dolfin team mailing list archive

["Martin Sandve Alnæs" <martinal@xxxxxxxxx>]

2008/5/19 Johan Hoffman <jhoffman@xxxxxxxxxx>:
>> On Sun 2008-05-18 22:55, Johan Hoffman wrote:
>>> > On Sun 2008-05-18 21:54, Johan Hoffman wrote:
>>> >> > On Sat, May 17, 2008 at 04:40:48PM +0200, Johan Hoffman wrote:
>>> >> >
>>> >> > 1. Solve time may dominate assemble anyway so that's where we
>>> should
>>> >> > optimize.
>>> >>
>>> >> Yes, there may be such cases, in particular for simple forms (Laplace
>>> >> equation etc.). For more complex forms with more terms and
>>> coefficients,
>>> >> assembly typically dominates, from what I have seen. This is the case
>>> >> for
>>> >> the flow problems of Murtazo for example.
>>> >
>>> > This probably depends if you use are using a projection method.  If
>>> you
>>> > are
>>> > solving the saddle point problem, you can forget about assembly time.
>>>
>>> Well, this is not what we see. I agree that this is what you would like,
>>> but this is not the case now. That is why we are now focusing on the
>>> assembly bottleneck.
>>
>> This just occurred to me.  If you have a Newtonian fluid, then the
>> momentum
>> equations are block diagonal, but this is not reflected in the matrix
>> structure.
>> Sure enough, run the stokes demo with -mat_view_draw -draw_pause -1 and
>> note
>> that the off-diagonal blocks of the momentum equations are cyan which
>> means they
>> are set, but have value zero.  This almost doubles the number of
>> insertions into
>> the global matrix.
>
> Good. You are right, this piece of information is not used.
>
> I guess the most general thing is to have ffc delete zero matrix entries
> in computing the sparsity pattern. I do not think this is done today?

We could add it with an appropriate
ufc::dof_map::tabulate_sparsity_pattern(...),
since the form compiler can figure out which entries are always zero.
Currently, this information is hidden from dolfin, and therefore it must
simply use the local blocks.

But A.add(...) calls a single block-addition function in PETSc
or Trilinos, does anyone know how these will perform if the values
contain zeros that are outside the initialized sparsity pattern?


>  Of course, if you really care about speed, you could
>> implement the momentum equations matrix-free with a custom preconditioner
>> that
>> only uses one block (since they are the same).
>>
>> Also, it seems like a strange design decision for general coupled systems
>> for
>> the blocks to be separate like this.  (Actually, ordering the unknowns
>> this way
>> makes some factorizations ``work'' even when the matrix is indefinite.)
>
>  Ok. We should look in to this.

The reasoning behind this decision was that it makes access to subvectors
for components of general hierarchial mixed elements easy. Vector elements
and mixed elements are treated as basically the same thing.

Thus, renumbering should preferably happen in dolfin, which will have to be
done for many occasions anyway.

-- 
Martin