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
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