[petsc-users] Trying to solve Ax = b problem with Boundary condition using ksp
Matthew Knepley
knepley at gmail.com
Thu Jul 12 06:22:31 CDT 2018
On Thu, Jul 12, 2018 at 1:00 AM Fazlul Huq <huq2090 at gmail.com> wrote:
> Hi,
> I am trying to solve this problem with the following code:
>
> static char help[] = "Solves a tridiagonal linear system with KSP.\n\n";
>
> /*T
> Concepts: KSP^solving a system of linear equations
> Processors: 1
> T*/
>
>
>
> /*
> Include "petscksp.h" so that we can use KSP solvers. Note that this file
> automatically includes:
> petscsys.h - base PETSc routines petscvec.h - vectors
> petscmat.h - matrices
> petscis.h - index sets petscksp.h - Krylov subspace
> methods
> petscviewer.h - viewers petscpc.h - preconditioners
>
> Note: The corresponding parallel example is ex23.c
> */
> #include <petscksp.h>
>
> int main(int argc,char **args)
> {
> Vec x, b, u; /* approx solution, RHS, exact solution */
> Mat A; /* linear system matrix */
> KSP ksp; /* linear solver context */
> PC pc; /* preconditioner context */
> PetscReal norm; /* norm of solution error */
> PetscErrorCode ierr;
> PetscInt i,n = 10,col[3],its;
> PetscMPIInt size;
> // PetscScalar zero = 0;
> PetscScalar hundredth = 0.01,value[3];
> PetscScalar one = 1.0;
> PetscScalar leftbc = 10.01;
> PetscScalar rightbc = 15.01;
> PetscBool nonzeroguess = PETSC_FALSE,changepcside = PETSC_FALSE;
>
> ierr = PetscInitialize(&argc,&args,(char*)0,help);if (ierr) return ierr;
> ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRQ(ierr);
> if (size != 1) SETERRQ(PETSC_COMM_WORLD,1,"This is a uniprocessor
> example only!");
> ierr = PetscOptionsGetInt(NULL,NULL,"-n",&n,NULL);CHKERRQ(ierr);
> ierr =
> PetscOptionsGetBool(NULL,NULL,"-nonzero_guess",&nonzeroguess,NULL);CHKERRQ(ierr);
>
>
> /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> Compute the matrix and right-hand-side vector that define
> the linear system, Ax = b.
> - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
>
> /*
> Create vectors. Note that we form 1 vector from scratch and
> then duplicate as needed.
> */
> ierr = VecCreate(PETSC_COMM_WORLD,&x);CHKERRQ(ierr);
> ierr = PetscObjectSetName((PetscObject) x, "Solution");CHKERRQ(ierr);
> ierr = VecSetSizes(x,PETSC_DECIDE,n);CHKERRQ(ierr);
> ierr = VecSetFromOptions(x);CHKERRQ(ierr);
> ierr = VecDuplicate(x,&b);CHKERRQ(ierr);
> ierr = VecDuplicate(x,&u);CHKERRQ(ierr);
>
> i=1;
> ierr = VecSetValues(b, 1, &i, &leftbc, INSERT_VALUES);CHKERRQ(ierr);
> for (i=2; i<n-1; i++){
> ierr = VecSetValues(b, n-2, &i, &hundredth,
> INSERT_VALUES);CHKERRQ(ierr);
> }
> i=n-1;
> ierr = VecSetValues(b, 1, &i, &rightbc, INSERT_VALUES);CHKERRQ(ierr);
> ierr = VecAssemblyBegin(b);CHKERRQ(ierr);
> ierr = VecAssemblyEnd(b);CHKERRQ(ierr);
>
> /*
> Create matrix. When using MatCreate(), the matrix format can
> be specified at runtime.
>
> Performance tuning note: For problems of substantial size,
> preallocation of matrix memory is crucial for attaining good
> performance. See the matrix chapter of the users manual for details.
> */
> ierr = MatCreate(PETSC_COMM_WORLD,&A);CHKERRQ(ierr);
> ierr = MatSetSizes(A,PETSC_DECIDE,PETSC_DECIDE,n,n);CHKERRQ(ierr);
> ierr = MatSetFromOptions(A);CHKERRQ(ierr);
> ierr = MatSetUp(A);CHKERRQ(ierr);
>
> /*
> Assemble matrix
> */
> value[0] = -1.0; value[1] = 2.0; value[2] = -1.0;
> for (i=1; i<n-1; i++) {
> col[0] = i-1; col[1] = i; col[2] = i+1;
> ierr = MatSetValues(A,1,&i,3,col,value,INSERT_VALUES);CHKERRQ(ierr);
> }
> i = n - 1; col[0] = n - 2; col[1] = n - 1;
> ierr = MatSetValues(A,1,&i,2,col,value,INSERT_VALUES);CHKERRQ(ierr);
> i = 0; col[0] = 0; col[1] = 1; value[0] = 2.0; value[1] = -1.0;
> ierr = MatSetValues(A,1,&i,2,col,value,INSERT_VALUES);CHKERRQ(ierr);
> ierr = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
> ierr = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
>
> /*
> Set exact solution; then compute right-hand-side vector.
> */
>
>
> ierr = VecSet(u,one);CHKERRQ(ierr);
> // ierr = MatMult(A,u,b);CHKERRQ(ierr);
>
> i=0;
> ierr = VecSetValues(b, 1, &i, &leftbc, INSERT_VALUES);CHKERRQ(ierr);
> for (i=1; i<n-1; i++){
> ierr = VecSetValues(b, n-2, &i, &hundredth,
> INSERT_VALUES);CHKERRQ(ierr);
>
What is the line above intended to do? You are telling it to take n-2
values, but only giving it
one value (hundreth) so it is indexing far outside the array.
Matt
> }
> i=n-1;
> ierr = VecSetValues(b, 1, &i, &rightbc, INSERT_VALUES);CHKERRQ(ierr);
> ierr = VecAssemblyBegin(b);CHKERRQ(ierr);
> ierr = VecAssemblyEnd(b);CHKERRQ(ierr);
>
> ierr = MatMult(A,u,b);CHKERRQ(ierr);
>
> /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> Create the linear solver and set various options
> - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
> /*
> Create linear solver context
> */
> ierr = KSPCreate(PETSC_COMM_WORLD,&ksp);CHKERRQ(ierr);
>
> /*
> Set operators. Here the matrix that defines the linear system
> also serves as the preconditioning matrix.
> */
> ierr = KSPSetOperators(ksp,A,A);CHKERRQ(ierr);
>
> /*
> Test if you can change the KSP side and type after they have been
> previously set
> */
> ierr =
> PetscOptionsGetBool(NULL,NULL,"-change_pc_side",&changepcside,NULL);CHKERRQ(ierr);
> if (changepcside) {
> ierr = KSPSetUp(ksp);CHKERRQ(ierr);
> ierr = PetscOptionsInsertString(NULL,"-ksp_norm_type unpreconditioned
> -ksp_pc_side right");CHKERRQ(ierr);
> ierr = KSPSetFromOptions(ksp);CHKERRQ(ierr);
> ierr = KSPSetUp(ksp);CHKERRQ(ierr);
> }
>
> /*
> Set linear solver defaults for this problem (optional).
> - By extracting the KSP and PC contexts from the KSP context,
> we can then directly call any KSP and PC routines to set
> various options.
> - The following four statements are optional; all of these
> parameters could alternatively be specified at runtime via
> KSPSetFromOptions();
> */
> ierr = KSPGetPC(ksp,&pc);CHKERRQ(ierr);
> ierr = PCSetType(pc,PCJACOBI);CHKERRQ(ierr);
> ierr =
> KSPSetTolerances(ksp,1.e-5,PETSC_DEFAULT,PETSC_DEFAULT,PETSC_DEFAULT);CHKERRQ(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.
> */
> ierr = KSPSetFromOptions(ksp);CHKERRQ(ierr);
>
> if (nonzeroguess) {
> PetscScalar p = .5;
> ierr = VecSet(x,p);CHKERRQ(ierr);
> ierr = KSPSetInitialGuessNonzero(ksp,PETSC_TRUE);CHKERRQ(ierr);
> }
>
> /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> Solve the linear system
> - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
> /*
> Solve linear system
> */
> ierr = KSPSolve(ksp,b,x);CHKERRQ(ierr);
>
> /*
> View solver info; we could instead use the option -ksp_view to
> print this info to the screen at the conclusion of KSPSolve().
> */
> ierr = KSPView(ksp,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
>
> /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> Check solution and clean up
> - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
> /*
> Check the error
> */
> ierr = VecAXPY(x,-1.0,u);CHKERRQ(ierr);
> ierr = VecNorm(x,NORM_2,&norm);CHKERRQ(ierr);
> ierr = KSPGetIterationNumber(ksp,&its);CHKERRQ(ierr);
> ierr = PetscPrintf(PETSC_COMM_WORLD,"Norm of error %g, Iterations
> %D\n",(double)norm,its);CHKERRQ(ierr);
>
> /*
> Free work space. All PETSc objects should be destroyed when they
> are no longer needed.
> */
> ierr = VecDestroy(&x);CHKERRQ(ierr); ierr = VecDestroy(&u);CHKERRQ(ierr);
> ierr = VecDestroy(&b);CHKERRQ(ierr); ierr = MatDestroy(&A);CHKERRQ(ierr);
> ierr = KSPDestroy(&ksp);CHKERRQ(ierr);
>
> /*
> Always call PetscFinalize() before exiting a program. This routine
> - finalizes the PETSc libraries as well as MPI
> - provides summary and diagnostic information if certain runtime
> options are chosen (e.g., -log_view).
> */
> ierr = PetscFinalize();
> return ierr;
> }
>
> But I got the following error message:
>
> [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: configure using --with-debugging=yes, recompile, link, and
> run
> [0]PETSC ERROR: to get more information on the crash.
> [0]PETSC ERROR: --------------------- Error Message
> --------------------------------------------------------------
> [0]PETSC ERROR: Signal received
> [0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html
> for trouble shooting.
> [0]PETSC ERROR: Petsc Release Version 3.8.3, Dec, 09, 2017
> [0]PETSC ERROR: ./ex1 on a arch-linux2-c-opt named huq2090 by huq2090 Wed
> Jul 11 23:48:10 2018
> [0]PETSC ERROR: Configure options
> --prefix=/opt/moose/petsc-3.8.3/mpich-3.2_gcc-7.3.0-opt --download-hypre=1
> --with-ssl=0 --with-debugging=no --with-pic=1 --with-shared-libraries=1
> --with-cc=mpicc --with-cxx=mpicxx --with-fc=mpif90 --download-fblaslapack=1
> --download-metis=1 --download-parmetis=1 --download-superlu_dist=1
> --download-mumps=1 --download-scalapack=1 -CC=mpicc -CXX=mpicxx -FC=mpif90
> -F77=mpif77 -F90=mpif90 -CFLAGS="-fPIC -fopenmp" -CXXFLAGS="-fPIC -fopenmp"
> -FFLAGS="-fPIC -fopenmp" -FCFLAGS="-fPIC -fopenmp" -F90FLAGS="-fPIC
> -fopenmp" -F77FLAGS="-fPIC -fopenmp"
> [0]PETSC ERROR: #1 User provided function() line 0 in unknown file
> application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0
> [unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=59
> :
> system msg for write_line failure : Bad file descriptor
>
> And again, when I tried to solve the same code with another pc, I got
> different error message attached herewith as an attachment.
>
> Can you please suggest me about what to do.
>
> Thanks.
>
> Best,
> Huq
>
>
>
>
> --
>
> Fazlul Huq
> Graduate Research Assistant
> Department of Nuclear, Plasma & Radiological Engineering (NPRE)
> University of Illinois at Urbana-Champaign (UIUC)
> E-mail: huq2090 at gmail.com
>
--
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
https://www.cse.buffalo.edu/~knepley/ <http://www.caam.rice.edu/~mk51/>
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