Performance issue with MatSetValues

Thu Aug 10 20:22:57 CDT 2006

Thank you. 
I knew it was kindly donated...and this is also  the reason why I am using the 
dev version of PETSC. I will look at the periodic implementation see if I can 
fix my problem.
Thank you for your precision.
Christophe

On Thursday 10 August 2006 06:01 pm, Barry Smith wrote:
>    This is just do to an incomplete implementation; a user kindly donated
> the code to use but did not add support for periodicity because he did not
> need it. If you look at src/dm/da/src/dainterp.c you will find the various
> routines for setting up the interpolations. If you look at the code
> for 3D_Q1 you will see how the periodic case is handled; you may be able
> to modify the 3D_Q0 code to also handle the periodic case. This will then
> resolve your difficulty.
>
> Good luck,
>
>     Barry
>
> On Thu, 10 Aug 2006, Christophe Picard wrote:
> > 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