I think the memory is indeed not preallocated. Yes my problem is periodic, but if I try to use a periodic DA, the multigrid solver complains about it (see the end of the message). I believe the source of that problem is DAGetInterpolation_3D_Q0().
The problem I am trying to solve is a 3D Poisson equation with Neuman/Robin/Periodic boundary conditions. The boundary conditions are decided at runtime. If I use if-else-if statements to choose the DA here is the message Thanks, Christophe [0]PETSC ERROR: --------------------- Error Message ------------------------------------ [0]PETSC ERROR: Invalid argument! [0]PETSC ERROR: Cannot handle periodic grid in x! [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: Petsc Development Version 2.3.1, Patch 14, Thu Jul 6 00:02:04 CDT 2006 HG revision: 97334a27165ab031dddd67964dd7a97955e75d20 [0]PETSC ERROR: See docs/changes/index.html for recent updates. [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting. [0]PETSC ERROR: See docs/index.html for manual pages. [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: ././oceanus on a linux-gnu named tux194.llnl.gov by picard1 Thu Aug 10 17:16:31 2006 [0]PETSC ERROR: Libraries linked from /home/picard1/Tools/Petsc-Dev/lib/linux-gnu-c-real-debug [0]PETSC ERROR: Configure run at Thu Jul 6 16:05:13 2006 [0]PETSC ERROR: Configure options --prefix=/home/picard1/Tools/Petsc-Dev --with-dynamic --with-shared --with-mpi=0 --with-superlu=1 --download-superlu=ifneeded [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: DAGetInterpolation_3D_Q0() line 498 in src/dm/da/src/dainterp.c [0]PETSC ERROR: DAGetInterpolation() line 874 in src/dm/da/src/dainterp.c [0]PETSC ERROR: DMGetInterpolation() line 117 in src/dm/da/utils/dm.c [0]PETSC ERROR: DMMGSetUp() line 215 in src/snes/utils/damg.c [0]PETSC ERROR: DMMGSetDM() line 180 in src/snes/utils/damg.c [0]PETSC ERROR: --------------------- Error Message ------------------------------------ [0]PETSC ERROR: Null argument, when expecting valid pointer! [0]PETSC ERROR: Null Object: Parameter # 1! [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: Petsc Development Version 2.3.1, Patch 14, Thu Jul 6 00:02:04 CDT 2006 HG revision: 97334a27165ab031dddd67964dd7a97955e75d20 [0]PETSC ERROR: See docs/changes/index.html for recent updates. [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting. [0]PETSC ERROR: See docs/index.html for manual pages. [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: ././oceanus on a linux-gnu named tux194.llnl.gov by picard1 Thu Aug 10 17:16:31 2006 [0]PETSC ERROR: Libraries linked from /home/picard1/Tools/Petsc-Dev/lib/linux-gnu-c-real-debug [0]PETSC ERROR: Configure run at Thu Jul 6 16:05:13 2006 [0]PETSC ERROR: Configure options --prefix=/home/picard1/Tools/Petsc-Dev --with-dynamic --with-shared --with-mpi=0 --with-superlu=1 --download-superlu=ifneeded [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: PetscObjectReference() line 106 in src/sys/objects/inherit.c [0]PETSC ERROR: MGSetInterpolate() line 136 in src/ksp/pc/impls/mg/mgfunc.c [0]PETSC ERROR: DMMGSetUpLevel() line 385 in src/snes/utils/damg.c [0]PETSC ERROR: DMMGSetKSP() line 452 in src/snes/utils/damg.c On Thursday 10 August 2006 04:53 pm, Matthew Knepley wrote: > It sounds like you are inserting values which were not preallocating. To > determine for sure, we would need to know more about the code. However, > if you have a periodic problem, why not use a periodic DA? > > Matt > > On 8/10/06, Christophe Picard <picard2 at llnl.gov> wrote: > > Hi, > > > > I have a performance issue while trying to insert values in the a matrix. > > I am using DMMG solver for cell-centered scheme in 3D from the > > petsc-snapshot to solve a Poisson equations. Inserting coefficients in > > the matrix for dirichlet or neumann boundary conditions, the insertion is > > instantaneous. But is I want to insert coefficients for periodic boundary > > conditions, I can notice a huge slow down in the insertion process (not > > in the resolution though). The smallest size I can notice the performance > > drop is 32*32*32. > > > > Is there any way to improve this? > > > > > > col.i = row.i+(mx-1); > > col.j = row.j; > > col.k = row.k; > > > > v[0] = 1; > > > > MatSetValuesStencil(*A,1,&row,1,&col,v,ADD_VALUES); > > > > > > > > Thans, > > > > Christophe
