1 /* 2 Routines to compute overlapping regions of a parallel MPI matrix 3 and to find submatrices that were shared across processors. 4 */ 5 #include <../src/mat/impls/baij/mpi/mpibaij.h> 6 #include <petscbt.h> 7 8 static PetscErrorCode MatIncreaseOverlap_MPIBAIJ_Local(Mat, PetscInt, char **, PetscInt *, PetscInt **); 9 static PetscErrorCode MatIncreaseOverlap_MPIBAIJ_Receive(Mat, PetscInt, PetscInt **, PetscInt **, PetscInt *); 10 extern PetscErrorCode MatGetRow_MPIBAIJ(Mat, PetscInt, PetscInt *, PetscInt **, PetscScalar **); 11 extern PetscErrorCode MatRestoreRow_MPIBAIJ(Mat, PetscInt, PetscInt *, PetscInt **, PetscScalar **); 12 13 PetscErrorCode MatIncreaseOverlap_MPIBAIJ(Mat C, PetscInt imax, IS is[], PetscInt ov) 14 { 15 PetscInt i, N = C->cmap->N, bs = C->rmap->bs, n; 16 const PetscInt *idx; 17 IS *is_new; 18 19 PetscFunctionBegin; 20 PetscCall(PetscMalloc1(imax, &is_new)); 21 /* Convert the indices into block format */ 22 PetscCall(ISCompressIndicesGeneral(N, C->rmap->n, bs, imax, is, is_new)); 23 PetscCheck(ov >= 0, PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Negative overlap specified"); 24 for (i = 0; i < ov; ++i) PetscCall(MatIncreaseOverlap_MPIBAIJ_Once(C, imax, is_new)); 25 for (i = 0; i < imax; i++) { 26 PetscCall(ISDestroy(&is[i])); 27 PetscCall(ISGetLocalSize(is_new[i], &n)); 28 PetscCall(ISGetIndices(is_new[i], &idx)); 29 PetscCall(ISCreateBlock(PetscObjectComm((PetscObject)is_new[i]), bs, n, idx, PETSC_COPY_VALUES, &is[i])); 30 PetscCall(ISDestroy(&is_new[i])); 31 } 32 PetscCall(PetscFree(is_new)); 33 PetscFunctionReturn(PETSC_SUCCESS); 34 } 35 36 /* 37 Sample message format: 38 If a processor A wants processor B to process some elements corresponding 39 to index sets is[1], is[5] 40 mesg [0] = 2 (no of index sets in the mesg) 41 ----------- 42 mesg [1] = 1 => is[1] 43 mesg [2] = sizeof(is[1]); 44 ----------- 45 mesg [5] = 5 => is[5] 46 mesg [6] = sizeof(is[5]); 47 ----------- 48 mesg [7] 49 mesg [n] data(is[1]) 50 ----------- 51 mesg[n+1] 52 mesg[m] data(is[5]) 53 ----------- 54 55 Notes: 56 nrqs - no of requests sent (or to be sent out) 57 nrqr - no of requests received (which have to be or which have been processed) 58 */ 59 PetscErrorCode MatIncreaseOverlap_MPIBAIJ_Once(Mat C, PetscInt imax, IS is[]) 60 { 61 Mat_MPIBAIJ *c = (Mat_MPIBAIJ *)C->data; 62 const PetscInt **idx, *idx_i; 63 PetscInt *n, *w3, *w4, **data, len; 64 PetscMPIInt size, rank, tag1, tag2, *w2, *w1, nrqr; 65 PetscInt Mbs, i, j, k, **rbuf, row, nrqs, msz, **outdat, **ptr; 66 PetscInt *ctr, *pa, *tmp, *isz, *isz1, **xdata, **rbuf2, *d_p; 67 PetscMPIInt *onodes1, *olengths1, *onodes2, *olengths2, proc = -1; 68 PetscBT *table; 69 MPI_Comm comm, *iscomms; 70 MPI_Request *s_waits1, *r_waits1, *s_waits2, *r_waits2; 71 char *t_p; 72 73 PetscFunctionBegin; 74 PetscCall(PetscObjectGetComm((PetscObject)C, &comm)); 75 size = c->size; 76 rank = c->rank; 77 Mbs = c->Mbs; 78 79 PetscCall(PetscObjectGetNewTag((PetscObject)C, &tag1)); 80 PetscCall(PetscObjectGetNewTag((PetscObject)C, &tag2)); 81 82 PetscCall(PetscMalloc2(imax, (PetscInt ***)&idx, imax, &n)); 83 84 for (i = 0; i < imax; i++) { 85 PetscCall(ISGetIndices(is[i], &idx[i])); 86 PetscCall(ISGetLocalSize(is[i], &n[i])); 87 } 88 89 /* evaluate communication - mesg to who,length of mesg, and buffer space 90 required. Based on this, buffers are allocated, and data copied into them*/ 91 PetscCall(PetscCalloc4(size, &w1, size, &w2, size, &w3, size, &w4)); 92 for (i = 0; i < imax; i++) { 93 PetscCall(PetscArrayzero(w4, size)); /* initialise work vector*/ 94 idx_i = idx[i]; 95 len = n[i]; 96 for (j = 0; j < len; j++) { 97 row = idx_i[j]; 98 PetscCheck(row >= 0, PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Index set cannot have negative entries"); 99 PetscCall(PetscLayoutFindOwner(C->rmap, row * C->rmap->bs, &proc)); 100 w4[proc]++; 101 } 102 for (j = 0; j < size; j++) { 103 if (w4[j]) { 104 w1[j] += w4[j]; 105 w3[j]++; 106 } 107 } 108 } 109 110 nrqs = 0; /* no of outgoing messages */ 111 msz = 0; /* total mesg length (for all proc */ 112 w1[rank] = 0; /* no mesg sent to itself */ 113 w3[rank] = 0; 114 for (i = 0; i < size; i++) { 115 if (w1[i]) { 116 w2[i] = 1; 117 nrqs++; 118 } /* there exists a message to proc i */ 119 } 120 /* pa - is list of processors to communicate with */ 121 PetscCall(PetscMalloc1(nrqs, &pa)); 122 for (i = 0, j = 0; i < size; i++) { 123 if (w1[i]) { 124 pa[j] = i; 125 j++; 126 } 127 } 128 129 /* Each message would have a header = 1 + 2*(no of IS) + data */ 130 for (i = 0; i < nrqs; i++) { 131 j = pa[i]; 132 w1[j] += w2[j] + 2 * w3[j]; 133 msz += w1[j]; 134 } 135 136 /* Determine the number of messages to expect, their lengths, from from-ids */ 137 PetscCall(PetscGatherNumberOfMessages(comm, w2, w1, &nrqr)); 138 PetscCall(PetscGatherMessageLengths(comm, nrqs, nrqr, w1, &onodes1, &olengths1)); 139 140 /* Now post the Irecvs corresponding to these messages */ 141 PetscCall(PetscPostIrecvInt(comm, tag1, nrqr, onodes1, olengths1, &rbuf, &r_waits1)); 142 143 /* Allocate Memory for outgoing messages */ 144 PetscCall(PetscMalloc4(size, &outdat, size, &ptr, msz, &tmp, size, &ctr)); 145 PetscCall(PetscArrayzero(outdat, size)); 146 PetscCall(PetscArrayzero(ptr, size)); 147 { 148 PetscInt *iptr = tmp, ict = 0; 149 for (i = 0; i < nrqs; i++) { 150 j = pa[i]; 151 iptr += ict; 152 outdat[j] = iptr; 153 ict = w1[j]; 154 } 155 } 156 157 /* Form the outgoing messages */ 158 /*plug in the headers*/ 159 for (i = 0; i < nrqs; i++) { 160 j = pa[i]; 161 outdat[j][0] = 0; 162 PetscCall(PetscArrayzero(outdat[j] + 1, 2 * w3[j])); 163 ptr[j] = outdat[j] + 2 * w3[j] + 1; 164 } 165 166 /* Memory for doing local proc's work*/ 167 { 168 PetscCall(PetscCalloc5(imax, &table, imax, &data, imax, &isz, Mbs * imax, &d_p, (Mbs / PETSC_BITS_PER_BYTE + 1) * imax, &t_p)); 169 170 for (i = 0; i < imax; i++) { 171 table[i] = t_p + (Mbs / PETSC_BITS_PER_BYTE + 1) * i; 172 data[i] = d_p + (Mbs)*i; 173 } 174 } 175 176 /* Parse the IS and update local tables and the outgoing buf with the data*/ 177 { 178 PetscInt n_i, *data_i, isz_i, *outdat_j, ctr_j; 179 PetscBT table_i; 180 181 for (i = 0; i < imax; i++) { 182 PetscCall(PetscArrayzero(ctr, size)); 183 n_i = n[i]; 184 table_i = table[i]; 185 idx_i = idx[i]; 186 data_i = data[i]; 187 isz_i = isz[i]; 188 for (j = 0; j < n_i; j++) { /* parse the indices of each IS */ 189 row = idx_i[j]; 190 PetscCall(PetscLayoutFindOwner(C->rmap, row * C->rmap->bs, &proc)); 191 if (proc != rank) { /* copy to the outgoing buffer */ 192 ctr[proc]++; 193 *ptr[proc] = row; 194 ptr[proc]++; 195 } else { /* Update the local table */ 196 if (!PetscBTLookupSet(table_i, row)) data_i[isz_i++] = row; 197 } 198 } 199 /* Update the headers for the current IS */ 200 for (j = 0; j < size; j++) { /* Can Optimise this loop by using pa[] */ 201 if ((ctr_j = ctr[j])) { 202 outdat_j = outdat[j]; 203 k = ++outdat_j[0]; 204 outdat_j[2 * k] = ctr_j; 205 outdat_j[2 * k - 1] = i; 206 } 207 } 208 isz[i] = isz_i; 209 } 210 } 211 212 /* Now post the sends */ 213 PetscCall(PetscMalloc1(nrqs, &s_waits1)); 214 for (i = 0; i < nrqs; ++i) { 215 j = pa[i]; 216 PetscCallMPI(MPI_Isend(outdat[j], w1[j], MPIU_INT, j, tag1, comm, s_waits1 + i)); 217 } 218 219 /* No longer need the original indices*/ 220 for (i = 0; i < imax; ++i) PetscCall(ISRestoreIndices(is[i], idx + i)); 221 PetscCall(PetscFree2(*(PetscInt ***)&idx, n)); 222 223 PetscCall(PetscMalloc1(imax, &iscomms)); 224 for (i = 0; i < imax; ++i) { 225 PetscCall(PetscCommDuplicate(PetscObjectComm((PetscObject)is[i]), &iscomms[i], NULL)); 226 PetscCall(ISDestroy(&is[i])); 227 } 228 229 /* Do Local work*/ 230 PetscCall(MatIncreaseOverlap_MPIBAIJ_Local(C, imax, table, isz, data)); 231 232 /* Receive messages*/ 233 PetscCallMPI(MPI_Waitall(nrqr, r_waits1, MPI_STATUSES_IGNORE)); 234 PetscCallMPI(MPI_Waitall(nrqs, s_waits1, MPI_STATUSES_IGNORE)); 235 236 /* Phase 1 sends are complete - deallocate buffers */ 237 PetscCall(PetscFree4(outdat, ptr, tmp, ctr)); 238 PetscCall(PetscFree4(w1, w2, w3, w4)); 239 240 PetscCall(PetscMalloc1(nrqr, &xdata)); 241 PetscCall(PetscMalloc1(nrqr, &isz1)); 242 PetscCall(MatIncreaseOverlap_MPIBAIJ_Receive(C, nrqr, rbuf, xdata, isz1)); 243 if (rbuf) { 244 PetscCall(PetscFree(rbuf[0])); 245 PetscCall(PetscFree(rbuf)); 246 } 247 248 /* Send the data back*/ 249 /* Do a global reduction to know the buffer space req for incoming messages*/ 250 { 251 PetscMPIInt *rw1; 252 253 PetscCall(PetscCalloc1(size, &rw1)); 254 255 for (i = 0; i < nrqr; ++i) { 256 proc = onodes1[i]; 257 rw1[proc] = isz1[i]; 258 } 259 260 /* Determine the number of messages to expect, their lengths, from from-ids */ 261 PetscCall(PetscGatherMessageLengths(comm, nrqr, nrqs, rw1, &onodes2, &olengths2)); 262 PetscCall(PetscFree(rw1)); 263 } 264 /* Now post the Irecvs corresponding to these messages */ 265 PetscCall(PetscPostIrecvInt(comm, tag2, nrqs, onodes2, olengths2, &rbuf2, &r_waits2)); 266 267 /* Now post the sends */ 268 PetscCall(PetscMalloc1(nrqr, &s_waits2)); 269 for (i = 0; i < nrqr; ++i) { 270 j = onodes1[i]; 271 PetscCallMPI(MPI_Isend(xdata[i], isz1[i], MPIU_INT, j, tag2, comm, s_waits2 + i)); 272 } 273 274 PetscCall(PetscFree(onodes1)); 275 PetscCall(PetscFree(olengths1)); 276 277 /* receive work done on other processors*/ 278 { 279 PetscMPIInt idex; 280 PetscInt is_no, ct1, max, *rbuf2_i, isz_i, *data_i, jmax; 281 PetscBT table_i; 282 283 for (i = 0; i < nrqs; ++i) { 284 PetscCallMPI(MPI_Waitany(nrqs, r_waits2, &idex, MPI_STATUS_IGNORE)); 285 /* Process the message*/ 286 rbuf2_i = rbuf2[idex]; 287 ct1 = 2 * rbuf2_i[0] + 1; 288 jmax = rbuf2[idex][0]; 289 for (j = 1; j <= jmax; j++) { 290 max = rbuf2_i[2 * j]; 291 is_no = rbuf2_i[2 * j - 1]; 292 isz_i = isz[is_no]; 293 data_i = data[is_no]; 294 table_i = table[is_no]; 295 for (k = 0; k < max; k++, ct1++) { 296 row = rbuf2_i[ct1]; 297 if (!PetscBTLookupSet(table_i, row)) data_i[isz_i++] = row; 298 } 299 isz[is_no] = isz_i; 300 } 301 } 302 PetscCallMPI(MPI_Waitall(nrqr, s_waits2, MPI_STATUSES_IGNORE)); 303 } 304 305 for (i = 0; i < imax; ++i) { 306 PetscCall(ISCreateGeneral(iscomms[i], isz[i], data[i], PETSC_COPY_VALUES, is + i)); 307 PetscCall(PetscCommDestroy(&iscomms[i])); 308 } 309 310 PetscCall(PetscFree(iscomms)); 311 PetscCall(PetscFree(onodes2)); 312 PetscCall(PetscFree(olengths2)); 313 314 PetscCall(PetscFree(pa)); 315 if (rbuf2) { 316 PetscCall(PetscFree(rbuf2[0])); 317 PetscCall(PetscFree(rbuf2)); 318 } 319 PetscCall(PetscFree(s_waits1)); 320 PetscCall(PetscFree(r_waits1)); 321 PetscCall(PetscFree(s_waits2)); 322 PetscCall(PetscFree(r_waits2)); 323 PetscCall(PetscFree5(table, data, isz, d_p, t_p)); 324 if (xdata) { 325 PetscCall(PetscFree(xdata[0])); 326 PetscCall(PetscFree(xdata)); 327 } 328 PetscCall(PetscFree(isz1)); 329 PetscFunctionReturn(PETSC_SUCCESS); 330 } 331 332 /* 333 MatIncreaseOverlap_MPIBAIJ_Local - Called by MatincreaseOverlap, to do 334 the work on the local processor. 335 336 Inputs: 337 C - MAT_MPIBAIJ; 338 imax - total no of index sets processed at a time; 339 table - an array of char - size = Mbs bits. 340 341 Output: 342 isz - array containing the count of the solution elements corresponding 343 to each index set; 344 data - pointer to the solutions 345 */ 346 static PetscErrorCode MatIncreaseOverlap_MPIBAIJ_Local(Mat C, PetscInt imax, PetscBT *table, PetscInt *isz, PetscInt **data) 347 { 348 Mat_MPIBAIJ *c = (Mat_MPIBAIJ *)C->data; 349 Mat A = c->A, B = c->B; 350 Mat_SeqBAIJ *a = (Mat_SeqBAIJ *)A->data, *b = (Mat_SeqBAIJ *)B->data; 351 PetscInt start, end, val, max, rstart, cstart, *ai, *aj; 352 PetscInt *bi, *bj, *garray, i, j, k, row, *data_i, isz_i; 353 PetscBT table_i; 354 355 PetscFunctionBegin; 356 rstart = c->rstartbs; 357 cstart = c->cstartbs; 358 ai = a->i; 359 aj = a->j; 360 bi = b->i; 361 bj = b->j; 362 garray = c->garray; 363 364 for (i = 0; i < imax; i++) { 365 data_i = data[i]; 366 table_i = table[i]; 367 isz_i = isz[i]; 368 for (j = 0, max = isz[i]; j < max; j++) { 369 row = data_i[j] - rstart; 370 start = ai[row]; 371 end = ai[row + 1]; 372 for (k = start; k < end; k++) { /* Amat */ 373 val = aj[k] + cstart; 374 if (!PetscBTLookupSet(table_i, val)) data_i[isz_i++] = val; 375 } 376 start = bi[row]; 377 end = bi[row + 1]; 378 for (k = start; k < end; k++) { /* Bmat */ 379 val = garray[bj[k]]; 380 if (!PetscBTLookupSet(table_i, val)) data_i[isz_i++] = val; 381 } 382 } 383 isz[i] = isz_i; 384 } 385 PetscFunctionReturn(PETSC_SUCCESS); 386 } 387 /* 388 MatIncreaseOverlap_MPIBAIJ_Receive - Process the received messages, 389 and return the output 390 391 Input: 392 C - the matrix 393 nrqr - no of messages being processed. 394 rbuf - an array of pointers to the received requests 395 396 Output: 397 xdata - array of messages to be sent back 398 isz1 - size of each message 399 400 For better efficiency perhaps we should malloc separately each xdata[i], 401 then if a remalloc is required we need only copy the data for that one row 402 rather than all previous rows as it is now where a single large chunk of 403 memory is used. 404 405 */ 406 static PetscErrorCode MatIncreaseOverlap_MPIBAIJ_Receive(Mat C, PetscInt nrqr, PetscInt **rbuf, PetscInt **xdata, PetscInt *isz1) 407 { 408 Mat_MPIBAIJ *c = (Mat_MPIBAIJ *)C->data; 409 Mat A = c->A, B = c->B; 410 Mat_SeqBAIJ *a = (Mat_SeqBAIJ *)A->data, *b = (Mat_SeqBAIJ *)B->data; 411 PetscInt rstart, cstart, *ai, *aj, *bi, *bj, *garray, i, j, k; 412 PetscInt row, total_sz, ct, ct1, ct2, ct3, mem_estimate, oct2, l, start, end; 413 PetscInt val, max1, max2, Mbs, no_malloc = 0, *tmp, new_estimate, ctr; 414 PetscInt *rbuf_i, kmax, rbuf_0; 415 PetscBT xtable; 416 417 PetscFunctionBegin; 418 Mbs = c->Mbs; 419 rstart = c->rstartbs; 420 cstart = c->cstartbs; 421 ai = a->i; 422 aj = a->j; 423 bi = b->i; 424 bj = b->j; 425 garray = c->garray; 426 427 for (i = 0, ct = 0, total_sz = 0; i < nrqr; ++i) { 428 rbuf_i = rbuf[i]; 429 rbuf_0 = rbuf_i[0]; 430 ct += rbuf_0; 431 for (j = 1; j <= rbuf_0; j++) total_sz += rbuf_i[2 * j]; 432 } 433 434 if (c->Mbs) max1 = ct * (a->nz + b->nz) / c->Mbs; 435 else max1 = 1; 436 mem_estimate = 3 * ((total_sz > max1 ? total_sz : max1) + 1); 437 if (nrqr) { 438 PetscCall(PetscMalloc1(mem_estimate, &xdata[0])); 439 ++no_malloc; 440 } 441 PetscCall(PetscBTCreate(Mbs, &xtable)); 442 PetscCall(PetscArrayzero(isz1, nrqr)); 443 444 ct3 = 0; 445 for (i = 0; i < nrqr; i++) { /* for easch mesg from proc i */ 446 rbuf_i = rbuf[i]; 447 rbuf_0 = rbuf_i[0]; 448 ct1 = 2 * rbuf_0 + 1; 449 ct2 = ct1; 450 ct3 += ct1; 451 for (j = 1; j <= rbuf_0; j++) { /* for each IS from proc i*/ 452 PetscCall(PetscBTMemzero(Mbs, xtable)); 453 oct2 = ct2; 454 kmax = rbuf_i[2 * j]; 455 for (k = 0; k < kmax; k++, ct1++) { 456 row = rbuf_i[ct1]; 457 if (!PetscBTLookupSet(xtable, row)) { 458 if (!(ct3 < mem_estimate)) { 459 new_estimate = (PetscInt)(1.5 * mem_estimate) + 1; 460 PetscCall(PetscMalloc1(new_estimate, &tmp)); 461 PetscCall(PetscArraycpy(tmp, xdata[0], mem_estimate)); 462 PetscCall(PetscFree(xdata[0])); 463 xdata[0] = tmp; 464 mem_estimate = new_estimate; 465 ++no_malloc; 466 for (ctr = 1; ctr <= i; ctr++) xdata[ctr] = xdata[ctr - 1] + isz1[ctr - 1]; 467 } 468 xdata[i][ct2++] = row; 469 ct3++; 470 } 471 } 472 for (k = oct2, max2 = ct2; k < max2; k++) { 473 row = xdata[i][k] - rstart; 474 start = ai[row]; 475 end = ai[row + 1]; 476 for (l = start; l < end; l++) { 477 val = aj[l] + cstart; 478 if (!PetscBTLookupSet(xtable, val)) { 479 if (!(ct3 < mem_estimate)) { 480 new_estimate = (PetscInt)(1.5 * mem_estimate) + 1; 481 PetscCall(PetscMalloc1(new_estimate, &tmp)); 482 PetscCall(PetscArraycpy(tmp, xdata[0], mem_estimate)); 483 PetscCall(PetscFree(xdata[0])); 484 xdata[0] = tmp; 485 mem_estimate = new_estimate; 486 ++no_malloc; 487 for (ctr = 1; ctr <= i; ctr++) xdata[ctr] = xdata[ctr - 1] + isz1[ctr - 1]; 488 } 489 xdata[i][ct2++] = val; 490 ct3++; 491 } 492 } 493 start = bi[row]; 494 end = bi[row + 1]; 495 for (l = start; l < end; l++) { 496 val = garray[bj[l]]; 497 if (!PetscBTLookupSet(xtable, val)) { 498 if (!(ct3 < mem_estimate)) { 499 new_estimate = (PetscInt)(1.5 * mem_estimate) + 1; 500 PetscCall(PetscMalloc1(new_estimate, &tmp)); 501 PetscCall(PetscArraycpy(tmp, xdata[0], mem_estimate)); 502 PetscCall(PetscFree(xdata[0])); 503 xdata[0] = tmp; 504 mem_estimate = new_estimate; 505 ++no_malloc; 506 for (ctr = 1; ctr <= i; ctr++) xdata[ctr] = xdata[ctr - 1] + isz1[ctr - 1]; 507 } 508 xdata[i][ct2++] = val; 509 ct3++; 510 } 511 } 512 } 513 /* Update the header*/ 514 xdata[i][2 * j] = ct2 - oct2; /* Undo the vector isz1 and use only a var*/ 515 xdata[i][2 * j - 1] = rbuf_i[2 * j - 1]; 516 } 517 xdata[i][0] = rbuf_0; 518 if (i + 1 < nrqr) xdata[i + 1] = xdata[i] + ct2; 519 isz1[i] = ct2; /* size of each message */ 520 } 521 PetscCall(PetscBTDestroy(&xtable)); 522 PetscCall(PetscInfo(C, "Allocated %" PetscInt_FMT " bytes, required %" PetscInt_FMT ", no of mallocs = %" PetscInt_FMT "\n", mem_estimate, ct3, no_malloc)); 523 PetscFunctionReturn(PETSC_SUCCESS); 524 } 525 526 PetscErrorCode MatCreateSubMatrices_MPIBAIJ(Mat C, PetscInt ismax, const IS isrow[], const IS iscol[], MatReuse scall, Mat *submat[]) 527 { 528 IS *isrow_block, *iscol_block; 529 Mat_MPIBAIJ *c = (Mat_MPIBAIJ *)C->data; 530 PetscInt nmax, nstages_local, nstages, i, pos, max_no, N = C->cmap->N, bs = C->rmap->bs; 531 Mat_SeqBAIJ *subc; 532 Mat_SubSppt *smat; 533 PetscBool sym = PETSC_FALSE, flg[2]; 534 535 PetscFunctionBegin; 536 PetscCall(PetscObjectTypeCompare((PetscObject)C, MATMPISBAIJ, flg)); 537 if (flg[0]) { 538 if (isrow == iscol) sym = PETSC_TRUE; 539 else { 540 flg[0] = flg[1] = PETSC_TRUE; 541 for (i = 0; i < ismax; i++) { 542 if (isrow[i] != iscol[i]) flg[0] = PETSC_FALSE; 543 PetscCall(ISGetLocalSize(iscol[0], &nmax)); 544 if (nmax == C->cmap->N && flg[1]) PetscCall(ISIdentity(iscol[0], flg + 1)); 545 } 546 sym = (PetscBool)(flg[0] || flg[1]); 547 } 548 } 549 /* The compression and expansion should be avoided. Doesn't point 550 out errors, might change the indices, hence buggey */ 551 PetscCall(PetscMalloc2(ismax, &isrow_block, ismax, &iscol_block)); 552 PetscCall(ISCompressIndicesGeneral(C->rmap->N, C->rmap->n, bs, ismax, isrow, isrow_block)); 553 if (isrow == iscol) { 554 for (i = 0; i < ismax; i++) { 555 iscol_block[i] = isrow_block[i]; 556 PetscCall(PetscObjectReference((PetscObject)iscol_block[i])); 557 } 558 } else PetscCall(ISCompressIndicesGeneral(N, C->cmap->n, bs, ismax, iscol, iscol_block)); 559 560 /* Determine the number of stages through which submatrices are done */ 561 if (!C->cmap->N) nmax = 20 * 1000000 / sizeof(PetscInt); 562 else nmax = 20 * 1000000 / (c->Nbs * sizeof(PetscInt)); 563 if (!nmax) nmax = 1; 564 565 if (scall == MAT_INITIAL_MATRIX) { 566 nstages_local = ismax / nmax + ((ismax % nmax) ? 1 : 0); /* local nstages */ 567 568 /* Make sure every processor loops through the nstages */ 569 PetscCall(MPIU_Allreduce(&nstages_local, &nstages, 1, MPIU_INT, MPI_MAX, PetscObjectComm((PetscObject)C))); 570 571 /* Allocate memory to hold all the submatrices and dummy submatrices */ 572 PetscCall(PetscCalloc1(ismax + nstages, submat)); 573 } else { /* MAT_REUSE_MATRIX */ 574 if (ismax) { 575 subc = (Mat_SeqBAIJ *)((*submat)[0]->data); 576 smat = subc->submatis1; 577 } else { /* (*submat)[0] is a dummy matrix */ 578 smat = (Mat_SubSppt *)(*submat)[0]->data; 579 } 580 PetscCheck(smat, PETSC_COMM_SELF, PETSC_ERR_ARG_NULL, "MatCreateSubMatrices(...,MAT_REUSE_MATRIX,...) requires submat"); 581 nstages = smat->nstages; 582 } 583 584 for (i = 0, pos = 0; i < nstages; i++) { 585 if (pos + nmax <= ismax) max_no = nmax; 586 else if (pos >= ismax) max_no = 0; 587 else max_no = ismax - pos; 588 589 PetscCall(MatCreateSubMatrices_MPIBAIJ_local(C, max_no, isrow_block + pos, iscol_block + pos, scall, *submat + pos, sym)); 590 if (!max_no) { 591 if (scall == MAT_INITIAL_MATRIX) { /* submat[pos] is a dummy matrix */ 592 smat = (Mat_SubSppt *)(*submat)[pos]->data; 593 smat->nstages = nstages; 594 } 595 pos++; /* advance to next dummy matrix if any */ 596 } else pos += max_no; 597 } 598 599 if (scall == MAT_INITIAL_MATRIX && ismax) { 600 /* save nstages for reuse */ 601 subc = (Mat_SeqBAIJ *)((*submat)[0]->data); 602 smat = subc->submatis1; 603 smat->nstages = nstages; 604 } 605 606 for (i = 0; i < ismax; i++) { 607 PetscCall(ISDestroy(&isrow_block[i])); 608 PetscCall(ISDestroy(&iscol_block[i])); 609 } 610 PetscCall(PetscFree2(isrow_block, iscol_block)); 611 PetscFunctionReturn(PETSC_SUCCESS); 612 } 613 614 /* This code is used for BAIJ and SBAIJ matrices (unfortunate dependency) */ 615 PetscErrorCode MatCreateSubMatrices_MPIBAIJ_local(Mat C, PetscInt ismax, const IS isrow[], const IS iscol[], MatReuse scall, Mat *submats, PetscBool sym) 616 { 617 Mat_MPIBAIJ *c = (Mat_MPIBAIJ *)C->data; 618 Mat A = c->A; 619 Mat_SeqBAIJ *a = (Mat_SeqBAIJ *)A->data, *b = (Mat_SeqBAIJ *)c->B->data, *subc; 620 const PetscInt **icol, **irow; 621 PetscInt *nrow, *ncol, start; 622 PetscMPIInt rank, size, tag0, tag2, tag3, tag4, *w1, *w2, *w3, *w4, nrqr; 623 PetscInt **sbuf1, **sbuf2, *sbuf2_i, i, j, k, l, ct1, ct2, **rbuf1, row, proc = -1; 624 PetscInt nrqs = 0, msz, **ptr = NULL, *req_size = NULL, *ctr = NULL, *pa, *tmp = NULL, tcol; 625 PetscInt **rbuf3 = NULL, *req_source1 = NULL, *req_source2, **sbuf_aj, **rbuf2 = NULL, max1, max2; 626 PetscInt **lens, is_no, ncols, *cols, mat_i, *mat_j, tmp2, jmax; 627 #if defined(PETSC_USE_CTABLE) 628 PetscHMapI *cmap, cmap_i = NULL, *rmap, rmap_i; 629 #else 630 PetscInt **cmap, *cmap_i = NULL, **rmap, *rmap_i; 631 #endif 632 const PetscInt *irow_i, *icol_i; 633 PetscInt ctr_j, *sbuf1_j, *sbuf_aj_i, *rbuf1_i, kmax, *lens_i; 634 MPI_Request *s_waits1, *r_waits1, *s_waits2, *r_waits2, *r_waits3; 635 MPI_Request *r_waits4, *s_waits3, *s_waits4; 636 MPI_Comm comm; 637 PetscScalar **rbuf4, *rbuf4_i = NULL, **sbuf_aa, *vals, *mat_a = NULL, *imat_a = NULL, *sbuf_aa_i; 638 PetscMPIInt *onodes1, *olengths1, end; 639 PetscInt **row2proc, *row2proc_i, *imat_ilen, *imat_j, *imat_i; 640 Mat_SubSppt *smat_i; 641 PetscBool *issorted, colflag, iscsorted = PETSC_TRUE; 642 PetscInt *sbuf1_i, *rbuf2_i, *rbuf3_i, ilen; 643 PetscInt bs = C->rmap->bs, bs2 = c->bs2, rstart = c->rstartbs; 644 PetscBool ijonly = c->ijonly; /* private flag indicates only matrix data structures are requested */ 645 PetscInt nzA, nzB, *a_i = a->i, *b_i = b->i, *a_j = a->j, *b_j = b->j, ctmp, imark, *cworkA, *cworkB; 646 PetscScalar *vworkA = NULL, *vworkB = NULL, *a_a = a->a, *b_a = b->a; 647 PetscInt cstart = c->cstartbs, *bmap = c->garray; 648 PetscBool *allrows, *allcolumns; 649 650 PetscFunctionBegin; 651 PetscCall(PetscObjectGetComm((PetscObject)C, &comm)); 652 size = c->size; 653 rank = c->rank; 654 655 PetscCall(PetscMalloc5(ismax, &row2proc, ismax, &cmap, ismax, &rmap, ismax + 1, &allcolumns, ismax, &allrows)); 656 PetscCall(PetscMalloc5(ismax, (PetscInt ***)&irow, ismax, (PetscInt ***)&icol, ismax, &nrow, ismax, &ncol, ismax, &issorted)); 657 658 for (i = 0; i < ismax; i++) { 659 PetscCall(ISSorted(iscol[i], &issorted[i])); 660 if (!issorted[i]) iscsorted = issorted[i]; /* columns are not sorted! */ 661 PetscCall(ISSorted(isrow[i], &issorted[i])); 662 663 /* Check for special case: allcolumns */ 664 PetscCall(ISIdentity(iscol[i], &colflag)); 665 PetscCall(ISGetLocalSize(iscol[i], &ncol[i])); 666 667 if (colflag && ncol[i] == c->Nbs) { 668 allcolumns[i] = PETSC_TRUE; 669 icol[i] = NULL; 670 } else { 671 allcolumns[i] = PETSC_FALSE; 672 PetscCall(ISGetIndices(iscol[i], &icol[i])); 673 } 674 675 /* Check for special case: allrows */ 676 PetscCall(ISIdentity(isrow[i], &colflag)); 677 PetscCall(ISGetLocalSize(isrow[i], &nrow[i])); 678 if (colflag && nrow[i] == c->Mbs) { 679 allrows[i] = PETSC_TRUE; 680 irow[i] = NULL; 681 } else { 682 allrows[i] = PETSC_FALSE; 683 PetscCall(ISGetIndices(isrow[i], &irow[i])); 684 } 685 } 686 687 if (scall == MAT_REUSE_MATRIX) { 688 /* Assumes new rows are same length as the old rows */ 689 for (i = 0; i < ismax; i++) { 690 subc = (Mat_SeqBAIJ *)submats[i]->data; 691 PetscCheck(subc->mbs == nrow[i] && subc->nbs == ncol[i], PETSC_COMM_SELF, PETSC_ERR_ARG_SIZ, "Cannot reuse matrix. wrong size"); 692 693 /* Initial matrix as if empty */ 694 PetscCall(PetscArrayzero(subc->ilen, subc->mbs)); 695 696 /* Initial matrix as if empty */ 697 submats[i]->factortype = C->factortype; 698 699 smat_i = subc->submatis1; 700 701 nrqs = smat_i->nrqs; 702 nrqr = smat_i->nrqr; 703 rbuf1 = smat_i->rbuf1; 704 rbuf2 = smat_i->rbuf2; 705 rbuf3 = smat_i->rbuf3; 706 req_source2 = smat_i->req_source2; 707 708 sbuf1 = smat_i->sbuf1; 709 sbuf2 = smat_i->sbuf2; 710 ptr = smat_i->ptr; 711 tmp = smat_i->tmp; 712 ctr = smat_i->ctr; 713 714 pa = smat_i->pa; 715 req_size = smat_i->req_size; 716 req_source1 = smat_i->req_source1; 717 718 allcolumns[i] = smat_i->allcolumns; 719 allrows[i] = smat_i->allrows; 720 row2proc[i] = smat_i->row2proc; 721 rmap[i] = smat_i->rmap; 722 cmap[i] = smat_i->cmap; 723 } 724 725 if (!ismax) { /* Get dummy submatrices and retrieve struct submatis1 */ 726 PetscCheck(submats[0], PETSC_COMM_SELF, PETSC_ERR_ARG_NULL, "submats are null, cannot reuse"); 727 smat_i = (Mat_SubSppt *)submats[0]->data; 728 729 nrqs = smat_i->nrqs; 730 nrqr = smat_i->nrqr; 731 rbuf1 = smat_i->rbuf1; 732 rbuf2 = smat_i->rbuf2; 733 rbuf3 = smat_i->rbuf3; 734 req_source2 = smat_i->req_source2; 735 736 sbuf1 = smat_i->sbuf1; 737 sbuf2 = smat_i->sbuf2; 738 ptr = smat_i->ptr; 739 tmp = smat_i->tmp; 740 ctr = smat_i->ctr; 741 742 pa = smat_i->pa; 743 req_size = smat_i->req_size; 744 req_source1 = smat_i->req_source1; 745 746 allcolumns[0] = PETSC_FALSE; 747 } 748 } else { /* scall == MAT_INITIAL_MATRIX */ 749 /* Get some new tags to keep the communication clean */ 750 PetscCall(PetscObjectGetNewTag((PetscObject)C, &tag2)); 751 PetscCall(PetscObjectGetNewTag((PetscObject)C, &tag3)); 752 753 /* evaluate communication - mesg to who, length of mesg, and buffer space 754 required. Based on this, buffers are allocated, and data copied into them*/ 755 PetscCall(PetscCalloc4(size, &w1, size, &w2, size, &w3, size, &w4)); /* mesg size, initialize work vectors */ 756 757 for (i = 0; i < ismax; i++) { 758 jmax = nrow[i]; 759 irow_i = irow[i]; 760 761 PetscCall(PetscMalloc1(jmax, &row2proc_i)); 762 row2proc[i] = row2proc_i; 763 764 if (issorted[i]) proc = 0; 765 for (j = 0; j < jmax; j++) { 766 if (!issorted[i]) proc = 0; 767 if (allrows[i]) row = j; 768 else row = irow_i[j]; 769 770 while (row >= c->rangebs[proc + 1]) proc++; 771 w4[proc]++; 772 row2proc_i[j] = proc; /* map row index to proc */ 773 } 774 for (j = 0; j < size; j++) { 775 if (w4[j]) { 776 w1[j] += w4[j]; 777 w3[j]++; 778 w4[j] = 0; 779 } 780 } 781 } 782 783 nrqs = 0; /* no of outgoing messages */ 784 msz = 0; /* total mesg length (for all procs) */ 785 w1[rank] = 0; /* no mesg sent to self */ 786 w3[rank] = 0; 787 for (i = 0; i < size; i++) { 788 if (w1[i]) { 789 w2[i] = 1; 790 nrqs++; 791 } /* there exists a message to proc i */ 792 } 793 PetscCall(PetscMalloc1(nrqs, &pa)); /*(proc -array)*/ 794 for (i = 0, j = 0; i < size; i++) { 795 if (w1[i]) { 796 pa[j] = i; 797 j++; 798 } 799 } 800 801 /* Each message would have a header = 1 + 2*(no of IS) + data */ 802 for (i = 0; i < nrqs; i++) { 803 j = pa[i]; 804 w1[j] += w2[j] + 2 * w3[j]; 805 msz += w1[j]; 806 } 807 PetscCall(PetscInfo(0, "Number of outgoing messages %" PetscInt_FMT " Total message length %" PetscInt_FMT "\n", nrqs, msz)); 808 809 /* Determine the number of messages to expect, their lengths, from from-ids */ 810 PetscCall(PetscGatherNumberOfMessages(comm, w2, w1, &nrqr)); 811 PetscCall(PetscGatherMessageLengths(comm, nrqs, nrqr, w1, &onodes1, &olengths1)); 812 813 /* Now post the Irecvs corresponding to these messages */ 814 PetscCall(PetscObjectGetNewTag((PetscObject)C, &tag0)); 815 PetscCall(PetscPostIrecvInt(comm, tag0, nrqr, onodes1, olengths1, &rbuf1, &r_waits1)); 816 817 /* Allocate Memory for outgoing messages */ 818 PetscCall(PetscMalloc4(size, &sbuf1, size, &ptr, 2 * msz, &tmp, size, &ctr)); 819 PetscCall(PetscArrayzero(sbuf1, size)); 820 PetscCall(PetscArrayzero(ptr, size)); 821 822 { 823 PetscInt *iptr = tmp; 824 k = 0; 825 for (i = 0; i < nrqs; i++) { 826 j = pa[i]; 827 iptr += k; 828 sbuf1[j] = iptr; 829 k = w1[j]; 830 } 831 } 832 833 /* Form the outgoing messages. Initialize the header space */ 834 for (i = 0; i < nrqs; i++) { 835 j = pa[i]; 836 sbuf1[j][0] = 0; 837 PetscCall(PetscArrayzero(sbuf1[j] + 1, 2 * w3[j])); 838 ptr[j] = sbuf1[j] + 2 * w3[j] + 1; 839 } 840 841 /* Parse the isrow and copy data into outbuf */ 842 for (i = 0; i < ismax; i++) { 843 row2proc_i = row2proc[i]; 844 PetscCall(PetscArrayzero(ctr, size)); 845 irow_i = irow[i]; 846 jmax = nrow[i]; 847 for (j = 0; j < jmax; j++) { /* parse the indices of each IS */ 848 proc = row2proc_i[j]; 849 if (allrows[i]) row = j; 850 else row = irow_i[j]; 851 852 if (proc != rank) { /* copy to the outgoing buf*/ 853 ctr[proc]++; 854 *ptr[proc] = row; 855 ptr[proc]++; 856 } 857 } 858 /* Update the headers for the current IS */ 859 for (j = 0; j < size; j++) { /* Can Optimise this loop too */ 860 if ((ctr_j = ctr[j])) { 861 sbuf1_j = sbuf1[j]; 862 k = ++sbuf1_j[0]; 863 sbuf1_j[2 * k] = ctr_j; 864 sbuf1_j[2 * k - 1] = i; 865 } 866 } 867 } 868 869 /* Now post the sends */ 870 PetscCall(PetscMalloc1(nrqs, &s_waits1)); 871 for (i = 0; i < nrqs; ++i) { 872 j = pa[i]; 873 PetscCallMPI(MPI_Isend(sbuf1[j], w1[j], MPIU_INT, j, tag0, comm, s_waits1 + i)); 874 } 875 876 /* Post Receives to capture the buffer size */ 877 PetscCall(PetscMalloc1(nrqs, &r_waits2)); 878 PetscCall(PetscMalloc3(nrqs, &req_source2, nrqs, &rbuf2, nrqs, &rbuf3)); 879 if (nrqs) rbuf2[0] = tmp + msz; 880 for (i = 1; i < nrqs; ++i) rbuf2[i] = rbuf2[i - 1] + w1[pa[i - 1]]; 881 for (i = 0; i < nrqs; ++i) { 882 j = pa[i]; 883 PetscCallMPI(MPI_Irecv(rbuf2[i], w1[j], MPIU_INT, j, tag2, comm, r_waits2 + i)); 884 } 885 886 /* Send to other procs the buf size they should allocate */ 887 /* Receive messages*/ 888 PetscCall(PetscMalloc1(nrqr, &s_waits2)); 889 PetscCall(PetscMalloc3(nrqr, &sbuf2, nrqr, &req_size, nrqr, &req_source1)); 890 891 PetscCallMPI(MPI_Waitall(nrqr, r_waits1, MPI_STATUSES_IGNORE)); 892 for (i = 0; i < nrqr; ++i) { 893 req_size[i] = 0; 894 rbuf1_i = rbuf1[i]; 895 start = 2 * rbuf1_i[0] + 1; 896 end = olengths1[i]; 897 PetscCall(PetscMalloc1(end, &sbuf2[i])); 898 sbuf2_i = sbuf2[i]; 899 for (j = start; j < end; j++) { 900 row = rbuf1_i[j] - rstart; 901 ncols = a_i[row + 1] - a_i[row] + b_i[row + 1] - b_i[row]; 902 sbuf2_i[j] = ncols; 903 req_size[i] += ncols; 904 } 905 req_source1[i] = onodes1[i]; 906 /* form the header */ 907 sbuf2_i[0] = req_size[i]; 908 for (j = 1; j < start; j++) sbuf2_i[j] = rbuf1_i[j]; 909 910 PetscCallMPI(MPI_Isend(sbuf2_i, end, MPIU_INT, req_source1[i], tag2, comm, s_waits2 + i)); 911 } 912 913 PetscCall(PetscFree(onodes1)); 914 PetscCall(PetscFree(olengths1)); 915 916 PetscCall(PetscFree(r_waits1)); 917 PetscCall(PetscFree4(w1, w2, w3, w4)); 918 919 /* Receive messages*/ 920 PetscCall(PetscMalloc1(nrqs, &r_waits3)); 921 922 PetscCallMPI(MPI_Waitall(nrqs, r_waits2, MPI_STATUSES_IGNORE)); 923 for (i = 0; i < nrqs; ++i) { 924 PetscCall(PetscMalloc1(rbuf2[i][0], &rbuf3[i])); 925 req_source2[i] = pa[i]; 926 PetscCallMPI(MPI_Irecv(rbuf3[i], rbuf2[i][0], MPIU_INT, req_source2[i], tag3, comm, r_waits3 + i)); 927 } 928 PetscCall(PetscFree(r_waits2)); 929 930 /* Wait on sends1 and sends2 */ 931 PetscCallMPI(MPI_Waitall(nrqs, s_waits1, MPI_STATUSES_IGNORE)); 932 PetscCallMPI(MPI_Waitall(nrqr, s_waits2, MPI_STATUSES_IGNORE)); 933 PetscCall(PetscFree(s_waits1)); 934 PetscCall(PetscFree(s_waits2)); 935 936 /* Now allocate sending buffers for a->j, and send them off */ 937 PetscCall(PetscMalloc1(nrqr, &sbuf_aj)); 938 for (i = 0, j = 0; i < nrqr; i++) j += req_size[i]; 939 if (nrqr) PetscCall(PetscMalloc1(j, &sbuf_aj[0])); 940 for (i = 1; i < nrqr; i++) sbuf_aj[i] = sbuf_aj[i - 1] + req_size[i - 1]; 941 942 PetscCall(PetscMalloc1(nrqr, &s_waits3)); 943 { 944 for (i = 0; i < nrqr; i++) { 945 rbuf1_i = rbuf1[i]; 946 sbuf_aj_i = sbuf_aj[i]; 947 ct1 = 2 * rbuf1_i[0] + 1; 948 ct2 = 0; 949 for (j = 1, max1 = rbuf1_i[0]; j <= max1; j++) { 950 kmax = rbuf1[i][2 * j]; 951 for (k = 0; k < kmax; k++, ct1++) { 952 row = rbuf1_i[ct1] - rstart; 953 nzA = a_i[row + 1] - a_i[row]; 954 nzB = b_i[row + 1] - b_i[row]; 955 ncols = nzA + nzB; 956 cworkA = PetscSafePointerPlusOffset(a_j, a_i[row]); 957 cworkB = PetscSafePointerPlusOffset(b_j, b_i[row]); 958 959 /* load the column indices for this row into cols */ 960 cols = sbuf_aj_i + ct2; 961 for (l = 0; l < nzB; l++) { 962 if ((ctmp = bmap[cworkB[l]]) < cstart) cols[l] = ctmp; 963 else break; 964 } 965 imark = l; 966 for (l = 0; l < nzA; l++) cols[imark + l] = cstart + cworkA[l]; 967 for (l = imark; l < nzB; l++) cols[nzA + l] = bmap[cworkB[l]]; 968 ct2 += ncols; 969 } 970 } 971 PetscCallMPI(MPI_Isend(sbuf_aj_i, req_size[i], MPIU_INT, req_source1[i], tag3, comm, s_waits3 + i)); 972 } 973 } 974 975 /* create col map: global col of C -> local col of submatrices */ 976 #if defined(PETSC_USE_CTABLE) 977 for (i = 0; i < ismax; i++) { 978 if (!allcolumns[i]) { 979 PetscCall(PetscHMapICreateWithSize(ncol[i], cmap + i)); 980 981 jmax = ncol[i]; 982 icol_i = icol[i]; 983 cmap_i = cmap[i]; 984 for (j = 0; j < jmax; j++) PetscCall(PetscHMapISet(cmap[i], icol_i[j] + 1, j + 1)); 985 } else cmap[i] = NULL; 986 } 987 #else 988 for (i = 0; i < ismax; i++) { 989 if (!allcolumns[i]) { 990 PetscCall(PetscCalloc1(c->Nbs, &cmap[i])); 991 jmax = ncol[i]; 992 icol_i = icol[i]; 993 cmap_i = cmap[i]; 994 for (j = 0; j < jmax; j++) cmap_i[icol_i[j]] = j + 1; 995 } else cmap[i] = NULL; 996 } 997 #endif 998 999 /* Create lens which is required for MatCreate... */ 1000 for (i = 0, j = 0; i < ismax; i++) j += nrow[i]; 1001 PetscCall(PetscMalloc1(ismax, &lens)); 1002 1003 if (ismax) PetscCall(PetscCalloc1(j, &lens[0])); 1004 for (i = 1; i < ismax; i++) lens[i] = PetscSafePointerPlusOffset(lens[i - 1], nrow[i - 1]); 1005 1006 /* Update lens from local data */ 1007 for (i = 0; i < ismax; i++) { 1008 row2proc_i = row2proc[i]; 1009 jmax = nrow[i]; 1010 if (!allcolumns[i]) cmap_i = cmap[i]; 1011 irow_i = irow[i]; 1012 lens_i = lens[i]; 1013 for (j = 0; j < jmax; j++) { 1014 if (allrows[i]) row = j; 1015 else row = irow_i[j]; /* global blocked row of C */ 1016 1017 proc = row2proc_i[j]; 1018 if (proc == rank) { 1019 /* Get indices from matA and then from matB */ 1020 #if defined(PETSC_USE_CTABLE) 1021 PetscInt tt; 1022 #endif 1023 row = row - rstart; 1024 nzA = a_i[row + 1] - a_i[row]; 1025 nzB = b_i[row + 1] - b_i[row]; 1026 cworkA = a_j + a_i[row]; 1027 cworkB = PetscSafePointerPlusOffset(b_j, b_i[row]); 1028 1029 if (!allcolumns[i]) { 1030 #if defined(PETSC_USE_CTABLE) 1031 for (k = 0; k < nzA; k++) { 1032 PetscCall(PetscHMapIGetWithDefault(cmap_i, cstart + cworkA[k] + 1, 0, &tt)); 1033 if (tt) lens_i[j]++; 1034 } 1035 for (k = 0; k < nzB; k++) { 1036 PetscCall(PetscHMapIGetWithDefault(cmap_i, bmap[cworkB[k]] + 1, 0, &tt)); 1037 if (tt) lens_i[j]++; 1038 } 1039 1040 #else 1041 for (k = 0; k < nzA; k++) { 1042 if (cmap_i[cstart + cworkA[k]]) lens_i[j]++; 1043 } 1044 for (k = 0; k < nzB; k++) { 1045 if (cmap_i[bmap[cworkB[k]]]) lens_i[j]++; 1046 } 1047 #endif 1048 } else { /* allcolumns */ 1049 lens_i[j] = nzA + nzB; 1050 } 1051 } 1052 } 1053 } 1054 1055 /* Create row map: global row of C -> local row of submatrices */ 1056 for (i = 0; i < ismax; i++) { 1057 if (!allrows[i]) { 1058 #if defined(PETSC_USE_CTABLE) 1059 PetscCall(PetscHMapICreateWithSize(nrow[i], rmap + i)); 1060 irow_i = irow[i]; 1061 jmax = nrow[i]; 1062 for (j = 0; j < jmax; j++) { 1063 if (allrows[i]) { 1064 PetscCall(PetscHMapISet(rmap[i], j + 1, j + 1)); 1065 } else { 1066 PetscCall(PetscHMapISet(rmap[i], irow_i[j] + 1, j + 1)); 1067 } 1068 } 1069 #else 1070 PetscCall(PetscCalloc1(c->Mbs, &rmap[i])); 1071 rmap_i = rmap[i]; 1072 irow_i = irow[i]; 1073 jmax = nrow[i]; 1074 for (j = 0; j < jmax; j++) { 1075 if (allrows[i]) rmap_i[j] = j; 1076 else rmap_i[irow_i[j]] = j; 1077 } 1078 #endif 1079 } else rmap[i] = NULL; 1080 } 1081 1082 /* Update lens from offproc data */ 1083 { 1084 PetscInt *rbuf2_i, *rbuf3_i, *sbuf1_i; 1085 1086 PetscCallMPI(MPI_Waitall(nrqs, r_waits3, MPI_STATUSES_IGNORE)); 1087 for (tmp2 = 0; tmp2 < nrqs; tmp2++) { 1088 sbuf1_i = sbuf1[pa[tmp2]]; 1089 jmax = sbuf1_i[0]; 1090 ct1 = 2 * jmax + 1; 1091 ct2 = 0; 1092 rbuf2_i = rbuf2[tmp2]; 1093 rbuf3_i = rbuf3[tmp2]; 1094 for (j = 1; j <= jmax; j++) { 1095 is_no = sbuf1_i[2 * j - 1]; 1096 max1 = sbuf1_i[2 * j]; 1097 lens_i = lens[is_no]; 1098 if (!allcolumns[is_no]) cmap_i = cmap[is_no]; 1099 rmap_i = rmap[is_no]; 1100 for (k = 0; k < max1; k++, ct1++) { 1101 if (allrows[is_no]) { 1102 row = sbuf1_i[ct1]; 1103 } else { 1104 #if defined(PETSC_USE_CTABLE) 1105 PetscCall(PetscHMapIGetWithDefault(rmap_i, sbuf1_i[ct1] + 1, 0, &row)); 1106 row--; 1107 PetscCheck(row >= 0, PETSC_COMM_SELF, PETSC_ERR_PLIB, "row not found in table"); 1108 #else 1109 row = rmap_i[sbuf1_i[ct1]]; /* the val in the new matrix to be */ 1110 #endif 1111 } 1112 max2 = rbuf2_i[ct1]; 1113 for (l = 0; l < max2; l++, ct2++) { 1114 if (!allcolumns[is_no]) { 1115 #if defined(PETSC_USE_CTABLE) 1116 PetscCall(PetscHMapIGetWithDefault(cmap_i, rbuf3_i[ct2] + 1, 0, &tcol)); 1117 #else 1118 tcol = cmap_i[rbuf3_i[ct2]]; 1119 #endif 1120 if (tcol) lens_i[row]++; 1121 } else { /* allcolumns */ 1122 lens_i[row]++; /* lens_i[row] += max2 ? */ 1123 } 1124 } 1125 } 1126 } 1127 } 1128 } 1129 PetscCall(PetscFree(r_waits3)); 1130 PetscCallMPI(MPI_Waitall(nrqr, s_waits3, MPI_STATUSES_IGNORE)); 1131 PetscCall(PetscFree(s_waits3)); 1132 1133 /* Create the submatrices */ 1134 for (i = 0; i < ismax; i++) { 1135 PetscInt bs_tmp; 1136 if (ijonly) bs_tmp = 1; 1137 else bs_tmp = bs; 1138 1139 PetscCall(MatCreate(PETSC_COMM_SELF, submats + i)); 1140 PetscCall(MatSetSizes(submats[i], nrow[i] * bs_tmp, ncol[i] * bs_tmp, PETSC_DETERMINE, PETSC_DETERMINE)); 1141 1142 PetscCall(MatSetType(submats[i], sym ? ((PetscObject)A)->type_name : MATSEQBAIJ)); 1143 PetscCall(MatSeqBAIJSetPreallocation(submats[i], bs_tmp, 0, lens[i])); 1144 PetscCall(MatSeqSBAIJSetPreallocation(submats[i], bs_tmp, 0, lens[i])); /* this subroutine is used by SBAIJ routines */ 1145 1146 /* create struct Mat_SubSppt and attached it to submat */ 1147 PetscCall(PetscNew(&smat_i)); 1148 subc = (Mat_SeqBAIJ *)submats[i]->data; 1149 subc->submatis1 = smat_i; 1150 1151 smat_i->destroy = submats[i]->ops->destroy; 1152 submats[i]->ops->destroy = MatDestroySubMatrix_SeqBAIJ; 1153 submats[i]->factortype = C->factortype; 1154 1155 smat_i->id = i; 1156 smat_i->nrqs = nrqs; 1157 smat_i->nrqr = nrqr; 1158 smat_i->rbuf1 = rbuf1; 1159 smat_i->rbuf2 = rbuf2; 1160 smat_i->rbuf3 = rbuf3; 1161 smat_i->sbuf2 = sbuf2; 1162 smat_i->req_source2 = req_source2; 1163 1164 smat_i->sbuf1 = sbuf1; 1165 smat_i->ptr = ptr; 1166 smat_i->tmp = tmp; 1167 smat_i->ctr = ctr; 1168 1169 smat_i->pa = pa; 1170 smat_i->req_size = req_size; 1171 smat_i->req_source1 = req_source1; 1172 1173 smat_i->allcolumns = allcolumns[i]; 1174 smat_i->allrows = allrows[i]; 1175 smat_i->singleis = PETSC_FALSE; 1176 smat_i->row2proc = row2proc[i]; 1177 smat_i->rmap = rmap[i]; 1178 smat_i->cmap = cmap[i]; 1179 } 1180 1181 if (!ismax) { /* Create dummy submats[0] for reuse struct subc */ 1182 PetscCall(MatCreate(PETSC_COMM_SELF, &submats[0])); 1183 PetscCall(MatSetSizes(submats[0], 0, 0, PETSC_DETERMINE, PETSC_DETERMINE)); 1184 PetscCall(MatSetType(submats[0], MATDUMMY)); 1185 1186 /* create struct Mat_SubSppt and attached it to submat */ 1187 PetscCall(PetscNew(&smat_i)); 1188 submats[0]->data = (void *)smat_i; 1189 1190 smat_i->destroy = submats[0]->ops->destroy; 1191 submats[0]->ops->destroy = MatDestroySubMatrix_Dummy; 1192 submats[0]->factortype = C->factortype; 1193 1194 smat_i->id = 0; 1195 smat_i->nrqs = nrqs; 1196 smat_i->nrqr = nrqr; 1197 smat_i->rbuf1 = rbuf1; 1198 smat_i->rbuf2 = rbuf2; 1199 smat_i->rbuf3 = rbuf3; 1200 smat_i->sbuf2 = sbuf2; 1201 smat_i->req_source2 = req_source2; 1202 1203 smat_i->sbuf1 = sbuf1; 1204 smat_i->ptr = ptr; 1205 smat_i->tmp = tmp; 1206 smat_i->ctr = ctr; 1207 1208 smat_i->pa = pa; 1209 smat_i->req_size = req_size; 1210 smat_i->req_source1 = req_source1; 1211 1212 smat_i->allcolumns = PETSC_FALSE; 1213 smat_i->singleis = PETSC_FALSE; 1214 smat_i->row2proc = NULL; 1215 smat_i->rmap = NULL; 1216 smat_i->cmap = NULL; 1217 } 1218 1219 if (ismax) PetscCall(PetscFree(lens[0])); 1220 PetscCall(PetscFree(lens)); 1221 if (sbuf_aj) { 1222 PetscCall(PetscFree(sbuf_aj[0])); 1223 PetscCall(PetscFree(sbuf_aj)); 1224 } 1225 1226 } /* endof scall == MAT_INITIAL_MATRIX */ 1227 1228 /* Post recv matrix values */ 1229 if (!ijonly) { 1230 PetscCall(PetscObjectGetNewTag((PetscObject)C, &tag4)); 1231 PetscCall(PetscMalloc1(nrqs, &rbuf4)); 1232 PetscCall(PetscMalloc1(nrqs, &r_waits4)); 1233 for (i = 0; i < nrqs; ++i) { 1234 PetscCall(PetscMalloc1(rbuf2[i][0] * bs2, &rbuf4[i])); 1235 PetscCallMPI(MPI_Irecv(rbuf4[i], rbuf2[i][0] * bs2, MPIU_SCALAR, req_source2[i], tag4, comm, r_waits4 + i)); 1236 } 1237 1238 /* Allocate sending buffers for a->a, and send them off */ 1239 PetscCall(PetscMalloc1(nrqr, &sbuf_aa)); 1240 for (i = 0, j = 0; i < nrqr; i++) j += req_size[i]; 1241 1242 if (nrqr) PetscCall(PetscMalloc1(j * bs2, &sbuf_aa[0])); 1243 for (i = 1; i < nrqr; i++) sbuf_aa[i] = sbuf_aa[i - 1] + req_size[i - 1] * bs2; 1244 1245 PetscCall(PetscMalloc1(nrqr, &s_waits4)); 1246 1247 for (i = 0; i < nrqr; i++) { 1248 rbuf1_i = rbuf1[i]; 1249 sbuf_aa_i = sbuf_aa[i]; 1250 ct1 = 2 * rbuf1_i[0] + 1; 1251 ct2 = 0; 1252 for (j = 1, max1 = rbuf1_i[0]; j <= max1; j++) { 1253 kmax = rbuf1_i[2 * j]; 1254 for (k = 0; k < kmax; k++, ct1++) { 1255 row = rbuf1_i[ct1] - rstart; 1256 nzA = a_i[row + 1] - a_i[row]; 1257 nzB = b_i[row + 1] - b_i[row]; 1258 ncols = nzA + nzB; 1259 cworkB = PetscSafePointerPlusOffset(b_j, b_i[row]); 1260 vworkA = PetscSafePointerPlusOffset(a_a, a_i[row] * bs2); 1261 vworkB = PetscSafePointerPlusOffset(b_a, b_i[row] * bs2); 1262 1263 /* load the column values for this row into vals*/ 1264 vals = sbuf_aa_i + ct2 * bs2; 1265 for (l = 0; l < nzB; l++) { 1266 if ((bmap[cworkB[l]]) < cstart) { 1267 PetscCall(PetscArraycpy(vals + l * bs2, vworkB + l * bs2, bs2)); 1268 } else break; 1269 } 1270 imark = l; 1271 for (l = 0; l < nzA; l++) PetscCall(PetscArraycpy(vals + (imark + l) * bs2, vworkA + l * bs2, bs2)); 1272 for (l = imark; l < nzB; l++) PetscCall(PetscArraycpy(vals + (nzA + l) * bs2, vworkB + l * bs2, bs2)); 1273 1274 ct2 += ncols; 1275 } 1276 } 1277 PetscCallMPI(MPI_Isend(sbuf_aa_i, req_size[i] * bs2, MPIU_SCALAR, req_source1[i], tag4, comm, s_waits4 + i)); 1278 } 1279 } 1280 1281 /* Assemble the matrices */ 1282 /* First assemble the local rows */ 1283 for (i = 0; i < ismax; i++) { 1284 row2proc_i = row2proc[i]; 1285 subc = (Mat_SeqBAIJ *)submats[i]->data; 1286 imat_ilen = subc->ilen; 1287 imat_j = subc->j; 1288 imat_i = subc->i; 1289 imat_a = subc->a; 1290 1291 if (!allcolumns[i]) cmap_i = cmap[i]; 1292 rmap_i = rmap[i]; 1293 irow_i = irow[i]; 1294 jmax = nrow[i]; 1295 for (j = 0; j < jmax; j++) { 1296 if (allrows[i]) row = j; 1297 else row = irow_i[j]; 1298 proc = row2proc_i[j]; 1299 1300 if (proc == rank) { 1301 row = row - rstart; 1302 nzA = a_i[row + 1] - a_i[row]; 1303 nzB = b_i[row + 1] - b_i[row]; 1304 cworkA = a_j + a_i[row]; 1305 cworkB = PetscSafePointerPlusOffset(b_j, b_i[row]); 1306 if (!ijonly) { 1307 vworkA = a_a + a_i[row] * bs2; 1308 vworkB = PetscSafePointerPlusOffset(b_a, b_i[row] * bs2); 1309 } 1310 1311 if (allrows[i]) { 1312 row = row + rstart; 1313 } else { 1314 #if defined(PETSC_USE_CTABLE) 1315 PetscCall(PetscHMapIGetWithDefault(rmap_i, row + rstart + 1, 0, &row)); 1316 row--; 1317 1318 PetscCheck(row >= 0, PETSC_COMM_SELF, PETSC_ERR_PLIB, "row not found in table"); 1319 #else 1320 row = rmap_i[row + rstart]; 1321 #endif 1322 } 1323 mat_i = imat_i[row]; 1324 if (!ijonly) mat_a = PetscSafePointerPlusOffset(imat_a, mat_i * bs2); 1325 mat_j = PetscSafePointerPlusOffset(imat_j, mat_i); 1326 ilen = imat_ilen[row]; 1327 1328 /* load the column indices for this row into cols*/ 1329 if (!allcolumns[i]) { 1330 for (l = 0; l < nzB; l++) { 1331 if ((ctmp = bmap[cworkB[l]]) < cstart) { 1332 #if defined(PETSC_USE_CTABLE) 1333 PetscCall(PetscHMapIGetWithDefault(cmap_i, ctmp + 1, 0, &tcol)); 1334 if (tcol) { 1335 #else 1336 if ((tcol = cmap_i[ctmp])) { 1337 #endif 1338 *mat_j++ = tcol - 1; 1339 PetscCall(PetscArraycpy(mat_a, vworkB + l * bs2, bs2)); 1340 mat_a += bs2; 1341 ilen++; 1342 } 1343 } else break; 1344 } 1345 imark = l; 1346 for (l = 0; l < nzA; l++) { 1347 #if defined(PETSC_USE_CTABLE) 1348 PetscCall(PetscHMapIGetWithDefault(cmap_i, cstart + cworkA[l] + 1, 0, &tcol)); 1349 if (tcol) { 1350 #else 1351 if ((tcol = cmap_i[cstart + cworkA[l]])) { 1352 #endif 1353 *mat_j++ = tcol - 1; 1354 if (!ijonly) { 1355 PetscCall(PetscArraycpy(mat_a, vworkA + l * bs2, bs2)); 1356 mat_a += bs2; 1357 } 1358 ilen++; 1359 } 1360 } 1361 for (l = imark; l < nzB; l++) { 1362 #if defined(PETSC_USE_CTABLE) 1363 PetscCall(PetscHMapIGetWithDefault(cmap_i, bmap[cworkB[l]] + 1, 0, &tcol)); 1364 if (tcol) { 1365 #else 1366 if ((tcol = cmap_i[bmap[cworkB[l]]])) { 1367 #endif 1368 *mat_j++ = tcol - 1; 1369 if (!ijonly) { 1370 PetscCall(PetscArraycpy(mat_a, vworkB + l * bs2, bs2)); 1371 mat_a += bs2; 1372 } 1373 ilen++; 1374 } 1375 } 1376 } else { /* allcolumns */ 1377 for (l = 0; l < nzB; l++) { 1378 if ((ctmp = bmap[cworkB[l]]) < cstart) { 1379 *mat_j++ = ctmp; 1380 PetscCall(PetscArraycpy(mat_a, vworkB + l * bs2, bs2)); 1381 mat_a += bs2; 1382 ilen++; 1383 } else break; 1384 } 1385 imark = l; 1386 for (l = 0; l < nzA; l++) { 1387 *mat_j++ = cstart + cworkA[l]; 1388 if (!ijonly) { 1389 PetscCall(PetscArraycpy(mat_a, vworkA + l * bs2, bs2)); 1390 mat_a += bs2; 1391 } 1392 ilen++; 1393 } 1394 for (l = imark; l < nzB; l++) { 1395 *mat_j++ = bmap[cworkB[l]]; 1396 if (!ijonly) { 1397 PetscCall(PetscArraycpy(mat_a, vworkB + l * bs2, bs2)); 1398 mat_a += bs2; 1399 } 1400 ilen++; 1401 } 1402 } 1403 imat_ilen[row] = ilen; 1404 } 1405 } 1406 } 1407 1408 /* Now assemble the off proc rows */ 1409 if (!ijonly) PetscCallMPI(MPI_Waitall(nrqs, r_waits4, MPI_STATUSES_IGNORE)); 1410 for (tmp2 = 0; tmp2 < nrqs; tmp2++) { 1411 sbuf1_i = sbuf1[pa[tmp2]]; 1412 jmax = sbuf1_i[0]; 1413 ct1 = 2 * jmax + 1; 1414 ct2 = 0; 1415 rbuf2_i = rbuf2[tmp2]; 1416 rbuf3_i = rbuf3[tmp2]; 1417 if (!ijonly) rbuf4_i = rbuf4[tmp2]; 1418 for (j = 1; j <= jmax; j++) { 1419 is_no = sbuf1_i[2 * j - 1]; 1420 rmap_i = rmap[is_no]; 1421 if (!allcolumns[is_no]) cmap_i = cmap[is_no]; 1422 subc = (Mat_SeqBAIJ *)submats[is_no]->data; 1423 imat_ilen = subc->ilen; 1424 imat_j = subc->j; 1425 imat_i = subc->i; 1426 if (!ijonly) imat_a = subc->a; 1427 max1 = sbuf1_i[2 * j]; 1428 for (k = 0; k < max1; k++, ct1++) { /* for each recved block row */ 1429 row = sbuf1_i[ct1]; 1430 1431 if (allrows[is_no]) { 1432 row = sbuf1_i[ct1]; 1433 } else { 1434 #if defined(PETSC_USE_CTABLE) 1435 PetscCall(PetscHMapIGetWithDefault(rmap_i, row + 1, 0, &row)); 1436 row--; 1437 PetscCheck(row >= 0, PETSC_COMM_SELF, PETSC_ERR_PLIB, "row not found in table"); 1438 #else 1439 row = rmap_i[row]; 1440 #endif 1441 } 1442 ilen = imat_ilen[row]; 1443 mat_i = imat_i[row]; 1444 if (!ijonly) mat_a = imat_a + mat_i * bs2; 1445 mat_j = imat_j + mat_i; 1446 max2 = rbuf2_i[ct1]; 1447 if (!allcolumns[is_no]) { 1448 for (l = 0; l < max2; l++, ct2++) { 1449 #if defined(PETSC_USE_CTABLE) 1450 PetscCall(PetscHMapIGetWithDefault(cmap_i, rbuf3_i[ct2] + 1, 0, &tcol)); 1451 #else 1452 tcol = cmap_i[rbuf3_i[ct2]]; 1453 #endif 1454 if (tcol) { 1455 *mat_j++ = tcol - 1; 1456 if (!ijonly) { 1457 PetscCall(PetscArraycpy(mat_a, rbuf4_i + ct2 * bs2, bs2)); 1458 mat_a += bs2; 1459 } 1460 ilen++; 1461 } 1462 } 1463 } else { /* allcolumns */ 1464 for (l = 0; l < max2; l++, ct2++) { 1465 *mat_j++ = rbuf3_i[ct2]; /* same global column index of C */ 1466 if (!ijonly) { 1467 PetscCall(PetscArraycpy(mat_a, rbuf4_i + ct2 * bs2, bs2)); 1468 mat_a += bs2; 1469 } 1470 ilen++; 1471 } 1472 } 1473 imat_ilen[row] = ilen; 1474 } 1475 } 1476 } 1477 1478 if (!iscsorted) { /* sort column indices of the rows */ 1479 MatScalar *work; 1480 1481 PetscCall(PetscMalloc1(bs2, &work)); 1482 for (i = 0; i < ismax; i++) { 1483 subc = (Mat_SeqBAIJ *)submats[i]->data; 1484 imat_ilen = subc->ilen; 1485 imat_j = subc->j; 1486 imat_i = subc->i; 1487 if (!ijonly) imat_a = subc->a; 1488 if (allcolumns[i]) continue; 1489 1490 jmax = nrow[i]; 1491 for (j = 0; j < jmax; j++) { 1492 mat_i = imat_i[j]; 1493 mat_j = imat_j + mat_i; 1494 ilen = imat_ilen[j]; 1495 if (ijonly) { 1496 PetscCall(PetscSortInt(ilen, mat_j)); 1497 } else { 1498 mat_a = imat_a + mat_i * bs2; 1499 PetscCall(PetscSortIntWithDataArray(ilen, mat_j, mat_a, bs2 * sizeof(MatScalar), work)); 1500 } 1501 } 1502 } 1503 PetscCall(PetscFree(work)); 1504 } 1505 1506 if (!ijonly) { 1507 PetscCall(PetscFree(r_waits4)); 1508 PetscCallMPI(MPI_Waitall(nrqr, s_waits4, MPI_STATUSES_IGNORE)); 1509 PetscCall(PetscFree(s_waits4)); 1510 } 1511 1512 /* Restore the indices */ 1513 for (i = 0; i < ismax; i++) { 1514 if (!allrows[i]) PetscCall(ISRestoreIndices(isrow[i], irow + i)); 1515 if (!allcolumns[i]) PetscCall(ISRestoreIndices(iscol[i], icol + i)); 1516 } 1517 1518 for (i = 0; i < ismax; i++) { 1519 PetscCall(MatAssemblyBegin(submats[i], MAT_FINAL_ASSEMBLY)); 1520 PetscCall(MatAssemblyEnd(submats[i], MAT_FINAL_ASSEMBLY)); 1521 } 1522 1523 PetscCall(PetscFree5(*(PetscInt ***)&irow, *(PetscInt ***)&icol, nrow, ncol, issorted)); 1524 PetscCall(PetscFree5(row2proc, cmap, rmap, allcolumns, allrows)); 1525 1526 if (!ijonly) { 1527 if (sbuf_aa) { 1528 PetscCall(PetscFree(sbuf_aa[0])); 1529 PetscCall(PetscFree(sbuf_aa)); 1530 } 1531 1532 for (i = 0; i < nrqs; ++i) PetscCall(PetscFree(rbuf4[i])); 1533 PetscCall(PetscFree(rbuf4)); 1534 } 1535 c->ijonly = PETSC_FALSE; /* set back to the default */ 1536 PetscFunctionReturn(PETSC_SUCCESS); 1537 } 1538