[petsc-dev] The problem about running an example in PETSc

Lulu Liu lulu.liu at kaust.edu.sa
Sun May 19 16:00:54 CDT 2013 

  ierr = DMDACreate(comm, da);CHKERRQ(ierr);
  ierr = DMDASetDim(*da, 3);CHKERRQ(ierr);                  // <-- fix this
line
  ierr = DMDASetSizes(*da, M, N, P);CHKERRQ(ierr);
  ierr = DMDASetNumProcs(*da, m, n, p);CHKERRQ(ierr);
  ierr = DMDASetBoundaryType(*da, bx, by, bz);CHKERRQ(ierr);
  ierr = DMDASetDof(*da, dof);CHKERRQ(ierr);
  ierr = DMDASetStencilType(*da, stencil_type);CHKERRQ(ierr);
  ierr = DMDASetStencilWidth(*da, s);CHKERRQ(ierr);
  ierr = DMDASetOwnershipRanges(*da, lx, ly, lz);CHKERRQ(ierr);
  /* This violates the behavior for other classes, but right now users
expect negative dimensions to be handled this way */
  ierr = DMSetFromOptions(*da);CHKERRQ(ierr);              // <--- delete
this line
  ierr = DMSetUp(*da);CHKERRQ(ierr);
  ierr = DMViewFromOptions(*da,"-dm_view");CHKERRQ(ierr);  // <--- delete
or set a prefix


If I delete  the line

 ierr = DMSetFromOptions(*da);CHKERRQ(ierr);

which implies the partition has no overlaps when in fact I put the option
-da_overlap 1 outside ( I need overlaps). How to fix it?

Thank you!



On Tue, Apr 30, 2013 at 9:20 PM, Jed Brown <jedbrown at mcs.anl.gov> wrote:

> Lulu Liu <lulu.liu at kaust.edu.sa> writes:
>
> > src/ts/examples/tutorials/ex29.c I want domain partition is 1x2
> >
> > mpiexec -n 2 ./ex29 -da_refine 4 -ts_max_steps 10 -ts_rtol 1e-3 -ts_atol
> > 1e-3   -ts_type arkimex -ts_monitor -snes_monitor -snes_type ngmres
> > -npc_snes_type nasm -npc_snes_nasm_type restrict -da_overlap 4
> >  -da_processors_x 1 -da_processors_y 2
>
> Thanks for sending the command to reproduce.
>
> > 0 TS dt 0.05 time 0
> >     0 SNES Function norm 1.762942085583e+01
> > [0]PETSC ERROR: --------------------- Error Message
> > ------------------------------------
> > [0]PETSC ERROR: Argument out of range!
> > [0]PETSC ERROR: Too many processors in Y direction: 2 1!
> > [0]PETSC ERROR: [1]PETSC ERROR: --------------------- Error Message
> > ------------------------------------
> > [1]PETSC ERROR: Argument out of range!
> > [1]PETSC ERROR: Too many processors in Y direction: 2 1!
> > [1]PETSC ERROR:
> > ------------------------------------------------------------------------
> > [1]PETSC ERROR: Petsc Development GIT revision:
> > bc51b945dfb4f1d1228fb677a132a806066a0f32  GIT Date: 2013-04-29 10:22:29
> > -0500
> > ------------------------------------------------------------------------
> > [0]PETSC ERROR: Petsc Development GIT revision:
> > bc51b945dfb4f1d1228fb677a132a806066a0f32  GIT Date: 2013-04-29 10:22:29
> > -0500
> > [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: ./ex29 on a arch-basic named kl-12681.local by liul Tue
> Apr
> > 30 21:07:37 2013
> > [0]PETSC ERROR: [1]PETSC ERROR: See docs/changes/index.html for recent
> > updates.
> > [1]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
> > [1]PETSC ERROR: See docs/index.html for manual pages.
> > [1]PETSC ERROR:
> > ------------------------------------------------------------------------
> > [1]PETSC ERROR: ./ex29 on a arch-basic named kl-12681.local by liul Tue
> Apr
> > 30 21:07:37 2013
> > [1]PETSC ERROR: Libraries linked from
> /Users/liul/soft/petsc/arch-basic/lib
> > [1]PETSC ERROR: Configure run at Tue Apr 30 15:46:16 2013
> > [1]PETSC ERROR: Configure options --download-cmake
> --download-f-blas-lapack
> > --download-mpich --with-cc=gcc --with-fc=gfortran PETSC_ARCH=arch-basic
> > [1]PETSC ERROR:
> > ------------------------------------------------------------------------
> > [1]PETSC ERROR: Libraries linked from
> /Users/liul/soft/petsc/arch-basic/lib
> > [0]PETSC ERROR: Configure run at Tue Apr 30 15:46:16 2013
> > [0]PETSC ERROR: Configure options --download-cmake
> --download-f-blas-lapack
> > --download-mpich --with-cc=gcc --with-fc=gfortran PETSC_ARCH=arch-basic
> > [0]PETSC ERROR:
> > ------------------------------------------------------------------------
> > [0]PETSC ERROR: DMSetUp_DA_2D() line 266 in
> > /Users/liul/soft/petsc/src/dm/impls/da/da2.c
> > DMSetUp_DA_2D() line 266 in /Users/liul/soft/petsc/src/dm/impls/da/da2.c
> > [1]PETSC ERROR: DMSetUp_DA() line 27 in
> > /Users/liul/soft/petsc/src/dm/impls/da/dareg.c
> > [1]PETSC ERROR: DMSetUp() line 469 in
> > /Users/liul/soft/petsc/src/dm/interface/dm.c
> > [1]PETSC ERROR: DMDACreate2d() line 888 in
> > /Users/liul/soft/petsc/src/dm/impls/da/da2.c
> > [1]PETSC ERROR: [0]PETSC ERROR: DMSetUp_DA() line 27 in
> > /Users/liul/soft/petsc/src/dm/impls/da/dareg.c
> > [0]PETSC ERROR: DMSetUp() line 469 in
> > /Users/liul/soft/petsc/src/dm/interface/dm.c
> > DMDAGetReducedDMDA() line 389 in
> > /Users/liul/soft/petsc/src/dm/impls/da/dacorn.c
> > [1]PETSC ERROR: CoefficientSubDomainRestrictHook() line 92 in
> > src/ts/examples/tutorials/ex29.c
> > [1]PETSC ERROR: DMCreateDomainDecomposition() line 1314 in
> > /Users/liul/soft/petsc/src/dm/interface/dm.c
> > [1]PETSC ERROR: SNESSetUp_NASM() line 112 in
> > /Users/liul/soft/petsc/src/snes/impls/nasm/nasm.c
> > [1]PETSC ERROR: SNESSetUp() line 2633 in
> > /Users/liul/soft/petsc/src/snes/interface/snes.c
> > [0]PETSC ERROR: DMDACreate2d() line 888 in
> > /Users/liul/soft/petsc/src/dm/impls/da/da2.c
> > [0]PETSC ERROR: DMDAGetReducedDMDA() line 389 in
> > /Users/liul/soft/petsc/src/dm/impls/da/dacorn.c
>
>   if (dim == 1) {
>     ierr =
> DMDACreate1d(PetscObjectComm((PetscObject)da),bx,M,nfields,s,dd->lx,nda);CHKERRQ(ierr);
>   } else if (dim == 2) {
>     ierr =
> DMDACreate2d(PetscObjectComm((PetscObject)da),bx,by,stencil_type,M,N,m,n,nfields,s,lx,ly,nda);CHKERRQ(ierr);
>   } else if (dim == 3) {
>     ierr =
> DMDACreate3d(PetscObjectComm((PetscObject)da),bx,by,bz,stencil_type,M,N,P,m,n,p,nfields,s,lx,ly,lz,nda);CHKERRQ(ierr);
>   }
>
> This code should be fixed to use the precise API instead of the
> convenience routines DMDACreate*d(), so that it does NOT call
> DMSetFromOptions (or if it does, call it after setting a prefix).
>
> Lulu, would you be up for taking a crack at this and submitting a patch?
> Just take the sequence of calls found in DMDACreate3d:
>
>   ierr = DMDACreate(comm, da);CHKERRQ(ierr);
>   ierr = DMDASetDim(*da, 3);CHKERRQ(ierr);                  // <-- fix
> this line
>   ierr = DMDASetSizes(*da, M, N, P);CHKERRQ(ierr);
>   ierr = DMDASetNumProcs(*da, m, n, p);CHKERRQ(ierr);
>   ierr = DMDASetBoundaryType(*da, bx, by, bz);CHKERRQ(ierr);
>   ierr = DMDASetDof(*da, dof);CHKERRQ(ierr);
>   ierr = DMDASetStencilType(*da, stencil_type);CHKERRQ(ierr);
>   ierr = DMDASetStencilWidth(*da, s);CHKERRQ(ierr);
>   ierr = DMDASetOwnershipRanges(*da, lx, ly, lz);CHKERRQ(ierr);
>   /* This violates the behavior for other classes, but right now users
> expect negative dimensions to be handled this way */
>   ierr = DMSetFromOptions(*da);CHKERRQ(ierr);              // <--- delete
> this
>   ierr = DMSetUp(*da);CHKERRQ(ierr);
>   ierr = DMViewFromOptions(*da,"-dm_view");CHKERRQ(ierr);  // <--- delete
> or set a prefix
>
> I can help if you get stuck.
>
> https://bitbucket.org/petsc/petsc/wiki/Home
>

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