1 2 #include <petscdmswarm.h> 3 #include <petsc/private/dmswarmimpl.h> /*I "petscdmswarm.h" I*/ 4 #include "data_bucket.h" 5 #include "data_ex.h" 6 7 8 /* 9 User loads desired location (MPI rank) into field DMSwarm_rank 10 */ 11 #undef __FUNCT__ 12 #define __FUNCT__ "DMSwarmMigrate_Push_Basic" 13 PetscErrorCode DMSwarmMigrate_Push_Basic(DM dm,PetscBool remove_sent_points) 14 { 15 DM_Swarm *swarm = (DM_Swarm*)dm->data; 16 PetscErrorCode ierr; 17 DataEx de; 18 PetscInt p,npoints,*rankval,n_points_recv; 19 PetscMPIInt rank,nrank; 20 void *point_buffer,*recv_points; 21 size_t sizeof_dmswarm_point; 22 23 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)dm),&rank);CHKERRQ(ierr); 24 25 ierr = DataBucketGetSizes(swarm->db,&npoints,NULL,NULL);CHKERRQ(ierr); 26 ierr = DMSwarmGetField(dm,DMSwarmField_rank,NULL,NULL,(void**)&rankval);CHKERRQ(ierr); 27 28 de = DataExCreate(PetscObjectComm((PetscObject)dm),0);CHKERRQ(ierr); 29 30 ierr = DataExTopologyInitialize(de);CHKERRQ(ierr); 31 for (p=0; p<npoints; p++) { 32 nrank = rankval[p]; 33 if (nrank != rank) { 34 ierr = DataExTopologyAddNeighbour(de,nrank);CHKERRQ(ierr); 35 } 36 } 37 ierr = DataExTopologyFinalize(de);CHKERRQ(ierr); 38 39 ierr = DataExInitializeSendCount(de);CHKERRQ(ierr); 40 for (p=0; p<npoints; p++) { 41 nrank = rankval[p]; 42 if (nrank != rank) { 43 ierr = DataExAddToSendCount(de,nrank,1);CHKERRQ(ierr); 44 } 45 } 46 ierr = DataExFinalizeSendCount(de);CHKERRQ(ierr); 47 48 ierr = DataBucketCreatePackedArray(swarm->db,&sizeof_dmswarm_point,&point_buffer);CHKERRQ(ierr); 49 ierr = DataExPackInitialize(de,sizeof_dmswarm_point);CHKERRQ(ierr); 50 for (p=0; p<npoints; p++) { 51 nrank = rankval[p]; 52 if (nrank != rank) { 53 /* copy point into buffer */ 54 ierr = DataBucketFillPackedArray(swarm->db,p,point_buffer);CHKERRQ(ierr); 55 /* insert point buffer into DataExchanger */ 56 ierr = DataExPackData(de,nrank,1,point_buffer);CHKERRQ(ierr); 57 } 58 } 59 ierr = DataExPackFinalize(de);CHKERRQ(ierr); 60 61 62 if (remove_sent_points) { 63 /* remove points which left processor */ 64 ierr = DataBucketGetSizes(swarm->db,&npoints,NULL,NULL);CHKERRQ(ierr); 65 for (p=0; p<npoints; p++) { 66 nrank = rankval[p]; 67 if (nrank != rank) { 68 /* kill point */ 69 ierr = DataBucketRemovePointAtIndex(swarm->db,p);CHKERRQ(ierr); 70 DataBucketGetSizes(swarm->db,&npoints,NULL,NULL);CHKERRQ(ierr); /* you need to update npoints as the list size decreases! */ 71 p--; /* check replacement point */ 72 } 73 } 74 } 75 ierr = DMSwarmRestoreField(dm,DMSwarmField_rank,NULL,NULL,(void**)&rankval);CHKERRQ(ierr); 76 77 ierr = DataExBegin(de);CHKERRQ(ierr); 78 ierr = DataExEnd(de);CHKERRQ(ierr); 79 80 ierr = DataExGetRecvData(de,&n_points_recv,(void**)&recv_points);CHKERRQ(ierr); 81 82 ierr = DataBucketGetSizes(swarm->db,&npoints,NULL,NULL);CHKERRQ(ierr); 83 ierr = DataBucketSetSizes(swarm->db,npoints + n_points_recv,-1);CHKERRQ(ierr); 84 for (p=0; p<n_points_recv; p++) { 85 void *data_p = (void*)( (char*)recv_points + p*sizeof_dmswarm_point ); 86 87 ierr = DataBucketInsertPackedArray(swarm->db,npoints+p,data_p);CHKERRQ(ierr); 88 } 89 ierr = DataExView(de);CHKERRQ(ierr); 90 ierr = DataBucketDestroyPackedArray(swarm->db,&point_buffer);CHKERRQ(ierr); 91 ierr = DataExDestroy(de);CHKERRQ(ierr); 92 93 PetscFunctionReturn(0); 94 } 95 96 #undef __FUNCT__ 97 #define __FUNCT__ "DMSwarmMigrate_DMNeighborScatter" 98 PetscErrorCode DMSwarmMigrate_DMNeighborScatter(DM dm,DM dmcell,PetscBool remove_sent_points,PetscInt *npoints_prior_migration) 99 { 100 DM_Swarm *swarm = (DM_Swarm*)dm->data; 101 PetscErrorCode ierr; 102 DataEx de; 103 PetscInt r,p,npoints,*rankval,n_points_recv; 104 PetscMPIInt rank,_rank; 105 const PetscMPIInt *neighbourranks; 106 void *point_buffer,*recv_points; 107 size_t sizeof_dmswarm_point; 108 PetscInt nneighbors; 109 PetscMPIInt mynneigh,*myneigh; 110 111 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)dm),&rank);CHKERRQ(ierr); 112 113 ierr = DataBucketGetSizes(swarm->db,&npoints,NULL,NULL);CHKERRQ(ierr); 114 ierr = DMSwarmGetField(dm,DMSwarmField_rank,NULL,NULL,(void**)&rankval);CHKERRQ(ierr); 115 116 de = DataExCreate(PetscObjectComm((PetscObject)dm),0);CHKERRQ(ierr); 117 118 ierr = DMGetNeighbors(dmcell,&nneighbors,&neighbourranks);CHKERRQ(ierr); 119 ierr = DataExTopologyInitialize(de);CHKERRQ(ierr); 120 for (r=0; r<nneighbors; r++) { 121 _rank = neighbourranks[r]; 122 if ((_rank != rank) && (_rank > 0)) { 123 ierr = DataExTopologyAddNeighbour(de,_rank);CHKERRQ(ierr); 124 } 125 } 126 ierr = DataExTopologyFinalize(de);CHKERRQ(ierr); 127 ierr = DataExTopologyGetNeighbours(de,&mynneigh,&myneigh);CHKERRQ(ierr); 128 129 ierr = DataExInitializeSendCount(de);CHKERRQ(ierr); 130 for (p=0; p<npoints; p++) { 131 if (rankval[p] == -1) { 132 for (r=0; r<mynneigh; r++) { 133 _rank = myneigh[r]; 134 ierr = DataExAddToSendCount(de,_rank,1);CHKERRQ(ierr); 135 } 136 } 137 } 138 ierr = DataExFinalizeSendCount(de);CHKERRQ(ierr); 139 140 ierr = DataBucketCreatePackedArray(swarm->db,&sizeof_dmswarm_point,&point_buffer);CHKERRQ(ierr); 141 ierr = DataExPackInitialize(de,sizeof_dmswarm_point);CHKERRQ(ierr); 142 for (p=0; p<npoints; p++) { 143 if (rankval[p] == -1) { 144 for (r=0; r<mynneigh; r++) { 145 _rank = myneigh[r]; 146 /* copy point into buffer */ 147 ierr = DataBucketFillPackedArray(swarm->db,p,point_buffer);CHKERRQ(ierr); 148 /* insert point buffer into DataExchanger */ 149 ierr = DataExPackData(de,_rank,1,point_buffer);CHKERRQ(ierr); 150 } 151 } 152 } 153 ierr = DataExPackFinalize(de);CHKERRQ(ierr); 154 ierr = DMSwarmRestoreField(dm,DMSwarmField_rank,NULL,NULL,(void**)&rankval);CHKERRQ(ierr); 155 156 if (remove_sent_points) { 157 DataField PField; 158 159 ierr = DataBucketGetDataFieldByName(swarm->db,DMSwarmField_rank,&PField);CHKERRQ(ierr); 160 ierr = DataFieldGetEntries(PField,(void**)&rankval);CHKERRQ(ierr); 161 162 /* remove points which left processor */ 163 ierr = DataBucketGetSizes(swarm->db,&npoints,NULL,NULL);CHKERRQ(ierr); 164 for (p=0; p<npoints; p++) { 165 if (rankval[p] == -1) { 166 /* kill point */ 167 ierr = DataBucketRemovePointAtIndex(swarm->db,p);CHKERRQ(ierr); 168 ierr = DataBucketGetSizes(swarm->db,&npoints,NULL,NULL);CHKERRQ(ierr); /* you need to update npoints as the list size decreases! */ 169 ierr = DataFieldGetEntries(PField,(void**)&rankval);CHKERRQ(ierr); /* update date point increase realloc performed */ 170 p--; /* check replacement point */ 171 } 172 } 173 } 174 ierr = DataBucketGetSizes(swarm->db,npoints_prior_migration,NULL,NULL);CHKERRQ(ierr); 175 176 ierr = DataExBegin(de);CHKERRQ(ierr); 177 ierr = DataExEnd(de);CHKERRQ(ierr); 178 179 ierr = DataExGetRecvData(de,&n_points_recv,(void**)&recv_points);CHKERRQ(ierr); 180 ierr = DataBucketGetSizes(swarm->db,&npoints,NULL,NULL);CHKERRQ(ierr); 181 ierr = DataBucketSetSizes(swarm->db,npoints + n_points_recv,-1);CHKERRQ(ierr); 182 for (p=0; p<n_points_recv; p++) { 183 void *data_p = (void*)( (char*)recv_points + p*sizeof_dmswarm_point ); 184 185 ierr = DataBucketInsertPackedArray(swarm->db,npoints+p,data_p);CHKERRQ(ierr); 186 } 187 188 //ierr = DataExView(de);CHKERRQ(ierr); 189 ierr = DataBucketDestroyPackedArray(swarm->db,&point_buffer);CHKERRQ(ierr); 190 ierr = DataExDestroy(de);CHKERRQ(ierr); 191 192 PetscFunctionReturn(0); 193 } 194 195 #undef __FUNCT__ 196 #define __FUNCT__ "DMSwarmMigrate_CellDMScatter" 197 PetscErrorCode DMSwarmMigrate_CellDMScatter(DM dm,PetscBool remove_sent_points) 198 { 199 DM_Swarm *swarm = (DM_Swarm*)dm->data; 200 PetscErrorCode ierr; 201 PetscInt p,npoints,npointsg=0,npoints2,npoints2g,len,*rankval,npoints_prior_migration; 202 const PetscInt *LA_iscell; 203 DM dmcell; 204 IS iscell; 205 Vec pos; 206 PetscBool error_check = swarm->migrate_error_on_missing_point; 207 PetscMPIInt commsize,rank; 208 209 ierr = DMSwarmGetCellDM(dm,&dmcell);CHKERRQ(ierr); 210 if (!dmcell) SETERRQ(PetscObjectComm((PetscObject)dm),PETSC_ERR_SUP,"Only valid if cell DM provided"); 211 212 ierr = MPI_Comm_size(PetscObjectComm((PetscObject)dm),&commsize);CHKERRQ(ierr); 213 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)dm),&rank);CHKERRQ(ierr); 214 if (commsize == 1) PetscFunctionReturn(0); 215 216 ierr = DMSwarmCreateGlobalVectorFromField(dm,DMSwarmPICField_coor,&pos);CHKERRQ(ierr); 217 ierr = DMLocatePoints(dmcell,pos,&iscell);CHKERRQ(ierr); 218 ierr = DMSwarmDestroyGlobalVectorFromField(dm,DMSwarmPICField_coor,&pos);CHKERRQ(ierr); 219 220 if (error_check) { 221 ierr = DMSwarmGetSize(dm,&npointsg);CHKERRQ(ierr); 222 } 223 ierr = DataBucketGetSizes(swarm->db,&npoints,NULL,NULL);CHKERRQ(ierr); 224 ierr = DMSwarmGetField(dm,DMSwarmField_rank,NULL,NULL,(void**)&rankval);CHKERRQ(ierr); 225 ierr = ISGetIndices(iscell,&LA_iscell);CHKERRQ(ierr); 226 for (p=0; p<npoints; p++) { 227 rankval[p] = LA_iscell[p]; 228 } 229 ierr = ISRestoreIndices(iscell,&LA_iscell);CHKERRQ(ierr); 230 ierr = DMSwarmRestoreField(dm,DMSwarmField_rank,NULL,NULL,(void**)&rankval);CHKERRQ(ierr); 231 ierr = ISDestroy(&iscell);CHKERRQ(ierr); 232 233 ierr = DMSwarmMigrate_DMNeighborScatter(dm,dmcell,remove_sent_points,&npoints_prior_migration);CHKERRQ(ierr); 234 235 /* locate points newly recevied */ 236 ierr = DataBucketGetSizes(swarm->db,&npoints2,NULL,NULL);CHKERRQ(ierr); 237 #if 0 238 len = npoints2 - npoints_prior_migration; 239 if (len > 0) { 240 PetscScalar *LA_coor; 241 PetscInt bs; 242 243 ierr = DMSwarmGetField(dm,DMSwarmPICField_coor,&bs,NULL,(void**)&LA_coor);CHKERRQ(ierr); 244 ierr = VecCreateSeqWithArray(PETSC_COMM_SELF,bs,bs*len,(const PetscScalar*)&LA_coor[bs*npoints_prior_migration],&pos);CHKERRQ(ierr); 245 246 ierr = DMLocatePoints(dmcell,pos,&iscell);CHKERRQ(ierr); 247 248 ierr = VecDestroy(&pos);CHKERRQ(ierr); 249 ierr = DMSwarmRestoreField(dm,DMSwarmPICField_coor,&bs,NULL,(void**)&LA_coor);CHKERRQ(ierr); 250 251 ierr = ISGetIndices(iscell,&LA_iscell);CHKERRQ(ierr); 252 ierr = DMSwarmGetField(dm,DMSwarmField_rank,NULL,NULL,(void**)&rankval);CHKERRQ(ierr); 253 for (p=0; p<len; p++) { 254 if (LA_iscell[p] == -1) { 255 rankval[npoints_prior_migration+p] = -1; 256 } 257 } 258 ierr = ISRestoreIndices(iscell,&LA_iscell);CHKERRQ(ierr); 259 ierr = ISDestroy(&iscell);CHKERRQ(ierr); 260 ierr = DMSwarmRestoreField(dm,DMSwarmField_rank,NULL,NULL,(void**)&rankval);CHKERRQ(ierr); 261 262 /* remove points which left processor */ 263 ierr = DataBucketGetDataFieldByName(swarm->db,DMSwarmField_rank,&PField);CHKERRQ(ierr); 264 ierr = DataFieldGetEntries(PField,(void**)&rankval);CHKERRQ(ierr); 265 266 ierr = DataBucketGetSizes(swarm->db,&npoints,NULL,NULL);CHKERRQ(ierr); 267 for (p=npoints_prior_migration; p<npoints2; p++) { 268 if (rankval[p] == -1) { 269 /* kill point */ 270 ierr = DataBucketRemovePointAtIndex(swarm->db,p);CHKERRQ(ierr); 271 ierr = DataBucketGetSizes(swarm->db,&npoints2,NULL,NULL);CHKERRQ(ierr); /* you need to update npoints as the list size decreases! */ 272 ierr = DataFieldGetEntries(PField,(void**)&rankval);CHKERRQ(ierr); /* update date point increase realloc performed */ 273 p--; /* check replacement point */ 274 } 275 } 276 277 } 278 #endif 279 280 { 281 PetscScalar *LA_coor; 282 PetscInt bs; 283 DataField PField; 284 285 ierr = DMSwarmGetField(dm,DMSwarmPICField_coor,&bs,NULL,(void**)&LA_coor);CHKERRQ(ierr); 286 ierr = VecCreateSeqWithArray(PETSC_COMM_SELF,bs,bs*npoints2,(const PetscScalar*)LA_coor,&pos);CHKERRQ(ierr); 287 ierr = DMLocatePoints(dmcell,pos,&iscell);CHKERRQ(ierr); 288 289 ierr = VecDestroy(&pos);CHKERRQ(ierr); 290 ierr = DMSwarmRestoreField(dm,DMSwarmPICField_coor,&bs,NULL,(void**)&LA_coor);CHKERRQ(ierr); 291 292 ierr = ISGetIndices(iscell,&LA_iscell);CHKERRQ(ierr); 293 ierr = DMSwarmGetField(dm,DMSwarmField_rank,NULL,NULL,(void**)&rankval);CHKERRQ(ierr); 294 for (p=0; p<npoints2; p++) { 295 rankval[p] = LA_iscell[p]; 296 } 297 ierr = ISRestoreIndices(iscell,&LA_iscell);CHKERRQ(ierr); 298 ierr = ISDestroy(&iscell);CHKERRQ(ierr); 299 ierr = DMSwarmRestoreField(dm,DMSwarmField_rank,NULL,NULL,(void**)&rankval);CHKERRQ(ierr); 300 301 /* remove points which left processor */ 302 ierr = DataBucketGetDataFieldByName(swarm->db,DMSwarmField_rank,&PField);CHKERRQ(ierr); 303 ierr = DataFieldGetEntries(PField,(void**)&rankval);CHKERRQ(ierr); 304 305 ierr = DataBucketGetSizes(swarm->db,&npoints2,NULL,NULL);CHKERRQ(ierr); 306 for (p=0; p<npoints2; p++) { 307 if (rankval[p] == -1) { 308 /* kill point */ 309 ierr = DataBucketRemovePointAtIndex(swarm->db,p);CHKERRQ(ierr); 310 ierr = DataBucketGetSizes(swarm->db,&npoints2,NULL,NULL);CHKERRQ(ierr); /* you need to update npoints as the list size decreases! */ 311 ierr = DataFieldGetEntries(PField,(void**)&rankval);CHKERRQ(ierr); /* update date point increase realloc performed */ 312 p--; /* check replacement point */ 313 } 314 } 315 316 } 317 318 /* check for error on removed points */ 319 if (error_check) { 320 ierr = DMSwarmGetSize(dm,&npoints2g);CHKERRQ(ierr); 321 if (npointsg != npoints2g) SETERRQ2(PetscObjectComm((PetscObject)dm),PETSC_ERR_USER,"Points from the DMSwarm must remain constant during migration (initial %D - final %D)",npointsg,npoints2g); 322 } 323 PetscFunctionReturn(0); 324 } 325 326 #undef __FUNCT__ 327 #define __FUNCT__ "DMSwarmMigrate_CellDMExact" 328 PetscErrorCode DMSwarmMigrate_CellDMExact(DM dm,PetscBool remove_sent_points) 329 { 330 // DM_Swarm *swarm = (DM_Swarm*)dm->data; 331 // PetscErrorCode ierr; 332 333 PetscFunctionReturn(0); 334 } 335 336 /* 337 Redundant as this assumes points can only be sent to a single rank 338 */ 339 #undef __FUNCT__ 340 #define __FUNCT__ "DMSwarmMigrate_GlobalToLocal_Basic" 341 PetscErrorCode DMSwarmMigrate_GlobalToLocal_Basic(DM dm,PetscInt *globalsize) 342 { 343 DM_Swarm *swarm = (DM_Swarm*)dm->data; 344 PetscErrorCode ierr; 345 DataEx de; 346 PetscInt p,npoints,*rankval,n_points_recv; 347 PetscMPIInt rank,nrank,negrank; 348 void *point_buffer,*recv_points; 349 size_t sizeof_dmswarm_point; 350 351 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)dm),&rank);CHKERRQ(ierr); 352 353 ierr = DataBucketGetSizes(swarm->db,&npoints,NULL,NULL);CHKERRQ(ierr); 354 *globalsize = npoints; 355 ierr = DMSwarmGetField(dm,DMSwarmField_rank,NULL,NULL,(void**)&rankval);CHKERRQ(ierr); 356 357 de = DataExCreate(PetscObjectComm((PetscObject)dm),0);CHKERRQ(ierr); 358 359 ierr = DataExTopologyInitialize(de);CHKERRQ(ierr); 360 for (p=0; p<npoints; p++) { 361 negrank = rankval[p]; 362 if (negrank < 0) { 363 nrank = -negrank - 1; 364 ierr = DataExTopologyAddNeighbour(de,nrank);CHKERRQ(ierr); 365 } 366 } 367 ierr = DataExTopologyFinalize(de);CHKERRQ(ierr); 368 369 ierr = DataExInitializeSendCount(de);CHKERRQ(ierr); 370 for (p=0; p<npoints; p++) { 371 negrank = rankval[p]; 372 if (negrank < 0) { 373 nrank = -negrank - 1; 374 ierr = DataExAddToSendCount(de,nrank,1);CHKERRQ(ierr); 375 } 376 } 377 ierr = DataExFinalizeSendCount(de);CHKERRQ(ierr); 378 379 ierr = DataBucketCreatePackedArray(swarm->db,&sizeof_dmswarm_point,&point_buffer);CHKERRQ(ierr); 380 ierr = DataExPackInitialize(de,sizeof_dmswarm_point);CHKERRQ(ierr); 381 for (p=0; p<npoints; p++) { 382 negrank = rankval[p]; 383 if (negrank < 0) { 384 nrank = -negrank - 1; 385 rankval[p] = nrank; 386 /* copy point into buffer */ 387 ierr = DataBucketFillPackedArray(swarm->db,p,point_buffer);CHKERRQ(ierr); 388 /* insert point buffer into DataExchanger */ 389 ierr = DataExPackData(de,nrank,1,point_buffer);CHKERRQ(ierr); 390 rankval[p] = negrank; 391 } 392 } 393 ierr = DataExPackFinalize(de);CHKERRQ(ierr); 394 395 ierr = DMSwarmRestoreField(dm,DMSwarmField_rank,NULL,NULL,(void**)&rankval);CHKERRQ(ierr); 396 397 ierr = DataExBegin(de);CHKERRQ(ierr); 398 ierr = DataExEnd(de);CHKERRQ(ierr); 399 400 ierr = DataExGetRecvData(de,&n_points_recv,(void**)&recv_points);CHKERRQ(ierr); 401 402 ierr = DataBucketGetSizes(swarm->db,&npoints,NULL,NULL);CHKERRQ(ierr); 403 ierr = DataBucketSetSizes(swarm->db,npoints + n_points_recv,-1);CHKERRQ(ierr); 404 for (p=0; p<n_points_recv; p++) { 405 void *data_p = (void*)( (char*)recv_points + p*sizeof_dmswarm_point ); 406 407 ierr = DataBucketInsertPackedArray(swarm->db,npoints+p,data_p);CHKERRQ(ierr); 408 } 409 ierr = DataExView(de);CHKERRQ(ierr); 410 ierr = DataBucketDestroyPackedArray(swarm->db,&point_buffer);CHKERRQ(ierr); 411 ierr = DataExDestroy(de);CHKERRQ(ierr); 412 413 PetscFunctionReturn(0); 414 } 415 416 typedef struct { 417 PetscMPIInt owner_rank; 418 PetscReal min[3],max[3]; 419 } CollectBBox; 420 421 #undef __FUNCT__ 422 #define __FUNCT__ "DMSwarmCollect_DMDABoundingBox" 423 PETSC_EXTERN PetscErrorCode DMSwarmCollect_DMDABoundingBox(DM dm,PetscInt *globalsize) 424 { 425 DM_Swarm *swarm = (DM_Swarm*)dm->data; 426 PetscErrorCode ierr; 427 DataEx de; 428 PetscInt p,pk,npoints,*rankval,n_points_recv,n_bbox_recv,dim,neighbour_cells; 429 PetscMPIInt rank,nrank; 430 void *point_buffer,*recv_points; 431 size_t sizeof_dmswarm_point,sizeof_bbox_ctx; 432 PetscBool isdmda; 433 CollectBBox *bbox,*recv_bbox; 434 const PetscMPIInt *dmneighborranks; 435 DM dmcell; 436 437 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)dm),&rank);CHKERRQ(ierr); 438 439 ierr = DMSwarmGetCellDM(dm,&dmcell);CHKERRQ(ierr); 440 if (!dmcell) SETERRQ(PetscObjectComm((PetscObject)dm),PETSC_ERR_SUP,"Only valid if cell DM provided"); 441 442 isdmda = PETSC_FALSE; 443 PetscObjectTypeCompare((PetscObject)dmcell,DMDA,&isdmda); 444 if (!isdmda) SETERRQ(PetscObjectComm((PetscObject)dm),PETSC_ERR_SUP,"Only DMDA support for CollectBoundingBox"); 445 446 ierr = DMGetDimension(dm,&dim);CHKERRQ(ierr); 447 448 sizeof_bbox_ctx = sizeof(CollectBBox); 449 PetscMalloc1(1,&bbox); 450 bbox->owner_rank = rank; 451 452 /* compute the bounding box based on the overlapping / stenctil size */ 453 //ierr = DMDAGetLocalBoundingBox(dmcell,bbox->min,bbox->max);CHKERRQ(ierr); 454 { 455 Vec lcoor; 456 457 ierr = DMGetCoordinatesLocal(dmcell,&lcoor);CHKERRQ(ierr); 458 459 if (dim >= 1) { 460 ierr = VecStrideMin(lcoor,0,NULL,&bbox->min[0]);CHKERRQ(ierr); 461 ierr = VecStrideMax(lcoor,0,NULL,&bbox->max[0]);CHKERRQ(ierr); 462 } 463 464 if (dim >= 2) { 465 ierr = VecStrideMin(lcoor,1,NULL,&bbox->min[1]);CHKERRQ(ierr); 466 ierr = VecStrideMax(lcoor,1,NULL,&bbox->max[1]);CHKERRQ(ierr); 467 } 468 469 if (dim == 3) { 470 ierr = VecStrideMin(lcoor,2,NULL,&bbox->min[2]);CHKERRQ(ierr); 471 ierr = VecStrideMax(lcoor,2,NULL,&bbox->max[2]);CHKERRQ(ierr); 472 } 473 } 474 475 ierr = DataBucketGetSizes(swarm->db,&npoints,NULL,NULL);CHKERRQ(ierr); 476 *globalsize = npoints; 477 ierr = DMSwarmGetField(dm,DMSwarmField_rank,NULL,NULL,(void**)&rankval);CHKERRQ(ierr); 478 479 de = DataExCreate(PetscObjectComm((PetscObject)dm),0);CHKERRQ(ierr); 480 481 /* use DMDA neighbours */ 482 ierr = DMDAGetNeighbors(dmcell,&dmneighborranks);CHKERRQ(ierr); 483 if (dim == 1) { 484 neighbour_cells = 3; 485 } else if (dim == 2) { 486 neighbour_cells = 9; 487 } else { 488 neighbour_cells = 27; 489 } 490 491 ierr = DataExTopologyInitialize(de);CHKERRQ(ierr); 492 for (p=0; p<neighbour_cells; p++) { 493 if ( (dmneighborranks[p] >= 0) && (dmneighborranks[p] != rank) ) { 494 ierr = DataExTopologyAddNeighbour(de,dmneighborranks[p]);CHKERRQ(ierr); 495 } 496 } 497 ierr = DataExTopologyFinalize(de);CHKERRQ(ierr); 498 499 ierr = DataExInitializeSendCount(de);CHKERRQ(ierr); 500 for (p=0; p<neighbour_cells; p++) { 501 if ( (dmneighborranks[p] >= 0) && (dmneighborranks[p] != rank) ) { 502 ierr = DataExAddToSendCount(de,dmneighborranks[p],1);CHKERRQ(ierr); 503 } 504 } 505 ierr = DataExFinalizeSendCount(de);CHKERRQ(ierr); 506 507 508 /* send bounding boxes */ 509 ierr = DataExPackInitialize(de,sizeof_bbox_ctx);CHKERRQ(ierr); 510 for (p=0; p<neighbour_cells; p++) { 511 nrank = dmneighborranks[p]; 512 if ( (nrank >= 0) && (nrank != rank) ) { 513 /* insert bbox buffer into DataExchanger */ 514 ierr = DataExPackData(de,nrank,1,bbox);CHKERRQ(ierr); 515 } 516 } 517 ierr = DataExPackFinalize(de);CHKERRQ(ierr); 518 519 /* recv bounding boxes */ 520 ierr = DataExBegin(de);CHKERRQ(ierr); 521 ierr = DataExEnd(de);CHKERRQ(ierr); 522 523 ierr = DataExGetRecvData(de,&n_bbox_recv,(void**)&recv_bbox);CHKERRQ(ierr); 524 525 526 for (p=0; p<n_bbox_recv; p++) { 527 printf("[rank %d]: box from %d : range[%+1.4e,%+1.4e]x[%+1.4e,%+1.4e]\n",rank,recv_bbox[p].owner_rank, 528 recv_bbox[p].min[0],recv_bbox[p].max[0],recv_bbox[p].min[1],recv_bbox[p].max[1]); 529 } 530 531 /* of course this is stupid as this "generic" function should have a better way to know what the coordinates are called */ 532 ierr = DataExInitializeSendCount(de);CHKERRQ(ierr); 533 for (pk=0; pk<n_bbox_recv; pk++) { 534 PetscReal *array_x,*array_y; 535 536 ierr = DMSwarmGetField(dm,"coorx",NULL,NULL,(void**)&array_x);CHKERRQ(ierr); 537 ierr = DMSwarmGetField(dm,"coory",NULL,NULL,(void**)&array_y);CHKERRQ(ierr); 538 539 for (p=0; p<npoints; p++) { 540 if ((array_x[p] >= recv_bbox[pk].min[0]) && (array_x[p] <= recv_bbox[pk].max[0]) ) { 541 if ((array_y[p] >= recv_bbox[pk].min[1]) && (array_y[p] <= recv_bbox[pk].max[1]) ) { 542 543 ierr = DataExAddToSendCount(de,recv_bbox[pk].owner_rank,1);CHKERRQ(ierr); 544 545 } 546 } 547 } 548 ierr = DMSwarmRestoreField(dm,"coory",NULL,NULL,(void**)&array_y);CHKERRQ(ierr); 549 ierr = DMSwarmRestoreField(dm,"coorx",NULL,NULL,(void**)&array_x);CHKERRQ(ierr); 550 } 551 ierr = DataExFinalizeSendCount(de);CHKERRQ(ierr); 552 553 554 555 ierr = DataBucketCreatePackedArray(swarm->db,&sizeof_dmswarm_point,&point_buffer);CHKERRQ(ierr); 556 ierr = DataExPackInitialize(de,sizeof_dmswarm_point);CHKERRQ(ierr); 557 for (pk=0; pk<n_bbox_recv; pk++) { 558 PetscReal *array_x,*array_y; 559 560 ierr = DMSwarmGetField(dm,"coorx",NULL,NULL,(void**)&array_x);CHKERRQ(ierr); 561 ierr = DMSwarmGetField(dm,"coory",NULL,NULL,(void**)&array_y);CHKERRQ(ierr); 562 563 for (p=0; p<npoints; p++) { 564 if ((array_x[p] >= recv_bbox[pk].min[0]) && (array_x[p] <= recv_bbox[pk].max[0]) ) { 565 if ((array_y[p] >= recv_bbox[pk].min[1]) && (array_y[p] <= recv_bbox[pk].max[1]) ) { 566 // copy point into buffer // 567 ierr = DataBucketFillPackedArray(swarm->db,p,point_buffer);CHKERRQ(ierr); 568 // insert point buffer into DataExchanger // 569 ierr = DataExPackData(de,recv_bbox[pk].owner_rank,1,point_buffer);CHKERRQ(ierr); 570 } 571 } 572 } 573 574 ierr = DMSwarmRestoreField(dm,"coory",NULL,NULL,(void**)&array_y);CHKERRQ(ierr); 575 ierr = DMSwarmRestoreField(dm,"coorx",NULL,NULL,(void**)&array_x);CHKERRQ(ierr); 576 } 577 578 ierr = DataExPackFinalize(de);CHKERRQ(ierr); 579 580 ierr = DMSwarmRestoreField(dm,DMSwarmField_rank,NULL,NULL,(void**)&rankval);CHKERRQ(ierr); 581 582 ierr = DataExBegin(de);CHKERRQ(ierr); 583 ierr = DataExEnd(de);CHKERRQ(ierr); 584 585 ierr = DataExGetRecvData(de,&n_points_recv,(void**)&recv_points);CHKERRQ(ierr); 586 587 ierr = DataBucketGetSizes(swarm->db,&npoints,NULL,NULL);CHKERRQ(ierr); 588 ierr = DataBucketSetSizes(swarm->db,npoints + n_points_recv,-1);CHKERRQ(ierr); 589 for (p=0; p<n_points_recv; p++) { 590 void *data_p = (void*)( (char*)recv_points + p*sizeof_dmswarm_point ); 591 592 ierr = DataBucketInsertPackedArray(swarm->db,npoints+p,data_p);CHKERRQ(ierr); 593 } 594 595 ierr = DataBucketDestroyPackedArray(swarm->db,&point_buffer);CHKERRQ(ierr); 596 PetscFree(bbox); 597 ierr = DataExView(de);CHKERRQ(ierr); 598 ierr = DataExDestroy(de);CHKERRQ(ierr); 599 600 PetscFunctionReturn(0); 601 } 602 603 604 /* General collection when no order, or neighbour information is provided */ 605 /* 606 User provides context and collect() method 607 Broadcast user context 608 609 for each context / rank { 610 collect(swarm,context,n,list) 611 } 612 613 */ 614 #undef __FUNCT__ 615 #define __FUNCT__ "DMSwarmCollect_General" 616 PETSC_EXTERN PetscErrorCode DMSwarmCollect_General(DM dm,PetscErrorCode (*collect)(DM,void*,PetscInt*,PetscInt**),size_t ctx_size,void *ctx,PetscInt *globalsize) 617 { 618 DM_Swarm *swarm = (DM_Swarm*)dm->data; 619 PetscErrorCode ierr; 620 DataEx de; 621 PetscInt p,r,npoints,n_points_recv; 622 PetscMPIInt commsize,rank; 623 void *point_buffer,*recv_points; 624 void *ctxlist; 625 PetscInt *n2collect,**collectlist; 626 size_t sizeof_dmswarm_point; 627 628 ierr = MPI_Comm_size(PetscObjectComm((PetscObject)dm),&commsize);CHKERRQ(ierr); 629 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject)dm),&rank);CHKERRQ(ierr); 630 631 ierr = DataBucketGetSizes(swarm->db,&npoints,NULL,NULL);CHKERRQ(ierr); 632 *globalsize = npoints; 633 634 /* Broadcast user context */ 635 PetscMalloc(ctx_size*commsize,&ctxlist); 636 ierr = MPI_Allgather(ctx,ctx_size,MPI_CHAR,ctxlist,ctx_size,MPI_CHAR,PetscObjectComm((PetscObject)dm));CHKERRQ(ierr); 637 638 PetscMalloc1(commsize,&n2collect); 639 PetscMalloc1(commsize,&collectlist); 640 641 for (r=0; r<commsize; r++) { 642 PetscInt _n2collect; 643 PetscInt *_collectlist; 644 void *_ctx_r; 645 646 _n2collect = 0; 647 _collectlist = NULL; 648 649 if (r != rank) { /* don't collect data from yourself */ 650 _ctx_r = (void*)( (char*)ctxlist + r * ctx_size ); 651 ierr = collect(dm,_ctx_r,&_n2collect,&_collectlist);CHKERRQ(ierr); 652 } 653 654 n2collect[r] = _n2collect; 655 collectlist[r] = _collectlist; 656 } 657 658 de = DataExCreate(PetscObjectComm((PetscObject)dm),0);CHKERRQ(ierr); 659 660 /* Define topology */ 661 ierr = DataExTopologyInitialize(de);CHKERRQ(ierr); 662 for (r=0; r<commsize; r++) { 663 if (n2collect[r] > 0) { 664 ierr = DataExTopologyAddNeighbour(de,(PetscMPIInt)r);CHKERRQ(ierr); 665 } 666 } 667 ierr = DataExTopologyFinalize(de);CHKERRQ(ierr); 668 669 /* Define send counts */ 670 ierr = DataExInitializeSendCount(de);CHKERRQ(ierr); 671 for (r=0; r<commsize; r++) { 672 if (n2collect[r] > 0) { 673 ierr = DataExAddToSendCount(de,r,n2collect[r]);CHKERRQ(ierr); 674 } 675 } 676 ierr = DataExFinalizeSendCount(de);CHKERRQ(ierr); 677 678 /* Pack data */ 679 ierr = DataBucketCreatePackedArray(swarm->db,&sizeof_dmswarm_point,&point_buffer);CHKERRQ(ierr); 680 681 ierr = DataExPackInitialize(de,sizeof_dmswarm_point);CHKERRQ(ierr); 682 for (r=0; r<commsize; r++) { 683 684 for (p=0; p<n2collect[r]; p++) { 685 ierr = DataBucketFillPackedArray(swarm->db,collectlist[r][p],point_buffer);CHKERRQ(ierr); 686 /* insert point buffer into the data exchanger */ 687 ierr = DataExPackData(de,r,1,point_buffer);CHKERRQ(ierr); 688 } 689 } 690 691 ierr = DataExPackFinalize(de);CHKERRQ(ierr); 692 693 /* Scatter */ 694 ierr = DataExBegin(de);CHKERRQ(ierr); 695 ierr = DataExEnd(de);CHKERRQ(ierr); 696 697 /* Collect data in DMSwarm container */ 698 ierr = DataExGetRecvData(de,&n_points_recv,(void**)&recv_points);CHKERRQ(ierr); 699 700 ierr = DataBucketGetSizes(swarm->db,&npoints,NULL,NULL);CHKERRQ(ierr); 701 ierr = DataBucketSetSizes(swarm->db,npoints + n_points_recv,-1);CHKERRQ(ierr); 702 for (p=0; p<n_points_recv; p++) { 703 void *data_p = (void*)( (char*)recv_points + p*sizeof_dmswarm_point ); 704 705 ierr = DataBucketInsertPackedArray(swarm->db,npoints+p,data_p);CHKERRQ(ierr); 706 } 707 708 /* Release memory */ 709 for (r=0; r<commsize; r++) { 710 if (collectlist[r]) PetscFree(collectlist[r]); 711 } 712 PetscFree(collectlist); 713 PetscFree(n2collect); 714 PetscFree(ctxlist); 715 ierr = DataBucketDestroyPackedArray(swarm->db,&point_buffer);CHKERRQ(ierr); 716 ierr = DataExView(de);CHKERRQ(ierr); 717 ierr = DataExDestroy(de);CHKERRQ(ierr); 718 719 PetscFunctionReturn(0); 720 } 721 722