Performance issue with MatSetValues

[Christophe Picard]

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