dolfin team mailing list archive

[Anders Logg <question135076@xxxxxxxxxxxxxxxxxxxxx>]

Question #135076 on DOLFIN changed:
https://answers.launchpad.net/dolfin/+question/135076

    Status: Open => Answered

Anders Logg proposed the following answer:
Can you try to isolate the form that gives rise to this and reproduce
it with a single call to assemble() for that form and still make it
crash. If so, it should be fairly easy for us to debug.

--
Anders


On Mon, Nov 22, 2010 at 06:19:42PM -0000, Martin Truffer wrote:
> New question #135076 on DOLFIN:
> https://answers.launchpad.net/dolfin/+question/135076
>
> A colleague of mine wrote some python code for a finite element project. It seems to run fine on his Mac, but I get the error below. I have been getting this error somewhat randomly at other times. Sometimes instant-clean will fix the problem, but not for everything. As is obvious from the traceback, this involves a lot of code that is not part of dolfin, but perhaps the error still makes sense?
> I am running fenics under Ubuntu Maverick and installed it through a ppa repository.
>
> Any help is appreciated.
>
>
> ERROR: An unexpected error occurred while tokenizing input
> The following traceback may be corrupted or invalid
> The error message is: ('EOF in multi-line statement', (10, 0))
>
> ---------------------------------------------------------------------------
> ValueError                                Traceback (most recent call last)
>
> /home/martin/matlab/UAF-inverse/maxwell_inverse/python/experiments/plap_vs_ssa1d/invert_ssa1d_from_plap.py in <module>()
>     164 params.forwardproblem.l2Weight = 1e-8
>     165 params.forwardproblem.useH1=True # Use H1 norm for bed strength functions
> --> 166 solver = InverseSolver(Vsurface,f,P,sigma,Bh,bcs=[bc],params=params)
>     167
>     168 # Perform the inversion starting with initial guess gamma0
>
>
> /home/martin/matlab/UAF-inverse/maxwell_inverse/python/inverseproblems/ssa1d.pyc in __init__(self, V, f, P, sigma, Bh, bcs, params)
>     270     InvertIGN.__init__(self,params)
>     271     self.V = V
> --> 272     self.forward_problem = SSA1dForward(V,f,P,sigma,Bh,bcs=bcs,params=self.params.forwardproblem)
>     273
>     274   def forwardProblem(self):
>
> /home/martin/matlab/UAF-inverse/maxwell_inverse/python/inverseproblems/ssa1d.pyc in __init__(self, V, f, P, sigma, Bh, bcs, params)
>      52         raise ValueError("Unsupported boundary condition")
>      53
> ---> 54     area = assemble(Constant(1)*dx,mesh=self.V.mesh())
>      55     self.range_form = assemble(Constant(1/area)*self.uu*self.vv*dx)
>      56     if self.params.useH1:
>
> /usr/lib/python2.6/dist-packages/dolfin/fem/assemble.pyc in assemble(form, tensor, mesh, coefficients, function_spaces, cell_domains, exterior_facet_domains, interior_facet_domains, reset_sparsity, add_values, backend, form_compiler_parameters)
>      98                        coefficients=coefficients,
>      99                        form_compiler_parameters=form_compiler_parameters,
> --> 100                        common_cell=common_cell)
>     101
>     102     # Set mesh if specified (important for functionals without a function spaces)
>
>
> /usr/lib/python2.6/dist-packages/dolfin/fem/form.pyc in __init__(self, form, function_spaces, coefficients, form_compiler_parameters, common_cell)
>      32         # Compile form if necessary
>
>      33         if not hasattr(form, "create_cell_integral"):
> ---> 34             (self._compiled_form, module, self.form_data) = jit(form, form_compiler_parameters, common_cell)
>      35
>      36         else:
>
> /usr/lib/python2.6/dist-packages/dolfin/compilemodules/jit.pyc in mpi_jit(*args, **kwargs)
>      45         # Just call JIT compiler when running in serial
>
>      46         if MPI.num_processes() == 1:
> ---> 47             return local_jit(*args, **kwargs)
>      48
>      49         # Compile first on process 0
>
>
> /usr/lib/python2.6/dist-packages/dolfin/compilemodules/jit.pyc in jit(form, form_compiler_parameters, common_cell)
>     112         raise RuntimeError, "Form compiler must implement the jit function."
>     113
> --> 114     return jit_compile(form, parameters=p, common_cell=common_cell)
>     115
>     116
>
> /usr/lib/python2.6/dist-packages/ffc/jitcompiler.pyc in jit(object, parameters, common_cell)
>      62         return jit_element(object, parameters)
>      63     else:
> ---> 64         return jit_form(object, parameters, common_cell)
>      65
>      66 def jit_form(form, parameters=None, common_cell=None):
>
> /usr/lib/python2.6/dist-packages/ffc/jitcompiler.pyc in jit_form(form, parameters, common_cell)
>     120
>     121     # Generate code
>
> --> 122     compile_form(preprocessed_form, prefix=jit_object.signature(), parameters=parameters)
>     123
>     124     # Build module using Instant (through UFC)
>
>
> /usr/lib/python2.6/dist-packages/ffc/compiler.pyc in compile_form(forms, object_names, prefix, parameters)
>     138     # Stage 2: intermediate representation
>
>     139     cpu_time = time()
> --> 140     ir = compute_ir(analysis, parameters)
>     141     _print_timing(2, time() - cpu_time)
>     142
>
> /usr/lib/python2.6/dist-packages/ffc/representation.pyc in compute_ir(analysis, parameters)
>      56     # Compute representation of elements
>
>      57     info("Computing representation of %d elements" % len(elements))
> ---> 58     ir_elements = [_compute_element_ir(e, i, element_map) for (i, e) in enumerate(elements)]
>      59
>      60     # Compute representation of dofmaps
>
>
> /usr/lib/python2.6/dist-packages/ffc/representation.pyc in _compute_element_ir(ufl_element, element_id, element_map)
>      93     ir["evaluate_basis"] = _evaluate_basis(element, cell)
>      94     ir["evaluate_dof"] = _evaluate_dof(element, cell)
> ---> 95     ir["interpolate_vertex_values"] = _interpolate_vertex_values(element, cell)
>      96     ir["num_sub_elements"] = ufl_element.num_sub_elements()
>      97     ir["create_sub_element"] = _create_sub_foo(ufl_element, element_map)
>
> /usr/lib/python2.6/dist-packages/ffc/representation.pyc in _interpolate_vertex_values(element, cell)
>     428                            "mapping": e.mapping()[0],
>     429                            "space_dim": e.space_dimension()}
> --> 430                           for e in all_elements(element)]
>     431     return ir
>     432
>
> /usr/lib/python2.6/dist-packages/FIAT/finite_element.pyc in tabulate(self, order, points)
>     106         """Return tabulated values of derivatives up to given order of
>     107         basis functions at given points."""
> --> 108         return self.poly_set.tabulate(points, order)
>     109
>     110     def value_shape(self):
>
> /usr/lib/python2.6/dist-packages/FIAT/polynomial_set.pyc in tabulate(self, pts, jet_order)
>      65         """Returns the values of the polynomial set."""
>      66         result = {}
> ---> 67         base_vals = self.expansion_set.tabulate( self.embedded_degree , pts )
>      68         for i in range( jet_order + 1 ):
>      69             alphas = mis( self.ref_el.get_spatial_dimension() , i )
>
> /usr/lib/python2.6/dist-packages/FIAT/expansions.pyc in tabulate(self, n, pts)
>     100             return numpy.array( [] )
>     101
> --> 102         ref_pts = [ self.mapping( pt ) for pt in pts ]
>     103
>     104         def idx(p,q):
>
> /usr/lib/python2.6/dist-packages/FIAT/expansions.pyc in <lambda>(x)
>      90         v2 = self.base_ref_el.get_vertices()
>      91         self.A,self.b = reference_element.make_affine_mapping( v1 , v2 )
> ---> 92         self.mapping = lambda x: numpy.dot( self.A , x ) + self.b
>      93 #        self.scale = numpy.sqrt( numpy.linalg.det( self.A ) )
>
>      94
>
> ValueError: matrices are not aligned
>
>

-- 
You received this question notification because you are a member of
DOLFIN Team, which is an answer contact for DOLFIN.