Date: 2021-03-03T22:26:42+00:00

Actual source code: sorder.c
petsc-3.14.5 2021-03-03
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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>

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

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

     14: PetscErrorCode MatGetOrdering_Flow(Mat mat,MatOrderingType type,IS *irow,IS *icol)
     15: {
     17:   SETERRQ(PetscObjectComm((PetscObject)mat),PETSC_ERR_SUP,"Cannot do default flow ordering for matrix type");
     18: }

     20: PETSC_INTERN PetscErrorCode MatGetOrdering_Natural(Mat mat,MatOrderingType type,IS *irow,IS *icol)
     21: {
     23:   PetscInt       n,i,*ii;
     24:   PetscBool      done;
     25:   MPI_Comm       comm;

     28:   PetscObjectGetComm((PetscObject)mat,&comm);
     29:   MatGetRowIJ(mat,0,PETSC_FALSE,PETSC_TRUE,&n,NULL,NULL,&done);
     30:   MatRestoreRowIJ(mat,0,PETSC_FALSE,PETSC_TRUE,NULL,NULL,NULL,&done);
     31:   if (done) { /* matrix may be "compressed" in symbolic factorization, due to i-nodes or block storage */
     32:     /*
     33:       We actually create general index sets because this avoids mallocs to
     34:       to obtain the indices in the MatSolve() routines.
     35:       ISCreateStride(PETSC_COMM_SELF,n,0,1,irow);
     36:       ISCreateStride(PETSC_COMM_SELF,n,0,1,icol);
     37:     */
     38:     PetscMalloc1(n,&ii);
     39:     for (i=0; i<n; i++) ii[i] = i;
     40:     ISCreateGeneral(PETSC_COMM_SELF,n,ii,PETSC_COPY_VALUES,irow);
     41:     ISCreateGeneral(PETSC_COMM_SELF,n,ii,PETSC_OWN_POINTER,icol);
     42:   } else {
     43:     PetscInt start,end;

     45:     MatGetOwnershipRange(mat,&start,&end);
     46:     ISCreateStride(comm,end-start,start,1,irow);
     47:     ISCreateStride(comm,end-start,start,1,icol);
     48:   }
     49:   ISSetIdentity(*irow);
     50:   ISSetIdentity(*icol);
     51:   return(0);
     52: }

     54: /*
     55:      Orders the rows (and columns) by the lengths of the rows.
     56:    This produces a symmetric Ordering but does not require a
     57:    matrix with symmetric non-zero structure.
     58: */
     59: PETSC_INTERN PetscErrorCode MatGetOrdering_RowLength(Mat mat,MatOrderingType type,IS *irow,IS *icol)
     60: {
     62:   PetscInt       n,*permr,*lens,i;
     63:   const PetscInt *ia,*ja;
     64:   PetscBool      done;

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

     70:   PetscMalloc2(n,&lens,n,&permr);
     71:   for (i=0; i<n; i++) {
     72:     lens[i]  = ia[i+1] - ia[i];
     73:     permr[i] = i;
     74:   }
     75:   MatRestoreRowIJ(mat,0,PETSC_FALSE,PETSC_TRUE,NULL,&ia,&ja,&done);

     77:   PetscSortIntWithPermutation(n,lens,permr);

     79:   ISCreateGeneral(PETSC_COMM_SELF,n,permr,PETSC_COPY_VALUES,irow);
     80:   ISCreateGeneral(PETSC_COMM_SELF,n,permr,PETSC_COPY_VALUES,icol);
     81:   PetscFree2(lens,permr);
     82:   return(0);
     83: }

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

     88:    Not Collective

     90:    Input Parameters:
     91: +  sname - name of ordering (for example MATORDERINGND)
     92: -  function - function pointer that creates the ordering

     94:    Level: developer

     96:    Sample usage:
     97: .vb
     98:    MatOrderingRegister("my_order", MyOrder);
     99: .ve

    101:    Then, your partitioner can be chosen with the procedural interface via
    102: $     MatOrderingSetType(part,"my_order)
    103:    or at runtime via the option
    104: $     -pc_factor_mat_ordering_type my_order

    106: .seealso: MatOrderingRegisterDestroy(), MatOrderingRegisterAll()
    107: @*/
    108: PetscErrorCode  MatOrderingRegister(const char sname[],PetscErrorCode (*function)(Mat,MatOrderingType,IS*,IS*))
    109: {

    113:   MatInitializePackage();
    114:   PetscFunctionListAdd(&MatOrderingList,sname,function);
    115:   return(0);
    116: }

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

    123:    Collective on Mat

    125:    Input Parameters:
    126: +  mat - the matrix
    127: -  type - type of reordering, one of the following:
    128: $      MATORDERINGNATURAL_OR_ND - Nested dissection unless matrix is SBAIJ then it is natural
    129: $      MATORDERINGNATURAL - Natural
    130: $      MATORDERINGND - Nested Dissection
    131: $      MATORDERING1WD - One-way Dissection
    132: $      MATORDERINGRCM - Reverse Cuthill-McKee
    133: $      MATORDERINGQMD - Quotient Minimum Degree
    134: $      MATORDERINGEXTERNAL - Use an ordering internal to the factorzation package and do not compute or use PETSc's

    136:    Output Parameters:
    137: +  rperm - row permutation indices
    138: -  cperm - column permutation indices

    140:    Options Database Key:
    141: + -mat_view_ordering draw - plots matrix nonzero structure in new ordering
    142: - -pc_factor_mat_ordering_type <nd,natural,..> - ordering to use with PCs based on factorization, LU, ILU, Cholesky, ICC

    144:    Level: intermediate

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

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

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

    155:    Some external packages that PETSc can use for direct factorization such as SuperLU do not accept orderings provided by
    156:    this call.

    158:    If MATORDERINGEXTERNAL is used then PETSc does not compute an ordering and utilizes one built into the factorization package

    160:            fill, reordering, natural, Nested Dissection,
    161:            One-way Dissection, Cholesky, Reverse Cuthill-McKee,
    162:            Quotient Minimum Degree

    164: .seealso:   MatOrderingRegister(), PCFactorSetMatOrderingType(), MatColoring, MatColoringCreate()
    165: @*/
    166: PetscErrorCode  MatGetOrdering(Mat mat,MatOrderingType type,IS *rperm,IS *cperm)
    167: {
    169:   PetscInt       mmat,nmat,mis,m;
    170:   PetscErrorCode (*r)(Mat,MatOrderingType,IS*,IS*);
    171:   PetscBool      flg = PETSC_FALSE,isseqdense,ismpidense,ismpiaij,ismpibaij,ismpisbaij,ismpiaijcusparse,iselemental,isscalapack,flg1;

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

    180:   PetscStrcmp(type,MATORDERINGEXTERNAL,&flg1);
    181:   if (flg1) {
    182:     *rperm = NULL;
    183:     *cperm = NULL;
    184:     return(0);
    185:   }

    187:   PetscStrcmp(type,MATORDERINGNATURAL_OR_ND,&flg1);
    188:   if (flg1) {
    189:     PetscBool isseqsbaij;
    190:     PetscObjectTypeCompareAny((PetscObject)mat,&isseqsbaij,MATSEQSBAIJ,MATSEQBAIJ,NULL);
    191:     if (isseqsbaij) {
    192:       type = MATORDERINGNATURAL;
    193:     } else {
    194:       type = MATORDERINGND;
    195:     }
    196:   }

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

    207:     MatMPIAIJGetSeqAIJ(mat,&Ad,&Ao,&colmap);
    208:     MatGetOrdering(Ad,type,&lrowperm,&lcolperm);
    209:     MatGetOwnershipRange(mat,&rstart,&rend);
    210:     /* Remap row index set to global space */
    211:     ISGetIndices(lrowperm,&lidx);
    212:     PetscMalloc1(rend-rstart,&idx);
    213:     for (i=0; i+rstart<rend; i++) idx[i] = rstart + lidx[i];
    214:     ISRestoreIndices(lrowperm,&lidx);
    215:     ISDestroy(&lrowperm);
    216:     ISCreateGeneral(PetscObjectComm((PetscObject)mat),rend-rstart,idx,PETSC_OWN_POINTER,rperm);
    217:     ISSetPermutation(*rperm);
    218:     /* Remap column index set to global space */
    219:     ISGetIndices(lcolperm,&lidx);
    220:     PetscMalloc1(rend-rstart,&idx);
    221:     for (i=0; i+rstart<rend; i++) idx[i] = rstart + lidx[i];
    222:     ISRestoreIndices(lcolperm,&lidx);
    223:     ISDestroy(&lcolperm);
    224:     ISCreateGeneral(PetscObjectComm((PetscObject)mat),rend-rstart,idx,PETSC_OWN_POINTER,cperm);
    225:     ISSetPermutation(*cperm);
    226:     return(0);
    227:   }

    229:   /* this chunk of code is REALLY bad, should maybe get the ordering from the factor matrix,
    230:      then those that don't support orderings will handle their cases themselves. */
    231:   PetscObjectTypeCompare((PetscObject)mat,MATSEQDENSE,&isseqdense);
    232:   PetscObjectTypeCompare((PetscObject)mat,MATMPIDENSE,&ismpidense);
    233:   PetscObjectTypeCompare((PetscObject)mat,MATMPIAIJCUSPARSE,&ismpiaijcusparse);
    234:   PetscObjectTypeCompare((PetscObject)mat,MATMPIBAIJ,&ismpibaij);
    235:   PetscObjectTypeCompare((PetscObject)mat,MATMPISBAIJ,&ismpisbaij);
    236:   PetscObjectTypeCompare((PetscObject)mat,MATELEMENTAL,&iselemental);
    237:   PetscObjectTypeCompare((PetscObject)mat,MATSCALAPACK,&isscalapack);
    238:   if (isseqdense || ismpidense || ismpibaij || ismpisbaij || ismpiaijcusparse || iselemental || isscalapack) {
    239:     MatGetLocalSize(mat,&m,NULL);
    240:     /*
    241:        These matrices only give natural ordering
    242:     */
    243:     ISCreateStride(PETSC_COMM_SELF,m,0,1,cperm);
    244:     ISCreateStride(PETSC_COMM_SELF,m,0,1,rperm);
    245:     ISSetIdentity(*cperm);
    246:     ISSetIdentity(*rperm);
    247:     return(0);
    248:   }

    250:   if (!mat->rmap->N) { /* matrix has zero rows */
    251:     ISCreateStride(PETSC_COMM_SELF,0,0,1,cperm);
    252:     ISCreateStride(PETSC_COMM_SELF,0,0,1,rperm);
    253:     ISSetIdentity(*cperm);
    254:     ISSetIdentity(*rperm);
    255:     return(0);
    256:   }

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

    261:   MatOrderingRegisterAll();
    262:   PetscFunctionListFind(MatOrderingList,type,&r);
    263:   if (!r) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Unknown or unregistered type: %s",type);

    265:   PetscLogEventBegin(MAT_GetOrdering,mat,0,0,0);
    266:   (*r)(mat,type,rperm,cperm);
    267:   ISSetPermutation(*rperm);
    268:   ISSetPermutation(*cperm);
    269:   /* Adjust for inode (reduced matrix ordering) only if row permutation is smaller the matrix size */
    270:   ISGetLocalSize(*rperm,&mis);
    271:   if (mmat > mis) {MatInodeAdjustForInodes(mat,rperm,cperm);}
    272:   PetscLogEventEnd(MAT_GetOrdering,mat,0,0,0);

    275:   PetscOptionsHasName(((PetscObject)mat)->options,((PetscObject)mat)->prefix,"-mat_view_ordering",&flg);
    276:   if (flg) {
    277:     Mat tmat;
    278:     MatPermute(mat,*rperm,*cperm,&tmat);
    279:     MatViewFromOptions(tmat,(PetscObject)mat,"-mat_view_ordering");
    280:     MatDestroy(&tmat);
    281:   }
    282:   return(0);
    283: }

    285: PetscErrorCode MatGetOrderingList(PetscFunctionList *list)
    286: {
    288:   *list = MatOrderingList;
    289:   return(0);
    290: }