[petsc-users] preconditioning with Matrix-Free SNES

Tue Jun 12 23:36:34 CDT 2012

Run in a debugger with -fp_trap to see where the bad value is generated.

Use SNESSetFunctionDomainError() if appropriate.

On Tue, Jun 12, 2012 at 11:32 PM, behzad baghapour <
behzad.baghapour at gmail.com> wrote:

> Thanks. I did above procedure to my ComputeJacobian (only set values for
> precondition matrix B and assemble both A and B). This tackles the problem
> but the linear solver did not converged and bring the below error:
>
> 0:   CFL = 100, Nonlinear = 0.0626958, Linear = (0,0,1e-05) 3.63577
>
> -----------------------------------------------------------------------------
>   Linear solve did not converge due to DIVERGED_ITS iterations 30
> 1:   CFL = 100, Nonlinear = 0.108225, Linear = (30,0.047985,0.3) 0.0569319
>
> -----------------------------------------------------------------------------
>
> [0]PETSC ERROR: --------------------- Error Message
> ------------------------------------
> [0]PETSC ERROR: Floating point exception!
> [0]PETSC ERROR: Infinite or not-a-number generated in norm!
>
> [0]PETSC ERROR:
> ------------------------------------------------------------------------
> [0]PETSC ERROR: Petsc Release Version 3.2.0, Patch 3, Fri Sep 30 10:28:33
> CDT 2011
> [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: ./code on a linux-gnu named baghapour by baghapour Wed Jun
> 13 08:54:57 2012
> [0]PETSC ERROR: Libraries linked from
> /home/baghapour/softs/petsc/linux-gnu-cxx-debug/lib
> [0]PETSC ERROR: Configure run at Wed Nov  9 19:16:47 2011
> [0]PETSC ERROR: Configure options --with-cc=gcc --with-fc=gfortran
> --with-cxx=g++ --download-f2cblaslapack=1 --download-mpich=1
> --with-clanguage=cxx --with-debugging=no --download-parms --download-hypre
> [0]PETSC ERROR:
> ------------------------------------------------------------------------
> [0]PETSC ERROR: VecNorm() line 167 in src/vec/vec/interface/rvector.c
> [0]PETSC ERROR: MatMFFDCompute_WP() line 75 in src/mat/impls/mffd/wp.c
> [0]PETSC ERROR: MatMult_MFFD() line 351 in src/mat/impls/mffd/mffd.c
> [0]PETSC ERROR: MatMult() line 2177 in src/mat/interface/matrix.c
> [0]PETSC ERROR: PCApplyBAorAB() line 610 in src/ksp/pc/interface/precon.c
> [0]PETSC ERROR: GMREScycle() line 156 in src/ksp/ksp/impls/gmres/gmres.c
> [0]PETSC ERROR: KSPSolve_GMRES() line 231 in
> src/ksp/ksp/impls/gmres/gmres.c
> [0]PETSC ERROR: KSPSolve() line 423 in src/ksp/ksp/interface/itfunc.c
> [0]PETSC ERROR: SNES_KSPSolve() line 3396 in src/snes/interface/snes.c
> [0]PETSC ERROR: SNESSolve_LS() line 190 in src/snes/impls/ls/ls.c
> [0]PETSC ERROR: SNESSolve() line 2676 in src/snes/interface/snes.c
> [0]PETSC ERROR: _petsc_NewtonTimeAdvance() line 141 in Newton.cpp
>
> Does it need to set specific options for linear solver (KSP) dealing with
> MF?
>
>
>
>
>
>
>
>
> On Wed, Jun 13, 2012 at 1:09 AM, Barry Smith <bsmith at mcs.anl.gov> wrote:
>
>>
>>   Like in your ComputeJacobian(     Mat *J,Mat *B, ...)
>>
>>    you are calling MatZeroEntries(*J....) and then MatSetValues(*J,....)
>>
>>    you should not do that. You should call the zero entries and set
>> values on B only. Then call MatAssemblyBegin/End() separately on BOTH
>> matrices.
>>
>>    Also if you checked the error code from MatZeroEntries() with a
>> CHKERRQ(ierr) instead of ignoring it you would likely not get the crash
>> below but would get stack frames instead.
>>
>>   Barry
>>
>> On Jun 12, 2012, at 12:54 PM, Matthew Knepley wrote:
>>
>> > On Wed, Jun 13, 2012 at 1:46 AM, behzad baghapour <
>> behzad.baghapour at gmail.com> wrote:
>> > You are right! I do calculate the Jacobian and Preconditioning matrice
>> in FormJacobian function with Mat context. When I used "-snes_mf_operator"
>> I received the error:
>> >
>> > Right, you only want to assemble the preconditioning matrix if you use
>> MF.
>> >
>> >    Matt
>> >
>> > [0]PETSC ERROR: --------------------- Error Message
>> ------------------------------------
>> > [0]PETSC ERROR: No support for this operation for this object type!
>> > [0]PETSC ERROR: Mat type mffd!
>> > [0]PETSC ERROR:
>> ------------------------------------------------------------------------
>> > [0]PETSC ERROR: Petsc Release Version 3.2.0, Patch 3, Fri Sep 30
>> 10:28:33 CDT 2011
>> > [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: ./code on a linux-gnu named behzad-desktop by behzad
>> Tue Jun 12 22:01:48 2012
>> > [0]PETSC ERROR: Libraries linked from
>> /home/behzad/softs/petsc/linux-gnu-cxx-debug/lib
>> > [0]PETSC ERROR: Configure run at Sat Dec 17 10:21:01 2011
>> > [0]PETSC ERROR: Configure options --with-cc=gcc --with-cxx=g++
>> --download-f2cblaslapack=1 --download-mpich=1 --download-hypre
>> --download-parms --with-clanguage=cxx -with-debugging=no
>> > [0]PETSC ERROR:
>> ------------------------------------------------------------------------
>> > [0]PETSC ERROR: MatZeroEntries() line 5186 in src/mat/interface/matrix.c
>> > [0]PETSC ERROR:
>> ------------------------------------------------------------------------
>> > [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation,
>> probably memory access out of range
>> > [0]PETSC ERROR: Try option -start_in_debugger or
>> -on_error_attach_debugger
>> > [0]PETSC ERROR: or see
>> http://www.mcs.anl.gov/petsc/petsc-as/documentation/faq.html#valgrind[0]PETSCERROR: or try
>> http://valgrind.org on GNU/linux and Apple Mac OS X to find memory
>> corruption errors
>> > [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link,
>> and run
>> > [0]PETSC ERROR: to get more information on the crash.
>> > [0]PETSC ERROR: --------------------- Error Message
>> ------------------------------------
>> > [0]PETSC ERROR: Signal received!
>> > [0]PETSC ERROR:
>> ------------------------------------------------------------------------
>> > [0]PETSC ERROR: Petsc Release Version 3.2.0, Patch 3, Fri Sep 30
>> 10:28:33 CDT 2011
>> > [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: ./code on a linux-gnu named behzad-desktop by behzad
>> Tue Jun 12 22:01:48 2012
>> > [0]PETSC ERROR: Libraries linked from
>> /home/behzad/softs/petsc/linux-gnu-cxx-debug/lib
>> > [0]PETSC ERROR: Configure run at Sat Dec 17 10:21:01 2011
>> > [0]PETSC ERROR: Configure options --with-cc=gcc --with-cxx=g++
>> --download-f2cblaslapack=1 --download-mpich=1 --download-hypre
>> --download-parms --with-clanguage=cxx -with-debugging=no
>> > [0]PETSC ERROR:
>> ------------------------------------------------------------------------
>> > [0]PETSC ERROR: User provided function() line 0 in unknown directory
>> unknown file
>> > application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0
>> > [cli_0]: aborting job:
>> > application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0
>> > make: [run] Error 59 (ignored)
>> >
>> >
>> >
>> > On Tue, Jun 12, 2012 at 8:47 PM, Jed Brown <jedbrown at mcs.anl.gov>
>> wrote:
>> > On Tue, Jun 12, 2012 at 11:12 AM, behzad baghapour <
>> behzad.baghapour at gmail.com> wrote:
>> > Thank you. Now, I received the error which I should change Mat into
>> mffd.
>> >
>> > Always include the entire error message!
>> >
>> > You have to assemble a matrix to use most preconditioners.
>> >
>> >
>> >
>> >
>> > --
>> > What most experimenters take for granted before they begin their
>> experiments is infinitely more interesting than any results to which their
>> experiments lead.
>> > -- Norbert Wiener
>>
>>
>
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