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
> "/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.
>>>