Actual source code: sbaij.c
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: diag = a->diag;
30: *missing = PETSC_FALSE;
31: for (i=0; i<a->mbs; i++) {
32: if (jj[diag[i]] != i) {
33: *missing = PETSC_TRUE;
34: if (dd) *dd = i;
35: break;
36: }
37: }
38: return(0);
39: }
43: PetscErrorCode MatMarkDiagonal_SeqSBAIJ(Mat A)
44: {
45: Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data;
47: PetscInt i;
50: if (!a->diag) {
51: PetscMalloc(a->mbs*sizeof(PetscInt),&a->diag);
52: PetscLogObjectMemory(A,a->mbs*sizeof(PetscInt));
53: a->free_diag = PETSC_TRUE;
54: }
55: for (i=0; i<a->mbs; i++) a->diag[i] = a->i[i];
56: return(0);
57: }
61: static PetscErrorCode MatGetRowIJ_SeqSBAIJ(Mat A,PetscInt oshift,PetscBool symmetric,PetscBool blockcompressed,PetscInt *nn,PetscInt *ia[],PetscInt *ja[],PetscBool *done)
62: {
63: Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data;
64: PetscInt i,j,n = a->mbs,nz = a->i[n],bs = A->rmap->bs;
68: *nn = n;
69: if (!ia) return(0);
70: if (!blockcompressed) {
71: /* malloc & create the natural set of indices */
72: PetscMalloc2((n+1)*bs,PetscInt,ia,nz*bs,PetscInt,ja);
73: for (i=0; i<n+1; i++) {
74: for (j=0; j<bs; j++) {
75: *ia[i*bs+j] = a->i[i]*bs+j+oshift;
76: }
77: }
78: for (i=0; i<nz; i++) {
79: for (j=0; j<bs; j++) {
80: *ja[i*bs+j] = a->j[i]*bs+j+oshift;
81: }
82: }
83: } else { /* blockcompressed */
84: if (oshift == 1) {
85: /* temporarily add 1 to i and j indices */
86: for (i=0; i<nz; i++) a->j[i]++;
87: for (i=0; i<n+1; i++) a->i[i]++;
88: }
89: *ia = a->i; *ja = a->j;
90: }
92: return(0);
93: }
97: static PetscErrorCode MatRestoreRowIJ_SeqSBAIJ(Mat A,PetscInt oshift,PetscBool symmetric,PetscBool blockcompressed,PetscInt *nn,PetscInt *ia[],PetscInt *ja[],PetscBool *done)
98: {
99: Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data;
100: PetscInt i,n = a->mbs,nz = a->i[n];
104: if (!ia) return(0);
106: if (!blockcompressed) {
107: PetscFree2(*ia,*ja);
108: } else if (oshift == 1) { /* blockcompressed */
109: for (i=0; i<nz; i++) a->j[i]--;
110: for (i=0; i<n+1; i++) a->i[i]--;
111: }
113: return(0);
114: }
118: PetscErrorCode MatDestroy_SeqSBAIJ(Mat A)
119: {
120: Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data;
124: #if defined(PETSC_USE_LOG)
125: PetscLogObjectState((PetscObject)A,"Rows=%D, NZ=%D",A->rmap->N,a->nz);
126: #endif
127: MatSeqXAIJFreeAIJ(A,&a->a,&a->j,&a->i);
128: if (a->free_diag){PetscFree(a->diag);}
129: ISDestroy(&a->row);
130: ISDestroy(&a->col);
131: ISDestroy(&a->icol);
132: PetscFree(a->idiag);
133: PetscFree(a->inode.size);
134: PetscFree(a->diag);
135: if (a->free_imax_ilen) {PetscFree2(a->imax,a->ilen);}
136: PetscFree(a->solve_work);
137: PetscFree(a->sor_work);
138: PetscFree(a->solves_work);
139: PetscFree(a->mult_work);
140: PetscFree(a->saved_values);
141: PetscFree(a->xtoy);
142: if (a->free_jshort) {PetscFree(a->jshort);}
143: PetscFree(a->inew);
144: MatDestroy(&a->parent);
145: PetscFree(A->data);
147: PetscObjectChangeTypeName((PetscObject)A,0);
148: PetscObjectComposeFunction((PetscObject)A,"MatStoreValues_C","",PETSC_NULL);
149: PetscObjectComposeFunction((PetscObject)A,"MatRetrieveValues_C","",PETSC_NULL);
150: PetscObjectComposeFunction((PetscObject)A,"MatSeqSBAIJSetColumnIndices_C","",PETSC_NULL);
151: PetscObjectComposeFunction((PetscObject)A,"MatConvert_seqsbaij_seqaij_C","",PETSC_NULL);
152: PetscObjectComposeFunction((PetscObject)A,"MatConvert_seqsbaij_seqbaij_C","",PETSC_NULL);
153: PetscObjectComposeFunction((PetscObject)A,"MatSeqSBAIJSetPreallocation_C","",PETSC_NULL);
154: PetscObjectComposeFunction((PetscObject)A,"MatConvert_seqsbaij_seqsbstrm_C","",PETSC_NULL);
155: return(0);
156: }
160: PetscErrorCode MatSetOption_SeqSBAIJ(Mat A,MatOption op,PetscBool flg)
161: {
162: Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data;
166: switch (op) {
167: case MAT_ROW_ORIENTED:
168: a->roworiented = flg;
169: break;
170: case MAT_KEEP_NONZERO_PATTERN:
171: a->keepnonzeropattern = flg;
172: break;
173: case MAT_NEW_NONZERO_LOCATIONS:
174: a->nonew = (flg ? 0 : 1);
175: break;
176: case MAT_NEW_NONZERO_LOCATION_ERR:
177: a->nonew = (flg ? -1 : 0);
178: break;
179: case MAT_NEW_NONZERO_ALLOCATION_ERR:
180: a->nonew = (flg ? -2 : 0);
181: break;
182: case MAT_UNUSED_NONZERO_LOCATION_ERR:
183: a->nounused = (flg ? -1 : 0);
184: break;
185: case MAT_NEW_DIAGONALS:
186: case MAT_IGNORE_OFF_PROC_ENTRIES:
187: case MAT_USE_HASH_TABLE:
188: PetscInfo1(A,"Option %s ignored\n",MatOptions[op]);
189: break;
190: case MAT_HERMITIAN:
191: if (!A->assembled) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Must call MatAssemblyEnd() first");
192: if (A->cmap->n < 65536 && A->cmap->bs == 1) {
193: A->ops->mult = MatMult_SeqSBAIJ_1_Hermitian_ushort;
194: } else if (A->cmap->bs == 1) {
195: A->ops->mult = MatMult_SeqSBAIJ_1_Hermitian;
196: } else SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"No support for Hermitian with block size greater than 1");
197: break;
198: case MAT_SPD:
199: A->spd_set = PETSC_TRUE;
200: A->spd = flg;
201: if (flg) {
202: A->symmetric = PETSC_TRUE;
203: A->structurally_symmetric = PETSC_TRUE;
204: A->symmetric_set = PETSC_TRUE;
205: A->structurally_symmetric_set = PETSC_TRUE;
206: }
207: break;
208: case MAT_SYMMETRIC:
209: case MAT_STRUCTURALLY_SYMMETRIC:
210: case MAT_SYMMETRY_ETERNAL:
211: if (!flg) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Matrix must be symmetric");
212: PetscInfo1(A,"Option %s not relevent\n",MatOptions[op]);
213: break;
214: case MAT_IGNORE_LOWER_TRIANGULAR:
215: a->ignore_ltriangular = flg;
216: break;
217: case MAT_ERROR_LOWER_TRIANGULAR:
218: a->ignore_ltriangular = flg;
219: break;
220: case MAT_GETROW_UPPERTRIANGULAR:
221: a->getrow_utriangular = flg;
222: break;
223: default:
224: SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP,"unknown option %d",op);
225: }
226: return(0);
227: }
231: PetscErrorCode MatGetRow_SeqSBAIJ(Mat A,PetscInt row,PetscInt *ncols,PetscInt **cols,PetscScalar **v)
232: {
233: Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data;
235: PetscInt itmp,i,j,k,M,*ai,*aj,bs,bn,bp,*cols_i,bs2;
236: MatScalar *aa,*aa_i;
237: PetscScalar *v_i;
240: 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()");
241: /* Get the upper triangular part of the row */
242: bs = A->rmap->bs;
243: ai = a->i;
244: aj = a->j;
245: aa = a->a;
246: bs2 = a->bs2;
247:
248: if (row < 0 || row >= A->rmap->N) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE, "Row %D out of range", row);
249:
250: bn = row/bs; /* Block number */
251: bp = row % bs; /* Block position */
252: M = ai[bn+1] - ai[bn];
253: *ncols = bs*M;
254:
255: if (v) {
256: *v = 0;
257: if (*ncols) {
258: PetscMalloc((*ncols+row)*sizeof(PetscScalar),v);
259: for (i=0; i<M; i++) { /* for each block in the block row */
260: v_i = *v + i*bs;
261: aa_i = aa + bs2*(ai[bn] + i);
262: for (j=bp,k=0; j<bs2; j+=bs,k++) {v_i[k] = aa_i[j];}
263: }
264: }
265: }
266:
267: if (cols) {
268: *cols = 0;
269: if (*ncols) {
270: PetscMalloc((*ncols+row)*sizeof(PetscInt),cols);
271: for (i=0; i<M; i++) { /* for each block in the block row */
272: cols_i = *cols + i*bs;
273: itmp = bs*aj[ai[bn] + i];
274: for (j=0; j<bs; j++) {cols_i[j] = itmp++;}
275: }
276: }
277: }
278:
279: /*search column A(0:row-1,row) (=A(row,0:row-1)). Could be expensive! */
280: /* this segment is currently removed, so only entries in the upper triangle are obtained */
281: #ifdef column_search
282: v_i = *v + M*bs;
283: cols_i = *cols + M*bs;
284: for (i=0; i<bn; i++){ /* for each block row */
285: M = ai[i+1] - ai[i];
286: for (j=0; j<M; j++){
287: itmp = aj[ai[i] + j]; /* block column value */
288: if (itmp == bn){
289: aa_i = aa + bs2*(ai[i] + j) + bs*bp;
290: for (k=0; k<bs; k++) {
291: *cols_i++ = i*bs+k;
292: *v_i++ = aa_i[k];
293: }
294: *ncols += bs;
295: break;
296: }
297: }
298: }
299: #endif
300: return(0);
301: }
305: PetscErrorCode MatRestoreRow_SeqSBAIJ(Mat A,PetscInt row,PetscInt *nz,PetscInt **idx,PetscScalar **v)
306: {
308:
310: if (idx) {PetscFree(*idx);}
311: if (v) {PetscFree(*v);}
312: return(0);
313: }
317: PetscErrorCode MatGetRowUpperTriangular_SeqSBAIJ(Mat A)
318: {
319: Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data;
322: a->getrow_utriangular = PETSC_TRUE;
323: return(0);
324: }
327: PetscErrorCode MatRestoreRowUpperTriangular_SeqSBAIJ(Mat A)
328: {
329: Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data;
332: a->getrow_utriangular = PETSC_FALSE;
333: return(0);
334: }
338: PetscErrorCode MatTranspose_SeqSBAIJ(Mat A,MatReuse reuse,Mat *B)
339: {
342: if (reuse == MAT_INITIAL_MATRIX || *B != A) {
343: MatDuplicate(A,MAT_COPY_VALUES,B);
344: }
345: return(0);
346: }
350: static PetscErrorCode MatView_SeqSBAIJ_ASCII(Mat A,PetscViewer viewer)
351: {
352: Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data;
353: PetscErrorCode ierr;
354: PetscInt i,j,bs = A->rmap->bs,k,l,bs2=a->bs2;
355: PetscViewerFormat format;
356: PetscInt *diag;
357:
359: PetscViewerGetFormat(viewer,&format);
360: if (format == PETSC_VIEWER_ASCII_INFO || format == PETSC_VIEWER_ASCII_INFO_DETAIL) {
361: PetscViewerASCIIPrintf(viewer," block size is %D\n",bs);
362: } else if (format == PETSC_VIEWER_ASCII_MATLAB) {
363: Mat aij;
364: if (A->factortype && bs>1){
365: PetscPrintf(PETSC_COMM_SELF,"Warning: matrix is factored with bs>1. MatView() with PETSC_VIEWER_ASCII_MATLAB is not supported and ignored!\n");
366: return(0);
367: }
368: MatConvert(A,MATSEQAIJ,MAT_INITIAL_MATRIX,&aij);
369: MatView(aij,viewer);
370: MatDestroy(&aij);
371: } else if (format == PETSC_VIEWER_ASCII_COMMON) {
372: PetscViewerASCIIUseTabs(viewer,PETSC_FALSE);
373: for (i=0; i<a->mbs; i++) {
374: for (j=0; j<bs; j++) {
375: PetscViewerASCIIPrintf(viewer,"row %D:",i*bs+j);
376: for (k=a->i[i]; k<a->i[i+1]; k++) {
377: for (l=0; l<bs; l++) {
378: #if defined(PETSC_USE_COMPLEX)
379: if (PetscImaginaryPart(a->a[bs2*k + l*bs + j]) > 0.0 && PetscRealPart(a->a[bs2*k + l*bs + j]) != 0.0) {
380: PetscViewerASCIIPrintf(viewer," (%D, %G + %G i) ",bs*a->j[k]+l,
381: PetscRealPart(a->a[bs2*k + l*bs + j]),PetscImaginaryPart(a->a[bs2*k + l*bs + j]));
382: } else if (PetscImaginaryPart(a->a[bs2*k + l*bs + j]) < 0.0 && PetscRealPart(a->a[bs2*k + l*bs + j]) != 0.0) {
383: PetscViewerASCIIPrintf(viewer," (%D, %G - %G i) ",bs*a->j[k]+l,
384: PetscRealPart(a->a[bs2*k + l*bs + j]),-PetscImaginaryPart(a->a[bs2*k + l*bs + j]));
385: } else if (PetscRealPart(a->a[bs2*k + l*bs + j]) != 0.0) {
386: PetscViewerASCIIPrintf(viewer," (%D, %G) ",bs*a->j[k]+l,PetscRealPart(a->a[bs2*k + l*bs + j]));
387: }
388: #else
389: if (a->a[bs2*k + l*bs + j] != 0.0) {
390: PetscViewerASCIIPrintf(viewer," (%D, %G) ",bs*a->j[k]+l,a->a[bs2*k + l*bs + j]);
391: }
392: #endif
393: }
394: }
395: PetscViewerASCIIPrintf(viewer,"\n");
396: }
397: }
398: PetscViewerASCIIUseTabs(viewer,PETSC_TRUE);
399: } else if (format == PETSC_VIEWER_ASCII_FACTOR_INFO) {
400: return(0);
401: } else {
402: PetscViewerASCIIUseTabs(viewer,PETSC_FALSE);
403: PetscObjectPrintClassNamePrefixType((PetscObject)A,viewer,"Matrix Object");
404: if (A->factortype){ /* for factored matrix */
405: if (bs>1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"matrix is factored with bs>1. Not implemented yet");
407: diag=a->diag;
408: for (i=0; i<a->mbs; i++) { /* for row block i */
409: PetscViewerASCIIPrintf(viewer,"row %D:",i);
410: /* diagonal entry */
411: #if defined(PETSC_USE_COMPLEX)
412: if (PetscImaginaryPart(a->a[diag[i]]) > 0.0) {
413: PetscViewerASCIIPrintf(viewer," (%D, %G + %G i) ",a->j[diag[i]],PetscRealPart(1.0/a->a[diag[i]]),PetscImaginaryPart(1.0/a->a[diag[i]]));
414: } else if (PetscImaginaryPart(a->a[diag[i]]) < 0.0) {
415: PetscViewerASCIIPrintf(viewer," (%D, %G - %G i) ",a->j[diag[i]],PetscRealPart(1.0/a->a[diag[i]]),-PetscImaginaryPart(1.0/a->a[diag[i]]));
416: } else {
417: PetscViewerASCIIPrintf(viewer," (%D, %G) ",a->j[diag[i]],PetscRealPart(1.0/a->a[diag[i]]));
418: }
419: #else
420: PetscViewerASCIIPrintf(viewer," (%D, %G) ",a->j[diag[i]],1.0/a->a[diag[i]]);
421: #endif
422: /* off-diagonal entries */
423: for (k=a->i[i]; k<a->i[i+1]-1; k++) {
424: #if defined(PETSC_USE_COMPLEX)
425: if (PetscImaginaryPart(a->a[k]) > 0.0) {
426: PetscViewerASCIIPrintf(viewer," (%D, %G + %G i) ",bs*a->j[k],PetscRealPart(a->a[k]),PetscImaginaryPart(a->a[k]));
427: } else if (PetscImaginaryPart(a->a[k]) < 0.0) {
428: PetscViewerASCIIPrintf(viewer," (%D, %G - %G i) ",bs*a->j[k],PetscRealPart(a->a[k]),-PetscImaginaryPart(a->a[k]));
429: } else {
430: PetscViewerASCIIPrintf(viewer," (%D, %G) ",bs*a->j[k],PetscRealPart(a->a[k]));
431: }
432: #else
433: PetscViewerASCIIPrintf(viewer," (%D, %G) ",a->j[k],a->a[k]);
434: #endif
435: }
436: PetscViewerASCIIPrintf(viewer,"\n");
437: }
438:
439: } else { /* for non-factored matrix */
440: for (i=0; i<a->mbs; i++) { /* for row block i */
441: for (j=0; j<bs; j++) { /* for row bs*i + j */
442: PetscViewerASCIIPrintf(viewer,"row %D:",i*bs+j);
443: for (k=a->i[i]; k<a->i[i+1]; k++) { /* for column block */
444: for (l=0; l<bs; l++) { /* for column */
445: #if defined(PETSC_USE_COMPLEX)
446: if (PetscImaginaryPart(a->a[bs2*k + l*bs + j]) > 0.0) {
447: PetscViewerASCIIPrintf(viewer," (%D, %G + %G i) ",bs*a->j[k]+l,
448: PetscRealPart(a->a[bs2*k + l*bs + j]),PetscImaginaryPart(a->a[bs2*k + l*bs + j]));
449: } else if (PetscImaginaryPart(a->a[bs2*k + l*bs + j]) < 0.0) {
450: PetscViewerASCIIPrintf(viewer," (%D, %G - %G i) ",bs*a->j[k]+l,
451: PetscRealPart(a->a[bs2*k + l*bs + j]),-PetscImaginaryPart(a->a[bs2*k + l*bs + j]));
452: } else {
453: PetscViewerASCIIPrintf(viewer," (%D, %G) ",bs*a->j[k]+l,PetscRealPart(a->a[bs2*k + l*bs + j]));
454: }
455: #else
456: PetscViewerASCIIPrintf(viewer," (%D, %G) ",bs*a->j[k]+l,a->a[bs2*k + l*bs + j]);
457: #endif
458: }
459: }
460: PetscViewerASCIIPrintf(viewer,"\n");
461: }
462: }
463: }
464: PetscViewerASCIIUseTabs(viewer,PETSC_TRUE);
465: }
466: PetscViewerFlush(viewer);
467: return(0);
468: }
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;
483:
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);
493:
494: PetscObjectQuery((PetscObject)A,"Zoomviewer",(PetscObject*)&viewer);
495:
496: PetscDrawGetCoordinates(draw,&xl,&yl,&xr,&yr);
497: PetscDrawString(draw, .3*(xl+xr), .3*(yl+yr), PETSC_DRAW_BLACK, "symmetric");
498:
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: }
528:
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;
554:
556: PetscViewerDrawGetDraw(viewer,0,&draw);
557: PetscDrawIsNull(draw,&isnull); if (isnull) return(0);
558:
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",PETSC_NULL);
565: return(0);
566: }
570: PetscErrorCode MatView_SeqSBAIJ(Mat A,PetscViewer viewer)
571: {
573: PetscBool iascii,isdraw;
574: FILE *file = 0;
577: PetscTypeCompare((PetscObject)viewer,PETSCVIEWERASCII,&iascii);
578: PetscTypeCompare((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;
606:
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;
655:
657: if (roworiented) {
658: stepval = (n-1)*bs;
659: } else {
660: stepval = (m-1)*bs;
661: }
662: for (k=0; k<m; k++) { /* loop over added rows */
663: row = im[k];
664: if (row < 0) continue;
665: #if defined(PETSC_USE_DEBUG)
666: if (row >= a->mbs) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Row too large: row %D max %D",row,a->mbs-1);
667: #endif
668: rp = aj + ai[row];
669: ap = aa + bs2*ai[row];
670: rmax = imax[row];
671: nrow = ailen[row];
672: low = 0;
673: high = nrow;
674: for (l=0; l<n; l++) { /* loop over added columns */
675: if (in[l] < 0) continue;
676: col = in[l];
677: #if defined(PETSC_USE_DEBUG)
678: if (col >= a->nbs) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Column too large: col %D max %D",col,a->nbs-1);
679: #endif
680: if (col < row) {
681: if (a->ignore_ltriangular) {
682: continue; /* ignore lower triangular block */
683: } else {
684: 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)");
685: }
686: }
687: if (roworiented) {
688: value = v + k*(stepval+bs)*bs + l*bs;
689: } else {
690: value = v + l*(stepval+bs)*bs + k*bs;
691: }
692: if (col <= lastcol) low = 0; else high = nrow;
693: lastcol = col;
694: while (high-low > 7) {
695: t = (low+high)/2;
696: if (rp[t] > col) high = t;
697: else low = t;
698: }
699: for (i=low; i<high; i++) {
700: if (rp[i] > col) break;
701: if (rp[i] == col) {
702: bap = ap + bs2*i;
703: if (roworiented) {
704: if (is == ADD_VALUES) {
705: for (ii=0; ii<bs; ii++,value+=stepval) {
706: for (jj=ii; jj<bs2; jj+=bs) {
707: bap[jj] += *value++;
708: }
709: }
710: } else {
711: for (ii=0; ii<bs; ii++,value+=stepval) {
712: for (jj=ii; jj<bs2; jj+=bs) {
713: bap[jj] = *value++;
714: }
715: }
716: }
717: } else {
718: if (is == ADD_VALUES) {
719: for (ii=0; ii<bs; ii++,value+=stepval) {
720: for (jj=0; jj<bs; jj++) {
721: *bap++ += *value++;
722: }
723: }
724: } else {
725: for (ii=0; ii<bs; ii++,value+=stepval) {
726: for (jj=0; jj<bs; jj++) {
727: *bap++ = *value++;
728: }
729: }
730: }
731: }
732: goto noinsert2;
733: }
734: }
735: if (nonew == 1) goto noinsert2;
736: if (nonew == -1) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Inserting a new nonzero (%D, %D) in the matrix", row, col);
737: MatSeqXAIJReallocateAIJ(A,a->mbs,bs2,nrow,row,col,rmax,aa,ai,aj,rp,ap,imax,nonew,MatScalar);
738: N = nrow++ - 1; high++;
739: /* shift up all the later entries in this row */
740: for (ii=N; ii>=i; ii--) {
741: rp[ii+1] = rp[ii];
742: PetscMemcpy(ap+bs2*(ii+1),ap+bs2*(ii),bs2*sizeof(MatScalar));
743: }
744: if (N >= i) {
745: PetscMemzero(ap+bs2*i,bs2*sizeof(MatScalar));
746: }
747: rp[i] = col;
748: bap = ap + bs2*i;
749: if (roworiented) {
750: for (ii=0; ii<bs; ii++,value+=stepval) {
751: for (jj=ii; jj<bs2; jj+=bs) {
752: bap[jj] = *value++;
753: }
754: }
755: } else {
756: for (ii=0; ii<bs; ii++,value+=stepval) {
757: for (jj=0; jj<bs; jj++) {
758: *bap++ = *value++;
759: }
760: }
761: }
762: noinsert2:;
763: low = i;
764: }
765: ailen[row] = nrow;
766: }
767: return(0);
768: }
770: /*
771: This is not yet used
772: */
775: PetscErrorCode MatAssemblyEnd_SeqSBAIJ_SeqAIJ_Inode(Mat A)
776: {
777: Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data;
778: PetscErrorCode ierr;
779: const PetscInt *ai = a->i, *aj = a->j,*cols;
780: PetscInt i = 0,j,blk_size,m = A->rmap->n,node_count = 0,nzx,nzy,*ns,row,nz,cnt,cnt2,*counts;
781: PetscBool flag;
784: PetscMalloc(m*sizeof(PetscInt),&ns);
785: while (i < m){
786: nzx = ai[i+1] - ai[i]; /* Number of nonzeros */
787: /* Limits the number of elements in a node to 'a->inode.limit' */
788: for (j=i+1,blk_size=1; j<m && blk_size <a->inode.limit; ++j,++blk_size) {
789: nzy = ai[j+1] - ai[j];
790: if (nzy != (nzx - j + i)) break;
791: PetscMemcmp(aj + ai[i] + j - i,aj + ai[j],nzy*sizeof(PetscInt),&flag);
792: if (!flag) break;
793: }
794: ns[node_count++] = blk_size;
795: i = j;
796: }
797: if (!a->inode.size && m && node_count > .9*m) {
798: PetscFree(ns);
799: PetscInfo2(A,"Found %D nodes out of %D rows. Not using Inode routines\n",node_count,m);
800: } else {
801: a->inode.node_count = node_count;
802: PetscMalloc(node_count*sizeof(PetscInt),&a->inode.size);
803: PetscLogObjectMemory(A,node_count*sizeof(PetscInt));
804: PetscMemcpy(a->inode.size,ns,node_count*sizeof(PetscInt));
805: PetscFree(ns);
806: PetscInfo3(A,"Found %D nodes of %D. Limit used: %D. Using Inode routines\n",node_count,m,a->inode.limit);
807:
808: /* count collections of adjacent columns in each inode */
809: row = 0;
810: cnt = 0;
811: for (i=0; i<node_count; i++) {
812: cols = aj + ai[row] + a->inode.size[i];
813: nz = ai[row+1] - ai[row] - a->inode.size[i];
814: for (j=1; j<nz; j++) {
815: if (cols[j] != cols[j-1]+1) {
816: cnt++;
817: }
818: }
819: cnt++;
820: row += a->inode.size[i];
821: }
822: PetscMalloc(2*cnt*sizeof(PetscInt),&counts);
823: cnt = 0;
824: row = 0;
825: for (i=0; i<node_count; i++) {
826: cols = aj + ai[row] + a->inode.size[i];
827: CHKMEMQ;
828: counts[2*cnt] = cols[0];
829: CHKMEMQ;
830: nz = ai[row+1] - ai[row] - a->inode.size[i];
831: cnt2 = 1;
832: for (j=1; j<nz; j++) {
833: if (cols[j] != cols[j-1]+1) {
834: CHKMEMQ;
835: counts[2*(cnt++)+1] = cnt2;
836: counts[2*cnt] = cols[j];
837: CHKMEMQ;
838: cnt2 = 1;
839: } else cnt2++;
840: }
841: CHKMEMQ;
842: counts[2*(cnt++)+1] = cnt2;
843: CHKMEMQ;
844: row += a->inode.size[i];
845: }
846: PetscIntView(2*cnt,counts,0);
847: }
848: return(0);
849: }
853: PetscErrorCode MatAssemblyEnd_SeqSBAIJ(Mat A,MatAssemblyType mode)
854: {
855: Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data;
857: PetscInt fshift = 0,i,j,*ai = a->i,*aj = a->j,*imax = a->imax;
858: PetscInt m = A->rmap->N,*ip,N,*ailen = a->ilen;
859: PetscInt mbs = a->mbs,bs2 = a->bs2,rmax = 0;
860: MatScalar *aa = a->a,*ap;
861:
863: if (mode == MAT_FLUSH_ASSEMBLY) return(0);
864:
865: if (m) rmax = ailen[0];
866: for (i=1; i<mbs; i++) {
867: /* move each row back by the amount of empty slots (fshift) before it*/
868: fshift += imax[i-1] - ailen[i-1];
869: rmax = PetscMax(rmax,ailen[i]);
870: if (fshift) {
871: ip = aj + ai[i]; ap = aa + bs2*ai[i];
872: N = ailen[i];
873: for (j=0; j<N; j++) {
874: ip[j-fshift] = ip[j];
875: PetscMemcpy(ap+(j-fshift)*bs2,ap+j*bs2,bs2*sizeof(MatScalar));
876: }
877: }
878: ai[i] = ai[i-1] + ailen[i-1];
879: }
880: if (mbs) {
881: fshift += imax[mbs-1] - ailen[mbs-1];
882: ai[mbs] = ai[mbs-1] + ailen[mbs-1];
883: }
884: /* reset ilen and imax for each row */
885: for (i=0; i<mbs; i++) {
886: ailen[i] = imax[i] = ai[i+1] - ai[i];
887: }
888: a->nz = ai[mbs];
889:
890: /* diagonals may have moved, reset it */
891: if (a->diag) {
892: PetscMemcpy(a->diag,ai,mbs*sizeof(PetscInt));
893: }
894: if (fshift && a->nounused == -1) {
895: 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);
896: }
897: 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);
898: PetscInfo1(A,"Number of mallocs during MatSetValues is %D\n",a->reallocs);
899: PetscInfo1(A,"Most nonzeros blocks in any row is %D\n",rmax);
900: A->info.mallocs += a->reallocs;
901: a->reallocs = 0;
902: A->info.nz_unneeded = (PetscReal)fshift*bs2;
903: a->idiagvalid = PETSC_FALSE;
905: if (A->cmap->n < 65536 && A->cmap->bs == 1) {
906: if (!a->jshort) {
907: PetscMalloc(a->i[A->rmap->n]*sizeof(unsigned short),&a->jshort);
908: PetscLogObjectMemory(A,a->i[A->rmap->n]*sizeof(unsigned short));
909: for (i=0; i<a->i[A->rmap->n]; i++) a->jshort[i] = a->j[i];
910: A->ops->mult = MatMult_SeqSBAIJ_1_ushort;
911: A->ops->sor = MatSOR_SeqSBAIJ_ushort;
912: a->free_jshort = PETSC_TRUE;
913: }
914: }
915: return(0);
916: }
918: /*
919: This function returns an array of flags which indicate the locations of contiguous
920: blocks that should be zeroed. for eg: if bs = 3 and is = [0,1,2,3,5,6,7,8,9]
921: then the resulting sizes = [3,1,1,3,1] correspondig to sets [(0,1,2),(3),(5),(6,7,8),(9)]
922: Assume: sizes should be long enough to hold all the values.
923: */
926: PetscErrorCode MatZeroRows_SeqSBAIJ_Check_Blocks(PetscInt idx[],PetscInt n,PetscInt bs,PetscInt sizes[], PetscInt *bs_max)
927: {
928: PetscInt i,j,k,row;
929: PetscBool flg;
930:
932: for (i=0,j=0; i<n; j++) {
933: row = idx[i];
934: if (row%bs!=0) { /* Not the begining of a block */
935: sizes[j] = 1;
936: i++;
937: } else if (i+bs > n) { /* Beginning of a block, but complete block doesn't exist (at idx end) */
938: sizes[j] = 1; /* Also makes sure atleast 'bs' values exist for next else */
939: i++;
940: } else { /* Begining of the block, so check if the complete block exists */
941: flg = PETSC_TRUE;
942: for (k=1; k<bs; k++) {
943: if (row+k != idx[i+k]) { /* break in the block */
944: flg = PETSC_FALSE;
945: break;
946: }
947: }
948: if (flg) { /* No break in the bs */
949: sizes[j] = bs;
950: i+= bs;
951: } else {
952: sizes[j] = 1;
953: i++;
954: }
955: }
956: }
957: *bs_max = j;
958: return(0);
959: }
962: /* Only add/insert a(i,j) with i<=j (blocks).
963: Any a(i,j) with i>j input by user is ingored.
964: */
968: PetscErrorCode MatSetValues_SeqSBAIJ(Mat A,PetscInt m,const PetscInt im[],PetscInt n,const PetscInt in[],const PetscScalar v[],InsertMode is)
969: {
970: Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data;
972: PetscInt *rp,k,low,high,t,ii,row,nrow,i,col,l,rmax,N,lastcol = -1;
973: PetscInt *imax=a->imax,*ai=a->i,*ailen=a->ilen,roworiented=a->roworiented;
974: PetscInt *aj=a->j,nonew=a->nonew,bs=A->rmap->bs,brow,bcol;
975: PetscInt ridx,cidx,bs2=a->bs2;
976: MatScalar *ap,value,*aa=a->a,*bap;
977:
980: for (k=0; k<m; k++) { /* loop over added rows */
981: row = im[k]; /* row number */
982: brow = row/bs; /* block row number */
983: if (row < 0) continue;
984: #if defined(PETSC_USE_DEBUG)
985: 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);
986: #endif
987: rp = aj + ai[brow]; /*ptr to beginning of column value of the row block*/
988: ap = aa + bs2*ai[brow]; /*ptr to beginning of element value of the row block*/
989: rmax = imax[brow]; /* maximum space allocated for this row */
990: nrow = ailen[brow]; /* actual length of this row */
991: low = 0;
992:
993: for (l=0; l<n; l++) { /* loop over added columns */
994: if (in[l] < 0) continue;
995: #if defined(PETSC_USE_DEBUG)
996: 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);
997: #endif
998: col = in[l];
999: bcol = col/bs; /* block col number */
1000:
1001: if (brow > bcol) {
1002: if (a->ignore_ltriangular){
1003: continue; /* ignore lower triangular values */
1004: } else {
1005: 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)");
1006: }
1007: }
1008:
1009: ridx = row % bs; cidx = col % bs; /*row and col index inside the block */
1010: if ((brow==bcol && ridx<=cidx) || (brow<bcol)){
1011: /* element value a(k,l) */
1012: if (roworiented) {
1013: value = v[l + k*n];
1014: } else {
1015: value = v[k + l*m];
1016: }
1017:
1018: /* move pointer bap to a(k,l) quickly and add/insert value */
1019: if (col <= lastcol) low = 0; high = nrow;
1020: lastcol = col;
1021: while (high-low > 7) {
1022: t = (low+high)/2;
1023: if (rp[t] > bcol) high = t;
1024: else low = t;
1025: }
1026: for (i=low; i<high; i++) {
1027: if (rp[i] > bcol) break;
1028: if (rp[i] == bcol) {
1029: bap = ap + bs2*i + bs*cidx + ridx;
1030: if (is == ADD_VALUES) *bap += value;
1031: else *bap = value;
1032: /* for diag block, add/insert its symmetric element a(cidx,ridx) */
1033: if (brow == bcol && ridx < cidx){
1034: bap = ap + bs2*i + bs*ridx + cidx;
1035: if (is == ADD_VALUES) *bap += value;
1036: else *bap = value;
1037: }
1038: goto noinsert1;
1039: }
1040: }
1041:
1042: if (nonew == 1) goto noinsert1;
1043: if (nonew == -1) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Inserting a new nonzero (%D, %D) in the matrix", row, col);
1044: MatSeqXAIJReallocateAIJ(A,a->mbs,bs2,nrow,brow,bcol,rmax,aa,ai,aj,rp,ap,imax,nonew,MatScalar);
1045:
1046: N = nrow++ - 1; high++;
1047: /* shift up all the later entries in this row */
1048: for (ii=N; ii>=i; ii--) {
1049: rp[ii+1] = rp[ii];
1050: PetscMemcpy(ap+bs2*(ii+1),ap+bs2*(ii),bs2*sizeof(MatScalar));
1051: }
1052: if (N>=i) {
1053: PetscMemzero(ap+bs2*i,bs2*sizeof(MatScalar));
1054: }
1055: rp[i] = bcol;
1056: ap[bs2*i + bs*cidx + ridx] = value;
1057: noinsert1:;
1058: low = i;
1059: }
1060: } /* end of loop over added columns */
1061: ailen[brow] = nrow;
1062: } /* end of loop over added rows */
1063: return(0);
1064: }
1068: PetscErrorCode MatICCFactor_SeqSBAIJ(Mat inA,IS row,const MatFactorInfo *info)
1069: {
1070: Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)inA->data;
1071: Mat outA;
1073: PetscBool row_identity;
1074:
1076: if (info->levels != 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Only levels=0 is supported for in-place icc");
1077: ISIdentity(row,&row_identity);
1078: if (!row_identity) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Matrix reordering is not supported");
1079: 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()! */
1081: outA = inA;
1082: inA->factortype = MAT_FACTOR_ICC;
1083:
1084: MatMarkDiagonal_SeqSBAIJ(inA);
1085: MatSeqSBAIJSetNumericFactorization_inplace(inA,row_identity);
1087: PetscObjectReference((PetscObject)row);
1088: ISDestroy(&a->row);
1089: a->row = row;
1090: PetscObjectReference((PetscObject)row);
1091: ISDestroy(&a->col);
1092: a->col = row;
1093:
1094: /* Create the invert permutation so that it can be used in MatCholeskyFactorNumeric() */
1095: if (a->icol) {ISInvertPermutation(row,PETSC_DECIDE, &a->icol);}
1096: PetscLogObjectParent(inA,a->icol);
1097:
1098: if (!a->solve_work) {
1099: PetscMalloc((inA->rmap->N+inA->rmap->bs)*sizeof(PetscScalar),&a->solve_work);
1100: PetscLogObjectMemory(inA,(inA->rmap->N+inA->rmap->bs)*sizeof(PetscScalar));
1101: }
1102:
1103: MatCholeskyFactorNumeric(outA,inA,info);
1104: return(0);
1105: }
1107: EXTERN_C_BEGIN
1110: PetscErrorCode MatSeqSBAIJSetColumnIndices_SeqSBAIJ(Mat mat,PetscInt *indices)
1111: {
1112: Mat_SeqSBAIJ *baij = (Mat_SeqSBAIJ *)mat->data;
1113: PetscInt i,nz,n;
1117: nz = baij->maxnz;
1118: n = mat->cmap->n;
1119: for (i=0; i<nz; i++) {
1120: baij->j[i] = indices[i];
1121: }
1122: baij->nz = nz;
1123: for (i=0; i<n; i++) {
1124: baij->ilen[i] = baij->imax[i];
1125: }
1126: MatSetOption(mat,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);
1127: return(0);
1128: }
1129: EXTERN_C_END
1133: /*@
1134: MatSeqSBAIJSetColumnIndices - Set the column indices for all the rows
1135: in the matrix.
1136:
1137: Input Parameters:
1138: + mat - the SeqSBAIJ matrix
1139: - indices - the column indices
1140:
1141: Level: advanced
1142:
1143: Notes:
1144: This can be called if you have precomputed the nonzero structure of the
1145: matrix and want to provide it to the matrix object to improve the performance
1146: of the MatSetValues() operation.
1147:
1148: You MUST have set the correct numbers of nonzeros per row in the call to
1149: MatCreateSeqSBAIJ(), and the columns indices MUST be sorted.
1150:
1151: MUST be called before any calls to MatSetValues()
1152:
1153: .seealso: MatCreateSeqSBAIJ
1154: @*/
1155: PetscErrorCode MatSeqSBAIJSetColumnIndices(Mat mat,PetscInt *indices)
1156: {
1158:
1162: PetscUseMethod(mat,"MatSeqSBAIJSetColumnIndices_C",(Mat,PetscInt *),(mat,indices));
1163: return(0);
1164: }
1168: PetscErrorCode MatCopy_SeqSBAIJ(Mat A,Mat B,MatStructure str)
1169: {
1173: /* If the two matrices have the same copy implementation, use fast copy. */
1174: if (str == SAME_NONZERO_PATTERN && (A->ops->copy == B->ops->copy)) {
1175: Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data;
1176: Mat_SeqSBAIJ *b = (Mat_SeqSBAIJ*)B->data;
1178: 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");
1179: PetscMemcpy(b->a,a->a,(a->i[A->rmap->N])*sizeof(PetscScalar));
1180: } else {
1181: MatGetRowUpperTriangular(A);
1182: MatCopy_Basic(A,B,str);
1183: MatRestoreRowUpperTriangular(A);
1184: }
1185: return(0);
1186: }
1190: PetscErrorCode MatSetUp_SeqSBAIJ(Mat A)
1191: {
1195: MatSeqSBAIJSetPreallocation_SeqSBAIJ(A,-PetscMax(A->rmap->bs,1),PETSC_DEFAULT,0);
1196: return(0);
1197: }
1201: PetscErrorCode MatGetArray_SeqSBAIJ(Mat A,PetscScalar *array[])
1202: {
1203: Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data;
1205: *array = a->a;
1206: return(0);
1207: }
1211: PetscErrorCode MatRestoreArray_SeqSBAIJ(Mat A,PetscScalar *array[])
1212: {
1214: return(0);
1215: }
1219: PetscErrorCode MatAXPY_SeqSBAIJ(Mat Y,PetscScalar a,Mat X,MatStructure str)
1220: {
1221: Mat_SeqSBAIJ *x=(Mat_SeqSBAIJ *)X->data, *y=(Mat_SeqSBAIJ *)Y->data;
1223: PetscInt i,bs=Y->rmap->bs,bs2=bs*bs,j;
1224: PetscBLASInt one = 1;
1225:
1227: if (str == SAME_NONZERO_PATTERN) {
1228: PetscScalar alpha = a;
1229: PetscBLASInt bnz = PetscBLASIntCast(x->nz*bs2);
1230: BLASaxpy_(&bnz,&alpha,x->a,&one,y->a,&one);
1231: } else if (str == SUBSET_NONZERO_PATTERN) { /* nonzeros of X is a subset of Y's */
1232: if (y->xtoy && y->XtoY != X) {
1233: PetscFree(y->xtoy);
1234: MatDestroy(&y->XtoY);
1235: }
1236: if (!y->xtoy) { /* get xtoy */
1237: MatAXPYGetxtoy_Private(x->mbs,x->i,x->j,PETSC_NULL, y->i,y->j,PETSC_NULL, &y->xtoy);
1238: y->XtoY = X;
1239: }
1240: for (i=0; i<x->nz; i++) {
1241: j = 0;
1242: while (j < bs2){
1243: y->a[bs2*y->xtoy[i]+j] += a*(x->a[bs2*i+j]);
1244: j++;
1245: }
1246: }
1247: PetscInfo3(Y,"ratio of nnz_s(X)/nnz_s(Y): %D/%D = %G\n",bs2*x->nz,bs2*y->nz,(PetscReal)(bs2*x->nz)/(bs2*y->nz));
1248: } else {
1249: MatGetRowUpperTriangular(X);
1250: MatAXPY_Basic(Y,a,X,str);
1251: MatRestoreRowUpperTriangular(X);
1252: }
1253: return(0);
1254: }
1258: PetscErrorCode MatSetBlockSize_SeqSBAIJ(Mat A,PetscInt bs)
1259: {
1260: PetscInt rbs,cbs;
1264: PetscLayoutGetBlockSize(A->rmap,&rbs);
1265: PetscLayoutGetBlockSize(A->cmap,&cbs);
1266: if (rbs != bs) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Attempt to set block size %d with SBAIJ %d",bs,rbs);
1267: if (cbs != bs) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Attempt to set block size %d with SBAIJ %d",bs,cbs);
1268: return(0);
1269: }
1273: PetscErrorCode MatIsSymmetric_SeqSBAIJ(Mat A,PetscReal tol,PetscBool *flg)
1274: {
1276: *flg = PETSC_TRUE;
1277: return(0);
1278: }
1282: PetscErrorCode MatIsStructurallySymmetric_SeqSBAIJ(Mat A,PetscBool *flg)
1283: {
1285: *flg = PETSC_TRUE;
1286: return(0);
1287: }
1291: PetscErrorCode MatIsHermitian_SeqSBAIJ(Mat A,PetscReal tol,PetscBool *flg)
1292: {
1294: *flg = PETSC_FALSE;
1295: return(0);
1296: }
1300: PetscErrorCode MatRealPart_SeqSBAIJ(Mat A)
1301: {
1302: Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data;
1303: PetscInt i,nz = a->bs2*a->i[a->mbs];
1304: MatScalar *aa = a->a;
1307: for (i=0; i<nz; i++) aa[i] = PetscRealPart(aa[i]);
1308: return(0);
1309: }
1313: PetscErrorCode MatImaginaryPart_SeqSBAIJ(Mat A)
1314: {
1315: Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data;
1316: PetscInt i,nz = a->bs2*a->i[a->mbs];
1317: MatScalar *aa = a->a;
1320: for (i=0; i<nz; i++) aa[i] = PetscImaginaryPart(aa[i]);
1321: return(0);
1322: }
1326: PetscErrorCode MatZeroRowsColumns_SeqSBAIJ(Mat A,PetscInt is_n,const PetscInt is_idx[],PetscScalar diag,Vec x, Vec b)
1327: {
1328: Mat_SeqSBAIJ *baij=(Mat_SeqSBAIJ*)A->data;
1329: PetscErrorCode ierr;
1330: PetscInt i,j,k,count;
1331: PetscInt bs=A->rmap->bs,bs2=baij->bs2,row,col;
1332: PetscScalar zero = 0.0;
1333: MatScalar *aa;
1334: const PetscScalar *xx;
1335: PetscScalar *bb;
1336: PetscBool *zeroed,vecs = PETSC_FALSE;
1339: /* fix right hand side if needed */
1340: if (x && b) {
1341: VecGetArrayRead(x,&xx);
1342: VecGetArray(b,&bb);
1343: vecs = PETSC_TRUE;
1344: }
1345: A->same_nonzero = PETSC_TRUE;
1347: /* zero the columns */
1348: PetscMalloc(A->rmap->n*sizeof(PetscBool),&zeroed);
1349: PetscMemzero(zeroed,A->rmap->n*sizeof(PetscBool));
1350: for (i=0; i<is_n; i++) {
1351: 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]);
1352: zeroed[is_idx[i]] = PETSC_TRUE;
1353: }
1354: if (vecs) {
1355: for (i=0; i<A->rmap->N; i++) {
1356: row = i/bs;
1357: for (j=baij->i[row]; j<baij->i[row+1]; j++) {
1358: for (k=0; k<bs; k++) {
1359: col = bs*baij->j[j] + k;
1360: if (col <= i) continue;
1361: aa = ((MatScalar*)(baij->a)) + j*bs2 + (i%bs) + bs*k;
1362: if (!zeroed[i] && zeroed[col]) {
1363: bb[i] -= aa[0]*xx[col];
1364: }
1365: if (zeroed[i] && !zeroed[col]) {
1366: bb[col] -= aa[0]*xx[i];
1367: }
1368: }
1369: }
1370: }
1371: for (i=0; i<is_n; i++) {
1372: bb[is_idx[i]] = diag*xx[is_idx[i]];
1373: }
1374: }
1376: for (i=0; i<A->rmap->N; i++) {
1377: if (!zeroed[i]) {
1378: row = i/bs;
1379: for (j=baij->i[row]; j<baij->i[row+1]; j++) {
1380: for (k=0; k<bs; k++) {
1381: col = bs*baij->j[j] + k;
1382: if (zeroed[col]) {
1383: aa = ((MatScalar*)(baij->a)) + j*bs2 + (i%bs) + bs*k;
1384: aa[0] = 0.0;
1385: }
1386: }
1387: }
1388: }
1389: }
1390: PetscFree(zeroed);
1391: if (vecs) {
1392: VecRestoreArrayRead(x,&xx);
1393: VecRestoreArray(b,&bb);
1394: }
1396: /* zero the rows */
1397: for (i=0; i<is_n; i++) {
1398: row = is_idx[i];
1399: count = (baij->i[row/bs +1] - baij->i[row/bs])*bs;
1400: aa = ((MatScalar*)(baij->a)) + baij->i[row/bs]*bs2 + (row%bs);
1401: for (k=0; k<count; k++) {
1402: aa[0] = zero;
1403: aa += bs;
1404: }
1405: if (diag != 0.0) {
1406: (*A->ops->setvalues)(A,1,&row,1,&row,&diag,INSERT_VALUES);
1407: }
1408: }
1409: MatAssemblyEnd_SeqSBAIJ(A,MAT_FINAL_ASSEMBLY);
1410: return(0);
1411: }
1413: /* -------------------------------------------------------------------*/
1414: static struct _MatOps MatOps_Values = {MatSetValues_SeqSBAIJ,
1415: MatGetRow_SeqSBAIJ,
1416: MatRestoreRow_SeqSBAIJ,
1417: MatMult_SeqSBAIJ_N,
1418: /* 4*/ MatMultAdd_SeqSBAIJ_N,
1419: MatMult_SeqSBAIJ_N, /* transpose versions are same as non-transpose versions */
1420: MatMultAdd_SeqSBAIJ_N,
1421: 0,
1422: 0,
1423: 0,
1424: /*10*/ 0,
1425: 0,
1426: MatCholeskyFactor_SeqSBAIJ,
1427: MatSOR_SeqSBAIJ,
1428: MatTranspose_SeqSBAIJ,
1429: /*15*/ MatGetInfo_SeqSBAIJ,
1430: MatEqual_SeqSBAIJ,
1431: MatGetDiagonal_SeqSBAIJ,
1432: MatDiagonalScale_SeqSBAIJ,
1433: MatNorm_SeqSBAIJ,
1434: /*20*/ 0,
1435: MatAssemblyEnd_SeqSBAIJ,
1436: MatSetOption_SeqSBAIJ,
1437: MatZeroEntries_SeqSBAIJ,
1438: /*24*/ 0,
1439: 0,
1440: 0,
1441: 0,
1442: 0,
1443: /*29*/ MatSetUp_SeqSBAIJ,
1444: 0,
1445: 0,
1446: MatGetArray_SeqSBAIJ,
1447: MatRestoreArray_SeqSBAIJ,
1448: /*34*/ MatDuplicate_SeqSBAIJ,
1449: 0,
1450: 0,
1451: 0,
1452: MatICCFactor_SeqSBAIJ,
1453: /*39*/ MatAXPY_SeqSBAIJ,
1454: MatGetSubMatrices_SeqSBAIJ,
1455: MatIncreaseOverlap_SeqSBAIJ,
1456: MatGetValues_SeqSBAIJ,
1457: MatCopy_SeqSBAIJ,
1458: /*44*/ 0,
1459: MatScale_SeqSBAIJ,
1460: 0,
1461: 0,
1462: MatZeroRowsColumns_SeqSBAIJ,
1463: /*49*/ MatSetBlockSize_SeqSBAIJ,
1464: MatGetRowIJ_SeqSBAIJ,
1465: MatRestoreRowIJ_SeqSBAIJ,
1466: 0,
1467: 0,
1468: /*54*/ 0,
1469: 0,
1470: 0,
1471: 0,
1472: MatSetValuesBlocked_SeqSBAIJ,
1473: /*59*/ MatGetSubMatrix_SeqSBAIJ,
1474: 0,
1475: 0,
1476: 0,
1477: 0,
1478: /*64*/ 0,
1479: 0,
1480: 0,
1481: 0,
1482: 0,
1483: /*69*/ MatGetRowMaxAbs_SeqSBAIJ,
1484: 0,
1485: 0,
1486: 0,
1487: 0,
1488: /*74*/ 0,
1489: 0,
1490: 0,
1491: 0,
1492: 0,
1493: /*79*/ 0,
1494: 0,
1495: 0,
1496: MatGetInertia_SeqSBAIJ,
1497: MatLoad_SeqSBAIJ,
1498: /*84*/ MatIsSymmetric_SeqSBAIJ,
1499: MatIsHermitian_SeqSBAIJ,
1500: MatIsStructurallySymmetric_SeqSBAIJ,
1501: 0,
1502: 0,
1503: /*89*/ 0,
1504: 0,
1505: 0,
1506: 0,
1507: 0,
1508: /*94*/ 0,
1509: 0,
1510: 0,
1511: 0,
1512: 0,
1513: /*99*/ 0,
1514: 0,
1515: 0,
1516: 0,
1517: 0,
1518: /*104*/0,
1519: MatRealPart_SeqSBAIJ,
1520: MatImaginaryPart_SeqSBAIJ,
1521: MatGetRowUpperTriangular_SeqSBAIJ,
1522: MatRestoreRowUpperTriangular_SeqSBAIJ,
1523: /*109*/0,
1524: 0,
1525: 0,
1526: 0,
1527: MatMissingDiagonal_SeqSBAIJ,
1528: /*114*/0,
1529: 0,
1530: 0,
1531: 0,
1532: 0,
1533: /*119*/0,
1534: 0,
1535: 0,
1536: 0
1537: };
1539: EXTERN_C_BEGIN
1542: PetscErrorCode MatStoreValues_SeqSBAIJ(Mat mat)
1543: {
1544: Mat_SeqSBAIJ *aij = (Mat_SeqSBAIJ *)mat->data;
1545: PetscInt nz = aij->i[mat->rmap->N]*mat->rmap->bs*aij->bs2;
1547:
1549: if (aij->nonew != 1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ORDER,"Must call MatSetOption(A,MAT_NEW_NONZERO_LOCATIONS,PETSC_FALSE);first");
1550:
1551: /* allocate space for values if not already there */
1552: if (!aij->saved_values) {
1553: PetscMalloc((nz+1)*sizeof(PetscScalar),&aij->saved_values);
1554: }
1555:
1556: /* copy values over */
1557: PetscMemcpy(aij->saved_values,aij->a,nz*sizeof(PetscScalar));
1558: return(0);
1559: }
1560: EXTERN_C_END
1562: EXTERN_C_BEGIN
1565: PetscErrorCode MatRetrieveValues_SeqSBAIJ(Mat mat)
1566: {
1567: Mat_SeqSBAIJ *aij = (Mat_SeqSBAIJ *)mat->data;
1569: PetscInt nz = aij->i[mat->rmap->N]*mat->rmap->bs*aij->bs2;
1570:
1572: if (aij->nonew != 1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ORDER,"Must call MatSetOption(A,MAT_NEW_NONZERO_LOCATIONS,PETSC_FALSE);first");
1573: if (!aij->saved_values) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ORDER,"Must call MatStoreValues(A);first");
1574:
1575: /* copy values over */
1576: PetscMemcpy(aij->a,aij->saved_values,nz*sizeof(PetscScalar));
1577: return(0);
1578: }
1579: EXTERN_C_END
1581: EXTERN_C_BEGIN
1584: PetscErrorCode MatSeqSBAIJSetPreallocation_SeqSBAIJ(Mat B,PetscInt bs,PetscInt nz,PetscInt *nnz)
1585: {
1586: Mat_SeqSBAIJ *b = (Mat_SeqSBAIJ*)B->data;
1588: PetscInt i,mbs,bs2, newbs = PetscAbs(bs);
1589: PetscBool skipallocation = PETSC_FALSE,flg = PETSC_FALSE,realalloc = PETSC_FALSE;
1592: if (nz >= 0 || nnz) realalloc = PETSC_TRUE;
1593: B->preallocated = PETSC_TRUE;
1594: if (bs < 0) {
1595: PetscOptionsBegin(((PetscObject)B)->comm,((PetscObject)B)->prefix,"Options for MPISBAIJ matrix","Mat");
1596: PetscOptionsInt("-mat_block_size","Set the blocksize used to store the matrix","MatSeqSBAIJSetPreallocation",newbs,&newbs,PETSC_NULL);
1597: PetscOptionsEnd();
1598: bs = PetscAbs(bs);
1599: }
1600: if (nnz && newbs != bs) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"Cannot change blocksize from command line if setting nnz");
1601: bs = newbs;
1603: PetscLayoutSetBlockSize(B->rmap,bs);
1604: PetscLayoutSetBlockSize(B->cmap,bs);
1605: PetscLayoutSetUp(B->rmap);
1606: PetscLayoutSetUp(B->cmap);
1608: mbs = B->rmap->N/bs;
1609: bs2 = bs*bs;
1610:
1611: if (mbs*bs != B->rmap->N) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Number rows, cols must be divisible by blocksize");
1612:
1613: if (nz == MAT_SKIP_ALLOCATION) {
1614: skipallocation = PETSC_TRUE;
1615: nz = 0;
1616: }
1618: if (nz == PETSC_DEFAULT || nz == PETSC_DECIDE) nz = 3;
1619: if (nz < 0) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"nz cannot be less than 0: value %D",nz);
1620: if (nnz) {
1621: for (i=0; i<mbs; i++) {
1622: 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]);
1623: 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);
1624: }
1625: }
1626:
1627: B->ops->mult = MatMult_SeqSBAIJ_N;
1628: B->ops->multadd = MatMultAdd_SeqSBAIJ_N;
1629: B->ops->multtranspose = MatMult_SeqSBAIJ_N;
1630: B->ops->multtransposeadd = MatMultAdd_SeqSBAIJ_N;
1631: PetscOptionsGetBool(((PetscObject)B)->prefix,"-mat_no_unroll",&flg,PETSC_NULL);
1632: if (!flg) {
1633: switch (bs) {
1634: case 1:
1635: B->ops->mult = MatMult_SeqSBAIJ_1;
1636: B->ops->multadd = MatMultAdd_SeqSBAIJ_1;
1637: B->ops->multtranspose = MatMult_SeqSBAIJ_1;
1638: B->ops->multtransposeadd = MatMultAdd_SeqSBAIJ_1;
1639: break;
1640: case 2:
1641: B->ops->mult = MatMult_SeqSBAIJ_2;
1642: B->ops->multadd = MatMultAdd_SeqSBAIJ_2;
1643: B->ops->multtranspose = MatMult_SeqSBAIJ_2;
1644: B->ops->multtransposeadd = MatMultAdd_SeqSBAIJ_2;
1645: break;
1646: case 3:
1647: B->ops->mult = MatMult_SeqSBAIJ_3;
1648: B->ops->multadd = MatMultAdd_SeqSBAIJ_3;
1649: B->ops->multtranspose = MatMult_SeqSBAIJ_3;
1650: B->ops->multtransposeadd = MatMultAdd_SeqSBAIJ_3;
1651: break;
1652: case 4:
1653: B->ops->mult = MatMult_SeqSBAIJ_4;
1654: B->ops->multadd = MatMultAdd_SeqSBAIJ_4;
1655: B->ops->multtranspose = MatMult_SeqSBAIJ_4;
1656: B->ops->multtransposeadd = MatMultAdd_SeqSBAIJ_4;
1657: break;
1658: case 5:
1659: B->ops->mult = MatMult_SeqSBAIJ_5;
1660: B->ops->multadd = MatMultAdd_SeqSBAIJ_5;
1661: B->ops->multtranspose = MatMult_SeqSBAIJ_5;
1662: B->ops->multtransposeadd = MatMultAdd_SeqSBAIJ_5;
1663: break;
1664: case 6:
1665: B->ops->mult = MatMult_SeqSBAIJ_6;
1666: B->ops->multadd = MatMultAdd_SeqSBAIJ_6;
1667: B->ops->multtranspose = MatMult_SeqSBAIJ_6;
1668: B->ops->multtransposeadd = MatMultAdd_SeqSBAIJ_6;
1669: break;
1670: case 7:
1671: B->ops->mult = MatMult_SeqSBAIJ_7;
1672: B->ops->multadd = MatMultAdd_SeqSBAIJ_7;
1673: B->ops->multtranspose = MatMult_SeqSBAIJ_7;
1674: B->ops->multtransposeadd = MatMultAdd_SeqSBAIJ_7;
1675: break;
1676: }
1677: }
1678:
1679: b->mbs = mbs;
1680: b->nbs = mbs;
1681: if (!skipallocation) {
1682: if (!b->imax) {
1683: PetscMalloc2(mbs,PetscInt,&b->imax,mbs,PetscInt,&b->ilen);
1684: b->free_imax_ilen = PETSC_TRUE;
1685: PetscLogObjectMemory(B,2*mbs*sizeof(PetscInt));
1686: }
1687: if (!nnz) {
1688: if (nz == PETSC_DEFAULT || nz == PETSC_DECIDE) nz = 5;
1689: else if (nz <= 0) nz = 1;
1690: for (i=0; i<mbs; i++) {
1691: b->imax[i] = nz;
1692: }
1693: nz = nz*mbs; /* total nz */
1694: } else {
1695: nz = 0;
1696: for (i=0; i<mbs; i++) {b->imax[i] = nnz[i]; nz += nnz[i];}
1697: }
1698: /* b->ilen will count nonzeros in each block row so far. */
1699: for (i=0; i<mbs; i++) { b->ilen[i] = 0;}
1700: /* nz=(nz+mbs)/2; */ /* total diagonal and superdiagonal nonzero blocks */
1701:
1702: /* allocate the matrix space */
1703: MatSeqXAIJFreeAIJ(B,&b->a,&b->j,&b->i);
1704: PetscMalloc3(bs2*nz,PetscScalar,&b->a,nz,PetscInt,&b->j,B->rmap->N+1,PetscInt,&b->i);
1705: PetscLogObjectMemory(B,(B->rmap->N+1)*sizeof(PetscInt)+nz*(bs2*sizeof(PetscScalar)+sizeof(PetscInt)));
1706: PetscMemzero(b->a,nz*bs2*sizeof(MatScalar));
1707: PetscMemzero(b->j,nz*sizeof(PetscInt));
1708: b->singlemalloc = PETSC_TRUE;
1709:
1710: /* pointer to beginning of each row */
1711: b->i[0] = 0;
1712: for (i=1; i<mbs+1; i++) {
1713: b->i[i] = b->i[i-1] + b->imax[i-1];
1714: }
1715: b->free_a = PETSC_TRUE;
1716: b->free_ij = PETSC_TRUE;
1717: } else {
1718: b->free_a = PETSC_FALSE;
1719: b->free_ij = PETSC_FALSE;
1720: }
1721:
1722: B->rmap->bs = bs;
1723: b->bs2 = bs2;
1724: b->nz = 0;
1725: b->maxnz = nz;
1726:
1727: b->inew = 0;
1728: b->jnew = 0;
1729: b->anew = 0;
1730: b->a2anew = 0;
1731: b->permute = PETSC_FALSE;
1732: if (realalloc) {MatSetOption(B,MAT_NEW_NONZERO_ALLOCATION_ERR,PETSC_TRUE);}
1733: return(0);
1734: }
1735: EXTERN_C_END
1737: /*
1738: This is used to set the numeric factorization for both Cholesky and ICC symbolic factorization
1739: */
1742: PetscErrorCode MatSeqSBAIJSetNumericFactorization_inplace(Mat B,PetscBool natural)
1743: {
1745: PetscBool flg = PETSC_FALSE;
1746: PetscInt bs = B->rmap->bs;
1749: PetscOptionsGetBool(((PetscObject)B)->prefix,"-mat_no_unroll",&flg,PETSC_NULL);
1750: if (flg) bs = 8;
1752: if (!natural) {
1753: switch (bs) {
1754: case 1:
1755: B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_1_inplace;
1756: break;
1757: case 2:
1758: B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_2;
1759: break;
1760: case 3:
1761: B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_3;
1762: break;
1763: case 4:
1764: B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_4;
1765: break;
1766: case 5:
1767: B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_5;
1768: break;
1769: case 6:
1770: B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_6;
1771: break;
1772: case 7:
1773: B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_7;
1774: break;
1775: default:
1776: B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_N;
1777: break;
1778: }
1779: } else {
1780: switch (bs) {
1781: case 1:
1782: B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_1_NaturalOrdering_inplace;
1783: break;
1784: case 2:
1785: B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_2_NaturalOrdering;
1786: break;
1787: case 3:
1788: B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_3_NaturalOrdering;
1789: break;
1790: case 4:
1791: B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_4_NaturalOrdering;
1792: break;
1793: case 5:
1794: B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_5_NaturalOrdering;
1795: break;
1796: case 6:
1797: B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_6_NaturalOrdering;
1798: break;
1799: case 7:
1800: B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_7_NaturalOrdering;
1801: break;
1802: default:
1803: B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_N_NaturalOrdering;
1804: break;
1805: }
1806: }
1807: return(0);
1808: }
1810: EXTERN_C_BEGIN
1811: extern PetscErrorCode MatConvert_SeqSBAIJ_SeqAIJ(Mat, MatType,MatReuse,Mat*);
1812: extern PetscErrorCode MatConvert_SeqSBAIJ_SeqBAIJ(Mat, MatType,MatReuse,Mat*);
1813: EXTERN_C_END
1815:
1816: EXTERN_C_BEGIN
1819: PetscErrorCode MatGetFactor_seqsbaij_petsc(Mat A,MatFactorType ftype,Mat *B)
1820: {
1821: PetscInt n = A->rmap->n;
1822: PetscErrorCode ierr;
1825: MatCreate(((PetscObject)A)->comm,B);
1826: MatSetSizes(*B,n,n,n,n);
1827: if (ftype == MAT_FACTOR_CHOLESKY || ftype == MAT_FACTOR_ICC) {
1828: MatSetType(*B,MATSEQSBAIJ);
1829: MatSeqSBAIJSetPreallocation(*B,1,MAT_SKIP_ALLOCATION,PETSC_NULL);
1830: (*B)->ops->choleskyfactorsymbolic = MatCholeskyFactorSymbolic_SeqSBAIJ;
1831: (*B)->ops->iccfactorsymbolic = MatICCFactorSymbolic_SeqSBAIJ;
1832: } else SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Factor type not supported");
1833: (*B)->factortype = ftype;
1834: return(0);
1835: }
1836: EXTERN_C_END
1838: EXTERN_C_BEGIN
1841: PetscErrorCode MatGetFactorAvailable_seqsbaij_petsc(Mat A,MatFactorType ftype,PetscBool *flg)
1842: {
1844: if (ftype == MAT_FACTOR_CHOLESKY || ftype == MAT_FACTOR_ICC) {
1845: *flg = PETSC_TRUE;
1846: } else {
1847: *flg = PETSC_FALSE;
1848: }
1849: return(0);
1850: }
1851: EXTERN_C_END
1853: EXTERN_C_BEGIN
1854: #if defined(PETSC_HAVE_MUMPS)
1855: extern PetscErrorCode MatGetFactor_sbaij_mumps(Mat,MatFactorType,Mat*);
1856: #endif
1857: #if defined(PETSC_HAVE_SPOOLES)
1858: extern PetscErrorCode MatGetFactor_seqsbaij_spooles(Mat,MatFactorType,Mat*);
1859: #endif
1860: #if defined(PETSC_HAVE_PASTIX)
1861: extern PetscErrorCode MatGetFactor_seqsbaij_pastix(Mat,MatFactorType,Mat*);
1862: #endif
1863: #if defined(PETSC_HAVE_CHOLMOD)
1864: extern PetscErrorCode MatGetFactor_seqsbaij_cholmod(Mat,MatFactorType,Mat*);
1865: #endif
1866: extern PetscErrorCode MatGetFactor_seqsbaij_sbstrm(Mat,MatFactorType,Mat*);
1867: EXTERN_C_END
1869: /*MC
1870: MATSEQSBAIJ - MATSEQSBAIJ = "seqsbaij" - A matrix type to be used for sequential symmetric block sparse matrices,
1871: based on block compressed sparse row format. Only the upper triangular portion of the matrix is stored.
1873: For complex numbers by default this matrix is symmetric, NOT Hermitian symmetric. To make it Hermitian symmetric you
1874: can call MatSetOption(Mat, MAT_HERMITIAN); after MatAssemblyEnd()
1876: Options Database Keys:
1877: . -mat_type seqsbaij - sets the matrix type to "seqsbaij" during a call to MatSetFromOptions()
1878:
1879: Notes: By default if you insert values into the lower triangular part of the matrix they are simply ignored (since they are not
1880: stored and it is assumed they symmetric to the upper triangular). If you call MatSetOption(Mat,MAT_IGNORE_LOWER_TRIANGULAR,PETSC_FALSE) or use
1881: 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.
1884: Level: beginner
1885:
1886: .seealso: MatCreateSeqSBAIJ
1887: M*/
1889: EXTERN_C_BEGIN
1890: extern PetscErrorCode MatConvert_SeqSBAIJ_SeqSBSTRM(Mat, MatType,MatReuse,Mat*);
1891: EXTERN_C_END
1894: EXTERN_C_BEGIN
1897: PetscErrorCode MatCreate_SeqSBAIJ(Mat B)
1898: {
1899: Mat_SeqSBAIJ *b;
1901: PetscMPIInt size;
1902: PetscBool no_unroll = PETSC_FALSE,no_inode = PETSC_FALSE;
1905: MPI_Comm_size(((PetscObject)B)->comm,&size);
1906: if (size > 1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"Comm must be of size 1");
1907:
1908: PetscNewLog(B,Mat_SeqSBAIJ,&b);
1909: B->data = (void*)b;
1910: PetscMemcpy(B->ops,&MatOps_Values,sizeof(struct _MatOps));
1911: B->ops->destroy = MatDestroy_SeqSBAIJ;
1912: B->ops->view = MatView_SeqSBAIJ;
1913: b->row = 0;
1914: b->icol = 0;
1915: b->reallocs = 0;
1916: b->saved_values = 0;
1917: b->inode.limit = 5;
1918: b->inode.max_limit = 5;
1919:
1920: b->roworiented = PETSC_TRUE;
1921: b->nonew = 0;
1922: b->diag = 0;
1923: b->solve_work = 0;
1924: b->mult_work = 0;
1925: B->spptr = 0;
1926: B->info.nz_unneeded = (PetscReal)b->maxnz*b->bs2;
1927: b->keepnonzeropattern = PETSC_FALSE;
1928: b->xtoy = 0;
1929: b->XtoY = 0;
1930:
1931: b->inew = 0;
1932: b->jnew = 0;
1933: b->anew = 0;
1934: b->a2anew = 0;
1935: b->permute = PETSC_FALSE;
1937: b->ignore_ltriangular = PETSC_TRUE;
1938: PetscOptionsGetBool(((PetscObject)B)->prefix,"-mat_ignore_lower_triangular",&b->ignore_ltriangular,PETSC_NULL);
1940: b->getrow_utriangular = PETSC_FALSE;
1941: PetscOptionsGetBool(((PetscObject)B)->prefix,"-mat_getrow_uppertriangular",&b->getrow_utriangular,PETSC_NULL);
1943: #if defined(PETSC_HAVE_PASTIX)
1944: PetscObjectComposeFunctionDynamic((PetscObject)B,"MatGetFactor_pastix_C",
1945: "MatGetFactor_seqsbaij_pastix",
1946: MatGetFactor_seqsbaij_pastix);
1947: #endif
1948: #if defined(PETSC_HAVE_SPOOLES)
1949: PetscObjectComposeFunctionDynamic((PetscObject)B,"MatGetFactor_spooles_C",
1950: "MatGetFactor_seqsbaij_spooles",
1951: MatGetFactor_seqsbaij_spooles);
1952: #endif
1953: #if defined(PETSC_HAVE_MUMPS)
1954: PetscObjectComposeFunctionDynamic((PetscObject)B,"MatGetFactor_mumps_C",
1955: "MatGetFactor_sbaij_mumps",
1956: MatGetFactor_sbaij_mumps);
1957: #endif
1958: #if defined(PETSC_HAVE_CHOLMOD)
1959: PetscObjectComposeFunctionDynamic((PetscObject)B,"MatGetFactor_cholmod_C",
1960: "MatGetFactor_seqsbaij_cholmod",
1961: MatGetFactor_seqsbaij_cholmod);
1962: #endif
1963: PetscObjectComposeFunctionDynamic((PetscObject)B,"MatGetFactorAvailable_petsc_C",
1964: "MatGetFactorAvailable_seqsbaij_petsc",
1965: MatGetFactorAvailable_seqsbaij_petsc);
1966: PetscObjectComposeFunctionDynamic((PetscObject)B,"MatGetFactor_petsc_C",
1967: "MatGetFactor_seqsbaij_petsc",
1968: MatGetFactor_seqsbaij_petsc);
1969: PetscObjectComposeFunctionDynamic((PetscObject)B,"MatGetFactor_sbstrm_C",
1970: "MatGetFactor_seqsbaij_sbstrm",
1971: MatGetFactor_seqsbaij_sbstrm);
1972: PetscObjectComposeFunctionDynamic((PetscObject)B,"MatStoreValues_C",
1973: "MatStoreValues_SeqSBAIJ",
1974: MatStoreValues_SeqSBAIJ);
1975: PetscObjectComposeFunctionDynamic((PetscObject)B,"MatRetrieveValues_C",
1976: "MatRetrieveValues_SeqSBAIJ",
1977: (void*)MatRetrieveValues_SeqSBAIJ);
1978: PetscObjectComposeFunctionDynamic((PetscObject)B,"MatSeqSBAIJSetColumnIndices_C",
1979: "MatSeqSBAIJSetColumnIndices_SeqSBAIJ",
1980: MatSeqSBAIJSetColumnIndices_SeqSBAIJ);
1981: PetscObjectComposeFunctionDynamic((PetscObject)B,"MatConvert_seqsbaij_seqaij_C",
1982: "MatConvert_SeqSBAIJ_SeqAIJ",
1983: MatConvert_SeqSBAIJ_SeqAIJ);
1984: PetscObjectComposeFunctionDynamic((PetscObject)B,"MatConvert_seqsbaij_seqbaij_C",
1985: "MatConvert_SeqSBAIJ_SeqBAIJ",
1986: MatConvert_SeqSBAIJ_SeqBAIJ);
1987: PetscObjectComposeFunctionDynamic((PetscObject)B,"MatSeqSBAIJSetPreallocation_C",
1988: "MatSeqSBAIJSetPreallocation_SeqSBAIJ",
1989: MatSeqSBAIJSetPreallocation_SeqSBAIJ);
1990: PetscObjectComposeFunctionDynamic((PetscObject)B,"MatConvert_seqsbaij_seqsbstrm_C",
1991: "MatConvert_SeqSBAIJ_SeqSBSTRM",
1992: MatConvert_SeqSBAIJ_SeqSBSTRM);
1994: B->symmetric = PETSC_TRUE;
1995: B->structurally_symmetric = PETSC_TRUE;
1996: B->symmetric_set = PETSC_TRUE;
1997: B->structurally_symmetric_set = PETSC_TRUE;
1998: PetscObjectChangeTypeName((PetscObject)B,MATSEQSBAIJ);
2000: PetscOptionsBegin(((PetscObject)B)->comm,((PetscObject)B)->prefix,"Options for SEQSBAIJ matrix","Mat");
2001: PetscOptionsBool("-mat_no_unroll","Do not optimize for inodes (slower)",PETSC_NULL,no_unroll,&no_unroll,PETSC_NULL);
2002: if (no_unroll) {PetscInfo(B,"Not using Inode routines due to -mat_no_unroll\n");}
2003: PetscOptionsBool("-mat_no_inode","Do not optimize for inodes (slower)",PETSC_NULL,no_inode,&no_inode,PETSC_NULL);
2004: if (no_inode) {PetscInfo(B,"Not using Inode routines due to -mat_no_inode\n");}
2005: PetscOptionsInt("-mat_inode_limit","Do not use inodes larger then this value",PETSC_NULL,b->inode.limit,&b->inode.limit,PETSC_NULL);
2006: PetscOptionsEnd();
2007: b->inode.use = (PetscBool)(!(no_unroll || no_inode));
2008: if (b->inode.limit > b->inode.max_limit) b->inode.limit = b->inode.max_limit;
2010: return(0);
2011: }
2012: EXTERN_C_END
2016: /*@C
2017: MatSeqSBAIJSetPreallocation - Creates a sparse symmetric matrix in block AIJ (block
2018: compressed row) format. For good matrix assembly performance the
2019: user should preallocate the matrix storage by setting the parameter nz
2020: (or the array nnz). By setting these parameters accurately, performance
2021: during matrix assembly can be increased by more than a factor of 50.
2023: Collective on Mat
2025: Input Parameters:
2026: + A - the symmetric matrix
2027: . bs - size of block
2028: . nz - number of block nonzeros per block row (same for all rows)
2029: - nnz - array containing the number of block nonzeros in the upper triangular plus
2030: diagonal portion of each block (possibly different for each block row) or PETSC_NULL
2032: Options Database Keys:
2033: . -mat_no_unroll - uses code that does not unroll the loops in the
2034: block calculations (much slower)
2035: . -mat_block_size - size of the blocks to use (only works if a negative bs is passed in
2037: Level: intermediate
2039: Notes:
2040: Specify the preallocated storage with either nz or nnz (not both).
2041: Set nz=PETSC_DEFAULT and nnz=PETSC_NULL for PETSc to control dynamic memory
2042: allocation. See the <a href="../../docs/manual.pdf#nameddest=ch_mat">Mat chapter of the users manual</a> for details.
2044: You can call MatGetInfo() to get information on how effective the preallocation was;
2045: for example the fields mallocs,nz_allocated,nz_used,nz_unneeded;
2046: You can also run with the option -info and look for messages with the string
2047: malloc in them to see if additional memory allocation was needed.
2049: If the nnz parameter is given then the nz parameter is ignored
2052: .seealso: MatCreate(), MatCreateSeqAIJ(), MatSetValues(), MatCreateMPISBAIJ()
2053: @*/
2054: PetscErrorCode MatSeqSBAIJSetPreallocation(Mat B,PetscInt bs,PetscInt nz,const PetscInt nnz[])
2055: {
2062: PetscTryMethod(B,"MatSeqSBAIJSetPreallocation_C",(Mat,PetscInt,PetscInt,const PetscInt[]),(B,bs,nz,nnz));
2063: return(0);
2064: }
2068: /*@C
2069: MatCreateSeqSBAIJ - Creates a sparse symmetric matrix in block AIJ (block
2070: compressed row) format. For good matrix assembly performance the
2071: user should preallocate the matrix storage by setting the parameter nz
2072: (or the array nnz). By setting these parameters accurately, performance
2073: during matrix assembly can be increased by more than a factor of 50.
2075: Collective on MPI_Comm
2077: Input Parameters:
2078: + comm - MPI communicator, set to PETSC_COMM_SELF
2079: . bs - size of block
2080: . m - number of rows, or number of columns
2081: . nz - number of block nonzeros per block row (same for all rows)
2082: - nnz - array containing the number of block nonzeros in the upper triangular plus
2083: diagonal portion of each block (possibly different for each block row) or PETSC_NULL
2085: Output Parameter:
2086: . A - the symmetric matrix
2088: Options Database Keys:
2089: . -mat_no_unroll - uses code that does not unroll the loops in the
2090: block calculations (much slower)
2091: . -mat_block_size - size of the blocks to use
2093: Level: intermediate
2095: It is recommended that one use the MatCreate(), MatSetType() and/or MatSetFromOptions(),
2096: MatXXXXSetPreallocation() paradgm instead of this routine directly.
2097: [MatXXXXSetPreallocation() is, for example, MatSeqAIJSetPreallocation]
2099: Notes:
2100: The number of rows and columns must be divisible by blocksize.
2101: This matrix type does not support complex Hermitian operation.
2103: Specify the preallocated storage with either nz or nnz (not both).
2104: Set nz=PETSC_DEFAULT and nnz=PETSC_NULL for PETSc to control dynamic memory
2105: allocation. See the <a href="../../docs/manual.pdf#nameddest=ch_mat">Mat chapter of the users manual</a> for details.
2107: If the nnz parameter is given then the nz parameter is ignored
2109: .seealso: MatCreate(), MatCreateSeqAIJ(), MatSetValues(), MatCreateMPISBAIJ()
2110: @*/
2111: PetscErrorCode MatCreateSeqSBAIJ(MPI_Comm comm,PetscInt bs,PetscInt m,PetscInt n,PetscInt nz,const PetscInt nnz[],Mat *A)
2112: {
2114:
2116: MatCreate(comm,A);
2117: MatSetSizes(*A,m,n,m,n);
2118: MatSetType(*A,MATSEQSBAIJ);
2119: MatSeqSBAIJSetPreallocation_SeqSBAIJ(*A,bs,nz,(PetscInt*)nnz);
2120: return(0);
2121: }
2125: PetscErrorCode MatDuplicate_SeqSBAIJ(Mat A,MatDuplicateOption cpvalues,Mat *B)
2126: {
2127: Mat C;
2128: Mat_SeqSBAIJ *c,*a = (Mat_SeqSBAIJ*)A->data;
2130: PetscInt i,mbs = a->mbs,nz = a->nz,bs2 =a->bs2;
2133: if (a->i[mbs] != nz) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Corrupt matrix");
2135: *B = 0;
2136: MatCreate(((PetscObject)A)->comm,&C);
2137: MatSetSizes(C,A->rmap->N,A->cmap->n,A->rmap->N,A->cmap->n);
2138: MatSetType(C,MATSEQSBAIJ);
2139: PetscMemcpy(C->ops,A->ops,sizeof(struct _MatOps));
2140: c = (Mat_SeqSBAIJ*)C->data;
2142: C->preallocated = PETSC_TRUE;
2143: C->factortype = A->factortype;
2144: c->row = 0;
2145: c->icol = 0;
2146: c->saved_values = 0;
2147: c->keepnonzeropattern = a->keepnonzeropattern;
2148: C->assembled = PETSC_TRUE;
2150: PetscLayoutReference(A->rmap,&C->rmap);
2151: PetscLayoutReference(A->cmap,&C->cmap);
2152: c->bs2 = a->bs2;
2153: c->mbs = a->mbs;
2154: c->nbs = a->nbs;
2156: if (cpvalues == MAT_SHARE_NONZERO_PATTERN) {
2157: c->imax = a->imax;
2158: c->ilen = a->ilen;
2159: c->free_imax_ilen = PETSC_FALSE;
2160: } else {
2161: PetscMalloc2((mbs+1),PetscInt,&c->imax,(mbs+1),PetscInt,&c->ilen);
2162: PetscLogObjectMemory(C,2*(mbs+1)*sizeof(PetscInt));
2163: for (i=0; i<mbs; i++) {
2164: c->imax[i] = a->imax[i];
2165: c->ilen[i] = a->ilen[i];
2166: }
2167: c->free_imax_ilen = PETSC_TRUE;
2168: }
2170: /* allocate the matrix space */
2171: if (cpvalues == MAT_SHARE_NONZERO_PATTERN) {
2172: PetscMalloc(bs2*nz*sizeof(MatScalar),&c->a);
2173: PetscLogObjectMemory(C,nz*bs2*sizeof(MatScalar));
2174: c->singlemalloc = PETSC_FALSE;
2175: c->free_ij = PETSC_FALSE;
2176: c->parent = A;
2177: PetscObjectReference((PetscObject)A);
2178: MatSetOption(A,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);
2179: MatSetOption(C,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);
2180: } else {
2181: PetscMalloc3(bs2*nz,MatScalar,&c->a,nz,PetscInt,&c->j,mbs+1,PetscInt,&c->i);
2182: PetscMemcpy(c->i,a->i,(mbs+1)*sizeof(PetscInt));
2183: PetscLogObjectMemory(C,(mbs+1)*sizeof(PetscInt) + nz*(bs2*sizeof(MatScalar) + sizeof(PetscInt)));
2184: c->singlemalloc = PETSC_TRUE;
2185: c->free_ij = PETSC_TRUE;
2186: }
2187: if (mbs > 0) {
2188: if (cpvalues != MAT_SHARE_NONZERO_PATTERN) {
2189: PetscMemcpy(c->j,a->j,nz*sizeof(PetscInt));
2190: }
2191: if (cpvalues == MAT_COPY_VALUES) {
2192: PetscMemcpy(c->a,a->a,bs2*nz*sizeof(MatScalar));
2193: } else {
2194: PetscMemzero(c->a,bs2*nz*sizeof(MatScalar));
2195: }
2196: if (a->jshort) {
2197: if (cpvalues == MAT_SHARE_NONZERO_PATTERN) {
2198: c->jshort = a->jshort;
2199: c->free_jshort = PETSC_FALSE;
2200: } else {
2201: PetscMalloc(nz*sizeof(unsigned short),&c->jshort);
2202: PetscLogObjectMemory(C,nz*sizeof(unsigned short));
2203: PetscMemcpy(c->jshort,a->jshort,nz*sizeof(unsigned short));
2204: c->free_jshort = PETSC_TRUE;
2205: }
2206: }
2207: }
2209: c->roworiented = a->roworiented;
2210: c->nonew = a->nonew;
2212: if (a->diag) {
2213: if (cpvalues == MAT_SHARE_NONZERO_PATTERN) {
2214: c->diag = a->diag;
2215: c->free_diag = PETSC_FALSE;
2216: } else {
2217: PetscMalloc(mbs*sizeof(PetscInt),&c->diag);
2218: PetscLogObjectMemory(C,mbs*sizeof(PetscInt));
2219: for (i=0; i<mbs; i++) {
2220: c->diag[i] = a->diag[i];
2221: }
2222: c->free_diag = PETSC_TRUE;
2223: }
2224: } else c->diag = 0;
2225: c->nz = a->nz;
2226: c->maxnz = a->nz; /* Since we allocate exactly the right amount */
2227: c->solve_work = 0;
2228: c->mult_work = 0;
2229: c->free_a = PETSC_TRUE;
2230: *B = C;
2231: PetscFListDuplicate(((PetscObject)A)->qlist,&((PetscObject)C)->qlist);
2232: return(0);
2233: }
2237: PetscErrorCode MatLoad_SeqSBAIJ(Mat newmat,PetscViewer viewer)
2238: {
2239: Mat_SeqSBAIJ *a;
2241: int fd;
2242: PetscMPIInt size;
2243: PetscInt i,nz,header[4],*rowlengths=0,M,N,bs=1;
2244: PetscInt *mask,mbs,*jj,j,rowcount,nzcount,k,*s_browlengths,maskcount;
2245: PetscInt kmax,jcount,block,idx,point,nzcountb,extra_rows,rows,cols;
2246: PetscInt *masked,nmask,tmp,bs2,ishift;
2247: PetscScalar *aa;
2248: MPI_Comm comm = ((PetscObject)viewer)->comm;
2251: PetscOptionsGetInt(((PetscObject)newmat)->prefix,"-matload_block_size",&bs,PETSC_NULL);
2252: bs2 = bs*bs;
2254: MPI_Comm_size(comm,&size);
2255: if (size > 1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"view must have one processor");
2256: PetscViewerBinaryGetDescriptor(viewer,&fd);
2257: PetscBinaryRead(fd,header,4,PETSC_INT);
2258: if (header[0] != MAT_FILE_CLASSID) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_FILE_UNEXPECTED,"not Mat object");
2259: M = header[1]; N = header[2]; nz = header[3];
2261: if (header[3] < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_FILE_UNEXPECTED,"Matrix stored in special format, cannot load as SeqSBAIJ");
2263: if (M != N) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Can only do square matrices");
2265: /*
2266: This code adds extra rows to make sure the number of rows is
2267: divisible by the blocksize
2268: */
2269: mbs = M/bs;
2270: extra_rows = bs - M + bs*(mbs);
2271: if (extra_rows == bs) extra_rows = 0;
2272: else mbs++;
2273: if (extra_rows) {
2274: PetscInfo(viewer,"Padding loaded matrix to match blocksize\n");
2275: }
2277: /* Set global sizes if not already set */
2278: if (newmat->rmap->n < 0 && newmat->rmap->N < 0 && newmat->cmap->n < 0 && newmat->cmap->N < 0) {
2279: MatSetSizes(newmat,PETSC_DECIDE,PETSC_DECIDE,M+extra_rows,N+extra_rows);
2280: } else { /* Check if the matrix global sizes are correct */
2281: MatGetSize(newmat,&rows,&cols);
2282: 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);
2283: }
2285: /* read in row lengths */
2286: PetscMalloc((M+extra_rows)*sizeof(PetscInt),&rowlengths);
2287: PetscBinaryRead(fd,rowlengths,M,PETSC_INT);
2288: for (i=0; i<extra_rows; i++) rowlengths[M+i] = 1;
2290: /* read in column indices */
2291: PetscMalloc((nz+extra_rows)*sizeof(PetscInt),&jj);
2292: PetscBinaryRead(fd,jj,nz,PETSC_INT);
2293: for (i=0; i<extra_rows; i++) jj[nz+i] = M+i;
2295: /* loop over row lengths determining block row lengths */
2296: PetscMalloc(mbs*sizeof(PetscInt),&s_browlengths);
2297: PetscMemzero(s_browlengths,mbs*sizeof(PetscInt));
2298: PetscMalloc2(mbs,PetscInt,&mask,mbs,PetscInt,&masked);
2299: PetscMemzero(mask,mbs*sizeof(PetscInt));
2300: rowcount = 0;
2301: nzcount = 0;
2302: for (i=0; i<mbs; i++) {
2303: nmask = 0;
2304: for (j=0; j<bs; j++) {
2305: kmax = rowlengths[rowcount];
2306: for (k=0; k<kmax; k++) {
2307: tmp = jj[nzcount++]/bs; /* block col. index */
2308: if (!mask[tmp] && tmp >= i) {masked[nmask++] = tmp; mask[tmp] = 1;}
2309: }
2310: rowcount++;
2311: }
2312: s_browlengths[i] += nmask;
2313:
2314: /* zero out the mask elements we set */
2315: for (j=0; j<nmask; j++) mask[masked[j]] = 0;
2316: }
2318: /* Do preallocation */
2319: MatSeqSBAIJSetPreallocation_SeqSBAIJ(newmat,bs,0,s_browlengths);
2320: a = (Mat_SeqSBAIJ*)newmat->data;
2322: /* set matrix "i" values */
2323: a->i[0] = 0;
2324: for (i=1; i<= mbs; i++) {
2325: a->i[i] = a->i[i-1] + s_browlengths[i-1];
2326: a->ilen[i-1] = s_browlengths[i-1];
2327: }
2328: a->nz = a->i[mbs];
2330: /* read in nonzero values */
2331: PetscMalloc((nz+extra_rows)*sizeof(PetscScalar),&aa);
2332: PetscBinaryRead(fd,aa,nz,PETSC_SCALAR);
2333: for (i=0; i<extra_rows; i++) aa[nz+i] = 1.0;
2335: /* set "a" and "j" values into matrix */
2336: nzcount = 0; jcount = 0;
2337: for (i=0; i<mbs; i++) {
2338: nzcountb = nzcount;
2339: nmask = 0;
2340: for (j=0; j<bs; j++) {
2341: kmax = rowlengths[i*bs+j];
2342: for (k=0; k<kmax; k++) {
2343: tmp = jj[nzcount++]/bs; /* block col. index */
2344: if (!mask[tmp] && tmp >= i) { masked[nmask++] = tmp; mask[tmp] = 1;}
2345: }
2346: }
2347: /* sort the masked values */
2348: PetscSortInt(nmask,masked);
2350: /* set "j" values into matrix */
2351: maskcount = 1;
2352: for (j=0; j<nmask; j++) {
2353: a->j[jcount++] = masked[j];
2354: mask[masked[j]] = maskcount++;
2355: }
2357: /* set "a" values into matrix */
2358: ishift = bs2*a->i[i];
2359: for (j=0; j<bs; j++) {
2360: kmax = rowlengths[i*bs+j];
2361: for (k=0; k<kmax; k++) {
2362: tmp = jj[nzcountb]/bs ; /* block col. index */
2363: if (tmp >= i){
2364: block = mask[tmp] - 1;
2365: point = jj[nzcountb] - bs*tmp;
2366: idx = ishift + bs2*block + j + bs*point;
2367: a->a[idx] = aa[nzcountb];
2368: }
2369: nzcountb++;
2370: }
2371: }
2372: /* zero out the mask elements we set */
2373: for (j=0; j<nmask; j++) mask[masked[j]] = 0;
2374: }
2375: if (jcount != a->nz) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_FILE_UNEXPECTED,"Bad binary matrix");
2377: PetscFree(rowlengths);
2378: PetscFree(s_browlengths);
2379: PetscFree(aa);
2380: PetscFree(jj);
2381: PetscFree2(mask,masked);
2383: MatAssemblyBegin(newmat,MAT_FINAL_ASSEMBLY);
2384: MatAssemblyEnd(newmat,MAT_FINAL_ASSEMBLY);
2385: MatView_Private(newmat);
2386: return(0);
2387: }
2391: /*@
2392: MatCreateSeqSBAIJWithArrays - Creates an sequential SBAIJ matrix using matrix elements
2393: (upper triangular entries in CSR format) provided by the user.
2395: Collective on MPI_Comm
2397: Input Parameters:
2398: + comm - must be an MPI communicator of size 1
2399: . bs - size of block
2400: . m - number of rows
2401: . n - number of columns
2402: . i - row indices
2403: . j - column indices
2404: - a - matrix values
2406: Output Parameter:
2407: . mat - the matrix
2409: Level: advanced
2411: Notes:
2412: The i, j, and a arrays are not copied by this routine, the user must free these arrays
2413: once the matrix is destroyed
2415: You cannot set new nonzero locations into this matrix, that will generate an error.
2417: The i and j indices are 0 based
2419: 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
2420: it is the regular CSR format excluding the lower triangular elements.
2422: .seealso: MatCreate(), MatCreateMPISBAIJ(), MatCreateSeqSBAIJ()
2424: @*/
2425: PetscErrorCode MatCreateSeqSBAIJWithArrays(MPI_Comm comm,PetscInt bs,PetscInt m,PetscInt n,PetscInt* i,PetscInt*j,PetscScalar *a,Mat *mat)
2426: {
2428: PetscInt ii;
2429: Mat_SeqSBAIJ *sbaij;
2432: if (bs != 1) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP,"block size %D > 1 is not supported yet",bs);
2433: if (i[0]) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"i (row indices) must start with 0");
2434:
2435: MatCreate(comm,mat);
2436: MatSetSizes(*mat,m,n,m,n);
2437: MatSetType(*mat,MATSEQSBAIJ);
2438: MatSeqSBAIJSetPreallocation_SeqSBAIJ(*mat,bs,MAT_SKIP_ALLOCATION,0);
2439: sbaij = (Mat_SeqSBAIJ*)(*mat)->data;
2440: PetscMalloc2(m,PetscInt,&sbaij->imax,m,PetscInt,&sbaij->ilen);
2441: PetscLogObjectMemory(*mat,2*m*sizeof(PetscInt));
2443: sbaij->i = i;
2444: sbaij->j = j;
2445: sbaij->a = a;
2446: sbaij->singlemalloc = PETSC_FALSE;
2447: sbaij->nonew = -1; /*this indicates that inserting a new value in the matrix that generates a new nonzero is an error*/
2448: sbaij->free_a = PETSC_FALSE;
2449: sbaij->free_ij = PETSC_FALSE;
2451: for (ii=0; ii<m; ii++) {
2452: sbaij->ilen[ii] = sbaij->imax[ii] = i[ii+1] - i[ii];
2453: #if defined(PETSC_USE_DEBUG)
2454: 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]);
2455: #endif
2456: }
2457: #if defined(PETSC_USE_DEBUG)
2458: for (ii=0; ii<sbaij->i[m]; ii++) {
2459: if (j[ii] < 0) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Negative column index at location = %d index = %d",ii,j[ii]);
2460: 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]);
2461: }
2462: #endif
2464: MatAssemblyBegin(*mat,MAT_FINAL_ASSEMBLY);
2465: MatAssemblyEnd(*mat,MAT_FINAL_ASSEMBLY);
2466: return(0);
2467: }