On Tue, May 6, 2014 at 10:53 PM, linjing bo <[email protected]> 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: [email protected] > To: [email protected] > CC: [email protected] > 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: [email protected] > To: [email protected] > CC: [email protected] > > On Mon, May 5, 2014 at 7:56 AM, linjing bo <[email protected]> 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: [email protected] > To: [email protected] > CC: [email protected] > > On Mon, May 5, 2014 at 7:25 AM, linjing bo <[email protected]> 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
