[petsc-users] VecValidValues() reports NaN found

Matthew Knepley knepley at gmail.com
Wed May 7 05:52:13 CDT 2014 

On Tue, May 6, 2014 at 10:53 PM, linjing bo <francium87 at hotmail.com> wrote:

> The Valgrind shows memory leak in memalign() called by KSPSetup and
> PCSetup. Is that normal?
>


Did you call KSPDestroy()?

  Matt

>
>
> ---------------------------------------------------------------------------------------------
> ==31551== 136 bytes in 1 blocks are definitely lost in loss record 2,636
> of 3,327
> ==31551==    at 0x4A05458: memalign (vg_replace_malloc.c:727)
> ==31551==    by 0x5498E79: PetscMallocAlign (mal.c:27)
> ==31551==    by 0x5DE9D5E: KSPSetUp_GMRES (gmres.c:75)
> ==31551==    by 0x5E1C41F: KSPSetUp (itfunc.c:239)
> ==31551==    by 0x5E1821D: KSPSolve (itfunc.c:399)
> ==31551==    by 0x5CAD7F1: kspsolve_ (itfuncf.c:219)
> ==31551==    by 0x8D9842: petsc_solver_defi_ (petsc_defi.F90:434)
> ==31551==    by 0x831618: field_solver_defi_ (field_defi.F90:57)
> ==31551==    by 0x46CB4E: MAIN__ (main.F90:96)
> ==31551==    by 0x41852B: main (in /home/jlin/defi_field/ftest/gtc)
>
> ...
>
> ==31551== 4,092 bytes in 1 blocks are definitely lost in loss record 3,113
> of 3,327
> ==31551==    at 0x4A05458: memalign (vg_replace_malloc.c:727)
> ==31551==    by 0x5498E79: PetscMallocAlign (mal.c:27)
> ==31551==    by 0x5A085AE: MatDuplicateNoCreate_SeqAIJ (aij.c:4011)
> ==31551==    by 0x5A2D24F: MatILUFactorSymbolic_SeqAIJ_ilu0
> (aijfact.c:1655)
> ==31551==    by 0x5A2B7CB: MatILUFactorSymbolic_SeqAIJ (aijfact.c:1756)
> ==31551==    by 0x573D152: MatILUFactorSymbolic (matrix.c:6240)
> ==31551==    by 0x5CFB843: PCSetUp_ILU (ilu.c:204)
> ==31551==    by 0x5D8BAA7: PCSetUp (precon.c:890)
> ==31551==    by 0x5E1C639: KSPSetUp (itfunc.c:278)
> ==31551==    by 0x5E1821D: KSPSolve (itfunc.c:399)
> ==31551==    by 0x5CAD7F1: kspsolve_ (itfuncf.c:219)
> ==31551==    by 0x8D9842: petsc_solver_defi_ (petsc_defi.F90:434)
> ==31551==    by 0x831618: field_solver_defi_ (field_defi.F90:57)
> ==31551==    by 0x46CB4E: MAIN__ (main.F90:96)
> ==31551==    by 0x41852B: main (in /home/jlin/defi_field/ftest/gtc)
>
>
> -------------------------------------------------------------------------------------------------
>
>
> ------------------------------
> From: francium87 at hotmail.com
> To: knepley at gmail.com
> CC: petsc-users at mcs.anl.gov
> Subject: RE: [petsc-users] VecValidValues() reports NaN found
> Date: Mon, 5 May 2014 13:15:38 +0000
>
> Ok, I will try it . Thanks for your advise.
>
> ------------------------------
> Date: Mon, 5 May 2014 08:12:05 -0500
> Subject: Re: [petsc-users] VecValidValues() reports NaN found
> From: knepley at gmail.com
> To: francium87 at hotmail.com
> CC: petsc-users at mcs.anl.gov
>
> On Mon, May 5, 2014 at 7:56 AM, linjing bo <francium87 at hotmail.com> wrote:
>
> I use JACOBI. The message showed is with JACOBI.
>
>
> Wired situation is that the backtrack information shows the location is
> before actually apply PC, so I guess the rhs vec is not changed at this
> point.
>
> Another wired thing is : Because the original code is to complex. I write
> out the A matrix in Ax=b, and write a small test code to read in this
> matrix and solve it, no error showed. The KSP, PC are all set to be the
> same.
>
> When I try to using ILU, more wired error happens, the backtrack info
> shows it died in a Flops logging function:
>
>
> 1) Run in serial until it works
>
> 2) It looks like you have memory overwriting problems. Run with valgrind
>
>    Matt
>
>
> [2]PETSC ERROR: --------------------- Error Message
> ------------------------------------
> [2]PETSC ERROR: Argument out of
> range!
> [2]PETSC ERROR: Cannot log negative
> flops!
> [2]PETSC ERROR:
> ------------------------------------------------------------------------
> [2]PETSC ERROR: Petsc Release Version 3.4.4, Mar, 13,
> 2014
> [2]PETSC ERROR: See docs/changes/index.html for recent
> updates.
> [2]PETSC ERROR: See docs/faq.html for hints about trouble
> shooting.
> [2]PETSC ERROR: See docs/index.html for manual
> pages.
> [2]PETSC ERROR:
> ------------------------------------------------------------------------
> [2]PETSC ERROR: ./gtc on a arch-linux2-c-debug named node2.indac.info by
> jlin Mon May  5 20:51:27
> 2014
>
> [2]PETSC ERROR: Libraries linked from
> /opt/sfw/petsc/3.4.4/intel/openmpi/lib
> [2]PETSC ERROR: Configure run at Sat Apr 26 20:19:41
> 2014
> [2]PETSC ERROR: Configure options
> --prefix=/opt/sfw/petsc/3.4.4/intel/openmpi
> --with-mpi-dir=/opt/sfw/openmpi/1.6.3/intel
> --with-blas-lapack-dir=/opt/sfw/intel/composer_xe_2011_sp1.7.256/mkl/lib/intel64
> --with-mpiexec=mpiexec
>
> [2]PETSC ERROR:
> ------------------------------------------------------------------------
>
> [2]PETSC ERROR: PetscLogFlops() line 204 in
> /tmp/petsc-3.4.4/include/petsclog.h
> [2]PETSC ERROR: MatLUFactorNumeric_SeqAIJ() line 552 in
> /tmp/petsc-3.4.4/src/mat/impls/aij/seq/aijfact.c
>
> [2]PETSC ERROR: MatLUFactorNumeric() line 2889 in
> /tmp/petsc-3.4.4/src/mat/interface/matrix.c
> [2]PETSC ERROR: PCSetUp_ILU() line 232 in
> /tmp/petsc-3.4.4/src/ksp/pc/impls/factor/ilu/ilu.c
> [2]PETSC ERROR: PCSetUp() line 890 in
> /tmp/petsc-3.4.4/src/ksp/pc/interface/precon.c
> [2]PETSC ERROR: KSPSetUp() line 278 in
> /tmp/petsc-3.4.4/src/ksp/ksp/interface/itfunc.c
> [2]PETSC ERROR: KSPSolve() line 399 in
> /tmp/petsc-3.4.4/src/ksp/ksp/interface/itfunc.c
>
>
>
>
> ------------------------------
> Date: Mon, 5 May 2014 07:27:52 -0500
> Subject: Re: [petsc-users] VecValidValues() reports NaN found
> From: knepley at gmail.com
> To: francium87 at hotmail.com
> CC: petsc-users at mcs.anl.gov
>
> On Mon, May 5, 2014 at 7:25 AM, linjing bo <francium87 at hotmail.com> wrote:
>
>  Hi, I'm trying to use PETSc's ksp method to solve a linear system. When
> running, Error is reported by VecValidValues() that NaN or Inf is found
> with error message listed below
>
>
> [3]PETSC ERROR: --------------------- Error Message
> ------------------------------------
> [3]PETSC ERROR: Floating point
> exception!
> [3]PETSC ERROR: Vec entry at local location 0 is not-a-number or infinite
> at beginning of function: Parameter number
> 2!
>
> [3]PETSC ERROR:
> ------------------------------------------------------------------------
>
> [3]PETSC ERROR: Petsc Release Version 3.4.4, Mar, 13,
> 2014
> [3]PETSC ERROR: See docs/changes/index.html for recent
> updates.
> [3]PETSC ERROR: See docs/faq.html for hints about trouble
> shooting.
> [3]PETSC ERROR: See docs/index.html for manual
> pages.
> [3]PETSC ERROR:
> ------------------------------------------------------------------------
>
> [3]PETSC ERROR: ./gtc on a arch-linux2-c-debug named node2.indac.info by
> jlin Mon May  5 20:03:20
> 2014
>
> [3]PETSC ERROR: Libraries linked from
> /opt/sfw/petsc/3.4.4/intel/openmpi/lib
> [3]PETSC ERROR: Configure run at Sat Apr 26 20:19:41
> 2014
> [3]PETSC ERROR: Configure options
> --prefix=/opt/sfw/petsc/3.4.4/intel/openmpi
> --with-mpi-dir=/opt/sfw/openmpi/1.6.3/intel
> --with-blas-lapack-dir=/opt/sfw/intel/composer_xe_2011_sp1.7.256/mkl/lib/intel64
> --with-mpiexec=mpiexec
>
> [3]PETSC ERROR:
> ------------------------------------------------------------------------
>
> [3]PETSC ERROR: VecValidValues() line 28 in
> /tmp/petsc-3.4.4/src/vec/vec/interface/rvector.c
>
>
> It looks like the vector after preconditioner application is bad. What is
> the preconditioner?
>
>   Matt
>
>
>
> [3]PETSC ERROR: PCApply() line 436 in
> /tmp/petsc-3.4.4/src/ksp/pc/interface/precon.c
> [3]PETSC ERROR: KSP_PCApply() line 227 in
> /tmp/petsc-3.4.4/include/petsc-private/kspimpl.h
> [3]PETSC ERROR: KSPInitialResidual() line 64 in
> /tmp/petsc-3.4.4/src/ksp/ksp/interface/itres.c
> [3]PETSC ERROR: KSPSolve_GMRES() line 239 in
> /tmp/petsc-3.4.4/src/ksp/ksp/impls/gmres/gmres.c
> [3]PETSC ERROR: KSPSolve() line 441 in
> /tmp/petsc-3.4.4/src/ksp/ksp/interface/itfunc.c
>
>
> After read the source code shown by backtrack informations, I realize the
> problem is in the right hand side vector. So I make a trial of set right
> hand side vector to ONE by VecSet, But the program still shows error
> message above, and using VecView or VecGetValue to investigate the first
> value of rhs vec shows the value is 1.0 as I set it to. Hope I clearly
> describe the problem. The code related is listed below
>
> ---------------------------Solver section--------------------------
>
>   call VecSet( pet_bp_b, one, ierr)
>
>   vecidx=[0,1]
>   call VecGetValues( pet_bp_b, 2, vecidx, first, ierr)
>   write(*,*) ' first two values ', first(1), first(2)
>
>   call KSPSetInitialGuessNonzero(solver_bp,Petsc_True,ierr)
>   call KSPSolve(solver_bp,pet_bp_b,pet_bp_x,ierr)
>   call KSPView(solver_bp, PETSC_VIEWER_STDOUT_SELF,ierr)
>   CHKERRQ(ierr)
>
>
>
>
>
> --
> 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
>
>
>
>
> --
> 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
>



-- 
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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