Actual source code: sbaij.c
petsc-3.5.4 2015-05-23
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,*ii = a->i,i;
28: MatMarkDiagonal_SeqSBAIJ(A);
29: *missing = PETSC_FALSE;
30: if (A->rmap->n > 0 && !ii) {
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 (diag[i] >= ii[i+1]) {
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,j;
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++) {
62: a->diag[i] = a->i[i+1];
63: for (j=a->i[i]; j<a->i[i+1]; j++) {
64: if (a->j[j] == i) {
65: a->diag[i] = j;
66: break;
67: }
68: }
69: }
70: return(0);
71: }
75: static PetscErrorCode MatGetRowIJ_SeqSBAIJ(Mat A,PetscInt oshift,PetscBool symmetric,PetscBool blockcompressed,PetscInt *nn,const PetscInt *inia[],const PetscInt *inja[],PetscBool *done)
76: {
77: Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data;
78: PetscInt i,j,n = a->mbs,nz = a->i[n],bs = A->rmap->bs;
79: PetscInt **ia = (PetscInt**)inia,**ja = (PetscInt**)inja;
83: *nn = n;
84: if (!ia) return(0);
85: if (!blockcompressed) {
86: /* malloc & create the natural set of indices */
87: PetscMalloc2((n+1)*bs,ia,nz*bs,ja);
88: for (i=0; i<n+1; i++) {
89: for (j=0; j<bs; j++) {
90: (*ia)[i*bs+j] = a->i[i]*bs+j+oshift;
91: }
92: }
93: for (i=0; i<nz; i++) {
94: for (j=0; j<bs; j++) {
95: (*ja)[i*bs+j] = a->j[i]*bs+j+oshift;
96: }
97: }
98: } else { /* blockcompressed */
99: if (oshift == 1) {
100: /* temporarily add 1 to i and j indices */
101: for (i=0; i<nz; i++) a->j[i]++;
102: for (i=0; i<n+1; i++) a->i[i]++;
103: }
104: *ia = a->i; *ja = a->j;
105: }
106: return(0);
107: }
111: static PetscErrorCode MatRestoreRowIJ_SeqSBAIJ(Mat A,PetscInt oshift,PetscBool symmetric,PetscBool blockcompressed,PetscInt *nn,const PetscInt *ia[],const PetscInt *ja[],PetscBool *done)
112: {
113: Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data;
114: PetscInt i,n = a->mbs,nz = a->i[n];
118: if (!ia) return(0);
120: if (!blockcompressed) {
121: PetscFree2(*ia,*ja);
122: } else if (oshift == 1) { /* blockcompressed */
123: for (i=0; i<nz; i++) a->j[i]--;
124: for (i=0; i<n+1; i++) a->i[i]--;
125: }
126: return(0);
127: }
131: PetscErrorCode MatDestroy_SeqSBAIJ(Mat A)
132: {
133: Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data;
137: #if defined(PETSC_USE_LOG)
138: PetscLogObjectState((PetscObject)A,"Rows=%D, NZ=%D",A->rmap->N,a->nz);
139: #endif
140: MatSeqXAIJFreeAIJ(A,&a->a,&a->j,&a->i);
141: if (a->free_diag) {PetscFree(a->diag);}
142: ISDestroy(&a->row);
143: ISDestroy(&a->col);
144: ISDestroy(&a->icol);
145: PetscFree(a->idiag);
146: PetscFree(a->inode.size);
147: if (a->free_imax_ilen) {PetscFree2(a->imax,a->ilen);}
148: PetscFree(a->solve_work);
149: PetscFree(a->sor_work);
150: PetscFree(a->solves_work);
151: PetscFree(a->mult_work);
152: PetscFree(a->saved_values);
153: PetscFree(a->xtoy);
154: if (a->free_jshort) {PetscFree(a->jshort);}
155: PetscFree(a->inew);
156: MatDestroy(&a->parent);
157: PetscFree(A->data);
159: PetscObjectChangeTypeName((PetscObject)A,0);
160: PetscObjectComposeFunction((PetscObject)A,"MatStoreValues_C",NULL);
161: PetscObjectComposeFunction((PetscObject)A,"MatRetrieveValues_C",NULL);
162: PetscObjectComposeFunction((PetscObject)A,"MatSeqSBAIJSetColumnIndices_C",NULL);
163: PetscObjectComposeFunction((PetscObject)A,"MatConvert_seqsbaij_seqaij_C",NULL);
164: PetscObjectComposeFunction((PetscObject)A,"MatConvert_seqsbaij_seqbaij_C",NULL);
165: PetscObjectComposeFunction((PetscObject)A,"MatSeqSBAIJSetPreallocation_C",NULL);
166: PetscObjectComposeFunction((PetscObject)A,"MatSeqSBAIJSetPreallocationCSR_C",NULL);
167: PetscObjectComposeFunction((PetscObject)A,"MatConvert_seqsbaij_seqsbstrm_C",NULL);
168: return(0);
169: }
173: PetscErrorCode MatSetOption_SeqSBAIJ(Mat A,MatOption op,PetscBool flg)
174: {
175: Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data;
179: switch (op) {
180: case MAT_ROW_ORIENTED:
181: a->roworiented = flg;
182: break;
183: case MAT_KEEP_NONZERO_PATTERN:
184: a->keepnonzeropattern = flg;
185: break;
186: case MAT_NEW_NONZERO_LOCATIONS:
187: a->nonew = (flg ? 0 : 1);
188: break;
189: case MAT_NEW_NONZERO_LOCATION_ERR:
190: a->nonew = (flg ? -1 : 0);
191: break;
192: case MAT_NEW_NONZERO_ALLOCATION_ERR:
193: a->nonew = (flg ? -2 : 0);
194: break;
195: case MAT_UNUSED_NONZERO_LOCATION_ERR:
196: a->nounused = (flg ? -1 : 0);
197: break;
198: case MAT_NEW_DIAGONALS:
199: case MAT_IGNORE_OFF_PROC_ENTRIES:
200: case MAT_USE_HASH_TABLE:
201: PetscInfo1(A,"Option %s ignored\n",MatOptions[op]);
202: break;
203: case MAT_HERMITIAN:
204: if (!A->assembled) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Must call MatAssemblyEnd() first");
205: if (A->cmap->n < 65536 && A->cmap->bs == 1) {
206: A->ops->mult = MatMult_SeqSBAIJ_1_Hermitian_ushort;
207: } else if (A->cmap->bs == 1) {
208: A->ops->mult = MatMult_SeqSBAIJ_1_Hermitian;
209: } else SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"No support for Hermitian with block size greater than 1");
210: break;
211: case MAT_SPD:
212: /* These options are handled directly by MatSetOption() */
213: break;
214: case MAT_SYMMETRIC:
215: case MAT_STRUCTURALLY_SYMMETRIC:
216: case MAT_SYMMETRY_ETERNAL:
217: if (!flg) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Matrix must be symmetric");
218: PetscInfo1(A,"Option %s not relevent\n",MatOptions[op]);
219: break;
220: case MAT_IGNORE_LOWER_TRIANGULAR:
221: a->ignore_ltriangular = flg;
222: break;
223: case MAT_ERROR_LOWER_TRIANGULAR:
224: a->ignore_ltriangular = flg;
225: break;
226: case MAT_GETROW_UPPERTRIANGULAR:
227: a->getrow_utriangular = flg;
228: break;
229: default:
230: SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP,"unknown option %d",op);
231: }
232: return(0);
233: }
237: PetscErrorCode MatGetRow_SeqSBAIJ(Mat A,PetscInt row,PetscInt *nz,PetscInt **idx,PetscScalar **v)
238: {
239: Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data;
243: 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()");
245: /* Get the upper triangular part of the row */
246: MatGetRow_SeqBAIJ_private(A,row,nz,idx,v,a->i,a->j,a->a);
247: return(0);
248: }
252: PetscErrorCode MatRestoreRow_SeqSBAIJ(Mat A,PetscInt row,PetscInt *nz,PetscInt **idx,PetscScalar **v)
253: {
257: if (idx) {PetscFree(*idx);}
258: if (v) {PetscFree(*v);}
259: return(0);
260: }
264: PetscErrorCode MatGetRowUpperTriangular_SeqSBAIJ(Mat A)
265: {
266: Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data;
269: a->getrow_utriangular = PETSC_TRUE;
270: return(0);
271: }
274: PetscErrorCode MatRestoreRowUpperTriangular_SeqSBAIJ(Mat A)
275: {
276: Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data;
279: a->getrow_utriangular = PETSC_FALSE;
280: return(0);
281: }
285: PetscErrorCode MatTranspose_SeqSBAIJ(Mat A,MatReuse reuse,Mat *B)
286: {
290: if (reuse == MAT_INITIAL_MATRIX || *B != A) {
291: MatDuplicate(A,MAT_COPY_VALUES,B);
292: }
293: return(0);
294: }
298: PetscErrorCode MatView_SeqSBAIJ_ASCII(Mat A,PetscViewer viewer)
299: {
300: Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data;
301: PetscErrorCode ierr;
302: PetscInt i,j,bs = A->rmap->bs,k,l,bs2=a->bs2;
303: PetscViewerFormat format;
304: PetscInt *diag;
307: PetscViewerGetFormat(viewer,&format);
308: if (format == PETSC_VIEWER_ASCII_INFO || format == PETSC_VIEWER_ASCII_INFO_DETAIL) {
309: PetscViewerASCIIPrintf(viewer," block size is %D\n",bs);
310: } else if (format == PETSC_VIEWER_ASCII_MATLAB) {
311: Mat aij;
312: const char *matname;
314: if (A->factortype && bs>1) {
315: PetscPrintf(PETSC_COMM_SELF,"Warning: matrix is factored with bs>1. MatView() with PETSC_VIEWER_ASCII_MATLAB is not supported and ignored!\n");
316: return(0);
317: }
318: MatConvert(A,MATSEQAIJ,MAT_INITIAL_MATRIX,&aij);
319: PetscObjectGetName((PetscObject)A,&matname);
320: PetscObjectSetName((PetscObject)aij,matname);
321: MatView(aij,viewer);
322: MatDestroy(&aij);
323: } else if (format == PETSC_VIEWER_ASCII_COMMON) {
324: PetscViewerASCIIUseTabs(viewer,PETSC_FALSE);
325: for (i=0; i<a->mbs; i++) {
326: for (j=0; j<bs; j++) {
327: PetscViewerASCIIPrintf(viewer,"row %D:",i*bs+j);
328: for (k=a->i[i]; k<a->i[i+1]; k++) {
329: for (l=0; l<bs; l++) {
330: #if defined(PETSC_USE_COMPLEX)
331: if (PetscImaginaryPart(a->a[bs2*k + l*bs + j]) > 0.0 && PetscRealPart(a->a[bs2*k + l*bs + j]) != 0.0) {
332: PetscViewerASCIIPrintf(viewer," (%D, %g + %g i) ",bs*a->j[k]+l,
333: (double)PetscRealPart(a->a[bs2*k + l*bs + j]),(double)PetscImaginaryPart(a->a[bs2*k + l*bs + j]));
334: } else if (PetscImaginaryPart(a->a[bs2*k + l*bs + j]) < 0.0 && PetscRealPart(a->a[bs2*k + l*bs + j]) != 0.0) {
335: PetscViewerASCIIPrintf(viewer," (%D, %g - %g i) ",bs*a->j[k]+l,
336: (double)PetscRealPart(a->a[bs2*k + l*bs + j]),-(double)PetscImaginaryPart(a->a[bs2*k + l*bs + j]));
337: } else if (PetscRealPart(a->a[bs2*k + l*bs + j]) != 0.0) {
338: PetscViewerASCIIPrintf(viewer," (%D, %g) ",bs*a->j[k]+l,(double)PetscRealPart(a->a[bs2*k + l*bs + j]));
339: }
340: #else
341: if (a->a[bs2*k + l*bs + j] != 0.0) {
342: PetscViewerASCIIPrintf(viewer," (%D, %g) ",bs*a->j[k]+l,(double)a->a[bs2*k + l*bs + j]);
343: }
344: #endif
345: }
346: }
347: PetscViewerASCIIPrintf(viewer,"\n");
348: }
349: }
350: PetscViewerASCIIUseTabs(viewer,PETSC_TRUE);
351: } else if (format == PETSC_VIEWER_ASCII_FACTOR_INFO) {
352: return(0);
353: } else {
354: PetscViewerASCIIUseTabs(viewer,PETSC_FALSE);
355: if (A->factortype) { /* for factored matrix */
356: if (bs>1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"matrix is factored with bs>1. Not implemented yet");
358: diag=a->diag;
359: for (i=0; i<a->mbs; i++) { /* for row block i */
360: PetscViewerASCIIPrintf(viewer,"row %D:",i);
361: /* diagonal entry */
362: #if defined(PETSC_USE_COMPLEX)
363: if (PetscImaginaryPart(a->a[diag[i]]) > 0.0) {
364: 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]]));
365: } else if (PetscImaginaryPart(a->a[diag[i]]) < 0.0) {
366: 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]]));
367: } else {
368: PetscViewerASCIIPrintf(viewer," (%D, %g) ",a->j[diag[i]],(double)PetscRealPart(1.0/a->a[diag[i]]));
369: }
370: #else
371: PetscViewerASCIIPrintf(viewer," (%D, %g) ",a->j[diag[i]],(double)(1.0/a->a[diag[i]]));
372: #endif
373: /* off-diagonal entries */
374: for (k=a->i[i]; k<a->i[i+1]-1; k++) {
375: #if defined(PETSC_USE_COMPLEX)
376: if (PetscImaginaryPart(a->a[k]) > 0.0) {
377: PetscViewerASCIIPrintf(viewer," (%D, %g + %g i) ",bs*a->j[k],(double)PetscRealPart(a->a[k]),(double)PetscImaginaryPart(a->a[k]));
378: } else if (PetscImaginaryPart(a->a[k]) < 0.0) {
379: PetscViewerASCIIPrintf(viewer," (%D, %g - %g i) ",bs*a->j[k],(double)PetscRealPart(a->a[k]),-(double)PetscImaginaryPart(a->a[k]));
380: } else {
381: PetscViewerASCIIPrintf(viewer," (%D, %g) ",bs*a->j[k],(double)PetscRealPart(a->a[k]));
382: }
383: #else
384: PetscViewerASCIIPrintf(viewer," (%D, %g) ",a->j[k],(double)a->a[k]);
385: #endif
386: }
387: PetscViewerASCIIPrintf(viewer,"\n");
388: }
390: } else { /* for non-factored matrix */
391: for (i=0; i<a->mbs; i++) { /* for row block i */
392: for (j=0; j<bs; j++) { /* for row bs*i + j */
393: PetscViewerASCIIPrintf(viewer,"row %D:",i*bs+j);
394: for (k=a->i[i]; k<a->i[i+1]; k++) { /* for column block */
395: for (l=0; l<bs; l++) { /* for column */
396: #if defined(PETSC_USE_COMPLEX)
397: if (PetscImaginaryPart(a->a[bs2*k + l*bs + j]) > 0.0) {
398: PetscViewerASCIIPrintf(viewer," (%D, %g + %g i) ",bs*a->j[k]+l,
399: (double)PetscRealPart(a->a[bs2*k + l*bs + j]),(double)PetscImaginaryPart(a->a[bs2*k + l*bs + j]));
400: } else if (PetscImaginaryPart(a->a[bs2*k + l*bs + j]) < 0.0) {
401: PetscViewerASCIIPrintf(viewer," (%D, %g - %g i) ",bs*a->j[k]+l,
402: (double)PetscRealPart(a->a[bs2*k + l*bs + j]),-(double)PetscImaginaryPart(a->a[bs2*k + l*bs + j]));
403: } else {
404: PetscViewerASCIIPrintf(viewer," (%D, %g) ",bs*a->j[k]+l,(double)PetscRealPart(a->a[bs2*k + l*bs + j]));
405: }
406: #else
407: PetscViewerASCIIPrintf(viewer," (%D, %g) ",bs*a->j[k]+l,(double)a->a[bs2*k + l*bs + j]);
408: #endif
409: }
410: }
411: PetscViewerASCIIPrintf(viewer,"\n");
412: }
413: }
414: }
415: PetscViewerASCIIUseTabs(viewer,PETSC_TRUE);
416: }
417: PetscViewerFlush(viewer);
418: return(0);
419: }
421: #include <petscdraw.h>
424: static PetscErrorCode MatView_SeqSBAIJ_Draw_Zoom(PetscDraw draw,void *Aa)
425: {
426: Mat A = (Mat) Aa;
427: Mat_SeqSBAIJ *a=(Mat_SeqSBAIJ*)A->data;
429: PetscInt row,i,j,k,l,mbs=a->mbs,color,bs=A->rmap->bs,bs2=a->bs2;
430: PetscMPIInt rank;
431: PetscReal xl,yl,xr,yr,x_l,x_r,y_l,y_r;
432: MatScalar *aa;
433: MPI_Comm comm;
434: PetscViewer viewer;
437: /*
438: This is nasty. If this is called from an originally parallel matrix
439: then all processes call this,but only the first has the matrix so the
440: rest should return immediately.
441: */
442: PetscObjectGetComm((PetscObject)draw,&comm);
443: MPI_Comm_rank(comm,&rank);
444: if (rank) return(0);
446: PetscObjectQuery((PetscObject)A,"Zoomviewer",(PetscObject*)&viewer);
448: PetscDrawGetCoordinates(draw,&xl,&yl,&xr,&yr);
449: PetscDrawString(draw, .3*(xl+xr), .3*(yl+yr), PETSC_DRAW_BLACK, "symmetric");
451: /* loop over matrix elements drawing boxes */
452: color = PETSC_DRAW_BLUE;
453: for (i=0,row=0; i<mbs; i++,row+=bs) {
454: for (j=a->i[i]; j<a->i[i+1]; j++) {
455: y_l = A->rmap->N - row - 1.0; y_r = y_l + 1.0;
456: x_l = a->j[j]*bs; x_r = x_l + 1.0;
457: aa = a->a + j*bs2;
458: for (k=0; k<bs; k++) {
459: for (l=0; l<bs; l++) {
460: if (PetscRealPart(*aa++) >= 0.) continue;
461: PetscDrawRectangle(draw,x_l+k,y_l-l,x_r+k,y_r-l,color,color,color,color);
462: }
463: }
464: }
465: }
466: color = PETSC_DRAW_CYAN;
467: for (i=0,row=0; i<mbs; i++,row+=bs) {
468: for (j=a->i[i]; j<a->i[i+1]; j++) {
469: y_l = A->rmap->N - row - 1.0; y_r = y_l + 1.0;
470: x_l = a->j[j]*bs; x_r = x_l + 1.0;
471: aa = a->a + j*bs2;
472: for (k=0; k<bs; k++) {
473: for (l=0; l<bs; l++) {
474: if (PetscRealPart(*aa++) != 0.) continue;
475: PetscDrawRectangle(draw,x_l+k,y_l-l,x_r+k,y_r-l,color,color,color,color);
476: }
477: }
478: }
479: }
481: color = PETSC_DRAW_RED;
482: for (i=0,row=0; i<mbs; i++,row+=bs) {
483: for (j=a->i[i]; j<a->i[i+1]; j++) {
484: y_l = A->rmap->N - row - 1.0; y_r = y_l + 1.0;
485: x_l = a->j[j]*bs; x_r = x_l + 1.0;
486: aa = a->a + j*bs2;
487: for (k=0; k<bs; k++) {
488: for (l=0; l<bs; l++) {
489: if (PetscRealPart(*aa++) <= 0.) continue;
490: PetscDrawRectangle(draw,x_l+k,y_l-l,x_r+k,y_r-l,color,color,color,color);
491: }
492: }
493: }
494: }
495: return(0);
496: }
500: static PetscErrorCode MatView_SeqSBAIJ_Draw(Mat A,PetscViewer viewer)
501: {
503: PetscReal xl,yl,xr,yr,w,h;
504: PetscDraw draw;
505: PetscBool isnull;
508: PetscViewerDrawGetDraw(viewer,0,&draw);
509: PetscDrawIsNull(draw,&isnull); if (isnull) return(0);
511: PetscObjectCompose((PetscObject)A,"Zoomviewer",(PetscObject)viewer);
512: xr = A->rmap->N; yr = A->rmap->N; h = yr/10.0; w = xr/10.0;
513: xr += w; yr += h; xl = -w; yl = -h;
514: PetscDrawSetCoordinates(draw,xl,yl,xr,yr);
515: PetscDrawZoom(draw,MatView_SeqSBAIJ_Draw_Zoom,A);
516: PetscObjectCompose((PetscObject)A,"Zoomviewer",NULL);
517: return(0);
518: }
522: PetscErrorCode MatView_SeqSBAIJ(Mat A,PetscViewer viewer)
523: {
525: PetscBool iascii,isdraw;
526: FILE *file = 0;
529: PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERASCII,&iascii);
530: PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERDRAW,&isdraw);
531: if (iascii) {
532: MatView_SeqSBAIJ_ASCII(A,viewer);
533: } else if (isdraw) {
534: MatView_SeqSBAIJ_Draw(A,viewer);
535: } else {
536: Mat B;
537: const char *matname;
538: MatConvert(A,MATSEQAIJ,MAT_INITIAL_MATRIX,&B);
539: PetscObjectGetName((PetscObject)A,&matname);
540: PetscObjectSetName((PetscObject)B,matname);
541: MatView(B,viewer);
542: MatDestroy(&B);
543: PetscViewerBinaryGetInfoPointer(viewer,&file);
544: if (file) {
545: fprintf(file,"-matload_block_size %d\n",(int)A->rmap->bs);
546: }
547: }
548: return(0);
549: }
554: PetscErrorCode MatGetValues_SeqSBAIJ(Mat A,PetscInt m,const PetscInt im[],PetscInt n,const PetscInt in[],PetscScalar v[])
555: {
556: Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data;
557: PetscInt *rp,k,low,high,t,row,nrow,i,col,l,*aj = a->j;
558: PetscInt *ai = a->i,*ailen = a->ilen;
559: PetscInt brow,bcol,ridx,cidx,bs=A->rmap->bs,bs2=a->bs2;
560: MatScalar *ap,*aa = a->a;
563: for (k=0; k<m; k++) { /* loop over rows */
564: row = im[k]; brow = row/bs;
565: if (row < 0) {v += n; continue;} /* SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Negative row: %D",row); */
566: 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);
567: rp = aj + ai[brow]; ap = aa + bs2*ai[brow];
568: nrow = ailen[brow];
569: for (l=0; l<n; l++) { /* loop over columns */
570: if (in[l] < 0) {v++; continue;} /* SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Negative column: %D",in[l]); */
571: 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);
572: col = in[l];
573: bcol = col/bs;
574: cidx = col%bs;
575: ridx = row%bs;
576: high = nrow;
577: low = 0; /* assume unsorted */
578: while (high-low > 5) {
579: t = (low+high)/2;
580: if (rp[t] > bcol) high = t;
581: else low = t;
582: }
583: for (i=low; i<high; i++) {
584: if (rp[i] > bcol) break;
585: if (rp[i] == bcol) {
586: *v++ = ap[bs2*i+bs*cidx+ridx];
587: goto finished;
588: }
589: }
590: *v++ = 0.0;
591: finished:;
592: }
593: }
594: return(0);
595: }
600: PetscErrorCode MatSetValuesBlocked_SeqSBAIJ(Mat A,PetscInt m,const PetscInt im[],PetscInt n,const PetscInt in[],const PetscScalar v[],InsertMode is)
601: {
602: Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data;
603: PetscErrorCode ierr;
604: PetscInt *rp,k,low,high,t,ii,jj,row,nrow,i,col,l,rmax,N,lastcol = -1;
605: PetscInt *imax =a->imax,*ai=a->i,*ailen=a->ilen;
606: PetscInt *aj =a->j,nonew=a->nonew,bs2=a->bs2,bs=A->rmap->bs,stepval;
607: PetscBool roworiented=a->roworiented;
608: const PetscScalar *value = v;
609: MatScalar *ap,*aa = a->a,*bap;
612: if (roworiented) stepval = (n-1)*bs;
613: else stepval = (m-1)*bs;
615: for (k=0; k<m; k++) { /* loop over added rows */
616: row = im[k];
617: if (row < 0) continue;
618: #if defined(PETSC_USE_DEBUG)
619: if (row >= a->mbs) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Row too large: row %D max %D",row,a->mbs-1);
620: #endif
621: rp = aj + ai[row];
622: ap = aa + bs2*ai[row];
623: rmax = imax[row];
624: nrow = ailen[row];
625: low = 0;
626: high = nrow;
627: for (l=0; l<n; l++) { /* loop over added columns */
628: if (in[l] < 0) continue;
629: col = in[l];
630: #if defined(PETSC_USE_DEBUG)
631: if (col >= a->nbs) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Column too large: col %D max %D",col,a->nbs-1);
632: #endif
633: if (col < row) {
634: if (a->ignore_ltriangular) continue; /* ignore lower triangular block */
635: 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)");
636: }
637: if (roworiented) value = v + k*(stepval+bs)*bs + l*bs;
638: else value = v + l*(stepval+bs)*bs + k*bs;
640: if (col <= lastcol) low = 0;
641: else high = nrow;
643: lastcol = col;
644: while (high-low > 7) {
645: t = (low+high)/2;
646: if (rp[t] > col) high = t;
647: else low = t;
648: }
649: for (i=low; i<high; i++) {
650: if (rp[i] > col) break;
651: if (rp[i] == col) {
652: bap = ap + bs2*i;
653: if (roworiented) {
654: if (is == ADD_VALUES) {
655: for (ii=0; ii<bs; ii++,value+=stepval) {
656: for (jj=ii; jj<bs2; jj+=bs) {
657: bap[jj] += *value++;
658: }
659: }
660: } else {
661: for (ii=0; ii<bs; ii++,value+=stepval) {
662: for (jj=ii; jj<bs2; jj+=bs) {
663: bap[jj] = *value++;
664: }
665: }
666: }
667: } else {
668: if (is == ADD_VALUES) {
669: for (ii=0; ii<bs; ii++,value+=stepval) {
670: for (jj=0; jj<bs; jj++) {
671: *bap++ += *value++;
672: }
673: }
674: } else {
675: for (ii=0; ii<bs; ii++,value+=stepval) {
676: for (jj=0; jj<bs; jj++) {
677: *bap++ = *value++;
678: }
679: }
680: }
681: }
682: goto noinsert2;
683: }
684: }
685: if (nonew == 1) goto noinsert2;
686: if (nonew == -1) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Inserting a new nonzero (%D, %D) in the matrix", row, col);
687: MatSeqXAIJReallocateAIJ(A,a->mbs,bs2,nrow,row,col,rmax,aa,ai,aj,rp,ap,imax,nonew,MatScalar);
688: N = nrow++ - 1; high++;
689: /* shift up all the later entries in this row */
690: for (ii=N; ii>=i; ii--) {
691: rp[ii+1] = rp[ii];
692: PetscMemcpy(ap+bs2*(ii+1),ap+bs2*(ii),bs2*sizeof(MatScalar));
693: }
694: if (N >= i) {
695: PetscMemzero(ap+bs2*i,bs2*sizeof(MatScalar));
696: }
697: rp[i] = col;
698: bap = ap + bs2*i;
699: if (roworiented) {
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=0; jj<bs; jj++) {
708: *bap++ = *value++;
709: }
710: }
711: }
712: noinsert2:;
713: low = i;
714: }
715: ailen[row] = nrow;
716: }
717: return(0);
718: }
720: /*
721: This is not yet used
722: */
725: PetscErrorCode MatAssemblyEnd_SeqSBAIJ_SeqAIJ_Inode(Mat A)
726: {
727: Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data;
729: const PetscInt *ai = a->i, *aj = a->j,*cols;
730: PetscInt i = 0,j,blk_size,m = A->rmap->n,node_count = 0,nzx,nzy,*ns,row,nz,cnt,cnt2,*counts;
731: PetscBool flag;
734: PetscMalloc1(m,&ns);
735: while (i < m) {
736: nzx = ai[i+1] - ai[i]; /* Number of nonzeros */
737: /* Limits the number of elements in a node to 'a->inode.limit' */
738: for (j=i+1,blk_size=1; j<m && blk_size <a->inode.limit; ++j,++blk_size) {
739: nzy = ai[j+1] - ai[j];
740: if (nzy != (nzx - j + i)) break;
741: PetscMemcmp(aj + ai[i] + j - i,aj + ai[j],nzy*sizeof(PetscInt),&flag);
742: if (!flag) break;
743: }
744: ns[node_count++] = blk_size;
746: i = j;
747: }
748: if (!a->inode.size && m && node_count > .9*m) {
749: PetscFree(ns);
750: PetscInfo2(A,"Found %D nodes out of %D rows. Not using Inode routines\n",node_count,m);
751: } else {
752: a->inode.node_count = node_count;
754: PetscMalloc1(node_count,&a->inode.size);
755: PetscLogObjectMemory((PetscObject)A,node_count*sizeof(PetscInt));
756: PetscMemcpy(a->inode.size,ns,node_count*sizeof(PetscInt));
757: PetscFree(ns);
758: PetscInfo3(A,"Found %D nodes of %D. Limit used: %D. Using Inode routines\n",node_count,m,a->inode.limit);
760: /* count collections of adjacent columns in each inode */
761: row = 0;
762: cnt = 0;
763: for (i=0; i<node_count; i++) {
764: cols = aj + ai[row] + a->inode.size[i];
765: nz = ai[row+1] - ai[row] - a->inode.size[i];
766: for (j=1; j<nz; j++) {
767: if (cols[j] != cols[j-1]+1) cnt++;
768: }
769: cnt++;
770: row += a->inode.size[i];
771: }
772: PetscMalloc1(2*cnt,&counts);
773: cnt = 0;
774: row = 0;
775: for (i=0; i<node_count; i++) {
776: cols = aj + ai[row] + a->inode.size[i];
777: counts[2*cnt] = cols[0];
778: nz = ai[row+1] - ai[row] - a->inode.size[i];
779: cnt2 = 1;
780: for (j=1; j<nz; j++) {
781: if (cols[j] != cols[j-1]+1) {
782: counts[2*(cnt++)+1] = cnt2;
783: counts[2*cnt] = cols[j];
784: cnt2 = 1;
785: } else cnt2++;
786: }
787: counts[2*(cnt++)+1] = cnt2;
788: row += a->inode.size[i];
789: }
790: PetscIntView(2*cnt,counts,0);
791: }
792: return(0);
793: }
797: PetscErrorCode MatAssemblyEnd_SeqSBAIJ(Mat A,MatAssemblyType mode)
798: {
799: Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data;
801: PetscInt fshift = 0,i,j,*ai = a->i,*aj = a->j,*imax = a->imax;
802: PetscInt m = A->rmap->N,*ip,N,*ailen = a->ilen;
803: PetscInt mbs = a->mbs,bs2 = a->bs2,rmax = 0;
804: MatScalar *aa = a->a,*ap;
807: if (mode == MAT_FLUSH_ASSEMBLY) return(0);
809: if (m) rmax = ailen[0];
810: for (i=1; i<mbs; i++) {
811: /* move each row back by the amount of empty slots (fshift) before it*/
812: fshift += imax[i-1] - ailen[i-1];
813: rmax = PetscMax(rmax,ailen[i]);
814: if (fshift) {
815: ip = aj + ai[i]; ap = aa + bs2*ai[i];
816: N = ailen[i];
817: for (j=0; j<N; j++) {
818: ip[j-fshift] = ip[j];
819: PetscMemcpy(ap+(j-fshift)*bs2,ap+j*bs2,bs2*sizeof(MatScalar));
820: }
821: }
822: ai[i] = ai[i-1] + ailen[i-1];
823: }
824: if (mbs) {
825: fshift += imax[mbs-1] - ailen[mbs-1];
826: ai[mbs] = ai[mbs-1] + ailen[mbs-1];
827: }
828: /* reset ilen and imax for each row */
829: for (i=0; i<mbs; i++) {
830: ailen[i] = imax[i] = ai[i+1] - ai[i];
831: }
832: a->nz = ai[mbs];
834: /* diagonals may have moved, reset it */
835: if (a->diag) {
836: PetscMemcpy(a->diag,ai,mbs*sizeof(PetscInt));
837: }
838: 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);
840: 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);
841: PetscInfo1(A,"Number of mallocs during MatSetValues is %D\n",a->reallocs);
842: PetscInfo1(A,"Most nonzeros blocks in any row is %D\n",rmax);
844: A->info.mallocs += a->reallocs;
845: a->reallocs = 0;
846: A->info.nz_unneeded = (PetscReal)fshift*bs2;
847: a->idiagvalid = PETSC_FALSE;
849: if (A->cmap->n < 65536 && A->cmap->bs == 1) {
850: if (a->jshort && a->free_jshort) {
851: /* when matrix data structure is changed, previous jshort must be replaced */
852: PetscFree(a->jshort);
853: }
854: PetscMalloc1(a->i[A->rmap->n],&a->jshort);
855: PetscLogObjectMemory((PetscObject)A,a->i[A->rmap->n]*sizeof(unsigned short));
856: for (i=0; i<a->i[A->rmap->n]; i++) a->jshort[i] = a->j[i];
857: A->ops->mult = MatMult_SeqSBAIJ_1_ushort;
858: A->ops->sor = MatSOR_SeqSBAIJ_ushort;
859: a->free_jshort = PETSC_TRUE;
860: }
861: return(0);
862: }
864: /*
865: This function returns an array of flags which indicate the locations of contiguous
866: blocks that should be zeroed. for eg: if bs = 3 and is = [0,1,2,3,5,6,7,8,9]
867: then the resulting sizes = [3,1,1,3,1] correspondig to sets [(0,1,2),(3),(5),(6,7,8),(9)]
868: Assume: sizes should be long enough to hold all the values.
869: */
872: PetscErrorCode MatZeroRows_SeqSBAIJ_Check_Blocks(PetscInt idx[],PetscInt n,PetscInt bs,PetscInt sizes[], PetscInt *bs_max)
873: {
874: PetscInt i,j,k,row;
875: PetscBool flg;
878: for (i=0,j=0; i<n; j++) {
879: row = idx[i];
880: if (row%bs!=0) { /* Not the begining of a block */
881: sizes[j] = 1;
882: i++;
883: } else if (i+bs > n) { /* Beginning of a block, but complete block doesn't exist (at idx end) */
884: sizes[j] = 1; /* Also makes sure atleast 'bs' values exist for next else */
885: i++;
886: } else { /* Begining of the block, so check if the complete block exists */
887: flg = PETSC_TRUE;
888: for (k=1; k<bs; k++) {
889: if (row+k != idx[i+k]) { /* break in the block */
890: flg = PETSC_FALSE;
891: break;
892: }
893: }
894: if (flg) { /* No break in the bs */
895: sizes[j] = bs;
896: i += bs;
897: } else {
898: sizes[j] = 1;
899: i++;
900: }
901: }
902: }
903: *bs_max = j;
904: return(0);
905: }
908: /* Only add/insert a(i,j) with i<=j (blocks).
909: Any a(i,j) with i>j input by user is ingored.
910: */
914: PetscErrorCode MatSetValues_SeqSBAIJ(Mat A,PetscInt m,const PetscInt im[],PetscInt n,const PetscInt in[],const PetscScalar v[],InsertMode is)
915: {
916: Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data;
918: PetscInt *rp,k,low,high,t,ii,row,nrow,i,col,l,rmax,N,lastcol = -1;
919: PetscInt *imax=a->imax,*ai=a->i,*ailen=a->ilen,roworiented=a->roworiented;
920: PetscInt *aj =a->j,nonew=a->nonew,bs=A->rmap->bs,brow,bcol;
921: PetscInt ridx,cidx,bs2=a->bs2;
922: MatScalar *ap,value,*aa=a->a,*bap;
925: for (k=0; k<m; k++) { /* loop over added rows */
926: row = im[k]; /* row number */
927: brow = row/bs; /* block row number */
928: if (row < 0) continue;
929: #if defined(PETSC_USE_DEBUG)
930: 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);
931: #endif
932: rp = aj + ai[brow]; /*ptr to beginning of column value of the row block*/
933: ap = aa + bs2*ai[brow]; /*ptr to beginning of element value of the row block*/
934: rmax = imax[brow]; /* maximum space allocated for this row */
935: nrow = ailen[brow]; /* actual length of this row */
936: low = 0;
938: for (l=0; l<n; l++) { /* loop over added columns */
939: if (in[l] < 0) continue;
940: #if defined(PETSC_USE_DEBUG)
941: 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);
942: #endif
943: col = in[l];
944: bcol = col/bs; /* block col number */
946: if (brow > bcol) {
947: if (a->ignore_ltriangular) continue; /* ignore lower triangular values */
948: 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)");
949: }
951: ridx = row % bs; cidx = col % bs; /*row and col index inside the block */
952: if ((brow==bcol && ridx<=cidx) || (brow<bcol)) {
953: /* element value a(k,l) */
954: if (roworiented) value = v[l + k*n];
955: else value = v[k + l*m];
957: /* move pointer bap to a(k,l) quickly and add/insert value */
958: if (col <= lastcol) low = 0;
959: high = nrow;
960: lastcol = col;
961: while (high-low > 7) {
962: t = (low+high)/2;
963: if (rp[t] > bcol) high = t;
964: else low = t;
965: }
966: for (i=low; i<high; i++) {
967: if (rp[i] > bcol) break;
968: if (rp[i] == bcol) {
969: bap = ap + bs2*i + bs*cidx + ridx;
970: if (is == ADD_VALUES) *bap += value;
971: else *bap = value;
972: /* for diag block, add/insert its symmetric element a(cidx,ridx) */
973: if (brow == bcol && ridx < cidx) {
974: bap = ap + bs2*i + bs*ridx + cidx;
975: if (is == ADD_VALUES) *bap += value;
976: else *bap = value;
977: }
978: goto noinsert1;
979: }
980: }
982: if (nonew == 1) goto noinsert1;
983: if (nonew == -1) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Inserting a new nonzero (%D, %D) in the matrix", row, col);
984: MatSeqXAIJReallocateAIJ(A,a->mbs,bs2,nrow,brow,bcol,rmax,aa,ai,aj,rp,ap,imax,nonew,MatScalar);
986: N = nrow++ - 1; high++;
987: /* shift up all the later entries in this row */
988: for (ii=N; ii>=i; ii--) {
989: rp[ii+1] = rp[ii];
990: PetscMemcpy(ap+bs2*(ii+1),ap+bs2*(ii),bs2*sizeof(MatScalar));
991: }
992: if (N>=i) {
993: PetscMemzero(ap+bs2*i,bs2*sizeof(MatScalar));
994: }
995: rp[i] = bcol;
996: ap[bs2*i + bs*cidx + ridx] = value;
997: A->nonzerostate++;
998: noinsert1:;
999: low = i;
1000: }
1001: } /* end of loop over added columns */
1002: ailen[brow] = nrow;
1003: } /* end of loop over added rows */
1004: return(0);
1005: }
1009: PetscErrorCode MatICCFactor_SeqSBAIJ(Mat inA,IS row,const MatFactorInfo *info)
1010: {
1011: Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)inA->data;
1012: Mat outA;
1014: PetscBool row_identity;
1017: if (info->levels != 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Only levels=0 is supported for in-place icc");
1018: ISIdentity(row,&row_identity);
1019: if (!row_identity) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Matrix reordering is not supported");
1020: 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()! */
1022: outA = inA;
1023: inA->factortype = MAT_FACTOR_ICC;
1025: MatMarkDiagonal_SeqSBAIJ(inA);
1026: MatSeqSBAIJSetNumericFactorization_inplace(inA,row_identity);
1028: PetscObjectReference((PetscObject)row);
1029: ISDestroy(&a->row);
1030: a->row = row;
1031: PetscObjectReference((PetscObject)row);
1032: ISDestroy(&a->col);
1033: a->col = row;
1035: /* Create the invert permutation so that it can be used in MatCholeskyFactorNumeric() */
1036: if (a->icol) {ISInvertPermutation(row,PETSC_DECIDE, &a->icol);}
1037: PetscLogObjectParent((PetscObject)inA,(PetscObject)a->icol);
1039: if (!a->solve_work) {
1040: PetscMalloc1((inA->rmap->N+inA->rmap->bs),&a->solve_work);
1041: PetscLogObjectMemory((PetscObject)inA,(inA->rmap->N+inA->rmap->bs)*sizeof(PetscScalar));
1042: }
1044: MatCholeskyFactorNumeric(outA,inA,info);
1045: return(0);
1046: }
1050: PetscErrorCode MatSeqSBAIJSetColumnIndices_SeqSBAIJ(Mat mat,PetscInt *indices)
1051: {
1052: Mat_SeqSBAIJ *baij = (Mat_SeqSBAIJ*)mat->data;
1053: PetscInt i,nz,n;
1057: nz = baij->maxnz;
1058: n = mat->cmap->n;
1059: for (i=0; i<nz; i++) baij->j[i] = indices[i];
1061: baij->nz = nz;
1062: for (i=0; i<n; i++) baij->ilen[i] = baij->imax[i];
1064: MatSetOption(mat,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);
1065: return(0);
1066: }
1070: /*@
1071: MatSeqSBAIJSetColumnIndices - Set the column indices for all the rows
1072: in the matrix.
1074: Input Parameters:
1075: + mat - the SeqSBAIJ matrix
1076: - indices - the column indices
1078: Level: advanced
1080: Notes:
1081: This can be called if you have precomputed the nonzero structure of the
1082: matrix and want to provide it to the matrix object to improve the performance
1083: of the MatSetValues() operation.
1085: You MUST have set the correct numbers of nonzeros per row in the call to
1086: MatCreateSeqSBAIJ(), and the columns indices MUST be sorted.
1088: MUST be called before any calls to MatSetValues()
1090: .seealso: MatCreateSeqSBAIJ
1091: @*/
1092: PetscErrorCode MatSeqSBAIJSetColumnIndices(Mat mat,PetscInt *indices)
1093: {
1099: PetscUseMethod(mat,"MatSeqSBAIJSetColumnIndices_C",(Mat,PetscInt*),(mat,indices));
1100: return(0);
1101: }
1105: PetscErrorCode MatCopy_SeqSBAIJ(Mat A,Mat B,MatStructure str)
1106: {
1110: /* If the two matrices have the same copy implementation, use fast copy. */
1111: if (str == SAME_NONZERO_PATTERN && (A->ops->copy == B->ops->copy)) {
1112: Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data;
1113: Mat_SeqSBAIJ *b = (Mat_SeqSBAIJ*)B->data;
1115: 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");
1116: PetscMemcpy(b->a,a->a,(a->i[A->rmap->N])*sizeof(PetscScalar));
1117: } else {
1118: MatGetRowUpperTriangular(A);
1119: MatCopy_Basic(A,B,str);
1120: MatRestoreRowUpperTriangular(A);
1121: }
1122: return(0);
1123: }
1127: PetscErrorCode MatSetUp_SeqSBAIJ(Mat A)
1128: {
1132: MatSeqSBAIJSetPreallocation_SeqSBAIJ(A,A->rmap->bs,PETSC_DEFAULT,0);
1133: return(0);
1134: }
1138: PetscErrorCode MatSeqSBAIJGetArray_SeqSBAIJ(Mat A,PetscScalar *array[])
1139: {
1140: Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data;
1143: *array = a->a;
1144: return(0);
1145: }
1149: PetscErrorCode MatSeqSBAIJRestoreArray_SeqSBAIJ(Mat A,PetscScalar *array[])
1150: {
1152: return(0);
1153: }
1157: PetscErrorCode MatAXPYGetPreallocation_SeqSBAIJ(Mat Y,Mat X,PetscInt *nnz)
1158: {
1159: PetscInt bs = Y->rmap->bs,mbs = Y->rmap->N/bs;
1160: Mat_SeqSBAIJ *x = (Mat_SeqSBAIJ*)X->data;
1161: Mat_SeqSBAIJ *y = (Mat_SeqSBAIJ*)Y->data;
1165: /* Set the number of nonzeros in the new matrix */
1166: MatAXPYGetPreallocation_SeqX_private(mbs,x->i,x->j,y->i,y->j,nnz);
1167: return(0);
1168: }
1172: PetscErrorCode MatAXPY_SeqSBAIJ(Mat Y,PetscScalar a,Mat X,MatStructure str)
1173: {
1174: Mat_SeqSBAIJ *x=(Mat_SeqSBAIJ*)X->data, *y=(Mat_SeqSBAIJ*)Y->data;
1176: PetscInt bs=Y->rmap->bs,bs2=bs*bs;
1177: PetscBLASInt one = 1;
1180: if (str == SAME_NONZERO_PATTERN) {
1181: PetscScalar alpha = a;
1182: PetscBLASInt bnz;
1183: PetscBLASIntCast(x->nz*bs2,&bnz);
1184: PetscStackCallBLAS("BLASaxpy",BLASaxpy_(&bnz,&alpha,x->a,&one,y->a,&one));
1185: PetscObjectStateIncrease((PetscObject)Y);
1186: } else if (str == SUBSET_NONZERO_PATTERN) { /* nonzeros of X is a subset of Y's */
1187: MatSetOption(X,MAT_GETROW_UPPERTRIANGULAR,PETSC_TRUE);
1188: MatAXPY_Basic(Y,a,X,str);
1189: MatSetOption(X,MAT_GETROW_UPPERTRIANGULAR,PETSC_FALSE);
1190: } else {
1191: Mat B;
1192: PetscInt *nnz;
1193: if (bs != X->rmap->bs) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Matrices must have same block size");
1194: MatGetRowUpperTriangular(X);
1195: MatGetRowUpperTriangular(Y);
1196: PetscMalloc1(Y->rmap->N,&nnz);
1197: MatCreate(PetscObjectComm((PetscObject)Y),&B);
1198: PetscObjectSetName((PetscObject)B,((PetscObject)Y)->name);
1199: MatSetSizes(B,Y->rmap->n,Y->cmap->n,Y->rmap->N,Y->cmap->N);
1200: MatSetBlockSizesFromMats(B,Y,Y);
1201: MatSetType(B,(MatType) ((PetscObject)Y)->type_name);
1202: MatAXPYGetPreallocation_SeqSBAIJ(Y,X,nnz);
1203: MatSeqSBAIJSetPreallocation(B,bs,0,nnz);
1204:
1205: MatAXPY_BasicWithPreallocation(B,Y,a,X,str);
1206:
1207: MatHeaderReplace(Y,B);
1208: PetscFree(nnz);
1209: MatRestoreRowUpperTriangular(X);
1210: MatRestoreRowUpperTriangular(Y);
1211: }
1212: return(0);
1213: }
1217: PetscErrorCode MatIsSymmetric_SeqSBAIJ(Mat A,PetscReal tol,PetscBool *flg)
1218: {
1220: *flg = PETSC_TRUE;
1221: return(0);
1222: }
1226: PetscErrorCode MatIsStructurallySymmetric_SeqSBAIJ(Mat A,PetscBool *flg)
1227: {
1229: *flg = PETSC_TRUE;
1230: return(0);
1231: }
1235: PetscErrorCode MatIsHermitian_SeqSBAIJ(Mat A,PetscReal tol,PetscBool *flg)
1236: {
1238: *flg = PETSC_FALSE;
1239: return(0);
1240: }
1244: PetscErrorCode MatRealPart_SeqSBAIJ(Mat A)
1245: {
1246: Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data;
1247: PetscInt i,nz = a->bs2*a->i[a->mbs];
1248: MatScalar *aa = a->a;
1251: for (i=0; i<nz; i++) aa[i] = PetscRealPart(aa[i]);
1252: return(0);
1253: }
1257: PetscErrorCode MatImaginaryPart_SeqSBAIJ(Mat A)
1258: {
1259: Mat_SeqSBAIJ *a = (Mat_SeqSBAIJ*)A->data;
1260: PetscInt i,nz = a->bs2*a->i[a->mbs];
1261: MatScalar *aa = a->a;
1264: for (i=0; i<nz; i++) aa[i] = PetscImaginaryPart(aa[i]);
1265: return(0);
1266: }
1270: PetscErrorCode MatZeroRowsColumns_SeqSBAIJ(Mat A,PetscInt is_n,const PetscInt is_idx[],PetscScalar diag,Vec x, Vec b)
1271: {
1272: Mat_SeqSBAIJ *baij=(Mat_SeqSBAIJ*)A->data;
1273: PetscErrorCode ierr;
1274: PetscInt i,j,k,count;
1275: PetscInt bs =A->rmap->bs,bs2=baij->bs2,row,col;
1276: PetscScalar zero = 0.0;
1277: MatScalar *aa;
1278: const PetscScalar *xx;
1279: PetscScalar *bb;
1280: PetscBool *zeroed,vecs = PETSC_FALSE;
1283: /* fix right hand side if needed */
1284: if (x && b) {
1285: VecGetArrayRead(x,&xx);
1286: VecGetArray(b,&bb);
1287: vecs = PETSC_TRUE;
1288: }
1290: /* zero the columns */
1291: PetscCalloc1(A->rmap->n,&zeroed);
1292: for (i=0; i<is_n; i++) {
1293: 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]);
1294: zeroed[is_idx[i]] = PETSC_TRUE;
1295: }
1296: if (vecs) {
1297: for (i=0; i<A->rmap->N; i++) {
1298: row = i/bs;
1299: for (j=baij->i[row]; j<baij->i[row+1]; j++) {
1300: for (k=0; k<bs; k++) {
1301: col = bs*baij->j[j] + k;
1302: if (col <= i) continue;
1303: aa = ((MatScalar*)(baij->a)) + j*bs2 + (i%bs) + bs*k;
1304: if (!zeroed[i] && zeroed[col]) bb[i] -= aa[0]*xx[col];
1305: if (zeroed[i] && !zeroed[col]) bb[col] -= aa[0]*xx[i];
1306: }
1307: }
1308: }
1309: for (i=0; i<is_n; i++) bb[is_idx[i]] = diag*xx[is_idx[i]];
1310: }
1312: for (i=0; i<A->rmap->N; i++) {
1313: if (!zeroed[i]) {
1314: row = i/bs;
1315: for (j=baij->i[row]; j<baij->i[row+1]; j++) {
1316: for (k=0; k<bs; k++) {
1317: col = bs*baij->j[j] + k;
1318: if (zeroed[col]) {
1319: aa = ((MatScalar*)(baij->a)) + j*bs2 + (i%bs) + bs*k;
1320: aa[0] = 0.0;
1321: }
1322: }
1323: }
1324: }
1325: }
1326: PetscFree(zeroed);
1327: if (vecs) {
1328: VecRestoreArrayRead(x,&xx);
1329: VecRestoreArray(b,&bb);
1330: }
1332: /* zero the rows */
1333: for (i=0; i<is_n; i++) {
1334: row = is_idx[i];
1335: count = (baij->i[row/bs +1] - baij->i[row/bs])*bs;
1336: aa = ((MatScalar*)(baij->a)) + baij->i[row/bs]*bs2 + (row%bs);
1337: for (k=0; k<count; k++) {
1338: aa[0] = zero;
1339: aa += bs;
1340: }
1341: if (diag != 0.0) {
1342: (*A->ops->setvalues)(A,1,&row,1,&row,&diag,INSERT_VALUES);
1343: }
1344: }
1345: MatAssemblyEnd_SeqSBAIJ(A,MAT_FINAL_ASSEMBLY);
1346: return(0);
1347: }
1349: /* -------------------------------------------------------------------*/
1350: static struct _MatOps MatOps_Values = {MatSetValues_SeqSBAIJ,
1351: MatGetRow_SeqSBAIJ,
1352: MatRestoreRow_SeqSBAIJ,
1353: MatMult_SeqSBAIJ_N,
1354: /* 4*/ MatMultAdd_SeqSBAIJ_N,
1355: MatMult_SeqSBAIJ_N, /* transpose versions are same as non-transpose versions */
1356: MatMultAdd_SeqSBAIJ_N,
1357: 0,
1358: 0,
1359: 0,
1360: /* 10*/ 0,
1361: 0,
1362: MatCholeskyFactor_SeqSBAIJ,
1363: MatSOR_SeqSBAIJ,
1364: MatTranspose_SeqSBAIJ,
1365: /* 15*/ MatGetInfo_SeqSBAIJ,
1366: MatEqual_SeqSBAIJ,
1367: MatGetDiagonal_SeqSBAIJ,
1368: MatDiagonalScale_SeqSBAIJ,
1369: MatNorm_SeqSBAIJ,
1370: /* 20*/ 0,
1371: MatAssemblyEnd_SeqSBAIJ,
1372: MatSetOption_SeqSBAIJ,
1373: MatZeroEntries_SeqSBAIJ,
1374: /* 24*/ 0,
1375: 0,
1376: 0,
1377: 0,
1378: 0,
1379: /* 29*/ MatSetUp_SeqSBAIJ,
1380: 0,
1381: 0,
1382: 0,
1383: 0,
1384: /* 34*/ MatDuplicate_SeqSBAIJ,
1385: 0,
1386: 0,
1387: 0,
1388: MatICCFactor_SeqSBAIJ,
1389: /* 39*/ MatAXPY_SeqSBAIJ,
1390: MatGetSubMatrices_SeqSBAIJ,
1391: MatIncreaseOverlap_SeqSBAIJ,
1392: MatGetValues_SeqSBAIJ,
1393: MatCopy_SeqSBAIJ,
1394: /* 44*/ 0,
1395: MatScale_SeqSBAIJ,
1396: 0,
1397: 0,
1398: MatZeroRowsColumns_SeqSBAIJ,
1399: /* 49*/ 0,
1400: MatGetRowIJ_SeqSBAIJ,
1401: MatRestoreRowIJ_SeqSBAIJ,
1402: 0,
1403: 0,
1404: /* 54*/ 0,
1405: 0,
1406: 0,
1407: 0,
1408: MatSetValuesBlocked_SeqSBAIJ,
1409: /* 59*/ MatGetSubMatrix_SeqSBAIJ,
1410: 0,
1411: 0,
1412: 0,
1413: 0,
1414: /* 64*/ 0,
1415: 0,
1416: 0,
1417: 0,
1418: 0,
1419: /* 69*/ MatGetRowMaxAbs_SeqSBAIJ,
1420: 0,
1421: 0,
1422: 0,
1423: 0,
1424: /* 74*/ 0,
1425: 0,
1426: 0,
1427: 0,
1428: 0,
1429: /* 79*/ 0,
1430: 0,
1431: 0,
1432: MatGetInertia_SeqSBAIJ,
1433: MatLoad_SeqSBAIJ,
1434: /* 84*/ MatIsSymmetric_SeqSBAIJ,
1435: MatIsHermitian_SeqSBAIJ,
1436: MatIsStructurallySymmetric_SeqSBAIJ,
1437: 0,
1438: 0,
1439: /* 89*/ 0,
1440: 0,
1441: 0,
1442: 0,
1443: 0,
1444: /* 94*/ 0,
1445: 0,
1446: 0,
1447: 0,
1448: 0,
1449: /* 99*/ 0,
1450: 0,
1451: 0,
1452: 0,
1453: 0,
1454: /*104*/ 0,
1455: MatRealPart_SeqSBAIJ,
1456: MatImaginaryPart_SeqSBAIJ,
1457: MatGetRowUpperTriangular_SeqSBAIJ,
1458: MatRestoreRowUpperTriangular_SeqSBAIJ,
1459: /*109*/ 0,
1460: 0,
1461: 0,
1462: 0,
1463: MatMissingDiagonal_SeqSBAIJ,
1464: /*114*/ 0,
1465: 0,
1466: 0,
1467: 0,
1468: 0,
1469: /*119*/ 0,
1470: 0,
1471: 0,
1472: 0,
1473: 0,
1474: /*124*/ 0,
1475: 0,
1476: 0,
1477: 0,
1478: 0,
1479: /*129*/ 0,
1480: 0,
1481: 0,
1482: 0,
1483: 0,
1484: /*134*/ 0,
1485: 0,
1486: 0,
1487: 0,
1488: 0,
1489: /*139*/ 0,
1490: 0,
1491: 0
1492: };
1496: PetscErrorCode MatStoreValues_SeqSBAIJ(Mat mat)
1497: {
1498: Mat_SeqSBAIJ *aij = (Mat_SeqSBAIJ*)mat->data;
1499: PetscInt nz = aij->i[mat->rmap->N]*mat->rmap->bs*aij->bs2;
1503: if (aij->nonew != 1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ORDER,"Must call MatSetOption(A,MAT_NEW_NONZERO_LOCATIONS,PETSC_FALSE);first");
1505: /* allocate space for values if not already there */
1506: if (!aij->saved_values) {
1507: PetscMalloc1((nz+1),&aij->saved_values);
1508: }
1510: /* copy values over */
1511: PetscMemcpy(aij->saved_values,aij->a,nz*sizeof(PetscScalar));
1512: return(0);
1513: }
1517: PetscErrorCode MatRetrieveValues_SeqSBAIJ(Mat mat)
1518: {
1519: Mat_SeqSBAIJ *aij = (Mat_SeqSBAIJ*)mat->data;
1521: PetscInt nz = aij->i[mat->rmap->N]*mat->rmap->bs*aij->bs2;
1524: if (aij->nonew != 1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ORDER,"Must call MatSetOption(A,MAT_NEW_NONZERO_LOCATIONS,PETSC_FALSE);first");
1525: if (!aij->saved_values) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ORDER,"Must call MatStoreValues(A);first");
1527: /* copy values over */
1528: PetscMemcpy(aij->a,aij->saved_values,nz*sizeof(PetscScalar));
1529: return(0);
1530: }
1534: PetscErrorCode MatSeqSBAIJSetPreallocation_SeqSBAIJ(Mat B,PetscInt bs,PetscInt nz,PetscInt *nnz)
1535: {
1536: Mat_SeqSBAIJ *b = (Mat_SeqSBAIJ*)B->data;
1538: PetscInt i,mbs,bs2;
1539: PetscBool skipallocation = PETSC_FALSE,flg = PETSC_FALSE,realalloc = PETSC_FALSE;
1542: if (nz >= 0 || nnz) realalloc = PETSC_TRUE;
1543: B->preallocated = PETSC_TRUE;
1545: MatSetBlockSize(B,PetscAbs(bs));
1546: PetscLayoutSetUp(B->rmap);
1547: PetscLayoutSetUp(B->cmap);
1548: PetscLayoutGetBlockSize(B->rmap,&bs);
1550: mbs = B->rmap->N/bs;
1551: bs2 = bs*bs;
1553: if (mbs*bs != B->rmap->N) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Number rows, cols must be divisible by blocksize");
1555: if (nz == MAT_SKIP_ALLOCATION) {
1556: skipallocation = PETSC_TRUE;
1557: nz = 0;
1558: }
1560: if (nz == PETSC_DEFAULT || nz == PETSC_DECIDE) nz = 3;
1561: if (nz < 0) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"nz cannot be less than 0: value %D",nz);
1562: if (nnz) {
1563: for (i=0; i<mbs; i++) {
1564: 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]);
1565: 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);
1566: }
1567: }
1569: B->ops->mult = MatMult_SeqSBAIJ_N;
1570: B->ops->multadd = MatMultAdd_SeqSBAIJ_N;
1571: B->ops->multtranspose = MatMult_SeqSBAIJ_N;
1572: B->ops->multtransposeadd = MatMultAdd_SeqSBAIJ_N;
1574: PetscOptionsGetBool(((PetscObject)B)->prefix,"-mat_no_unroll",&flg,NULL);
1575: if (!flg) {
1576: switch (bs) {
1577: case 1:
1578: B->ops->mult = MatMult_SeqSBAIJ_1;
1579: B->ops->multadd = MatMultAdd_SeqSBAIJ_1;
1580: B->ops->multtranspose = MatMult_SeqSBAIJ_1;
1581: B->ops->multtransposeadd = MatMultAdd_SeqSBAIJ_1;
1582: break;
1583: case 2:
1584: B->ops->mult = MatMult_SeqSBAIJ_2;
1585: B->ops->multadd = MatMultAdd_SeqSBAIJ_2;
1586: B->ops->multtranspose = MatMult_SeqSBAIJ_2;
1587: B->ops->multtransposeadd = MatMultAdd_SeqSBAIJ_2;
1588: break;
1589: case 3:
1590: B->ops->mult = MatMult_SeqSBAIJ_3;
1591: B->ops->multadd = MatMultAdd_SeqSBAIJ_3;
1592: B->ops->multtranspose = MatMult_SeqSBAIJ_3;
1593: B->ops->multtransposeadd = MatMultAdd_SeqSBAIJ_3;
1594: break;
1595: case 4:
1596: B->ops->mult = MatMult_SeqSBAIJ_4;
1597: B->ops->multadd = MatMultAdd_SeqSBAIJ_4;
1598: B->ops->multtranspose = MatMult_SeqSBAIJ_4;
1599: B->ops->multtransposeadd = MatMultAdd_SeqSBAIJ_4;
1600: break;
1601: case 5:
1602: B->ops->mult = MatMult_SeqSBAIJ_5;
1603: B->ops->multadd = MatMultAdd_SeqSBAIJ_5;
1604: B->ops->multtranspose = MatMult_SeqSBAIJ_5;
1605: B->ops->multtransposeadd = MatMultAdd_SeqSBAIJ_5;
1606: break;
1607: case 6:
1608: B->ops->mult = MatMult_SeqSBAIJ_6;
1609: B->ops->multadd = MatMultAdd_SeqSBAIJ_6;
1610: B->ops->multtranspose = MatMult_SeqSBAIJ_6;
1611: B->ops->multtransposeadd = MatMultAdd_SeqSBAIJ_6;
1612: break;
1613: case 7:
1614: B->ops->mult = MatMult_SeqSBAIJ_7;
1615: B->ops->multadd = MatMultAdd_SeqSBAIJ_7;
1616: B->ops->multtranspose = MatMult_SeqSBAIJ_7;
1617: B->ops->multtransposeadd = MatMultAdd_SeqSBAIJ_7;
1618: break;
1619: }
1620: }
1622: b->mbs = mbs;
1623: b->nbs = mbs;
1624: if (!skipallocation) {
1625: if (!b->imax) {
1626: PetscMalloc2(mbs,&b->imax,mbs,&b->ilen);
1628: b->free_imax_ilen = PETSC_TRUE;
1630: PetscLogObjectMemory((PetscObject)B,2*mbs*sizeof(PetscInt));
1631: }
1632: if (!nnz) {
1633: if (nz == PETSC_DEFAULT || nz == PETSC_DECIDE) nz = 5;
1634: else if (nz <= 0) nz = 1;
1635: for (i=0; i<mbs; i++) b->imax[i] = nz;
1636: nz = nz*mbs; /* total nz */
1637: } else {
1638: nz = 0;
1639: for (i=0; i<mbs; i++) {b->imax[i] = nnz[i]; nz += nnz[i];}
1640: }
1641: /* b->ilen will count nonzeros in each block row so far. */
1642: for (i=0; i<mbs; i++) b->ilen[i] = 0;
1643: /* nz=(nz+mbs)/2; */ /* total diagonal and superdiagonal nonzero blocks */
1645: /* allocate the matrix space */
1646: MatSeqXAIJFreeAIJ(B,&b->a,&b->j,&b->i);
1647: PetscMalloc3(bs2*nz,&b->a,nz,&b->j,B->rmap->N+1,&b->i);
1648: PetscLogObjectMemory((PetscObject)B,(B->rmap->N+1)*sizeof(PetscInt)+nz*(bs2*sizeof(PetscScalar)+sizeof(PetscInt)));
1649: PetscMemzero(b->a,nz*bs2*sizeof(MatScalar));
1650: PetscMemzero(b->j,nz*sizeof(PetscInt));
1652: b->singlemalloc = PETSC_TRUE;
1654: /* pointer to beginning of each row */
1655: b->i[0] = 0;
1656: for (i=1; i<mbs+1; i++) b->i[i] = b->i[i-1] + b->imax[i-1];
1658: b->free_a = PETSC_TRUE;
1659: b->free_ij = PETSC_TRUE;
1660: } else {
1661: b->free_a = PETSC_FALSE;
1662: b->free_ij = PETSC_FALSE;
1663: }
1665: B->rmap->bs = bs;
1666: b->bs2 = bs2;
1667: b->nz = 0;
1668: b->maxnz = nz;
1670: b->inew = 0;
1671: b->jnew = 0;
1672: b->anew = 0;
1673: b->a2anew = 0;
1674: b->permute = PETSC_FALSE;
1675: if (realalloc) {MatSetOption(B,MAT_NEW_NONZERO_ALLOCATION_ERR,PETSC_TRUE);}
1676: return(0);
1677: }
1681: PetscErrorCode MatSeqSBAIJSetPreallocationCSR_SeqSBAIJ(Mat B,PetscInt bs,const PetscInt ii[],const PetscInt jj[], const PetscScalar V[])
1682: {
1683: PetscInt i,j,m,nz,nz_max=0,*nnz;
1684: PetscScalar *values=0;
1685: PetscBool roworiented = ((Mat_SeqSBAIJ*)B->data)->roworiented;
1688: if (bs < 1) SETERRQ1(PetscObjectComm((PetscObject)B),PETSC_ERR_ARG_OUTOFRANGE,"Invalid block size specified, must be positive but it is %D",bs);
1689: PetscLayoutSetBlockSize(B->rmap,bs);
1690: PetscLayoutSetBlockSize(B->cmap,bs);
1691: PetscLayoutSetUp(B->rmap);
1692: PetscLayoutSetUp(B->cmap);
1693: PetscLayoutGetBlockSize(B->rmap,&bs);
1694: m = B->rmap->n/bs;
1696: if (ii[0]) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"ii[0] must be 0 but it is %D",ii[0]);
1697: PetscMalloc1((m+1),&nnz);
1698: for (i=0; i<m; i++) {
1699: nz = ii[i+1] - ii[i];
1700: if (nz < 0) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Row %D has a negative number of columns %D",i,nz);
1701: nz_max = PetscMax(nz_max,nz);
1702: nnz[i] = nz;
1703: }
1704: MatSeqSBAIJSetPreallocation(B,bs,0,nnz);
1705: PetscFree(nnz);
1707: values = (PetscScalar*)V;
1708: if (!values) {
1709: PetscCalloc1(bs*bs*nz_max,&values);
1710: }
1711: for (i=0; i<m; i++) {
1712: PetscInt ncols = ii[i+1] - ii[i];
1713: const PetscInt *icols = jj + ii[i];
1714: if (!roworiented || bs == 1) {
1715: const PetscScalar *svals = values + (V ? (bs*bs*ii[i]) : 0);
1716: MatSetValuesBlocked_SeqSBAIJ(B,1,&i,ncols,icols,svals,INSERT_VALUES);
1717: } else {
1718: for (j=0; j<ncols; j++) {
1719: const PetscScalar *svals = values + (V ? (bs*bs*(ii[i]+j)) : 0);
1720: MatSetValuesBlocked_SeqSBAIJ(B,1,&i,1,&icols[j],svals,INSERT_VALUES);
1721: }
1722: }
1723: }
1724: if (!V) { PetscFree(values); }
1725: MatAssemblyBegin(B,MAT_FINAL_ASSEMBLY);
1726: MatAssemblyEnd(B,MAT_FINAL_ASSEMBLY);
1727: MatSetOption(B,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);
1728: return(0);
1729: }
1731: /*
1732: This is used to set the numeric factorization for both Cholesky and ICC symbolic factorization
1733: */
1736: PetscErrorCode MatSeqSBAIJSetNumericFactorization_inplace(Mat B,PetscBool natural)
1737: {
1739: PetscBool flg = PETSC_FALSE;
1740: PetscInt bs = B->rmap->bs;
1743: PetscOptionsGetBool(((PetscObject)B)->prefix,"-mat_no_unroll",&flg,NULL);
1744: if (flg) bs = 8;
1746: if (!natural) {
1747: switch (bs) {
1748: case 1:
1749: B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_1_inplace;
1750: break;
1751: case 2:
1752: B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_2;
1753: break;
1754: case 3:
1755: B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_3;
1756: break;
1757: case 4:
1758: B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_4;
1759: break;
1760: case 5:
1761: B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_5;
1762: break;
1763: case 6:
1764: B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_6;
1765: break;
1766: case 7:
1767: B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_7;
1768: break;
1769: default:
1770: B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_N;
1771: break;
1772: }
1773: } else {
1774: switch (bs) {
1775: case 1:
1776: B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_1_NaturalOrdering_inplace;
1777: break;
1778: case 2:
1779: B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_2_NaturalOrdering;
1780: break;
1781: case 3:
1782: B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_3_NaturalOrdering;
1783: break;
1784: case 4:
1785: B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_4_NaturalOrdering;
1786: break;
1787: case 5:
1788: B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_5_NaturalOrdering;
1789: break;
1790: case 6:
1791: B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_6_NaturalOrdering;
1792: break;
1793: case 7:
1794: B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_7_NaturalOrdering;
1795: break;
1796: default:
1797: B->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_SeqSBAIJ_N_NaturalOrdering;
1798: break;
1799: }
1800: }
1801: return(0);
1802: }
1804: PETSC_EXTERN PetscErrorCode MatConvert_SeqSBAIJ_SeqAIJ(Mat, MatType,MatReuse,Mat*);
1805: PETSC_EXTERN PetscErrorCode MatConvert_SeqSBAIJ_SeqBAIJ(Mat, MatType,MatReuse,Mat*);
1809: PETSC_EXTERN PetscErrorCode MatGetFactor_seqsbaij_petsc(Mat A,MatFactorType ftype,Mat *B)
1810: {
1811: PetscInt n = A->rmap->n;
1815: #if defined(PETSC_USE_COMPLEX)
1816: if (A->hermitian) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Hermitian Factor is not supported");
1817: #endif
1818: MatCreate(PetscObjectComm((PetscObject)A),B);
1819: MatSetSizes(*B,n,n,n,n);
1820: if (ftype == MAT_FACTOR_CHOLESKY || ftype == MAT_FACTOR_ICC) {
1821: MatSetType(*B,MATSEQSBAIJ);
1822: MatSeqSBAIJSetPreallocation(*B,A->rmap->bs,MAT_SKIP_ALLOCATION,NULL);
1824: (*B)->ops->choleskyfactorsymbolic = MatCholeskyFactorSymbolic_SeqSBAIJ;
1825: (*B)->ops->iccfactorsymbolic = MatICCFactorSymbolic_SeqSBAIJ;
1826: } else SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Factor type not supported");
1827: (*B)->factortype = ftype;
1828: return(0);
1829: }
1833: PetscErrorCode MatGetFactorAvailable_seqsbaij_petsc(Mat A,MatFactorType ftype,PetscBool *flg)
1834: {
1836: if (ftype == MAT_FACTOR_CHOLESKY || ftype == MAT_FACTOR_ICC) {
1837: *flg = PETSC_TRUE;
1838: } else {
1839: *flg = PETSC_FALSE;
1840: }
1841: return(0);
1842: }
1844: #if defined(PETSC_HAVE_MUMPS)
1845: PETSC_EXTERN PetscErrorCode MatGetFactor_sbaij_mumps(Mat,MatFactorType,Mat*);
1846: #endif
1847: #if defined(PETSC_HAVE_PASTIX)
1848: PETSC_EXTERN PetscErrorCode MatGetFactor_seqsbaij_pastix(Mat,MatFactorType,Mat*);
1849: #endif
1850: #if defined(PETSC_HAVE_SUITESPARSE)
1851: PETSC_EXTERN PetscErrorCode MatGetFactor_seqsbaij_cholmod(Mat,MatFactorType,Mat*);
1852: #endif
1853: PETSC_EXTERN PetscErrorCode MatGetFactor_seqsbaij_sbstrm(Mat,MatFactorType,Mat*);
1855: /*MC
1856: MATSEQSBAIJ - MATSEQSBAIJ = "seqsbaij" - A matrix type to be used for sequential symmetric block sparse matrices,
1857: based on block compressed sparse row format. Only the upper triangular portion of the matrix is stored.
1859: For complex numbers by default this matrix is symmetric, NOT Hermitian symmetric. To make it Hermitian symmetric you
1860: can call MatSetOption(Mat, MAT_HERMITIAN); after MatAssemblyEnd()
1862: Options Database Keys:
1863: . -mat_type seqsbaij - sets the matrix type to "seqsbaij" during a call to MatSetFromOptions()
1865: Notes: By default if you insert values into the lower triangular part of the matrix they are simply ignored (since they are not
1866: stored and it is assumed they symmetric to the upper triangular). If you call MatSetOption(Mat,MAT_IGNORE_LOWER_TRIANGULAR,PETSC_FALSE) or use
1867: 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.
1870: Level: beginner
1872: .seealso: MatCreateSeqSBAIJ
1873: M*/
1875: PETSC_EXTERN PetscErrorCode MatConvert_SeqSBAIJ_SeqSBSTRM(Mat, MatType,MatReuse,Mat*);
1879: PETSC_EXTERN PetscErrorCode MatCreate_SeqSBAIJ(Mat B)
1880: {
1881: Mat_SeqSBAIJ *b;
1883: PetscMPIInt size;
1884: PetscBool no_unroll = PETSC_FALSE,no_inode = PETSC_FALSE;
1887: MPI_Comm_size(PetscObjectComm((PetscObject)B),&size);
1888: if (size > 1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"Comm must be of size 1");
1890: PetscNewLog(B,&b);
1891: B->data = (void*)b;
1892: PetscMemcpy(B->ops,&MatOps_Values,sizeof(struct _MatOps));
1894: B->ops->destroy = MatDestroy_SeqSBAIJ;
1895: B->ops->view = MatView_SeqSBAIJ;
1896: b->row = 0;
1897: b->icol = 0;
1898: b->reallocs = 0;
1899: b->saved_values = 0;
1900: b->inode.limit = 5;
1901: b->inode.max_limit = 5;
1903: b->roworiented = PETSC_TRUE;
1904: b->nonew = 0;
1905: b->diag = 0;
1906: b->solve_work = 0;
1907: b->mult_work = 0;
1908: B->spptr = 0;
1909: B->info.nz_unneeded = (PetscReal)b->maxnz*b->bs2;
1910: b->keepnonzeropattern = PETSC_FALSE;
1911: b->xtoy = 0;
1912: b->XtoY = 0;
1914: b->inew = 0;
1915: b->jnew = 0;
1916: b->anew = 0;
1917: b->a2anew = 0;
1918: b->permute = PETSC_FALSE;
1920: b->ignore_ltriangular = PETSC_TRUE;
1922: PetscOptionsGetBool(((PetscObject)B)->prefix,"-mat_ignore_lower_triangular",&b->ignore_ltriangular,NULL);
1924: b->getrow_utriangular = PETSC_FALSE;
1926: PetscOptionsGetBool(((PetscObject)B)->prefix,"-mat_getrow_uppertriangular",&b->getrow_utriangular,NULL);
1928: #if defined(PETSC_HAVE_PASTIX)
1929: PetscObjectComposeFunction((PetscObject)B,"MatGetFactor_pastix_C",MatGetFactor_seqsbaij_pastix);
1930: #endif
1931: #if defined(PETSC_HAVE_MUMPS)
1932: PetscObjectComposeFunction((PetscObject)B,"MatGetFactor_mumps_C",MatGetFactor_sbaij_mumps);
1933: #endif
1934: #if defined(PETSC_HAVE_SUITESPARSE)
1935: PetscObjectComposeFunction((PetscObject)B,"MatGetFactor_cholmod_C",MatGetFactor_seqsbaij_cholmod);
1936: #endif
1937: PetscObjectComposeFunction((PetscObject)B,"MatGetFactorAvailable_petsc_C",MatGetFactorAvailable_seqsbaij_petsc);
1938: PetscObjectComposeFunction((PetscObject)B,"MatGetFactor_petsc_C",MatGetFactor_seqsbaij_petsc);
1939: PetscObjectComposeFunction((PetscObject)B,"MatGetFactor_sbstrm_C",MatGetFactor_seqsbaij_sbstrm);
1940: PetscObjectComposeFunction((PetscObject)B,"MatStoreValues_C",MatStoreValues_SeqSBAIJ);
1941: PetscObjectComposeFunction((PetscObject)B,"MatRetrieveValues_C",MatRetrieveValues_SeqSBAIJ);
1942: PetscObjectComposeFunction((PetscObject)B,"MatSeqSBAIJSetColumnIndices_C",MatSeqSBAIJSetColumnIndices_SeqSBAIJ);
1943: PetscObjectComposeFunction((PetscObject)B,"MatConvert_seqsbaij_seqaij_C",MatConvert_SeqSBAIJ_SeqAIJ);
1944: PetscObjectComposeFunction((PetscObject)B,"MatConvert_seqsbaij_seqbaij_C",MatConvert_SeqSBAIJ_SeqBAIJ);
1945: PetscObjectComposeFunction((PetscObject)B,"MatSeqSBAIJSetPreallocation_C",MatSeqSBAIJSetPreallocation_SeqSBAIJ);
1946: PetscObjectComposeFunction((PetscObject)B,"MatSeqSBAIJSetPreallocationCSR_C",MatSeqSBAIJSetPreallocationCSR_SeqSBAIJ);
1947: PetscObjectComposeFunction((PetscObject)B,"MatConvert_seqsbaij_seqsbstrm_C",MatConvert_SeqSBAIJ_SeqSBSTRM);
1949: B->symmetric = PETSC_TRUE;
1950: B->structurally_symmetric = PETSC_TRUE;
1951: B->symmetric_set = PETSC_TRUE;
1952: B->structurally_symmetric_set = PETSC_TRUE;
1954: PetscObjectChangeTypeName((PetscObject)B,MATSEQSBAIJ);
1956: PetscOptionsBegin(PetscObjectComm((PetscObject)B),((PetscObject)B)->prefix,"Options for SEQSBAIJ matrix","Mat");
1957: PetscOptionsBool("-mat_no_unroll","Do not optimize for inodes (slower)",NULL,no_unroll,&no_unroll,NULL);
1958: if (no_unroll) {
1959: PetscInfo(B,"Not using Inode routines due to -mat_no_unroll\n");
1960: }
1961: PetscOptionsBool("-mat_no_inode","Do not optimize for inodes (slower)",NULL,no_inode,&no_inode,NULL);
1962: if (no_inode) {
1963: PetscInfo(B,"Not using Inode routines due to -mat_no_inode\n");
1964: }
1965: PetscOptionsInt("-mat_inode_limit","Do not use inodes larger then this value",NULL,b->inode.limit,&b->inode.limit,NULL);
1966: PetscOptionsEnd();
1967: b->inode.use = (PetscBool)(!(no_unroll || no_inode));
1968: if (b->inode.limit > b->inode.max_limit) b->inode.limit = b->inode.max_limit;
1969: return(0);
1970: }
1974: /*@C
1975: MatSeqSBAIJSetPreallocation - Creates a sparse symmetric matrix in block AIJ (block
1976: compressed row) format. For good matrix assembly performance the
1977: user should preallocate the matrix storage by setting the parameter nz
1978: (or the array nnz). By setting these parameters accurately, performance
1979: during matrix assembly can be increased by more than a factor of 50.
1981: Collective on Mat
1983: Input Parameters:
1984: + B - the symmetric matrix
1985: . bs - size of block
1986: . nz - number of block nonzeros per block row (same for all rows)
1987: - nnz - array containing the number of block nonzeros in the upper triangular plus
1988: diagonal portion of each block (possibly different for each block row) or NULL
1990: Options Database Keys:
1991: . -mat_no_unroll - uses code that does not unroll the loops in the
1992: block calculations (much slower)
1993: . -mat_block_size - size of the blocks to use (only works if a negative bs is passed in
1995: Level: intermediate
1997: Notes:
1998: Specify the preallocated storage with either nz or nnz (not both).
1999: Set nz=PETSC_DEFAULT and nnz=NULL for PETSc to control dynamic memory
2000: allocation. See Users-Manual: ch_mat for details.
2002: You can call MatGetInfo() to get information on how effective the preallocation was;
2003: for example the fields mallocs,nz_allocated,nz_used,nz_unneeded;
2004: You can also run with the option -info and look for messages with the string
2005: malloc in them to see if additional memory allocation was needed.
2007: If the nnz parameter is given then the nz parameter is ignored
2010: .seealso: MatCreate(), MatCreateSeqAIJ(), MatSetValues(), MatCreateSBAIJ()
2011: @*/
2012: PetscErrorCode MatSeqSBAIJSetPreallocation(Mat B,PetscInt bs,PetscInt nz,const PetscInt nnz[])
2013: {
2020: PetscTryMethod(B,"MatSeqSBAIJSetPreallocation_C",(Mat,PetscInt,PetscInt,const PetscInt[]),(B,bs,nz,nnz));
2021: return(0);
2022: }
2024: #undef __FUNCT__
2026: /*@C
2027: MatSeqSBAIJSetPreallocationCSR - Allocates memory for a sparse sequential matrix in symmetric block AIJ format.
2029: Input Parameters:
2030: + B - the matrix
2031: . i - the indices into j for the start of each local row (starts with zero)
2032: . j - the column indices for each local row (starts with zero) these must be sorted for each row
2033: - v - optional values in the matrix
2035: Level: developer
2037: Notes:
2038: The order of the entries in values is specified by the MatOption MAT_ROW_ORIENTED. For example, C programs
2039: may want to use the default MAT_ROW_ORIENTED=PETSC_TRUE and use an array v[nnz][bs][bs] where the second index is
2040: over rows within a block and the last index is over columns within a block row. Fortran programs will likely set
2041: MAT_ROW_ORIENTED=PETSC_FALSE and use a Fortran array v(bs,bs,nnz) in which the first index is over rows within a
2042: block column and the second index is over columns within a block.
2044: .keywords: matrix, block, aij, compressed row, sparse
2046: .seealso: MatCreate(), MatCreateSeqSBAIJ(), MatSetValuesBlocked(), MatSeqSBAIJSetPreallocation(), MATSEQSBAIJ
2047: @*/
2048: PetscErrorCode MatSeqSBAIJSetPreallocationCSR(Mat B,PetscInt bs,const PetscInt i[],const PetscInt j[], const PetscScalar v[])
2049: {
2056: PetscTryMethod(B,"MatSeqSBAIJSetPreallocationCSR_C",(Mat,PetscInt,const PetscInt[],const PetscInt[],const PetscScalar[]),(B,bs,i,j,v));
2057: return(0);
2058: }
2062: /*@C
2063: MatCreateSeqSBAIJ - Creates a sparse symmetric matrix in block AIJ (block
2064: compressed row) format. For good matrix assembly performance the
2065: user should preallocate the matrix storage by setting the parameter nz
2066: (or the array nnz). By setting these parameters accurately, performance
2067: during matrix assembly can be increased by more than a factor of 50.
2069: Collective on MPI_Comm
2071: Input Parameters:
2072: + comm - MPI communicator, set to PETSC_COMM_SELF
2073: . bs - size of block
2074: . m - number of rows, or number of columns
2075: . nz - number of block nonzeros per block row (same for all rows)
2076: - nnz - array containing the number of block nonzeros in the upper triangular plus
2077: diagonal portion of each block (possibly different for each block row) or NULL
2079: Output Parameter:
2080: . A - the symmetric matrix
2082: Options Database Keys:
2083: . -mat_no_unroll - uses code that does not unroll the loops in the
2084: block calculations (much slower)
2085: . -mat_block_size - size of the blocks to use
2087: Level: intermediate
2089: It is recommended that one use the MatCreate(), MatSetType() and/or MatSetFromOptions(),
2090: MatXXXXSetPreallocation() paradgm instead of this routine directly.
2091: [MatXXXXSetPreallocation() is, for example, MatSeqAIJSetPreallocation]
2093: Notes:
2094: The number of rows and columns must be divisible by blocksize.
2095: This matrix type does not support complex Hermitian operation.
2097: Specify the preallocated storage with either nz or nnz (not both).
2098: Set nz=PETSC_DEFAULT and nnz=NULL for PETSc to control dynamic memory
2099: allocation. See Users-Manual: ch_mat for details.
2101: If the nnz parameter is given then the nz parameter is ignored
2103: .seealso: MatCreate(), MatCreateSeqAIJ(), MatSetValues(), MatCreateSBAIJ()
2104: @*/
2105: PetscErrorCode MatCreateSeqSBAIJ(MPI_Comm comm,PetscInt bs,PetscInt m,PetscInt n,PetscInt nz,const PetscInt nnz[],Mat *A)
2106: {
2110: MatCreate(comm,A);
2111: MatSetSizes(*A,m,n,m,n);
2112: MatSetType(*A,MATSEQSBAIJ);
2113: MatSeqSBAIJSetPreallocation_SeqSBAIJ(*A,bs,nz,(PetscInt*)nnz);
2114: return(0);
2115: }
2119: PetscErrorCode MatDuplicate_SeqSBAIJ(Mat A,MatDuplicateOption cpvalues,Mat *B)
2120: {
2121: Mat C;
2122: Mat_SeqSBAIJ *c,*a = (Mat_SeqSBAIJ*)A->data;
2124: PetscInt i,mbs = a->mbs,nz = a->nz,bs2 =a->bs2;
2127: if (a->i[mbs] != nz) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Corrupt matrix");
2129: *B = 0;
2130: MatCreate(PetscObjectComm((PetscObject)A),&C);
2131: MatSetSizes(C,A->rmap->N,A->cmap->n,A->rmap->N,A->cmap->n);
2132: MatSetType(C,MATSEQSBAIJ);
2133: PetscMemcpy(C->ops,A->ops,sizeof(struct _MatOps));
2134: c = (Mat_SeqSBAIJ*)C->data;
2136: C->preallocated = PETSC_TRUE;
2137: C->factortype = A->factortype;
2138: c->row = 0;
2139: c->icol = 0;
2140: c->saved_values = 0;
2141: c->keepnonzeropattern = a->keepnonzeropattern;
2142: C->assembled = PETSC_TRUE;
2144: PetscLayoutReference(A->rmap,&C->rmap);
2145: PetscLayoutReference(A->cmap,&C->cmap);
2146: c->bs2 = a->bs2;
2147: c->mbs = a->mbs;
2148: c->nbs = a->nbs;
2150: if (cpvalues == MAT_SHARE_NONZERO_PATTERN) {
2151: c->imax = a->imax;
2152: c->ilen = a->ilen;
2153: c->free_imax_ilen = PETSC_FALSE;
2154: } else {
2155: PetscMalloc2((mbs+1),&c->imax,(mbs+1),&c->ilen);
2156: PetscLogObjectMemory((PetscObject)C,2*(mbs+1)*sizeof(PetscInt));
2157: for (i=0; i<mbs; i++) {
2158: c->imax[i] = a->imax[i];
2159: c->ilen[i] = a->ilen[i];
2160: }
2161: c->free_imax_ilen = PETSC_TRUE;
2162: }
2164: /* allocate the matrix space */
2165: if (cpvalues == MAT_SHARE_NONZERO_PATTERN) {
2166: PetscMalloc1(bs2*nz,&c->a);
2167: PetscLogObjectMemory((PetscObject)C,nz*bs2*sizeof(MatScalar));
2168: c->i = a->i;
2169: c->j = a->j;
2170: c->singlemalloc = PETSC_FALSE;
2171: c->free_a = PETSC_TRUE;
2172: c->free_ij = PETSC_FALSE;
2173: c->parent = A;
2174: PetscObjectReference((PetscObject)A);
2175: MatSetOption(A,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);
2176: MatSetOption(C,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_TRUE);
2177: } else {
2178: PetscMalloc3(bs2*nz,&c->a,nz,&c->j,mbs+1,&c->i);
2179: PetscMemcpy(c->i,a->i,(mbs+1)*sizeof(PetscInt));
2180: PetscLogObjectMemory((PetscObject)C,(mbs+1)*sizeof(PetscInt) + nz*(bs2*sizeof(MatScalar) + sizeof(PetscInt)));
2181: c->singlemalloc = PETSC_TRUE;
2182: c->free_a = PETSC_TRUE;
2183: c->free_ij = PETSC_TRUE;
2184: }
2185: if (mbs > 0) {
2186: if (cpvalues != MAT_SHARE_NONZERO_PATTERN) {
2187: PetscMemcpy(c->j,a->j,nz*sizeof(PetscInt));
2188: }
2189: if (cpvalues == MAT_COPY_VALUES) {
2190: PetscMemcpy(c->a,a->a,bs2*nz*sizeof(MatScalar));
2191: } else {
2192: PetscMemzero(c->a,bs2*nz*sizeof(MatScalar));
2193: }
2194: if (a->jshort) {
2195: /* cannot share jshort, it is reallocated in MatAssemblyEnd_SeqSBAIJ() */
2196: /* if the parent matrix is reassembled, this child matrix will never notice */
2197: PetscMalloc1(nz,&c->jshort);
2198: PetscLogObjectMemory((PetscObject)C,nz*sizeof(unsigned short));
2199: PetscMemcpy(c->jshort,a->jshort,nz*sizeof(unsigned short));
2201: c->free_jshort = PETSC_TRUE;
2202: }
2203: }
2205: c->roworiented = a->roworiented;
2206: c->nonew = a->nonew;
2208: if (a->diag) {
2209: if (cpvalues == MAT_SHARE_NONZERO_PATTERN) {
2210: c->diag = a->diag;
2211: c->free_diag = PETSC_FALSE;
2212: } else {
2213: PetscMalloc1(mbs,&c->diag);
2214: PetscLogObjectMemory((PetscObject)C,mbs*sizeof(PetscInt));
2215: for (i=0; i<mbs; i++) c->diag[i] = a->diag[i];
2216: c->free_diag = PETSC_TRUE;
2217: }
2218: }
2219: c->nz = a->nz;
2220: c->maxnz = a->nz; /* Since we allocate exactly the right amount */
2221: c->solve_work = 0;
2222: c->mult_work = 0;
2224: *B = C;
2225: PetscFunctionListDuplicate(((PetscObject)A)->qlist,&((PetscObject)C)->qlist);
2226: return(0);
2227: }
2231: PetscErrorCode MatLoad_SeqSBAIJ(Mat newmat,PetscViewer viewer)
2232: {
2233: Mat_SeqSBAIJ *a;
2235: int fd;
2236: PetscMPIInt size;
2237: PetscInt i,nz,header[4],*rowlengths=0,M,N,bs = newmat->rmap->bs;
2238: PetscInt *mask,mbs,*jj,j,rowcount,nzcount,k,*s_browlengths,maskcount;
2239: PetscInt kmax,jcount,block,idx,point,nzcountb,extra_rows,rows,cols;
2240: PetscInt *masked,nmask,tmp,bs2,ishift;
2241: PetscScalar *aa;
2242: MPI_Comm comm;
2245: PetscObjectGetComm((PetscObject)viewer,&comm);
2246: PetscOptionsGetInt(((PetscObject)newmat)->prefix,"-matload_block_size",&bs,NULL);
2247: if (bs < 0) bs = 1;
2248: bs2 = bs*bs;
2250: MPI_Comm_size(comm,&size);
2251: if (size > 1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"view must have one processor");
2252: PetscViewerBinaryGetDescriptor(viewer,&fd);
2253: PetscBinaryRead(fd,header,4,PETSC_INT);
2254: if (header[0] != MAT_FILE_CLASSID) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_FILE_UNEXPECTED,"not Mat object");
2255: M = header[1]; N = header[2]; nz = header[3];
2257: if (header[3] < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_FILE_UNEXPECTED,"Matrix stored in special format, cannot load as SeqSBAIJ");
2259: if (M != N) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"Can only do square matrices");
2261: /*
2262: This code adds extra rows to make sure the number of rows is
2263: divisible by the blocksize
2264: */
2265: mbs = M/bs;
2266: extra_rows = bs - M + bs*(mbs);
2267: if (extra_rows == bs) extra_rows = 0;
2268: else mbs++;
2269: if (extra_rows) {
2270: PetscInfo(viewer,"Padding loaded matrix to match blocksize\n");
2271: }
2273: /* Set global sizes if not already set */
2274: if (newmat->rmap->n < 0 && newmat->rmap->N < 0 && newmat->cmap->n < 0 && newmat->cmap->N < 0) {
2275: MatSetSizes(newmat,PETSC_DECIDE,PETSC_DECIDE,M+extra_rows,N+extra_rows);
2276: } else { /* Check if the matrix global sizes are correct */
2277: MatGetSize(newmat,&rows,&cols);
2278: 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);
2279: }
2281: /* read in row lengths */
2282: PetscMalloc1((M+extra_rows),&rowlengths);
2283: PetscBinaryRead(fd,rowlengths,M,PETSC_INT);
2284: for (i=0; i<extra_rows; i++) rowlengths[M+i] = 1;
2286: /* read in column indices */
2287: PetscMalloc1((nz+extra_rows),&jj);
2288: PetscBinaryRead(fd,jj,nz,PETSC_INT);
2289: for (i=0; i<extra_rows; i++) jj[nz+i] = M+i;
2291: /* loop over row lengths determining block row lengths */
2292: PetscCalloc1(mbs,&s_browlengths);
2293: PetscMalloc2(mbs,&mask,mbs,&masked);
2294: PetscMemzero(mask,mbs*sizeof(PetscInt));
2295: rowcount = 0;
2296: nzcount = 0;
2297: for (i=0; i<mbs; i++) {
2298: nmask = 0;
2299: for (j=0; j<bs; j++) {
2300: kmax = rowlengths[rowcount];
2301: for (k=0; k<kmax; k++) {
2302: tmp = jj[nzcount++]/bs; /* block col. index */
2303: if (!mask[tmp] && tmp >= i) {masked[nmask++] = tmp; mask[tmp] = 1;}
2304: }
2305: rowcount++;
2306: }
2307: s_browlengths[i] += nmask;
2309: /* zero out the mask elements we set */
2310: for (j=0; j<nmask; j++) mask[masked[j]] = 0;
2311: }
2313: /* Do preallocation */
2314: MatSeqSBAIJSetPreallocation_SeqSBAIJ(newmat,bs,0,s_browlengths);
2315: a = (Mat_SeqSBAIJ*)newmat->data;
2317: /* set matrix "i" values */
2318: a->i[0] = 0;
2319: for (i=1; i<= mbs; i++) {
2320: a->i[i] = a->i[i-1] + s_browlengths[i-1];
2321: a->ilen[i-1] = s_browlengths[i-1];
2322: }
2323: a->nz = a->i[mbs];
2325: /* read in nonzero values */
2326: PetscMalloc1((nz+extra_rows),&aa);
2327: PetscBinaryRead(fd,aa,nz,PETSC_SCALAR);
2328: for (i=0; i<extra_rows; i++) aa[nz+i] = 1.0;
2330: /* set "a" and "j" values into matrix */
2331: nzcount = 0; jcount = 0;
2332: for (i=0; i<mbs; i++) {
2333: nzcountb = nzcount;
2334: nmask = 0;
2335: for (j=0; j<bs; j++) {
2336: kmax = rowlengths[i*bs+j];
2337: for (k=0; k<kmax; k++) {
2338: tmp = jj[nzcount++]/bs; /* block col. index */
2339: if (!mask[tmp] && tmp >= i) { masked[nmask++] = tmp; mask[tmp] = 1;}
2340: }
2341: }
2342: /* sort the masked values */
2343: PetscSortInt(nmask,masked);
2345: /* set "j" values into matrix */
2346: maskcount = 1;
2347: for (j=0; j<nmask; j++) {
2348: a->j[jcount++] = masked[j];
2349: mask[masked[j]] = maskcount++;
2350: }
2352: /* set "a" values into matrix */
2353: ishift = bs2*a->i[i];
2354: for (j=0; j<bs; j++) {
2355: kmax = rowlengths[i*bs+j];
2356: for (k=0; k<kmax; k++) {
2357: tmp = jj[nzcountb]/bs; /* block col. index */
2358: if (tmp >= i) {
2359: block = mask[tmp] - 1;
2360: point = jj[nzcountb] - bs*tmp;
2361: idx = ishift + bs2*block + j + bs*point;
2362: a->a[idx] = aa[nzcountb];
2363: }
2364: nzcountb++;
2365: }
2366: }
2367: /* zero out the mask elements we set */
2368: for (j=0; j<nmask; j++) mask[masked[j]] = 0;
2369: }
2370: if (jcount != a->nz) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_FILE_UNEXPECTED,"Bad binary matrix");
2372: PetscFree(rowlengths);
2373: PetscFree(s_browlengths);
2374: PetscFree(aa);
2375: PetscFree(jj);
2376: PetscFree2(mask,masked);
2378: MatAssemblyBegin(newmat,MAT_FINAL_ASSEMBLY);
2379: MatAssemblyEnd(newmat,MAT_FINAL_ASSEMBLY);
2380: return(0);
2381: }
2385: /*@
2386: MatCreateSeqSBAIJWithArrays - Creates an sequential SBAIJ matrix using matrix elements
2387: (upper triangular entries in CSR format) provided by the user.
2389: Collective on MPI_Comm
2391: Input Parameters:
2392: + comm - must be an MPI communicator of size 1
2393: . bs - size of block
2394: . m - number of rows
2395: . n - number of columns
2396: . i - row indices
2397: . j - column indices
2398: - a - matrix values
2400: Output Parameter:
2401: . mat - the matrix
2403: Level: advanced
2405: Notes:
2406: The i, j, and a arrays are not copied by this routine, the user must free these arrays
2407: once the matrix is destroyed
2409: You cannot set new nonzero locations into this matrix, that will generate an error.
2411: The i and j indices are 0 based
2413: 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
2414: it is the regular CSR format excluding the lower triangular elements.
2416: .seealso: MatCreate(), MatCreateSBAIJ(), MatCreateSeqSBAIJ()
2418: @*/
2419: PetscErrorCode MatCreateSeqSBAIJWithArrays(MPI_Comm comm,PetscInt bs,PetscInt m,PetscInt n,PetscInt *i,PetscInt *j,PetscScalar *a,Mat *mat)
2420: {
2422: PetscInt ii;
2423: Mat_SeqSBAIJ *sbaij;
2426: if (bs != 1) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP,"block size %D > 1 is not supported yet",bs);
2427: if (i[0]) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"i (row indices) must start with 0");
2429: MatCreate(comm,mat);
2430: MatSetSizes(*mat,m,n,m,n);
2431: MatSetType(*mat,MATSEQSBAIJ);
2432: MatSeqSBAIJSetPreallocation_SeqSBAIJ(*mat,bs,MAT_SKIP_ALLOCATION,0);
2433: sbaij = (Mat_SeqSBAIJ*)(*mat)->data;
2434: PetscMalloc2(m,&sbaij->imax,m,&sbaij->ilen);
2435: PetscLogObjectMemory((PetscObject)*mat,2*m*sizeof(PetscInt));
2437: sbaij->i = i;
2438: sbaij->j = j;
2439: sbaij->a = a;
2441: sbaij->singlemalloc = PETSC_FALSE;
2442: sbaij->nonew = -1; /*this indicates that inserting a new value in the matrix that generates a new nonzero is an error*/
2443: sbaij->free_a = PETSC_FALSE;
2444: sbaij->free_ij = PETSC_FALSE;
2446: for (ii=0; ii<m; ii++) {
2447: sbaij->ilen[ii] = sbaij->imax[ii] = i[ii+1] - i[ii];
2448: #if defined(PETSC_USE_DEBUG)
2449: 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]);
2450: #endif
2451: }
2452: #if defined(PETSC_USE_DEBUG)
2453: for (ii=0; ii<sbaij->i[m]; ii++) {
2454: if (j[ii] < 0) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Negative column index at location = %d index = %d",ii,j[ii]);
2455: 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]);
2456: }
2457: #endif
2459: MatAssemblyBegin(*mat,MAT_FINAL_ASSEMBLY);
2460: MatAssemblyEnd(*mat,MAT_FINAL_ASSEMBLY);
2461: return(0);
2462: }