On Fri, Jan 27, 2012 at 10:32 AM, Tabrez Ali <stali at geology.wisc.edu> wrote:
> PETSc Gurus > > First I want to thank you for patiently answering questions that I have > asked in past regarding preallocation. Unfortunately I am still having > problems. > > I have a small unstructured FE (elasticity) code that uses PETSc. > > Unfortunately I am not yet able to find an _efficient_ way of calculating > the non-zero structure so I simply overestimate the o_nz and d_nz values (= > dimension x max_number_of nodes _a_node_contributes_to) which means that my > stiffness matrix consumes at least 2X more memory. For example, for a > perfectly structured mesh of linear hexes this number is 3*27=81=o_nz=d_nz. > In complicated 3D linear tet/hex meshes that I have generated I rarely need > to set a value greater than 150. In general I have found that as long as I > keep DOF/core between 100-200K (assuming 1GB/per core) there is enough > local RAM left even when memory for stiffness matrix is overestimated by > 2X-6X. > > In any case now I do want to preallocate exactly for better memory > performance and the ambiguity involved in choosing a reasonable o_nz/d_nz. > The way I am trying to do it involves loops like ... > > do i=1, num_local_elements > do j=1, num_total_nodes > ... > end do > end do > > or using lists that involve searches. > > This unfortunately takes much time (much more than assembly and solve) due > to the second loop. I am aware of many posts/slides by PETSc authors that > mention that the non-zero structure can be found simply by looping once > through elements but what to do next is not quite clear. > > I am also aware of this post by Barry [ http://lists.mcs.anl.gov/** > pipermail/petsc-users/2008-**May/003020.html<http://lists.mcs.anl.gov/pipermail/petsc-users/2008-May/003020.html>] > but I cannot get it to work for a simple 4 element problem. Can some one > please expand on the strategy being suggested by Barry specially where the > loops are discussed (I understand the arrays and the vecscatter part). I am > also not sure how does using a t of 0.5 and 1 prevents double counting. > Shouldn't it be 0 and 1? > > I am also aware of some capabilities in DMMESH but right now I dont > understand it well enough to utilize it. > I agree with you here. Its not easy enough to use. However, I have rewritten the basics of it completely in C, which will all have easy Fortran bindings. You can specify your mesh with adjacency lists using Fortran arrays. The last part I am working on is matrix preallocation. I would not normally ask you to wait, but I think I am pretty close. Mail me directly if you want more info. I think it should only take me a few weeks to finish. Thanks, Matt Alternatively does PETSc support MATMPIAIJ of size=integer(1)/logical > instead of real(8) which I can use to put zeros/ones (when I loop over > elements the first time) to get the non-zero structure? > > Thanks in advance. > > Tabrez > -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener -------------- next part -------------- An HTML attachment was scrubbed... URL: <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20120127/f58dfd9b/attachment.htm>
