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:   PetscErrorCode  ierr;
 13:   PetscInt        innz = 0, ionz = 0, nlsiz;
 14:   DM_Moab         *dmmoab = (DM_Moab*)dm->data;
 15:   PetscInt        *nnz = 0, *onz = 0;
 16:   char            *tmp = 0;
 17:   Mat             A;
 18:   MatType         mtype;


 24:   /* next, need to allocate the non-zero arrays to enable pre-allocation */
 25:   mtype = dm->mattype;
 26:   PetscStrstr(mtype, MATBAIJ, &tmp);
 27:   nlsiz = (tmp ? dmmoab->nloc : dmmoab->nloc * dmmoab->numFields);

 29:   /* allocate the nnz, onz arrays based on block size and local nodes */
 30:   PetscCalloc2(nlsiz, &nnz, nlsiz, &onz);

 32:   /* compute the nonzero pattern based on MOAB connectivity data for local elements */
 33:   DMMoab_Compute_NNZ_From_Connectivity(dm, &innz, nnz, &ionz, onz, (tmp ? PETSC_TRUE : PETSC_FALSE));

 35:   /* create the Matrix and set its type as specified by user */
 36:   MatCreate((((PetscObject)dm)->comm), &A);
 37:   MatSetSizes(A, dmmoab->nloc * dmmoab->numFields, dmmoab->nloc * dmmoab->numFields, PETSC_DETERMINE, PETSC_DETERMINE);
 38:   MatSetType(A, mtype);
 39:   MatSetBlockSize(A, dmmoab->bs);
 40:   MatSetDM(A, dm); /* set DM reference */
 41:   MatSetFromOptions(A);

 43:   if (!dmmoab->ltog_map) SETERRQ((((PetscObject)dm)->comm), PETSC_ERR_ORDER, "Cannot create a DMMoab Mat without calling DMSetUp first.");
 44:   MatSetLocalToGlobalMapping(A, dmmoab->ltog_map, dmmoab->ltog_map);

 46:   /* set preallocation based on different supported Mat types */
 47:   MatSeqAIJSetPreallocation(A, innz, nnz);
 48:   MatMPIAIJSetPreallocation(A, innz, nnz, ionz, onz);
 49:   MatSeqBAIJSetPreallocation(A, dmmoab->bs, innz, nnz);
 50:   MatMPIBAIJSetPreallocation(A, dmmoab->bs, innz, nnz, ionz, onz);

 52:   /* clean up temporary memory */
 53:   PetscFree2(nnz, onz);

 55:   /* set up internal matrix data-structures */
 56:   MatSetUp(A);

 58:   /* MatSetOption(A, MAT_NEW_NONZERO_ALLOCATION_ERR, PETSC_FALSE); */

 60:   *J = A;
 61:   return(0);
 62: }

 64: PETSC_EXTERN PetscErrorCode DMMoab_Compute_NNZ_From_Connectivity(DM dm, PetscInt* innz, PetscInt* nnz, PetscInt* ionz, PetscInt* onz, PetscBool isbaij)
 65: {
 66:   PetscInt        i, f, nloc, vpere, bs, n_nnz, n_onz, ivtx = 0;
 67:   PetscInt        ibs, jbs, inbsize, iobsize, nfields, nlsiz;
 68:   DM_Moab         *dmmoab = (DM_Moab*)dm->data;
 69:   moab::Range     found;
 70:   std::vector<moab::EntityHandle> adjs, storage;
 71:   PetscBool isinterlaced;
 72:   moab::EntityHandle vtx;
 73:   moab::ErrorCode merr;

 76:   bs = dmmoab->bs;
 77:   nloc = dmmoab->nloc;
 78:   nfields = dmmoab->numFields;
 79:   isinterlaced = (isbaij || bs == nfields ? PETSC_TRUE : PETSC_FALSE);
 80:   nlsiz = (isinterlaced ? nloc : nloc * nfields);

 82:   /* loop over the locally owned vertices and figure out the NNZ pattern using connectivity information */
 83:   for (moab::Range::const_iterator iter = dmmoab->vowned->begin(); iter != dmmoab->vowned->end(); iter++, ivtx++) {

 85:     vtx = *iter;
 86:     /* Get adjacency information for current vertex - i.e., all elements of dimension (dim) that connects
 87:        to the current vertex. We can then decipher if a vertex is ghosted or not and compute the
 88:        non-zero pattern accordingly. */
 89:     adjs.clear();
 90:     if (dmmoab->hlevel && (dmmoab->pcomm->size() == 1)) {
 91:       merr = dmmoab->hierarchy->get_adjacencies(vtx, dmmoab->dim, adjs); MBERRNM(merr);
 92:     }
 93:     else {
 94:       merr = dmmoab->mbiface->get_adjacencies(&vtx, 1, dmmoab->dim, true, adjs, moab::Interface::UNION); MBERRNM(merr);
 95:     }

 97:     /* reset counters */
 98:     n_nnz = n_onz = 0;
 99:     found.clear();

101:     /* loop over vertices and update the number of connectivity */
102:     for (unsigned jter = 0; jter < adjs.size(); ++jter) {

104:       /* Get connectivity information in canonical ordering for the local element */
105:       const moab::EntityHandle *connect;
106:       std::vector<moab::EntityHandle> cconnect;
107:       merr = dmmoab->mbiface->get_connectivity(adjs[jter], connect, vpere, false, &storage); MBERRNM(merr);

109:       /* loop over each element connected to the adjacent vertex and update as needed */
110:       for (i = 0; i < vpere; ++i) {
111:         /* find the truly user-expected layer of ghosted entities to decipher NNZ pattern */
112:         if (connect[i] == vtx || found.find(connect[i]) != found.end()) continue; /* make sure we don't double count shared vertices */
113:         if (dmmoab->vghost->find(connect[i]) != dmmoab->vghost->end()) n_onz++; /* update out-of-proc onz */
114:         else n_nnz++; /* else local vertex */
115:         found.insert(connect[i]);
116:       }
117:     }
118:     storage.clear();

120:     if (isbaij) {
121:       nnz[ivtx] = n_nnz;  /* leave out self to avoid repeats -> node shared by multiple elements */
122:       if (onz) {
123:         onz[ivtx] = n_onz; /* add ghost non-owned nodes */
124:       }
125:     }
126:     else { /* AIJ matrices */
127:       if (!isinterlaced) {
128:         for (f = 0; f < nfields; f++) {
129:           nnz[f * nloc + ivtx] = n_nnz; /* leave out self to avoid repeats -> node shared by multiple elements */
130:           if (onz)
131:             onz[f * nloc + ivtx] = n_onz; /* add ghost non-owned nodes */
132:         }
133:       }
134:       else {
135:         for (f = 0; f < nfields; f++) {
136:           nnz[nfields * ivtx + f] = n_nnz; /* leave out self to avoid repeats -> node shared by multiple elements */
137:           if (onz)
138:             onz[nfields * ivtx + f] = n_onz; /* add ghost non-owned nodes */
139:         }
140:       }
141:     }
142:   }

144:   for (i = 0; i < nlsiz; i++)
145:     nnz[i] += 1; /* self count the node */

147:   for (ivtx = 0; ivtx < nloc; ivtx++) {
148:     if (!isbaij) {
149:       for (ibs = 0; ibs < nfields; ibs++) {
150:         if (dmmoab->dfill) {  /* first address the diagonal block */
151:           /* just add up the ints -- easier/faster rather than branching based on "1" */
152:           for (jbs = 0, inbsize = 0; jbs < nfields; jbs++)
153:             inbsize += dmmoab->dfill[ibs * nfields + jbs];
154:         }
155:         else inbsize = nfields; /* dense coupling since user didn't specify the component fill explicitly */
156:         if (isinterlaced) nnz[ivtx * nfields + ibs] *= inbsize;
157:         else nnz[ibs * nloc + ivtx] *= inbsize;

159:         if (onz) {
160:           if (dmmoab->ofill) {  /* next address the off-diagonal block */
161:             /* just add up the ints -- easier/faster rather than branching based on "1" */
162:             for (jbs = 0, iobsize = 0; jbs < nfields; jbs++)
163:               iobsize += dmmoab->dfill[ibs * nfields + jbs];
164:           }
165:           else iobsize = nfields; /* dense coupling since user didn't specify the component fill explicitly */
166:           if (isinterlaced) onz[ivtx * nfields + ibs] *= iobsize;
167:           else onz[ibs * nloc + ivtx] *= iobsize;
168:         }
169:       }
170:     }
171:     else {
172:       /* check if we got overzealous in our nnz and onz computations */
173:       nnz[ivtx] = (nnz[ivtx] > dmmoab->nloc ? dmmoab->nloc : nnz[ivtx]);
174:       if (onz) onz[ivtx] = (onz[ivtx] > dmmoab->nloc ? dmmoab->nloc : onz[ivtx]);
175:     }
176:   }
177:   /* update innz and ionz based on local maxima */
178:   if (innz || ionz) {
179:     if (innz) *innz = 0;
180:     if (ionz) *ionz = 0;
181:     for (i = 0; i < nlsiz; i++) {
182:       if (innz && (nnz[i] > *innz)) *innz = nnz[i];
183:       if ((ionz && onz) && (onz[i] > *ionz)) *ionz = onz[i];
184:     }
185:   }
186:   return(0);
187: }

189: static PetscErrorCode DMMoabSetBlockFills_Private(PetscInt w, const PetscInt *fill, PetscInt **rfill)
190: {
192:   PetscInt       i, j, *ifill;

195:   if (!fill) return(0);
196:   PetscMalloc1(w * w, &ifill);
197:   for (i = 0; i < w; i++) {
198:     for (j = 0; j < w; j++)
199:       ifill[i * w + j] = fill[i * w + j];
200:   }

202:   *rfill = ifill;
203:   return(0);
204: }

206: /*@C
207:     DMMoabSetBlockFills - Sets the fill pattern in each block for a multi-component problem
208:     of the matrix returned by DMCreateMatrix().

210:     Logically Collective on da

212:     Input Parameters:
213: +   dm - the DMMoab object
214: .   dfill - the fill pattern in the diagonal block (may be NULL, means use dense block)
215: -   ofill - the fill pattern in the off-diagonal blocks

217:     Level: developer

219:     Notes:
220:     This only makes sense when you are doing multicomponent problems but using the
221:        MPIAIJ matrix format

223:            The format for dfill and ofill is a 2 dimensional dof by dof matrix with 1 entries
224:        representing coupling and 0 entries for missing coupling. For example
225: $             dfill[9] = {1, 0, 0,
226: $                         1, 1, 0,
227: $                         0, 1, 1}
228:        means that row 0 is coupled with only itself in the diagonal block, row 1 is coupled with
229:        itself and row 0 (in the diagonal block) and row 2 is coupled with itself and row 1 (in the
230:        diagonal block).

232:      DMDASetGetMatrix() allows you to provide general code for those more complicated nonzero patterns then
233:      can be represented in the dfill, ofill format

235:    Contributed by Glenn Hammond

237: .seealso DMCreateMatrix(), DMDASetGetMatrix(), DMSetMatrixPreallocateOnly()

239: @*/
240: PetscErrorCode  DMMoabSetBlockFills(DM dm, const PetscInt *dfill, const PetscInt *ofill)
241: {
242:   DM_Moab       *dmmoab = (DM_Moab*)dm->data;

247:   DMMoabSetBlockFills_Private(dmmoab->numFields, dfill, &dmmoab->dfill);
248:   DMMoabSetBlockFills_Private(dmmoab->numFields, ofill, &dmmoab->ofill);
249:   return(0);
250: }