dolfin team mailing list archive

[Anders Logg <logg@xxxxxxxxx>]

On Wed, Jul 16, 2008 at 11:01:46PM +0200, Dag Lindbo wrote:
> > Very nice!
> >
> 
> Thanks :)
> 
> > Some comments:
> >
> > 1. Beating uBLAS by a factor 3 is not that hard. 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.
> >
> 
> I think this simplifies it too much.

Not that much. Look at SparsityPatternBuilder. It's basically the
assembly algorithm with tabulate_tensor commented out. This is step
(ii).

Then step (iii) is uBlasMatrix::init():

  for(set = pattern.begin(); set != pattern.end(); ++set)
    for(element = set->begin(); element != set->end(); ++element)
      A.push_back(set - pattern.begin(), *element, 0.0);

which for some of our test cases takes 50% of the time used by step
(ii).

> Ublas has a matrix type called
> "generalized vector of vector" (gvov) that one can assemble into without
> (i) and (ii) but then one has to copy the whole matrix to a compressed row
> major afterwards. Artefacts of this pre-SP "assembly matrix" can still be
> found in DOLFIN.
> 
> That MTL can take you from a fresh bilinear form to a matrix ripe for
> Krylov iteration three times faster is, in my opinion, impressive.

Don't get me wrong. I agree that MTL is very impressive. I'm just
saying that what we have now in DOLFIN is not. :-)

-- 
Anders


> > We've just started and don't have anything to present yet.
> >
> > 2. I've also looked at MTL before. We even considered using it as the
> > main LA backend a (long) while back.
> >
> > 3. With the new LA interfaces in place, I wouldn't mind having MTL as
> > an optional backend.
> >
> >
> >
> > On Tue, Jul 15, 2008 at 11:58:05PM +0200, Dag Lindbo wrote:
> >> Hello!
> >>
> >> In light of the long and interesting discussion we had a while ago about
> >> assembler performance I decided to try to squeeze more out of the uBlas
> >> backend. This was not very successful.
> >>
> >> However, I've been following the development of MTL4
> >> (http://www.osl.iu.edu/research/mtl/mtl4/) with a keen eye on the
> >> interesting insertion scheme they provide. I implemented a backend --
> >> without sparsity pattern computation -- for the dolfin assembler and
> >> here
> >> are some first benchmarks results:
> >>
> >> Incomp Navier Stokes on 50x50x50 unit cube
> >>
> >> MTL --------------------------------------------------------
> >> assembly time: 8.510000
> >> reassembly time: 6.750000
> >> vecor assembly time: 6.070000
> >>
> >> memory: 230 mb
> >>
> >> UBLAS ------------------------------------------------------
> >> assembly time: 23.030000
> >> reassembly time: 12.140000
> >> vector assembly time: 6.030000
> >>
> >> memory: 642 mb
> >>
> >> Poisson on 2000x2000 unit square
> >>
> >> MTL --------------------------------------------------------
> >> assembly time: 9.520000
> >> reassembly time: 6.650000
> >> assembly time: 4.730000
> >> vector linear solve: 0.000000
> >>
> >> memory: 452 mb
> >>
> >> UBLAS ------------------------------------------------------
> >> assembly time: 15.400000
> >> reassembly time: 7.520000
> >> vector assembly time: 5.020000
> >>
> >> memory: 1169 mb
> >>
> >> Conclusions? MTL is more than twice as fast and allocates less than half
> >> the memory (since there is no sparsity pattern computation) across a set
> >> of forms I've tested.
> >>
> >> The code is not perfectly done yet, but I'd still be happy to share it
> >> with whoever wants to mess around with it.
> >>
> >> Cheers!
> >>
> >> /Dag
> >>
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> >
> 
> 
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