Actual source code: sbaijcholmod.c
2: /*
3: Provides an interface to the CHOLMOD sparse solver available through SuiteSparse version 4.2.1
5: When built with PETSC_USE_64BIT_INDICES this will use Suitesparse_long as the
6: integer type in UMFPACK, otherwise it will use int. This means
7: all integers in this file as simply declared as PetscInt. Also it means
8: that one cannot use 64BIT_INDICES on 32-bit pointer systems [as Suitesparse_long is 32-bit only]
10: */
12: #include <../src/mat/impls/sbaij/seq/sbaij.h>
13: #include <../src/mat/impls/sbaij/seq/cholmod/cholmodimpl.h>
15: /*
16: This is a terrible hack, but it allows the error handler to retain a context.
17: Note that this hack really cannot be made both reentrant and concurrent.
18: */
19: static Mat static_F;
21: static void CholmodErrorHandler(int status, const char *file, int line, const char *message)
22: {
23: PetscFunctionBegin;
24: if (status > CHOLMOD_OK) {
25: PetscCallVoid(PetscInfo(static_F, "CHOLMOD warning %d at %s:%d: %s\n", status, file, line, message));
26: } else if (status == CHOLMOD_OK) { /* Documentation says this can happen, but why? */
27: PetscCallVoid(PetscInfo(static_F, "CHOLMOD OK at %s:%d: %s\n", file, line, message));
28: } else {
29: PetscCallVoid(PetscErrorPrintf("CHOLMOD error %d at %s:%d: %s\n", status, file, line, message));
30: }
31: PetscFunctionReturnVoid();
32: }
34: #define CHOLMOD_OPTION_DOUBLE(name, help) \
35: do { \
36: PetscReal tmp = (PetscReal)c->name; \
37: PetscCall(PetscOptionsReal("-mat_cholmod_" #name, help, "None", tmp, &tmp, NULL)); \
38: c->name = (double)tmp; \
39: } while (0)
41: #define CHOLMOD_OPTION_INT(name, help) \
42: do { \
43: PetscInt tmp = (PetscInt)c->name; \
44: PetscCall(PetscOptionsInt("-mat_cholmod_" #name, help, "None", tmp, &tmp, NULL)); \
45: c->name = (int)tmp; \
46: } while (0)
48: #define CHOLMOD_OPTION_SIZE_T(name, help) \
49: do { \
50: PetscReal tmp = (PetscInt)c->name; \
51: PetscCall(PetscOptionsReal("-mat_cholmod_" #name, help, "None", tmp, &tmp, NULL)); \
52: PetscCheck(tmp >= 0, PetscObjectComm((PetscObject)F), PETSC_ERR_ARG_OUTOFRANGE, "value must be positive"); \
53: c->name = (size_t)tmp; \
54: } while (0)
56: #define CHOLMOD_OPTION_BOOL(name, help) \
57: do { \
58: PetscBool tmp = (PetscBool) !!c->name; \
59: PetscCall(PetscOptionsBool("-mat_cholmod_" #name, help, "None", tmp, &tmp, NULL)); \
60: c->name = (int)tmp; \
61: } while (0)
63: static PetscErrorCode CholmodSetOptions(Mat F)
64: {
65: Mat_CHOLMOD *chol = (Mat_CHOLMOD *)F->data;
66: cholmod_common *c = chol->common;
67: PetscBool flg;
69: PetscFunctionBegin;
70: PetscOptionsBegin(PetscObjectComm((PetscObject)F), ((PetscObject)F)->prefix, "CHOLMOD Options", "Mat");
71: CHOLMOD_OPTION_INT(nmethods, "Number of different ordering methods to try");
73: #if defined(PETSC_USE_SUITESPARSE_GPU)
74: c->useGPU = 1;
75: CHOLMOD_OPTION_INT(useGPU, "Use GPU for BLAS 1, otherwise 0");
76: CHOLMOD_OPTION_SIZE_T(maxGpuMemBytes, "Maximum memory to allocate on the GPU");
77: CHOLMOD_OPTION_DOUBLE(maxGpuMemFraction, "Fraction of available GPU memory to allocate");
78: #endif
80: /* CHOLMOD handles first-time packing and refactor-packing separately, but we usually want them to be the same. */
81: chol->pack = (PetscBool)c->final_pack;
82: PetscCall(PetscOptionsBool("-mat_cholmod_pack", "Pack factors after factorization [disable for frequent repeat factorization]", "None", chol->pack, &chol->pack, NULL));
83: c->final_pack = (int)chol->pack;
85: CHOLMOD_OPTION_DOUBLE(dbound, "Minimum absolute value of diagonal entries of D");
86: CHOLMOD_OPTION_DOUBLE(grow0, "Global growth ratio when factors are modified");
87: CHOLMOD_OPTION_DOUBLE(grow1, "Column growth ratio when factors are modified");
88: CHOLMOD_OPTION_SIZE_T(grow2, "Affine column growth constant when factors are modified");
89: CHOLMOD_OPTION_SIZE_T(maxrank, "Max rank of update, larger values are faster but use more memory [2,4,8]");
90: {
91: static const char *const list[] = {"SIMPLICIAL", "AUTO", "SUPERNODAL", "MatCholmodFactorType", "MAT_CHOLMOD_FACTOR_", 0};
92: PetscCall(PetscOptionsEnum("-mat_cholmod_factor", "Factorization method", "None", list, (PetscEnum)c->supernodal, (PetscEnum *)&c->supernodal, NULL));
93: }
94: if (c->supernodal) CHOLMOD_OPTION_DOUBLE(supernodal_switch, "flop/nnz_L threshold for switching to supernodal factorization");
95: CHOLMOD_OPTION_BOOL(final_asis, "Leave factors \"as is\"");
96: CHOLMOD_OPTION_BOOL(final_pack, "Pack the columns when finished (use FALSE if the factors will be updated later)");
97: if (!c->final_asis) {
98: CHOLMOD_OPTION_BOOL(final_super, "Leave supernodal factors instead of converting to simplicial");
99: CHOLMOD_OPTION_BOOL(final_ll, "Turn LDL' factorization into LL'");
100: CHOLMOD_OPTION_BOOL(final_monotonic, "Ensure columns are monotonic when done");
101: CHOLMOD_OPTION_BOOL(final_resymbol, "Remove numerically zero values resulting from relaxed supernodal amalgamation");
102: }
103: {
104: PetscReal tmp[] = {(PetscReal)c->zrelax[0], (PetscReal)c->zrelax[1], (PetscReal)c->zrelax[2]};
105: PetscInt n = 3;
106: PetscCall(PetscOptionsRealArray("-mat_cholmod_zrelax", "3 real supernodal relaxed amalgamation parameters", "None", tmp, &n, &flg));
107: PetscCheck(!flg || n == 3, PetscObjectComm((PetscObject)F), PETSC_ERR_ARG_OUTOFRANGE, "must provide exactly 3 parameters to -mat_cholmod_zrelax");
108: if (flg)
109: while (n--) c->zrelax[n] = (double)tmp[n];
110: }
111: {
112: PetscInt n, tmp[] = {(PetscInt)c->nrelax[0], (PetscInt)c->nrelax[1], (PetscInt)c->nrelax[2]};
113: PetscCall(PetscOptionsIntArray("-mat_cholmod_nrelax", "3 size_t supernodal relaxed amalgamation parameters", "None", tmp, &n, &flg));
114: PetscCheck(!flg || n == 3, PetscObjectComm((PetscObject)F), PETSC_ERR_ARG_OUTOFRANGE, "must provide exactly 3 parameters to -mat_cholmod_nrelax");
115: if (flg)
116: while (n--) c->nrelax[n] = (size_t)tmp[n];
117: }
118: CHOLMOD_OPTION_BOOL(prefer_upper, "Work with upper triangular form [faster when using fill-reducing ordering, slower in natural ordering]");
119: CHOLMOD_OPTION_BOOL(default_nesdis, "Use NESDIS instead of METIS for nested dissection");
120: CHOLMOD_OPTION_INT(print, "Verbosity level");
121: PetscOptionsEnd();
122: PetscFunctionReturn(PETSC_SUCCESS);
123: }
125: PetscErrorCode CholmodStart(Mat F)
126: {
127: Mat_CHOLMOD *chol = (Mat_CHOLMOD *)F->data;
128: cholmod_common *c;
130: PetscFunctionBegin;
131: if (chol->common) PetscFunctionReturn(PETSC_SUCCESS);
132: PetscCall(PetscMalloc1(1, &chol->common));
133: PetscCallExternal(!cholmod_X_start, chol->common);
135: c = chol->common;
136: c->error_handler = CholmodErrorHandler;
137: PetscFunctionReturn(PETSC_SUCCESS);
138: }
140: static PetscErrorCode MatWrapCholmod_seqsbaij(Mat A, PetscBool values, cholmod_sparse *C, PetscBool *aijalloc, PetscBool *valloc)
141: {
142: Mat_SeqSBAIJ *sbaij = (Mat_SeqSBAIJ *)A->data;
143: PetscBool vallocin = PETSC_FALSE;
145: PetscFunctionBegin;
146: PetscCall(PetscMemzero(C, sizeof(*C)));
147: /* CHOLMOD uses column alignment, SBAIJ stores the upper factor, so we pass it on as a lower factor, swapping the meaning of row and column */
148: C->nrow = (size_t)A->cmap->n;
149: C->ncol = (size_t)A->rmap->n;
150: C->nzmax = (size_t)sbaij->maxnz;
151: C->p = sbaij->i;
152: C->i = sbaij->j;
153: if (values) {
154: #if defined(PETSC_USE_COMPLEX)
155: /* we need to pass CHOLMOD the conjugate matrix */
156: PetscScalar *v;
157: PetscInt i;
159: PetscCall(PetscMalloc1(sbaij->maxnz, &v));
160: for (i = 0; i < sbaij->maxnz; i++) v[i] = PetscConj(sbaij->a[i]);
161: C->x = v;
162: vallocin = PETSC_TRUE;
163: #else
164: C->x = sbaij->a;
165: #endif
166: }
167: C->stype = -1;
168: C->itype = CHOLMOD_INT_TYPE;
169: C->xtype = values ? CHOLMOD_SCALAR_TYPE : CHOLMOD_PATTERN;
170: C->dtype = CHOLMOD_DOUBLE;
171: C->sorted = 1;
172: C->packed = 1;
173: *aijalloc = PETSC_FALSE;
174: *valloc = vallocin;
175: PetscFunctionReturn(PETSC_SUCCESS);
176: }
178: #define GET_ARRAY_READ 0
179: #define GET_ARRAY_WRITE 1
181: PetscErrorCode VecWrapCholmod(Vec X, PetscInt rw, cholmod_dense *Y)
182: {
183: PetscScalar *x;
184: PetscInt n;
186: PetscFunctionBegin;
187: PetscCall(PetscMemzero(Y, sizeof(*Y)));
188: switch (rw) {
189: case GET_ARRAY_READ:
190: PetscCall(VecGetArrayRead(X, (const PetscScalar **)&x));
191: break;
192: case GET_ARRAY_WRITE:
193: PetscCall(VecGetArrayWrite(X, &x));
194: break;
195: default:
196: SETERRQ(PETSC_COMM_SELF, PETSC_ERR_SUP, "Case %" PetscInt_FMT " not handled", rw);
197: break;
198: }
199: PetscCall(VecGetSize(X, &n));
201: Y->x = x;
202: Y->nrow = n;
203: Y->ncol = 1;
204: Y->nzmax = n;
205: Y->d = n;
206: Y->xtype = CHOLMOD_SCALAR_TYPE;
207: Y->dtype = CHOLMOD_DOUBLE;
208: PetscFunctionReturn(PETSC_SUCCESS);
209: }
211: PetscErrorCode VecUnWrapCholmod(Vec X, PetscInt rw, cholmod_dense *Y)
212: {
213: PetscFunctionBegin;
214: switch (rw) {
215: case GET_ARRAY_READ:
216: PetscCall(VecRestoreArrayRead(X, (const PetscScalar **)&Y->x));
217: break;
218: case GET_ARRAY_WRITE:
219: PetscCall(VecRestoreArrayWrite(X, (PetscScalar **)&Y->x));
220: break;
221: default:
222: SETERRQ(PETSC_COMM_SELF, PETSC_ERR_SUP, "Case %" PetscInt_FMT " not handled", rw);
223: break;
224: }
225: PetscFunctionReturn(PETSC_SUCCESS);
226: }
228: PetscErrorCode MatDenseWrapCholmod(Mat X, PetscInt rw, cholmod_dense *Y)
229: {
230: PetscScalar *x;
231: PetscInt m, n, lda;
233: PetscFunctionBegin;
234: PetscCall(PetscMemzero(Y, sizeof(*Y)));
235: switch (rw) {
236: case GET_ARRAY_READ:
237: PetscCall(MatDenseGetArrayRead(X, (const PetscScalar **)&x));
238: break;
239: case GET_ARRAY_WRITE:
240: PetscCall(MatDenseGetArrayWrite(X, &x));
241: break;
242: default:
243: SETERRQ(PETSC_COMM_SELF, PETSC_ERR_SUP, "Case %" PetscInt_FMT " not handled", rw);
244: break;
245: }
246: PetscCall(MatDenseGetLDA(X, &lda));
247: PetscCall(MatGetLocalSize(X, &m, &n));
249: Y->x = x;
250: Y->nrow = m;
251: Y->ncol = n;
252: Y->nzmax = lda * n;
253: Y->d = lda;
254: Y->xtype = CHOLMOD_SCALAR_TYPE;
255: Y->dtype = CHOLMOD_DOUBLE;
256: PetscFunctionReturn(PETSC_SUCCESS);
257: }
259: PetscErrorCode MatDenseUnWrapCholmod(Mat X, PetscInt rw, cholmod_dense *Y)
260: {
261: PetscFunctionBegin;
262: switch (rw) {
263: case GET_ARRAY_READ:
264: PetscCall(MatDenseRestoreArrayRead(X, (const PetscScalar **)&Y->x));
265: break;
266: case GET_ARRAY_WRITE:
267: /* we don't have MatDenseRestoreArrayWrite */
268: PetscCall(MatDenseRestoreArray(X, (PetscScalar **)&Y->x));
269: break;
270: default:
271: SETERRQ(PETSC_COMM_SELF, PETSC_ERR_SUP, "Case %" PetscInt_FMT " not handled", rw);
272: break;
273: }
274: PetscFunctionReturn(PETSC_SUCCESS);
275: }
277: PETSC_INTERN PetscErrorCode MatDestroy_CHOLMOD(Mat F)
278: {
279: Mat_CHOLMOD *chol = (Mat_CHOLMOD *)F->data;
281: PetscFunctionBegin;
282: if (chol->spqrfact) PetscCallExternal(!SuiteSparseQR_C_free, &chol->spqrfact, chol->common);
283: if (chol->factor) PetscCallExternal(!cholmod_X_free_factor, &chol->factor, chol->common);
284: if (chol->common->itype == CHOLMOD_INT) {
285: PetscCallExternal(!cholmod_finish, chol->common);
286: } else {
287: PetscCallExternal(!cholmod_l_finish, chol->common);
288: }
289: PetscCall(PetscFree(chol->common));
290: PetscCall(PetscFree(chol->matrix));
291: PetscCall(PetscObjectComposeFunction((PetscObject)F, "MatFactorGetSolverType_C", NULL));
292: PetscCall(PetscObjectComposeFunction((PetscObject)F, "MatQRFactorSymbolic_C", NULL));
293: PetscCall(PetscObjectComposeFunction((PetscObject)F, "MatQRFactorNumeric_C", NULL));
294: PetscCall(PetscFree(F->data));
295: PetscFunctionReturn(PETSC_SUCCESS);
296: }
298: static PetscErrorCode MatSolve_CHOLMOD(Mat, Vec, Vec);
299: static PetscErrorCode MatMatSolve_CHOLMOD(Mat, Mat, Mat);
301: /*static const char *const CholmodOrderingMethods[] = {"User","AMD","METIS","NESDIS(default)","Natural","NESDIS(small=20000)","NESDIS(small=4,no constrained)","NESDIS()"};*/
303: static PetscErrorCode MatView_Info_CHOLMOD(Mat F, PetscViewer viewer)
304: {
305: Mat_CHOLMOD *chol = (Mat_CHOLMOD *)F->data;
306: const cholmod_common *c = chol->common;
307: PetscInt i;
309: PetscFunctionBegin;
310: if (F->ops->solve != MatSolve_CHOLMOD) PetscFunctionReturn(PETSC_SUCCESS);
311: PetscCall(PetscViewerASCIIPrintf(viewer, "CHOLMOD run parameters:\n"));
312: PetscCall(PetscViewerASCIIPushTab(viewer));
313: PetscCall(PetscViewerASCIIPrintf(viewer, "Pack factors after symbolic factorization: %s\n", chol->pack ? "TRUE" : "FALSE"));
314: PetscCall(PetscViewerASCIIPrintf(viewer, "Common.dbound %g (Smallest absolute value of diagonal entries of D)\n", c->dbound));
315: PetscCall(PetscViewerASCIIPrintf(viewer, "Common.grow0 %g\n", c->grow0));
316: PetscCall(PetscViewerASCIIPrintf(viewer, "Common.grow1 %g\n", c->grow1));
317: PetscCall(PetscViewerASCIIPrintf(viewer, "Common.grow2 %u\n", (unsigned)c->grow2));
318: PetscCall(PetscViewerASCIIPrintf(viewer, "Common.maxrank %u\n", (unsigned)c->maxrank));
319: PetscCall(PetscViewerASCIIPrintf(viewer, "Common.supernodal_switch %g\n", c->supernodal_switch));
320: PetscCall(PetscViewerASCIIPrintf(viewer, "Common.supernodal %d\n", c->supernodal));
321: PetscCall(PetscViewerASCIIPrintf(viewer, "Common.final_asis %d\n", c->final_asis));
322: PetscCall(PetscViewerASCIIPrintf(viewer, "Common.final_super %d\n", c->final_super));
323: PetscCall(PetscViewerASCIIPrintf(viewer, "Common.final_ll %d\n", c->final_ll));
324: PetscCall(PetscViewerASCIIPrintf(viewer, "Common.final_pack %d\n", c->final_pack));
325: PetscCall(PetscViewerASCIIPrintf(viewer, "Common.final_monotonic %d\n", c->final_monotonic));
326: PetscCall(PetscViewerASCIIPrintf(viewer, "Common.final_resymbol %d\n", c->final_resymbol));
327: PetscCall(PetscViewerASCIIPrintf(viewer, "Common.zrelax [%g,%g,%g]\n", c->zrelax[0], c->zrelax[1], c->zrelax[2]));
328: PetscCall(PetscViewerASCIIPrintf(viewer, "Common.nrelax [%u,%u,%u]\n", (unsigned)c->nrelax[0], (unsigned)c->nrelax[1], (unsigned)c->nrelax[2]));
329: PetscCall(PetscViewerASCIIPrintf(viewer, "Common.prefer_upper %d\n", c->prefer_upper));
330: PetscCall(PetscViewerASCIIPrintf(viewer, "Common.print %d\n", c->print));
331: for (i = 0; i < c->nmethods; i++) {
332: PetscCall(PetscViewerASCIIPrintf(viewer, "Ordering method %" PetscInt_FMT "%s:\n", i, i == c->selected ? " [SELECTED]" : ""));
333: PetscCall(PetscViewerASCIIPrintf(viewer, " lnz %g, fl %g, prune_dense %g, prune_dense2 %g\n", c->method[i].lnz, c->method[i].fl, c->method[i].prune_dense, c->method[i].prune_dense2));
334: }
335: PetscCall(PetscViewerASCIIPrintf(viewer, "Common.postorder %d\n", c->postorder));
336: PetscCall(PetscViewerASCIIPrintf(viewer, "Common.default_nesdis %d (use NESDIS instead of METIS for nested dissection)\n", c->default_nesdis));
337: /* Statistics */
338: PetscCall(PetscViewerASCIIPrintf(viewer, "Common.fl %g (flop count from most recent analysis)\n", c->fl));
339: PetscCall(PetscViewerASCIIPrintf(viewer, "Common.lnz %g (fundamental nz in L)\n", c->lnz));
340: PetscCall(PetscViewerASCIIPrintf(viewer, "Common.anz %g\n", c->anz));
341: PetscCall(PetscViewerASCIIPrintf(viewer, "Common.modfl %g (flop count from most recent update)\n", c->modfl));
342: PetscCall(PetscViewerASCIIPrintf(viewer, "Common.malloc_count %g (number of live objects)\n", (double)c->malloc_count));
343: PetscCall(PetscViewerASCIIPrintf(viewer, "Common.memory_usage %g (peak memory usage in bytes)\n", (double)c->memory_usage));
344: PetscCall(PetscViewerASCIIPrintf(viewer, "Common.memory_inuse %g (current memory usage in bytes)\n", (double)c->memory_inuse));
345: PetscCall(PetscViewerASCIIPrintf(viewer, "Common.nrealloc_col %g (number of column reallocations)\n", c->nrealloc_col));
346: PetscCall(PetscViewerASCIIPrintf(viewer, "Common.nrealloc_factor %g (number of factor reallocations due to column reallocations)\n", c->nrealloc_factor));
347: PetscCall(PetscViewerASCIIPrintf(viewer, "Common.ndbounds_hit %g (number of times diagonal was modified by dbound)\n", c->ndbounds_hit));
348: PetscCall(PetscViewerASCIIPrintf(viewer, "Common.rowfacfl %g (number of flops in last call to cholmod_rowfac)\n", c->rowfacfl));
349: PetscCall(PetscViewerASCIIPrintf(viewer, "Common.aatfl %g (number of flops to compute A(:,f)*A(:,f)')\n", c->aatfl));
350: #if defined(PETSC_USE_SUITESPARSE_GPU)
351: PetscCall(PetscViewerASCIIPrintf(viewer, "Common.useGPU %d\n", c->useGPU));
352: #endif
353: PetscCall(PetscViewerASCIIPopTab(viewer));
354: PetscFunctionReturn(PETSC_SUCCESS);
355: }
357: PETSC_INTERN PetscErrorCode MatView_CHOLMOD(Mat F, PetscViewer viewer)
358: {
359: PetscBool iascii;
360: PetscViewerFormat format;
362: PetscFunctionBegin;
363: PetscCall(PetscObjectTypeCompare((PetscObject)viewer, PETSCVIEWERASCII, &iascii));
364: if (iascii) {
365: PetscCall(PetscViewerGetFormat(viewer, &format));
366: if (format == PETSC_VIEWER_ASCII_INFO) PetscCall(MatView_Info_CHOLMOD(F, viewer));
367: }
368: PetscFunctionReturn(PETSC_SUCCESS);
369: }
371: static PetscErrorCode MatSolve_CHOLMOD(Mat F, Vec B, Vec X)
372: {
373: Mat_CHOLMOD *chol = (Mat_CHOLMOD *)F->data;
374: cholmod_dense cholB, cholX, *X_handle, *Y_handle = NULL, *E_handle = NULL;
376: PetscFunctionBegin;
377: static_F = F;
378: PetscCall(VecWrapCholmod(B, GET_ARRAY_READ, &cholB));
379: PetscCall(VecWrapCholmod(X, GET_ARRAY_WRITE, &cholX));
380: X_handle = &cholX;
381: PetscCallExternal(!cholmod_X_solve2, CHOLMOD_A, chol->factor, &cholB, NULL, &X_handle, NULL, &Y_handle, &E_handle, chol->common);
382: PetscCallExternal(!cholmod_X_free_dense, &Y_handle, chol->common);
383: PetscCallExternal(!cholmod_X_free_dense, &E_handle, chol->common);
384: PetscCall(VecUnWrapCholmod(B, GET_ARRAY_READ, &cholB));
385: PetscCall(VecUnWrapCholmod(X, GET_ARRAY_WRITE, &cholX));
386: PetscCall(PetscLogFlops(4.0 * chol->common->lnz));
387: PetscFunctionReturn(PETSC_SUCCESS);
388: }
390: static PetscErrorCode MatMatSolve_CHOLMOD(Mat F, Mat B, Mat X)
391: {
392: Mat_CHOLMOD *chol = (Mat_CHOLMOD *)F->data;
393: cholmod_dense cholB, cholX, *X_handle, *Y_handle = NULL, *E_handle = NULL;
395: PetscFunctionBegin;
396: static_F = F;
397: PetscCall(MatDenseWrapCholmod(B, GET_ARRAY_READ, &cholB));
398: PetscCall(MatDenseWrapCholmod(X, GET_ARRAY_WRITE, &cholX));
399: X_handle = &cholX;
400: PetscCallExternal(!cholmod_X_solve2, CHOLMOD_A, chol->factor, &cholB, NULL, &X_handle, NULL, &Y_handle, &E_handle, chol->common);
401: PetscCallExternal(!cholmod_X_free_dense, &Y_handle, chol->common);
402: PetscCallExternal(!cholmod_X_free_dense, &E_handle, chol->common);
403: PetscCall(MatDenseUnWrapCholmod(B, GET_ARRAY_READ, &cholB));
404: PetscCall(MatDenseUnWrapCholmod(X, GET_ARRAY_WRITE, &cholX));
405: PetscCall(PetscLogFlops(4.0 * B->cmap->n * chol->common->lnz));
406: PetscFunctionReturn(PETSC_SUCCESS);
407: }
409: static PetscErrorCode MatCholeskyFactorNumeric_CHOLMOD(Mat F, Mat A, const MatFactorInfo *info)
410: {
411: Mat_CHOLMOD *chol = (Mat_CHOLMOD *)F->data;
412: cholmod_sparse cholA;
413: PetscBool aijalloc, valloc;
414: int err;
416: PetscFunctionBegin;
417: PetscCall((*chol->Wrap)(A, PETSC_TRUE, &cholA, &aijalloc, &valloc));
418: static_F = F;
419: err = !cholmod_X_factorize(&cholA, chol->factor, chol->common);
420: PetscCheck(!err, PetscObjectComm((PetscObject)F), PETSC_ERR_LIB, "CHOLMOD factorization failed with status %d", chol->common->status);
421: PetscCheck(chol->common->status != CHOLMOD_NOT_POSDEF, PetscObjectComm((PetscObject)F), PETSC_ERR_MAT_CH_ZRPVT, "CHOLMOD detected that the matrix is not positive definite, failure at column %u", (unsigned)chol->factor->minor);
423: PetscCall(PetscLogFlops(chol->common->fl));
424: if (aijalloc) PetscCall(PetscFree2(cholA.p, cholA.i));
425: if (valloc) PetscCall(PetscFree(cholA.x));
426: #if defined(PETSC_USE_SUITESPARSE_GPU)
427: PetscCall(PetscLogGpuTimeAdd(chol->common->CHOLMOD_GPU_GEMM_TIME + chol->common->CHOLMOD_GPU_SYRK_TIME + chol->common->CHOLMOD_GPU_TRSM_TIME + chol->common->CHOLMOD_GPU_POTRF_TIME));
428: #endif
430: F->ops->solve = MatSolve_CHOLMOD;
431: F->ops->solvetranspose = MatSolve_CHOLMOD;
432: F->ops->matsolve = MatMatSolve_CHOLMOD;
433: F->ops->matsolvetranspose = MatMatSolve_CHOLMOD;
434: PetscFunctionReturn(PETSC_SUCCESS);
435: }
437: PETSC_INTERN PetscErrorCode MatCholeskyFactorSymbolic_CHOLMOD(Mat F, Mat A, IS perm, const MatFactorInfo *info)
438: {
439: Mat_CHOLMOD *chol = (Mat_CHOLMOD *)F->data;
440: int err;
441: cholmod_sparse cholA;
442: PetscBool aijalloc, valloc;
443: PetscInt *fset = 0;
444: size_t fsize = 0;
446: PetscFunctionBegin;
447: /* Set options to F */
448: PetscCall(CholmodSetOptions(F));
450: PetscCall((*chol->Wrap)(A, PETSC_FALSE, &cholA, &aijalloc, &valloc));
451: static_F = F;
452: if (chol->factor) {
453: err = !cholmod_X_resymbol(&cholA, fset, fsize, (int)chol->pack, chol->factor, chol->common);
454: PetscCheck(!err, PetscObjectComm((PetscObject)F), PETSC_ERR_LIB, "CHOLMOD analysis failed with status %d", chol->common->status);
455: } else if (perm) {
456: const PetscInt *ip;
457: PetscCall(ISGetIndices(perm, &ip));
458: chol->factor = cholmod_X_analyze_p(&cholA, (PetscInt *)ip, fset, fsize, chol->common);
459: PetscCheck(chol->factor, PetscObjectComm((PetscObject)F), PETSC_ERR_LIB, "CHOLMOD analysis failed using PETSc ordering with status %d", chol->common->status);
460: PetscCall(ISRestoreIndices(perm, &ip));
461: } else {
462: chol->factor = cholmod_X_analyze(&cholA, chol->common);
463: PetscCheck(chol->factor, PetscObjectComm((PetscObject)F), PETSC_ERR_LIB, "CHOLMOD analysis failed using internal ordering with status %d", chol->common->status);
464: }
466: if (aijalloc) PetscCall(PetscFree2(cholA.p, cholA.i));
467: if (valloc) PetscCall(PetscFree(cholA.x));
469: F->ops->choleskyfactornumeric = MatCholeskyFactorNumeric_CHOLMOD;
470: PetscFunctionReturn(PETSC_SUCCESS);
471: }
473: static PetscErrorCode MatFactorGetSolverType_seqsbaij_cholmod(Mat A, MatSolverType *type)
474: {
475: PetscFunctionBegin;
476: *type = MATSOLVERCHOLMOD;
477: PetscFunctionReturn(PETSC_SUCCESS);
478: }
480: PETSC_INTERN PetscErrorCode MatGetInfo_CHOLMOD(Mat F, MatInfoType flag, MatInfo *info)
481: {
482: Mat_CHOLMOD *chol = (Mat_CHOLMOD *)F->data;
484: PetscFunctionBegin;
485: info->block_size = 1.0;
486: info->nz_allocated = chol->common->lnz;
487: info->nz_used = chol->common->lnz;
488: info->nz_unneeded = 0.0;
489: info->assemblies = 0.0;
490: info->mallocs = 0.0;
491: info->memory = chol->common->memory_inuse;
492: info->fill_ratio_given = 0;
493: info->fill_ratio_needed = 0;
494: info->factor_mallocs = chol->common->malloc_count;
495: PetscFunctionReturn(PETSC_SUCCESS);
496: }
498: /*MC
499: MATSOLVERCHOLMOD
501: A matrix type providing direct solvers (Cholesky) for sequential matrices
502: via the external package CHOLMOD.
504: Use `./configure --download-suitesparse` to install PETSc to use CHOLMOD
506: Use `-pc_type cholesky` `-pc_factor_mat_solver_type cholmod` to use this direct solver
508: Consult CHOLMOD documentation for more information about the common parameters
509: which correspond to the options database keys below.
511: Options Database Keys:
512: + -mat_cholmod_dbound <0> - Minimum absolute value of diagonal entries of D (None)
513: . -mat_cholmod_grow0 <1.2> - Global growth ratio when factors are modified (None)
514: . -mat_cholmod_grow1 <1.2> - Column growth ratio when factors are modified (None)
515: . -mat_cholmod_grow2 <5> - Affine column growth constant when factors are modified (None)
516: . -mat_cholmod_maxrank <8> - Max rank of update, larger values are faster but use more memory [2,4,8] (None)
517: . -mat_cholmod_factor <AUTO> - (choose one of) `SIMPLICIAL`, `AUTO`, `SUPERNODAL`
518: . -mat_cholmod_supernodal_switch <40> - flop/nnz_L threshold for switching to supernodal factorization (None)
519: . -mat_cholmod_final_asis <TRUE> - Leave factors "as is" (None)
520: . -mat_cholmod_final_pack <TRUE> - Pack the columns when finished (use FALSE if the factors will be updated later) (None)
521: . -mat_cholmod_zrelax <0.8> - 3 real supernodal relaxed amalgamation parameters (None)
522: . -mat_cholmod_nrelax <4> - 3 size_t supernodal relaxed amalgamation parameters (None)
523: . -mat_cholmod_prefer_upper <TRUE> - Work with upper triangular form (faster when using fill-reducing ordering, slower in natural ordering) (None)
524: . -mat_cholmod_print <3> - Verbosity level (None)
525: - -mat_ordering_type internal - Use the ordering provided by Cholmod
527: Level: beginner
529: Note:
530: CHOLMOD is part of SuiteSparse http://faculty.cse.tamu.edu/davis/suitesparse.html
532: .seealso: [](ch_matrices), `Mat`, `PCCHOLESKY`, `PCFactorSetMatSolverType()`, `MatSolverType`
533: M*/
535: PETSC_INTERN PetscErrorCode MatGetFactor_seqsbaij_cholmod(Mat A, MatFactorType ftype, Mat *F)
536: {
537: Mat B;
538: Mat_CHOLMOD *chol;
539: PetscInt m = A->rmap->n, n = A->cmap->n, bs;
541: PetscFunctionBegin;
542: PetscCall(MatGetBlockSize(A, &bs));
543: PetscCheck(bs == 1, PetscObjectComm((PetscObject)A), PETSC_ERR_SUP, "CHOLMOD only supports block size=1, given %" PetscInt_FMT, bs);
544: #if defined(PETSC_USE_COMPLEX)
545: PetscCheck(A->hermitian == PETSC_BOOL3_TRUE, PetscObjectComm((PetscObject)A), PETSC_ERR_SUP, "Only for Hermitian matrices");
546: #endif
547: /* Create the factorization matrix F */
548: PetscCall(MatCreate(PetscObjectComm((PetscObject)A), &B));
549: PetscCall(MatSetSizes(B, PETSC_DECIDE, PETSC_DECIDE, m, n));
550: PetscCall(PetscStrallocpy("cholmod", &((PetscObject)B)->type_name));
551: PetscCall(MatSetUp(B));
552: PetscCall(PetscNew(&chol));
554: chol->Wrap = MatWrapCholmod_seqsbaij;
555: B->data = chol;
557: B->ops->getinfo = MatGetInfo_CHOLMOD;
558: B->ops->view = MatView_CHOLMOD;
559: B->ops->choleskyfactorsymbolic = MatCholeskyFactorSymbolic_CHOLMOD;
560: B->ops->destroy = MatDestroy_CHOLMOD;
561: PetscCall(PetscObjectComposeFunction((PetscObject)B, "MatFactorGetSolverType_C", MatFactorGetSolverType_seqsbaij_cholmod));
562: B->factortype = MAT_FACTOR_CHOLESKY;
563: B->assembled = PETSC_TRUE;
564: B->preallocated = PETSC_TRUE;
566: PetscCall(CholmodStart(B));
568: PetscCall(PetscFree(B->solvertype));
569: PetscCall(PetscStrallocpy(MATSOLVERCHOLMOD, &B->solvertype));
570: B->canuseordering = PETSC_TRUE;
571: PetscCall(PetscStrallocpy(MATORDERINGEXTERNAL, (char **)&B->preferredordering[MAT_FACTOR_CHOLESKY]));
572: *F = B;
573: PetscFunctionReturn(PETSC_SUCCESS);
574: }