test_input_stokes_slip_bc.py, but this is not a big issue. Now that Sfepy is installed, the fun begins.
Thanks a lot!
Hth, have a good fun :)
r.
participants (3)
-
Robert Cimrman -
Serge-Étienne Parent -
Vladimír Lukeš