Does the same happen with MatDuplicate? It overwrites the MatSeqAIJSetPreallocation? In this case, can I redefine the nonzero places?
I need it for the case of creating the preconditioner by changing the jacobian slightly. Margarita On 3 February 2012 22:58, Matthew Knepley <knepley at gmail.com> wrote: > On Fri, Feb 3, 2012 at 4:46 PM, Margarita Satraki < > margarita.satraki at gmail.com> wrote: > >> Hi Jed, >> >> Thanks for the reply. >> I've defined 2 nonzeros per row so it should consider them to be in the >> correct place (1 for diagonal and 1 for the 1st off diagonal). I do not >> want to delete anything, just experiment with inserting new entries. This >> is a simple example to demonstrate my problem with a more complicated code >> of nonlinear elasticity. > > > Assembly of a matrix compresses it, throwing away extra allocated places > that were not used. > > Matt > > > >> Margarita >> >> >> On 3 February 2012 22:41, Jed Brown <jedbrown at mcs.anl.gov> wrote: >> >>> On Sat, Feb 4, 2012 at 01:35, Margarita Satraki < >>> margarita.satraki at gmail.com> wrote: >>> >>>> It seems that only the 1st case gives good results in the sense that by >>>> increasing the size of the matrix you increase the time needed by >>>> MatSetValues linearly. Both the 2nd and the 3rd case give similar results, >>>> much worse than the 1st. I understand that the 1st case has the advantage >>>> because of accurate memory allocation but shouldn't the 2ndcase be better >>>> than the 3rd since it at least defines the number of nonzeros per row so it >>>> again allocates memory more accurately? >>> >>> >>> Those nonzeros are in the wrong place and PETSc does not know that you >>> want to "delete" the old entries. >>> >>> Just preallocate the correct number of nonzeros and it will be fast, >>> don't bother with copying in a "similar" matrix. >>> >> >> > > > -- > 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/20120203/8697f7d8/attachment.htm>
