dolfin team mailing list archive

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

Quoting Anders Logg <logg@xxxxxxxxx>:

> On Sat, Apr 01, 2006 at 12:05:43AM +0200, Garth N. Wells wrote:
> > Quoting Anders Logg <logg@xxxxxxxxx>:
> > 
> > > On Fri, Mar 31, 2006 at 06:16:51PM +0200, Garth N. Wells wrote:
> > > > On Fri, 2006-03-31 at 10:10 -0600, Robert C.Kirby wrote:
> > > > > >
> > > > > > The more I look at it, the more I like it.
> > > > > >
> > > > > > For the benchmarks I made, there was no optimisation (it was  
> > > > > > missing from dolfin-config --cflags). When using optimisation,  
> > > > > > uBlas outperforms the simple functions I wrote for inserting and  
> > > > > > retrieving values from an array. It also provides a LU solver  
> > > > > > (which I need to compute inverses of small matrices).
> > > > > >
> > > > > > It compiled fine with the Intel Linux compiler, and I'm testing it 
> 
> > > > > > now under Cygwin.
> > > > > >
> > > > > 
> > > > > Can you install just ublas (without the boost build system), or do  
> > > > > you have to go through the whole boost build process?
> > > > > 
> > > > 
> > > > There is no need build boost when using ublas.
> > > > 
> > > > If you want to build uBlas, it does have it's own build system but
> there
> > > > is also a configure script so you can do the usual ./configure, make
> > > > install.
> > > > 
> > > > Garth
> > > 
> > > It seems obvious we need something other than PETSc for dense linear
> > > algebra and ublas seems to be a good option.
> > > 
> > > How do we make it fit into DOLFIN? There are some different options:
> > > 
> > > 1. Wrap it as we do with most other stuff, so we would create
> > > something like a class DenseMatrix that wraps a ublas dense matrix.
> > > 
> > > Then the question is how DenseMatrix interacts with the class Vector
> > > which is a PETSc vector. Do we also need a DenseVector?
> > 
> > This would be quick, and we wouldn't have wrap many (if any functions) as
> uBlass
> > is C++ and the functions are intuitive. If we wrap everthing, what's the
> point
> > in using uBlas?
> > 
> > We would need a DenseVector to operate with a dense matrix when taking
> slices,
> > solving, mutliplying, etc.
> > 
> > This could be a good start to play around with uBlas and see if it's really
> what
> > we want.
> 
> Maybe that's the best thing, just create a DenseMatrix and DenseVector
> that wrap (or inherit or typedef) the corresponding data structures in
> ublas.

OK, sounds good. I'll create DenseMatrix and DenseVector classes that inherit
the ublas data structures.

> 
> Then if there should be need for it, we can merge the two matrix types
> Matrix (PETSc matrix) and DenseMatrix with a common interface.
> 
> Also, putting ublas in a subdirectory contrib/ublas seems like a good
> option. Just make sure to put in the proper credits and license for
> ublas.
> 

I'll drop it in shortly.

> Is ublas stable or do we need to track it's development to update for
> new versions?
> 

It seems pretty stable. We can passively keep an eye out for updates.

Garth

> /Anders
> 
> 
> > > 
> > > Should the assembly routines be able to accept a DenseMatrix etc?
> > > 
> > 
> > I can think of examples where this would be useful for me, but not urgent.
> > 
> > > 2. Use a common interface for all linear algebra: Matrix and Vector
> > > which can be PETSc or ublas or ... This is similar to what we had
> > > before with our own implementations in SparseMatrix and DenseMatrix,
> > > only now we would wrap PETSc and ublas instead. This might impose a
> > > slight overhead in addressing entries.
> > > 
> > > We might remove the overhead with a template solution rather than the
> > > class hierarchy (envelope-letter) we used before.
> > > 
> > > This way, we would also need to design a common interface for both
> > > dense and sparse matrices. We could do this, but it would require some
> > > thought to get it right. (Or we just go ahead and implement it and to
> > > get something that works...)
> > > 
> > 
> > A truly common interface would be difficult to define as some operations
> will
> > differ. We could define a basic set of operations which are common.
> > 
> > Garth
> > 
> > > There is a fairly new project called GLAS for Generic Linear Algebra
> > > Software that aims at creating a C++ template library for linear
> > > algebra with multiple backends. I don't think they have anything
> > > useful yet but they seem to have a plan for handling multiple backends
> > > while providing a common interface.
> > > 
> > > 3. Just use ublas from within DOLFIN the way we use STL in some
> > > places.
> > > 
> > > I'm very keen on keeping a simple user interface so in my ideal world
> > > there is just one class Matrix and one class Vector (perhaps with
> > > multiple backends).
> > > 
> > > /Anders
> > > 
> > > _______________________________________________
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> > > DOLFIN-dev@xxxxxxxxxx
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> > > 
> > 
> 
> -- 
> Anders Logg
> Research Assistant Professor
> Toyota Technological Institute at Chicago
> http://www.tti-c.org/logg/
> 
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