Actual source code: dmmbmat.cxx
1: #include <petsc/private/dmmbimpl.h>
2: #include <petsc/private/vecimpl.h>
4: #include <petscdmmoab.h>
5: #include <MBTagConventions.hpp>
6: #include <moab/NestedRefine.hpp>
8: PETSC_EXTERN PetscErrorCode DMMoab_Compute_NNZ_From_Connectivity(DM, PetscInt *, PetscInt *, PetscInt *, PetscInt *, PetscBool);
10: PETSC_EXTERN PetscErrorCode DMCreateMatrix_Moab(DM dm, Mat *J)
11: {
12: PetscInt innz = 0, ionz = 0, nlsiz;
13: DM_Moab *dmmoab = (DM_Moab *)dm->data;
14: PetscInt *nnz = 0, *onz = 0;
15: char *tmp = 0;
16: Mat A;
17: MatType mtype;
22: /* next, need to allocate the non-zero arrays to enable pre-allocation */
23: mtype = dm->mattype;
24: PetscStrstr(mtype, MATBAIJ, &tmp);
25: nlsiz = (tmp ? dmmoab->nloc : dmmoab->nloc * dmmoab->numFields);
27: /* allocate the nnz, onz arrays based on block size and local nodes */
28: PetscCalloc2(nlsiz, &nnz, nlsiz, &onz);
30: /* compute the nonzero pattern based on MOAB connectivity data for local elements */
31: DMMoab_Compute_NNZ_From_Connectivity(dm, &innz, nnz, &ionz, onz, (tmp ? PETSC_TRUE : PETSC_FALSE));
33: /* create the Matrix and set its type as specified by user */
34: MatCreate((((PetscObject)dm)->comm), &A);
35: MatSetSizes(A, dmmoab->nloc * dmmoab->numFields, dmmoab->nloc * dmmoab->numFields, PETSC_DETERMINE, PETSC_DETERMINE);
36: MatSetType(A, mtype);
37: MatSetBlockSize(A, dmmoab->bs);
38: MatSetDM(A, dm); /* set DM reference */
39: MatSetFromOptions(A);
42: MatSetLocalToGlobalMapping(A, dmmoab->ltog_map, dmmoab->ltog_map);
44: /* set preallocation based on different supported Mat types */
45: MatSeqAIJSetPreallocation(A, innz, nnz);
46: MatMPIAIJSetPreallocation(A, innz, nnz, ionz, onz);
47: MatSeqBAIJSetPreallocation(A, dmmoab->bs, innz, nnz);
48: MatMPIBAIJSetPreallocation(A, dmmoab->bs, innz, nnz, ionz, onz);
50: /* clean up temporary memory */
51: PetscFree2(nnz, onz);
53: /* set up internal matrix data-structures */
54: MatSetUp(A);
56: /* MatSetOption(A, MAT_NEW_NONZERO_ALLOCATION_ERR, PETSC_FALSE); */
58: *J = A;
59: return 0;
60: }
62: PETSC_EXTERN PetscErrorCode DMMoab_Compute_NNZ_From_Connectivity(DM dm, PetscInt *innz, PetscInt *nnz, PetscInt *ionz, PetscInt *onz, PetscBool isbaij)
63: {
64: PetscInt i, f, nloc, vpere, bs, n_nnz, n_onz, ivtx = 0;
65: PetscInt ibs, jbs, inbsize, iobsize, nfields, nlsiz;
66: DM_Moab *dmmoab = (DM_Moab *)dm->data;
67: moab::Range found;
68: std::vector<moab::EntityHandle> adjs, storage;
69: PetscBool isinterlaced;
70: moab::EntityHandle vtx;
71: moab::ErrorCode merr;
73: bs = dmmoab->bs;
74: nloc = dmmoab->nloc;
75: nfields = dmmoab->numFields;
76: isinterlaced = (isbaij || bs == nfields ? PETSC_TRUE : PETSC_FALSE);
77: nlsiz = (isinterlaced ? nloc : nloc * nfields);
79: /* loop over the locally owned vertices and figure out the NNZ pattern using connectivity information */
80: for (moab::Range::const_iterator iter = dmmoab->vowned->begin(); iter != dmmoab->vowned->end(); iter++, ivtx++) {
81: vtx = *iter;
82: /* Get adjacency information for current vertex - i.e., all elements of dimension (dim) that connects
83: to the current vertex. We can then decipher if a vertex is ghosted or not and compute the
84: non-zero pattern accordingly. */
85: adjs.clear();
86: if (dmmoab->hlevel && (dmmoab->pcomm->size() == 1)) {
87: merr = dmmoab->hierarchy->get_adjacencies(vtx, dmmoab->dim, adjs);
88: MBERRNM(merr);
89: } else {
90: merr = dmmoab->mbiface->get_adjacencies(&vtx, 1, dmmoab->dim, true, adjs, moab::Interface::UNION);
91: MBERRNM(merr);
92: }
94: /* reset counters */
95: n_nnz = n_onz = 0;
96: found.clear();
98: /* loop over vertices and update the number of connectivity */
99: for (unsigned jter = 0; jter < adjs.size(); ++jter) {
100: /* Get connectivity information in canonical ordering for the local element */
101: const moab::EntityHandle *connect;
102: std::vector<moab::EntityHandle> cconnect;
103: merr = dmmoab->mbiface->get_connectivity(adjs[jter], connect, vpere, false, &storage);
104: MBERRNM(merr);
106: /* loop over each element connected to the adjacent vertex and update as needed */
107: for (i = 0; i < vpere; ++i) {
108: /* find the truly user-expected layer of ghosted entities to decipher NNZ pattern */
109: if (connect[i] == vtx || found.find(connect[i]) != found.end()) continue; /* make sure we don't double count shared vertices */
110: if (dmmoab->vghost->find(connect[i]) != dmmoab->vghost->end()) n_onz++; /* update out-of-proc onz */
111: else n_nnz++; /* else local vertex */
112: found.insert(connect[i]);
113: }
114: }
115: storage.clear();
117: if (isbaij) {
118: nnz[ivtx] = n_nnz; /* leave out self to avoid repeats -> node shared by multiple elements */
119: if (onz) { onz[ivtx] = n_onz; /* add ghost non-owned nodes */ }
120: } else { /* AIJ matrices */
121: if (!isinterlaced) {
122: for (f = 0; f < nfields; f++) {
123: nnz[f * nloc + ivtx] = n_nnz; /* leave out self to avoid repeats -> node shared by multiple elements */
124: if (onz) onz[f * nloc + ivtx] = n_onz; /* add ghost non-owned nodes */
125: }
126: } else {
127: for (f = 0; f < nfields; f++) {
128: nnz[nfields * ivtx + f] = n_nnz; /* leave out self to avoid repeats -> node shared by multiple elements */
129: if (onz) onz[nfields * ivtx + f] = n_onz; /* add ghost non-owned nodes */
130: }
131: }
132: }
133: }
135: for (i = 0; i < nlsiz; i++) nnz[i] += 1; /* self count the node */
137: for (ivtx = 0; ivtx < nloc; ivtx++) {
138: if (!isbaij) {
139: for (ibs = 0; ibs < nfields; ibs++) {
140: if (dmmoab->dfill) { /* first address the diagonal block */
141: /* just add up the ints -- easier/faster rather than branching based on "1" */
142: for (jbs = 0, inbsize = 0; jbs < nfields; jbs++) inbsize += dmmoab->dfill[ibs * nfields + jbs];
143: } else inbsize = nfields; /* dense coupling since user didn't specify the component fill explicitly */
144: if (isinterlaced) nnz[ivtx * nfields + ibs] *= inbsize;
145: else nnz[ibs * nloc + ivtx] *= inbsize;
147: if (onz) {
148: if (dmmoab->ofill) { /* next address the off-diagonal block */
149: /* just add up the ints -- easier/faster rather than branching based on "1" */
150: for (jbs = 0, iobsize = 0; jbs < nfields; jbs++) iobsize += dmmoab->dfill[ibs * nfields + jbs];
151: } else iobsize = nfields; /* dense coupling since user didn't specify the component fill explicitly */
152: if (isinterlaced) onz[ivtx * nfields + ibs] *= iobsize;
153: else onz[ibs * nloc + ivtx] *= iobsize;
154: }
155: }
156: } else {
157: /* check if we got overzealous in our nnz and onz computations */
158: nnz[ivtx] = (nnz[ivtx] > dmmoab->nloc ? dmmoab->nloc : nnz[ivtx]);
159: if (onz) onz[ivtx] = (onz[ivtx] > dmmoab->nloc ? dmmoab->nloc : onz[ivtx]);
160: }
161: }
162: /* update innz and ionz based on local maxima */
163: if (innz || ionz) {
164: if (innz) *innz = 0;
165: if (ionz) *ionz = 0;
166: for (i = 0; i < nlsiz; i++) {
167: if (innz && (nnz[i] > *innz)) *innz = nnz[i];
168: if ((ionz && onz) && (onz[i] > *ionz)) *ionz = onz[i];
169: }
170: }
171: return 0;
172: }
174: static PetscErrorCode DMMoabSetBlockFills_Private(PetscInt w, const PetscInt *fill, PetscInt **rfill)
175: {
176: PetscInt i, j, *ifill;
178: if (!fill) return 0;
179: PetscMalloc1(w * w, &ifill);
180: for (i = 0; i < w; i++) {
181: for (j = 0; j < w; j++) ifill[i * w + j] = fill[i * w + j];
182: }
184: *rfill = ifill;
185: return 0;
186: }
188: /*@C
189: DMMoabSetBlockFills - Sets the fill pattern in each block for a multi-component problem
190: of the matrix returned by DMCreateMatrix().
192: Logically Collective on da
194: Input Parameters:
195: + dm - the DMMoab object
196: . dfill - the fill pattern in the diagonal block (may be NULL, means use dense block)
197: - ofill - the fill pattern in the off-diagonal blocks
199: Level: developer
201: Notes:
202: This only makes sense when you are doing multicomponent problems but using the
203: MPIAIJ matrix format
205: The format for dfill and ofill is a 2 dimensional dof by dof matrix with 1 entries
206: representing coupling and 0 entries for missing coupling. For example
207: $ dfill[9] = {1, 0, 0,
208: $ 1, 1, 0,
209: $ 0, 1, 1}
210: means that row 0 is coupled with only itself in the diagonal block, row 1 is coupled with
211: itself and row 0 (in the diagonal block) and row 2 is coupled with itself and row 1 (in the
212: diagonal block).
214: DMDASetGetMatrix() allows you to provide general code for those more complicated nonzero patterns then
215: can be represented in the dfill, ofill format
217: Contributed by Glenn Hammond
219: .seealso `DMCreateMatrix()`, `DMDASetGetMatrix()`, `DMSetMatrixPreallocateOnly()`
221: @*/
222: PetscErrorCode DMMoabSetBlockFills(DM dm, const PetscInt *dfill, const PetscInt *ofill)
223: {
224: DM_Moab *dmmoab = (DM_Moab *)dm->data;
227: DMMoabSetBlockFills_Private(dmmoab->numFields, dfill, &dmmoab->dfill);
228: DMMoabSetBlockFills_Private(dmmoab->numFields, ofill, &dmmoab->ofill);
229: return 0;
230: }