Actual source code: sorder.c

petsc-3.4.4 2014-03-13
  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:     PetscMalloc(n*sizeof(PetscInt),&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,PetscInt,&lens,n,PetscInt,&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:     PetscMalloc((rend-rstart)*sizeof(PetscInt),&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:     PetscMalloc((rend-rstart)*sizeof(PetscInt),&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:     ISSetPermutation(*rperm);
242:     ISSetPermutation(*cperm);
243:     return(0);
244:   }

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

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

259:   if (!MatOrderingRegisterAllCalled) {MatOrderingRegisterAll();}
260:   PetscFunctionListFind(MatOrderingList,type,&r);
261:   if (!r) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Unknown or unregistered type: %s",type);

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


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

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