On Sun, 6 May 2018 at 10:40, Robert Speck <r.sp...@fz-juelich.de> wrote:
> Hi! > > I would like to do a matrix-vector multiplication (besides using linear > solvers and so on) with petsc4py. I took the matrix from this example > (https://bitbucket.org/petsc/petsc4py/src/master/demo/kspsolve/petsc-mat.py) This example only produces a matrix. And from the code the matrix produced is identical in serial or parallel. > and applied it to a PETSc Vector. All works well in serial, but in > parallel (in particular if ordering becomes relevant) the resulting > vector looks very different. Given this, the way you defined the x vector in y = A x must be different when run on 1 versus N mpi ranks. Using the shell matrix of this example > ( > https://bitbucket.org/petsc/petsc4py/src/master/demo/poisson2d/poisson2d.py > ) > helps, but then I cannot use matrix-based preconditioners for KSP > directly (right?). I also tried using DMDA for creating vectors and > matrix and for taking care of their ordering (which seems to be my > problem here), but that did not help either. > > So, my question is this: How do I do easy parallel matrix-vector > multiplication with petsc4py in a way that allows me to use parallel > linear solvers etc. later on? I want to deal with spatial decomposition > as little as possible. What's the context - are you solving a PDE? Assuming you are using your own grid object (e.g. as you might have if solving a PDE), and assuming you are not solving a 1D problem, you actually have to "deal" with the spatial decomposition otherwise performance could be quite terrible - even for something simple like a 5 point Laplacian on a structured grid in 2D What data structures should I use? DMDA or > PETSc.Vec() and PETSc.Mat() or something else? The mat vec product is not causing you a problem. Your issue appears to be that you do not have a way to label entries in a vector in a consistent manner. What's the objective? Are you solving a PDE? If yes, structured grid? If yes again, use the DMDA. It takes care of all the local-to-global and global-to-local mapping you need. Thanks, Dave > > Thanks! > -Robert- > > -- > Dr. Robert Speck > Juelich Supercomputing Centre > Institute for Advanced Simulation > Forschungszentrum Juelich GmbH > 52425 Juelich, Germany > > Tel: +49 2461 61 1644 > Fax: +49 2461 61 6656 > > Email: r.sp...@fz-juelich.de > Website: http://www.fz-juelich.de/ias/jsc/speck_r > PinT: http://www.fz-juelich.de/ias/jsc/pint > > > > > ------------------------------------------------------------------------------------------------ > > ------------------------------------------------------------------------------------------------ > Forschungszentrum Juelich GmbH > 52425 Juelich > Sitz der Gesellschaft: Juelich > Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 > Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher > Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), > Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, > Prof. Dr. Sebastian M. Schmidt > > ------------------------------------------------------------------------------------------------ > > ------------------------------------------------------------------------------------------------ > >