dolfin team mailing list archive

[Anders Logg <logg@xxxxxxxxx>]

On Tue, Jan 16, 2007 at 10:13:04AM -0600, Garth N. Wells wrote:
> 
> 
> 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.

That's a good point. When we have all the functionality in place, we
should provide some options for assembling with or without building
the DofMap so the assembly can be tuned to different situations (one
or more calls).

> Are you using uBLAS or PETSc matrices?

uBLAS

/Anders


> 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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> >>>>>
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