Actual source code: sbaij.c

petsc-dev 2014-02-02
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  2: /*
  3:     Defines the basic matrix operations for the SBAIJ (compressed row)
  4:   matrix storage format.
  5: */
  6: #include <../src/mat/impls/baij/seq/baij.h>         /*I "petscmat.h" I*/
  7: #include <../src/mat/impls/sbaij/seq/sbaij.h>
  8: #include <petscblaslapack.h>

 10: #include <../src/mat/impls/sbaij/seq/relax.h>
 11: #define USESHORT
 12: #include <../src/mat/impls/sbaij/seq/relax.h>

 14: extern PetscErrorCode MatSeqSBAIJSetNumericFactorization_inplace(Mat,PetscBool);

 16: /*
 17:      Checks for missing diagonals
 18: */
 21: PetscErrorCode MatMissingDiagonal_SeqSBAIJ(Mat A,PetscBool  *missing,PetscInt *dd)
 22: {
 23:   Mat_SeqSBAIJ   *a = (Mat_SeqSBAIJ*)A->data;
 25:   PetscInt       *diag,*jj = a->j,i;

 28:   MatMarkDiagonal_SeqSBAIJ(A);
 29:   *missing = PETSC_FALSE;
 30:   if (A->rmap->n > 0 && !jj) {
 31:     *missing = PETSC_TRUE;
 32:     if (dd) *dd = 0;
 33:     PetscInfo(A,"Matrix has no entries therefore is missing diagonal");
 34:   } else {
 35:     diag = a->diag;
 36:     for (i=0; i<a->mbs; i++) {
 37:       if (jj[diag[i]] != i) {
 38:         *missing = PETSC_TRUE;
 39:         if (dd) *dd = i;
 40:         break;
 41:       }
 42:     }
 43:   }
 44:   return(0);
 45: }

 49: PetscErrorCode MatMarkDiagonal_SeqSBAIJ(Mat A)
 50: {
 51:   Mat_SeqSBAIJ   *a = (Mat_SeqSBAIJ*)A->data;
 53:   PetscInt       i;

 56:   if (!a->diag) {
 57:     PetscMalloc1(a->mbs,&a->diag);
 58:     PetscLogObjectMemory((PetscObject)A,a->mbs*sizeof(PetscInt));
 59:     a->free_diag = PETSC_TRUE;
 60:   }
 61:   for (i=0; i<a->mbs; i++) a->diag[i] = a->i[i];
 62:   return(0);
 63: }

 67: static PetscErrorCode MatGetRowIJ_SeqSBAIJ(Mat A,PetscInt oshift,PetscBool symmetric,PetscBool blockcompressed,PetscInt *nn,const PetscInt *inia[],const PetscInt *inja[],PetscBool  *done)
 68: {
 69:   Mat_SeqSBAIJ   *a = (Mat_SeqSBAIJ*)A->data;
 70:   PetscInt       i,j,n = a->mbs,nz = a->i[n],bs = A->rmap->bs;
 71:   PetscInt       **ia = (PetscInt**)inia,**ja = (PetscInt**)inja;

 75:   *nn = n;
 76:   if (!ia) return(0);
 77:   if (!blockcompressed) {
 78:     /* malloc & create the natural set of indices */
 79:     PetscMalloc2((n+1)*bs,ia,nz*bs,ja);
 80:     for (i=0; i<n+1; i++) {
 81:       for (j=0; j<bs; j++) {
 82:         *ia[i*bs+j] = a->i[i]*bs+j+oshift;
 83:       }
 84:     }
 85:     for (i=0; i<nz; i++) {
 86:       for (j=0; j<bs; j++) {
 87:         *ja[i*bs+j] = a->j[i]*bs+j+oshift;
 88:       }
 89:     }
 90:   } else { /* blockcompressed */
 91:     if (oshift == 1) {
 92:       /* temporarily add 1 to i and j indices */
 93:       for (i=0; i<nz; i++) a->j[i]++;
 94:       for (i=0; i<n+1; i++) a->i[i]++;
 95:     }
 96:     *ia = a->i; *ja = a->j;
 97:   }
 98:   return(0);
 99: }

103: static PetscErrorCode MatRestoreRowIJ_SeqSBAIJ(Mat A,PetscInt oshift,PetscBool symmetric,PetscBool blockcompressed,PetscInt *nn,const PetscInt *ia[],const PetscInt *ja[],PetscBool  *done)
104: {
105:   Mat_SeqSBAIJ   *a = (Mat_SeqSBAIJ*)A->data;
106:   PetscInt       i,n = a->mbs,nz = a->i[n];

110:   if (!ia) return(0);

112:   if (!blockcompressed) {
113:     PetscFree2(*ia,*ja);
114:   } else if (oshift == 1) { /* blockcompressed */
115:     for (i=0; i<nz; i++) a->j[i]--;
116:     for (i=0; i<n+1; i++) a->i[i]--;
117:   }
118:   return(0);
119: }

123: PetscErrorCode MatDestroy_SeqSBAIJ(Mat A)
124: {
125:   Mat_SeqSBAIJ   *a = (Mat_SeqSBAIJ*)A->data;

129: #if defined(PETSC_USE_LOG)
130:   PetscLogObjectState((PetscObject)A,"Rows=%D, NZ=%D",A->rmap->N,a->nz);
131: #endif
132:   MatSeqXAIJFreeAIJ(A,&a->a,&a->j,&a->i);
133:   if (a->free_diag) {PetscFree(a->diag);}
134:   ISDestroy(&a->row);
135:   ISDestroy(&a->col);
136:   ISDestroy(&a->icol);
137:   PetscFree(a->idiag);
138:   PetscFree(a->inode.size);
139:   if (a->free_imax_ilen) {PetscFree2(a->imax,a->ilen);}
140:   PetscFree(a->solve_work);
141:   PetscFree(a->sor_work);
142:   PetscFree(a->solves_work);
143:   PetscFree(a->mult_work);
144:   PetscFree(a->saved_values);
145:   PetscFree(a->xtoy);
146:   if (a->free_jshort) {PetscFree(a->jshort);}
147:   PetscFree(a->inew);
148:   MatDestroy(&a->parent);
149:   PetscFree(A->data);

151:   PetscObjectChangeTypeName((PetscObject)A,0);
152:   PetscObjectComposeFunction((PetscObject)A,"MatStoreValues_C",NULL);
153:   PetscObjectComposeFunction((PetscObject)A,"MatRetrieveValues_C",NULL);
154:   PetscObjectComposeFunction((PetscObject)A,"MatSeqSBAIJSetColumnIndices_C",NULL);
155:   PetscObjectComposeFunction((PetscObject)A,"MatConvert_seqsbaij_seqaij_C",NULL);
156:   PetscObjectComposeFunction((PetscObject)A,"MatConvert_seqsbaij_seqbaij_C",NULL);
157:   PetscObjectComposeFunction((PetscObject)A,"MatSeqSBAIJSetPreallocation_C",NULL);
158:   PetscObjectComposeFunction((PetscObject)A,"MatSeqSBAIJSetPreallocationCSR_C",NULL);
159:   PetscObjectComposeFunction((PetscObject)A,"MatConvert_seqsbaij_seqsbstrm_C",NULL);
160:   return(0);
161: }

165: PetscErrorCode MatSetOption_SeqSBAIJ(Mat A,MatOption op,PetscBool flg)
166: {
167:   Mat_SeqSBAIJ   *a = (Mat_SeqSBAIJ*)A->data;

171:   switch (op) {
172:   case MAT_ROW_ORIENTED:
173:     a->roworiented = flg;
174:     break;
175:   case MAT_KEEP_NONZERO_PATTERN:
176:     a->keepnonzeropattern = flg;
177:     break;
178:   case MAT_NEW_NONZERO_LOCATIONS:
179:     a->nonew = (flg ? 0 : 1);
180:     break;
181:   case MAT_NEW_NONZERO_LOCATION_ERR:
182:     a->nonew = (flg ? -1 : 0);
183:     break;
184:   case MAT_NEW_NONZERO_ALLOCATION_ERR:
185:     a->nonew = (flg ? -2 : 0);
186:     break;
187:   case MAT_UNUSED_NONZERO_LOCATION_ERR:
188:     a->nounused = (flg ? -1 : 0);
189:     break;
190:   case MAT_NEW_DIAGONALS:
191:   case MAT_IGNORE_OFF_PROC_ENTRIES:
192:   case MAT_USE_HASH_TABLE:
193:     PetscInfo1(A,"Option %s ignored\n",MatOptions[op]);
194:     break;
195:   case MAT_HERMITIAN:
196:     if (!A->assembled) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Must call MatAssemblyEnd() first");
197:     if (A->cmap->n < 65536 && A->cmap->bs == 1) {
198:       A->ops->mult = MatMult_SeqSBAIJ_1_Hermitian_ushort;
199:     } else if (A->cmap->bs == 1) {
200:       A->ops->mult = MatMult_SeqSBAIJ_1_Hermitian;
201:     } else SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"No support for Hermitian with block size greater than 1");
202:     break;
203:   case MAT_SPD:
204:     /* These options are handled directly by MatSetOption() */
205:     break;
206:   case MAT_SYMMETRIC:
207:   case MAT_STRUCTURALLY_SYMMETRIC:
208:   case MAT_SYMMETRY_ETERNAL:
209:     if (!flg) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Matrix must be symmetric");
210:     PetscInfo1(A,"Option %s not relevent\n",MatOptions[op]);
211:     break;
212:   case MAT_IGNORE_LOWER_TRIANGULAR:
213:     a->ignore_ltriangular = flg;
214:     break;
215:   case MAT_ERROR_LOWER_TRIANGULAR:
216:     a->ignore_ltriangular = flg;
217:     break;
218:   case MAT_GETROW_UPPERTRIANGULAR:
219:     a->getrow_utriangular = flg;
220:     break;
221:   default:
222:     SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP,"unknown option %d",op);
223:   }
224:   return(0);
225: }

229: PetscErrorCode MatGetRow_SeqSBAIJ(Mat A,PetscInt row,PetscInt *ncols,PetscInt **cols,PetscScalar **v)
230: {
231:   Mat_SeqSBAIJ   *a = (Mat_SeqSBAIJ*)A->data;
233:   PetscInt       itmp,i,j,k,M,*ai,*aj,bs,bn,bp,*cols_i,bs2;
234:   MatScalar      *aa,*aa_i;
235:   PetscScalar    *v_i;

238:   if (A && !a->getrow_utriangular) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"MatGetRow is not supported for SBAIJ matrix format. Getting the upper triangular part of row, run with -mat_getrow_uppertriangular, call MatSetOption(mat,MAT_GETROW_UPPERTRIANGULAR,PETSC_TRUE) or MatGetRowUpperTriangular()");
239:   /* Get the upper triangular part of the row */
240:   bs  = A->rmap->bs;
241:   ai  = a->i;
242:   aj  = a->j;
243:   aa  = a->a;
244:   bs2 = a->bs2;

246:   if (row < 0 || row >= A->rmap->N) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE, "Row %D out of range", row);

248:   bn     = row/bs; /* Block number */
249:   bp     = row % bs; /* Block position */
250:   M      = ai[bn+1] - ai[bn];
251:   *ncols = bs*M;

253:   if (v) {
254:     *v = 0;
255:     if (*ncols) {
256:       PetscMalloc1((*ncols+row),v);
257:       for (i=0; i<M; i++) { /* for each block in the block row */
258:         v_i  = *v + i*bs;
259:         aa_i = aa + bs2*(ai[bn] + i);
260:         for (j=bp,k=0; j<bs2; j+=bs,k++) v_i[k] = aa_i[j];
261:       }
262:     }
263:   }

265:   if (cols) {
266:     *cols = 0;
267:     if (*ncols) {
268:       PetscMalloc1((*ncols+row),cols);
269:       for (i=0; i<M; i++) { /* for each block in the block row */
270:         cols_i = *cols + i*bs;
271:         itmp   = bs*aj[ai[bn] + i];
272:         for (j=0; j<bs; j++) cols_i[j] = itmp++;
273:       }
274:     }
275:   }

277:   /*search column A(0:row-1,row) (=A(row,0:row-1)). Could be expensive! */
278:   /* this segment is currently removed, so only entries in the upper triangle are obtained */
279: #if defined(column_search)
280:   v_i    = *v    + M*bs;
281:   cols_i = *cols + M*bs;
282:   for (i=0; i<bn; i++) { /* for each block row */
283:     M = ai[i+1] - ai[i];
284:     for (j=0; j<M; j++) {
285:       itmp = aj[ai[i] + j];    /* block column value */
286:       if (itmp == bn) {
287:         aa_i = aa + bs2*(ai[i] + j) + bs*bp;
288:         for (k=0; k<bs; k++) {
289:           *cols_i++ = i*bs+k;
290:           *v_i++    = aa_i[k];
291:         }
292:         *ncols += bs;
293:         break;
294:       }
295:     }
296:   }
297: #endif
298:   return(0);
299: }

303: PetscErrorCode MatRestoreRow_SeqSBAIJ(Mat A,PetscInt row,PetscInt *nz,PetscInt **idx,PetscScalar **v)
304: {

308:   if (idx) {PetscFree(*idx);}
309:   if (v)   {PetscFree(*v);}
310:   return(0);
311: }

315: PetscErrorCode MatGetRowUpperTriangular_SeqSBAIJ(Mat A)
316: {
317:   Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data;

320:   a->getrow_utriangular = PETSC_TRUE;
321:   return(0);
322: }
325: PetscErrorCode MatRestoreRowUpperTriangular_SeqSBAIJ(Mat A)
326: {
327:   Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data;

330:   a->getrow_utriangular = PETSC_FALSE;
331:   return(0);
332: }

336: PetscErrorCode MatTranspose_SeqSBAIJ(Mat A,MatReuse reuse,Mat *B)
337: {

341:   if (reuse == MAT_INITIAL_MATRIX || *B != A) {
342:     MatDuplicate(A,MAT_COPY_VALUES,B);
343:   }
344:   return(0);
345: }

349: static PetscErrorCode MatView_SeqSBAIJ_ASCII(Mat A,PetscViewer viewer)
350: {
351:   Mat_SeqSBAIJ      *a = (Mat_SeqSBAIJ*)A->data;
352:   PetscErrorCode    ierr;
353:   PetscInt          i,j,bs = A->rmap->bs,k,l,bs2=a->bs2;
354:   PetscViewerFormat format;
355:   PetscInt          *diag;

358:   PetscViewerGetFormat(viewer,&format);
359:   if (format == PETSC_VIEWER_ASCII_INFO || format == PETSC_VIEWER_ASCII_INFO_DETAIL) {
360:     PetscViewerASCIIPrintf(viewer,"  block size is %D\n",bs);
361:   } else if (format == PETSC_VIEWER_ASCII_MATLAB) {
362:     Mat aij;
363:     if (A->factortype && bs>1) {
364:       PetscPrintf(PETSC_COMM_SELF,"Warning: matrix is factored with bs>1. MatView() with PETSC_VIEWER_ASCII_MATLAB is not supported and ignored!\n");
365:       return(0);
366:     }
367:     MatConvert(A,MATSEQAIJ,MAT_INITIAL_MATRIX,&aij);
368:     MatView(aij,viewer);
369:     MatDestroy(&aij);
370:   } else if (format == PETSC_VIEWER_ASCII_COMMON) {
371:     PetscViewerASCIIUseTabs(viewer,PETSC_FALSE);
372:     for (i=0; i<a->mbs; i++) {
373:       for (j=0; j<bs; j++) {
374:         PetscViewerASCIIPrintf(viewer,"row %D:",i*bs+j);
375:         for (k=a->i[i]; k<a->i[i+1]; k++) {
376:           for (l=0; l<bs; l++) {
377: #if defined(PETSC_USE_COMPLEX)
378:             if (PetscImaginaryPart(a->a[bs2*k + l*bs + j]) > 0.0 && PetscRealPart(a->a[bs2*k + l*bs + j]) != 0.0) {
379:               PetscViewerASCIIPrintf(viewer," (%D, %g + %g i) ",bs*a->j[k]+l,
380:                                             (double)PetscRealPart(a->a[bs2*k + l*bs + j]),(double)PetscImaginaryPart(a->a[bs2*k + l*bs + j]));
381:             } else if (PetscImaginaryPart(a->a[bs2*k + l*bs + j]) < 0.0 && PetscRealPart(a->a[bs2*k + l*bs + j]) != 0.0) {
382:               PetscViewerASCIIPrintf(viewer," (%D, %g - %g i) ",bs*a->j[k]+l,
383:                                             (double)PetscRealPart(a->a[bs2*k + l*bs + j]),-(double)PetscImaginaryPart(a->a[bs2*k + l*bs + j]));
384:             } else if (PetscRealPart(a->a[bs2*k + l*bs + j]) != 0.0) {
385:               PetscViewerASCIIPrintf(viewer," (%D, %g) ",bs*a->j[k]+l,(double)PetscRealPart(a->a[bs2*k + l*bs + j]));
386:             }
387: #else
388:             if (a->a[bs2*k + l*bs + j] != 0.0) {
389:               PetscViewerASCIIPrintf(viewer," (%D, %g) ",bs*a->j[k]+l,(double)a->a[bs2*k + l*bs + j]);
390:             }
391: #endif
392:           }
393:         }
394:         PetscViewerASCIIPrintf(viewer,"\n");
395:       }
396:     }
397:     PetscViewerASCIIUseTabs(viewer,PETSC_TRUE);
398:   } else if (format == PETSC_VIEWER_ASCII_FACTOR_INFO) {
399:     return(0);
400:   } else {
401:     PetscViewerASCIIUseTabs(viewer,PETSC_FALSE);
402:     PetscObjectPrintClassNamePrefixType((PetscObject)A,viewer);
403:     if (A->factortype) { /* for factored matrix */
404:       if (bs>1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"matrix is factored with bs>1. Not implemented yet");

406:       diag=a->diag;
407:       for (i=0; i<a->mbs; i++) { /* for row block i */
408:         PetscViewerASCIIPrintf(viewer,"row %D:",i);
409:         /* diagonal entry */
410: #if defined(PETSC_USE_COMPLEX)
411:         if (PetscImaginaryPart(a->a[diag[i]]) > 0.0) {
412:           PetscViewerASCIIPrintf(viewer," (%D, %g + %g i) ",a->j[diag[i]],(double)PetscRealPart(1.0/a->a[diag[i]]),(double)PetscImaginaryPart(1.0/a->a[diag[i]]));
413:         } else if (PetscImaginaryPart(a->a[diag[i]]) < 0.0) {
414:           PetscViewerASCIIPrintf(viewer," (%D, %g - %g i) ",a->j[diag[i]],(double)PetscRealPart(1.0/a->a[diag[i]]),-(double)PetscImaginaryPart(1.0/a->a[diag[i]]));
415:         } else {
416:           PetscViewerASCIIPrintf(viewer," (%D, %g) ",a->j[diag[i]],(double)PetscRealPart(1.0/a->a[diag[i]]));
417:         }
418: #else
419:         PetscViewerASCIIPrintf(viewer," (%D, %g) ",a->j[diag[i]],(double)(1.0/a->a[diag[i]]));
420: #endif
421:         /* off-diagonal entries */
422:         for (k=a->i[i]; k<a->i[i+1]-1; k++) {
423: #if defined(PETSC_USE_COMPLEX)
424:           if (PetscImaginaryPart(a->a[k]) > 0.0) {
425:             PetscViewerASCIIPrintf(viewer," (%D, %g + %g i) ",bs*a->j[k],(double)PetscRealPart(a->a[k]),(double)PetscImaginaryPart(a->a[k]));
426:           } else if (PetscImaginaryPart(a->a[k]) < 0.0) {
427:             PetscViewerASCIIPrintf(viewer," (%D, %g - %g i) ",bs*a->j[k],(double)PetscRealPart(a->a[k]),-(double)PetscImaginaryPart(a->a[k]));
428:           } else {
429:             PetscViewerASCIIPrintf(viewer," (%D, %g) ",bs*a->j[k],(double)PetscRealPart(a->a[k]));
430:           }
431: #else
432:           PetscViewerASCIIPrintf(viewer," (%D, %g) ",a->j[k],(double)a->a[k]);
433: #endif
434:         }
435:         PetscViewerASCIIPrintf(viewer,"\n");
436:       }

438:     } else { /* for non-factored matrix */
439:       for (i=0; i<a->mbs; i++) { /* for row block i */
440:         for (j=0; j<bs; j++) {   /* for row bs*i + j */
441:           PetscViewerASCIIPrintf(viewer,"row %D:",i*bs+j);
442:           for (k=a->i[i]; k<a->i[i+1]; k++) { /* for column block */
443:             for (l=0; l<bs; l++) {            /* for column */
444: #if defined(PETSC_USE_COMPLEX)
445:               if (PetscImaginaryPart(a->a[bs2*k + l*bs + j]) > 0.0) {
446:                 PetscViewerASCIIPrintf(viewer," (%D, %g + %g i) ",bs*a->j[k]+l,
447:                                               (double)PetscRealPart(a->a[bs2*k + l*bs + j]),(double)PetscImaginaryPart(a->a[bs2*k + l*bs + j]));
448:               } else if (PetscImaginaryPart(a->a[bs2*k + l*bs + j]) < 0.0) {
449:                 PetscViewerASCIIPrintf(viewer," (%D, %g - %g i) ",bs*a->j[k]+l,
450:                                               (double)PetscRealPart(a->a[bs2*k + l*bs + j]),-(double)PetscImaginaryPart(a->a[bs2*k + l*bs + j]));
451:               } else {
452:                 PetscViewerASCIIPrintf(viewer," (%D, %g) ",bs*a->j[k]+l,(double)PetscRealPart(a->a[bs2*k + l*bs + j]));
453:               }
454: #else
455:               PetscViewerASCIIPrintf(viewer," (%D, %g) ",bs*a->j[k]+l,(double)a->a[bs2*k + l*bs + j]);
456: #endif
457:             }
458:           }
459:           PetscViewerASCIIPrintf(viewer,"\n");
460:         }
461:       }
462:     }
463:     PetscViewerASCIIUseTabs(viewer,PETSC_TRUE);
464:   }
465:   PetscViewerFlush(viewer);
466:   return(0);
467: }

469: #include <petscdraw.h>
472: static PetscErrorCode MatView_SeqSBAIJ_Draw_Zoom(PetscDraw draw,void *Aa)
473: {
474:   Mat            A = (Mat) Aa;
475:   Mat_SeqSBAIJ   *a=(Mat_SeqSBAIJ*)A->data;
477:   PetscInt       row,i,j,k,l,mbs=a->mbs,color,bs=A->rmap->bs,bs2=a->bs2;
478:   PetscMPIInt    rank;
479:   PetscReal      xl,yl,xr,yr,x_l,x_r,y_l,y_r;
480:   MatScalar      *aa;
481:   MPI_Comm       comm;
482:   PetscViewer    viewer;

485:   /*
486:     This is nasty. If this is called from an originally parallel matrix
487:     then all processes call this,but only the first has the matrix so the
488:     rest should return immediately.
489:   */
490:   PetscObjectGetComm((PetscObject)draw,&comm);
491:   MPI_Comm_rank(comm,&rank);
492:   if (rank) return(0);

494:   PetscObjectQuery((PetscObject)A,"Zoomviewer",(PetscObject*)&viewer);

496:   PetscDrawGetCoordinates(draw,&xl,&yl,&xr,&yr);
497:   PetscDrawString(draw, .3*(xl+xr), .3*(yl+yr), PETSC_DRAW_BLACK, "symmetric");

499:   /* loop over matrix elements drawing boxes */
500:   color = PETSC_DRAW_BLUE;
501:   for (i=0,row=0; i<mbs; i++,row+=bs) {
502:     for (j=a->i[i]; j<a->i[i+1]; j++) {
503:       y_l = A->rmap->N - row - 1.0; y_r = y_l + 1.0;
504:       x_l = a->j[j]*bs; x_r = x_l + 1.0;
505:       aa  = a->a + j*bs2;
506:       for (k=0; k<bs; k++) {
507:         for (l=0; l<bs; l++) {
508:           if (PetscRealPart(*aa++) >=  0.) continue;
509:           PetscDrawRectangle(draw,x_l+k,y_l-l,x_r+k,y_r-l,color,color,color,color);
510:         }
511:       }
512:     }
513:   }
514:   color = PETSC_DRAW_CYAN;
515:   for (i=0,row=0; i<mbs; i++,row+=bs) {
516:     for (j=a->i[i]; j<a->i[i+1]; j++) {
517:       y_l = A->rmap->N - row - 1.0; y_r = y_l + 1.0;
518:       x_l = a->j[j]*bs; x_r = x_l + 1.0;
519:       aa = a->a + j*bs2;
520:       for (k=0; k<bs; k++) {
521:         for (l=0; l<bs; l++) {
522:           if (PetscRealPart(*aa++) != 0.) continue;
523:           PetscDrawRectangle(draw,x_l+k,y_l-l,x_r+k,y_r-l,color,color,color,color);
524:         }
525:       }
526:     }
527:   }

529:   color = PETSC_DRAW_RED;
530:   for (i=0,row=0; i<mbs; i++,row+=bs) {
531:     for (j=a->i[i]; j<a->i[i+1]; j++) {
532:       y_l = A->rmap->N - row - 1.0; y_r = y_l + 1.0;
533:       x_l = a->j[j]*bs; x_r = x_l + 1.0;
534:       aa = a->a + j*bs2;
535:       for (k=0; k<bs; k++) {
536:         for (l=0; l<bs; l++) {
537:           if (PetscRealPart(*aa++) <= 0.) continue;
538:           PetscDrawRectangle(draw,x_l+k,y_l-l,x_r+k,y_r-l,color,color,color,color);
539:         }
540:       }
541:     }
542:   }
543:   return(0);
544: }

548: static PetscErrorCode MatView_SeqSBAIJ_Draw(Mat A,PetscViewer viewer)
549: {
551:   PetscReal      xl,yl,xr,yr,w,h;
552:   PetscDraw      draw;
553:   PetscBool      isnull;

556:   PetscViewerDrawGetDraw(viewer,0,&draw);
557:   PetscDrawIsNull(draw,&isnull); if (isnull) return(0);

559:   PetscObjectCompose((PetscObject)A,"Zoomviewer",(PetscObject)viewer);
560:   xr   = A->rmap->N; yr = A->rmap->N; h = yr/10.0; w = xr/10.0;
561:   xr  += w;    yr += h;  xl = -w;     yl = -h;
562:   PetscDrawSetCoordinates(draw,xl,yl,xr,yr);
563:   PetscDrawZoom(draw,MatView_SeqSBAIJ_Draw_Zoom,A);
564:   PetscObjectCompose((PetscObject)A,"Zoomviewer",NULL);
565:   return(0);
566: }

570: PetscErrorCode MatView_SeqSBAIJ(Mat A,PetscViewer viewer)
571: {
573:   PetscBool      iascii,isdraw;
574:   FILE           *file = 0;

577:   PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERASCII,&iascii);
578:   PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERDRAW,&isdraw);
579:   if (iascii) {
580:     MatView_SeqSBAIJ_ASCII(A,viewer);
581:   } else if (isdraw) {
582:     MatView_SeqSBAIJ_Draw(A,viewer);
583:   } else {
584:     Mat B;
585:     MatConvert(A,MATSEQAIJ,MAT_INITIAL_MATRIX,&B);
586:     MatView(B,viewer);
587:     MatDestroy(&B);
588:     PetscViewerBinaryGetInfoPointer(viewer,&file);
589:     if (file) {
590:       fprintf(file,"-matload_block_size %d\n",(int)A->rmap->bs);
591:     }
592:   }
593:   return(0);
594: }


599: PetscErrorCode MatGetValues_SeqSBAIJ(Mat A,PetscInt m,const PetscInt im[],PetscInt n,const PetscInt in[],PetscScalar v[])
600: {
601:   Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data;
602:   PetscInt     *rp,k,low,high,t,row,nrow,i,col,l,*aj = a->j;
603:   PetscInt     *ai = a->i,*ailen = a->ilen;
604:   PetscInt     brow,bcol,ridx,cidx,bs=A->rmap->bs,bs2=a->bs2;
605:   MatScalar    *ap,*aa = a->a;

608:   for (k=0; k<m; k++) { /* loop over rows */
609:     row = im[k]; brow = row/bs;
610:     if (row < 0) {v += n; continue;} /* SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Negative row: %D",row); */
611:     if (row >= A->rmap->N) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Row too large: row %D max %D",row,A->rmap->N-1);
612:     rp   = aj + ai[brow]; ap = aa + bs2*ai[brow];
613:     nrow = ailen[brow];
614:     for (l=0; l<n; l++) { /* loop over columns */
615:       if (in[l] < 0) {v++; continue;} /* SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Negative column: %D",in[l]); */
616:       if (in[l] >= A->cmap->n) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Column too large: col %D max %D",in[l],A->cmap->n-1);
617:       col  = in[l];
618:       bcol = col/bs;
619:       cidx = col%bs;
620:       ridx = row%bs;
621:       high = nrow;
622:       low  = 0; /* assume unsorted */
623:       while (high-low > 5) {
624:         t = (low+high)/2;
625:         if (rp[t] > bcol) high = t;
626:         else              low  = t;
627:       }
628:       for (i=low; i<high; i++) {
629:         if (rp[i] > bcol) break;
630:         if (rp[i] == bcol) {
631:           *v++ = ap[bs2*i+bs*cidx+ridx];
632:           goto finished;
633:         }
634:       }
635:       *v++ = 0.0;
636: finished:;
637:     }
638:   }
639:   return(0);
640: }


645: PetscErrorCode MatSetValuesBlocked_SeqSBAIJ(Mat A,PetscInt m,const PetscInt im[],PetscInt n,const PetscInt in[],const PetscScalar v[],InsertMode is)
646: {
647:   Mat_SeqSBAIJ      *a = (Mat_SeqSBAIJ*)A->data;
648:   PetscErrorCode    ierr;
649:   PetscInt          *rp,k,low,high,t,ii,jj,row,nrow,i,col,l,rmax,N,lastcol = -1;
650:   PetscInt          *imax      =a->imax,*ai=a->i,*ailen=a->ilen;
651:   PetscInt          *aj        =a->j,nonew=a->nonew,bs2=a->bs2,bs=A->rmap->bs,stepval;
652:   PetscBool         roworiented=a->roworiented;
653:   const PetscScalar *value     = v;
654:   MatScalar         *ap,*aa = a->a,*bap;

657:   if (roworiented) stepval = (n-1)*bs;
658:   else stepval = (m-1)*bs;

660:   for (k=0; k<m; k++) { /* loop over added rows */
661:     row = im[k];
662:     if (row < 0) continue;
663: #if defined(PETSC_USE_DEBUG)
664:     if (row >= a->mbs) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Row too large: row %D max %D",row,a->mbs-1);
665: #endif
666:     rp   = aj + ai[row];
667:     ap   = aa + bs2*ai[row];
668:     rmax = imax[row];
669:     nrow = ailen[row];
670:     low  = 0;
671:     high = nrow;
672:     for (l=0; l<n; l++) { /* loop over added columns */
673:       if (in[l] < 0) continue;
674:       col = in[l];
675: #if defined(PETSC_USE_DEBUG)
676:       if (col >= a->nbs) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Column too large: col %D max %D",col,a->nbs-1);
677: #endif
678:       if (col < row) {
679:         if (a->ignore_ltriangular) continue; /* ignore lower triangular block */
680:         else SETERRQ(PETSC_COMM_SELF,PETSC_ERR_USER,"Lower triangular value cannot be set for sbaij format. Ignoring these values, run with -mat_ignore_lower_triangular or call MatSetOption(mat,MAT_IGNORE_LOWER_TRIANGULAR,PETSC_TRUE)");
681:       }
682:       if (roworiented) value = v + k*(stepval+bs)*bs + l*bs;
683:       else value = v + l*(stepval+bs)*bs + k*bs;

685:       if (col <= lastcol) low = 0;
686:       else high = nrow;

688:       lastcol = col;
689:       while (high-low > 7) {
690:         t = (low+high)/2;
691:         if (rp[t] > col) high = t;
692:         else             low  = t;
693:       }
694:       for (i=low; i<high; i++) {
695:         if (rp[i] > col) break;
696:         if (rp[i] == col) {
697:           bap = ap +  bs2*i;
698:           if (roworiented) {
699:             if (is == ADD_VALUES) {
700:               for (ii=0; ii<bs; ii++,value+=stepval) {
701:                 for (jj=ii; jj<bs2; jj+=bs) {
702:                   bap[jj] += *value++;
703:                 }
704:               }
705:             } else {
706:               for (ii=0; ii<bs; ii++,value+=stepval) {
707:                 for (jj=ii; jj<bs2; jj+=bs) {
708:                   bap[jj] = *value++;
709:                 }
710:                }
711:             }
712:           } else {
713:             if (is == ADD_VALUES) {
714:               for (ii=0; ii<bs; ii++,value+=stepval) {
715:                 for (jj=0; jj<bs; jj++) {
716:                   *bap++ += *value++;
717:                 }
718:               }
719:             } else {
720:               for (ii=0; ii<bs; ii++,value+=stepval) {
721:                 for (jj=0; jj<bs; jj++) {
722:                   *bap++  = *value++;
723:                 }
724:               }
725:             }
726:           }
727:           goto noinsert2;
728:         }
729:       }
730:       if (nonew == 1) goto noinsert2;
731:       if (nonew == -1) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Inserting a new nonzero (%D, %D) in the matrix", row, col);
732:       MatSeqXAIJReallocateAIJ(A,a->mbs,bs2,nrow,row,col,rmax,aa,ai,aj,rp,ap,imax,nonew,MatScalar);
733:       N = nrow++ - 1; high++;
734:       /* shift up all the later entries in this row */
735:       for (ii=N; ii>=i; ii--) {
736:         rp[ii+1] = rp[ii];
737:         PetscMemcpy(ap+bs2*(ii+1),ap+bs2*(ii),bs2*sizeof(MatScalar));
738:       }
739:       if (N >= i) {
740:         PetscMemzero(ap+bs2*i,bs2*sizeof(MatScalar));
741:       }
742:       rp[i] = col;
743:       bap   = ap +  bs2*i;
744:       if (roworiented) {
745:         for (ii=0; ii<bs; ii++,value+=stepval) {
746:           for (jj=ii; jj<bs2; jj+=bs) {
747:             bap[jj] = *value++;
748:           }
749:         }
750:       } else {
751:         for (ii=0; ii<bs; ii++,value+=stepval) {
752:           for (jj=0; jj<bs; jj++) {
753:             *bap++ = *value++;
754:           }
755:         }
756:        }
757:     noinsert2:;
758:       low = i;
759:     }
760:     ailen[row] = nrow;
761:   }
762:   return(0);
763: }

765: /*
766:     This is not yet used
767: */
770: PetscErrorCode MatAssemblyEnd_SeqSBAIJ_SeqAIJ_Inode(Mat A)
771: {
772:   Mat_SeqSBAIJ   *a = (Mat_SeqSBAIJ*)A->data;
774:   const PetscInt *ai = a->i, *aj = a->j,*cols;
775:   PetscInt       i   = 0,j,blk_size,m = A->rmap->n,node_count = 0,nzx,nzy,*ns,row,nz,cnt,cnt2,*counts;
776:   PetscBool      flag;

779:   PetscMalloc1(m,&ns);
780:   while (i < m) {
781:     nzx = ai[i+1] - ai[i];       /* Number of nonzeros */
782:     /* Limits the number of elements in a node to 'a->inode.limit' */
783:     for (j=i+1,blk_size=1; j<m && blk_size <a->inode.limit; ++j,++blk_size) {
784:       nzy = ai[j+1] - ai[j];
785:       if (nzy != (nzx - j + i)) break;
786:       PetscMemcmp(aj + ai[i] + j - i,aj + ai[j],nzy*sizeof(PetscInt),&flag);
787:       if (!flag) break;
788:     }
789:     ns[node_count++] = blk_size;

791:     i = j;
792:   }
793:   if (!a->inode.size && m && node_count > .9*m) {
794:     PetscFree(ns);
795:     PetscInfo2(A,"Found %D nodes out of %D rows. Not using Inode routines\n",node_count,m);
796:   } else {
797:     a->inode.node_count = node_count;

799:     PetscMalloc1(node_count,&a->inode.size);
800:     PetscLogObjectMemory((PetscObject)A,node_count*sizeof(PetscInt));
801:     PetscMemcpy(a->inode.size,ns,node_count*sizeof(PetscInt));
802:     PetscFree(ns);
803:     PetscInfo3(A,"Found %D nodes of %D. Limit used: %D. Using Inode routines\n",node_count,m,a->inode.limit);

805:     /* count collections of adjacent columns in each inode */
806:     row = 0;
807:     cnt = 0;
808:     for (i=0; i<node_count; i++) {
809:       cols = aj + ai[row] + a->inode.size[i];
810:       nz   = ai[row+1] - ai[row] - a->inode.size[i];
811:       for (j=1; j<nz; j++) {
812:         if (cols[j] != cols[j-1]+1) cnt++;
813:       }
814:       cnt++;
815:       row += a->inode.size[i];
816:     }
817:     PetscMalloc1(2*cnt,&counts);
818:     cnt  = 0;
819:     row  = 0;
820:     for (i=0; i<node_count; i++) {
821:       cols = aj + ai[row] + a->inode.size[i];
822:       counts[2*cnt] = cols[0];
823:       nz   = ai[row+1] - ai[row] - a->inode.size[i];
824:       cnt2 = 1;
825:       for (j=1; j<nz; j++) {
826:         if (cols[j] != cols[j-1]+1) {
827:           counts[2*(cnt++)+1] = cnt2;
828:           counts[2*cnt]       = cols[j];
829:           cnt2 = 1;
830:         } else cnt2++;
831:       }
832:       counts[2*(cnt++)+1] = cnt2;
833:       row += a->inode.size[i];
834:     }
835:     PetscIntView(2*cnt,counts,0);
836:   }
837:   return(0);
838: }

842: PetscErrorCode MatAssemblyEnd_SeqSBAIJ(Mat A,MatAssemblyType mode)
843: {
844:   Mat_SeqSBAIJ   *a = (Mat_SeqSBAIJ*)A->data;
846:   PetscInt       fshift = 0,i,j,*ai = a->i,*aj = a->j,*imax = a->imax;
847:   PetscInt       m      = A->rmap->N,*ip,N,*ailen = a->ilen;
848:   PetscInt       mbs    = a->mbs,bs2 = a->bs2,rmax = 0;
849:   MatScalar      *aa    = a->a,*ap;

852:   if (mode == MAT_FLUSH_ASSEMBLY) return(0);

854:   if (m) rmax = ailen[0];
855:   for (i=1; i<mbs; i++) {
856:     /* move each row back by the amount of empty slots (fshift) before it*/
857:     fshift += imax[i-1] - ailen[i-1];
858:     rmax    = PetscMax(rmax,ailen[i]);
859:     if (fshift) {
860:       ip = aj + ai[i]; ap = aa + bs2*ai[i];
861:       N  = ailen[i];
862:       for (j=0; j<N; j++) {
863:         ip[j-fshift] = ip[j];
864:         PetscMemcpy(ap+(j-fshift)*bs2,ap+j*bs2,bs2*sizeof(MatScalar));
865:       }
866:     }
867:     ai[i] = ai[i-1] + ailen[i-1];
868:   }
869:   if (mbs) {
870:     fshift += imax[mbs-1] - ailen[mbs-1];
871:     ai[mbs] = ai[mbs-1] + ailen[mbs-1];
872:   }
873:   /* reset ilen and imax for each row */
874:   for (i=0; i<mbs; i++) {
875:     ailen[i] = imax[i] = ai[i+1] - ai[i];
876:   }
877:   a->nz = ai[mbs];

879:   /* diagonals may have moved, reset it */
880:   if (a->diag) {
881:     PetscMemcpy(a->diag,ai,mbs*sizeof(PetscInt));
882:   }
883:   if (fshift && a->nounused == -1) SETERRQ4(PETSC_COMM_SELF,PETSC_ERR_PLIB, "Unused space detected in matrix: %D X %D block size %D, %D unneeded", m, A->cmap->n, A->rmap->bs, fshift*bs2);

885:   PetscInfo5(A,"Matrix size: %D X %D, block size %D; storage space: %D unneeded, %D used\n",m,A->rmap->N,A->rmap->bs,fshift*bs2,a->nz*bs2);
886:   PetscInfo1(A,"Number of mallocs during MatSetValues is %D\n",a->reallocs);
887:   PetscInfo1(A,"Most nonzeros blocks in any row is %D\n",rmax);

889:   A->info.mallocs    += a->reallocs;
890:   a->reallocs         = 0;
891:   A->info.nz_unneeded = (PetscReal)fshift*bs2;
892:   a->idiagvalid       = PETSC_FALSE;

894:   if (A->cmap->n < 65536 && A->cmap->bs == 1) {
895:     if (a->jshort && a->free_jshort) {
896:       /* when matrix data structure is changed, previous jshort must be replaced */
897:       PetscFree(a->jshort);
898:     }
899:     PetscMalloc1(a->i[A->rmap->n],&a->jshort);
900:     PetscLogObjectMemory((PetscObject)A,a->i[A->rmap->n]*sizeof(unsigned short));
901:     for (i=0; i<a->i[A->rmap->n]; i++) a->jshort[i] = a->j[i];
902:     A->ops->mult   = MatMult_SeqSBAIJ_1_ushort;
903:     A->ops->sor    = MatSOR_SeqSBAIJ_ushort;
904:     a->free_jshort = PETSC_TRUE;
905:   }
906:   return(0);
907: }

909: /*
910:    This function returns an array of flags which indicate the locations of contiguous
911:    blocks that should be zeroed. for eg: if bs = 3  and is = [0,1,2,3,5,6,7,8,9]
912:    then the resulting sizes = [3,1,1,3,1] correspondig to sets [(0,1,2),(3),(5),(6,7,8),(9)]
913:    Assume: sizes should be long enough to hold all the values.
914: */
917: PetscErrorCode MatZeroRows_SeqSBAIJ_Check_Blocks(PetscInt idx[],PetscInt n,PetscInt bs,PetscInt sizes[], PetscInt *bs_max)
918: {
919:   PetscInt  i,j,k,row;
920:   PetscBool flg;

923:   for (i=0,j=0; i<n; j++) {
924:     row = idx[i];
925:     if (row%bs!=0) { /* Not the begining of a block */
926:       sizes[j] = 1;
927:       i++;
928:     } else if (i+bs > n) { /* Beginning of a block, but complete block doesn't exist (at idx end) */
929:       sizes[j] = 1;         /* Also makes sure atleast 'bs' values exist for next else */
930:       i++;
931:     } else { /* Begining of the block, so check if the complete block exists */
932:       flg = PETSC_TRUE;
933:       for (k=1; k<bs; k++) {
934:         if (row+k != idx[i+k]) { /* break in the block */
935:           flg = PETSC_FALSE;
936:           break;
937:         }
938:       }
939:       if (flg) { /* No break in the bs */
940:         sizes[j] = bs;
941:         i       += bs;
942:       } else {
943:         sizes[j] = 1;
944:         i++;
945:       }
946:     }
947:   }
948:   *bs_max = j;
949:   return(0);
950: }


953: /* Only add/insert a(i,j) with i<=j (blocks).
954:    Any a(i,j) with i>j input by user is ingored.
955: */

959: PetscErrorCode MatSetValues_SeqSBAIJ(Mat A,PetscInt m,const PetscInt im[],PetscInt n,const PetscInt in[],const PetscScalar v[],InsertMode is)
960: {
961:   Mat_SeqSBAIJ   *a = (Mat_SeqSBAIJ*)A->data;
963:   PetscInt       *rp,k,low,high,t,ii,row,nrow,i,col,l,rmax,N,lastcol = -1;
964:   PetscInt       *imax=a->imax,*ai=a->i,*ailen=a->ilen,roworiented=a->roworiented;
965:   PetscInt       *aj  =a->j,nonew=a->nonew,bs=A->rmap->bs,brow,bcol;
966:   PetscInt       ridx,cidx,bs2=a->bs2;
967:   MatScalar      *ap,value,*aa=a->a,*bap;

971:   for (k=0; k<m; k++) { /* loop over added rows */
972:     row  = im[k];       /* row number */
973:     brow = row/bs;      /* block row number */
974:     if (row < 0) continue;
975: #if defined(PETSC_USE_DEBUG)
976:     if (row >= A->rmap->N) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Row too large: row %D max %D",row,A->rmap->N-1);
977: #endif
978:     rp   = aj + ai[brow]; /*ptr to beginning of column value of the row block*/
979:     ap   = aa + bs2*ai[brow]; /*ptr to beginning of element value of the row block*/
980:     rmax = imax[brow];  /* maximum space allocated for this row */
981:     nrow = ailen[brow]; /* actual length of this row */
982:     low  = 0;

984:     for (l=0; l<n; l++) { /* loop over added columns */
985:       if (in[l] < 0) continue;
986: #if defined(PETSC_USE_DEBUG)
987:       if (in[l] >= A->rmap->N) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Column too large: col %D max %D",in[l],A->rmap->N-1);
988: #endif
989:       col  = in[l];
990:       bcol = col/bs;              /* block col number */

992:       if (brow > bcol) {
993:         if (a->ignore_ltriangular) continue; /* ignore lower triangular values */
994:         else SETERRQ(PETSC_COMM_SELF,PETSC_ERR_USER,"Lower triangular value cannot be set for sbaij format. Ignoring these values, run with -mat_ignore_lower_triangular or call MatSetOption(mat,MAT_IGNORE_LOWER_TRIANGULAR,PETSC_TRUE)");
995:       }

997:       ridx = row % bs; cidx = col % bs; /*row and col index inside the block */
998:       if ((brow==bcol && ridx<=cidx) || (brow<bcol)) {
999:         /* element value a(k,l) */
1000:         if (roworiented) value = v[l + k*n];
1001:         else value = v[k + l*m];

1003:         /* move pointer bap to a(k,l) quickly and add/insert value */
1004:         if (col <= lastcol) low = 0;
1005:         high = nrow;
1006:         lastcol = col;
1007:         while (high-low > 7) {
1008:           t = (low+high)/2;
1009:           if (rp[t] > bcol) high = t;
1010:           else              low  = t;
1011:         }
1012:         for (i=low; i<high; i++) {
1013:           if (rp[i] > bcol) break;
1014:           if (rp[i] == bcol) {
1015:             bap = ap +  bs2*i + bs*cidx + ridx;
1016:             if (is == ADD_VALUES) *bap += value;
1017:             else                  *bap  = value;
1018:             /* for diag block, add/insert its symmetric element a(cidx,ridx) */
1019:             if (brow == bcol && ridx < cidx) {
1020:               bap = ap +  bs2*i + bs*ridx + cidx;
1021:               if (is == ADD_VALUES) *bap += value;
1022:               else                  *bap  = value;
1023:             }
1024:             goto noinsert1;
1025:           }
1026:         }

1028:         if (nonew == 1) goto noinsert1;
1029:         if (nonew == -1) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Inserting a new nonzero (%D, %D) in the matrix", row, col);
1030:         MatSeqXAIJReallocateAIJ(A,a->mbs,bs2,nrow,brow,bcol,rmax,aa,ai,aj,rp,ap,imax,nonew,MatScalar);

1032:         N = nrow++ - 1; high++;
1033:         /* shift up all the later entries in this row */
1034:         for (ii=N; ii>=i; ii--) {
1035:           rp[ii+1] = rp[ii];
1036:           PetscMemcpy(ap+bs2*(ii+1),ap+bs2*(ii),bs2*sizeof(MatScalar));
1037:         }
1038:         if (N>=i) {
1039:           PetscMemzero(ap+bs2*i,bs2*sizeof(MatScalar));
1040:         }
1041:         rp[i]                      = bcol;
1042:         ap[bs2*i + bs*cidx + ridx] = value;
1043: noinsert1:;
1044:         low = i;
1045:       }
1046:     }   /* end of loop over added columns */
1047:     ailen[brow] = nrow;
1048:   }   /* end of loop over added rows */
1049:   return(0);
1050: }

1054: PetscErrorCode MatICCFactor_SeqSBAIJ(Mat inA,IS row,const MatFactorInfo *info)
1055: {
1056:   Mat_SeqSBAIJ   *a = (Mat_SeqSBAIJ*)inA->data;
1057:   Mat            outA;
1059:   PetscBool      row_identity;

1062:   if (info->levels != 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Only levels=0 is supported for in-place icc");
1063:   ISIdentity(row,&row_identity);
1064:   if (!row_identity) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Matrix reordering is not supported");
1065:   if (inA->rmap->bs != 1) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP,"Matrix block size %D is not supported",inA->rmap->bs); /* Need to replace MatCholeskyFactorSymbolic_SeqSBAIJ_MSR()! */

1067:   outA            = inA;
1068:   inA->factortype = MAT_FACTOR_ICC;

1070:   MatMarkDiagonal_SeqSBAIJ(inA);
1071:   MatSeqSBAIJSetNumericFactorization_inplace(inA,row_identity);

1073:   PetscObjectReference((PetscObject)row);
1074:   ISDestroy(&a->row);
1075:   a->row = row;
1076:   PetscObjectReference((PetscObject)row);
1077:   ISDestroy(&a->col);
1078:   a->col = row;

1080:   /* Create the invert permutation so that it can be used in MatCholeskyFactorNumeric() */
1081:   if (a->icol) {ISInvertPermutation(row,PETSC_DECIDE, &a->icol);}
1082:   PetscLogObjectParent((PetscObject)inA,(PetscObject)a->icol);

1084:   if (!a->solve_work) {
1085:     PetscMalloc1((inA->rmap->N+inA->rmap->bs),&a->solve_work);
1086:     PetscLogObjectMemory((PetscObject)inA,(inA->rmap->N+inA->rmap->bs)*sizeof(PetscScalar));
1087:   }

1089:   MatCholeskyFactorNumeric(outA,inA,info);
1090:   return(0);
1091: }

1095: PetscErrorCode  MatSeqSBAIJSetColumnIndices_SeqSBAIJ(Mat mat,PetscInt *indices)
1096: {
1097:   Mat_SeqSBAIJ   *baij = (Mat_SeqSBAIJ*)mat->data;
1098:   PetscInt       i,nz,n;

1102:   nz = baij->maxnz;
1103:   n  = mat->cmap->n;
1104:   for (i=0; i<nz; i++) baij->j[i] = indices[i];

1106:   baij->nz = nz;
1107:   for (i=0; i<n; i++) baij->ilen[i] = baij->imax[i];

1109:   MatSetOption(mat,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);
1110:   return(0);
1111: }

1115: /*@
1116:   MatSeqSBAIJSetColumnIndices - Set the column indices for all the rows
1117:   in the matrix.

1119:   Input Parameters:
1120:   +  mat     - the SeqSBAIJ matrix
1121:   -  indices - the column indices

1123:   Level: advanced

1125:   Notes:
1126:   This can be called if you have precomputed the nonzero structure of the
1127:   matrix and want to provide it to the matrix object to improve the performance
1128:   of the MatSetValues() operation.

1130:   You MUST have set the correct numbers of nonzeros per row in the call to
1131:   MatCreateSeqSBAIJ(), and the columns indices MUST be sorted.

1133:   MUST be called before any calls to MatSetValues()

1135:   .seealso: MatCreateSeqSBAIJ
1136: @*/
1137: PetscErrorCode  MatSeqSBAIJSetColumnIndices(Mat mat,PetscInt *indices)
1138: {

1144:   PetscUseMethod(mat,"MatSeqSBAIJSetColumnIndices_C",(Mat,PetscInt*),(mat,indices));
1145:   return(0);
1146: }

1150: PetscErrorCode MatCopy_SeqSBAIJ(Mat A,Mat B,MatStructure str)
1151: {

1155:   /* If the two matrices have the same copy implementation, use fast copy. */
1156:   if (str == SAME_NONZERO_PATTERN && (A->ops->copy == B->ops->copy)) {
1157:     Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data;
1158:     Mat_SeqSBAIJ *b = (Mat_SeqSBAIJ*)B->data;

1160:     if (a->i[A->rmap->N] != b->i[B->rmap->N]) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_INCOMP,"Number of nonzeros in two matrices are different");
1161:     PetscMemcpy(b->a,a->a,(a->i[A->rmap->N])*sizeof(PetscScalar));
1162:   } else {
1163:     MatGetRowUpperTriangular(A);
1164:     MatCopy_Basic(A,B,str);
1165:     MatRestoreRowUpperTriangular(A);
1166:   }
1167:   return(0);
1168: }

1172: PetscErrorCode MatSetUp_SeqSBAIJ(Mat A)
1173: {

1177:    MatSeqSBAIJSetPreallocation_SeqSBAIJ(A,A->rmap->bs,PETSC_DEFAULT,0);
1178:   return(0);
1179: }

1183: PetscErrorCode MatSeqSBAIJGetArray_SeqSBAIJ(Mat A,PetscScalar *array[])
1184: {
1185:   Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data;

1188:   *array = a->a;
1189:   return(0);
1190: }

1194: PetscErrorCode MatSeqSBAIJRestoreArray_SeqSBAIJ(Mat A,PetscScalar *array[])
1195: {
1197:   return(0);
1198: }

1202: PetscErrorCode MatAXPY_SeqSBAIJ(Mat Y,PetscScalar a,Mat X,MatStructure str)
1203: {
1204:   Mat_SeqSBAIJ   *x=(Mat_SeqSBAIJ*)X->data, *y=(Mat_SeqSBAIJ*)Y->data;
1206:   PetscInt       i,bs=Y->rmap->bs,bs2=bs*bs,j;
1207:   PetscBLASInt   one = 1;

1210:   if (str == SAME_NONZERO_PATTERN) {
1211:     PetscScalar  alpha = a;
1212:     PetscBLASInt bnz;
1213:     PetscBLASIntCast(x->nz*bs2,&bnz);
1214:     PetscStackCallBLAS("BLASaxpy",BLASaxpy_(&bnz,&alpha,x->a,&one,y->a,&one));
1215:   } else if (str == SUBSET_NONZERO_PATTERN) { /* nonzeros of X is a subset of Y's */
1216:     if (y->xtoy && y->XtoY != X) {
1217:       PetscFree(y->xtoy);
1218:       MatDestroy(&y->XtoY);
1219:     }
1220:     if (!y->xtoy) { /* get xtoy */
1221:       MatAXPYGetxtoy_Private(x->mbs,x->i,x->j,NULL, y->i,y->j,NULL, &y->xtoy);
1222:       y->XtoY = X;
1223:     }
1224:     for (i=0; i<x->nz; i++) {
1225:       j = 0;
1226:       while (j < bs2) {
1227:         y->a[bs2*y->xtoy[i]+j] += a*(x->a[bs2*i+j]);
1228:         j++;
1229:       }
1230:     }
1231:     PetscInfo3(Y,"ratio of nnz_s(X)/nnz_s(Y): %D/%D = %g\n",bs2*x->nz,bs2*y->nz,(double)((PetscReal)(bs2*x->nz)/(PetscReal)(bs2*y->nz)));
1232:   } else {
1233:     MatGetRowUpperTriangular(X);
1234:     MatAXPY_Basic(Y,a,X,str);
1235:     MatRestoreRowUpperTriangular(X);
1236:   }
1237:   return(0);
1238: }

1242: PetscErrorCode MatIsSymmetric_SeqSBAIJ(Mat A,PetscReal tol,PetscBool  *flg)
1243: {
1245:   *flg = PETSC_TRUE;
1246:   return(0);
1247: }

1251: PetscErrorCode MatIsStructurallySymmetric_SeqSBAIJ(Mat A,PetscBool  *flg)
1252: {
1254:   *flg = PETSC_TRUE;
1255:   return(0);
1256: }

1260: PetscErrorCode MatIsHermitian_SeqSBAIJ(Mat A,PetscReal tol,PetscBool  *flg)
1261: {
1263:   *flg = PETSC_FALSE;
1264:   return(0);
1265: }

1269: PetscErrorCode MatRealPart_SeqSBAIJ(Mat A)
1270: {
1271:   Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data;
1272:   PetscInt     i,nz = a->bs2*a->i[a->mbs];
1273:   MatScalar    *aa = a->a;

1276:   for (i=0; i<nz; i++) aa[i] = PetscRealPart(aa[i]);
1277:   return(0);
1278: }

1282: PetscErrorCode MatImaginaryPart_SeqSBAIJ(Mat A)
1283: {
1284:   Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data;
1285:   PetscInt     i,nz = a->bs2*a->i[a->mbs];
1286:   MatScalar    *aa = a->a;

1289:   for (i=0; i<nz; i++) aa[i] = PetscImaginaryPart(aa[i]);
1290:   return(0);
1291: }

1295: PetscErrorCode MatZeroRowsColumns_SeqSBAIJ(Mat A,PetscInt is_n,const PetscInt is_idx[],PetscScalar diag,Vec x, Vec b)
1296: {
1297:   Mat_SeqSBAIJ      *baij=(Mat_SeqSBAIJ*)A->data;
1298:   PetscErrorCode    ierr;
1299:   PetscInt          i,j,k,count;
1300:   PetscInt          bs   =A->rmap->bs,bs2=baij->bs2,row,col;
1301:   PetscScalar       zero = 0.0;
1302:   MatScalar         *aa;
1303:   const PetscScalar *xx;
1304:   PetscScalar       *bb;
1305:   PetscBool         *zeroed,vecs = PETSC_FALSE;

1308:   /* fix right hand side if needed */
1309:   if (x && b) {
1310:     VecGetArrayRead(x,&xx);
1311:     VecGetArray(b,&bb);
1312:     vecs = PETSC_TRUE;
1313:   }
1314:   A->same_nonzero = PETSC_TRUE;

1316:   /* zero the columns */
1317:   PetscCalloc1(A->rmap->n,&zeroed);
1318:   for (i=0; i<is_n; i++) {
1319:     if (is_idx[i] < 0 || is_idx[i] >= A->rmap->N) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"row %D out of range",is_idx[i]);
1320:     zeroed[is_idx[i]] = PETSC_TRUE;
1321:   }
1322:   if (vecs) {
1323:     for (i=0; i<A->rmap->N; i++) {
1324:       row = i/bs;
1325:       for (j=baij->i[row]; j<baij->i[row+1]; j++) {
1326:         for (k=0; k<bs; k++) {
1327:           col = bs*baij->j[j] + k;
1328:           if (col <= i) continue;
1329:           aa = ((MatScalar*)(baij->a)) + j*bs2 + (i%bs) + bs*k;
1330:           if (!zeroed[i] && zeroed[col]) bb[i]   -= aa[0]*xx[col];
1331:           if (zeroed[i] && !zeroed[col]) bb[col] -= aa[0]*xx[i];
1332:         }
1333:       }
1334:     }
1335:     for (i=0; i<is_n; i++) bb[is_idx[i]] = diag*xx[is_idx[i]];
1336:   }

1338:   for (i=0; i<A->rmap->N; i++) {
1339:     if (!zeroed[i]) {
1340:       row = i/bs;
1341:       for (j=baij->i[row]; j<baij->i[row+1]; j++) {
1342:         for (k=0; k<bs; k++) {
1343:           col = bs*baij->j[j] + k;
1344:           if (zeroed[col]) {
1345:             aa = ((MatScalar*)(baij->a)) + j*bs2 + (i%bs) + bs*k;
1346:             aa[0] = 0.0;
1347:           }
1348:         }
1349:       }
1350:     }
1351:   }
1352:   PetscFree(zeroed);
1353:   if (vecs) {
1354:     VecRestoreArrayRead(x,&xx);
1355:     VecRestoreArray(b,&bb);
1356:   }

1358:   /* zero the rows */
1359:   for (i=0; i<is_n; i++) {
1360:     row   = is_idx[i];
1361:     count = (baij->i[row/bs +1] - baij->i[row/bs])*bs;
1362:     aa    = ((MatScalar*)(baij->a)) + baij->i[row/bs]*bs2 + (row%bs);
1363:     for (k=0; k<count; k++) {
1364:       aa[0] =  zero;
1365:       aa   += bs;
1366:     }
1367:     if (diag != 0.0) {
1368:       (*A->ops->setvalues)(A,1,&row,1,&row,&diag,INSERT_VALUES);
1369:     }
1370:   }
1371:   MatAssemblyEnd_SeqSBAIJ(A,MAT_FINAL_ASSEMBLY);
1372:   return(0);
1373: }

1375: /* -------------------------------------------------------------------*/
1376: static struct _MatOps MatOps_Values = {MatSetValues_SeqSBAIJ,
1377:                                        MatGetRow_SeqSBAIJ,
1378:                                        MatRestoreRow_SeqSBAIJ,
1379:                                        MatMult_SeqSBAIJ_N,
1380:                                /*  4*/ MatMultAdd_SeqSBAIJ_N,
1381:                                        MatMult_SeqSBAIJ_N,       /* transpose versions are same as non-transpose versions */
1382:                                        MatMultAdd_SeqSBAIJ_N,
1383:                                        0,
1384:                                        0,
1385:                                        0,
1386:                                /* 10*/ 0,
1387:                                        0,
1388:                                        MatCholeskyFactor_SeqSBAIJ,
1389:                                        MatSOR_SeqSBAIJ,
1390:                                        MatTranspose_SeqSBAIJ,
1391:                                /* 15*/ MatGetInfo_SeqSBAIJ,
1392:                                        MatEqual_SeqSBAIJ,
1393:                                        MatGetDiagonal_SeqSBAIJ,
1394:                                        MatDiagonalScale_SeqSBAIJ,
1395:                                        MatNorm_SeqSBAIJ,
1396:                                /* 20*/ 0,
1397:                                        MatAssemblyEnd_SeqSBAIJ,
1398:                                        MatSetOption_SeqSBAIJ,
1399:                                        MatZeroEntries_SeqSBAIJ,
1400:                                /* 24*/ 0,
1401:                                        0,
1402:                                        0,
1403:                                        0,
1404:                                        0,
1405:                                /* 29*/ MatSetUp_SeqSBAIJ,
1406:                                        0,
1407:                                        0,
1408:                                        0,
1409:                                        0,
1410:                                /* 34*/ MatDuplicate_SeqSBAIJ,
1411:                                        0,
1412:                                        0,
1413:                                        0,
1414:                                        MatICCFactor_SeqSBAIJ,
1415:                                /* 39*/ MatAXPY_SeqSBAIJ,
1416:                                        MatGetSubMatrices_SeqSBAIJ,
1417:                                        MatIncreaseOverlap_SeqSBAIJ,
1418:                                        MatGetValues_SeqSBAIJ,
1419:                                        MatCopy_SeqSBAIJ,
1420:                                /* 44*/ 0,
1421:                                        MatScale_SeqSBAIJ,
1422:                                        0,
1423:                                        0,
1424:                                        MatZeroRowsColumns_SeqSBAIJ,
1425:                                /* 49*/ 0,
1426:                                        MatGetRowIJ_SeqSBAIJ,
1427:                                        MatRestoreRowIJ_SeqSBAIJ,
1428:                                        0,
1429:                                        0,
1430:                                /* 54*/ 0,
1431:                                        0,
1432:                                        0,
1433:                                        0,
1434:                                        MatSetValuesBlocked_SeqSBAIJ,
1435:                                /* 59*/ MatGetSubMatrix_SeqSBAIJ,
1436:                                        0,
1437:                                        0,
1438:                                        0,
1439:                                        0,
1440:                                /* 64*/ 0,
1441:                                        0,
1442:                                        0,
1443:                                        0,
1444:                                        0,
1445:                                /* 69*/ MatGetRowMaxAbs_SeqSBAIJ,
1446:                                        0,
1447:                                        0,
1448:                                        0,
1449:                                        0,
1450:                                /* 74*/ 0,
1451:                                        0,
1452:                                        0,
1453:                                        0,
1454:                                        0,
1455:                                /* 79*/ 0,
1456:                                        0,
1457:                                        0,
1458:                                        MatGetInertia_SeqSBAIJ,
1459:                                        MatLoad_SeqSBAIJ,
1460:                                /* 84*/ MatIsSymmetric_SeqSBAIJ,
1461:                                        MatIsHermitian_SeqSBAIJ,
1462:                                        MatIsStructurallySymmetric_SeqSBAIJ,
1463:                                        0,
1464:                                        0,
1465:                                /* 89*/ 0,
1466:                                        0,
1467:                                        0,
1468:                                        0,
1469:                                        0,
1470:                                /* 94*/ 0,
1471:                                        0,
1472:                                        0,
1473:                                        0,
1474:                                        0,
1475:                                /* 99*/ 0,
1476:                                        0,
1477:                                        0,
1478:                                        0,
1479:                                        0,
1480:                                /*104*/ 0,
1481:                                        MatRealPart_SeqSBAIJ,
1482:                                        MatImaginaryPart_SeqSBAIJ,
1483:                                        MatGetRowUpperTriangular_SeqSBAIJ,
1484:                                        MatRestoreRowUpperTriangular_SeqSBAIJ,
1485:                                /*109*/ 0,
1486:                                        0,
1487:                                        0,
1488:                                        0,
1489:                                        MatMissingDiagonal_SeqSBAIJ,
1490:                                /*114*/ 0,
1491:                                        0,
1492:                                        0,
1493:                                        0,
1494:                                        0,
1495:                                /*119*/ 0,
1496:                                        0,
1497:                                        0,
1498:                                        0,
1499:                                        0,
1500:                                /*124*/ 0,
1501:                                        0,
1502:                                        0,
1503:                                        0,
1504:                                        0,
1505:                                /*129*/ 0,
1506:                                        0,
1507:                                        0,
1508:                                        0,
1509:                                        0,
1510:                                /*134*/ 0,
1511:                                        0,
1512:                                        0,
1513:                                        0,
1514:                                        0,
1515:                                /*139*/ 0,
1516:                                        0,
1517:                                        0
1518: };

1522: PetscErrorCode  MatStoreValues_SeqSBAIJ(Mat mat)
1523: {
1524:   Mat_SeqSBAIJ   *aij = (Mat_SeqSBAIJ*)mat->data;
1525:   PetscInt       nz   = aij->i[mat->rmap->N]*mat->rmap->bs*aij->bs2;

1529:   if (aij->nonew != 1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ORDER,"Must call MatSetOption(A,MAT_NEW_NONZERO_LOCATIONS,PETSC_FALSE);first");

1531:   /* allocate space for values if not already there */
1532:   if (!aij->saved_values) {
1533:     PetscMalloc1((nz+1),&aij->saved_values);
1534:   }

1536:   /* copy values over */
1537:   PetscMemcpy(aij->saved_values,aij->a,nz*sizeof(PetscScalar));
1538:   return(0);
1539: }

1543: PetscErrorCode  MatRetrieveValues_SeqSBAIJ(Mat mat)
1544: {
1545:   Mat_SeqSBAIJ   *aij = (Mat_SeqSBAIJ*)mat->data;
1547:   PetscInt       nz = aij->i[mat->rmap->N]*mat->rmap->bs*aij->bs2;

1550:   if (aij->nonew != 1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ORDER,"Must call MatSetOption(A,MAT_NEW_NONZERO_LOCATIONS,PETSC_FALSE);first");
1551:   if (!aij->saved_values) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ORDER,"Must call MatStoreValues(A);first");

1553:   /* copy values over */
1554:   PetscMemcpy(aij->a,aij->saved_values,nz*sizeof(PetscScalar));
1555:   return(0);
1556: }

1560: PetscErrorCode  MatSeqSBAIJSetPreallocation_SeqSBAIJ(Mat B,PetscInt bs,PetscInt nz,PetscInt *nnz)
1561: {
1562:   Mat_SeqSBAIJ   *b = (Mat_SeqSBAIJ*)B->data;
1564:   PetscInt       i,mbs,bs2;
1565:   PetscBool      skipallocation = PETSC_FALSE,flg = PETSC_FALSE,realalloc = PETSC_FALSE;

1568:   if (nz >= 0 || nnz) realalloc = PETSC_TRUE;
1569:   B->preallocated = PETSC_TRUE;

1571:   PetscLayoutSetBlockSize(B->rmap,bs);
1572:   PetscLayoutSetBlockSize(B->cmap,bs);
1573:   PetscLayoutSetUp(B->rmap);
1574:   PetscLayoutSetUp(B->cmap);
1575:   PetscLayoutGetBlockSize(B->rmap,&bs);

1577:   mbs = B->rmap->N/bs;
1578:   bs2 = bs*bs;

1580:   if (mbs*bs != B->rmap->N) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Number rows, cols must be divisible by blocksize");

1582:   if (nz == MAT_SKIP_ALLOCATION) {
1583:     skipallocation = PETSC_TRUE;
1584:     nz             = 0;
1585:   }

1587:   if (nz == PETSC_DEFAULT || nz == PETSC_DECIDE) nz = 3;
1588:   if (nz < 0) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"nz cannot be less than 0: value %D",nz);
1589:   if (nnz) {
1590:     for (i=0; i<mbs; i++) {
1591:       if (nnz[i] < 0) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"nnz cannot be less than 0: local row %D value %D",i,nnz[i]);
1592:       if (nnz[i] > mbs) SETERRQ3(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"nnz cannot be greater than block row length: local row %D value %D rowlength %D",i,nnz[i],mbs);
1593:     }
1594:   }

1596:   B->ops->mult             = MatMult_SeqSBAIJ_N;
1597:   B->ops->multadd          = MatMultAdd_SeqSBAIJ_N;
1598:   B->ops->multtranspose    = MatMult_SeqSBAIJ_N;
1599:   B->ops->multtransposeadd = MatMultAdd_SeqSBAIJ_N;

1601:   PetscOptionsGetBool(((PetscObject)B)->prefix,"-mat_no_unroll",&flg,NULL);
1602:   if (!flg) {
1603:     switch (bs) {
1604:     case 1:
1605:       B->ops->mult             = MatMult_SeqSBAIJ_1;
1606:       B->ops->multadd          = MatMultAdd_SeqSBAIJ_1;
1607:       B->ops->multtranspose    = MatMult_SeqSBAIJ_1;
1608:       B->ops->multtransposeadd = MatMultAdd_SeqSBAIJ_1;
1609:       break;
1610:     case 2:
1611:       B->ops->mult             = MatMult_SeqSBAIJ_2;
1612:       B->ops->multadd          = MatMultAdd_SeqSBAIJ_2;
1613:       B->ops->multtranspose    = MatMult_SeqSBAIJ_2;
1614:       B->ops->multtransposeadd = MatMultAdd_SeqSBAIJ_2;
1615:       break;
1616:     case 3:
1617:       B->ops->mult             = MatMult_SeqSBAIJ_3;
1618:       B->ops->multadd          = MatMultAdd_SeqSBAIJ_3;
1619:       B->ops->multtranspose    = MatMult_SeqSBAIJ_3;
1620:       B->ops->multtransposeadd = MatMultAdd_SeqSBAIJ_3;
1621:       break;
1622:     case 4:
1623:       B->ops->mult             = MatMult_SeqSBAIJ_4;
1624:       B->ops->multadd          = MatMultAdd_SeqSBAIJ_4;
1625:       B->ops->multtranspose    = MatMult_SeqSBAIJ_4;
1626:       B->ops->multtransposeadd = MatMultAdd_SeqSBAIJ_4;
1627:       break;
1628:     case 5:
1629:       B->ops->mult             = MatMult_SeqSBAIJ_5;
1630:       B->ops->multadd          = MatMultAdd_SeqSBAIJ_5;
1631:       B->ops->multtranspose    = MatMult_SeqSBAIJ_5;
1632:       B->ops->multtransposeadd = MatMultAdd_SeqSBAIJ_5;
1633:       break;
1634:     case 6:
1635:       B->ops->mult             = MatMult_SeqSBAIJ_6;
1636:       B->ops->multadd          = MatMultAdd_SeqSBAIJ_6;
1637:       B->ops->multtranspose    = MatMult_SeqSBAIJ_6;
1638:       B->ops->multtransposeadd = MatMultAdd_SeqSBAIJ_6;
1639:       break;
1640:     case 7:
1641:       B->ops->mult             = MatMult_SeqSBAIJ_7;
1642:       B->ops->multadd          = MatMultAdd_SeqSBAIJ_7;
1643:       B->ops->multtranspose    = MatMult_SeqSBAIJ_7;
1644:       B->ops->multtransposeadd = MatMultAdd_SeqSBAIJ_7;
1645:       break;
1646:     }
1647:   }

1649:   b->mbs = mbs;
1650:   b->nbs = mbs;
1651:   if (!skipallocation) {
1652:     if (!b->imax) {
1653:       PetscMalloc2(mbs,&b->imax,mbs,&b->ilen);

1655:       b->free_imax_ilen = PETSC_TRUE;

1657:       PetscLogObjectMemory((PetscObject)B,2*mbs*sizeof(PetscInt));
1658:     }
1659:     if (!nnz) {
1660:       if (nz == PETSC_DEFAULT || nz == PETSC_DECIDE) nz = 5;
1661:       else if (nz <= 0) nz = 1;
1662:       for (i=0; i<mbs; i++) b->imax[i] = nz;
1663:       nz = nz*mbs; /* total nz */
1664:     } else {
1665:       nz = 0;
1666:       for (i=0; i<mbs; i++) {b->imax[i] = nnz[i]; nz += nnz[i];}
1667:     }
1668:     /* b->ilen will count nonzeros in each block row so far. */
1669:     for (i=0; i<mbs; i++) b->ilen[i] = 0;
1670:     /* nz=(nz+mbs)/2; */ /* total diagonal and superdiagonal nonzero blocks */

1672:     /* allocate the matrix space */
1673:     MatSeqXAIJFreeAIJ(B,&b->a,&b->j,&b->i);
1674:     PetscMalloc3(bs2*nz,&b->a,nz,&b->j,B->rmap->N+1,&b->i);
1675:     PetscLogObjectMemory((PetscObject)B,(B->rmap->N+1)*sizeof(PetscInt)+nz*(bs2*sizeof(PetscScalar)+sizeof(PetscInt)));
1676:     PetscMemzero(b->a,nz*bs2*sizeof(MatScalar));
1677:     PetscMemzero(b->j,nz*sizeof(PetscInt));

1679:     b->singlemalloc = PETSC_TRUE;

1681:     /* pointer to beginning of each row */
1682:     b->i[0] = 0;
1683:     for (i=1; i<mbs+1; i++) b->i[i] = b->i[i-1] + b->imax[i-1];

1685:     b->free_a  = PETSC_TRUE;
1686:     b->free_ij = PETSC_TRUE;
1687:   } else {
1688:     b->free_a  = PETSC_FALSE;
1689:     b->free_ij = PETSC_FALSE;
1690:   }

1692:   B->rmap->bs = bs;
1693:   b->bs2      = bs2;
1694:   b->nz       = 0;
1695:   b->maxnz    = nz;

1697:   b->inew    = 0;
1698:   b->jnew    = 0;
1699:   b->anew    = 0;
1700:   b->a2anew  = 0;
1701:   b->permute = PETSC_FALSE;
1702:   if (realalloc) {MatSetOption(B,MAT_NEW_NONZERO_ALLOCATION_ERR,PETSC_TRUE);}
1703:   return(0);
1704: }

1708: PetscErrorCode MatSeqSBAIJSetPreallocationCSR_SeqSBAIJ(Mat B,PetscInt bs,const PetscInt ii[],const PetscInt jj[], const PetscScalar V[])
1709: {
1710:   PetscInt       i,j,m,nz,nz_max=0,*nnz;
1711:   PetscScalar    *values=0;
1712:   PetscBool      roworiented = ((Mat_SeqSBAIJ*)B->data)->roworiented;
1715:   if (bs < 1) SETERRQ1(PetscObjectComm((PetscObject)B),PETSC_ERR_ARG_OUTOFRANGE,"Invalid block size specified, must be positive but it is %D",bs);
1716:   PetscLayoutSetBlockSize(B->rmap,bs);
1717:   PetscLayoutSetBlockSize(B->cmap,bs);
1718:   PetscLayoutSetUp(B->rmap);
1719:   PetscLayoutSetUp(B->cmap);
1720:   PetscLayoutGetBlockSize(B->rmap,&bs);
1721:   m      = B->rmap->n/bs;

1723:   if (ii[0]) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"ii[0] must be 0 but it is %D",ii[0]);
1724:   PetscMalloc1((m+1),&nnz);
1725:   for (i=0; i<m; i++) {
1726:     nz = ii[i+1] - ii[i];
1727:     if (nz < 0) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Row %D has a negative number of columns %D",i,nz);
1728:     nz_max = PetscMax(nz_max,nz);
1729:     nnz[i] = nz;
1730:   }
1731:   MatSeqSBAIJSetPreallocation(B,bs,0,nnz);
1732:   PetscFree(nnz);

1734:   values = (PetscScalar*)V;
1735:   if (!values) {
1736:     PetscCalloc1(bs*bs*nz_max,&values);
1737:   }
1738:   for (i=0; i<m; i++) {
1739:     PetscInt          ncols  = ii[i+1] - ii[i];
1740:     const PetscInt    *icols = jj + ii[i];
1741:     if (!roworiented || bs == 1) {
1742:       const PetscScalar *svals = values + (V ? (bs*bs*ii[i]) : 0);
1743:       MatSetValuesBlocked_SeqSBAIJ(B,1,&i,ncols,icols,svals,INSERT_VALUES);
1744:     } else {
1745:       for (j=0; j<ncols; j++) {
1746:         const PetscScalar *svals = values + (V ? (bs*bs*(ii[i]+j)) : 0);
1747:         MatSetValuesBlocked_SeqSBAIJ(B,1,&i,1,&icols[j],svals,INSERT_VALUES);
1748:       }
1749:     }
1750:   }
1751:   if (!V) { PetscFree(values); }
1752:   MatAssemblyBegin(B,MAT_FINAL_ASSEMBLY);
1753:   MatAssemblyEnd(B,MAT_FINAL_ASSEMBLY);
1754:   MatSetOption(B,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);
1755:   return(0);
1756: }

1758: /*
1759:    This is used to set the numeric factorization for both Cholesky and ICC symbolic factorization
1760: */
1763: PetscErrorCode MatSeqSBAIJSetNumericFactorization_inplace(Mat B,PetscBool natural)
1764: {
1766:   PetscBool      flg = PETSC_FALSE;
1767:   PetscInt       bs  = B->rmap->bs;

1770:   PetscOptionsGetBool(((PetscObject)B)->prefix,"-mat_no_unroll",&flg,NULL);
1771:   if (flg) bs = 8;

1773:   if (!natural) {
1774:     switch (bs) {
1775:     case 1:
1776:       B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_1_inplace;
1777:       break;
1778:     case 2:
1779:       B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_2;
1780:       break;
1781:     case 3:
1782:       B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_3;
1783:       break;
1784:     case 4:
1785:       B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_4;
1786:       break;
1787:     case 5:
1788:       B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_5;
1789:       break;
1790:     case 6:
1791:       B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_6;
1792:       break;
1793:     case 7:
1794:       B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_7;
1795:       break;
1796:     default:
1797:       B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_N;
1798:       break;
1799:     }
1800:   } else {
1801:     switch (bs) {
1802:     case 1:
1803:       B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_1_NaturalOrdering_inplace;
1804:       break;
1805:     case 2:
1806:       B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_2_NaturalOrdering;
1807:       break;
1808:     case 3:
1809:       B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_3_NaturalOrdering;
1810:       break;
1811:     case 4:
1812:       B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_4_NaturalOrdering;
1813:       break;
1814:     case 5:
1815:       B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_5_NaturalOrdering;
1816:       break;
1817:     case 6:
1818:       B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_6_NaturalOrdering;
1819:       break;
1820:     case 7:
1821:       B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_7_NaturalOrdering;
1822:       break;
1823:     default:
1824:       B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_N_NaturalOrdering;
1825:       break;
1826:     }
1827:   }
1828:   return(0);
1829: }

1831: PETSC_EXTERN PetscErrorCode MatConvert_SeqSBAIJ_SeqAIJ(Mat, MatType,MatReuse,Mat*);
1832: PETSC_EXTERN PetscErrorCode MatConvert_SeqSBAIJ_SeqBAIJ(Mat, MatType,MatReuse,Mat*);

1836: PETSC_EXTERN PetscErrorCode MatGetFactor_seqsbaij_petsc(Mat A,MatFactorType ftype,Mat *B)
1837: {
1838:   PetscInt       n = A->rmap->n;

1842: #if defined(PETSC_USE_COMPLEX)
1843:   if (A->hermitian) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Hermitian Factor is not supported");
1844: #endif
1845:   MatCreate(PetscObjectComm((PetscObject)A),B);
1846:   MatSetSizes(*B,n,n,n,n);
1847:   if (ftype == MAT_FACTOR_CHOLESKY || ftype == MAT_FACTOR_ICC) {
1848:     MatSetType(*B,MATSEQSBAIJ);
1849:     MatSeqSBAIJSetPreallocation(*B,A->rmap->bs,MAT_SKIP_ALLOCATION,NULL);

1851:     (*B)->ops->choleskyfactorsymbolic = MatCholeskyFactorSymbolic_SeqSBAIJ;
1852:     (*B)->ops->iccfactorsymbolic      = MatICCFactorSymbolic_SeqSBAIJ;
1853:   } else SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Factor type not supported");
1854:   (*B)->factortype = ftype;
1855:   return(0);
1856: }

1860: PetscErrorCode MatGetFactorAvailable_seqsbaij_petsc(Mat A,MatFactorType ftype,PetscBool  *flg)
1861: {
1863:   if (ftype == MAT_FACTOR_CHOLESKY || ftype == MAT_FACTOR_ICC) {
1864:     *flg = PETSC_TRUE;
1865:   } else {
1866:     *flg = PETSC_FALSE;
1867:   }
1868:   return(0);
1869: }

1871: #if defined(PETSC_HAVE_MUMPS)
1872: PETSC_EXTERN PetscErrorCode MatGetFactor_sbaij_mumps(Mat,MatFactorType,Mat*);
1873: #endif
1874: #if defined(PETSC_HAVE_PASTIX)
1875: PETSC_EXTERN PetscErrorCode MatGetFactor_seqsbaij_pastix(Mat,MatFactorType,Mat*);
1876: #endif
1877: #if defined(PETSC_HAVE_CHOLMOD)
1878: PETSC_EXTERN PetscErrorCode MatGetFactor_seqsbaij_cholmod(Mat,MatFactorType,Mat*);
1879: #endif
1880: PETSC_EXTERN PetscErrorCode MatGetFactor_seqsbaij_sbstrm(Mat,MatFactorType,Mat*);

1882: /*MC
1883:   MATSEQSBAIJ - MATSEQSBAIJ = "seqsbaij" - A matrix type to be used for sequential symmetric block sparse matrices,
1884:   based on block compressed sparse row format.  Only the upper triangular portion of the matrix is stored.

1886:   For complex numbers by default this matrix is symmetric, NOT Hermitian symmetric. To make it Hermitian symmetric you
1887:   can call MatSetOption(Mat, MAT_HERMITIAN); after MatAssemblyEnd()

1889:   Options Database Keys:
1890:   . -mat_type seqsbaij - sets the matrix type to "seqsbaij" during a call to MatSetFromOptions()

1892:   Notes: By default if you insert values into the lower triangular part of the matrix they are simply ignored (since they are not
1893:      stored and it is assumed they symmetric to the upper triangular). If you call MatSetOption(Mat,MAT_IGNORE_LOWER_TRIANGULAR,PETSC_FALSE) or use
1894:      the options database -mat_ignore_lower_triangular false it will generate an error if you try to set a value in the lower triangular portion.


1897:   Level: beginner

1899:   .seealso: MatCreateSeqSBAIJ
1900: M*/

1902: PETSC_EXTERN PetscErrorCode MatConvert_SeqSBAIJ_SeqSBSTRM(Mat, MatType,MatReuse,Mat*);

1906: PETSC_EXTERN PetscErrorCode MatCreate_SeqSBAIJ(Mat B)
1907: {
1908:   Mat_SeqSBAIJ   *b;
1910:   PetscMPIInt    size;
1911:   PetscBool      no_unroll = PETSC_FALSE,no_inode = PETSC_FALSE;

1914:   MPI_Comm_size(PetscObjectComm((PetscObject)B),&size);
1915:   if (size > 1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"Comm must be of size 1");

1917:   PetscNewLog(B,&b);
1918:   B->data = (void*)b;
1919:   PetscMemcpy(B->ops,&MatOps_Values,sizeof(struct _MatOps));

1921:   B->ops->destroy    = MatDestroy_SeqSBAIJ;
1922:   B->ops->view       = MatView_SeqSBAIJ;
1923:   b->row             = 0;
1924:   b->icol            = 0;
1925:   b->reallocs        = 0;
1926:   b->saved_values    = 0;
1927:   b->inode.limit     = 5;
1928:   b->inode.max_limit = 5;

1930:   b->roworiented        = PETSC_TRUE;
1931:   b->nonew              = 0;
1932:   b->diag               = 0;
1933:   b->solve_work         = 0;
1934:   b->mult_work          = 0;
1935:   B->spptr              = 0;
1936:   B->info.nz_unneeded   = (PetscReal)b->maxnz*b->bs2;
1937:   b->keepnonzeropattern = PETSC_FALSE;
1938:   b->xtoy               = 0;
1939:   b->XtoY               = 0;

1941:   b->inew    = 0;
1942:   b->jnew    = 0;
1943:   b->anew    = 0;
1944:   b->a2anew  = 0;
1945:   b->permute = PETSC_FALSE;

1947:   b->ignore_ltriangular = PETSC_TRUE;

1949:   PetscOptionsGetBool(((PetscObject)B)->prefix,"-mat_ignore_lower_triangular",&b->ignore_ltriangular,NULL);

1951:   b->getrow_utriangular = PETSC_FALSE;

1953:   PetscOptionsGetBool(((PetscObject)B)->prefix,"-mat_getrow_uppertriangular",&b->getrow_utriangular,NULL);

1955: #if defined(PETSC_HAVE_PASTIX)
1956:   PetscObjectComposeFunction((PetscObject)B,"MatGetFactor_pastix_C",MatGetFactor_seqsbaij_pastix);
1957: #endif
1958: #if defined(PETSC_HAVE_MUMPS)
1959:   PetscObjectComposeFunction((PetscObject)B,"MatGetFactor_mumps_C",MatGetFactor_sbaij_mumps);
1960: #endif
1961: #if defined(PETSC_HAVE_CHOLMOD)
1962:   PetscObjectComposeFunction((PetscObject)B,"MatGetFactor_cholmod_C",MatGetFactor_seqsbaij_cholmod);
1963: #endif
1964:   PetscObjectComposeFunction((PetscObject)B,"MatGetFactorAvailable_petsc_C",MatGetFactorAvailable_seqsbaij_petsc);
1965:   PetscObjectComposeFunction((PetscObject)B,"MatGetFactor_petsc_C",MatGetFactor_seqsbaij_petsc);
1966:   PetscObjectComposeFunction((PetscObject)B,"MatGetFactor_sbstrm_C",MatGetFactor_seqsbaij_sbstrm);
1967:   PetscObjectComposeFunction((PetscObject)B,"MatStoreValues_C",MatStoreValues_SeqSBAIJ);
1968:   PetscObjectComposeFunction((PetscObject)B,"MatRetrieveValues_C",MatRetrieveValues_SeqSBAIJ);
1969:   PetscObjectComposeFunction((PetscObject)B,"MatSeqSBAIJSetColumnIndices_C",MatSeqSBAIJSetColumnIndices_SeqSBAIJ);
1970:   PetscObjectComposeFunction((PetscObject)B,"MatConvert_seqsbaij_seqaij_C",MatConvert_SeqSBAIJ_SeqAIJ);
1971:   PetscObjectComposeFunction((PetscObject)B,"MatConvert_seqsbaij_seqbaij_C",MatConvert_SeqSBAIJ_SeqBAIJ);
1972:   PetscObjectComposeFunction((PetscObject)B,"MatSeqSBAIJSetPreallocation_C",MatSeqSBAIJSetPreallocation_SeqSBAIJ);
1973:   PetscObjectComposeFunction((PetscObject)B,"MatSeqSBAIJSetPreallocationCSR_C",MatSeqSBAIJSetPreallocationCSR_SeqSBAIJ);
1974:   PetscObjectComposeFunction((PetscObject)B,"MatConvert_seqsbaij_seqsbstrm_C",MatConvert_SeqSBAIJ_SeqSBSTRM);

1976:   B->symmetric                  = PETSC_TRUE;
1977:   B->structurally_symmetric     = PETSC_TRUE;
1978:   B->symmetric_set              = PETSC_TRUE;
1979:   B->structurally_symmetric_set = PETSC_TRUE;

1981:   PetscObjectChangeTypeName((PetscObject)B,MATSEQSBAIJ);

1983:   PetscOptionsBegin(PetscObjectComm((PetscObject)B),((PetscObject)B)->prefix,"Options for SEQSBAIJ matrix","Mat");
1984:   PetscOptionsBool("-mat_no_unroll","Do not optimize for inodes (slower)",NULL,no_unroll,&no_unroll,NULL);
1985:   if (no_unroll) {
1986:     PetscInfo(B,"Not using Inode routines due to -mat_no_unroll\n");
1987:   }
1988:   PetscOptionsBool("-mat_no_inode","Do not optimize for inodes (slower)",NULL,no_inode,&no_inode,NULL);
1989:   if (no_inode) {
1990:     PetscInfo(B,"Not using Inode routines due to -mat_no_inode\n");
1991:   }
1992:   PetscOptionsInt("-mat_inode_limit","Do not use inodes larger then this value",NULL,b->inode.limit,&b->inode.limit,NULL);
1993:   PetscOptionsEnd();
1994:   b->inode.use = (PetscBool)(!(no_unroll || no_inode));
1995:   if (b->inode.limit > b->inode.max_limit) b->inode.limit = b->inode.max_limit;
1996:   return(0);
1997: }

2001: /*@C
2002:    MatSeqSBAIJSetPreallocation - Creates a sparse symmetric matrix in block AIJ (block
2003:    compressed row) format.  For good matrix assembly performance the
2004:    user should preallocate the matrix storage by setting the parameter nz
2005:    (or the array nnz).  By setting these parameters accurately, performance
2006:    during matrix assembly can be increased by more than a factor of 50.

2008:    Collective on Mat

2010:    Input Parameters:
2011: +  A - the symmetric matrix
2012: .  bs - size of block
2013: .  nz - number of block nonzeros per block row (same for all rows)
2014: -  nnz - array containing the number of block nonzeros in the upper triangular plus
2015:          diagonal portion of each block (possibly different for each block row) or NULL

2017:    Options Database Keys:
2018: .   -mat_no_unroll - uses code that does not unroll the loops in the
2019:                      block calculations (much slower)
2020: .    -mat_block_size - size of the blocks to use (only works if a negative bs is passed in

2022:    Level: intermediate

2024:    Notes:
2025:    Specify the preallocated storage with either nz or nnz (not both).
2026:    Set nz=PETSC_DEFAULT and nnz=NULL for PETSc to control dynamic memory
2027:    allocation.  See the <a href="../../docs/manual.pdf#nameddest=ch_mat">Mat chapter of the users manual</a> for details.

2029:    You can call MatGetInfo() to get information on how effective the preallocation was;
2030:    for example the fields mallocs,nz_allocated,nz_used,nz_unneeded;
2031:    You can also run with the option -info and look for messages with the string
2032:    malloc in them to see if additional memory allocation was needed.

2034:    If the nnz parameter is given then the nz parameter is ignored


2037: .seealso: MatCreate(), MatCreateSeqAIJ(), MatSetValues(), MatCreateSBAIJ()
2038: @*/
2039: PetscErrorCode  MatSeqSBAIJSetPreallocation(Mat B,PetscInt bs,PetscInt nz,const PetscInt nnz[])
2040: {

2047:   PetscTryMethod(B,"MatSeqSBAIJSetPreallocation_C",(Mat,PetscInt,PetscInt,const PetscInt[]),(B,bs,nz,nnz));
2048:   return(0);
2049: }

2051: #undef  __FUNCT__
2053: /*@C
2054:    MatSeqSBAIJSetPreallocationCSR - Allocates memory for a sparse sequential matrix in symmetric block AIJ format.

2056:    Input Parameters:
2057: +  A - the matrix
2058: .  i - the indices into j for the start of each local row (starts with zero)
2059: .  j - the column indices for each local row (starts with zero) these must be sorted for each row
2060: -  v - optional values in the matrix

2062:    Level: developer

2064:    Notes:
2065:    The order of the entries in values is specified by the MatOption MAT_ROW_ORIENTED.  For example, C programs
2066:    may want to use the default MAT_ROW_ORIENTED=PETSC_TRUE and use an array v[nnz][bs][bs] where the second index is
2067:    over rows within a block and the last index is over columns within a block row.  Fortran programs will likely set
2068:    MAT_ROW_ORIENTED=PETSC_FALSE and use a Fortran array v(bs,bs,nnz) in which the first index is over rows within a
2069:    block column and the second index is over columns within a block.

2071: .keywords: matrix, block, aij, compressed row, sparse

2073: .seealso: MatCreate(), MatCreateSeqSBAIJ(), MatSetValuesBlocked(), MatSeqSBAIJSetPreallocation(), MATSEQSBAIJ
2074: @*/
2075: PetscErrorCode MatSeqSBAIJSetPreallocationCSR(Mat B,PetscInt bs,const PetscInt i[],const PetscInt j[], const PetscScalar v[])
2076: {

2083:   PetscTryMethod(B,"MatSeqSBAIJSetPreallocationCSR_C",(Mat,PetscInt,const PetscInt[],const PetscInt[],const PetscScalar[]),(B,bs,i,j,v));
2084:   return(0);
2085: }

2089: /*@C
2090:    MatCreateSeqSBAIJ - Creates a sparse symmetric matrix in block AIJ (block
2091:    compressed row) format.  For good matrix assembly performance the
2092:    user should preallocate the matrix storage by setting the parameter nz
2093:    (or the array nnz).  By setting these parameters accurately, performance
2094:    during matrix assembly can be increased by more than a factor of 50.

2096:    Collective on MPI_Comm

2098:    Input Parameters:
2099: +  comm - MPI communicator, set to PETSC_COMM_SELF
2100: .  bs - size of block
2101: .  m - number of rows, or number of columns
2102: .  nz - number of block nonzeros per block row (same for all rows)
2103: -  nnz - array containing the number of block nonzeros in the upper triangular plus
2104:          diagonal portion of each block (possibly different for each block row) or NULL

2106:    Output Parameter:
2107: .  A - the symmetric matrix

2109:    Options Database Keys:
2110: .   -mat_no_unroll - uses code that does not unroll the loops in the
2111:                      block calculations (much slower)
2112: .    -mat_block_size - size of the blocks to use

2114:    Level: intermediate

2116:    It is recommended that one use the MatCreate(), MatSetType() and/or MatSetFromOptions(),
2117:    MatXXXXSetPreallocation() paradgm instead of this routine directly.
2118:    [MatXXXXSetPreallocation() is, for example, MatSeqAIJSetPreallocation]

2120:    Notes:
2121:    The number of rows and columns must be divisible by blocksize.
2122:    This matrix type does not support complex Hermitian operation.

2124:    Specify the preallocated storage with either nz or nnz (not both).
2125:    Set nz=PETSC_DEFAULT and nnz=NULL for PETSc to control dynamic memory
2126:    allocation.  See the <a href="../../docs/manual.pdf#nameddest=ch_mat">Mat chapter of the users manual</a> for details.

2128:    If the nnz parameter is given then the nz parameter is ignored

2130: .seealso: MatCreate(), MatCreateSeqAIJ(), MatSetValues(), MatCreateSBAIJ()
2131: @*/
2132: PetscErrorCode  MatCreateSeqSBAIJ(MPI_Comm comm,PetscInt bs,PetscInt m,PetscInt n,PetscInt nz,const PetscInt nnz[],Mat *A)
2133: {

2137:   MatCreate(comm,A);
2138:   MatSetSizes(*A,m,n,m,n);
2139:   MatSetType(*A,MATSEQSBAIJ);
2140:   MatSeqSBAIJSetPreallocation_SeqSBAIJ(*A,bs,nz,(PetscInt*)nnz);
2141:   return(0);
2142: }

2146: PetscErrorCode MatDuplicate_SeqSBAIJ(Mat A,MatDuplicateOption cpvalues,Mat *B)
2147: {
2148:   Mat            C;
2149:   Mat_SeqSBAIJ   *c,*a = (Mat_SeqSBAIJ*)A->data;
2151:   PetscInt       i,mbs = a->mbs,nz = a->nz,bs2 =a->bs2;

2154:   if (a->i[mbs] != nz) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Corrupt matrix");

2156:   *B   = 0;
2157:   MatCreate(PetscObjectComm((PetscObject)A),&C);
2158:   MatSetSizes(C,A->rmap->N,A->cmap->n,A->rmap->N,A->cmap->n);
2159:   MatSetType(C,MATSEQSBAIJ);
2160:   PetscMemcpy(C->ops,A->ops,sizeof(struct _MatOps));
2161:   c    = (Mat_SeqSBAIJ*)C->data;

2163:   C->preallocated       = PETSC_TRUE;
2164:   C->factortype         = A->factortype;
2165:   c->row                = 0;
2166:   c->icol               = 0;
2167:   c->saved_values       = 0;
2168:   c->keepnonzeropattern = a->keepnonzeropattern;
2169:   C->assembled          = PETSC_TRUE;

2171:   PetscLayoutReference(A->rmap,&C->rmap);
2172:   PetscLayoutReference(A->cmap,&C->cmap);
2173:   c->bs2 = a->bs2;
2174:   c->mbs = a->mbs;
2175:   c->nbs = a->nbs;

2177:   if  (cpvalues == MAT_SHARE_NONZERO_PATTERN) {
2178:     c->imax           = a->imax;
2179:     c->ilen           = a->ilen;
2180:     c->free_imax_ilen = PETSC_FALSE;
2181:   } else {
2182:     PetscMalloc2((mbs+1),&c->imax,(mbs+1),&c->ilen);
2183:     PetscLogObjectMemory((PetscObject)C,2*(mbs+1)*sizeof(PetscInt));
2184:     for (i=0; i<mbs; i++) {
2185:       c->imax[i] = a->imax[i];
2186:       c->ilen[i] = a->ilen[i];
2187:     }
2188:     c->free_imax_ilen = PETSC_TRUE;
2189:   }

2191:   /* allocate the matrix space */
2192:   if (cpvalues == MAT_SHARE_NONZERO_PATTERN) {
2193:     PetscMalloc1(bs2*nz,&c->a);
2194:     PetscLogObjectMemory((PetscObject)C,nz*bs2*sizeof(MatScalar));
2195:     c->i            = a->i;
2196:     c->j            = a->j;
2197:     c->singlemalloc = PETSC_FALSE;
2198:     c->free_a       = PETSC_TRUE;
2199:     c->free_ij      = PETSC_FALSE;
2200:     c->parent       = A;
2201:     PetscObjectReference((PetscObject)A);
2202:     MatSetOption(A,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);
2203:     MatSetOption(C,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);
2204:   } else {
2205:     PetscMalloc3(bs2*nz,&c->a,nz,&c->j,mbs+1,&c->i);
2206:     PetscMemcpy(c->i,a->i,(mbs+1)*sizeof(PetscInt));
2207:     PetscLogObjectMemory((PetscObject)C,(mbs+1)*sizeof(PetscInt) + nz*(bs2*sizeof(MatScalar) + sizeof(PetscInt)));
2208:     c->singlemalloc = PETSC_TRUE;
2209:     c->free_a       = PETSC_TRUE;
2210:     c->free_ij      = PETSC_TRUE;
2211:   }
2212:   if (mbs > 0) {
2213:     if (cpvalues != MAT_SHARE_NONZERO_PATTERN) {
2214:       PetscMemcpy(c->j,a->j,nz*sizeof(PetscInt));
2215:     }
2216:     if (cpvalues == MAT_COPY_VALUES) {
2217:       PetscMemcpy(c->a,a->a,bs2*nz*sizeof(MatScalar));
2218:     } else {
2219:       PetscMemzero(c->a,bs2*nz*sizeof(MatScalar));
2220:     }
2221:     if (a->jshort) {
2222:       /* cannot share jshort, it is reallocated in MatAssemblyEnd_SeqSBAIJ() */
2223:       /* if the parent matrix is reassembled, this child matrix will never notice */
2224:       PetscMalloc1(nz,&c->jshort);
2225:       PetscLogObjectMemory((PetscObject)C,nz*sizeof(unsigned short));
2226:       PetscMemcpy(c->jshort,a->jshort,nz*sizeof(unsigned short));

2228:       c->free_jshort = PETSC_TRUE;
2229:     }
2230:   }

2232:   c->roworiented = a->roworiented;
2233:   c->nonew       = a->nonew;

2235:   if (a->diag) {
2236:     if (cpvalues == MAT_SHARE_NONZERO_PATTERN) {
2237:       c->diag      = a->diag;
2238:       c->free_diag = PETSC_FALSE;
2239:     } else {
2240:       PetscMalloc1(mbs,&c->diag);
2241:       PetscLogObjectMemory((PetscObject)C,mbs*sizeof(PetscInt));
2242:       for (i=0; i<mbs; i++) c->diag[i] = a->diag[i];
2243:       c->free_diag = PETSC_TRUE;
2244:     }
2245:   }
2246:   c->nz         = a->nz;
2247:   c->maxnz      = a->nz; /* Since we allocate exactly the right amount */
2248:   c->solve_work = 0;
2249:   c->mult_work  = 0;

2251:   *B   = C;
2252:   PetscFunctionListDuplicate(((PetscObject)A)->qlist,&((PetscObject)C)->qlist);
2253:   return(0);
2254: }

2258: PetscErrorCode MatLoad_SeqSBAIJ(Mat newmat,PetscViewer viewer)
2259: {
2260:   Mat_SeqSBAIJ   *a;
2262:   int            fd;
2263:   PetscMPIInt    size;
2264:   PetscInt       i,nz,header[4],*rowlengths=0,M,N,bs=1;
2265:   PetscInt       *mask,mbs,*jj,j,rowcount,nzcount,k,*s_browlengths,maskcount;
2266:   PetscInt       kmax,jcount,block,idx,point,nzcountb,extra_rows,rows,cols;
2267:   PetscInt       *masked,nmask,tmp,bs2,ishift;
2268:   PetscScalar    *aa;
2269:   MPI_Comm       comm;

2272:   PetscObjectGetComm((PetscObject)viewer,&comm);
2273:   PetscOptionsGetInt(((PetscObject)newmat)->prefix,"-matload_block_size",&bs,NULL);
2274:   bs2  = bs*bs;

2276:   MPI_Comm_size(comm,&size);
2277:   if (size > 1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"view must have one processor");
2278:   PetscViewerBinaryGetDescriptor(viewer,&fd);
2279:   PetscBinaryRead(fd,header,4,PETSC_INT);
2280:   if (header[0] != MAT_FILE_CLASSID) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_FILE_UNEXPECTED,"not Mat object");
2281:   M = header[1]; N = header[2]; nz = header[3];

2283:   if (header[3] < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_FILE_UNEXPECTED,"Matrix stored in special format, cannot load as SeqSBAIJ");

2285:   if (M != N) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Can only do square matrices");

2287:   /*
2288:      This code adds extra rows to make sure the number of rows is
2289:     divisible by the blocksize
2290:   */
2291:   mbs        = M/bs;
2292:   extra_rows = bs - M + bs*(mbs);
2293:   if (extra_rows == bs) extra_rows = 0;
2294:   else                  mbs++;
2295:   if (extra_rows) {
2296:     PetscInfo(viewer,"Padding loaded matrix to match blocksize\n");
2297:   }

2299:   /* Set global sizes if not already set */
2300:   if (newmat->rmap->n < 0 && newmat->rmap->N < 0 && newmat->cmap->n < 0 && newmat->cmap->N < 0) {
2301:     MatSetSizes(newmat,PETSC_DECIDE,PETSC_DECIDE,M+extra_rows,N+extra_rows);
2302:   } else { /* Check if the matrix global sizes are correct */
2303:     MatGetSize(newmat,&rows,&cols);
2304:     if (M != rows ||  N != cols) SETERRQ4(PETSC_COMM_SELF,PETSC_ERR_FILE_UNEXPECTED,"Matrix in file of different length (%d, %d) than the input matrix (%d, %d)",M,N,rows,cols);
2305:   }

2307:   /* read in row lengths */
2308:   PetscMalloc1((M+extra_rows),&rowlengths);
2309:   PetscBinaryRead(fd,rowlengths,M,PETSC_INT);
2310:   for (i=0; i<extra_rows; i++) rowlengths[M+i] = 1;

2312:   /* read in column indices */
2313:   PetscMalloc1((nz+extra_rows),&jj);
2314:   PetscBinaryRead(fd,jj,nz,PETSC_INT);
2315:   for (i=0; i<extra_rows; i++) jj[nz+i] = M+i;

2317:   /* loop over row lengths determining block row lengths */
2318:   PetscCalloc1(mbs,&s_browlengths);
2319:   PetscMalloc2(mbs,&mask,mbs,&masked);
2320:   PetscMemzero(mask,mbs*sizeof(PetscInt));
2321:   rowcount = 0;
2322:   nzcount  = 0;
2323:   for (i=0; i<mbs; i++) {
2324:     nmask = 0;
2325:     for (j=0; j<bs; j++) {
2326:       kmax = rowlengths[rowcount];
2327:       for (k=0; k<kmax; k++) {
2328:         tmp = jj[nzcount++]/bs;   /* block col. index */
2329:         if (!mask[tmp] && tmp >= i) {masked[nmask++] = tmp; mask[tmp] = 1;}
2330:       }
2331:       rowcount++;
2332:     }
2333:     s_browlengths[i] += nmask;

2335:     /* zero out the mask elements we set */
2336:     for (j=0; j<nmask; j++) mask[masked[j]] = 0;
2337:   }

2339:   /* Do preallocation */
2340:   MatSeqSBAIJSetPreallocation_SeqSBAIJ(newmat,bs,0,s_browlengths);
2341:   a    = (Mat_SeqSBAIJ*)newmat->data;

2343:   /* set matrix "i" values */
2344:   a->i[0] = 0;
2345:   for (i=1; i<= mbs; i++) {
2346:     a->i[i]      = a->i[i-1] + s_browlengths[i-1];
2347:     a->ilen[i-1] = s_browlengths[i-1];
2348:   }
2349:   a->nz = a->i[mbs];

2351:   /* read in nonzero values */
2352:   PetscMalloc1((nz+extra_rows),&aa);
2353:   PetscBinaryRead(fd,aa,nz,PETSC_SCALAR);
2354:   for (i=0; i<extra_rows; i++) aa[nz+i] = 1.0;

2356:   /* set "a" and "j" values into matrix */
2357:   nzcount = 0; jcount = 0;
2358:   for (i=0; i<mbs; i++) {
2359:     nzcountb = nzcount;
2360:     nmask    = 0;
2361:     for (j=0; j<bs; j++) {
2362:       kmax = rowlengths[i*bs+j];
2363:       for (k=0; k<kmax; k++) {
2364:         tmp = jj[nzcount++]/bs; /* block col. index */
2365:         if (!mask[tmp] && tmp >= i) { masked[nmask++] = tmp; mask[tmp] = 1;}
2366:       }
2367:     }
2368:     /* sort the masked values */
2369:     PetscSortInt(nmask,masked);

2371:     /* set "j" values into matrix */
2372:     maskcount = 1;
2373:     for (j=0; j<nmask; j++) {
2374:       a->j[jcount++]  = masked[j];
2375:       mask[masked[j]] = maskcount++;
2376:     }

2378:     /* set "a" values into matrix */
2379:     ishift = bs2*a->i[i];
2380:     for (j=0; j<bs; j++) {
2381:       kmax = rowlengths[i*bs+j];
2382:       for (k=0; k<kmax; k++) {
2383:         tmp = jj[nzcountb]/bs;        /* block col. index */
2384:         if (tmp >= i) {
2385:           block     = mask[tmp] - 1;
2386:           point     = jj[nzcountb] - bs*tmp;
2387:           idx       = ishift + bs2*block + j + bs*point;
2388:           a->a[idx] = aa[nzcountb];
2389:         }
2390:         nzcountb++;
2391:       }
2392:     }
2393:     /* zero out the mask elements we set */
2394:     for (j=0; j<nmask; j++) mask[masked[j]] = 0;
2395:   }
2396:   if (jcount != a->nz) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_FILE_UNEXPECTED,"Bad binary matrix");

2398:   PetscFree(rowlengths);
2399:   PetscFree(s_browlengths);
2400:   PetscFree(aa);
2401:   PetscFree(jj);
2402:   PetscFree2(mask,masked);

2404:   MatAssemblyBegin(newmat,MAT_FINAL_ASSEMBLY);
2405:   MatAssemblyEnd(newmat,MAT_FINAL_ASSEMBLY);
2406:   return(0);
2407: }

2411: /*@
2412:      MatCreateSeqSBAIJWithArrays - Creates an sequential SBAIJ matrix using matrix elements
2413:               (upper triangular entries in CSR format) provided by the user.

2415:      Collective on MPI_Comm

2417:    Input Parameters:
2418: +  comm - must be an MPI communicator of size 1
2419: .  bs - size of block
2420: .  m - number of rows
2421: .  n - number of columns
2422: .  i - row indices
2423: .  j - column indices
2424: -  a - matrix values

2426:    Output Parameter:
2427: .  mat - the matrix

2429:    Level: advanced

2431:    Notes:
2432:        The i, j, and a arrays are not copied by this routine, the user must free these arrays
2433:     once the matrix is destroyed

2435:        You cannot set new nonzero locations into this matrix, that will generate an error.

2437:        The i and j indices are 0 based

2439:        When block size is greater than 1 the matrix values must be stored using the SBAIJ storage format (see the SBAIJ code to determine this). For block size of 1
2440:        it is the regular CSR format excluding the lower triangular elements.

2442: .seealso: MatCreate(), MatCreateSBAIJ(), MatCreateSeqSBAIJ()

2444: @*/
2445: PetscErrorCode  MatCreateSeqSBAIJWithArrays(MPI_Comm comm,PetscInt bs,PetscInt m,PetscInt n,PetscInt *i,PetscInt *j,PetscScalar *a,Mat *mat)
2446: {
2448:   PetscInt       ii;
2449:   Mat_SeqSBAIJ   *sbaij;

2452:   if (bs != 1) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP,"block size %D > 1 is not supported yet",bs);
2453:   if (i[0]) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"i (row indices) must start with 0");

2455:   MatCreate(comm,mat);
2456:   MatSetSizes(*mat,m,n,m,n);
2457:   MatSetType(*mat,MATSEQSBAIJ);
2458:   MatSeqSBAIJSetPreallocation_SeqSBAIJ(*mat,bs,MAT_SKIP_ALLOCATION,0);
2459:   sbaij = (Mat_SeqSBAIJ*)(*mat)->data;
2460:   PetscMalloc2(m,&sbaij->imax,m,&sbaij->ilen);
2461:   PetscLogObjectMemory((PetscObject)*mat,2*m*sizeof(PetscInt));

2463:   sbaij->i = i;
2464:   sbaij->j = j;
2465:   sbaij->a = a;

2467:   sbaij->singlemalloc = PETSC_FALSE;
2468:   sbaij->nonew        = -1;             /*this indicates that inserting a new value in the matrix that generates a new nonzero is an error*/
2469:   sbaij->free_a       = PETSC_FALSE;
2470:   sbaij->free_ij      = PETSC_FALSE;

2472:   for (ii=0; ii<m; ii++) {
2473:     sbaij->ilen[ii] = sbaij->imax[ii] = i[ii+1] - i[ii];
2474: #if defined(PETSC_USE_DEBUG)
2475:     if (i[ii+1] - i[ii] < 0) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Negative row length in i (row indices) row = %d length = %d",ii,i[ii+1] - i[ii]);
2476: #endif
2477:   }
2478: #if defined(PETSC_USE_DEBUG)
2479:   for (ii=0; ii<sbaij->i[m]; ii++) {
2480:     if (j[ii] < 0) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Negative column index at location = %d index = %d",ii,j[ii]);
2481:     if (j[ii] > n - 1) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Column index to large at location = %d index = %d",ii,j[ii]);
2482:   }
2483: #endif

2485:   MatAssemblyBegin(*mat,MAT_FINAL_ASSEMBLY);
2486:   MatAssemblyEnd(*mat,MAT_FINAL_ASSEMBLY);
2487:   return(0);
2488: }