Nov. 13, 2014
2:25 p.m.
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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