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

Jed Brown jedbrown at mcs.anl.gov
Tue Apr 30 14:37:50 CDT 2013 

Please always use "reply-all" so that your messages go to the list.

Lulu Liu <lulu.liu at kaust.edu.sa> writes:

>  ierr = DMDACreate(comm, da);CHKERRQ(ierr);
>   ierr = DMDASetDim(*da, 3);CHKERRQ(ierr);                  // <-- fix this
> line  Why do we fix this line?

Just pass 'dim' so that it works for any dimension.

>   ierr = DMDASetSizes(*da, M, N, P);CHKERRQ(ierr);   I think that we should
> fix this line...
>
>      The error shown like:
>
>      Partition in x direction is too fine! -6 1!

Hmm, that error should only be able to occur before the DM is set up.  M
should be positive after setup.

>   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
>
>
> 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
>>
>
>
>
> -- 
> Best wishes,
> Lulu Liu
> Applied Mathematics and Computational Science
> King Abdullah University of Science and Technology
> Tel：＋966－0544701599
>
> -- 
>
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