Actual source code: mpiadj.c
1: #define PETSCMAT_DLL
3: /*
4: Defines the basic matrix operations for the ADJ adjacency list matrix data-structure.
5: */
6: #include ../src/mat/impls/adj/mpi/mpiadj.h
7: #include petscsys.h
11: PetscErrorCode MatView_MPIAdj_ASCII(Mat A,PetscViewer viewer)
12: {
13: Mat_MPIAdj *a = (Mat_MPIAdj*)A->data;
14: PetscErrorCode ierr;
15: PetscInt i,j,m = A->rmap->n;
16: const char *name;
17: PetscViewerFormat format;
20: PetscObjectGetName((PetscObject)A,&name);
21: PetscViewerGetFormat(viewer,&format);
22: if (format == PETSC_VIEWER_ASCII_INFO) {
23: return(0);
24: } else if (format == PETSC_VIEWER_ASCII_MATLAB) {
25: SETERRQ(PETSC_ERR_SUP,"Matlab format not supported");
26: } else {
27: PetscViewerASCIIUseTabs(viewer,PETSC_NO);
28: for (i=0; i<m; i++) {
29: PetscViewerASCIISynchronizedPrintf(viewer,"row %D:",i+A->rmap->rstart);
30: for (j=a->i[i]; j<a->i[i+1]; j++) {
31: PetscViewerASCIISynchronizedPrintf(viewer," %D ",a->j[j]);
32: }
33: PetscViewerASCIISynchronizedPrintf(viewer,"\n");
34: }
35: PetscViewerASCIIUseTabs(viewer,PETSC_YES);
36: }
37: PetscViewerFlush(viewer);
38: return(0);
39: }
43: PetscErrorCode MatView_MPIAdj(Mat A,PetscViewer viewer)
44: {
46: PetscTruth iascii;
49: PetscTypeCompare((PetscObject)viewer,PETSC_VIEWER_ASCII,&iascii);
50: if (iascii) {
51: MatView_MPIAdj_ASCII(A,viewer);
52: } else {
53: SETERRQ1(PETSC_ERR_SUP,"Viewer type %s not supported by MPIAdj",((PetscObject)viewer)->type_name);
54: }
55: return(0);
56: }
60: PetscErrorCode MatDestroy_MPIAdj(Mat mat)
61: {
62: Mat_MPIAdj *a = (Mat_MPIAdj*)mat->data;
66: #if defined(PETSC_USE_LOG)
67: PetscLogObjectState((PetscObject)mat,"Rows=%D, Cols=%D, NZ=%D",mat->rmap->n,mat->cmap->n,a->nz);
68: #endif
69: PetscFree(a->diag);
70: if (a->freeaij) {
71: PetscFree(a->i);
72: PetscFree(a->j);
73: PetscFree(a->values);
74: }
75: PetscFree(a);
76: PetscObjectChangeTypeName((PetscObject)mat,0);
77: PetscObjectComposeFunction((PetscObject)mat,"MatMPIAdjSetPreallocation_C","",PETSC_NULL);
78: return(0);
79: }
83: PetscErrorCode MatSetOption_MPIAdj(Mat A,MatOption op,PetscTruth flg)
84: {
85: Mat_MPIAdj *a = (Mat_MPIAdj*)A->data;
89: switch (op) {
90: case MAT_SYMMETRIC:
91: case MAT_STRUCTURALLY_SYMMETRIC:
92: case MAT_HERMITIAN:
93: a->symmetric = flg;
94: break;
95: case MAT_SYMMETRY_ETERNAL:
96: break;
97: default:
98: PetscInfo1(A,"Option %s ignored\n",MatOptions[op]);
99: break;
100: }
101: return(0);
102: }
105: /*
106: Adds diagonal pointers to sparse matrix structure.
107: */
111: PetscErrorCode MatMarkDiagonal_MPIAdj(Mat A)
112: {
113: Mat_MPIAdj *a = (Mat_MPIAdj*)A->data;
115: PetscInt i,j,m = A->rmap->n;
118: PetscMalloc(m*sizeof(PetscInt),&a->diag);
119: PetscLogObjectMemory(A,m*sizeof(PetscInt));
120: for (i=0; i<A->rmap->n; i++) {
121: for (j=a->i[i]; j<a->i[i+1]; j++) {
122: if (a->j[j] == i) {
123: a->diag[i] = j;
124: break;
125: }
126: }
127: }
128: return(0);
129: }
133: PetscErrorCode MatGetRow_MPIAdj(Mat A,PetscInt row,PetscInt *nz,PetscInt **idx,PetscScalar **v)
134: {
135: Mat_MPIAdj *a = (Mat_MPIAdj*)A->data;
136: PetscInt *itmp;
139: row -= A->rmap->rstart;
141: if (row < 0 || row >= A->rmap->n) SETERRQ(PETSC_ERR_ARG_OUTOFRANGE,"Row out of range");
143: *nz = a->i[row+1] - a->i[row];
144: if (v) *v = PETSC_NULL;
145: if (idx) {
146: itmp = a->j + a->i[row];
147: if (*nz) {
148: *idx = itmp;
149: }
150: else *idx = 0;
151: }
152: return(0);
153: }
157: PetscErrorCode MatRestoreRow_MPIAdj(Mat A,PetscInt row,PetscInt *nz,PetscInt **idx,PetscScalar **v)
158: {
160: return(0);
161: }
165: PetscErrorCode MatEqual_MPIAdj(Mat A,Mat B,PetscTruth* flg)
166: {
167: Mat_MPIAdj *a = (Mat_MPIAdj *)A->data,*b = (Mat_MPIAdj *)B->data;
169: PetscTruth flag;
172: /* If the matrix dimensions are not equal,or no of nonzeros */
173: if ((A->rmap->n != B->rmap->n) ||(a->nz != b->nz)) {
174: flag = PETSC_FALSE;
175: }
176:
177: /* if the a->i are the same */
178: PetscMemcmp(a->i,b->i,(A->rmap->n+1)*sizeof(PetscInt),&flag);
179:
180: /* if a->j are the same */
181: PetscMemcmp(a->j,b->j,(a->nz)*sizeof(PetscInt),&flag);
183: MPI_Allreduce(&flag,flg,1,MPI_INT,MPI_LAND,((PetscObject)A)->comm);
184: return(0);
185: }
189: PetscErrorCode MatGetRowIJ_MPIAdj(Mat A,PetscInt oshift,PetscTruth symmetric,PetscTruth blockcompressed,PetscInt *m,PetscInt *ia[],PetscInt *ja[],PetscTruth *done)
190: {
192: PetscMPIInt size;
193: PetscInt i;
194: Mat_MPIAdj *a = (Mat_MPIAdj *)A->data;
197: MPI_Comm_size(((PetscObject)A)->comm,&size);
198: if (size > 1) {*done = PETSC_FALSE; return(0);}
199: *m = A->rmap->n;
200: *ia = a->i;
201: *ja = a->j;
202: *done = PETSC_TRUE;
203: if (oshift) {
204: for (i=0; i<(*ia)[*m]; i++) {
205: (*ja)[i]++;
206: }
207: for (i=0; i<=(*m); i++) (*ia)[i]++;
208: }
209: return(0);
210: }
214: PetscErrorCode MatRestoreRowIJ_MPIAdj(Mat A,PetscInt oshift,PetscTruth symmetric,PetscTruth blockcompressed,PetscInt *m,PetscInt *ia[],PetscInt *ja[],PetscTruth *done)
215: {
216: PetscInt i;
217: Mat_MPIAdj *a = (Mat_MPIAdj *)A->data;
220: if (ia && a->i != *ia) SETERRQ(PETSC_ERR_ARG_WRONGSTATE,"ia passed back is not one obtained with MatGetRowIJ()");
221: if (ja && a->j != *ja) SETERRQ(PETSC_ERR_ARG_WRONGSTATE,"ja passed back is not one obtained with MatGetRowIJ()");
222: if (oshift) {
223: for (i=0; i<=(*m); i++) (*ia)[i]--;
224: for (i=0; i<(*ia)[*m]; i++) {
225: (*ja)[i]--;
226: }
227: }
228: return(0);
229: }
233: PetscErrorCode MatConvertFrom_MPIAdj(Mat A,const MatType type,MatReuse reuse,Mat *newmat)
234: {
235: Mat B;
236: PetscErrorCode ierr;
237: PetscInt i,m,N,nzeros = 0,*ia,*ja,len,rstart,cnt,j,*a;
238: const PetscInt *rj;
239: const PetscScalar *ra;
240: MPI_Comm comm;
243: MatGetSize(A,PETSC_NULL,&N);
244: MatGetLocalSize(A,&m,PETSC_NULL);
245: MatGetOwnershipRange(A,&rstart,PETSC_NULL);
246:
247: /* count the number of nonzeros per row */
248: for (i=0; i<m; i++) {
249: MatGetRow(A,i+rstart,&len,&rj,PETSC_NULL);
250: for (j=0; j<len; j++) {
251: if (rj[j] == i+rstart) {len--; break;} /* don't count diagonal */
252: }
253: MatRestoreRow(A,i+rstart,&len,&rj,PETSC_NULL);
254: nzeros += len;
255: }
257: /* malloc space for nonzeros */
258: PetscMalloc((nzeros+1)*sizeof(PetscInt),&a);
259: PetscMalloc((N+1)*sizeof(PetscInt),&ia);
260: PetscMalloc((nzeros+1)*sizeof(PetscInt),&ja);
262: nzeros = 0;
263: ia[0] = 0;
264: for (i=0; i<m; i++) {
265: MatGetRow(A,i+rstart,&len,&rj,&ra);
266: cnt = 0;
267: for (j=0; j<len; j++) {
268: if (rj[j] != i+rstart) { /* if not diagonal */
269: a[nzeros+cnt] = (PetscInt) PetscAbsScalar(ra[j]);
270: ja[nzeros+cnt++] = rj[j];
271: }
272: }
273: MatRestoreRow(A,i+rstart,&len,&rj,&ra);
274: nzeros += cnt;
275: ia[i+1] = nzeros;
276: }
278: PetscObjectGetComm((PetscObject)A,&comm);
279: MatCreate(comm,&B);
280: MatSetSizes(B,m,PETSC_DETERMINE,PETSC_DETERMINE,N);
281: MatSetType(B,type);
282: MatMPIAdjSetPreallocation(B,ia,ja,a);
284: if (reuse == MAT_REUSE_MATRIX) {
285: MatHeaderReplace(A,B);
286: } else {
287: *newmat = B;
288: }
289: return(0);
290: }
292: /* -------------------------------------------------------------------*/
293: static struct _MatOps MatOps_Values = {0,
294: MatGetRow_MPIAdj,
295: MatRestoreRow_MPIAdj,
296: 0,
297: /* 4*/ 0,
298: 0,
299: 0,
300: 0,
301: 0,
302: 0,
303: /*10*/ 0,
304: 0,
305: 0,
306: 0,
307: 0,
308: /*15*/ 0,
309: MatEqual_MPIAdj,
310: 0,
311: 0,
312: 0,
313: /*20*/ 0,
314: 0,
315: 0,
316: MatSetOption_MPIAdj,
317: 0,
318: /*25*/ 0,
319: 0,
320: 0,
321: 0,
322: 0,
323: /*30*/ 0,
324: 0,
325: 0,
326: 0,
327: 0,
328: /*35*/ 0,
329: 0,
330: 0,
331: 0,
332: 0,
333: /*40*/ 0,
334: 0,
335: 0,
336: 0,
337: 0,
338: /*45*/ 0,
339: 0,
340: 0,
341: 0,
342: 0,
343: /*50*/ 0,
344: MatGetRowIJ_MPIAdj,
345: MatRestoreRowIJ_MPIAdj,
346: 0,
347: 0,
348: /*55*/ 0,
349: 0,
350: 0,
351: 0,
352: 0,
353: /*60*/ 0,
354: MatDestroy_MPIAdj,
355: MatView_MPIAdj,
356: MatConvertFrom_MPIAdj,
357: 0,
358: /*65*/ 0,
359: 0,
360: 0,
361: 0,
362: 0,
363: /*70*/ 0,
364: 0,
365: 0,
366: 0,
367: 0,
368: /*75*/ 0,
369: 0,
370: 0,
371: 0,
372: 0,
373: /*80*/ 0,
374: 0,
375: 0,
376: 0,
377: 0,
378: /*85*/ 0,
379: 0,
380: 0,
381: 0,
382: 0,
383: /*90*/ 0,
384: 0,
385: 0,
386: 0,
387: 0,
388: /*95*/ 0,
389: 0,
390: 0,
391: 0};
396: PetscErrorCode MatMPIAdjSetPreallocation_MPIAdj(Mat B,PetscInt *i,PetscInt *j,PetscInt *values)
397: {
398: Mat_MPIAdj *b = (Mat_MPIAdj *)B->data;
400: #if defined(PETSC_USE_DEBUG)
401: PetscInt ii;
402: #endif
405: PetscMapSetBlockSize(B->rmap,1);
406: PetscMapSetBlockSize(B->cmap,1);
407: PetscMapSetUp(B->rmap);
408: PetscMapSetUp(B->cmap);
410: #if defined(PETSC_USE_DEBUG)
411: if (i[0] != 0) SETERRQ1(PETSC_ERR_ARG_OUTOFRANGE,"First i[] index must be zero, instead it is %D\n",i[0]);
412: for (ii=1; ii<B->rmap->n; ii++) {
413: if (i[ii] < 0 || i[ii] < i[ii-1]) {
414: SETERRQ4(PETSC_ERR_ARG_OUTOFRANGE,"i[%D]=%D index is out of range: i[%D]=%D",ii,i[ii],ii-1,i[ii-1]);
415: }
416: }
417: for (ii=0; ii<i[B->rmap->n]; ii++) {
418: if (j[ii] < 0 || j[ii] >= B->cmap->N) {
419: SETERRQ2(PETSC_ERR_ARG_OUTOFRANGE,"Column index %D out of range %D\n",ii,j[ii]);
420: }
421: }
422: #endif
423: B->preallocated = PETSC_TRUE;
425: b->j = j;
426: b->i = i;
427: b->values = values;
429: b->nz = i[B->rmap->n];
430: b->diag = 0;
431: b->symmetric = PETSC_FALSE;
432: b->freeaij = PETSC_TRUE;
434: MatAssemblyBegin(B,MAT_FINAL_ASSEMBLY);
435: MatAssemblyEnd(B,MAT_FINAL_ASSEMBLY);
436: return(0);
437: }
440: /*MC
441: MATMPIADJ - MATMPIADJ = "mpiadj" - A matrix type to be used for distributed adjacency matrices,
442: intended for use constructing orderings and partitionings.
444: Level: beginner
446: .seealso: MatCreateMPIAdj
447: M*/
452: PetscErrorCode MatCreate_MPIAdj(Mat B)
453: {
454: Mat_MPIAdj *b;
456: PetscMPIInt size,rank;
459: MPI_Comm_size(((PetscObject)B)->comm,&size);
460: MPI_Comm_rank(((PetscObject)B)->comm,&rank);
462: PetscNewLog(B,Mat_MPIAdj,&b);
463: B->data = (void*)b;
464: PetscMemcpy(B->ops,&MatOps_Values,sizeof(struct _MatOps));
465: B->mapping = 0;
466: B->assembled = PETSC_FALSE;
467:
468: PetscObjectComposeFunctionDynamic((PetscObject)B,"MatMPIAdjSetPreallocation_C",
469: "MatMPIAdjSetPreallocation_MPIAdj",
470: MatMPIAdjSetPreallocation_MPIAdj);
471: PetscObjectChangeTypeName((PetscObject)B,MATMPIADJ);
472: return(0);
473: }
478: /*@C
479: MatMPIAdjSetPreallocation - Sets the array used for storing the matrix elements
481: Collective on MPI_Comm
483: Input Parameters:
484: + A - the matrix
485: . i - the indices into j for the start of each row
486: . j - the column indices for each row (sorted for each row).
487: The indices in i and j start with zero (NOT with one).
488: - values - [optional] edge weights
490: Level: intermediate
492: .seealso: MatCreate(), MatCreateMPIAdj(), MatSetValues()
493: @*/
494: PetscErrorCode MatMPIAdjSetPreallocation(Mat B,PetscInt *i,PetscInt *j,PetscInt *values)
495: {
496: PetscErrorCode ierr,(*f)(Mat,PetscInt*,PetscInt*,PetscInt*);
499: PetscObjectQueryFunction((PetscObject)B,"MatMPIAdjSetPreallocation_C",(void (**)(void))&f);
500: if (f) {
501: (*f)(B,i,j,values);
502: }
503: return(0);
504: }
508: /*@C
509: MatCreateMPIAdj - Creates a sparse matrix representing an adjacency list.
510: The matrix does not have numerical values associated with it, but is
511: intended for ordering (to reduce bandwidth etc) and partitioning.
513: Collective on MPI_Comm
515: Input Parameters:
516: + comm - MPI communicator
517: . m - number of local rows
518: . N - number of global columns
519: . i - the indices into j for the start of each row
520: . j - the column indices for each row (sorted for each row).
521: The indices in i and j start with zero (NOT with one).
522: - values -[optional] edge weights
524: Output Parameter:
525: . A - the matrix
527: Level: intermediate
529: Notes: This matrix object does not support most matrix operations, include
530: MatSetValues().
531: You must NOT free the ii, values and jj arrays yourself. PETSc will free them
532: when the matrix is destroyed; you must allocate them with PetscMalloc(). If you
533: call from Fortran you need not create the arrays with PetscMalloc().
534: Should not include the matrix diagonals.
536: If you already have a matrix, you can create its adjacency matrix by a call
537: to MatConvert, specifying a type of MATMPIADJ.
539: Possible values for MatSetOption() - MAT_STRUCTURALLY_SYMMETRIC
541: .seealso: MatCreate(), MatConvert(), MatGetOrdering()
542: @*/
543: PetscErrorCode MatCreateMPIAdj(MPI_Comm comm,PetscInt m,PetscInt N,PetscInt *i,PetscInt *j,PetscInt *values,Mat *A)
544: {
548: MatCreate(comm,A);
549: MatSetSizes(*A,m,PETSC_DETERMINE,PETSC_DETERMINE,N);
550: MatSetType(*A,MATMPIADJ);
551: MatMPIAdjSetPreallocation(*A,i,j,values);
552: return(0);
553: }