Sfepy Giving up | Ccore error

[gustxsr]

Hello!
I am working with a partially modified version of the Interactive Example from the Sfepy Documentation in a Jupyter Notebook but when I run vec = pb.solve(status = status), the program outputs sfepy: giving up and at the end ValueError: ccore error (see above). I am using the tetrahedral mesh of a rectangular prism (16x16x1) that has 64 evenly spaced cylinders inside (this is the mesh):

Is there something wrong with my mesh? I could also share the mesh file and jupyter notebook.
Thank you!

This is the whole error message:

---

ValueError Traceback (most recent call last)
in ()
----> 1 vec = pb.solve(status = status)

~/anaconda3/lib/python3.6/site-packages/sfepy/discrete/problem.py in solve(self, state0, status, force_values, var_data, update_bcs, update_materials, save_results, step_hook, post_process_hook, post_process_hook_final, verbose)
1381 prestep_fun=prestep_fun,
1382 poststep_fun=poststep_fun,
-> 1383 status=status)
1384 output('solved in %d steps in %.2f seconds'
1385 % (status['n_step'], status['time']), verbose=verbose)

~/anaconda3/lib/python3.6/site-packages/sfepy/solvers/ts_solvers.py in _standard_ts_call(self, vec0, nls, init_fun, prestep_fun, poststep_fun, status, **kwargs)
32 result = call(self, vec0=vec0, nls=nls, init_fun=init_fun,
33 prestep_fun=prestep_fun, poststep_fun=poststep_fun,
---> 34 status=status, **kwargs)
35
36 ttt = time.clock() - tt

~/anaconda3/lib/python3.6/site-packages/sfepy/solvers/ts_solvers.py in call(self, vec0, nls, init_fun, prestep_fun, poststep_fun, status, **kwargs)
73 prestep_fun(ts, vec0)
74
---> 75 vec = nls(vec0)
76
77 poststep_fun(ts, vec)

~/anaconda3/lib/python3.6/site-packages/sfepy/solvers/nls.py in call(self, vec_x0, conf, fun, fun_grad, lin_solver, iter_hook, status)
256
257 try:
--> 258 vec_r = fun(vec_x)
259
260 except ValueError:

~/anaconda3/lib/python3.6/site-packages/sfepy/discrete/evaluate.py in eval_residual(self, vec, is_full)
74 vec = self.make_full_vec(vec)
75
---> 76 vec_r = self.problem.equations.eval_residuals(vec)
77 if self.matrix_hook is not None:
78 vec_r = self.matrix_hook(vec_r, self.problem, call_mode='residual')

~/anaconda3/lib/python3.6/site-packages/sfepy/discrete/equations.py in eval_residuals(self, state, by_blocks, names)
699 out = self.create_stripped_state_vector()
700
--> 701 self.evaluate(mode='weak', dw_mode='vector', asm_obj=out)
702
703 return out

~/anaconda3/lib/python3.6/site-packages/sfepy/discrete/equations.py in evaluate(self, names, mode, dw_mode, term_mode, asm_obj)
632 for eq in eqs:
633 out = eq.evaluate(mode=mode, dw_mode=dw_mode,
--> 634 term_mode=term_mode, asm_obj=asm_obj)
635 if isinstance(out, tuple): extras.extend(out[1])
636

~/anaconda3/lib/python3.6/site-packages/sfepy/discrete/equations.py in evaluate(self, mode, dw_mode, term_mode, asm_obj)
851 term_mode=term_mode,
852 standalone=False,
--> 853 ret_status=True)
854 term.assemble_to(asm_obj, val, iels, mode=dw_mode)
855

~/anaconda3/lib/python3.6/site-packages/sfepy/terms/terms.py in evaluate(self, mode, diff_var, standalone, ret_status, **kwargs)
1409 else:
1410 _args = tuple(args) + (mode, term_mode, diff_var)
-> 1411 fargs = self.call_get_fargs(_args, kwargs)
1412
1413 if varr.dtype == nm.float64:

~/anaconda3/lib/python3.6/site-packages/sfepy/terms/terms.py in call_get_fargs(self, args, kwargs)
1245 def call_get_fargs(self, args, kwargs):
1246 try:
-> 1247 fargs = self.get_fargs(*args, **kwargs)
1248
1249 except (RuntimeError, ValueError):

~/anaconda3/lib/python3.6/site-packages/sfepy/terms/terms_elastic.py in get_fargs(self, mat, virtual, state, mode, term_mode, diff_var, **kwargs)
54 def get_fargs(self, mat, virtual, state,
55 mode=None, term_mode=None, diff_var=None, **kwargs):
---> 56 vg, _ = self.get_mapping(state)
57
58 if mode == 'weak':

~/anaconda3/lib/python3.6/site-packages/sfepy/terms/terms.py in get_mapping(self, variable, get_saved, return_key)
1032 self.integral, integration,
1033 get_saved=get_saved,
-> 1034 return_key=return_key)
1035
1036 return out

~/anaconda3/lib/python3.6/site-packages/sfepy/discrete/common/fields.py in get_mapping(self, region, integral, integration, get_saved, return_key)
241
242 if out is None:
--> 243 out = self.create_mapping(region, integral, integration)
244 self.mappings[key] = out
245

~/anaconda3/lib/python3.6/site-packages/sfepy/discrete/fem/fields_base.py in create_mapping(self, region, integral, integration, return_mapping)
1010 vg = mapping.get_mapping(qp.vals, qp.weights, poly_space=ps,
1011 ori=self.ori,
-> 1012 transform=self.basis_transform)
1013
1014 out = vg

~/anaconda3/lib/python3.6/site-packages/sfepy/discrete/fem/mappings.py in get_mapping(self, qp_coors, weights, poly_space, ori, transform)
97 cmap = CMapping(self.n_el, qp_coors.shape[0], self.dim,
98 poly_space.n_nod, mode='volume', flag=flag)
---> 99 cmap.describe(self.coors, self.conn, bf_g, ebf_g, weights)
100
101 return cmap

sfepy/discrete/common/extmods/mappings.pyx in sfepy.discrete.common.extmods.mappings.CMapping.describe()

ValueError: ccore error (see above)

[rc]

Yes, sharing the mesh and code reproducing the error would be helpful.

[gustxsr]

Here I send the Jupyter Note?book and two meshes (one that is all tetrahedral (ends in tet) and the other that is hexahedral (ends in hex)). The filename in the notebook has to be changed to run the program.

…

________________________________ De: Robert Cimrman <notifications@github.com> Enviado: viernes, 02 de agosto de 2019 04:55 p.m. Para: sfepy/sfepy Cc: Gustavo X Santiago-Reyes; Author Asunto: Re: [sfepy/sfepy] Sfepy Giving up | Ccore error (#543) Yes, sharing the mesh and code reproducing the error would be helpful. - You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub<#543?email_source=notifications&email_token=ALCJDKPJKJVUPGCWZH3TUADQCSNNTA5CNFSM4II7AWH2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD3O2FRI#issuecomment-517841605>, or mute the thread<https://github.com/notifications/unsubscribe-auth/ALCJDKNGJ6MOD6A7OBILLLDQCSNNTANCNFSM4II7AWHQ>.

[rc]

@gustxsr have you really attached the files? I cannot see them.

[rc]

Stale issue cleanup, feel free to ask more.