dolfin team mailing list archive

["Garth N. Wells" <g.n.wells@xxxxxxxxxx>]

This has been fixed in dolfin-stable.

Garth

Alessio Quaglino wrote:
> > Send the simplest possible C++ program that leads to the problem and
> > I'll take a look.
> >
> > Garth
>
> Ok thanks. Put this into /src/demo/pde/poisson:
>
> #include <dolfin.h>
> #include "Poisson.h"
>
> using namespace dolfin;
>
> void solvePoissonBug(Mesh& mesh)
> {
>   // Linear system and solver
>   Matrix A;
>   Vector b;
>
>   // Create forms
>   Function f = 0.0;
>   Function g = 0.0;
>   Poisson::BilinearForm a;
>   Poisson::LinearForm L(f,g);
>
>   // Assemble
>   FEM::assemble(a, A, mesh);
>   FEM::assemble(L, b, mesh);
>
>   int rows[1];
>   int cols[1];
>   real block[1];
>
>   rows[0] = 1;
>   cols[0] = 1;
>   block[0] = 1.0;
>
>   A.add(block, rows, 0, cols, 0);
> }
>
> int main()
> {
>   Mesh mesh("../../../../data/meshes/dolfin-2.xml.gz");
>   solvePoissonBug(mesh);
> }
>
> Regards,
> Alessio
>
>
> > Alessio Quaglino wrote:
> > > > Alessio Quaglino wrote:
> > > > > Anyway, I just have a small (but important) bug with uBlas and dolfin
> > > > > 0.6.3 that Johan Jansson couldnt solve so if you (or someone else if
> > > > > you
> > > > > don't have time) could help me I would really appreciate.
> > > > Is the bug present in the later release (0.6.4)?
> > > >
> > > > Garth
> > >
> > > Yes. Gbd gives the following output:
> > >
> > > Program received signal SIGSEGV, Segmentation fault.
> > > [Switching to Thread -1209726752 (LWP 3498)]
> > > 0xb7cd53dc in
> > > boost::numeric::ublas::matrix_assign<boost::numeric::ublas::scalar_assign,
> > > boost::numeric::ublas::basic_full<unsigned int>,
> > > boost::numeric::ublas::generalized_vector_of_vector<double,
> > > boost::numeric::ublas::basic_row_major<unsigned int, int>,
> > > boost::numeric::ublas::vector<boost::numeric::ublas::compressed_vector<double,
> > > 0u, boost::numeric::ublas::unbounded_array<unsigned int,
> > > std::allocator<unsigned int> >,
> > > boost::numeric::ublas::unbounded_array<double, std::allocator<double> >
> > > > ,
> > > boost::numeric::ublas::unbounded_array<boost::numeric::ublas::compressed_vector<double,
> > > 0u, boost::numeric::ublas::unbounded_array<unsigned int,
> > > std::allocator<unsigned int> >,
> > > boost::numeric::ublas::unbounded_array<double, std::allocator<double> >
> > > > ,
> > > std::allocator<boost::numeric::ublas::compressed_vector<double, 0u,
> > > boost::numeric::ublas::unbounded_array<unsigned int,
> > > std::allocator<unsigned int> >,
> > > boost::numeric::ublas::unbounded_array<double, std::allocator<double> >
> > > > > > > , boost::numeric::ublas::compressed_matrix<double,
> > > boost::numeric::ublas::basic_row_major<unsigned int, int>, 0u,
> > > boost::numeric::ublas::unbounded_array<unsigned int,
> > > std::allocator<unsigned int> >,
> > > boost::numeric::ublas::unbounded_array<double, std::allocator<double> >
> > > > (m=@0x8242b7c, e=@0x8242b44) at vector_sparse.hpp:957
> > > 957                 *it = k_based (i);
> > >
> > > The simple example uses the Python interface and the Poisson equation.
> > > I've inserted inside uBlasMatrix.h the following function, which does
> > > exactly what add() does, but with different arguments.
> > >
> > >    template <class Mat>
> > >    inline void uBlasMatrix<Mat>::diagSum(const uBlasVector& x)
> > >    {
> > >      if( assembled )
> > >      {
> > >        Assembly_matrix.assign(*this);
> > >        assembled = false;
> > >      }
> > >      else
> > >        dolfin_error("Matrix has not been assembled. Did you forget to
> > >  call
> > >  A.apply()?");
> > >
> > >      uint s = Assembly_matrix.size1();
> > >      uint r = Assembly_matrix.size2();
> > >
> > >      if( s != r )
> > >        dolfin_error("Matrix is not square!");
> > >
> > >      for( uint i = 0; i < s; i++ )
> > >      {
> > >        Assembly_matrix(i , i) += x[i];
> > >      }
> > >    }
> > >
> > > My simple test case just import the form file already defined for
> > > Poisson
> > > euqation, uses dolfin mesh generator and then assemble the matrix A:
> > >
> > >     # Create a mesh of the unit square
> > >     mesh = UnitSquare(100, 100)
> > >
> > >     # Import forms (compiled just-in-time with FFC)
> > >     forms = import_formfile("Poisson.form")
> > >     import poisson as forms
> > >
> > >     # Assemble linear system
> > >     a = forms.PoissonBilinearForm()
> > >     A = Matrix()
> > >     FEM_assemble(a, A, mesh)
> > >
> > >     # Sum a vector
> > >     b = Vector(A.size(0))
> > >     b.operator=(2.0)
> > >     A.diagSum(b)
> > >
> > > I've also already tried to call A.apply() before but it does not help.
> > > The
> > > segmentation fault comes from the following line (inside uBlasMatrix.h):
> > >
> > > Assembly_matrix.assign(*this);
> > >
> > > However, there is no segmentation fault if I call A.zero() after
> > > FEM_assemble(), so my guess is that this depends on the matrix
> > > representation. Thank you for the help.
> > >
> > > Regards,
> > > Alessio Quaglino
> > >
> > >
> > > > > Best regards,
> > > > > Alessio Quaglino