[petsc-users] Problem of solving simple example in SNES in parallel
Mark F. Adams
mark.adams at columbia.edu
Fri Mar 22 11:47:06 CDT 2013
You seem to be running the serial code in FormFunction. You are setting all 3 equation but you only have 1 or 2 (probably with 2 processor) so you are overwriting memory with your f[2] = ….
You need to just set the equations that you have locally. You seem to call VecGetSizem call VecGetLocalSize and and figure out which equations you own and any set them.
On Mar 22, 2013, at 11:59 AM, Gaurish Telang <gaurish108 at gmail.com> wrote:
> Hello,
>
> I am trying to learn SNES to solve some non-linear equations.
>
> Consider the following non-linear equation which has solution (x,y,z) = (2,3,4)
>
> x^2 - y^2 + z^2 = 11
> xy + y^2 - 3z = 3
> x - xz + yz = 6
>
> For solving this, I am able to get the following simple code I wrote to work on 1 processor, but it seems to be failing for 2 or more processors.
>
> The errors I am getting when I run with two processors (mpirun -n 2 ./a.out -snes_monitor )
> Can anybody suggestions to fix this issue? It looks like a very trivial problem, but I am not sure what is wrong.
>
> (The code I wrote is after the error)
>
> %---------------------------------------------------
> The error is
> [0]PETSC ERROR: PetscMallocValidate: error detected at SNESComputeFunction() line 1889 in /home/gaurish108/Software/petsc-3.3-p5/src/snes/interface/snes.c
> [0]PETSC ERROR: Memory [id=0(16)] at address 0xa1933f0 is corrupted (probably write past end of array)
> [0]PETSC ERROR: Memory originally allocated in VecCreate_MPI_Private() line 193 in /home/gaurish108/Software/petsc-3.3-p5/src/vec/vec/impls/mpi/pbvec.c
> [1]PETSC ERROR: PetscMallocValidate: error detected at SNESComputeFunction() line 1889 in /home/gaurish108/Software/petsc-3.3-p5/src/snes/interface/snes.c
> [1]PETSC ERROR: Memory [id=0(16)] at address 0xa04c350 is corrupted (probably write past end of array)
> [1]PETSC ERROR: Memory originally allocated in VecCreate_MPI_Private() line 193 in /home/gaurish108/Software/petsc-3.3-p5/src/vec/vec/impls/mpi/pbvec.c
> [1]PETSC ERROR: --------------------- Error Message ------------------------------------
> [1]PETSC ERROR: Memory corruption!
> [1]PETSC ERROR: !
> [1]PETSC ERROR: ------------------------------------------------------------------------
> [1]PETSC ERROR: Petsc Release Version 3.3.0, Patch 5, Sat Dec 1 15:10:41 CST 2012
> [1]PETSC ERROR: See docs/changes/index.html for recent updates.
> [1]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
> [0]PETSC ERROR: --------------------- Error Message ------------------------------------
> [0]PETSC ERROR: Memory corruption!
> [0]PETSC ERROR: !
> [0]PETSC ERROR: ------------------------------------------------------------------------
> [0]PETSC ERROR: Petsc Release Version 3.3.0, Patch 5, Sat Dec 1 15:10:41 CST 2012
> [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: [1]PETSC ERROR: See docs/index.html for manual pages.
> [1]PETSC ERROR: ------------------------------------------------------------------------
> [1]PETSC ERROR: ./gaurish on a linux-gnu named gaurish108 by gaurish108 Fri Mar 22 11:58:01 2013
> [1]PETSC ERROR: Libraries linked from /home/gaurish108/Software/petsc-3.3-p5/linux-gnu-c-yes-debug-refblas/lib
> [1]PETSC ERROR: Configure run at Tue Feb 19 20:22:20 2013
> [1]PETSC ERROR: Configure options --download-f-blas-lapack=1
> [1]PETSC ERROR: ------------------------------------------------------------------------
> [1]PETSC ERROR: PetscMallocValidate() line 150 in /home/gaurish108/Software/petsc-3.3-p5/src/sys/memory/mtr.c
> [1]PETSC ERROR: SNESComputeFunction() line 1889 in /home/gaurish108/Software/petsc-3.3-p5/src/snes/interface/snes.c
> [1]PETSC ERROR: SNESSolve_LS() line 161 in /home/gaurish108/Software/petsc-3.3-p5/src/snes/impls/ls/ls.c
> [1]PETSC ERROR: SNESSolve() line 3536 in /home/gaurish108/Software/petsc-3.3-p5/src/snes/interface/snes.c
> [1]PETSC ERROR: main() line 69 in gaurish.c
> See docs/index.html for manual pages.
> [0]PETSC ERROR: ------------------------------------------------------------------------
> [0]PETSC ERROR: ./gaurish on a linux-gnu named gaurish108 by gaurish108 Fri Mar 22 11:58:01 2013
> [0]PETSC ERROR: Libraries linked from /home/gaurish108/Software/petsc-3.3-p5/linux-gnu-c-yes-debug-refblas/lib
> [0]PETSC ERROR: Configure run at Tue Feb 19 20:22:20 2013
> [0]PETSC ERROR: Configure options --download-f-blas-lapack=1
> [0]PETSC ERROR: ------------------------------------------------------------------------
> [0]PETSC ERROR: PetscMallocValidate() line 150 in /home/gaurish108/Software/petsc-3.3-p5/src/sys/memory/mtr.c
> [0]PETSC ERROR: SNESComputeFunction() line 1889 in /home/gaurish108/Software/petsc-3.3-p5/src/snes/interface/snes.c
> [0]PETSC ERROR: SNESSolve_LS() line 161 in /home/gaurish108/Software/petsc-3.3-p5/src/snes/impls/ls/ls.c
> [0]PETSC ERROR: SNESSolve() line 3536 in /home/gaurish108/Software/petsc-3.3-p5/src/snes/interface/snes.c
> [0]PETSC ERROR: main() line 69 in gaurish.c
> --------------------------------------------------------------------------
> MPI_ABORT was invoked on rank 1 in communicator MPI_COMM_WORLD
> with errorcode 78.
>
> NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
> You may or may not see output from other processes, depending on
> exactly when Open MPI kills them.
> --------------------------------------------------------------------------
> --------------------------------------------------------------------------
> mpirun has exited due to process rank 1 with PID 17933 on
> node gaurish108 exiting without calling "finalize". This may
> have caused other processes in the application to be
> terminated by signals sent by mpirun (as reported here).
> --------------------------------------------------------------------------
> [gaurish108:17931] 1 more process has sent help message help-mpi-api.txt / mpi-abort
> [gaurish108:17931] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages
>
>
>
> %------------------------------------------------------
> The code is
>
> static char help[] = "Shows solve a nonlinear equation using Newton iteration method.\n\n";
> #include <petscsnes.h>
> #include <math.h>
> #include <petscsys.h>
> #include <stdio.h>
> #include <petsctime.h>
> /* User-defined routines*/
> extern PetscErrorCode FormJacobian(SNES,Vec,Mat*,Mat*,MatStructure*,void*);
> extern PetscErrorCode FormFunction(SNES,Vec,Vec,void*);
> extern PetscErrorCode FormInitialGuess(Vec);
> extern PetscErrorCode Monitor(SNES,PetscInt,PetscReal,void *);
> #undef __FUNCT__
> #define __FUNCT__ "main"
> int main(int argc,char **argv)
> { SNES snes; /* SNES context */
> Vec x,r,F; /* vectors */
> Mat J; /* Jacobian matrix */
> PetscErrorCode ierr;
> PetscInt its,n = 3,i,maxit,maxf;
> PetscMPIInt size;
> PetscScalar iniRHS[3];
>
> PetscInitialize(&argc,&argv,(char *)0,help);
> ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRQ(ierr);
> ierr = PetscOptionsGetInt(PETSC_NULL,"-n",&n,PETSC_NULL);CHKERRQ(ierr);
> //-------------------------------------------------------------------------------
> ierr = SNESCreate(PETSC_COMM_WORLD,&snes);CHKERRQ(ierr);
>
> ierr = VecCreate(PETSC_COMM_WORLD,&x);CHKERRQ(ierr);
> ierr = VecSetSizes(x,PETSC_DECIDE,n);CHKERRQ(ierr);
> ierr = VecSetFromOptions(x);CHKERRQ(ierr);
> ierr = VecDuplicate(x,&r);CHKERRQ(ierr);
> ierr = VecDuplicate(x,&F);CHKERRQ(ierr);
>
> ierr = SNESSetFunction(snes,r,FormFunction,(void*)F);CHKERRQ(ierr);
>
> ierr = MatCreate(PETSC_COMM_WORLD,&J);CHKERRQ(ierr);
> ierr = MatSetSizes(J,PETSC_DECIDE,PETSC_DECIDE,n,n);CHKERRQ(ierr);
> ierr = MatSetFromOptions(J);CHKERRQ(ierr);
> ierr = MatSetUp(J);CHKERRQ(ierr);
> ierr = SNESSetJacobian(snes,J,J,FormJacobian,PETSC_NULL);CHKERRQ(ierr);
>
> ierr = SNESSetFromOptions(snes);CHKERRQ(ierr);
>
> // Set RHS of equation to F
> iniRHS[0]=11; iniRHS[1]=3; iniRHS[2]=6;
> for (i=0;i<n;i++)
> {
> ierr = VecSetValues(F,1,&i,&iniRHS[i],INSERT_VALUES);CHKERRQ(ierr);
> }
> // initial guess
> ierr = FormInitialGuess(x);CHKERRQ(ierr);
>
> ierr = SNESSolve(snes,PETSC_NULL,x);CHKERRQ(ierr); // The command to call to solve the equation.
>
> /* Free work space. All PETSc objects should be destroyed when they are no longer needed*/
> ierr = VecDestroy(&x);CHKERRQ(ierr); ierr = VecDestroy(&r);CHKERRQ(ierr);
> ierr = VecDestroy(&F);CHKERRQ(ierr);
> ierr = MatDestroy(&J);CHKERRQ(ierr); ierr = SNESDestroy(&snes);CHKERRQ(ierr);
> ierr = PetscFinalize();
> return 0;
> }
>
>
> #undef __FUNCT__
> #define __FUNCT__ "FormInitialGuess"
> /*
> FormInitialGuess - Computes initial guess.
>
> Input/Output Parameter:
> . x - the solution vector
> */
> PetscErrorCode FormInitialGuess(Vec x)
> {
> PetscErrorCode ierr;
> PetscScalar pfive =10;
> ierr = VecSet(x,pfive);CHKERRQ(ierr);
> return 0;
> }
>
>
> /* ------------------------------------------------------------------- */
> #undef __FUNCT__
> #define __FUNCT__ "FormFunction"
> /*
> FormFunction - Evaluates nonlinear function, F(x).
>
> Input Parameters:
> . snes - the SNES context
> . x - input vector
> . ctx - optional user-defined context, as set by SNESSetFunction()
>
> Output Parameter:
> . f - function vector
>
> Note:
> The user-defined context can contain any application-specific data
> needed for the function evaluation (such as various parameters, work
> vectors, and grid information). In this program the context is just
> a vector containing the right-hand-side of the discretized PDE.
> */
>
> PetscErrorCode FormFunction(SNES snes,Vec x,Vec f,void *ctx)
> {
> Vec g = (Vec)ctx;
> PetscScalar *xx,*ff,*gg;
> PetscErrorCode ierr;
> PetscInt n;
>
> /*
> Get pointers to vector data.
> - For default PETSc vectors, VecGetArray() returns a pointer to
> the data array. Otherwise, the routine is implementation dependent.
> - You MUST call VecRestoreArray() when you no longer need access to
> the array.
> */
> ierr = VecGetArray(x,&xx);CHKERRQ(ierr);
> ierr = VecGetArray(f,&ff);CHKERRQ(ierr);
> ierr = VecGetArray(g,&gg);CHKERRQ(ierr);
>
> /*
> Compute function
> */
> ierr = VecGetSize(x,&n);CHKERRQ(ierr);
>
> ff[0]=pow(xx[0],2)-pow(xx[1],2)+pow(xx[2],2)-gg[0];
> ff[1]=xx[0]*xx[1]+pow(xx[1],2)-3.0*xx[2]-gg[1];
> ff[2]=xx[0]-xx[0]*xx[2]+xx[1]*xx[2]-gg[2];
>
> /*
> Restore vectors
> */
> ierr = VecRestoreArray(x,&xx);CHKERRQ(ierr);
> ierr = VecRestoreArray(f,&ff);CHKERRQ(ierr);
> ierr = VecRestoreArray(g,&gg);CHKERRQ(ierr);
> return 0;
> }
>
>
>
> /* ------------------------------------------------------------------- */
> #undef __FUNCT__
> #define __FUNCT__ "FormJacobian"
> /*
> FormJacobian - Evaluates Jacobian matrix.
>
> Input Parameters:
> . snes - the SNES context
> . x - input vector
> . dummy - optional user-defined context (not used here)
>
> Output Parameters:
> . jac - Jacobian matrix
> . B - optionally different preconditioning matrix
> . flag - flag indicating matrix structure
> */
>
> PetscErrorCode FormJacobian(SNES snes,Vec x,Mat *jac,Mat *B,MatStructure*flag,void *dummy)
> {
> PetscScalar *xx,A[3];
> PetscErrorCode ierr;
> PetscInt i,n,j[3];
>
> /*
> Get pointer to vector data
> */
> ierr = VecGetArray(x,&xx);CHKERRQ(ierr);
>
> /*
> Compute Jacobian entries and insert into matrix.
> - Note that in this case we set all elements for a particular
> row at once.
> */
> ierr = VecGetSize(x,&n);CHKERRQ(ierr);
> j[0] = 0; j[1] = 1; j[2] = 2;
> /*set the first row of jacobian*/
> i=0;
> A[0]=2*xx[0]; A[1]=-2*xx[1]; A[2]=2*xx[2];
> ierr = MatSetValues(*jac,1,&i,3,j,A,INSERT_VALUES);CHKERRQ(ierr);
> /*set the second row of jacobian*/
> i=1;
> A[0]=xx[1]; A[1]=xx[0]+2*xx[1]; A[2]=-3.0;
> ierr = MatSetValues(*jac,1,&i,3,j,A,INSERT_VALUES);CHKERRQ(ierr);
> /*set the third row of jacobian*/
> i=2;
> A[0]=1-xx[2]; A[1]=xx[2]; A[2]=-xx[0]+xx[1];
> ierr = MatSetValues(*jac,1,&i,3,j,A,INSERT_VALUES);CHKERRQ(ierr);
>
>
>
> ierr = VecRestoreArray(x,&xx);CHKERRQ(ierr);
>
> /*
> Assemble matrix
> */
> ierr = MatAssemblyBegin(*jac,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
> ierr = MatAssemblyEnd(*jac,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
>
> return 0;
> }
>
>
>
>
>
>
More information about the petsc-users
mailing list