1 #include <petsc/private/dmmbimpl.h> /*I "petscdmmoab.h" I*/ 2 #include <petsc/private/vecimpl.h> 3 4 #include <petscdmmoab.h> 5 #include <MBTagConventions.hpp> 6 #include <moab/NestedRefine.hpp> 7 8 PETSC_EXTERN PetscErrorCode DMMoab_Compute_NNZ_From_Connectivity(DM, PetscInt*, PetscInt*, PetscInt*, PetscInt*, PetscBool); 9 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; 19 20 PetscFunctionBegin; 21 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 22 PetscValidPointer(J, 3); 23 24 /* next, need to allocate the non-zero arrays to enable pre-allocation */ 25 mtype = dm->mattype; 26 ierr = PetscStrstr(mtype, MATBAIJ, &tmp);CHKERRQ(ierr); 27 nlsiz = (tmp ? dmmoab->nloc : dmmoab->nloc * dmmoab->numFields); 28 29 /* allocate the nnz, onz arrays based on block size and local nodes */ 30 ierr = PetscCalloc2(nlsiz, &nnz, nlsiz, &onz);CHKERRQ(ierr); 31 32 /* compute the nonzero pattern based on MOAB connectivity data for local elements */ 33 ierr = DMMoab_Compute_NNZ_From_Connectivity(dm, &innz, nnz, &ionz, onz, (tmp ? PETSC_TRUE : PETSC_FALSE));CHKERRQ(ierr); 34 35 /* create the Matrix and set its type as specified by user */ 36 ierr = MatCreate((((PetscObject)dm)->comm), &A);CHKERRQ(ierr); 37 ierr = MatSetSizes(A, dmmoab->nloc * dmmoab->numFields, dmmoab->nloc * dmmoab->numFields, PETSC_DETERMINE, PETSC_DETERMINE);CHKERRQ(ierr); 38 ierr = MatSetType(A, mtype);CHKERRQ(ierr); 39 ierr = MatSetBlockSize(A, dmmoab->bs);CHKERRQ(ierr); 40 ierr = MatSetDM(A, dm);CHKERRQ(ierr); /* set DM reference */ 41 ierr = MatSetFromOptions(A);CHKERRQ(ierr); 42 43 if (!dmmoab->ltog_map) SETERRQ((((PetscObject)dm)->comm), PETSC_ERR_ORDER, "Cannot create a DMMoab Mat without calling DMSetUp first."); 44 ierr = MatSetLocalToGlobalMapping(A, dmmoab->ltog_map, dmmoab->ltog_map);CHKERRQ(ierr); 45 46 /* set preallocation based on different supported Mat types */ 47 ierr = MatSeqAIJSetPreallocation(A, innz, nnz);CHKERRQ(ierr); 48 ierr = MatMPIAIJSetPreallocation(A, innz, nnz, ionz, onz);CHKERRQ(ierr); 49 ierr = MatSeqBAIJSetPreallocation(A, dmmoab->bs, innz, nnz);CHKERRQ(ierr); 50 ierr = MatMPIBAIJSetPreallocation(A, dmmoab->bs, innz, nnz, ionz, onz);CHKERRQ(ierr); 51 52 /* clean up temporary memory */ 53 ierr = PetscFree2(nnz, onz);CHKERRQ(ierr); 54 55 /* set up internal matrix data-structures */ 56 ierr = MatSetUp(A);CHKERRQ(ierr); 57 58 /* MatSetOption(A, MAT_NEW_NONZERO_ALLOCATION_ERR, PETSC_FALSE); */ 59 60 *J = A; 61 PetscFunctionReturn(0); 62 } 63 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; 74 75 PetscFunctionBegin; 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); 81 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++) { 84 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 } 96 97 /* reset counters */ 98 n_nnz = n_onz = 0; 99 found.clear(); 100 101 /* loop over vertices and update the number of connectivity */ 102 for (unsigned jter = 0; jter < adjs.size(); ++jter) { 103 104 /* 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); 108 109 /* 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(); 119 120 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 } 143 144 for (i = 0; i < nlsiz; i++) 145 nnz[i] += 1; /* self count the node */ 146 147 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; 158 159 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 PetscFunctionReturn(0); 187 } 188 189 static PetscErrorCode DMMoabSetBlockFills_Private(PetscInt w, const PetscInt *fill, PetscInt **rfill) 190 { 191 PetscErrorCode ierr; 192 PetscInt i, j, *ifill; 193 194 PetscFunctionBegin; 195 if (!fill) PetscFunctionReturn(0); 196 ierr = PetscMalloc1(w * w, &ifill);CHKERRQ(ierr); 197 for (i = 0; i < w; i++) { 198 for (j = 0; j < w; j++) 199 ifill[i * w + j] = fill[i * w + j]; 200 } 201 202 *rfill = ifill; 203 PetscFunctionReturn(0); 204 } 205 206 /*@C 207 DMMoabSetBlockFills - Sets the fill pattern in each block for a multi-component problem 208 of the matrix returned by DMCreateMatrix(). 209 210 Logically Collective on da 211 212 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 216 217 Level: developer 218 219 Notes: 220 This only makes sense when you are doing multicomponent problems but using the 221 MPIAIJ matrix format 222 223 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). 231 232 DMDASetGetMatrix() allows you to provide general code for those more complicated nonzero patterns then 233 can be represented in the dfill, ofill format 234 235 Contributed by Glenn Hammond 236 237 .seealso DMCreateMatrix(), DMDASetGetMatrix(), DMSetMatrixPreallocateOnly() 238 239 @*/ 240 PetscErrorCode DMMoabSetBlockFills(DM dm, const PetscInt *dfill, const PetscInt *ofill) 241 { 242 DM_Moab *dmmoab = (DM_Moab*)dm->data; 243 PetscErrorCode ierr; 244 245 PetscFunctionBegin; 246 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 247 ierr = DMMoabSetBlockFills_Private(dmmoab->numFields, dfill, &dmmoab->dfill);CHKERRQ(ierr); 248 ierr = DMMoabSetBlockFills_Private(dmmoab->numFields, ofill, &dmmoab->ofill);CHKERRQ(ierr); 249 PetscFunctionReturn(0); 250 } 251