dolfin team mailing list archive

[Anders Logg <logg@xxxxxxxxx>]

On Wed, Jul 16, 2008 at 09:59:10PM +0100, Garth N. Wells wrote:
> 
> 
> Anders Logg wrote:
> > On Wed, Jul 16, 2008 at 09:48:16PM +0100, Garth N. Wells wrote:
> >>
> >> Anders Logg wrote:
> >>> Very nice!
> >>>
> >>> Some comments:
> >>>
> >>> 1. Beating uBLAS by a factor 3 is not that hard. 
> >> A factor 3 is quite something if the matrix is in compressed row format. 
> >>   DOLFIN assembly times into uBLAS, PETSc and Trilinos matrices are all 
> >> very close to each other.
> >>
> >> Didem Unat (PhD
> >>> student at UCSD/Simula) and Ilmar have been looking at the assembly in
> >>> DOLFIN recently. We've done some initial benchmarks and have started
> >>> investigating how to speedup the assembly. Take a look at what happens
> >>> when we assemble into uBLAS:
> >>>
> >>>   (i)   Compute sparsity pattern
> >>>   (ii)  Reset tensor
> >>>   (iii) Assemble
> >>>
> >>> For uBLAS, each of these steps is approximately an assembly process.
> >>> I don't remember the exact numbers, but by just using an
> >>> std::vector<std::map<int, double> > instead of a uBLAS matrix, one may
> >>> skip (i) and (ii) and get a speedup.
> >>>
> >> You can do this with uBLAS too by using the uBLAS mapped_matrix (uses 
> >> std::map internally) instead of compressed_matrix. The problem is that 
> >> it is dead slow for matrix-vector multiplications. Most uBLAS sparse 
> >> matrix types are faster to assemble than the compressed_matrix, but are 
> >> slower to traverse.
> >>
> >> Before the computation of the sparsity pattern was implemented, DOLFIN 
> >> assembled into a uBLAS vector-of-compressed-vectors because it is quite 
> >> fast to assemble uninitialised and can be converted quite quickly to a 
> >> compressed row matrix. This approach may still have merit for some problems.
> >>
> >> Garth
> > 
> > I think eventually we should assemble into a special-purpose data
> > structure that is fast for assembly and the convert row-wise (which is
> > fast) into something suitable for linear algebra.
> >
> 
> This is what we did before (into a vector of vectors, then convert),
> and it wasn't faster overall.
> 
> Garth

What was the cost of the conversion?

-- 
Anders

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