Actual source code: sorder.c


  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: 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;
170:   PetscErrorCode (*r)(Mat,MatOrderingType,IS*,IS*);
171:   PetscBool      flg,ismpiaij;

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");
179:   if (!type) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_NULL,"Ordering type cannot be null");

181:   PetscStrcmp(type,MATORDERINGEXTERNAL,&flg);
182:   if (flg) {
183:     *rperm = NULL;
184:     *cperm = NULL;
185:     return(0);
186:   }

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

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

219:   if (!mat->rmap->N) { /* matrix has zero rows */
220:     ISCreateStride(PETSC_COMM_SELF,0,0,1,cperm);
221:     ISCreateStride(PETSC_COMM_SELF,0,0,1,rperm);
222:     ISSetIdentity(*cperm);
223:     ISSetIdentity(*rperm);
224:     return(0);
225:   }

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

230:   MatOrderingRegisterAll();
231:   PetscFunctionListFind(MatOrderingList,type,&r);
232:   if (!r) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Unknown or unregistered type: %s",type);

234:   PetscLogEventBegin(MAT_GetOrdering,mat,0,0,0);
235:   (*r)(mat,type,rperm,cperm);
236:   ISSetPermutation(*rperm);
237:   ISSetPermutation(*cperm);
238:   /* Adjust for inode (reduced matrix ordering) only if row permutation is smaller the matrix size */
239:   ISGetLocalSize(*rperm,&mis);
240:   if (mmat > mis) {MatInodeAdjustForInodes(mat,rperm,cperm);}
241:   PetscLogEventEnd(MAT_GetOrdering,mat,0,0,0);

243:   PetscOptionsHasName(((PetscObject)mat)->options,((PetscObject)mat)->prefix,"-mat_view_ordering",&flg);
244:   if (flg) {
245:     Mat tmat;
246:     MatPermute(mat,*rperm,*cperm,&tmat);
247:     MatViewFromOptions(tmat,(PetscObject)mat,"-mat_view_ordering");
248:     MatDestroy(&tmat);
249:   }
250:   return(0);
251: }

253: PetscErrorCode MatGetOrderingList(PetscFunctionList *list)
254: {
256:   *list = MatOrderingList;
257:   return(0);
258: }