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