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 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; 18 19 PetscFunctionBegin; 20 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 21 PetscValidPointer(J, 3); 22 23 /* next, need to allocate the non-zero arrays to enable pre-allocation */ 24 mtype = dm->mattype; 25 PetscCall(PetscStrstr(mtype, MATBAIJ, &tmp)); 26 nlsiz = (tmp ? dmmoab->nloc : dmmoab->nloc * dmmoab->numFields); 27 28 /* allocate the nnz, onz arrays based on block size and local nodes */ 29 PetscCall(PetscCalloc2(nlsiz, &nnz, nlsiz, &onz)); 30 31 /* compute the nonzero pattern based on MOAB connectivity data for local elements */ 32 PetscCall(DMMoab_Compute_NNZ_From_Connectivity(dm, &innz, nnz, &ionz, onz, (tmp ? PETSC_TRUE : PETSC_FALSE))); 33 34 /* create the Matrix and set its type as specified by user */ 35 PetscCall(MatCreate((((PetscObject)dm)->comm), &A)); 36 PetscCall(MatSetSizes(A, dmmoab->nloc * dmmoab->numFields, dmmoab->nloc * dmmoab->numFields, PETSC_DETERMINE, PETSC_DETERMINE)); 37 PetscCall(MatSetType(A, mtype)); 38 PetscCall(MatSetBlockSize(A, dmmoab->bs)); 39 PetscCall(MatSetDM(A, dm)); /* set DM reference */ 40 PetscCall(MatSetFromOptions(A)); 41 42 PetscCheck(dmmoab->ltog_map,(((PetscObject)dm)->comm), PETSC_ERR_ORDER, "Cannot create a DMMoab Mat without calling DMSetUp first."); 43 PetscCall(MatSetLocalToGlobalMapping(A, dmmoab->ltog_map, dmmoab->ltog_map)); 44 45 /* set preallocation based on different supported Mat types */ 46 PetscCall(MatSeqAIJSetPreallocation(A, innz, nnz)); 47 PetscCall(MatMPIAIJSetPreallocation(A, innz, nnz, ionz, onz)); 48 PetscCall(MatSeqBAIJSetPreallocation(A, dmmoab->bs, innz, nnz)); 49 PetscCall(MatMPIBAIJSetPreallocation(A, dmmoab->bs, innz, nnz, ionz, onz)); 50 51 /* clean up temporary memory */ 52 PetscCall(PetscFree2(nnz, onz)); 53 54 /* set up internal matrix data-structures */ 55 PetscCall(MatSetUp(A)); 56 57 /* MatSetOption(A, MAT_NEW_NONZERO_ALLOCATION_ERR, PETSC_FALSE); */ 58 59 *J = A; 60 PetscFunctionReturn(0); 61 } 62 63 PETSC_EXTERN PetscErrorCode DMMoab_Compute_NNZ_From_Connectivity(DM dm, PetscInt* innz, PetscInt* nnz, PetscInt* ionz, PetscInt* onz, PetscBool isbaij) 64 { 65 PetscInt i, f, nloc, vpere, bs, n_nnz, n_onz, ivtx = 0; 66 PetscInt ibs, jbs, inbsize, iobsize, nfields, nlsiz; 67 DM_Moab *dmmoab = (DM_Moab*)dm->data; 68 moab::Range found; 69 std::vector<moab::EntityHandle> adjs, storage; 70 PetscBool isinterlaced; 71 moab::EntityHandle vtx; 72 moab::ErrorCode merr; 73 74 PetscFunctionBegin; 75 bs = dmmoab->bs; 76 nloc = dmmoab->nloc; 77 nfields = dmmoab->numFields; 78 isinterlaced = (isbaij || bs == nfields ? PETSC_TRUE : PETSC_FALSE); 79 nlsiz = (isinterlaced ? nloc : nloc * nfields); 80 81 /* loop over the locally owned vertices and figure out the NNZ pattern using connectivity information */ 82 for (moab::Range::const_iterator iter = dmmoab->vowned->begin(); iter != dmmoab->vowned->end(); iter++, ivtx++) { 83 84 vtx = *iter; 85 /* Get adjacency information for current vertex - i.e., all elements of dimension (dim) that connects 86 to the current vertex. We can then decipher if a vertex is ghosted or not and compute the 87 non-zero pattern accordingly. */ 88 adjs.clear(); 89 if (dmmoab->hlevel && (dmmoab->pcomm->size() == 1)) { 90 merr = dmmoab->hierarchy->get_adjacencies(vtx, dmmoab->dim, adjs); MBERRNM(merr); 91 } 92 else { 93 merr = dmmoab->mbiface->get_adjacencies(&vtx, 1, dmmoab->dim, true, adjs, moab::Interface::UNION); MBERRNM(merr); 94 } 95 96 /* reset counters */ 97 n_nnz = n_onz = 0; 98 found.clear(); 99 100 /* loop over vertices and update the number of connectivity */ 101 for (unsigned jter = 0; jter < adjs.size(); ++jter) { 102 103 /* Get connectivity information in canonical ordering for the local element */ 104 const moab::EntityHandle *connect; 105 std::vector<moab::EntityHandle> cconnect; 106 merr = dmmoab->mbiface->get_connectivity(adjs[jter], connect, vpere, false, &storage); MBERRNM(merr); 107 108 /* loop over each element connected to the adjacent vertex and update as needed */ 109 for (i = 0; i < vpere; ++i) { 110 /* find the truly user-expected layer of ghosted entities to decipher NNZ pattern */ 111 if (connect[i] == vtx || found.find(connect[i]) != found.end()) continue; /* make sure we don't double count shared vertices */ 112 if (dmmoab->vghost->find(connect[i]) != dmmoab->vghost->end()) n_onz++; /* update out-of-proc onz */ 113 else n_nnz++; /* else local vertex */ 114 found.insert(connect[i]); 115 } 116 } 117 storage.clear(); 118 119 if (isbaij) { 120 nnz[ivtx] = n_nnz; /* leave out self to avoid repeats -> node shared by multiple elements */ 121 if (onz) { 122 onz[ivtx] = n_onz; /* add ghost non-owned nodes */ 123 } 124 } 125 else { /* AIJ matrices */ 126 if (!isinterlaced) { 127 for (f = 0; f < nfields; f++) { 128 nnz[f * nloc + ivtx] = n_nnz; /* leave out self to avoid repeats -> node shared by multiple elements */ 129 if (onz) 130 onz[f * nloc + ivtx] = n_onz; /* add ghost non-owned nodes */ 131 } 132 } 133 else { 134 for (f = 0; f < nfields; f++) { 135 nnz[nfields * ivtx + f] = n_nnz; /* leave out self to avoid repeats -> node shared by multiple elements */ 136 if (onz) 137 onz[nfields * ivtx + f] = n_onz; /* add ghost non-owned nodes */ 138 } 139 } 140 } 141 } 142 143 for (i = 0; i < nlsiz; i++) 144 nnz[i] += 1; /* self count the node */ 145 146 for (ivtx = 0; ivtx < nloc; ivtx++) { 147 if (!isbaij) { 148 for (ibs = 0; ibs < nfields; ibs++) { 149 if (dmmoab->dfill) { /* first address the diagonal block */ 150 /* just add up the ints -- easier/faster rather than branching based on "1" */ 151 for (jbs = 0, inbsize = 0; jbs < nfields; jbs++) 152 inbsize += dmmoab->dfill[ibs * nfields + jbs]; 153 } 154 else inbsize = nfields; /* dense coupling since user didn't specify the component fill explicitly */ 155 if (isinterlaced) nnz[ivtx * nfields + ibs] *= inbsize; 156 else nnz[ibs * nloc + ivtx] *= inbsize; 157 158 if (onz) { 159 if (dmmoab->ofill) { /* next address the off-diagonal block */ 160 /* just add up the ints -- easier/faster rather than branching based on "1" */ 161 for (jbs = 0, iobsize = 0; jbs < nfields; jbs++) 162 iobsize += dmmoab->dfill[ibs * nfields + jbs]; 163 } 164 else iobsize = nfields; /* dense coupling since user didn't specify the component fill explicitly */ 165 if (isinterlaced) onz[ivtx * nfields + ibs] *= iobsize; 166 else onz[ibs * nloc + ivtx] *= iobsize; 167 } 168 } 169 } 170 else { 171 /* check if we got overzealous in our nnz and onz computations */ 172 nnz[ivtx] = (nnz[ivtx] > dmmoab->nloc ? dmmoab->nloc : nnz[ivtx]); 173 if (onz) onz[ivtx] = (onz[ivtx] > dmmoab->nloc ? dmmoab->nloc : onz[ivtx]); 174 } 175 } 176 /* update innz and ionz based on local maxima */ 177 if (innz || ionz) { 178 if (innz) *innz = 0; 179 if (ionz) *ionz = 0; 180 for (i = 0; i < nlsiz; i++) { 181 if (innz && (nnz[i] > *innz)) *innz = nnz[i]; 182 if ((ionz && onz) && (onz[i] > *ionz)) *ionz = onz[i]; 183 } 184 } 185 PetscFunctionReturn(0); 186 } 187 188 static PetscErrorCode DMMoabSetBlockFills_Private(PetscInt w, const PetscInt *fill, PetscInt **rfill) 189 { 190 PetscInt i, j, *ifill; 191 192 PetscFunctionBegin; 193 if (!fill) PetscFunctionReturn(0); 194 PetscCall(PetscMalloc1(w * w, &ifill)); 195 for (i = 0; i < w; i++) { 196 for (j = 0; j < w; j++) 197 ifill[i * w + j] = fill[i * w + j]; 198 } 199 200 *rfill = ifill; 201 PetscFunctionReturn(0); 202 } 203 204 /*@C 205 DMMoabSetBlockFills - Sets the fill pattern in each block for a multi-component problem 206 of the matrix returned by DMCreateMatrix(). 207 208 Logically Collective on da 209 210 Input Parameters: 211 + dm - the DMMoab object 212 . dfill - the fill pattern in the diagonal block (may be NULL, means use dense block) 213 - ofill - the fill pattern in the off-diagonal blocks 214 215 Level: developer 216 217 Notes: 218 This only makes sense when you are doing multicomponent problems but using the 219 MPIAIJ matrix format 220 221 The format for dfill and ofill is a 2 dimensional dof by dof matrix with 1 entries 222 representing coupling and 0 entries for missing coupling. For example 223 $ dfill[9] = {1, 0, 0, 224 $ 1, 1, 0, 225 $ 0, 1, 1} 226 means that row 0 is coupled with only itself in the diagonal block, row 1 is coupled with 227 itself and row 0 (in the diagonal block) and row 2 is coupled with itself and row 1 (in the 228 diagonal block). 229 230 DMDASetGetMatrix() allows you to provide general code for those more complicated nonzero patterns then 231 can be represented in the dfill, ofill format 232 233 Contributed by Glenn Hammond 234 235 .seealso DMCreateMatrix(), DMDASetGetMatrix(), DMSetMatrixPreallocateOnly() 236 237 @*/ 238 PetscErrorCode DMMoabSetBlockFills(DM dm, const PetscInt *dfill, const PetscInt *ofill) 239 { 240 DM_Moab *dmmoab = (DM_Moab*)dm->data; 241 242 PetscFunctionBegin; 243 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 244 PetscCall(DMMoabSetBlockFills_Private(dmmoab->numFields, dfill, &dmmoab->dfill)); 245 PetscCall(DMMoabSetBlockFills_Private(dmmoab->numFields, ofill, &dmmoab->ofill)); 246 PetscFunctionReturn(0); 247 } 248