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
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 "/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.
>
> *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
>