[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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