1 #define PETSCDM_DLL 2 3 #include "petscda.h" /*I "petscda.h" I*/ 4 #include "petscmat.h" /*I "petscmat.h" I*/ 5 #include "private/dmimpl.h" /*I "petscmat.h" I*/ 6 7 /* CSR storage of the nonzero structure of a bs*bs matrix */ 8 typedef struct { 9 PetscInt bs,nz,*i,*j; 10 } DMSlicedBlockFills; 11 12 typedef struct { 13 Vec globalvector; 14 PetscInt bs,n,N,Nghosts,*ghosts; 15 PetscInt d_nz,o_nz,*d_nnz,*o_nnz; 16 DMSlicedBlockFills *dfill,*ofill; 17 } DM_Sliced; 18 19 #undef __FUNCT__ 20 #define __FUNCT__ "DMGetMatrix_Sliced" 21 PetscErrorCode PETSCDM_DLLEXPORT DMGetMatrix_Sliced(DM dm, const MatType mtype,Mat *J) 22 { 23 PetscErrorCode ierr; 24 PetscInt *globals,*sd_nnz,*so_nnz,rstart,bs,i; 25 ISLocalToGlobalMapping lmap,blmap; 26 void (*aij)(void) = PETSC_NULL; 27 DM_Sliced *slice = (DM_Sliced*)dm->data; 28 29 PetscFunctionBegin; 30 bs = slice->bs; 31 ierr = MatCreate(((PetscObject)dm)->comm,J);CHKERRQ(ierr); 32 ierr = MatSetSizes(*J,slice->n*bs,slice->n*bs,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 33 ierr = MatSetType(*J,mtype);CHKERRQ(ierr); 34 ierr = MatSeqBAIJSetPreallocation(*J,bs,slice->d_nz,slice->d_nnz);CHKERRQ(ierr); 35 ierr = MatMPIBAIJSetPreallocation(*J,bs,slice->d_nz,slice->d_nnz,slice->o_nz,slice->o_nnz);CHKERRQ(ierr); 36 /* In general, we have to do extra work to preallocate for scalar (AIJ) matrices so we check whether it will do any 37 * good before going on with it. */ 38 ierr = PetscObjectQueryFunction((PetscObject)*J,"MatMPIAIJSetPreallocation_C",&aij);CHKERRQ(ierr); 39 if (!aij) { 40 ierr = PetscObjectQueryFunction((PetscObject)*J,"MatSeqAIJSetPreallocation_C",&aij);CHKERRQ(ierr); 41 } 42 if (aij) { 43 if (bs == 1) { 44 ierr = MatSeqAIJSetPreallocation(*J,slice->d_nz,slice->d_nnz);CHKERRQ(ierr); 45 ierr = MatMPIAIJSetPreallocation(*J,slice->d_nz,slice->d_nnz,slice->o_nz,slice->o_nnz);CHKERRQ(ierr); 46 } else if (!slice->d_nnz) { 47 ierr = MatSeqAIJSetPreallocation(*J,slice->d_nz*bs,PETSC_NULL);CHKERRQ(ierr); 48 ierr = MatMPIAIJSetPreallocation(*J,slice->d_nz*bs,PETSC_NULL,slice->o_nz*bs,PETSC_NULL);CHKERRQ(ierr); 49 } else { 50 /* The user has provided preallocation per block-row, convert it to per scalar-row respecting DMSlicedSetBlockFills() if applicable */ 51 ierr = PetscMalloc2(slice->n*bs,PetscInt,&sd_nnz,(!!slice->o_nnz)*slice->n*bs,PetscInt,&so_nnz);CHKERRQ(ierr); 52 for (i=0; i<slice->n*bs; i++) { 53 sd_nnz[i] = (slice->d_nnz[i/bs]-1) * (slice->ofill ? slice->ofill->i[i%bs+1]-slice->ofill->i[i%bs] : bs) 54 + (slice->dfill ? slice->dfill->i[i%bs+1]-slice->dfill->i[i%bs] : bs); 55 if (so_nnz) { 56 so_nnz[i] = slice->o_nnz[i/bs] * (slice->ofill ? slice->ofill->i[i%bs+1]-slice->ofill->i[i%bs] : bs); 57 } 58 } 59 ierr = MatSeqAIJSetPreallocation(*J,slice->d_nz*bs,sd_nnz);CHKERRQ(ierr); 60 ierr = MatMPIAIJSetPreallocation(*J,slice->d_nz*bs,sd_nnz,slice->o_nz*bs,so_nnz);CHKERRQ(ierr); 61 ierr = PetscFree2(sd_nnz,so_nnz);CHKERRQ(ierr); 62 } 63 } 64 65 ierr = MatSetBlockSize(*J,bs);CHKERRQ(ierr); 66 67 /* Set up the local to global map. For the scalar map, we have to translate to entry-wise indexing instead of block-wise. */ 68 ierr = PetscMalloc((slice->n+slice->Nghosts)*bs*sizeof(PetscInt),&globals);CHKERRQ(ierr); 69 ierr = MatGetOwnershipRange(*J,&rstart,PETSC_NULL);CHKERRQ(ierr); 70 for (i=0; i<slice->n*bs; i++) { 71 globals[i] = rstart + i; 72 } 73 for (i=0; i<slice->Nghosts*bs; i++) { 74 globals[slice->n*bs+i] = slice->ghosts[i/bs]*bs + i%bs; 75 } 76 ierr = ISLocalToGlobalMappingCreate(PETSC_COMM_SELF,(slice->n+slice->Nghosts)*bs,globals,PETSC_OWN_POINTER,&lmap);CHKERRQ(ierr); 77 ierr = ISLocalToGlobalMappingBlock(lmap,bs,&blmap);CHKERRQ(ierr); 78 ierr = MatSetLocalToGlobalMapping(*J,lmap);CHKERRQ(ierr); 79 ierr = MatSetLocalToGlobalMappingBlock(*J,blmap);CHKERRQ(ierr); 80 ierr = ISLocalToGlobalMappingDestroy(lmap);CHKERRQ(ierr); 81 ierr = ISLocalToGlobalMappingDestroy(blmap);CHKERRQ(ierr); 82 PetscFunctionReturn(0); 83 } 84 85 #undef __FUNCT__ 86 #define __FUNCT__ "DMSlicedSetGhosts" 87 /*@C 88 DMSlicedSetGhosts - Sets the global indices of other processes elements that will 89 be ghosts on this process 90 91 Not Collective 92 93 Input Parameters: 94 + slice - the DM object 95 . bs - block size 96 . nlocal - number of local (owned, non-ghost) blocks 97 . Nghosts - number of ghost blocks on this process 98 - ghosts - global indices of each ghost block 99 100 Level: advanced 101 102 .seealso DMDestroy(), DMCreateGlobalVector(), DMSlicedGetGlobalIndices() 103 104 @*/ 105 PetscErrorCode PETSCDM_DLLEXPORT DMSlicedSetGhosts(DM dm,PetscInt bs,PetscInt nlocal,PetscInt Nghosts,const PetscInt ghosts[]) 106 { 107 PetscErrorCode ierr; 108 DM_Sliced *slice = (DM_Sliced*)dm->data; 109 110 PetscFunctionBegin; 111 PetscValidHeaderSpecific(dm,DM_CLASSID,1); 112 ierr = PetscFree(slice->ghosts);CHKERRQ(ierr); 113 ierr = PetscMalloc(Nghosts*sizeof(PetscInt),&slice->ghosts);CHKERRQ(ierr); 114 ierr = PetscMemcpy(slice->ghosts,ghosts,Nghosts*sizeof(PetscInt));CHKERRQ(ierr); 115 slice->bs = bs; 116 slice->n = nlocal; 117 slice->Nghosts = Nghosts; 118 PetscFunctionReturn(0); 119 } 120 121 #undef __FUNCT__ 122 #define __FUNCT__ "DMSlicedSetPreallocation" 123 /*@C 124 DMSlicedSetPreallocation - sets the matrix memory preallocation for matrices computed by DMSliced 125 126 Not Collective 127 128 Input Parameters: 129 + slice - the DM object 130 . d_nz - number of block nonzeros per block row in diagonal portion of local 131 submatrix (same for all local rows) 132 . d_nnz - array containing the number of block nonzeros in the various block rows 133 of the in diagonal portion of the local (possibly different for each block 134 row) or PETSC_NULL. You must leave room for the diagonal entry even if it is zero. 135 . o_nz - number of block nonzeros per block row in the off-diagonal portion of local 136 submatrix (same for all local rows). 137 - o_nnz - array containing the number of nonzeros in the various block rows of the 138 off-diagonal portion of the local submatrix (possibly different for 139 each block row) or PETSC_NULL. 140 141 Notes: 142 See MatMPIBAIJSetPreallocation() for more details on preallocation. If a scalar matrix (AIJ) is 143 obtained with DMSlicedGetMatrix(), the correct preallocation will be set, respecting DMSlicedSetBlockFills(). 144 145 Level: advanced 146 147 .seealso DMDestroy(), DMCreateGlobalVector(), DMSlicedGetGlobalIndices(), MatMPIAIJSetPreallocation(), 148 MatMPIBAIJSetPreallocation(), DMSlicedGetMatrix(), DMSlicedSetBlockFills() 149 150 @*/ 151 PetscErrorCode PETSCDM_DLLEXPORT DMSlicedSetPreallocation(DM dm,PetscInt d_nz,const PetscInt d_nnz[],PetscInt o_nz,const PetscInt o_nnz[]) 152 { 153 DM_Sliced *slice = (DM_Sliced*)dm->data; 154 155 PetscFunctionBegin; 156 PetscValidHeaderSpecific(dm,DM_CLASSID,1); 157 slice->d_nz = d_nz; 158 slice->d_nnz = (PetscInt*)d_nnz; 159 slice->o_nz = o_nz; 160 slice->o_nnz = (PetscInt*)o_nnz; 161 PetscFunctionReturn(0); 162 } 163 164 #undef __FUNCT__ 165 #define __FUNCT__ "DMSlicedSetBlockFills_Private" 166 static PetscErrorCode DMSlicedSetBlockFills_Private(PetscInt bs,const PetscInt *fill,DMSlicedBlockFills **inf) 167 { 168 PetscErrorCode ierr; 169 PetscInt i,j,nz,*fi,*fj; 170 DMSlicedBlockFills *f; 171 172 PetscFunctionBegin; 173 PetscValidPointer(inf,3); 174 if (*inf) {ierr = PetscFree3((*inf)->i,(*inf)->j,*inf);CHKERRQ(ierr);} 175 if (!fill) PetscFunctionReturn(0); 176 for (i=0,nz=0; i<bs*bs; i++) if (fill[i]) nz++; 177 ierr = PetscMalloc3(1,DMSlicedBlockFills,&f,bs+1,PetscInt,&fi,nz,PetscInt,&fj);CHKERRQ(ierr); 178 f->bs = bs; 179 f->nz = nz; 180 f->i = fi; 181 f->j = fj; 182 for (i=0,nz=0; i<bs; i++) { 183 fi[i] = nz; 184 for (j=0; j<bs; j++) if (fill[i*bs+j]) fj[nz++] = j; 185 } 186 fi[i] = nz; 187 *inf = f; 188 PetscFunctionReturn(0); 189 } 190 191 #undef __FUNCT__ 192 #define __FUNCT__ "DMSlicedSetBlockFills" 193 /*@C 194 DMSlicedSetBlockFills - Sets the fill pattern in each block for a multi-component problem 195 of the matrix returned by DMSlicedGetMatrix(). 196 197 Logically Collective on DM 198 199 Input Parameter: 200 + sliced - the DM object 201 . dfill - the fill pattern in the diagonal block (may be PETSC_NULL, means use dense block) 202 - ofill - the fill pattern in the off-diagonal blocks 203 204 Notes: 205 This only makes sense for multicomponent problems using scalar matrix formats (AIJ). 206 See DASetBlockFills() for example usage. 207 208 Level: advanced 209 210 .seealso DMSlicedGetMatrix(), DASetBlockFills() 211 @*/ 212 PetscErrorCode PETSCDM_DLLEXPORT DMSlicedSetBlockFills(DM dm,const PetscInt *dfill,const PetscInt *ofill) 213 { 214 DM_Sliced *slice = (DM_Sliced*)dm->data; 215 PetscErrorCode ierr; 216 217 PetscFunctionBegin; 218 PetscValidHeaderSpecific(dm,DM_CLASSID,1); 219 ierr = DMSlicedSetBlockFills_Private(slice->bs,dfill,&slice->dfill);CHKERRQ(ierr); 220 ierr = DMSlicedSetBlockFills_Private(slice->bs,ofill,&slice->ofill);CHKERRQ(ierr); 221 PetscFunctionReturn(0); 222 } 223 224 extern PetscErrorCode DMDestroy_Private(DM,PetscBool *); 225 226 #undef __FUNCT__ 227 #define __FUNCT__ "DMDestroy_Sliced" 228 PetscErrorCode PETSCDM_DLLEXPORT DMDestroy_Sliced(DM dm) 229 { 230 PetscErrorCode ierr; 231 PetscBool done; 232 DM_Sliced *slice = (DM_Sliced*)dm->data; 233 234 PetscFunctionBegin; 235 ierr = DMDestroy_Private(dm,&done);CHKERRQ(ierr); 236 if (!done) PetscFunctionReturn(0); 237 238 if (slice->globalvector) {ierr = VecDestroy(slice->globalvector);CHKERRQ(ierr);} 239 ierr = PetscFree(slice->ghosts);CHKERRQ(ierr); 240 if (slice->dfill) {ierr = PetscFree3(slice->dfill,slice->dfill->i,slice->dfill->j);CHKERRQ(ierr);} 241 if (slice->ofill) {ierr = PetscFree3(slice->ofill,slice->ofill->i,slice->ofill->j);CHKERRQ(ierr);} 242 ierr = PetscFree(dm->data);CHKERRQ(ierr); 243 ierr = PetscHeaderDestroy(dm);CHKERRQ(ierr); 244 PetscFunctionReturn(0); 245 } 246 247 #undef __FUNCT__ 248 #define __FUNCT__ "DMCreateGlobalVector_Sliced" 249 PetscErrorCode PETSCDM_DLLEXPORT DMCreateGlobalVector_Sliced(DM dm,Vec *gvec) 250 { 251 PetscErrorCode ierr; 252 PetscInt bs,cnt; 253 DM_Sliced *slice = (DM_Sliced*)dm->data; 254 255 PetscFunctionBegin; 256 PetscValidHeaderSpecific(dm,DM_CLASSID,1); 257 PetscValidPointer(gvec,2); 258 *gvec = 0; 259 if (slice->globalvector) { 260 ierr = PetscObjectGetReference((PetscObject)slice->globalvector,&cnt);CHKERRQ(ierr); 261 if (cnt == 1) { /* Nobody else has a reference so we can just reference it and give it away */ 262 *gvec = slice->globalvector; 263 ierr = PetscObjectReference((PetscObject)*gvec);CHKERRQ(ierr); 264 ierr = VecZeroEntries(*gvec);CHKERRQ(ierr); 265 } else { /* Someone else has a reference so we duplicate the global vector */ 266 ierr = VecDuplicate(slice->globalvector,gvec);CHKERRQ(ierr); 267 } 268 } else { 269 bs = slice->bs; 270 ierr = VecCreateGhostBlock(((PetscObject)dm)->comm,bs,slice->n*bs,PETSC_DETERMINE,slice->Nghosts,slice->ghosts,&slice->globalvector);CHKERRQ(ierr); 271 *gvec = slice->globalvector; 272 ierr = PetscObjectReference((PetscObject)*gvec);CHKERRQ(ierr); 273 } 274 PetscFunctionReturn(0); 275 } 276 277 #undef __FUNCT__ 278 #define __FUNCT__ "DMSlicedCreate" 279 /*@C 280 DMSlicedCreate - Creates a DM object, used to manage data for a unstructured problem 281 282 Collective on MPI_Comm 283 284 Input Parameter: 285 . comm - the processors that will share the global vector 286 287 Output Parameters: 288 . slice - the slice object 289 290 Level: advanced 291 292 .seealso DMDestroy(), DMCreateGlobalVector(), DMSlicedGetGlobalIndices() 293 294 @*/ 295 PetscErrorCode PETSCDM_DLLEXPORT DMSlicedCreate(MPI_Comm comm,DM *dm) 296 { 297 PetscErrorCode ierr; 298 DM p; 299 DM_Sliced *slice; 300 301 PetscFunctionBegin; 302 PetscValidPointer(dm,2); 303 #ifndef PETSC_USE_DYNAMIC_LIBRARIES 304 ierr = DMInitializePackage(PETSC_NULL);CHKERRQ(ierr); 305 #endif 306 307 ierr = PetscHeaderCreate(p,_p_DM,struct _DMOps,DM_CLASSID,0,"DM",comm,DMDestroy,DMView);CHKERRQ(ierr); 308 ierr = PetscNewLog(p,DM_Sliced,&slice);CHKERRQ(ierr); 309 p->data = slice; 310 311 ierr = PetscObjectChangeTypeName((PetscObject)p,"Sliced");CHKERRQ(ierr); 312 p->ops->createglobalvector = DMCreateGlobalVector_Sliced; 313 p->ops->getmatrix = DMGetMatrix_Sliced; 314 p->ops->destroy = DMDestroy_Sliced; 315 *dm = p; 316 PetscFunctionReturn(0); 317 } 318 319 320 #undef __FUNCT__ 321 #define __FUNCT__ "DMSlicedGetGlobalIndices" 322 /*@C 323 DMSlicedGetGlobalIndices - Gets the global indices for all the local entries 324 325 Collective on DM 326 327 Input Parameter: 328 . slice - the slice object 329 330 Output Parameters: 331 . idx - the individual indices for each packed vector/array 332 333 Level: advanced 334 335 Notes: 336 The idx parameters should be freed by the calling routine with PetscFree() 337 338 .seealso DMSlicedDestroy(), DMSlicedCreateGlobalVector(), DMSlicedCreate() 339 340 @*/ 341 PetscErrorCode PETSCDM_DLLEXPORT DMSlicedGetGlobalIndices(DM dm,PetscInt *idx[]) 342 { 343 PetscFunctionReturn(0); 344 } 345 346 347 /* Explanation of the missing functions for DA-style handling of the local vector: 348 349 DMSlicedCreateLocalVector() 350 DMSlicedGlobalToLocalBegin() 351 DMSlicedGlobalToLocalEnd() 352 353 There is no way to get the global form from a local form, so DMSlicedCreateLocalVector() is a memory leak without 354 external accounting for the global vector. Also, DMSliced intends the user to work with the VecGhost interface since the 355 ghosts are already ordered after the owned entries. Contrast this to a DA where the local vector has a special 356 ordering described by the structured grid, hence it cannot share memory with the global form. For this reason, users 357 of DMSliced should work with the global vector and use 358 359 VecGhostGetLocalForm(), VecGhostRestoreLocalForm() 360 VecGhostUpdateBegin(), VecGhostUpdateEnd() 361 362 rather than the missing DA-style functions. This is conceptually simpler and offers better performance than is 363 possible with the DA-style interface. 364 */ 365