[petsc-users] Problem with GAMG elasticity case:'createdefaultdata' not set(?) need to support NULL data!
Mark F. Adams
mfadams at lbl.gov
Sat Oct 19 15:36:06 CDT 2013
You can try running a problem that finishes with
-malloc
-malloc_debug
-malloc_dump
to see if there are any memory issues. It looks like you are completely destroying the solver object each time and starting over. Valgrind would be very useful here because it looks like memory is getting corrupted if the same code runs many times.
On Oct 19, 2013, at 3:39 PM, Einar Sørheim <einar.sorheim at gmail.com> wrote:
> yes, I call the given code many times, what i have seen so far is that changing e.g. the order of destruction statements changes the time of failure,I will try to debug to get more details
>
>
> 2013/10/18 Mark F. Adams <mfadams at lbl.gov>
> 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>
>
>
>
>
> --
> Einar Sørheim
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