[petsc-users] Problem with GAMG elasticity case:'createdefaultdata' not set(?) need to support NULL data!

Mark F. Adams mfadams at lbl.gov
Fri Oct 18 09:08:26 CDT 2013


I would guess there is some memory corruption or leak someplace.  Try running with -on_error_attach_debugger, and try to get some more information.  Do you just repeat a call to the code below many times?  Is this deterministic, does it fail on the same solve each time? 


On Oct 18, 2013, at 9:30 AM, Einar Sørheim <einar.sorheim at gmail.com> wrote:

> Uncommenting  KSPSetFromOptions solved my intial problem, however I got a new problem that occurs after many timesteps, in our code we use petsc gamg as a solver for several problems(e.g. thermal and mechanical) at each time step, I have a suspicion it might have something to do with cleanup after solving, the rror appears after many calls to the petsc gamg solver interface, the error message is the following:
> 
> [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/documentation/faq.html#valgrind[0]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS X to find memory corruption errors
> [0]PETSC ERROR: likely location of problem given in stack below
> [0]PETSC ERROR: ---------------------  Stack Frames ------------------------------------
> [0]PETSC ERROR: Note: The EXACT line numbers in the stack are not available,
> [0]PETSC ERROR:       INSTEAD the line number of the start of the function
> [0]PETSC ERROR:       is given.
> [0]PETSC ERROR: [0] MatSetNearNullSpace line 7580 src/mat/interface/D:\PROGRA~1\PETSC-~1.3\src\mat\INTERF~1\matrix.c
> [0]PETSC ERROR: --------------------- Error Message ------------------------------------
> [0]PETSC ERROR: Signal received!
> [0]PETSC ERROR: ------------------------------------------------------------------------
> [0]PETSC ERROR: Petsc Release Version 3.4.3, Oct, 15, 2013 
> [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: D:\Programming\gits\Alsim\SharedModules - Copy\Source\Release\Alsim_nypetsc.exe on a arch-mswin-c-debug named CMP3 by admeinar Fri Oct 18 12:26:04 2013
> [0]PETSC ERROR: Libraries linked from /cygdrive/d/Programming/petsc-3.4.3/arch-mswin-c-debug/lib
> [0]PETSC ERROR: Configure run at Thu Oct 17 08:23:18 2013
> [0]PETSC ERROR: Configure options --with-debugging=1 --with-openmp=yes --with-pthread=no --with-cc="win32fe icl" --with-fc="win32fe ifort" --with-cxx="win32fe icl" --with-blas-lapack-dir="C:/Program Files (x86)/Intel/Composer XE 2013/mkl/lib/intel64" --download-superlu --with-sowing=0 --with-c2html=0 --with-mpi-dir="C:/Program Files (x86)/Intel/MPI/4.1.0.028/em64t" --useThreads=0 --useThreads=0
> 
> The source code for the petsc interface: 
> 
>       subroutine petscsolver(i_nodes,r_elements_,i_rowstart_,i_columnindex_,r_x_,r_b_,i_Nnz,i_Precond, i_Solver
>      $     ,coords_,i_nodedof)
> #include <finclude/petscsys.h>
> #include <finclude/petscvec.h>
> #include <finclude/petscmat.h>
> #include <finclude/petscpc.h>
> #include <finclude/petscksp.h>
> #include <finclude/petscviewer.h>
> 
>       integer i_nodes, i_Nnz, i_Precond, i_solver, i_nodedof
>       integer i_rowstart_(*),i_columnindex_(*)
>       double precision r_elements_(*),r_x_(*), r_b_(*),coords_(*)
>       integer, allocatable  :: i_indices_(:)
> !     Variables:
> !
> !  A       - matrix that defines linear system
> !  ksp    - KSP context
> !  ksp     - KSP context
> !  x, b, u - approx solution, RHS, exact solution vectors
> !
> !      implicit none
>       Vec     x,u,b,vec_coords
>       PC      pc
>       Mat     A,F,Matnull
>       KSP    ksp
>       PetscInt i,j,II,JJ,m,n,i1,imaxiter
>       PetscInt Istart,Iend
>       PetscInt nsteps,one, neg_one
>       PetscErrorCode ierr
>       PetscBool  flg
>       PetscScalar  v,x_array_(1), norm, tol, t0,t1
>       PetscOffset i_x
>       PetscViewer viewer
> 
> 
>       call PetscTime(t0,ierr)
>       write(*,*) "Enter petsc"
> 
>       n      = 1
>       nsteps = 1
>       one    = 1
>       neg_one = 1
>       i1 = 1
>       imaxiter = 1200
> 
> 
>       call MatCreate(PETSC_COMM_WORLD,A,ierr)
>       call MatSetSizes(A,PETSC_DECIDE,PETSC_DECIDE,i_nodes,i_nodes,ierr)
>       call MatSetType(A, MATSEQAIJ,ierr)
>       call MatSetUp(A,ierr)
>       call MatSeqAIJSetPreallocation(A,100,PETSC_NULL_INTEGER,ierr)
> !  The matrix is partitioned by contiguous chunks of rows across the
> !  processors.  Determine which rows of the matrix are locally owned. 
> 
>       call MatGetOwnershipRange(A,Istart,Iend,ierr)
> 
> 
>       write(*,*) "Start of matrix fill", i_nodes, Istart, Iend
>       do i=1,i_nodes
> !         write(*,*) "Start of loop",i !!, i_indices_(i+1)
> !         i_indices_(i+1) = i
> !         write(*,*) "Start of loop2"
>          do j=i_rowstart_(i),i_rowstart_(i+1)-1
> !            write(*,*) "Start of loop 3"
>             v = r_elements_(j)
> !            write(*,*) i1,i,i1,j-1,v
>             call MatSetValues(A,i1,i-1,i1,i_columnindex_(j)-1,v,INSERT_VALUES,ierr)
>             if (ierr.gt.0) stop
>          end do
>       end do
> !      write(*,*) "End of matrix fill"
> 
> !  Assemble matrix, using the 2-step process:
> !       MatAssemblyBegin(), MatAssemblyEnd()
> !  Computations can be done while messages are in transition
> !  by placing code between these two statements.
> 
>       call MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY,ierr)
>       call MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY,ierr)
> 
> !  Create parallel vectors.
> !   - When using VecCreate(), the parallel partitioning of the vector
> !     is determined by PETSc at runtime.
> !   - Note: We form 1 vector from scratch and then duplicate as needed.
> !      write(*,*) "Start of vector fill"
>       call VecCreate(PETSC_COMM_WORLD,u,ierr)
>       call VecSetType(u, VECSEQ,ierr)
>       call VecSetSizes(u,PETSC_DECIDE,i_nodes,ierr)
> !      call VecSetFromOptions(u,ierr)      
>       call VecDuplicate(u,b,ierr)
>       call VecDuplicate(b,x,ierr)
>       do i=1,i_nodes
>          call VecSetValues(x,i1,i-1,r_x_(i),INSERT_VALUES,ierr)
>          call VecSetValues(b,i1,i-1,r_b_(i),INSERT_VALUES,ierr)
>       enddo
> !  Assemble vector
> 
>        call VecAssemblyBegin(x,ierr)
>        call VecAssemblyEnd(x,ierr)
>        call VecAssemblyBegin(b,ierr)
>        call VecAssemblyEnd(b,ierr)
>        call PetscTime(t1,ierr)
> !       write(*,*) "End of vec fill time spent :", t1-t0
> !  Create linear solver context
> 
>       call KSPCreate(PETSC_COMM_WORLD,ksp,ierr)
> 
> 
> !  Set operators. Here the matrix that defines the linear system
> !  also serves as the preconditioning matrix.
> 
>       call KSPSetOperators(ksp,A,A,DIFFERENT_NONZERO_PATTERN,ierr)
> 
> 
>       call KSPGetPC(ksp,pc,ierr)
>       tol = 1.e-20
>       call KSPSetTolerances(ksp,tol,PETSC_DEFAULT_DOUBLE_PRECISION,PETSC_DEFAULT_DOUBLE_PRECISION,imaxiter,ierr)
>       select case (i_Precond)
>       case ( 1 )
>          call PCSetType(pc,PCJACOBI,ierr)
>       case ( 2 )
>          call PCSetType(pc,PCILU,ierr)
>          call PCFactorSetMatSolverPackage(pc,MATSOLVERSUPERLU,ierr);
>          call PCFactorSetUpMatSolverPackage(pc,ierr); 
>          call PCFactorGetMatrix(pc,F);
>          call MatSuperluSetILUDropTol(F,1.e-4);
>       case ( 3 )
>          call PCSetType(pc,PCGAMG,ierr)
> !         call PCGAMGInitializePackage()
> !         call PCCreate_GAMG(pc,ierr)
>       case DEFAULT
>          call PCSetType(pc,PCJACOBI,ierr)
>       end select
> 
> !      call PCSetType(pc,PCJACOBI,ierr)
>       select case (i_solver)
>       case ( 0 )
>          call KSPSetType(ksp,KSPCG,ierr)
>       case DEFAULT
>          call KSPSetType(ksp,KSPCG,ierr)
>       end select
>       call KSPCGSetType(ksp,KSP_CG_SYMMETRIC,ierr)
>       if (i_nodedof==3) then
>          write(*,*) "Set coord, number of nodes is:", i_nodes/i_nodedof
>          call VecCreateSeqWithArray(MPI_COMM_SELF,3,i_nodes,coords_,vec_coords,ierr)
>          call MatNullSpaceCreateRigidBody(vec_coords,Matnull,ierr)
>          call MatSetNearNullSpace(A,Matnull,ierr)
>          call MatNullSpaceDestroy(Matnull,ierr)
> 
>          write(*,*) "Finish setting null space ierr =", ierr
> !         call PCSetCoordinates( pc, 3,i_nodes/i_nodedof, coords_, ierr )
> 
>       end if
> !      call KSPMonitorSet(ksp, KSPMonitorDefault, PETSC_NULL, PETSC_NULL,ierr)
> !  Set runtime options, e.g.,
> !      -ksp_type <type> -pc_type <type> -ksp_monitor -ksp_rtol <rtol>
> !  These options will override those specified above as long as
> !  KSPSetFromOptions() is called _after_ any other customization
> !  routines.
> 
>       call KSPSetFromOptions(ksp,ierr)
>       call KSPSetInitialGuessNonzero(ksp,PETSC_TRUE,ierr)
>       call KSPSetUp(ksp,ierr)
>       call PetscTime(t0,ierr)
>       write(*,*) "Time setup", t0-t1
> ! - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 
> !                      Solve the linear system
> ! - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 
> 
>       call KSPSolve(ksp,b,x,ierr)
>       call PetscTime(t1,ierr)
>       write(*,*) "end solve, time used:",t1-t0
>       call KSPGetSolution(ksp,x,ierr)
>       call VecGetArray(x,x_array_,i_x,ierr)
>       do i=1,i_nodes
>          r_x_(i) = x_array_(i_x + i)
>       enddo
>       call VecRestoreArray(x,x_array_,i_x,ierr)
> 
> 
> !  Free work space.  All PETSc objects should be destroyed when they
> !  are no longer needed.
> !      call PCDestroy(pc,ierr)
> 
>       call VecDestroy(u,ierr)
>       call VecDestroy(x,ierr)
>       call VecDestroy(b,ierr)
>       call MatDestroy(A,ierr)
>       if (i_nodedof==3) then
>          call VecDestroy(vec_coords,ierr)
>          call MatDestroy(Matnull,ierr)
>       endif
>       call KSPDestroy(ksp,ierr)
>       call PetscTime(t0,ierr)
>       write(*,*) "time celan up :", t0-t1
> 
>       end
> 
> -- 
> Einar Sørheim
> <Mail Attachment>

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