Beispiel #1
0
/*@
   MatSubMatrixUpdate - Updates a submatrix

   Collective on Mat

   Input Parameters:
+  N - submatrix to update
.  A - full matrix in the submatrix
.  isrow - rows in the update (same as the first time the submatrix was created)
-  iscol - columns in the update (same as the first time the submatrix was created)

   Level: developer

   Notes:
   Most will use MatGetSubMatrix which provides a more efficient representation if it is available.

.seealso: MatGetSubMatrix(), MatCreateSubMatrix()
@*/
PetscErrorCode  MatSubMatrixUpdate(Mat N,Mat A,IS isrow,IS iscol)
{
  PetscErrorCode ierr;
  PetscBool      flg;
  Mat_SubMatrix  *Na;

  PetscFunctionBegin;
  PetscValidHeaderSpecific(N,MAT_CLASSID,1);
  PetscValidHeaderSpecific(A,MAT_CLASSID,2);
  PetscValidHeaderSpecific(isrow,IS_CLASSID,3);
  PetscValidHeaderSpecific(iscol,IS_CLASSID,4);
  ierr = PetscObjectTypeCompare((PetscObject)N,MATSUBMATRIX,&flg);CHKERRQ(ierr);
  if (!flg) SETERRQ(PetscObjectComm((PetscObject)A),PETSC_ERR_ARG_WRONG,"Matrix has wrong type");

  Na   = (Mat_SubMatrix*)N->data;
  ierr = ISEqual(isrow,Na->isrow,&flg);CHKERRQ(ierr);
  if (!flg) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_INCOMP,"Cannot update submatrix with different row indices");
  ierr = ISEqual(iscol,Na->iscol,&flg);CHKERRQ(ierr);
  if (!flg) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_INCOMP,"Cannot update submatrix with different column indices");

  ierr  = PetscObjectReference((PetscObject)A);CHKERRQ(ierr);
  ierr  = MatDestroy(&Na->A);CHKERRQ(ierr);
  Na->A = A;

  Na->scale = 1.0;
  ierr      = VecDestroy(&Na->left);CHKERRQ(ierr);
  ierr      = VecDestroy(&Na->right);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}
Beispiel #2
0
int main(int argc,char **argv)
{
  PetscErrorCode         ierr;
  PetscInt               n = 3,ix[2][3] = {{3,5,4},{1,7,9}};
  IS                     isx,il;
  PetscMPIInt            size,rank;
  PetscViewer            vx,vl;
  PetscBool              equal;

  ierr = PetscInitialize(&argc,&argv,(char*)0,help);CHKERRQ(ierr);
  ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr);
  ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRQ(ierr);
  if (size > 2) SETERRQ(PETSC_COMM_WORLD,PETSC_ERR_ARG_SIZ,"Example only works with one or two processes");
  ierr = ISCreateGeneral(PETSC_COMM_WORLD,n,ix[rank],PETSC_COPY_VALUES,&isx);CHKERRQ(ierr);
  ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,"testfile",FILE_MODE_WRITE,&vx);CHKERRQ(ierr);
  ierr = ISView(isx,vx);CHKERRQ(ierr);
  ierr = PetscViewerDestroy(&vx);CHKERRQ(ierr);

  ierr = ISCreate(PETSC_COMM_WORLD,&il);CHKERRQ(ierr);
  ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,"testfile",FILE_MODE_READ,&vl);CHKERRQ(ierr);
  ierr = ISLoad(il,vl);CHKERRQ(ierr);
  ierr = PetscViewerDestroy(&vl);CHKERRQ(ierr);

  ierr = ISEqual(il,isx,&equal);CHKERRQ(ierr);
  if (!equal) SETERRQ(PETSC_COMM_WORLD,PETSC_ERR_PLIB,"Index set loaded from file does not match index set to file");
  ierr = ISDestroy(&il);CHKERRQ(ierr);
  ierr = ISDestroy(&isx);CHKERRQ(ierr);
  ierr = PetscFinalize();
  return ierr;
}
Beispiel #3
0
PetscErrorCode MatEqual_SMF(Mat A,Mat B,PetscBool *flg)
{
  PetscErrorCode    ierr;
  MatSubMatFreeCtx  ctx1,ctx2;
  PetscBool         flg1,flg2,flg3;

  PetscFunctionBegin;
  ierr = MatShellGetContext(A,(void **)&ctx1);CHKERRQ(ierr);
  ierr = MatShellGetContext(B,(void **)&ctx2);CHKERRQ(ierr);
  ierr = ISEqual(ctx1->Rows,ctx2->Rows,&flg2);CHKERRQ(ierr);
  ierr = ISEqual(ctx1->Cols,ctx2->Cols,&flg3);CHKERRQ(ierr);
  if (flg2==PETSC_FALSE || flg3==PETSC_FALSE){
    *flg=PETSC_FALSE;
  } else {
    ierr = MatEqual(ctx1->A,ctx2->A,&flg1);CHKERRQ(ierr);
    if (flg1==PETSC_FALSE){ *flg=PETSC_FALSE;}
    else { *flg=PETSC_TRUE;}
  }
  PetscFunctionReturn(0);
}
Beispiel #4
0
static PetscErrorCode  VecGetSubVector_Nest(Vec X,IS is,Vec *x)
{
  Vec_Nest       *bx = (Vec_Nest*)X->data;
  PetscInt       i;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  *x = NULL;
  for (i=0; i<bx->nb; i++) {
    PetscBool issame = PETSC_FALSE;
    ierr = ISEqual(is,bx->is[i],&issame);CHKERRQ(ierr);
    if (issame) {
      *x   = bx->v[i];
      ierr = PetscObjectReference((PetscObject)(*x));CHKERRQ(ierr);
      break;
    }
  }
  if (!*x) SETERRQ(PetscObjectComm((PetscObject)is),PETSC_ERR_ARG_OUTOFRANGE,"Index set not found in nested Vec");
  PetscFunctionReturn(0);
}
Beispiel #5
0
int main(int argc,char **args)
{
    Mat            C;
    PetscErrorCode ierr;
    PetscInt       i,m = 2,N,M,idx[4],Nsub1,Nsub2,ol=1,x1,x2;
    PetscScalar    Ke[16];
    PetscReal      x,y,h;
    IS             *is1,*is2;
    PetscBool      flg;

    PetscInitialize(&argc,&args,(char *)0,help);
    ierr = PetscOptionsGetInt(PETSC_NULL,"-m",&m,PETSC_NULL);
    CHKERRQ(ierr);
    N = (m+1)*(m+1); /* dimension of matrix */
    M = m*m; /* number of elements */
    h = 1.0/m;       /* mesh width */
    x1= (m+1)/2;
    x2= x1;
    ierr = PetscOptionsGetInt(PETSC_NULL,"-x1",&x1,PETSC_NULL);
    CHKERRQ(ierr);
    ierr = PetscOptionsGetInt(PETSC_NULL,"-x2",&x2,PETSC_NULL);
    CHKERRQ(ierr);
    /* create stiffness matrix */
    ierr = MatCreateSeqAIJ(PETSC_COMM_SELF,N,N,9,PETSC_NULL,&C);
    CHKERRQ(ierr);

    /* forms the element stiffness for the Laplacian */
    ierr = FormElementStiffness(h*h,Ke);
    CHKERRQ(ierr);
    for (i=0; i<M; i++) {
        /* location of lower left corner of element */
        x = h*(i % m);
        y = h*(i/m);
        /* node numbers for the four corners of element */
        idx[0] = (m+1)*(i/m) + (i % m);
        idx[1] = idx[0]+1;
        idx[2] = idx[1] + m + 1;
        idx[3] = idx[2] - 1;
        ierr = MatSetValues(C,4,idx,4,idx,Ke,ADD_VALUES);
        CHKERRQ(ierr);
    }
    ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);
    CHKERRQ(ierr);
    ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);
    CHKERRQ(ierr);

    for (ol=0; ol<m+2; ++ol) {

        ierr = PCASMCreateSubdomains2D(m+1,m+1,x1,x2,1,0,&Nsub1,&is1);
        CHKERRQ(ierr);
        ierr = MatIncreaseOverlap(C,Nsub1,is1,ol);
        CHKERRQ(ierr);
        ierr = PCASMCreateSubdomains2D(m+1,m+1,x1,x2,1,ol,&Nsub2,&is2);
        CHKERRQ(ierr);

        ierr = PetscPrintf(PETSC_COMM_SELF,"flg == 1 => both index sets are same\n");
        CHKERRQ(ierr);
        if(Nsub1 != Nsub2) {
            ierr = PetscPrintf(PETSC_COMM_SELF,"Error: No of indes sets don't match\n");
            CHKERRQ(ierr);
        }

        for (i=0; i<Nsub1; ++i) {
            ierr = ISEqual(is1[i],is2[i],&flg);
            CHKERRQ(ierr);
            ierr = PetscPrintf(PETSC_COMM_SELF,"i =  %D,flg = %d \n",i,(int)flg);
            CHKERRQ(ierr);

        }
        for (i=0; i<Nsub1; ++i) {
            ierr = ISDestroy(&&is1[i]);
            CHKERRQ(ierr);
        }
        for (i=0; i<Nsub2; ++i) {
            ierr = ISDestroy(&&is2[i]);
            CHKERRQ(ierr);
        }


        ierr = PetscFree(is1);
        CHKERRQ(ierr);
        ierr = PetscFree(is2);
        CHKERRQ(ierr);
    }
    ierr = MatDestroy(&C);
    CHKERRQ(ierr);
    ierr = PetscFinalize();
    return 0;
}
Beispiel #6
0
int main(int argc,char **argv)
{
  PetscMPIInt    rank,size;
  PetscInt       i,n,*indices;
  const PetscInt *ii;
  IS             is,newis;
  PetscBool      flg;
  PetscErrorCode ierr;

  ierr = PetscInitialize(&argc,&argv,(char*)0,help);if (ierr) return ierr;
  ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr);
  ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRQ(ierr);

  /*
     Test IS of size 0
  */
  ierr = ISCreateGeneral(PETSC_COMM_SELF,0,&n,PETSC_COPY_VALUES,&is);CHKERRQ(ierr);
  ierr = ISGetSize(is,&n);CHKERRQ(ierr);
  if (n != 0) SETERRQ(PETSC_COMM_SELF,1,"ISGetSize");
  ierr = ISDestroy(&is);CHKERRQ(ierr);

  /*
     Create large IS and test ISGetIndices()
  */
  n    = 10000 + rank;
  ierr = PetscMalloc1(n,&indices);CHKERRQ(ierr);
  for (i=0; i<n; i++) indices[i] = rank + i;
  ierr = ISCreateGeneral(PETSC_COMM_SELF,n,indices,PETSC_COPY_VALUES,&is);CHKERRQ(ierr);
  ierr = ISGetIndices(is,&ii);CHKERRQ(ierr);
  for (i=0; i<n; i++) {
    if (ii[i] != indices[i]) SETERRQ(PETSC_COMM_SELF,1,"ISGetIndices");
  }
  ierr = ISRestoreIndices(is,&ii);CHKERRQ(ierr);

  /*
     Check identity and permutation
  */
  ierr = ISPermutation(is,&flg);CHKERRQ(ierr);
  if (flg) SETERRQ(PETSC_COMM_SELF,1,"ISPermutation");
  ierr = ISIdentity(is,&flg);CHKERRQ(ierr);
  if (!flg) SETERRQ(PETSC_COMM_SELF,1,"ISIdentity");
  ierr = ISSetPermutation(is);CHKERRQ(ierr);
  ierr = ISSetIdentity(is);CHKERRQ(ierr);
  ierr = ISPermutation(is,&flg);CHKERRQ(ierr);
  if (!flg) SETERRQ(PETSC_COMM_SELF,1,"ISPermutation");
  ierr = ISIdentity(is,&flg);CHKERRQ(ierr);
  if (!flg) SETERRQ(PETSC_COMM_SELF,1,"ISIdentity");

  /*
     Check equality of index sets
  */
  ierr = ISEqual(is,is,&flg);CHKERRQ(ierr);
  if (!flg) SETERRQ(PETSC_COMM_SELF,1,"ISEqual");

  /*
     Sorting
  */
  ierr = ISSort(is);CHKERRQ(ierr);
  ierr = ISSorted(is,&flg);CHKERRQ(ierr);
  if (!flg) SETERRQ(PETSC_COMM_SELF,1,"ISSort");

  /*
     Thinks it is a different type?
  */
  ierr = PetscObjectTypeCompare((PetscObject)is,ISSTRIDE,&flg);CHKERRQ(ierr);
  if (flg) SETERRQ(PETSC_COMM_SELF,1,"ISStride");
  ierr = PetscObjectTypeCompare((PetscObject)is,ISBLOCK,&flg);CHKERRQ(ierr);
  if (flg) SETERRQ(PETSC_COMM_SELF,1,"ISBlock");

  ierr = ISDestroy(&is);CHKERRQ(ierr);

  /*
     Inverting permutation
  */
  for (i=0; i<n; i++) indices[i] = n - i - 1;
  ierr = ISCreateGeneral(PETSC_COMM_SELF,n,indices,PETSC_COPY_VALUES,&is);CHKERRQ(ierr);
  ierr = PetscFree(indices);CHKERRQ(ierr);
  ierr = ISSetPermutation(is);CHKERRQ(ierr);
  ierr = ISInvertPermutation(is,PETSC_DECIDE,&newis);CHKERRQ(ierr);
  ierr = ISGetIndices(newis,&ii);CHKERRQ(ierr);
  for (i=0; i<n; i++) {
    if (ii[i] != n - i - 1) SETERRQ(PETSC_COMM_SELF,1,"ISInvertPermutation");
  }
  ierr = ISRestoreIndices(newis,&ii);CHKERRQ(ierr);
  ierr = ISDestroy(&newis);CHKERRQ(ierr);
  ierr = ISDestroy(&is);CHKERRQ(ierr);
  ierr = PetscFinalize();
  return ierr;
}
Beispiel #7
0
PetscErrorCode SNESSolve_VINEWTONRSLS(SNES snes)
{
  SNES_VINEWTONRSLS  *vi = (SNES_VINEWTONRSLS*)snes->data;
  PetscErrorCode     ierr;
  PetscInt           maxits,i,lits;
  PetscBool          lssucceed;
  MatStructure       flg = DIFFERENT_NONZERO_PATTERN;
  PetscReal          fnorm,gnorm,xnorm=0,ynorm;
  Vec                Y,X,F;
  KSPConvergedReason kspreason;

  PetscFunctionBegin;

  snes->numFailures            = 0;
  snes->numLinearSolveFailures = 0;
  snes->reason                 = SNES_CONVERGED_ITERATING;

  maxits        = snes->max_its;        /* maximum number of iterations */
  X             = snes->vec_sol;        /* solution vector */
  F             = snes->vec_func;       /* residual vector */
  Y             = snes->work[0];        /* work vectors */

  ierr = SNESLineSearchSetVIFunctions(snes->linesearch, SNESVIProjectOntoBounds, SNESVIComputeInactiveSetFnorm);CHKERRQ(ierr);
  ierr = SNESLineSearchSetVecs(snes->linesearch, X, PETSC_NULL, PETSC_NULL, PETSC_NULL, PETSC_NULL);CHKERRQ(ierr);
  ierr = SNESLineSearchSetUp(snes->linesearch);CHKERRQ(ierr);

  ierr = PetscObjectTakeAccess(snes);CHKERRQ(ierr);
  snes->iter = 0;
  snes->norm = 0.0;
  ierr = PetscObjectGrantAccess(snes);CHKERRQ(ierr);

  ierr = SNESVIProjectOntoBounds(snes,X);CHKERRQ(ierr);
  ierr = SNESComputeFunction(snes,X,F);CHKERRQ(ierr);
  if (snes->domainerror) {
    snes->reason = SNES_DIVERGED_FUNCTION_DOMAIN;
    PetscFunctionReturn(0);
  }
  ierr = SNESVIComputeInactiveSetFnorm(snes,F,X,&fnorm);CHKERRQ(ierr);
  ierr = VecNormBegin(X,NORM_2,&xnorm);CHKERRQ(ierr);        /* xnorm <- ||x||  */
  ierr = VecNormEnd(X,NORM_2,&xnorm);CHKERRQ(ierr);
  if (PetscIsInfOrNanReal(fnorm)) SETERRQ(((PetscObject)X)->comm,PETSC_ERR_FP,"User provided compute function generated a Not-a-Number");

  ierr = PetscObjectTakeAccess(snes);CHKERRQ(ierr);
  snes->norm = fnorm;
  ierr = PetscObjectGrantAccess(snes);CHKERRQ(ierr);
  SNESLogConvHistory(snes,fnorm,0);
  ierr = SNESMonitor(snes,0,fnorm);CHKERRQ(ierr);

  /* set parameter for default relative tolerance convergence test */
  snes->ttol = fnorm*snes->rtol;
  /* test convergence */
  ierr = (*snes->ops->converged)(snes,0,0.0,0.0,fnorm,&snes->reason,snes->cnvP);CHKERRQ(ierr);
  if (snes->reason) PetscFunctionReturn(0);


  for (i=0; i<maxits; i++) {

    IS         IS_act,IS_inact; /* _act -> active set _inact -> inactive set */
    IS         IS_redact; /* redundant active set */
    VecScatter scat_act,scat_inact;
    PetscInt   nis_act,nis_inact;
    Vec        Y_act,Y_inact,F_inact;
    Mat        jac_inact_inact,prejac_inact_inact;
    PetscBool  isequal;

    /* Call general purpose update function */
    if (snes->ops->update) {
      ierr = (*snes->ops->update)(snes, snes->iter);CHKERRQ(ierr);
    }
    ierr = SNESComputeJacobian(snes,X,&snes->jacobian,&snes->jacobian_pre,&flg);CHKERRQ(ierr);


        /* Create active and inactive index sets */

    /*original
    ierr = SNESVICreateIndexSets_RS(snes,X,F,&IS_act,&IS_inact);CHKERRQ(ierr);
     */
    ierr = SNESVIGetActiveSetIS(snes,X,F,&IS_act);CHKERRQ(ierr);

    if (vi->checkredundancy) {
      (*vi->checkredundancy)(snes,IS_act,&IS_redact,vi->ctxP);CHKERRQ(ierr);
      if (IS_redact){
        ierr = ISSort(IS_redact);CHKERRQ(ierr);
        ierr = ISComplement(IS_redact,X->map->rstart,X->map->rend,&IS_inact);CHKERRQ(ierr);
        ierr = ISDestroy(&IS_redact);CHKERRQ(ierr);
      }
      else {
        ierr = ISComplement(IS_act,X->map->rstart,X->map->rend,&IS_inact);CHKERRQ(ierr);
      }
    } else {
      ierr = ISComplement(IS_act,X->map->rstart,X->map->rend,&IS_inact);CHKERRQ(ierr);
    }


    /* Create inactive set submatrix */
    ierr = MatGetSubMatrix(snes->jacobian,IS_inact,IS_inact,MAT_INITIAL_MATRIX,&jac_inact_inact);CHKERRQ(ierr);

    if (0) {                    /* Dead code (temporary developer hack) */
      IS keptrows;
      ierr = MatFindNonzeroRows(jac_inact_inact,&keptrows);CHKERRQ(ierr);
      if (keptrows) {
        PetscInt       cnt,*nrows,k;
        const PetscInt *krows,*inact;
        PetscInt       rstart=jac_inact_inact->rmap->rstart;

        ierr = MatDestroy(&jac_inact_inact);CHKERRQ(ierr);
        ierr = ISDestroy(&IS_act);CHKERRQ(ierr);

        ierr = ISGetLocalSize(keptrows,&cnt);CHKERRQ(ierr);
        ierr = ISGetIndices(keptrows,&krows);CHKERRQ(ierr);
        ierr = ISGetIndices(IS_inact,&inact);CHKERRQ(ierr);
        ierr = PetscMalloc(cnt*sizeof(PetscInt),&nrows);CHKERRQ(ierr);
        for (k=0; k<cnt; k++) {
          nrows[k] = inact[krows[k]-rstart];
        }
        ierr = ISRestoreIndices(keptrows,&krows);CHKERRQ(ierr);
        ierr = ISRestoreIndices(IS_inact,&inact);CHKERRQ(ierr);
        ierr = ISDestroy(&keptrows);CHKERRQ(ierr);
        ierr = ISDestroy(&IS_inact);CHKERRQ(ierr);

        ierr = ISCreateGeneral(((PetscObject)snes)->comm,cnt,nrows,PETSC_OWN_POINTER,&IS_inact);CHKERRQ(ierr);
        ierr = ISComplement(IS_inact,F->map->rstart,F->map->rend,&IS_act);CHKERRQ(ierr);
        ierr = MatGetSubMatrix(snes->jacobian,IS_inact,IS_inact,MAT_INITIAL_MATRIX,&jac_inact_inact);CHKERRQ(ierr);
      }
    }
    ierr = DMSetVI(snes->dm,IS_inact);CHKERRQ(ierr);
    /* remove later */

    /*
  ierr = VecView(vi->xu,PETSC_VIEWER_BINARY_(((PetscObject)(vi->xu))->comm));CHKERRQ(ierr);
  ierr = VecView(vi->xl,PETSC_VIEWER_BINARY_(((PetscObject)(vi->xl))->comm));CHKERRQ(ierr);
  ierr = VecView(X,PETSC_VIEWER_BINARY_(((PetscObject)X)->comm));CHKERRQ(ierr);
  ierr = VecView(F,PETSC_VIEWER_BINARY_(((PetscObject)F)->comm));CHKERRQ(ierr);
  ierr = ISView(IS_inact,PETSC_VIEWER_BINARY_(((PetscObject)IS_inact)->comm));CHKERRQ(ierr);
     */

    /* Get sizes of active and inactive sets */
    ierr = ISGetLocalSize(IS_act,&nis_act);CHKERRQ(ierr);
    ierr = ISGetLocalSize(IS_inact,&nis_inact);CHKERRQ(ierr);

    /* Create active and inactive set vectors */
    ierr = SNESCreateSubVectors_VINEWTONRSLS(snes,nis_inact,&F_inact);CHKERRQ(ierr);
    ierr = SNESCreateSubVectors_VINEWTONRSLS(snes,nis_act,&Y_act);CHKERRQ(ierr);
    ierr = SNESCreateSubVectors_VINEWTONRSLS(snes,nis_inact,&Y_inact);CHKERRQ(ierr);

    /* Create scatter contexts */
    ierr = VecScatterCreate(Y,IS_act,Y_act,PETSC_NULL,&scat_act);CHKERRQ(ierr);
    ierr = VecScatterCreate(Y,IS_inact,Y_inact,PETSC_NULL,&scat_inact);CHKERRQ(ierr);

    /* Do a vec scatter to active and inactive set vectors */
    ierr = VecScatterBegin(scat_inact,F,F_inact,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr);
    ierr = VecScatterEnd(scat_inact,F,F_inact,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr);

    ierr = VecScatterBegin(scat_act,Y,Y_act,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr);
    ierr = VecScatterEnd(scat_act,Y,Y_act,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr);

    ierr = VecScatterBegin(scat_inact,Y,Y_inact,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr);
    ierr = VecScatterEnd(scat_inact,Y,Y_inact,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr);

    /* Active set direction = 0 */
    ierr = VecSet(Y_act,0);CHKERRQ(ierr);
    if (snes->jacobian != snes->jacobian_pre) {
      ierr = MatGetSubMatrix(snes->jacobian_pre,IS_inact,IS_inact,MAT_INITIAL_MATRIX,&prejac_inact_inact);CHKERRQ(ierr);
    } else prejac_inact_inact = jac_inact_inact;

    ierr = ISEqual(vi->IS_inact_prev,IS_inact,&isequal);CHKERRQ(ierr);
    if (!isequal) {
      ierr = SNESVIResetPCandKSP(snes,jac_inact_inact,prejac_inact_inact);CHKERRQ(ierr);
      flg  = DIFFERENT_NONZERO_PATTERN;
    }

    /*      ierr = ISView(IS_inact,0);CHKERRQ(ierr); */
    /*      ierr = ISView(IS_act,0);CHKERRQ(ierr);*/
    /*      ierr = MatView(snes->jacobian_pre,0); */



    ierr = KSPSetOperators(snes->ksp,jac_inact_inact,prejac_inact_inact,flg);CHKERRQ(ierr);
    ierr = KSPSetUp(snes->ksp);CHKERRQ(ierr);
    {
      PC        pc;
      PetscBool flg;
      ierr = KSPGetPC(snes->ksp,&pc);CHKERRQ(ierr);
      ierr = PetscObjectTypeCompare((PetscObject)pc,PCFIELDSPLIT,&flg);CHKERRQ(ierr);
      if (flg) {
        KSP      *subksps;
        ierr = PCFieldSplitGetSubKSP(pc,PETSC_NULL,&subksps);CHKERRQ(ierr);
        ierr = KSPGetPC(subksps[0],&pc);CHKERRQ(ierr);
        ierr = PetscFree(subksps);CHKERRQ(ierr);
        ierr = PetscObjectTypeCompare((PetscObject)pc,PCBJACOBI,&flg);CHKERRQ(ierr);
        if (flg) {
          PetscInt       n,N = 101*101,j,cnts[3] = {0,0,0};
          const PetscInt *ii;

          ierr = ISGetSize(IS_inact,&n);CHKERRQ(ierr);
          ierr = ISGetIndices(IS_inact,&ii);CHKERRQ(ierr);
          for (j=0; j<n; j++) {
            if (ii[j] < N) cnts[0]++;
            else if (ii[j] < 2*N) cnts[1]++;
            else if (ii[j] < 3*N) cnts[2]++;
          }
          ierr = ISRestoreIndices(IS_inact,&ii);CHKERRQ(ierr);

          ierr = PCBJacobiSetTotalBlocks(pc,3,cnts);CHKERRQ(ierr);
        }
      }
    }

    ierr = SNES_KSPSolve(snes,snes->ksp,F_inact,Y_inact);CHKERRQ(ierr);
    ierr = KSPGetConvergedReason(snes->ksp,&kspreason);CHKERRQ(ierr);
    if (kspreason < 0) {
      if (++snes->numLinearSolveFailures >= snes->maxLinearSolveFailures) {
        ierr = PetscInfo2(snes,"iter=%D, number linear solve failures %D greater than current SNES allowed, stopping solve\n",snes->iter,snes->numLinearSolveFailures);CHKERRQ(ierr);
        snes->reason = SNES_DIVERGED_LINEAR_SOLVE;
        break;
      }
     }

    ierr = VecScatterBegin(scat_act,Y_act,Y,INSERT_VALUES,SCATTER_REVERSE);CHKERRQ(ierr);
    ierr = VecScatterEnd(scat_act,Y_act,Y,INSERT_VALUES,SCATTER_REVERSE);CHKERRQ(ierr);
    ierr = VecScatterBegin(scat_inact,Y_inact,Y,INSERT_VALUES,SCATTER_REVERSE);CHKERRQ(ierr);
    ierr = VecScatterEnd(scat_inact,Y_inact,Y,INSERT_VALUES,SCATTER_REVERSE);CHKERRQ(ierr);

    ierr = VecDestroy(&F_inact);CHKERRQ(ierr);
    ierr = VecDestroy(&Y_act);CHKERRQ(ierr);
    ierr = VecDestroy(&Y_inact);CHKERRQ(ierr);
    ierr = VecScatterDestroy(&scat_act);CHKERRQ(ierr);
    ierr = VecScatterDestroy(&scat_inact);CHKERRQ(ierr);
    ierr = ISDestroy(&IS_act);CHKERRQ(ierr);
    if (!isequal) {
      ierr = ISDestroy(&vi->IS_inact_prev);CHKERRQ(ierr);
      ierr = ISDuplicate(IS_inact,&vi->IS_inact_prev);CHKERRQ(ierr);
    }
    ierr = ISDestroy(&IS_inact);CHKERRQ(ierr);
    ierr = MatDestroy(&jac_inact_inact);CHKERRQ(ierr);
    if (snes->jacobian != snes->jacobian_pre) {
      ierr = MatDestroy(&prejac_inact_inact);CHKERRQ(ierr);
    }
    ierr = KSPGetIterationNumber(snes->ksp,&lits);CHKERRQ(ierr);
    snes->linear_its += lits;
    ierr = PetscInfo2(snes,"iter=%D, linear solve iterations=%D\n",snes->iter,lits);CHKERRQ(ierr);
    /*
    if (snes->ops->precheck) {
      PetscBool changed_y = PETSC_FALSE;
      ierr = (*snes->ops->precheck)(snes,X,Y,snes->precheck,&changed_y);CHKERRQ(ierr);
    }

    if (PetscLogPrintInfo){
      ierr = SNESVICheckResidual_Private(snes,snes->jacobian,F,Y,G,W);CHKERRQ(ierr);
    }
    */
    /* Compute a (scaled) negative update in the line search routine:
         Y <- X - lambda*Y
       and evaluate G = function(Y) (depends on the line search).
    */
    ierr = VecCopy(Y,snes->vec_sol_update);CHKERRQ(ierr);
    ynorm = 1; gnorm = fnorm;
    ierr = SNESLineSearchApply(snes->linesearch, X, F, &gnorm, Y);CHKERRQ(ierr);
    ierr = SNESLineSearchGetNorms(snes->linesearch, &xnorm, &gnorm, &ynorm);CHKERRQ(ierr);
    ierr = PetscInfo4(snes,"fnorm=%18.16e, gnorm=%18.16e, ynorm=%18.16e, lssucceed=%d\n",(double)fnorm,(double)gnorm,(double)ynorm,(int)lssucceed);CHKERRQ(ierr);
    if (snes->reason == SNES_DIVERGED_FUNCTION_COUNT) break;
    if (snes->domainerror) {
      snes->reason = SNES_DIVERGED_FUNCTION_DOMAIN;
      ierr = DMDestroyVI(snes->dm);CHKERRQ(ierr);
      PetscFunctionReturn(0);
    }
    ierr = SNESLineSearchGetSuccess(snes->linesearch, &lssucceed);CHKERRQ(ierr);

    if (!lssucceed) {
      if (++snes->numFailures >= snes->maxFailures) {
        PetscBool ismin;
        snes->reason = SNES_DIVERGED_LINE_SEARCH;
        ierr = SNESVICheckLocalMin_Private(snes,snes->jacobian,F,X,gnorm,&ismin);CHKERRQ(ierr);
        if (ismin) snes->reason = SNES_DIVERGED_LOCAL_MIN;
        break;
      }
    }
    /* Update function and solution vectors */
    fnorm = gnorm;
    /* Monitor convergence */
    ierr = PetscObjectTakeAccess(snes);CHKERRQ(ierr);
    snes->iter = i+1;
    snes->norm = fnorm;
    ierr = PetscObjectGrantAccess(snes);CHKERRQ(ierr);
    SNESLogConvHistory(snes,snes->norm,lits);
    ierr = SNESMonitor(snes,snes->iter,snes->norm);CHKERRQ(ierr);
    /* Test for convergence, xnorm = || X || */
    if (snes->ops->converged != SNESSkipConverged) { ierr = VecNorm(X,NORM_2,&xnorm);CHKERRQ(ierr); }
    ierr = (*snes->ops->converged)(snes,snes->iter,xnorm,ynorm,fnorm,&snes->reason,snes->cnvP);CHKERRQ(ierr);
    if (snes->reason) break;
  }
  ierr = DMDestroyVI(snes->dm);CHKERRQ(ierr);
  if (i == maxits) {
    ierr = PetscInfo1(snes,"Maximum number of iterations has been reached: %D\n",maxits);CHKERRQ(ierr);
    if (!snes->reason) snes->reason = SNES_DIVERGED_MAX_IT;
  }
  PetscFunctionReturn(0);
}
Beispiel #8
0
int main(int argc,char **args)
{
  Mat            A,Atrans,sA,*submatA,*submatsA;
  PetscErrorCode ierr;
  PetscMPIInt    size,rank;
  PetscInt       bs=1,mbs=10,ov=1,i,j,k,*rows,*cols,nd=2,*idx,rstart,rend,sz,M,N,Mbs;
  PetscScalar    *vals,rval,one=1.0;
  IS             *is1,*is2;
  PetscRandom    rand;
  PetscBool      flg,TestOverlap,TestSubMat,TestAllcols,test_sorted=PETSC_FALSE;
  PetscInt       vid = -1;
#if defined(PETSC_USE_LOG)
  PetscLogStage  stages[2];
#endif

  ierr = PetscInitialize(&argc,&args,(char*)0,help);if (ierr) return ierr;
  ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRQ(ierr);
  ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr);

  ierr = PetscOptionsGetInt(NULL,NULL,"-mat_block_size",&bs,NULL);CHKERRQ(ierr);
  ierr = PetscOptionsGetInt(NULL,NULL,"-mat_mbs",&mbs,NULL);CHKERRQ(ierr);
  ierr = PetscOptionsGetInt(NULL,NULL,"-ov",&ov,NULL);CHKERRQ(ierr);
  ierr = PetscOptionsGetInt(NULL,NULL,"-nd",&nd,NULL);CHKERRQ(ierr);
  ierr = PetscOptionsGetInt(NULL,NULL,"-view_id",&vid,NULL);CHKERRQ(ierr);
  ierr = PetscOptionsHasName(NULL,NULL, "-test_overlap", &TestOverlap);CHKERRQ(ierr);
  ierr = PetscOptionsHasName(NULL,NULL, "-test_submat", &TestSubMat);CHKERRQ(ierr);
  ierr = PetscOptionsHasName(NULL,NULL, "-test_allcols", &TestAllcols);CHKERRQ(ierr);
  ierr = PetscOptionsGetBool(NULL,NULL,"-test_sorted",&test_sorted,NULL);CHKERRQ(ierr);

  ierr = MatCreate(PETSC_COMM_WORLD,&A);CHKERRQ(ierr);
  ierr = MatSetSizes(A,mbs*bs,mbs*bs,PETSC_DECIDE,PETSC_DECIDE);CHKERRQ(ierr);
  ierr = MatSetType(A,MATBAIJ);CHKERRQ(ierr);
  ierr = MatSeqBAIJSetPreallocation(A,bs,PETSC_DEFAULT,NULL);CHKERRQ(ierr);
  ierr = MatMPIBAIJSetPreallocation(A,bs,PETSC_DEFAULT,NULL,PETSC_DEFAULT,NULL);CHKERRQ(ierr);

  ierr = PetscRandomCreate(PETSC_COMM_WORLD,&rand);CHKERRQ(ierr);
  ierr = PetscRandomSetFromOptions(rand);CHKERRQ(ierr);

  ierr = MatGetOwnershipRange(A,&rstart,&rend);CHKERRQ(ierr);
  ierr = MatGetSize(A,&M,&N);CHKERRQ(ierr);
  Mbs  = M/bs;

  ierr = PetscMalloc1(bs,&rows);CHKERRQ(ierr);
  ierr = PetscMalloc1(bs,&cols);CHKERRQ(ierr);
  ierr = PetscMalloc1(bs*bs,&vals);CHKERRQ(ierr);
  ierr = PetscMalloc1(M,&idx);CHKERRQ(ierr);

  /* Now set blocks of values */
  for (j=0; j<bs*bs; j++) vals[j] = 0.0;
  for (i=0; i<Mbs; i++) {
    cols[0] = i*bs; rows[0] = i*bs;
    for (j=1; j<bs; j++) {
      rows[j] = rows[j-1]+1;
      cols[j] = cols[j-1]+1;
    }
    ierr = MatSetValues(A,bs,rows,bs,cols,vals,ADD_VALUES);CHKERRQ(ierr);
  }
  /* second, add random blocks */
  for (i=0; i<20*bs; i++) {
    ierr    = PetscRandomGetValue(rand,&rval);CHKERRQ(ierr);
    cols[0] = bs*(PetscInt)(PetscRealPart(rval)*Mbs);
    ierr    = PetscRandomGetValue(rand,&rval);CHKERRQ(ierr);
    rows[0] = rstart + bs*(PetscInt)(PetscRealPart(rval)*mbs);
    for (j=1; j<bs; j++) {
      rows[j] = rows[j-1]+1;
      cols[j] = cols[j-1]+1;
    }

    for (j=0; j<bs*bs; j++) {
      ierr    = PetscRandomGetValue(rand,&rval);CHKERRQ(ierr);
      vals[j] = rval;
    }
    ierr = MatSetValues(A,bs,rows,bs,cols,vals,ADD_VALUES);CHKERRQ(ierr);
  }

  ierr = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
  ierr = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);

  /* make A a symmetric matrix: A <- A^T + A */
  ierr = MatTranspose(A,MAT_INITIAL_MATRIX, &Atrans);CHKERRQ(ierr);
  ierr = MatAXPY(A,one,Atrans,DIFFERENT_NONZERO_PATTERN);CHKERRQ(ierr);
  ierr = MatDestroy(&Atrans);CHKERRQ(ierr);
  ierr = MatTranspose(A,MAT_INITIAL_MATRIX, &Atrans);CHKERRQ(ierr);
  ierr = MatEqual(A, Atrans, &flg);CHKERRQ(ierr);
  if (flg) {
    ierr = MatSetOption(A,MAT_SYMMETRIC,PETSC_TRUE);CHKERRQ(ierr);
  } else SETERRQ(PETSC_COMM_SELF,1,"A+A^T is non-symmetric");
  ierr = MatDestroy(&Atrans);CHKERRQ(ierr);

  /* create a SeqSBAIJ matrix sA (= A) */
  ierr = MatConvert(A,MATSBAIJ,MAT_INITIAL_MATRIX,&sA);CHKERRQ(ierr);
  if (vid >= 0 && vid < size) {
    if (!rank) printf("A: \n");
    ierr = MatView(A,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
    if (!rank) printf("sA: \n");
    ierr = MatView(sA,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
  }

  /* Test sA==A through MatMult() */
  ierr = MatMultEqual(A,sA,10,&flg);CHKERRQ(ierr);
  if (!flg) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"Error in MatConvert(): A != sA");

  /* Test MatIncreaseOverlap() */
  ierr = PetscMalloc1(nd,&is1);CHKERRQ(ierr);
  ierr = PetscMalloc1(nd,&is2);CHKERRQ(ierr);

  for (i=0; i<nd; i++) {
    if (!TestAllcols) {
      ierr = PetscRandomGetValue(rand,&rval);CHKERRQ(ierr);
      sz   = (PetscInt)((0.5+0.2*PetscRealPart(rval))*mbs); /* 0.5*mbs < sz < 0.7*mbs */

      for (j=0; j<sz; j++) {
        ierr      = PetscRandomGetValue(rand,&rval);CHKERRQ(ierr);
        idx[j*bs] = bs*(PetscInt)(PetscRealPart(rval)*Mbs);
        for (k=1; k<bs; k++) idx[j*bs+k] = idx[j*bs]+k;
      }
      ierr = ISCreateGeneral(PETSC_COMM_SELF,sz*bs,idx,PETSC_COPY_VALUES,is1+i);CHKERRQ(ierr);
      ierr = ISCreateGeneral(PETSC_COMM_SELF,sz*bs,idx,PETSC_COPY_VALUES,is2+i);CHKERRQ(ierr);
      if (rank == vid) {
        ierr = PetscPrintf(PETSC_COMM_SELF," [%d] IS sz[%d]: %d\n",rank,i,sz);CHKERRQ(ierr);
        ierr = ISView(is2[i],PETSC_VIEWER_STDOUT_SELF);CHKERRQ(ierr);
      }
    } else { /* Test all rows and colums */
      sz   = M;
      ierr = ISCreateStride(PETSC_COMM_SELF,sz,0,1,is1+i);CHKERRQ(ierr);
      ierr = ISCreateStride(PETSC_COMM_SELF,sz,0,1,is2+i);CHKERRQ(ierr);

      if (rank == vid) {
        PetscBool colflag;
        ierr = ISIdentity(is2[i],&colflag);CHKERRQ(ierr);
        printf("[%d] is2[%d], colflag %d\n",rank,(int)i,(int)colflag);
        ierr = ISView(is2[i],PETSC_VIEWER_STDOUT_SELF);CHKERRQ(ierr);
      }
    }
  }

  ierr = PetscLogStageRegister("MatOv_SBAIJ",&stages[0]);CHKERRQ(ierr);
  ierr = PetscLogStageRegister("MatOv_BAIJ",&stages[1]);CHKERRQ(ierr);

  /* Test MatIncreaseOverlap */
  if (TestOverlap) {
    ierr = PetscLogStagePush(stages[0]);CHKERRQ(ierr);
    ierr = MatIncreaseOverlap(sA,nd,is2,ov);CHKERRQ(ierr);
    ierr = PetscLogStagePop();CHKERRQ(ierr);

    ierr = PetscLogStagePush(stages[1]);CHKERRQ(ierr);
    ierr = MatIncreaseOverlap(A,nd,is1,ov);CHKERRQ(ierr);
    ierr = PetscLogStagePop();CHKERRQ(ierr);

    if (rank == vid) {
      printf("\n[%d] IS from BAIJ:\n",rank);
      ierr = ISView(is1[0],PETSC_VIEWER_STDOUT_SELF);CHKERRQ(ierr);
      printf("\n[%d] IS from SBAIJ:\n",rank);
      ierr = ISView(is2[0],PETSC_VIEWER_STDOUT_SELF);CHKERRQ(ierr);
    }

    for (i=0; i<nd; ++i) {
      ierr = ISEqual(is1[i],is2[i],&flg);CHKERRQ(ierr);
      if (!flg) {
        if (!rank) {
          ierr = ISSort(is1[i]);CHKERRQ(ierr);
          /* ISView(is1[i],PETSC_VIEWER_STDOUT_SELF);CHKERRQ(ierr); */
          ierr = ISSort(is2[i]);CHKERRQ(ierr);
          /* ISView(is2[i],PETSC_VIEWER_STDOUT_SELF);CHKERRQ(ierr); */
        }
        SETERRQ1(PETSC_COMM_SELF,1,"i=%D, is1 != is2",i);
      }
    }
  }

  /* Test MatCreateSubmatrices */
  if (TestSubMat) {
    if (test_sorted) {
      for (i = 0; i < nd; ++i) {
        ierr = ISSort(is1[i]);CHKERRQ(ierr);
      }
    }
    ierr = MatCreateSubMatrices(A,nd,is1,is1,MAT_INITIAL_MATRIX,&submatA);CHKERRQ(ierr);
    ierr = MatCreateSubMatrices(sA,nd,is1,is1,MAT_INITIAL_MATRIX,&submatsA);CHKERRQ(ierr);

    ierr = MatMultEqual(A,sA,10,&flg);CHKERRQ(ierr);
    if (!flg) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"A != sA");

    /* Now test MatCreateSubmatrices with MAT_REUSE_MATRIX option */
    ierr = MatCreateSubMatrices(A,nd,is1,is1,MAT_REUSE_MATRIX,&submatA);CHKERRQ(ierr);
    ierr = MatCreateSubMatrices(sA,nd,is1,is1,MAT_REUSE_MATRIX,&submatsA);CHKERRQ(ierr);
    ierr = MatMultEqual(A,sA,10,&flg);CHKERRQ(ierr);
    if (!flg) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"MatCreateSubmatrices(): A != sA");

    ierr = MatDestroySubMatrices(nd,&submatA);CHKERRQ(ierr);
    ierr = MatDestroySubMatrices(nd,&submatsA);CHKERRQ(ierr);
  }

  /* Free allocated memory */
  for (i=0; i<nd; ++i) {
    ierr = ISDestroy(&is1[i]);CHKERRQ(ierr);
    ierr = ISDestroy(&is2[i]);CHKERRQ(ierr);
  }
  ierr = PetscFree(is1);CHKERRQ(ierr);
  ierr = PetscFree(is2);CHKERRQ(ierr);
  ierr = PetscFree(idx);CHKERRQ(ierr);
  ierr = PetscFree(rows);CHKERRQ(ierr);
  ierr = PetscFree(cols);CHKERRQ(ierr);
  ierr = PetscFree(vals);CHKERRQ(ierr);
  ierr = MatDestroy(&A);CHKERRQ(ierr);
  ierr = MatDestroy(&sA);CHKERRQ(ierr);
  ierr = PetscRandomDestroy(&rand);CHKERRQ(ierr);
  ierr = PetscFinalize();
  return ierr;
}
Beispiel #9
0
static PetscErrorCode  VecNestSetSubVec_Private(Vec X,PetscInt idxm,Vec x)
{
  Vec_Nest       *bx = (Vec_Nest*)X->data;
  PetscInt       i,offset=0,n=0,bs;
  IS             is;
  PetscErrorCode ierr;
  PetscBool      issame = PETSC_FALSE;
  PetscInt       N=0;

  /* check if idxm < bx->nb */
  if (idxm >= bx->nb) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Out of range index value %D maximum %D",idxm,bx->nb);

  PetscFunctionBegin;
  ierr = VecDestroy(&bx->v[idxm]);CHKERRQ(ierr);       /* destroy the existing vector */
  ierr = VecDuplicate(x,&bx->v[idxm]);CHKERRQ(ierr);   /* duplicate the layout of given vector */
  ierr = VecCopy(x,bx->v[idxm]);CHKERRQ(ierr);         /* copy the contents of the given vector */

  /* check if we need to update the IS for the block */
  offset = X->map->rstart;
  for (i=0; i<idxm; i++) {
    n=0;
    ierr = VecGetLocalSize(bx->v[i],&n);CHKERRQ(ierr);
    offset += n;
  }

  /* get the local size and block size */
  ierr = VecGetLocalSize(x,&n);CHKERRQ(ierr);
  ierr = VecGetBlockSize(x,&bs);CHKERRQ(ierr);

  /* create the new IS */
  ierr = ISCreateStride(PetscObjectComm((PetscObject)x),n,offset,1,&is);CHKERRQ(ierr);
  ierr = ISSetBlockSize(is,bs);CHKERRQ(ierr);

  /* check if they are equal */
  ierr = ISEqual(is,bx->is[idxm],&issame);CHKERRQ(ierr);

  if (!issame) {
    /* The IS of given vector has a different layout compared to the existing block vector.
     Destroy the existing reference and update the IS. */
    ierr = ISDestroy(&bx->is[idxm]);CHKERRQ(ierr);
    ierr = ISDuplicate(is,&bx->is[idxm]);CHKERRQ(ierr);
    ierr = ISCopy(is,bx->is[idxm]);CHKERRQ(ierr);

    offset += n;
    /* Since the current IS[idxm] changed, we need to update all the subsequent IS */
    for (i=idxm+1; i<bx->nb; i++) {
      /* get the local size and block size */
      ierr = VecGetLocalSize(bx->v[i],&n);CHKERRQ(ierr);
      ierr = VecGetBlockSize(bx->v[i],&bs);CHKERRQ(ierr);

      /* destroy the old and create the new IS */
      ierr = ISDestroy(&bx->is[i]);CHKERRQ(ierr);
      ierr = ISCreateStride(((PetscObject)bx->v[i])->comm,n,offset,1,&bx->is[i]);CHKERRQ(ierr);
      ierr = ISSetBlockSize(bx->is[i],bs);CHKERRQ(ierr);

      offset += n;
    }

    n=0;
    ierr = VecSize_Nest_Recursive(X,PETSC_TRUE,&N);CHKERRQ(ierr);
    ierr = VecSize_Nest_Recursive(X,PETSC_FALSE,&n);CHKERRQ(ierr);
    ierr = PetscLayoutSetSize(X->map,N);CHKERRQ(ierr);
    ierr = PetscLayoutSetLocalSize(X->map,n);CHKERRQ(ierr);
  }

  ierr = ISDestroy(&is);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}
Beispiel #10
0
PETSC_EXTERN void PETSC_STDCALL  isequal_(IS is1,IS is2,PetscBool  *flg, int *__ierr ){
*__ierr = ISEqual(
	(IS)PetscToPointer((is1) ),
	(IS)PetscToPointer((is2) ),flg);
}
Beispiel #11
0
PetscErrorCode MatGetSubMatrix_BlockMat(Mat A,IS isrow,IS iscol,MatReuse scall,Mat *B)
{
  Mat_BlockMat   *a = (Mat_BlockMat*)A->data;
  Mat_SeqAIJ     *c;
  PetscErrorCode ierr;
  PetscInt       i,k,first,step,lensi,nrows,ncols;
  PetscInt       *j_new,*i_new,*aj = a->j,*ailen = a->ilen;
  PetscScalar    *a_new;
  Mat            C,*aa = a->a;
  PetscBool      stride,equal;

  PetscFunctionBegin;
  ierr = ISEqual(isrow,iscol,&equal);CHKERRQ(ierr);
  if (!equal) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Only for idential column and row indices");
  ierr = PetscObjectTypeCompare((PetscObject)iscol,ISSTRIDE,&stride);CHKERRQ(ierr);
  if (!stride) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Only for stride indices");
  ierr = ISStrideGetInfo(iscol,&first,&step);CHKERRQ(ierr);
  if (step != A->rmap->bs) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Can only select one entry from each block");

  ierr  = ISGetLocalSize(isrow,&nrows);CHKERRQ(ierr);
  ncols = nrows;

  /* create submatrix */
  if (scall == MAT_REUSE_MATRIX) {
    PetscInt n_cols,n_rows;
    C    = *B;
    ierr = MatGetSize(C,&n_rows,&n_cols);CHKERRQ(ierr);
    if (n_rows != nrows || n_cols != ncols) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Reused submatrix wrong size");
    ierr = MatZeroEntries(C);CHKERRQ(ierr);
  } else {
    ierr = MatCreate(PetscObjectComm((PetscObject)A),&C);CHKERRQ(ierr);
    ierr = MatSetSizes(C,nrows,ncols,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr);
    if (A->symmetric) {
      ierr = MatSetType(C,MATSEQSBAIJ);CHKERRQ(ierr);
    } else {
      ierr = MatSetType(C,MATSEQAIJ);CHKERRQ(ierr);
    }
    ierr = MatSeqAIJSetPreallocation(C,0,ailen);CHKERRQ(ierr);
    ierr = MatSeqSBAIJSetPreallocation(C,1,0,ailen);CHKERRQ(ierr);
  }
  c = (Mat_SeqAIJ*)C->data;

  /* loop over rows inserting into submatrix */
  a_new = c->a;
  j_new = c->j;
  i_new = c->i;

  for (i=0; i<nrows; i++) {
    lensi = ailen[i];
    for (k=0; k<lensi; k++) {
      *j_new++ = *aj++;
      ierr     = MatGetValue(*aa++,first,first,a_new++);CHKERRQ(ierr);
    }
    i_new[i+1] = i_new[i] + lensi;
    c->ilen[i] = lensi;
  }

  ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
  ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
  *B   = C;
  PetscFunctionReturn(0);
}
Beispiel #12
0
int main(int argc,char **args)
{
  Mat            A,B,*submatA,*submatB;
  PetscInt       bs=1,m=11,ov=1,i,j,k,*rows,*cols,nd=5,*idx,rstart,rend,sz,mm,nn,M,N,Mbs;
  PetscErrorCode ierr;
  PetscMPIInt    size,rank;
  PetscScalar    *vals,rval;
  IS             *is1,*is2;
  PetscRandom    rdm;
  Vec            xx,s1,s2;
  PetscReal      s1norm,s2norm,rnorm,tol = 100*PETSC_SMALL;
  PetscBool      flg,test_nd0=PETSC_FALSE;

  ierr = PetscInitialize(&argc,&args,(char*)0,help);if (ierr) return ierr;
  ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRQ(ierr);
  ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr);

  ierr = PetscOptionsGetInt(NULL,NULL,"-mat_block_size",&bs,NULL);CHKERRQ(ierr);
  ierr = PetscOptionsGetInt(NULL,NULL,"-mat_size",&m,NULL);CHKERRQ(ierr);
  ierr = PetscOptionsGetInt(NULL,NULL,"-ov",&ov,NULL);CHKERRQ(ierr);
  ierr = PetscOptionsGetInt(NULL,NULL,"-nd",&nd,NULL);CHKERRQ(ierr);
  ierr = PetscOptionsGetBool(NULL,NULL,"-test_nd0",&test_nd0,NULL);CHKERRQ(ierr);

  /* Create a AIJ matrix A */
  ierr = MatCreate(PETSC_COMM_WORLD,&A);CHKERRQ(ierr);
  ierr = MatSetSizes(A,m*bs,m*bs,PETSC_DECIDE,PETSC_DECIDE);CHKERRQ(ierr);
  ierr = MatSetType(A,MATAIJ);CHKERRQ(ierr);
  ierr = MatSeqAIJSetPreallocation(A,PETSC_DEFAULT,NULL);CHKERRQ(ierr);
  ierr = MatMPIAIJSetPreallocation(A,PETSC_DEFAULT,NULL,PETSC_DEFAULT,NULL);CHKERRQ(ierr);
  ierr = MatSetFromOptions(A);CHKERRQ(ierr);
  ierr = MatSetOption(A,MAT_NEW_NONZERO_ALLOCATION_ERR,PETSC_FALSE);CHKERRQ(ierr);

  /* Create a BAIJ matrix B */
  ierr = MatCreate(PETSC_COMM_WORLD,&B);CHKERRQ(ierr);
  ierr = MatSetSizes(B,m*bs,m*bs,PETSC_DECIDE,PETSC_DECIDE);CHKERRQ(ierr);
  ierr = MatSetType(B,MATBAIJ);CHKERRQ(ierr);
  ierr = MatSeqBAIJSetPreallocation(B,bs,PETSC_DEFAULT,NULL);CHKERRQ(ierr);
  ierr = MatMPIBAIJSetPreallocation(B,bs,PETSC_DEFAULT,NULL,PETSC_DEFAULT,NULL);CHKERRQ(ierr);
  ierr = MatSetFromOptions(B);CHKERRQ(ierr);
  ierr = MatSetOption(B,MAT_NEW_NONZERO_ALLOCATION_ERR,PETSC_FALSE);CHKERRQ(ierr);

  ierr = PetscRandomCreate(PETSC_COMM_WORLD,&rdm);CHKERRQ(ierr);
  ierr = PetscRandomSetFromOptions(rdm);CHKERRQ(ierr);

  ierr = MatGetOwnershipRange(A,&rstart,&rend);CHKERRQ(ierr);
  ierr = MatGetSize(A,&M,&N);CHKERRQ(ierr);
  Mbs  = M/bs;

  ierr = PetscMalloc1(bs,&rows);CHKERRQ(ierr);
  ierr = PetscMalloc1(bs,&cols);CHKERRQ(ierr);
  ierr = PetscMalloc1(bs*bs,&vals);CHKERRQ(ierr);
  ierr = PetscMalloc1(M,&idx);CHKERRQ(ierr);

  /* Now set blocks of values */
  for (i=0; i<40*bs; i++) {
    ierr    = PetscRandomGetValue(rdm,&rval);CHKERRQ(ierr);
    cols[0] = bs*(int)(PetscRealPart(rval)*Mbs);
    ierr    = PetscRandomGetValue(rdm,&rval);CHKERRQ(ierr);
    rows[0] = rstart + bs*(int)(PetscRealPart(rval)*m);
    for (j=1; j<bs; j++) {
      rows[j] = rows[j-1]+1;
      cols[j] = cols[j-1]+1;
    }

    for (j=0; j<bs*bs; j++) {
      ierr    = PetscRandomGetValue(rdm,&rval);CHKERRQ(ierr);
      vals[j] = rval;
    }
    ierr = MatSetValues(A,bs,rows,bs,cols,vals,ADD_VALUES);CHKERRQ(ierr);
    ierr = MatSetValues(B,bs,rows,bs,cols,vals,ADD_VALUES);CHKERRQ(ierr);
  }

  ierr = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
  ierr = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
  ierr = MatAssemblyBegin(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
  ierr = MatAssemblyEnd(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);

  /* Test MatIncreaseOverlap() */
  ierr = PetscMalloc1(nd,&is1);CHKERRQ(ierr);
  ierr = PetscMalloc1(nd,&is2);CHKERRQ(ierr);

  if (!rank && test_nd0) nd = 0; /* test case */

  for (i=0; i<nd; i++) {
    ierr = PetscRandomGetValue(rdm,&rval);CHKERRQ(ierr);
    sz   = (int)(PetscRealPart(rval)*m);
    for (j=0; j<sz; j++) {
      ierr      = PetscRandomGetValue(rdm,&rval);CHKERRQ(ierr);
      idx[j*bs] = bs*(int)(PetscRealPart(rval)*Mbs);
      for (k=1; k<bs; k++) idx[j*bs+k] = idx[j*bs]+k;
    }
    ierr = ISCreateGeneral(PETSC_COMM_SELF,sz*bs,idx,PETSC_COPY_VALUES,is1+i);CHKERRQ(ierr);
    ierr = ISCreateGeneral(PETSC_COMM_SELF,sz*bs,idx,PETSC_COPY_VALUES,is2+i);CHKERRQ(ierr);
  }
  ierr = MatIncreaseOverlap(A,nd,is1,ov);CHKERRQ(ierr);
  ierr = MatIncreaseOverlap(B,nd,is2,ov);CHKERRQ(ierr);

  for (i=0; i<nd; ++i) {
    ierr = ISEqual(is1[i],is2[i],&flg);CHKERRQ(ierr);

    if (!flg) {
      ierr = PetscPrintf(PETSC_COMM_SELF,"i=%D, flg=%d :bs=%D m=%D ov=%D nd=%D np=%D\n",i,flg,bs,m,ov,nd,size);CHKERRQ(ierr);
    }
  }

  for (i=0; i<nd; ++i) {
    ierr = ISSort(is1[i]);CHKERRQ(ierr);
    ierr = ISSort(is2[i]);CHKERRQ(ierr);
  }

  ierr = MatCreateSubMatrices(B,nd,is2,is2,MAT_INITIAL_MATRIX,&submatB);CHKERRQ(ierr);
  ierr = MatCreateSubMatrices(A,nd,is1,is1,MAT_INITIAL_MATRIX,&submatA);CHKERRQ(ierr);

  /* Test MatMult() */
  for (i=0; i<nd; i++) {
    ierr = MatGetSize(submatA[i],&mm,&nn);CHKERRQ(ierr);
    ierr = VecCreateSeq(PETSC_COMM_SELF,mm,&xx);CHKERRQ(ierr);
    ierr = VecDuplicate(xx,&s1);CHKERRQ(ierr);
    ierr = VecDuplicate(xx,&s2);CHKERRQ(ierr);
    for (j=0; j<3; j++) {
      ierr  = VecSetRandom(xx,rdm);CHKERRQ(ierr);
      ierr  = MatMult(submatA[i],xx,s1);CHKERRQ(ierr);
      ierr  = MatMult(submatB[i],xx,s2);CHKERRQ(ierr);
      ierr  = VecNorm(s1,NORM_2,&s1norm);CHKERRQ(ierr);
      ierr  = VecNorm(s2,NORM_2,&s2norm);CHKERRQ(ierr);
      rnorm = s2norm-s1norm;
      if (rnorm<-tol || rnorm>tol) {
        ierr = PetscPrintf(PETSC_COMM_SELF,"[%d]Error:MatMult - Norm1=%16.14e Norm2=%16.14e\n",rank,s1norm,s2norm);CHKERRQ(ierr);
      }
    }
    ierr = VecDestroy(&xx);CHKERRQ(ierr);
    ierr = VecDestroy(&s1);CHKERRQ(ierr);
    ierr = VecDestroy(&s2);CHKERRQ(ierr);
  }

  /* Now test MatCreateSubmatrices with MAT_REUSE_MATRIX option */
  ierr = MatCreateSubMatrices(A,nd,is1,is1,MAT_REUSE_MATRIX,&submatA);CHKERRQ(ierr);
  ierr = MatCreateSubMatrices(B,nd,is2,is2,MAT_REUSE_MATRIX,&submatB);CHKERRQ(ierr);

  /* Test MatMult() */
  for (i=0; i<nd; i++) {
    ierr = MatGetSize(submatA[i],&mm,&nn);CHKERRQ(ierr);
    ierr = VecCreateSeq(PETSC_COMM_SELF,mm,&xx);CHKERRQ(ierr);
    ierr = VecDuplicate(xx,&s1);CHKERRQ(ierr);
    ierr = VecDuplicate(xx,&s2);CHKERRQ(ierr);
    for (j=0; j<3; j++) {
      ierr  = VecSetRandom(xx,rdm);CHKERRQ(ierr);
      ierr  = MatMult(submatA[i],xx,s1);CHKERRQ(ierr);
      ierr  = MatMult(submatB[i],xx,s2);CHKERRQ(ierr);
      ierr  = VecNorm(s1,NORM_2,&s1norm);CHKERRQ(ierr);
      ierr  = VecNorm(s2,NORM_2,&s2norm);CHKERRQ(ierr);
      rnorm = s2norm-s1norm;
      if (rnorm<-tol || rnorm>tol) {
        ierr = PetscPrintf(PETSC_COMM_SELF,"[%d]Error:MatMult - Norm1=%16.14e Norm2=%16.14e\n",rank,s1norm,s2norm);CHKERRQ(ierr);
      }
    }
    ierr = VecDestroy(&xx);CHKERRQ(ierr);
    ierr = VecDestroy(&s1);CHKERRQ(ierr);
    ierr = VecDestroy(&s2);CHKERRQ(ierr);
  }

  /* Free allocated memory */
  for (i=0; i<nd; ++i) {
    ierr = ISDestroy(&is1[i]);CHKERRQ(ierr);
    ierr = ISDestroy(&is2[i]);CHKERRQ(ierr);
  }
  ierr = MatDestroySubMatrices(nd,&submatA);CHKERRQ(ierr);
  ierr = MatDestroySubMatrices(nd,&submatB);CHKERRQ(ierr);

  ierr = PetscFree(is1);CHKERRQ(ierr);
  ierr = PetscFree(is2);CHKERRQ(ierr);
  ierr = PetscFree(idx);CHKERRQ(ierr);
  ierr = PetscFree(rows);CHKERRQ(ierr);
  ierr = PetscFree(cols);CHKERRQ(ierr);
  ierr = PetscFree(vals);CHKERRQ(ierr);
  ierr = MatDestroy(&A);CHKERRQ(ierr);
  ierr = MatDestroy(&B);CHKERRQ(ierr);
  ierr = PetscRandomDestroy(&rdm);CHKERRQ(ierr);
  ierr = PetscFinalize();
  return ierr;
}
Beispiel #13
0
int main(int argc,char **args)
{
  Mat            A,Atrans,sA,*submatA,*submatsA;
  PetscInt       bs=1,m=43,ov=1,i,j,k,*rows,*cols,M,nd=5,*idx,mm,nn;
  PetscErrorCode ierr;
  PetscMPIInt    size;
  PetscScalar    *vals,rval,one=1.0;
  IS             *is1,*is2;
  PetscRandom    rand;
  Vec            xx,s1,s2;
  PetscReal      s1norm,s2norm,rnorm,tol = 1.e-10;
  PetscBool      flg;

  PetscInitialize(&argc,&args,(char *)0,help);
 

  ierr = PetscOptionsGetInt(PETSC_NULL,"-mat_block_size",&bs,PETSC_NULL);CHKERRQ(ierr);
  ierr = PetscOptionsGetInt(PETSC_NULL,"-mat_size",&m,PETSC_NULL);CHKERRQ(ierr);
  ierr = PetscOptionsGetInt(PETSC_NULL,"-ov",&ov,PETSC_NULL);CHKERRQ(ierr);
  ierr = PetscOptionsGetInt(PETSC_NULL,"-nd",&nd,PETSC_NULL);CHKERRQ(ierr);

  /* create a SeqBAIJ matrix A */
  M    = m*bs;
  ierr = MatCreateSeqBAIJ(PETSC_COMM_SELF,bs,M,M,1,PETSC_NULL,&A);CHKERRQ(ierr);
  ierr = PetscRandomCreate(PETSC_COMM_SELF,&rand);CHKERRQ(ierr);
  ierr = PetscRandomSetFromOptions(rand);CHKERRQ(ierr);

  ierr = PetscMalloc(bs*sizeof(PetscInt),&rows);CHKERRQ(ierr);
  ierr = PetscMalloc(bs*sizeof(PetscInt),&cols);CHKERRQ(ierr);
  ierr = PetscMalloc(bs*bs*sizeof(PetscScalar),&vals);CHKERRQ(ierr);
  ierr = PetscMalloc(M*sizeof(PetscScalar),&idx);CHKERRQ(ierr);
  
  /* Now set blocks of random values */
  /* first, set diagonal blocks as zero */
  for (j=0; j<bs*bs; j++) vals[j] = 0.0;
  for (i=0; i<m; i++){
    cols[0] = i*bs; rows[0] = i*bs; 
    for (j=1; j<bs; j++) {
      rows[j] = rows[j-1]+1;
      cols[j] = cols[j-1]+1;
    }
    ierr = MatSetValues(A,bs,rows,bs,cols,vals,ADD_VALUES);CHKERRQ(ierr);
  }
  /* second, add random blocks */
  for (i=0; i<20*bs; i++) {
      ierr = PetscRandomGetValue(rand,&rval);CHKERRQ(ierr);
      cols[0] = bs*(int)(PetscRealPart(rval)*m);
      ierr = PetscRandomGetValue(rand,&rval);CHKERRQ(ierr);
      rows[0] = bs*(int)(PetscRealPart(rval)*m);
      for (j=1; j<bs; j++) {
        rows[j] = rows[j-1]+1;
        cols[j] = cols[j-1]+1;
      }

      for (j=0; j<bs*bs; j++) {
        ierr = PetscRandomGetValue(rand,&rval);CHKERRQ(ierr);
        vals[j] = rval;
      }
      ierr = MatSetValues(A,bs,rows,bs,cols,vals,ADD_VALUES);CHKERRQ(ierr);
  }

  ierr = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
  ierr = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);

  /* make A a symmetric matrix: A <- A^T + A */
  ierr = MatTranspose(A,MAT_INITIAL_MATRIX, &Atrans);CHKERRQ(ierr);
  ierr = MatAXPY(A,one,Atrans,DIFFERENT_NONZERO_PATTERN);CHKERRQ(ierr); 
  ierr = MatDestroy(&Atrans);CHKERRQ(ierr);
  ierr = MatTranspose(A,MAT_INITIAL_MATRIX, &Atrans);
  ierr = MatEqual(A, Atrans, &flg);
  if (!flg) {
    SETERRQ(PETSC_COMM_SELF,1,"A+A^T is non-symmetric");
  }
  ierr = MatDestroy(&Atrans);CHKERRQ(ierr);

  /* create a SeqSBAIJ matrix sA (= A) */
  ierr = MatConvert(A,MATSEQSBAIJ,MAT_INITIAL_MATRIX,&sA);CHKERRQ(ierr); 
 
  /* Test sA==A through MatMult() */
  for (i=0; i<nd; i++) {
    ierr = MatGetSize(A,&mm,&nn);CHKERRQ(ierr);
    ierr = VecCreateSeq(PETSC_COMM_SELF,mm,&xx);CHKERRQ(ierr);
    ierr = VecDuplicate(xx,&s1);CHKERRQ(ierr);
    ierr = VecDuplicate(xx,&s2);CHKERRQ(ierr);
    for (j=0; j<3; j++) {
      ierr = VecSetRandom(xx,rand);CHKERRQ(ierr);
      ierr = MatMult(A,xx,s1);CHKERRQ(ierr);
      ierr = MatMult(sA,xx,s2);CHKERRQ(ierr);
      ierr = VecNorm(s1,NORM_2,&s1norm);CHKERRQ(ierr);
      ierr = VecNorm(s2,NORM_2,&s2norm);CHKERRQ(ierr);
      rnorm = s2norm-s1norm;
      if (rnorm<-tol || rnorm>tol) { 
        ierr = PetscPrintf(PETSC_COMM_SELF,"Error:MatMult - Norm1=%16.14e Norm2=%16.14e\n",s1norm,s2norm);CHKERRQ(ierr);
      }
    }
    ierr = VecDestroy(&xx);CHKERRQ(ierr);
    ierr = VecDestroy(&s1);CHKERRQ(ierr);
    ierr = VecDestroy(&s2);CHKERRQ(ierr);
  } 

  /* Test MatIncreaseOverlap() */
  ierr = PetscMalloc(nd*sizeof(IS **),&is1);CHKERRQ(ierr);
  ierr = PetscMalloc(nd*sizeof(IS **),&is2);CHKERRQ(ierr);

  
  for (i=0; i<nd; i++) {
    ierr = PetscRandomGetValue(rand,&rval);CHKERRQ(ierr);
    size = (int)(PetscRealPart(rval)*m);
    for (j=0; j<size; j++) {
      ierr = PetscRandomGetValue(rand,&rval);CHKERRQ(ierr);
      idx[j*bs] = bs*(int)(PetscRealPart(rval)*m);
      for (k=1; k<bs; k++) idx[j*bs+k] = idx[j*bs]+k;
    }
    ierr = ISCreateGeneral(PETSC_COMM_SELF,size*bs,idx,PETSC_COPY_VALUES,is1+i);CHKERRQ(ierr);
    ierr = ISCreateGeneral(PETSC_COMM_SELF,size*bs,idx,PETSC_COPY_VALUES,is2+i);CHKERRQ(ierr);
  }
  /* for debugging */
  /*
  ierr = MatView(A,PETSC_VIEWER_STDOUT_SELF);CHKERRQ(ierr); 
  ierr = MatView(sA,PETSC_VIEWER_STDOUT_SELF);CHKERRQ(ierr); 
  */

  ierr = MatIncreaseOverlap(A,nd,is1,ov);CHKERRQ(ierr);
  ierr = MatIncreaseOverlap(sA,nd,is2,ov);CHKERRQ(ierr);

  for (i=0; i<nd; ++i) { 
    ierr = ISSort(is1[i]);CHKERRQ(ierr);
    ierr = ISSort(is2[i]);CHKERRQ(ierr);
  }

  for (i=0; i<nd; ++i) {
    ierr = ISEqual(is1[i],is2[i],&flg);CHKERRQ(ierr);
    if (!flg){
      /* ISView(is1[i],PETSC_VIEWER_STDOUT_SELF);CHKERRQ(ierr);
         ISView(is2[i],PETSC_VIEWER_STDOUT_SELF);CHKERRQ(ierr); */
      SETERRQ1(PETSC_COMM_SELF,1,"i=%d, is1 != is2",i);
    }
  }
  
  ierr = MatGetSubMatrices(A,nd,is1,is1,MAT_INITIAL_MATRIX,&submatA);CHKERRQ(ierr);
  ierr = MatGetSubMatrices(sA,nd,is2,is2,MAT_INITIAL_MATRIX,&submatsA);CHKERRQ(ierr);

  /* Test MatMult() */
  for (i=0; i<nd; i++) {
    ierr = MatGetSize(submatA[i],&mm,&nn);CHKERRQ(ierr);
    ierr = VecCreateSeq(PETSC_COMM_SELF,mm,&xx);CHKERRQ(ierr);
    ierr = VecDuplicate(xx,&s1);CHKERRQ(ierr);
    ierr = VecDuplicate(xx,&s2);CHKERRQ(ierr);
    for (j=0; j<3; j++) {
      ierr = VecSetRandom(xx,rand);CHKERRQ(ierr);
      ierr = MatMult(submatA[i],xx,s1);CHKERRQ(ierr);
      ierr = MatMult(submatsA[i],xx,s2);CHKERRQ(ierr);
      ierr = VecNorm(s1,NORM_2,&s1norm);CHKERRQ(ierr);
      ierr = VecNorm(s2,NORM_2,&s2norm);CHKERRQ(ierr);
      rnorm = s2norm-s1norm;
      if (rnorm<-tol || rnorm>tol) { 
        ierr = PetscPrintf(PETSC_COMM_SELF,"Error:MatMult - Norm1=%16.14e Norm2=%16.14e\n",s1norm,s2norm);CHKERRQ(ierr);
      }
    }
    ierr = VecDestroy(&xx);CHKERRQ(ierr);
    ierr = VecDestroy(&s1);CHKERRQ(ierr);
    ierr = VecDestroy(&s2);CHKERRQ(ierr);
  } 

  /* Now test MatGetSubmatrices with MAT_REUSE_MATRIX option */
  ierr = MatGetSubMatrices(A,nd,is1,is1,MAT_REUSE_MATRIX,&submatA);CHKERRQ(ierr);
  ierr = MatGetSubMatrices(sA,nd,is2,is2,MAT_REUSE_MATRIX,&submatsA);CHKERRQ(ierr);
  
  /* Test MatMult() */
  for (i=0; i<nd; i++) {
    ierr = MatGetSize(submatA[i],&mm,&nn);CHKERRQ(ierr);
    ierr = VecCreateSeq(PETSC_COMM_SELF,mm,&xx);CHKERRQ(ierr);
    ierr = VecDuplicate(xx,&s1);CHKERRQ(ierr);
    ierr = VecDuplicate(xx,&s2);CHKERRQ(ierr);
    for (j=0; j<3; j++) {
      ierr = VecSetRandom(xx,rand);CHKERRQ(ierr);
      ierr = MatMult(submatA[i],xx,s1);CHKERRQ(ierr);
      ierr = MatMult(submatsA[i],xx,s2);CHKERRQ(ierr);
      ierr = VecNorm(s1,NORM_2,&s1norm);CHKERRQ(ierr);
      ierr = VecNorm(s2,NORM_2,&s2norm);CHKERRQ(ierr);
      rnorm = s2norm-s1norm;
      if (rnorm<-tol || rnorm>tol) { 
        ierr = PetscPrintf(PETSC_COMM_SELF,"Error:MatMult - Norm1=%16.14e Norm2=%16.14e\n",s1norm,s2norm);CHKERRQ(ierr);
      }
    }
    ierr = VecDestroy(&xx);CHKERRQ(ierr);
    ierr = VecDestroy(&s1);CHKERRQ(ierr);
    ierr = VecDestroy(&s2);CHKERRQ(ierr);
  } 
    
  /* Free allocated memory */
  for (i=0; i<nd; ++i) { 
    ierr = ISDestroy(&is1[i]);CHKERRQ(ierr);
    ierr = ISDestroy(&is2[i]);CHKERRQ(ierr);
    
    ierr = MatDestroy(&submatA[i]);CHKERRQ(ierr);
    ierr = MatDestroy(&submatsA[i]);CHKERRQ(ierr);
    
  }
  
  ierr = PetscFree(submatA);CHKERRQ(ierr);
  ierr = PetscFree(submatsA);CHKERRQ(ierr);
  
  ierr = PetscFree(is1);CHKERRQ(ierr);
  ierr = PetscFree(is2);CHKERRQ(ierr);
  ierr = PetscFree(idx);CHKERRQ(ierr);
  ierr = PetscFree(rows);CHKERRQ(ierr);
  ierr = PetscFree(cols);CHKERRQ(ierr);
  ierr = PetscFree(vals);CHKERRQ(ierr);
  ierr = MatDestroy(&A);CHKERRQ(ierr);
  ierr = MatDestroy(&sA);CHKERRQ(ierr);
  ierr = PetscRandomDestroy(&rand);CHKERRQ(ierr);
  ierr = PetscFinalize();
  return 0;
}
Beispiel #14
0
static PetscErrorCode PCSetUp_Cholesky(PC pc)
{
    PetscErrorCode         ierr;
    PetscBool              flg;
    PC_Cholesky            *dir = (PC_Cholesky*)pc->data;
    const MatSolverPackage stype;
    MatFactorError         err;

    PetscFunctionBegin;
    pc->failedreason = PC_NOERROR;
    if (dir->hdr.reusefill && pc->setupcalled) ((PC_Factor*)dir)->info.fill = dir->hdr.actualfill;

    ierr = MatSetErrorIfFailure(pc->pmat,pc->erroriffailure);
    CHKERRQ(ierr);
    if (dir->hdr.inplace) {
        if (dir->row && dir->col && (dir->row != dir->col)) {
            ierr = ISDestroy(&dir->row);
            CHKERRQ(ierr);
        }
        ierr = ISDestroy(&dir->col);
        CHKERRQ(ierr);
        ierr = MatGetOrdering(pc->pmat,((PC_Factor*)dir)->ordering,&dir->row,&dir->col);
        CHKERRQ(ierr);
        if (dir->col && (dir->row != dir->col)) {  /* only use row ordering for SBAIJ */
            ierr = ISDestroy(&dir->col);
            CHKERRQ(ierr);
        }
        if (dir->row) {
            ierr = PetscLogObjectParent((PetscObject)pc,(PetscObject)dir->row);
            CHKERRQ(ierr);
        }
        ierr = MatCholeskyFactor(pc->pmat,dir->row,&((PC_Factor*)dir)->info);
        CHKERRQ(ierr);
        ierr = MatFactorGetError(pc->pmat,&err);
        CHKERRQ(ierr);
        if (err) { /* Factor() fails */
            pc->failedreason = (PCFailedReason)err;
            PetscFunctionReturn(0);
        }

        ((PC_Factor*)dir)->fact = pc->pmat;
    } else {
        MatInfo info;

        if (!pc->setupcalled) {
            ierr = MatGetOrdering(pc->pmat,((PC_Factor*)dir)->ordering,&dir->row,&dir->col);
            CHKERRQ(ierr);
            /* check if dir->row == dir->col */
            ierr = ISEqual(dir->row,dir->col,&flg);
            CHKERRQ(ierr);
            if (!flg) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_INCOMP,"row and column permutations must equal");
            ierr = ISDestroy(&dir->col);
            CHKERRQ(ierr); /* only pass one ordering into CholeskyFactor */

            flg  = PETSC_FALSE;
            ierr = PetscOptionsGetBool(((PetscObject)pc)->options,((PetscObject)pc)->prefix,"-pc_factor_nonzeros_along_diagonal",&flg,NULL);
            CHKERRQ(ierr);
            if (flg) {
                PetscReal tol = 1.e-10;
                ierr = PetscOptionsGetReal(((PetscObject)pc)->options,((PetscObject)pc)->prefix,"-pc_factor_nonzeros_along_diagonal",&tol,NULL);
                CHKERRQ(ierr);
                ierr = MatReorderForNonzeroDiagonal(pc->pmat,tol,dir->row,dir->row);
                CHKERRQ(ierr);
            }
            if (dir->row) {
                ierr = PetscLogObjectParent((PetscObject)pc,(PetscObject)dir->row);
                CHKERRQ(ierr);
            }
            if (!((PC_Factor*)dir)->fact) {
                ierr = MatGetFactor(pc->pmat,((PC_Factor*)dir)->solvertype,MAT_FACTOR_CHOLESKY,&((PC_Factor*)dir)->fact);
                CHKERRQ(ierr);
            }
            ierr                = MatCholeskyFactorSymbolic(((PC_Factor*)dir)->fact,pc->pmat,dir->row,&((PC_Factor*)dir)->info);
            CHKERRQ(ierr);
            ierr                = MatGetInfo(((PC_Factor*)dir)->fact,MAT_LOCAL,&info);
            CHKERRQ(ierr);
            dir->hdr.actualfill = info.fill_ratio_needed;
            ierr                = PetscLogObjectParent((PetscObject)pc,(PetscObject)((PC_Factor*)dir)->fact);
            CHKERRQ(ierr);
        } else if (pc->flag != SAME_NONZERO_PATTERN) {
            if (!dir->hdr.reuseordering) {
                ierr = ISDestroy(&dir->row);
                CHKERRQ(ierr);
                ierr = MatGetOrdering(pc->pmat,((PC_Factor*)dir)->ordering,&dir->row,&dir->col);
                CHKERRQ(ierr);
                ierr = ISDestroy(&dir->col);
                CHKERRQ(ierr); /* only use dir->row ordering in CholeskyFactor */

                flg  = PETSC_FALSE;
                ierr = PetscOptionsGetBool(((PetscObject)pc)->options,((PetscObject)pc)->prefix,"-pc_factor_nonzeros_along_diagonal",&flg,NULL);
                CHKERRQ(ierr);
                if (flg) {
                    PetscReal tol = 1.e-10;
                    ierr = PetscOptionsGetReal(((PetscObject)pc)->options,((PetscObject)pc)->prefix,"-pc_factor_nonzeros_along_diagonal",&tol,NULL);
                    CHKERRQ(ierr);
                    ierr = MatReorderForNonzeroDiagonal(pc->pmat,tol,dir->row,dir->row);
                    CHKERRQ(ierr);
                }
                if (dir->row) {
                    ierr = PetscLogObjectParent((PetscObject)pc,(PetscObject)dir->row);
                    CHKERRQ(ierr);
                }
            }
            ierr                = MatDestroy(&((PC_Factor*)dir)->fact);
            CHKERRQ(ierr);
            ierr                = MatGetFactor(pc->pmat,((PC_Factor*)dir)->solvertype,MAT_FACTOR_CHOLESKY,&((PC_Factor*)dir)->fact);
            CHKERRQ(ierr);
            ierr                = MatCholeskyFactorSymbolic(((PC_Factor*)dir)->fact,pc->pmat,dir->row,&((PC_Factor*)dir)->info);
            CHKERRQ(ierr);
            ierr                = MatGetInfo(((PC_Factor*)dir)->fact,MAT_LOCAL,&info);
            CHKERRQ(ierr);
            dir->hdr.actualfill = info.fill_ratio_needed;
            ierr                = PetscLogObjectParent((PetscObject)pc,(PetscObject)((PC_Factor*)dir)->fact);
            CHKERRQ(ierr);
        } else {
            ierr = MatFactorGetError(((PC_Factor*)dir)->fact,&err);
            CHKERRQ(ierr);
            if (err == MAT_FACTOR_NUMERIC_ZEROPIVOT) {
                ierr = MatFactorClearError(((PC_Factor*)dir)->fact);
                CHKERRQ(ierr);
                pc->failedreason = PC_NOERROR;
            }
        }
        ierr = MatFactorGetError(((PC_Factor*)dir)->fact,&err);
        CHKERRQ(ierr);
        if (err) { /* FactorSymbolic() fails */
            pc->failedreason = (PCFailedReason)err;
            PetscFunctionReturn(0);
        }

        ierr = MatCholeskyFactorNumeric(((PC_Factor*)dir)->fact,pc->pmat,&((PC_Factor*)dir)->info);
        CHKERRQ(ierr);
        ierr = MatFactorGetError(((PC_Factor*)dir)->fact,&err);
        CHKERRQ(ierr);
        if (err) { /* FactorNumeric() fails */
            pc->failedreason = (PCFailedReason)err;
        }
    }

    ierr = PCFactorGetMatSolverPackage(pc,&stype);
    CHKERRQ(ierr);
    if (!stype) {
        const MatSolverPackage solverpackage;
        ierr = MatFactorGetSolverPackage(((PC_Factor*)dir)->fact,&solverpackage);
        CHKERRQ(ierr);
        ierr = PCFactorSetMatSolverPackage(pc,solverpackage);
        CHKERRQ(ierr);
    }
    PetscFunctionReturn(0);
}
Beispiel #15
0
static PetscErrorCode PCSetUp_Cholesky(PC pc)
{
  PetscErrorCode ierr;
  PetscBool      flg;
  PC_Cholesky    *dir = (PC_Cholesky*)pc->data;

  PetscFunctionBegin;
  if (dir->reusefill && pc->setupcalled) ((PC_Factor*)dir)->info.fill = dir->actualfill;

  if (dir->inplace) {
    if (dir->row && dir->col && (dir->row != dir->col)) {
      ierr = ISDestroy(&dir->row);CHKERRQ(ierr);
    }
    ierr = ISDestroy(&dir->col);CHKERRQ(ierr);
    ierr = MatGetOrdering(pc->pmat,((PC_Factor*)dir)->ordering,&dir->row,&dir->col);CHKERRQ(ierr);
    if (dir->col && (dir->row != dir->col)) {  /* only use row ordering for SBAIJ */
      ierr = ISDestroy(&dir->col);CHKERRQ(ierr);
    }
    if (dir->row) {ierr = PetscLogObjectParent(pc,dir->row);CHKERRQ(ierr);}
    ierr = MatCholeskyFactor(pc->pmat,dir->row,&((PC_Factor*)dir)->info);CHKERRQ(ierr);
    ((PC_Factor*)dir)->fact = pc->pmat;
  } else {
    MatInfo info;
    if (!pc->setupcalled) {
      ierr = MatGetOrdering(pc->pmat,((PC_Factor*)dir)->ordering,&dir->row,&dir->col);CHKERRQ(ierr);
      /* check if dir->row == dir->col */
      ierr = ISEqual(dir->row,dir->col,&flg);CHKERRQ(ierr);
      if (!flg) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_INCOMP,"row and column permutations must equal");
      ierr = ISDestroy(&dir->col);CHKERRQ(ierr); /* only pass one ordering into CholeskyFactor */

      flg  = PETSC_FALSE;
      ierr = PetscOptionsGetBool(((PetscObject)pc)->prefix,"-pc_factor_nonzeros_along_diagonal",&flg,PETSC_NULL);CHKERRQ(ierr);
      if (flg) {
        PetscReal tol = 1.e-10;
        ierr = PetscOptionsGetReal(((PetscObject)pc)->prefix,"-pc_factor_nonzeros_along_diagonal",&tol,PETSC_NULL);CHKERRQ(ierr);
        ierr = MatReorderForNonzeroDiagonal(pc->pmat,tol,dir->row,dir->row);CHKERRQ(ierr);
      }
      if (dir->row) {ierr = PetscLogObjectParent(pc,dir->row);CHKERRQ(ierr);}
      if (!((PC_Factor*)dir)->fact){
        ierr = MatGetFactor(pc->pmat,((PC_Factor*)dir)->solvertype,MAT_FACTOR_CHOLESKY,&((PC_Factor*)dir)->fact);CHKERRQ(ierr);
      }
      ierr = MatCholeskyFactorSymbolic(((PC_Factor*)dir)->fact,pc->pmat,dir->row,&((PC_Factor*)dir)->info);CHKERRQ(ierr);
      ierr = MatGetInfo(((PC_Factor*)dir)->fact,MAT_LOCAL,&info);CHKERRQ(ierr);
      dir->actualfill = info.fill_ratio_needed;
      ierr = PetscLogObjectParent(pc,((PC_Factor*)dir)->fact);CHKERRQ(ierr);
    } else if (pc->flag != SAME_NONZERO_PATTERN) {
      if (!dir->reuseordering) {
        ierr = ISDestroy(&dir->row);CHKERRQ(ierr);
        ierr = MatGetOrdering(pc->pmat,((PC_Factor*)dir)->ordering,&dir->row,&dir->col);CHKERRQ(ierr);
        ierr = ISDestroy(&dir->col);CHKERRQ(ierr); /* only use dir->row ordering in CholeskyFactor */

        flg  = PETSC_FALSE;
        ierr = PetscOptionsGetBool(((PetscObject)pc)->prefix,"-pc_factor_nonzeros_along_diagonal",&flg,PETSC_NULL);CHKERRQ(ierr);
        if (flg) {
          PetscReal tol = 1.e-10;
          ierr = PetscOptionsGetReal(((PetscObject)pc)->prefix,"-pc_factor_nonzeros_along_diagonal",&tol,PETSC_NULL);CHKERRQ(ierr);
          ierr = MatReorderForNonzeroDiagonal(pc->pmat,tol,dir->row,dir->row);CHKERRQ(ierr);
        }
        if (dir->row) {ierr = PetscLogObjectParent(pc,dir->row);CHKERRQ(ierr);}
      }
      ierr = MatDestroy(&((PC_Factor*)dir)->fact);CHKERRQ(ierr);
      ierr = MatGetFactor(pc->pmat,((PC_Factor*)dir)->solvertype,MAT_FACTOR_CHOLESKY,&((PC_Factor*)dir)->fact);CHKERRQ(ierr);
      ierr = MatCholeskyFactorSymbolic(((PC_Factor*)dir)->fact,pc->pmat,dir->row,&((PC_Factor*)dir)->info);CHKERRQ(ierr);
      ierr = MatGetInfo(((PC_Factor*)dir)->fact,MAT_LOCAL,&info);CHKERRQ(ierr);
      dir->actualfill = info.fill_ratio_needed;
      ierr = PetscLogObjectParent(pc,((PC_Factor*)dir)->fact);CHKERRQ(ierr);
    }
    ierr = MatCholeskyFactorNumeric(((PC_Factor*)dir)->fact,pc->pmat,&((PC_Factor*)dir)->info);CHKERRQ(ierr);
  }
  PetscFunctionReturn(0);
}
Beispiel #16
0
  -ov <overlap>   : >=0  amount of overlap between domains\n\n";

#include <petscmat.h>

int main(int argc,char **args)
{
  PetscErrorCode ierr;
  PetscInt       nd = 2,ov=1,i,start,m,n,end,lsize;
  PetscMPIInt    rank;
  PetscBool      flg;
  Mat            A,B;
  char           file[PETSC_MAX_PATH_LEN];
  PetscViewer    fd;
  IS             *is1,*is2;
  PetscRandom    r;
  PetscScalar    rand;

  ierr = PetscInitialize(&argc,&args,(char*)0,help);if (ierr) return ierr;
#if defined(PETSC_USE_COMPLEX)
  SETERRQ(PETSC_COMM_WORLD,1,"This example does not work with complex numbers");
#else

  ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr);
  ierr = PetscOptionsGetString(NULL,NULL,"-f",file,PETSC_MAX_PATH_LEN,&flg);CHKERRQ(ierr);
  if (!flg) SETERRQ(PETSC_COMM_WORLD,1,"Must use -f filename to indicate a file containing a PETSc binary matrix");
  ierr = PetscOptionsGetInt(NULL,NULL,"-nd",&nd,NULL);CHKERRQ(ierr);
  ierr = PetscOptionsGetInt(NULL,NULL,"-ov",&ov,NULL);CHKERRQ(ierr);

  /* Read matrix and RHS */
  ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,file,FILE_MODE_READ,&fd);CHKERRQ(ierr);
  ierr = MatCreate(PETSC_COMM_WORLD,&A);CHKERRQ(ierr);
  ierr = MatSetType(A,MATMPIAIJ);CHKERRQ(ierr);
  ierr = MatLoad(A,fd);CHKERRQ(ierr);
  ierr = MatSetFromOptions(A);CHKERRQ(ierr);
  ierr = PetscViewerDestroy(&fd);CHKERRQ(ierr);

  /* Read the matrix again as a sequential matrix */
  ierr = PetscViewerBinaryOpen(PETSC_COMM_SELF,file,FILE_MODE_READ,&fd);CHKERRQ(ierr);
  ierr = MatCreate(PETSC_COMM_SELF,&B);CHKERRQ(ierr);
  ierr = MatSetType(B,MATSEQAIJ);CHKERRQ(ierr);
  ierr = MatLoad(B,fd);CHKERRQ(ierr);
  ierr = MatSetFromOptions(B);CHKERRQ(ierr);
  ierr = PetscViewerDestroy(&fd);CHKERRQ(ierr);

  /* Create the IS corresponding to subdomains */
  ierr = PetscMalloc1(nd,&is1);CHKERRQ(ierr);
  ierr = PetscMalloc1(nd,&is2);CHKERRQ(ierr);

  /* Create the random Index Sets */
  ierr = MatGetSize(A,&m,&n);CHKERRQ(ierr);
  ierr = PetscRandomCreate(PETSC_COMM_SELF,&r);CHKERRQ(ierr);
  ierr = PetscRandomSetFromOptions(r);CHKERRQ(ierr);
  for (i=0; i<nd; i++) {
    ierr  = PetscRandomGetValue(r,&rand);CHKERRQ(ierr);
    start = (PetscInt)(rand*m);
    ierr  = PetscRandomGetValue(r,&rand);CHKERRQ(ierr);
    end   = (PetscInt)(rand*m);
    lsize =  end - start;
    if (start > end) { start = end; lsize = -lsize;}
    ierr = ISCreateStride(PETSC_COMM_SELF,lsize,start,1,is1+i);CHKERRQ(ierr);
    ierr = ISCreateStride(PETSC_COMM_SELF,lsize,start,1,is2+i);CHKERRQ(ierr);
  }
  ierr = MatIncreaseOverlap(A,nd,is1,ov);CHKERRQ(ierr);
  ierr = MatIncreaseOverlap(B,nd,is2,ov);CHKERRQ(ierr);
  /* Now see if the serial and parallel case have the same answers */
  for (i=0; i<nd; ++i) {
    ierr = ISEqual(is1[i],is2[i],&flg);CHKERRQ(ierr);
    ierr = PetscPrintf(PETSC_COMM_SELF,"proc:[%d], i=%D, flg =%d\n",rank,i,(int)flg);CHKERRQ(ierr);
  }

  /* Free allocated memory */
  for (i=0; i<nd; ++i) {
    ierr = ISDestroy(&is1[i]);CHKERRQ(ierr);
    ierr = ISDestroy(&is2[i]);CHKERRQ(ierr);
  }
  ierr = PetscFree(is1);CHKERRQ(ierr);
  ierr = PetscFree(is2);CHKERRQ(ierr);
  ierr = PetscRandomDestroy(&r);CHKERRQ(ierr);
  ierr = MatDestroy(&A);CHKERRQ(ierr);
  ierr = MatDestroy(&B);CHKERRQ(ierr);
#endif
  ierr = PetscFinalize();
  return ierr;
}