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: {
 16:   SETERRQ(PetscObjectComm((PetscObject)mat),PETSC_ERR_SUP,"Cannot do default flow ordering for matrix type");
 17: }

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

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

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

 51: /*
 52:      Orders the rows (and columns) by the lengths of the rows.
 53:    This produces a symmetric Ordering but does not require a
 54:    matrix with symmetric non-zero structure.
 55: */
 56: PETSC_INTERN PetscErrorCode MatGetOrdering_RowLength(Mat mat,MatOrderingType type,IS *irow,IS *icol)
 57: {
 58:   PetscInt       n,*permr,*lens,i;
 59:   const PetscInt *ia,*ja;
 60:   PetscBool      done;

 62:   MatGetRowIJ(mat,0,PETSC_FALSE,PETSC_TRUE,&n,&ia,&ja,&done);

 65:   PetscMalloc2(n,&lens,n,&permr);
 66:   for (i=0; i<n; i++) {
 67:     lens[i]  = ia[i+1] - ia[i];
 68:     permr[i] = i;
 69:   }
 70:   MatRestoreRowIJ(mat,0,PETSC_FALSE,PETSC_TRUE,NULL,&ia,&ja,&done);

 72:   PetscSortIntWithPermutation(n,lens,permr);

 74:   ISCreateGeneral(PETSC_COMM_SELF,n,permr,PETSC_COPY_VALUES,irow);
 75:   ISCreateGeneral(PETSC_COMM_SELF,n,permr,PETSC_COPY_VALUES,icol);
 76:   PetscFree2(lens,permr);
 77:   return 0;
 78: }

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

 83:    Not Collective

 85:    Input Parameters:
 86: +  sname - name of ordering (for example MATORDERINGND)
 87: -  function - function pointer that creates the ordering

 89:    Level: developer

 91:    Sample usage:
 92: .vb
 93:    MatOrderingRegister("my_order", MyOrder);
 94: .ve

 96:    Then, your partitioner can be chosen with the procedural interface via
 97: $     MatOrderingSetType(part,"my_order)
 98:    or at runtime via the option
 99: $     -pc_factor_mat_ordering_type my_order

101: .seealso: MatOrderingRegisterAll()
102: @*/
103: PetscErrorCode  MatOrderingRegister(const char sname[],PetscErrorCode (*function)(Mat,MatOrderingType,IS*,IS*))
104: {
105:   MatInitializePackage();
106:   PetscFunctionListAdd(&MatOrderingList,sname,function);
107:   return 0;
108: }

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

115:    Collective on Mat

117:    Input Parameters:
118: +  mat - the matrix
119: -  type - type of reordering, one of the following:
120: $      MATORDERINGNATURAL_OR_ND - Nested dissection unless matrix is SBAIJ then it is natural
121: $      MATORDERINGNATURAL - Natural
122: $      MATORDERINGND - Nested Dissection
123: $      MATORDERING1WD - One-way Dissection
124: $      MATORDERINGRCM - Reverse Cuthill-McKee
125: $      MATORDERINGQMD - Quotient Minimum Degree
126: $      MATORDERINGEXTERNAL - Use an ordering internal to the factorzation package and do not compute or use PETSc's

128:    Output Parameters:
129: +  rperm - row permutation indices
130: -  cperm - column permutation indices

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

136:    Level: intermediate

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

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

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

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

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

152:            fill, reordering, natural, Nested Dissection,
153:            One-way Dissection, Cholesky, Reverse Cuthill-McKee,
154:            Quotient Minimum Degree

156: .seealso:   MatOrderingRegister(), PCFactorSetMatOrderingType(), MatColoring, MatColoringCreate()
157: @*/
158: PetscErrorCode  MatGetOrdering(Mat mat,MatOrderingType type,IS *rperm,IS *cperm)
159: {
160:   PetscInt       mmat,nmat,mis;
161:   PetscErrorCode (*r)(Mat,MatOrderingType,IS*,IS*);
162:   PetscBool      flg,ismpiaij;


171:   PetscStrcmp(type,MATORDERINGEXTERNAL,&flg);
172:   if (flg) {
173:     *rperm = NULL;
174:     *cperm = NULL;
175:     return 0;
176:   }

178:   /* This code is terrible. MatGetOrdering() multiple dispatch should use matrix and this code should move to impls/aij/mpi. */
179:   PetscObjectTypeCompare((PetscObject)mat,MATMPIAIJ,&ismpiaij);
180:   if (ismpiaij) {               /* Reorder using diagonal block */
181:     Mat            Ad,Ao;
182:     const PetscInt *colmap;
183:     IS             lrowperm,lcolperm;
184:     PetscInt       i,rstart,rend,*idx;
185:     const PetscInt *lidx;

187:     MatMPIAIJGetSeqAIJ(mat,&Ad,&Ao,&colmap);
188:     MatGetOrdering(Ad,type,&lrowperm,&lcolperm);
189:     MatGetOwnershipRange(mat,&rstart,&rend);
190:     /* Remap row index set to global space */
191:     ISGetIndices(lrowperm,&lidx);
192:     PetscMalloc1(rend-rstart,&idx);
193:     for (i=0; i+rstart<rend; i++) idx[i] = rstart + lidx[i];
194:     ISRestoreIndices(lrowperm,&lidx);
195:     ISDestroy(&lrowperm);
196:     ISCreateGeneral(PetscObjectComm((PetscObject)mat),rend-rstart,idx,PETSC_OWN_POINTER,rperm);
197:     ISSetPermutation(*rperm);
198:     /* Remap column index set to global space */
199:     ISGetIndices(lcolperm,&lidx);
200:     PetscMalloc1(rend-rstart,&idx);
201:     for (i=0; i+rstart<rend; i++) idx[i] = rstart + lidx[i];
202:     ISRestoreIndices(lcolperm,&lidx);
203:     ISDestroy(&lcolperm);
204:     ISCreateGeneral(PetscObjectComm((PetscObject)mat),rend-rstart,idx,PETSC_OWN_POINTER,cperm);
205:     ISSetPermutation(*cperm);
206:     return 0;
207:   }

209:   if (!mat->rmap->N) { /* matrix has zero rows */
210:     ISCreateStride(PETSC_COMM_SELF,0,0,1,cperm);
211:     ISCreateStride(PETSC_COMM_SELF,0,0,1,rperm);
212:     ISSetIdentity(*cperm);
213:     ISSetIdentity(*rperm);
214:     return 0;
215:   }

217:   MatGetLocalSize(mat,&mmat,&nmat);

220:   MatOrderingRegisterAll();
221:   PetscFunctionListFind(MatOrderingList,type,&r);

224:   PetscLogEventBegin(MAT_GetOrdering,mat,0,0,0);
225:   (*r)(mat,type,rperm,cperm);
226:   ISSetPermutation(*rperm);
227:   ISSetPermutation(*cperm);
228:   /* Adjust for inode (reduced matrix ordering) only if row permutation is smaller the matrix size */
229:   ISGetLocalSize(*rperm,&mis);
230:   if (mmat > mis) MatInodeAdjustForInodes(mat,rperm,cperm);
231:   PetscLogEventEnd(MAT_GetOrdering,mat,0,0,0);

233:   PetscOptionsHasName(((PetscObject)mat)->options,((PetscObject)mat)->prefix,"-mat_view_ordering",&flg);
234:   if (flg) {
235:     Mat tmat;
236:     MatPermute(mat,*rperm,*cperm,&tmat);
237:     MatViewFromOptions(tmat,(PetscObject)mat,"-mat_view_ordering");
238:     MatDestroy(&tmat);
239:   }
240:   return 0;
241: }

243: PetscErrorCode MatGetOrderingList(PetscFunctionList *list)
244: {
245:   *list = MatOrderingList;
246:   return 0;
247: }