Date: 2015-10-02T22:12:35+00:00

Actual source code: sorder.c
petsc-3.6.2 2015-10-02
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      2: /*
      3:      Provides the code that allows PETSc users to register their own
      4:   sequential matrix Ordering routines.
      5: */
      6: #include <petsc/private/matimpl.h>
      7: #include <petscmat.h>  /*I "petscmat.h" I*/

      9: PetscFunctionList MatOrderingList              = 0;
     10: PetscBool         MatOrderingRegisterAllCalled = PETSC_FALSE;

     12: extern PetscErrorCode MatGetOrdering_Flow_SeqAIJ(Mat,MatOrderingType,IS*,IS*);

     16: PetscErrorCode MatGetOrdering_Flow(Mat mat,MatOrderingType type,IS *irow,IS *icol)
     17: {
     19:   SETERRQ(PetscObjectComm((PetscObject)mat),PETSC_ERR_SUP,"Cannot do default flow ordering for matrix type");
     20: #if !defined(PETSC_USE_DEBUG)
     21:   return(0);
     22: #endif
     23: }

     27: PETSC_EXTERN PetscErrorCode MatGetOrdering_Natural(Mat mat,MatOrderingType type,IS *irow,IS *icol)
     28: {
     30:   PetscInt       n,i,*ii;
     31:   PetscBool      done;
     32:   MPI_Comm       comm;

     35:   PetscObjectGetComm((PetscObject)mat,&comm);
     36:   MatGetRowIJ(mat,0,PETSC_FALSE,PETSC_TRUE,&n,NULL,NULL,&done);
     37:   MatRestoreRowIJ(mat,0,PETSC_FALSE,PETSC_TRUE,NULL,NULL,NULL,&done);
     38:   if (done) { /* matrix may be "compressed" in symbolic factorization, due to i-nodes or block storage */
     39:     /*
     40:       We actually create general index sets because this avoids mallocs to
     41:       to obtain the indices in the MatSolve() routines.
     42:       ISCreateStride(PETSC_COMM_SELF,n,0,1,irow);
     43:       ISCreateStride(PETSC_COMM_SELF,n,0,1,icol);
     44:     */
     45:     PetscMalloc1(n,&ii);
     46:     for (i=0; i<n; i++) ii[i] = i;
     47:     ISCreateGeneral(PETSC_COMM_SELF,n,ii,PETSC_COPY_VALUES,irow);
     48:     ISCreateGeneral(PETSC_COMM_SELF,n,ii,PETSC_OWN_POINTER,icol);
     49:   } else {
     50:     PetscInt start,end;

     52:     MatGetOwnershipRange(mat,&start,&end);
     53:     ISCreateStride(comm,end-start,start,1,irow);
     54:     ISCreateStride(comm,end-start,start,1,icol);
     55:   }
     56:   ISSetIdentity(*irow);
     57:   ISSetIdentity(*icol);
     58:   return(0);
     59: }

     61: /*
     62:      Orders the rows (and columns) by the lengths of the rows.
     63:    This produces a symmetric Ordering but does not require a
     64:    matrix with symmetric non-zero structure.
     65: */
     68: PETSC_EXTERN PetscErrorCode MatGetOrdering_RowLength(Mat mat,MatOrderingType type,IS *irow,IS *icol)
     69: {
     71:   PetscInt       n,*permr,*lens,i;
     72:   const PetscInt *ia,*ja;
     73:   PetscBool      done;

     76:   MatGetRowIJ(mat,0,PETSC_FALSE,PETSC_TRUE,&n,&ia,&ja,&done);
     77:   if (!done) SETERRQ(PetscObjectComm((PetscObject)mat),PETSC_ERR_SUP,"Cannot get rows for matrix");

     79:   PetscMalloc2(n,&lens,n,&permr);
     80:   for (i=0; i<n; i++) {
     81:     lens[i]  = ia[i+1] - ia[i];
     82:     permr[i] = i;
     83:   }
     84:   MatRestoreRowIJ(mat,0,PETSC_FALSE,PETSC_TRUE,NULL,&ia,&ja,&done);

     86:   PetscSortIntWithPermutation(n,lens,permr);

     88:   ISCreateGeneral(PETSC_COMM_SELF,n,permr,PETSC_COPY_VALUES,irow);
     89:   ISCreateGeneral(PETSC_COMM_SELF,n,permr,PETSC_COPY_VALUES,icol);
     90:   PetscFree2(lens,permr);
     91:   return(0);
     92: }

     96: /*@C
     97:    MatOrderingRegister - Adds a new sparse matrix ordering to the matrix package.

     99:    Not Collective

    101:    Input Parameters:
    102: +  sname - name of ordering (for example MATORDERINGND)
    103: -  function - function pointer that creates the ordering

    105:    Level: developer

    107:    Sample usage:
    108: .vb
    109:    MatOrderingRegister("my_order", MyOrder);
    110: .ve

    112:    Then, your partitioner can be chosen with the procedural interface via
    113: $     MatOrderingSetType(part,"my_order)
    114:    or at runtime via the option
    115: $     -pc_factor_mat_ordering_type my_order

    117: .keywords: matrix, ordering, register

    119: .seealso: MatOrderingRegisterDestroy(), MatOrderingRegisterAll()
    120: @*/
    121: PetscErrorCode  MatOrderingRegister(const char sname[],PetscErrorCode (*function)(Mat,MatOrderingType,IS*,IS*))
    122: {

    126:   PetscFunctionListAdd(&MatOrderingList,sname,function);
    127:   return(0);
    128: }

    130: #include <../src/mat/impls/aij/mpi/mpiaij.h>
    133: /*@C
    134:    MatGetOrdering - Gets a reordering for a matrix to reduce fill or to
    135:    improve numerical stability of LU factorization.

    137:    Collective on Mat

    139:    Input Parameters:
    140: +  mat - the matrix
    141: -  type - type of reordering, one of the following:
    142: $      MATORDERINGNATURAL - Natural
    143: $      MATORDERINGND - Nested Dissection
    144: $      MATORDERING1WD - One-way Dissection
    145: $      MATORDERINGRCM - Reverse Cuthill-McKee
    146: $      MATORDERINGQMD - Quotient Minimum Degree

    148:    Output Parameters:
    149: +  rperm - row permutation indices
    150: -  cperm - column permutation indices

    153:    Options Database Key:
    154: . -mat_view_ordering draw - plots matrix nonzero structure in new ordering

    156:    Level: intermediate

    158:    Notes:
    159:       This DOES NOT actually reorder the matrix; it merely returns two index sets
    160:    that define a reordering. This is usually not used directly, rather use the
    161:    options PCFactorSetMatOrderingType()

    163:    The user can define additional orderings; see MatOrderingRegister().

    165:    These are generally only implemented for sequential sparse matrices.

    167:    The external packages that PETSc can use for direct factorization such as SuperLU do not accept orderings provided by
    168:    this call.

    171: .keywords: matrix, set, ordering, factorization, direct, ILU, LU,
    172:            fill, reordering, natural, Nested Dissection,
    173:            One-way Dissection, Cholesky, Reverse Cuthill-McKee,
    174:            Quotient Minimum Degree

    176: .seealso:   MatOrderingRegister(), PCFactorSetMatOrderingType()
    177: @*/
    178: PetscErrorCode  MatGetOrdering(Mat mat,MatOrderingType type,IS *rperm,IS *cperm)
    179: {
    181:   PetscInt       mmat,nmat,mis,m;
    182:   PetscErrorCode (*r)(Mat,MatOrderingType,IS*,IS*);
    183:   PetscBool      flg = PETSC_FALSE,isseqdense,ismpidense,ismpiaij,ismpibaij,ismpisbaij,ismpiaijcusp,ismpiaijcusparse,iselemental;

    189:   if (!mat->assembled) SETERRQ(PetscObjectComm((PetscObject)mat),PETSC_ERR_ARG_WRONGSTATE,"Not for unassembled matrix");
    190:   if (mat->factortype) SETERRQ(PetscObjectComm((PetscObject)mat),PETSC_ERR_ARG_WRONGSTATE,"Not for factored matrix");

    192:   /* This code is terrible. MatGetOrdering() multiple dispatch should use matrix and this code should move to impls/aij/mpi. */
    193:   PetscObjectTypeCompare((PetscObject)mat,MATMPIAIJ,&ismpiaij);
    194:   if (ismpiaij) {               /* Reorder using diagonal block */
    195:     Mat            Ad,Ao;
    196:     const PetscInt *colmap;
    197:     IS             lrowperm,lcolperm;
    198:     PetscInt       i,rstart,rend,*idx;
    199:     const PetscInt *lidx;

    201:     MatMPIAIJGetSeqAIJ(mat,&Ad,&Ao,&colmap);
    202:     MatGetOrdering(Ad,type,&lrowperm,&lcolperm);
    203:     MatGetOwnershipRange(mat,&rstart,&rend);
    204:     /* Remap row index set to global space */
    205:     ISGetIndices(lrowperm,&lidx);
    206:     PetscMalloc1(rend-rstart,&idx);
    207:     for (i=0; i+rstart<rend; i++) idx[i] = rstart + lidx[i];
    208:     ISRestoreIndices(lrowperm,&lidx);
    209:     ISDestroy(&lrowperm);
    210:     ISCreateGeneral(PetscObjectComm((PetscObject)mat),rend-rstart,idx,PETSC_OWN_POINTER,rperm);
    211:     ISSetPermutation(*rperm);
    212:     /* Remap column index set to global space */
    213:     ISGetIndices(lcolperm,&lidx);
    214:     PetscMalloc1(rend-rstart,&idx);
    215:     for (i=0; i+rstart<rend; i++) idx[i] = rstart + lidx[i];
    216:     ISRestoreIndices(lcolperm,&lidx);
    217:     ISDestroy(&lcolperm);
    218:     ISCreateGeneral(PetscObjectComm((PetscObject)mat),rend-rstart,idx,PETSC_OWN_POINTER,cperm);
    219:     ISSetPermutation(*cperm);
    220:     return(0);
    221:   }

    223:   /* this chunk of code is REALLY bad, should maybe get the ordering from the factor matrix,
    224:      then those that don't support orderings will handle their cases themselves. */
    225:   PetscObjectTypeCompare((PetscObject)mat,MATSEQDENSE,&isseqdense);
    226:   PetscObjectTypeCompare((PetscObject)mat,MATMPIDENSE,&ismpidense);
    227:   PetscObjectTypeCompare((PetscObject)mat,MATMPIAIJCUSP,&ismpiaijcusp);
    228:   PetscObjectTypeCompare((PetscObject)mat,MATMPIAIJCUSPARSE,&ismpiaijcusparse);
    229:   PetscObjectTypeCompare((PetscObject)mat,MATMPIBAIJ,&ismpibaij);
    230:   PetscObjectTypeCompare((PetscObject)mat,MATMPISBAIJ,&ismpisbaij);
    231:   PetscObjectTypeCompare((PetscObject)mat,MATELEMENTAL,&iselemental);
    232:   if (isseqdense || ismpidense || ismpibaij || ismpisbaij || ismpiaijcusp || ismpiaijcusparse || iselemental) {
    233:     MatGetLocalSize(mat,&m,NULL);
    234:     /*
    235:        These matrices only give natural ordering
    236:     */
    237:     ISCreateStride(PETSC_COMM_SELF,m,0,1,cperm);
    238:     ISCreateStride(PETSC_COMM_SELF,m,0,1,rperm);
    239:     ISSetIdentity(*cperm);
    240:     ISSetIdentity(*rperm);
    241:     return(0);
    242:   }

    244:   if (!mat->rmap->N) { /* matrix has zero rows */
    245:     ISCreateStride(PETSC_COMM_SELF,0,0,1,cperm);
    246:     ISCreateStride(PETSC_COMM_SELF,0,0,1,rperm);
    247:     ISSetIdentity(*cperm);
    248:     ISSetIdentity(*rperm);
    249:     return(0);
    250:   }

    252:   MatGetLocalSize(mat,&mmat,&nmat);
    253:   if (mmat != nmat) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"Must be square matrix, rows %D columns %D",mmat,nmat);

    255:   MatOrderingRegisterAll();
    256:   PetscFunctionListFind(MatOrderingList,type,&r);
    257:   if (!r) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Unknown or unregistered type: %s",type);

    259:   PetscLogEventBegin(MAT_GetOrdering,mat,0,0,0);
    260:   (*r)(mat,type,rperm,cperm);
    261:   ISSetPermutation(*rperm);
    262:   ISSetPermutation(*cperm);
    263:   /* Adjust for inode (reduced matrix ordering) only if row permutation is smaller the matrix size */
    264:   ISGetLocalSize(*rperm,&mis);
    265:   if (mmat > mis) {MatInodeAdjustForInodes(mat,rperm,cperm);}
    266:   PetscLogEventEnd(MAT_GetOrdering,mat,0,0,0);

    269:   PetscOptionsHasName(((PetscObject)mat)->prefix,"-mat_view_ordering",&flg);
    270:   if (flg) {
    271:     Mat tmat;
    272:     MatPermute(mat,*rperm,*cperm,&tmat);
    273:     MatViewFromOptions(tmat,(PetscObject)mat,"-mat_view_ordering");
    274:     MatDestroy(&tmat);
    275:   }
    276:   return(0);
    277: }

    281: PetscErrorCode MatGetOrderingList(PetscFunctionList *list)
    282: {
    284:   *list = MatOrderingList;
    285:   return(0);
    286: }