dolfin team mailing list archive

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

Anders Logg wrote:
> I've run the old and new assembly through valgrind --tool=callgrind
> and here's a summary of the results:
>
> Old assembly, below assembleCommonOld():
>
>     assembleElementOld()         86.74%
>     other                        13.26%
>
> New assembly, below assembleCommon():
>
>     assembleElementTensor()      42.73%
>     DofMap::numNonZeroesRow()    39.19%
>     DofMap::~DofMap()            12.09%
>     other                         5.99%
>
> So in summary the DofMap class adds about 100% in extra work.

A problem is that DofMap is called at each assemble, whereas it should 
only be called for the first assemble.

Are you using uBLAS or PETSc matrices?

Garth

> (The 60% for running the benchmark is because the benchmark also
> includes running some local benchmarks for the element tensor which is
> not affected by the DofMap.)
>
> /Anders
>
>
> On Tue, Jan 16, 2007 at 10:04:30AM +0100, Anders Logg wrote:
> > I have added an old version of the assembly to FEM. Running the
> > benchmark in src/bench/fem/assembly/ with the old assembly confirms
> > the result that the new assembly is about 60% slower.
> >
> > To change between the two (old and new), edit lines 81-82 in
> > src/bench/fem/assembly/main.cpp.
> >
> > /Anders
> >
> >
> >
> > On Tue, Jan 16, 2007 at 12:06:10AM +0100, Anders Logg wrote:
> > > On Mon, Jan 15, 2007 at 10:54:18PM +0100, Garth N. Wells wrote:
> > > > The extra time could be in the mesh initialisation. DofMap is pretty fast.
> > > I'm not sure. The benchmark initializes the mesh connectivity before
> > > assembling and then assembles 100 times, so at least the last 99 times
> > > the mesh initialization should not do anything. (Calling init() on the
> > > mesh twice does not do anything the second time.)
> > >
> > > > What needs to be done is to use the DofMap to initialise the sparse 
> > > > matrix pattern (at least for uBLAS). What happens now is that everything 
> > > > is assembled into a uBLAS vector-of-compressed-vectors (fast assembly), 
> > > > which is then copied to a CSR matrix (for fast matrix vector mult or for 
> > > > passing to UMFPACK). Using DofMap, the CSR matrix could be initialised. 
> > > > This should make things faster and use less memory
> > > ok, let's do that.
> > >
> > > > Also, which problem are you assembling? Scalar Poisson equation can be 
> > > > misleading as it tends to fill sparse matrices quite fast even if they 
> > > > are not well initialised. This tends to show up with vector equations.
> > > Advection operator for cubic Lagrange in 3D:
> > >
> > >     a = v*c[i]*U.dx(i)*dx
> > >
> > > /Anders
> > >
> > >
> > > > Garth
> > > >
> > > > Anders Logg wrote:
> > > > > There is a benchmark for assembly in src/bench/fem/assembly/.
> > > > > We should use this to track the speed of assembly during the
> > > > > planned changes to the Assembly and DofMap classes.
> > > > >
> > > > > The assembly is now 59% slower than it was before the DofMap (and
> > > > > maybe other changes).
> > > > >
> > > > >   0.63-dev (changeset 1d485299d95)
> > > > >   CPU time: 87.8056
> > > > >
> > > > >   0.6.4 (changeset 49bf8f3ca3d9)
> > > > >   CPU time: 139.686
> > > > >
> > > > > Note that the benchmarks are run with --enable-optimization.
> > > > >
> > > > > Let's try to get back to the speed we had before or at least find out
> > > > > exactly what takes time. It might be that computing the nonzero
> > > > > pattern is what takes more time, but that this is necessary to reduce
> > > > > the memory usage.
> > > > >
> > > > > /Anders
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