dolfin team mailing list archive

[Anders Logg <logg@xxxxxxxxx>]

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.
(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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> > > > DOLFIN-dev@xxxxxxxxxx
> > > > http://www.fenics.org/mailman/listinfo/dolfin-dev
> > > > 
> > > 
> > > 
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