On 26 September 2011 15:21, Andre Massing <mass...@simula.no> wrote: > On 09/26/2011 01:15 PM, Anders Logg wrote: >> On Mon, Sep 26, 2011 at 12:06:55AM -0700, Johan Hake wrote: >>> On Sunday September 25 2011 23:54:57 Anders Logg wrote: >>>> As part of assembling systems on overlapping meshes (for Nitsche type >>>> methods), my student Andre Massing is calling the regular DOLFIN >>>> assemble function for part of the domain and then calling a special >>>> purpose assembler (currently residing in a branch called dolfin-olm) >>>> for terms that are not supported by the regular assembler. >>>> >>>> For this to work out well, I'd like to propose the following changes >>>> to the assembler: >>>> >>>> 1. Make the assemble_cells, assemble_exterior/interior_facets public >>>> >>>> We need to access these separately. >>>> >>>> 2. Add options for controlling if and how we call A.apply() >>> >>> Wouldn't this be unnesseary if 1 is implemented? Then you just impement your >>> own more flexible assemble routine? >> >> Good point. >> >> Andre: Would that be enough? Note that apply() is not called from the >> assemble_cells/interior/exterior_facets functions, only from the main >> (currently public) assemble function. > > In principle that would be okay. But it enforces the user > to reimplement (or basically to copy paste) the entire > > void Assembler::assemble(GenericTensor& A, > const Form& a, > const MeshFunction<uint>* cell_domains, > const MeshFunction<uint>* exterior_facet_domains, > const MeshFunction<uint>* interior_facet_domains, > bool reset_sparsity, > bool add_values) > > even if the user only wants to first do an regular assemble (via that > function) and then add/insert manually new entries. > Top copy paste the entire assemble function just to get rid of one apply > call at the end seems not to be really user friendly. > > One nice example is the use of the ident_zeros function which as of > today is "damm" slow :) if there are many zeros along the diagonal. > That is because the Matrix will be called with an apply() at the end > of the assemble routine and hence adding values afterwards via > ident_zeros is very expensive.
My understanding is that it does not add entries. Someone did add some hacks which I never understood the need for. A good solution is to not use Assembler but SystemAssembler. The latter should really be the default in DOLFIN since it preserves symmetry. I haven't tested, but I don't know if, for PETSc, MatZeroRows can be called post set/insert but pre apply. The function Assembler::assemble referred to above could have something like 'bool finalise_matrix=true' added to the function signature. Garth > Naturally a user want to assemble, ident_zeros and then call apply. > Basically copy pasting the the whole assemble function > only to omit the postpone the one apply call at the end of assemble > function seems to be an overkill. > > So one thing is the possibility to omit the apply at the end the > assemble. The other thing is to make assemble_cells, etc. public or > protected to ease the implementation of new assemblers. As you said > there are related, but I can think of simple scenarios where a > completely new assembler is not needed but just a tiny function to add > some elements. There, the missing option of postponing the apply makes > it rather cumbersome to reuse the nice functionality which already is > provided in DOLFIN. > > -- > Andre > > > > > > > > >> >> -- >> Anders >> >> >>> Johan >>> >>>> A.apply() calls PETSc MatAssemblyBegin/End with MAT_FINAL_ASSEMBLY. >>>> This makes it *very* expensive for us since we need to switch between >>>> inserting and adding values to the matrix. We need to instead use the >>>> option MAT_FLUSH_ASSEMBLY. It would further be useful to have an >>>> option of not calling A.apply() at all. >>>> >>>> I'm not sure how this should be handled in the GenericTensor interface >>>> since Trilinos does not seem to have a corresponding option. >>>> >>>> A first step would be to just add a boolean option to the assembler: >>>> >>>> call_apply=false >>>> >>>> Then we could manually flush the values in between calls. >>>> >>>> Opinions? >>>> >> >> _______________________________________________ >> Mailing list: https://launchpad.net/~dolfin >> Post to : dolfin@lists.launchpad.net >> Unsubscribe : https://launchpad.net/~dolfin >> More help : https://help.launchpad.net/ListHelp > > > _______________________________________________ > Mailing list: https://launchpad.net/~dolfin > Post to : dolfin@lists.launchpad.net > Unsubscribe : https://launchpad.net/~dolfin > More help : https://help.launchpad.net/ListHelp > _______________________________________________ Mailing list: https://launchpad.net/~dolfin Post to : dolfin@lists.launchpad.net Unsubscribe : https://launchpad.net/~dolfin More help : https://help.launchpad.net/ListHelp
