On 17 Nov 2011, at 02:31, Andre Massing <email address hidden> wrote:

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> I looked into this and it seems to me that is a bit more involved, so
> here is what I have come up with so far. comments, corrections etc.
> are very welcome!
> 
> At you might have seen I stumbled across 2 other bugs 891448 and 891452
> which did not make it easier to find reasons or solutions for that bug :)
> 
> The implementation of PeriodicBC implicitly assumes that  master and
> slave dofs have the same row sparsity pattern as revealed by the
> following lines ( PeriodicBC.cpp:180 )
> 
> // Add slave rows to master rows
>  for (uint i = 0; i < num_dof_pairs; ++i)
>  {
>    // Add slave row to master row in A
>    if (A)
>    {
>      std::vector<uint> columns;
>      std::vector<double> values;
>      A->getrow(slave_dofs[i], columns, values);
>      A->add(&values[0], 1, &master_dofs[i], columns.size(), &columns[0]);
>      A->apply("add");
>    }
> However, it cannot be assumed that the row sparsity patter for the
> master and slave are the same, since the sparsity pattern builder does
> not take PeriodicBC into account (for instance by adding connectivity
> information for dofs which are mapped to each other)
> 
> In addition states trilinos documentation that
> 
> """
> Note that, even after a matrix is constructed (FillComplete has been
> called), it is possible to update existing matrix entries. It is not
> possible to create new entries.
> """
> see
> http://trilinos.sandia.gov/packages/docs/r10.8/packages/epetra/doc/html/classEpetra__CrsMatrix.html#a1291bfb498b94ac4f1563b48d11dfae5
> 
> And the program crashes exactly when a row patterns occur that do not
> match (So a crossed mesh would be actually a "workaround" ;) ),
> since the matrix is finalized when passed to the PeriodicBC::apply
> function.
> 
> One could try to circumvent this by finalizing the matrix in the solve
> function *after* assembling and the call to all boundary conditions,
> which would require to
> 1. fixed the other aforementioned bugs regarding the unintentional
> finalization of the Matrix
> 2. introduce a way to do several boundary condition apply calls
> without assembling the matrix (up to now, apply does that in any case)
> 
> Nevertheless it still feels wrong, since the main reason for the bug
> is the incomplete sparsity pattern which will result in bad
> performance anyway. Or to put in a very "handwaving way", since the
> Functionspace does not have a notion of constraints and we therefore
> follow the procedure 1. finalize assemble 2. then modify A, b on a
> algebraic level to take constraints into account, constraints are not
> considered when the sparsity has to be computed.
> 

I registered a blueprint a while ago on this, which proposed taking the bcs  into account when building the sparsity pattern. Modifying the sparsity of a matrix post-assembly is bad. Some backends allow it, but performance is usually poor, and other backends don't permit it.

Garth



> Sorry for the detailed and elaborate email, I was to tired to write a
> short one :)
> 
> Andre
> 
> 
> 
> 
> 
> 
> 
> On 11/16/2011 04:45 PM, Andre Massing wrote:
>> ** Changed in: dolfin Status: Confirmed => In Progress
>> 
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> https://bugs.launchpad.net/bugs/864741
> 
> Title:
>  Periodic bc demos fail with Trilinos
> 
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