1 2 /* 3 Routines to compute overlapping regions of a parallel MPI matrix 4 and to find submatrices that were shared across processors. 5 */ 6 #include <../src/mat/impls/baij/mpi/mpibaij.h> 7 #include <petscbt.h> 8 9 static PetscErrorCode MatIncreaseOverlap_MPIBAIJ_Local(Mat,PetscInt,char**,PetscInt*,PetscInt**); 10 static PetscErrorCode MatIncreaseOverlap_MPIBAIJ_Receive(Mat,PetscInt,PetscInt**,PetscInt**,PetscInt*); 11 extern PetscErrorCode MatGetRow_MPIBAIJ(Mat,PetscInt,PetscInt*,PetscInt**,PetscScalar**); 12 extern PetscErrorCode MatRestoreRow_MPIBAIJ(Mat,PetscInt,PetscInt*,PetscInt**,PetscScalar**); 13 14 PetscErrorCode MatIncreaseOverlap_MPIBAIJ(Mat C,PetscInt imax,IS is[],PetscInt ov) 15 { 16 PetscErrorCode ierr; 17 PetscInt i,N=C->cmap->N, bs=C->rmap->bs; 18 IS *is_new; 19 20 PetscFunctionBegin; 21 ierr = PetscMalloc1(imax,&is_new);CHKERRQ(ierr); 22 /* Convert the indices into block format */ 23 ierr = ISCompressIndicesGeneral(N,C->rmap->n,bs,imax,is,is_new);CHKERRQ(ierr); 24 if (ov < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Negative overlap specified\n"); 25 for (i=0; i<ov; ++i) { 26 ierr = MatIncreaseOverlap_MPIBAIJ_Once(C,imax,is_new);CHKERRQ(ierr); 27 } 28 for (i=0; i<imax; i++) {ierr = ISDestroy(&is[i]);CHKERRQ(ierr);} 29 ierr = ISExpandIndicesGeneral(N,N,bs,imax,is_new,is);CHKERRQ(ierr); 30 for (i=0; i<imax; i++) {ierr = ISDestroy(&is_new[i]);CHKERRQ(ierr);} 31 ierr = PetscFree(is_new);CHKERRQ(ierr); 32 PetscFunctionReturn(0); 33 } 34 35 /* 36 Sample message format: 37 If a processor A wants processor B to process some elements corresponding 38 to index sets is[1], is[5] 39 mesg [0] = 2 (no of index sets in the mesg) 40 ----------- 41 mesg [1] = 1 => is[1] 42 mesg [2] = sizeof(is[1]); 43 ----------- 44 mesg [5] = 5 => is[5] 45 mesg [6] = sizeof(is[5]); 46 ----------- 47 mesg [7] 48 mesg [n] data(is[1]) 49 ----------- 50 mesg[n+1] 51 mesg[m] data(is[5]) 52 ----------- 53 54 Notes: 55 nrqs - no of requests sent (or to be sent out) 56 nrqr - no of requests recieved (which have to be or which have been processed 57 */ 58 PetscErrorCode MatIncreaseOverlap_MPIBAIJ_Once(Mat C,PetscInt imax,IS is[]) 59 { 60 Mat_MPIBAIJ *c = (Mat_MPIBAIJ*)C->data; 61 const PetscInt **idx,*idx_i; 62 PetscInt *n,*w3,*w4,**data,len; 63 PetscErrorCode ierr; 64 PetscMPIInt size,rank,tag1,tag2,*w2,*w1,nrqr; 65 PetscInt Mbs,i,j,k,**rbuf,row,proc=-1,nrqs,msz,**outdat,**ptr; 66 PetscInt *ctr,*pa,*tmp,*isz,*isz1,**xdata,**rbuf2,*d_p; 67 PetscMPIInt *onodes1,*olengths1,*onodes2,*olengths2; 68 PetscBT *table; 69 MPI_Comm comm; 70 MPI_Request *s_waits1,*r_waits1,*s_waits2,*r_waits2; 71 MPI_Status *s_status,*recv_status; 72 char *t_p; 73 74 PetscFunctionBegin; 75 ierr = PetscObjectGetComm((PetscObject)C,&comm);CHKERRQ(ierr); 76 size = c->size; 77 rank = c->rank; 78 Mbs = c->Mbs; 79 80 ierr = PetscObjectGetNewTag((PetscObject)C,&tag1);CHKERRQ(ierr); 81 ierr = PetscObjectGetNewTag((PetscObject)C,&tag2);CHKERRQ(ierr); 82 83 ierr = PetscMalloc2(imax+1,&idx,imax,&n);CHKERRQ(ierr); 84 85 for (i=0; i<imax; i++) { 86 ierr = ISGetIndices(is[i],&idx[i]);CHKERRQ(ierr); 87 ierr = ISGetLocalSize(is[i],&n[i]);CHKERRQ(ierr); 88 } 89 90 /* evaluate communication - mesg to who,length of mesg, and buffer space 91 required. Based on this, buffers are allocated, and data copied into them*/ 92 ierr = PetscCalloc4(size,&w1,size,&w2,size,&w3,size,&w4);CHKERRQ(ierr); 93 for (i=0; i<imax; i++) { 94 ierr = PetscMemzero(w4,size*sizeof(PetscInt));CHKERRQ(ierr); /* initialise work vector*/ 95 idx_i = idx[i]; 96 len = n[i]; 97 for (j=0; j<len; j++) { 98 row = idx_i[j]; 99 if (row < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Index set cannot have negative entries"); 100 ierr = PetscLayoutFindOwner(C->rmap,row*C->rmap->bs,&proc);CHKERRQ(ierr); 101 w4[proc]++; 102 } 103 for (j=0; j<size; j++) { 104 if (w4[j]) { w1[j] += w4[j]; w3[j]++;} 105 } 106 } 107 108 nrqs = 0; /* no of outgoing messages */ 109 msz = 0; /* total mesg length (for all proc */ 110 w1[rank] = 0; /* no mesg sent to itself */ 111 w3[rank] = 0; 112 for (i=0; i<size; i++) { 113 if (w1[i]) {w2[i] = 1; nrqs++;} /* there exists a message to proc i */ 114 } 115 /* pa - is list of processors to communicate with */ 116 ierr = PetscMalloc1(nrqs+1,&pa);CHKERRQ(ierr); 117 for (i=0,j=0; i<size; i++) { 118 if (w1[i]) {pa[j] = i; j++;} 119 } 120 121 /* Each message would have a header = 1 + 2*(no of IS) + data */ 122 for (i=0; i<nrqs; i++) { 123 j = pa[i]; 124 w1[j] += w2[j] + 2*w3[j]; 125 msz += w1[j]; 126 } 127 128 /* Determine the number of messages to expect, their lengths, from from-ids */ 129 ierr = PetscGatherNumberOfMessages(comm,w2,w1,&nrqr);CHKERRQ(ierr); 130 ierr = PetscGatherMessageLengths(comm,nrqs,nrqr,w1,&onodes1,&olengths1);CHKERRQ(ierr); 131 132 /* Now post the Irecvs corresponding to these messages */ 133 ierr = PetscPostIrecvInt(comm,tag1,nrqr,onodes1,olengths1,&rbuf,&r_waits1);CHKERRQ(ierr); 134 135 /* Allocate Memory for outgoing messages */ 136 ierr = PetscMalloc4(size,&outdat,size,&ptr,msz,&tmp,size,&ctr);CHKERRQ(ierr); 137 ierr = PetscMemzero(outdat,size*sizeof(PetscInt*));CHKERRQ(ierr); 138 ierr = PetscMemzero(ptr,size*sizeof(PetscInt*));CHKERRQ(ierr); 139 { 140 PetscInt *iptr = tmp,ict = 0; 141 for (i=0; i<nrqs; i++) { 142 j = pa[i]; 143 iptr += ict; 144 outdat[j] = iptr; 145 ict = w1[j]; 146 } 147 } 148 149 /* Form the outgoing messages */ 150 /*plug in the headers*/ 151 for (i=0; i<nrqs; i++) { 152 j = pa[i]; 153 outdat[j][0] = 0; 154 ierr = PetscMemzero(outdat[j]+1,2*w3[j]*sizeof(PetscInt));CHKERRQ(ierr); 155 ptr[j] = outdat[j] + 2*w3[j] + 1; 156 } 157 158 /* Memory for doing local proc's work*/ 159 { 160 ierr = PetscCalloc5(imax,&table, imax,&data, imax,&isz, Mbs*imax,&d_p, (Mbs/PETSC_BITS_PER_BYTE+1)*imax,&t_p);CHKERRQ(ierr); 161 162 for (i=0; i<imax; i++) { 163 table[i] = t_p + (Mbs/PETSC_BITS_PER_BYTE+1)*i; 164 data[i] = d_p + (Mbs)*i; 165 } 166 } 167 168 /* Parse the IS and update local tables and the outgoing buf with the data*/ 169 { 170 PetscInt n_i,*data_i,isz_i,*outdat_j,ctr_j; 171 PetscBT table_i; 172 173 for (i=0; i<imax; i++) { 174 ierr = PetscMemzero(ctr,size*sizeof(PetscInt));CHKERRQ(ierr); 175 n_i = n[i]; 176 table_i = table[i]; 177 idx_i = idx[i]; 178 data_i = data[i]; 179 isz_i = isz[i]; 180 for (j=0; j<n_i; j++) { /* parse the indices of each IS */ 181 row = idx_i[j]; 182 ierr = PetscLayoutFindOwner(C->rmap,row*C->rmap->bs,&proc);CHKERRQ(ierr); 183 if (proc != rank) { /* copy to the outgoing buffer */ 184 ctr[proc]++; 185 *ptr[proc] = row; 186 ptr[proc]++; 187 } else { /* Update the local table */ 188 if (!PetscBTLookupSet(table_i,row)) data_i[isz_i++] = row; 189 } 190 } 191 /* Update the headers for the current IS */ 192 for (j=0; j<size; j++) { /* Can Optimise this loop by using pa[] */ 193 if ((ctr_j = ctr[j])) { 194 outdat_j = outdat[j]; 195 k = ++outdat_j[0]; 196 outdat_j[2*k] = ctr_j; 197 outdat_j[2*k-1] = i; 198 } 199 } 200 isz[i] = isz_i; 201 } 202 } 203 204 /* Now post the sends */ 205 ierr = PetscMalloc1(nrqs+1,&s_waits1);CHKERRQ(ierr); 206 for (i=0; i<nrqs; ++i) { 207 j = pa[i]; 208 ierr = MPI_Isend(outdat[j],w1[j],MPIU_INT,j,tag1,comm,s_waits1+i);CHKERRQ(ierr); 209 } 210 211 /* No longer need the original indices*/ 212 for (i=0; i<imax; ++i) { 213 ierr = ISRestoreIndices(is[i],idx+i);CHKERRQ(ierr); 214 } 215 ierr = PetscFree2(idx,n);CHKERRQ(ierr); 216 217 for (i=0; i<imax; ++i) { 218 ierr = ISDestroy(&is[i]);CHKERRQ(ierr); 219 } 220 221 /* Do Local work*/ 222 ierr = MatIncreaseOverlap_MPIBAIJ_Local(C,imax,table,isz,data);CHKERRQ(ierr); 223 224 /* Receive messages*/ 225 ierr = PetscMalloc1(nrqr+1,&recv_status);CHKERRQ(ierr); 226 if (nrqr) {ierr = MPI_Waitall(nrqr,r_waits1,recv_status);CHKERRQ(ierr);} 227 228 ierr = PetscMalloc1(nrqs+1,&s_status);CHKERRQ(ierr); 229 if (nrqs) {ierr = MPI_Waitall(nrqs,s_waits1,s_status);CHKERRQ(ierr);} 230 231 /* Phase 1 sends are complete - deallocate buffers */ 232 ierr = PetscFree4(outdat,ptr,tmp,ctr);CHKERRQ(ierr); 233 ierr = PetscFree4(w1,w2,w3,w4);CHKERRQ(ierr); 234 235 ierr = PetscMalloc1(nrqr+1,&xdata);CHKERRQ(ierr); 236 ierr = PetscMalloc1(nrqr+1,&isz1);CHKERRQ(ierr); 237 ierr = MatIncreaseOverlap_MPIBAIJ_Receive(C,nrqr,rbuf,xdata,isz1);CHKERRQ(ierr); 238 ierr = PetscFree(rbuf[0]);CHKERRQ(ierr); 239 ierr = PetscFree(rbuf);CHKERRQ(ierr); 240 241 /* Send the data back*/ 242 /* Do a global reduction to know the buffer space req for incoming messages*/ 243 { 244 PetscMPIInt *rw1; 245 246 ierr = PetscCalloc1(size,&rw1);CHKERRQ(ierr); 247 248 for (i=0; i<nrqr; ++i) { 249 proc = recv_status[i].MPI_SOURCE; 250 if (proc != onodes1[i]) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"MPI_SOURCE mismatch"); 251 rw1[proc] = isz1[i]; 252 } 253 254 ierr = PetscFree(onodes1);CHKERRQ(ierr); 255 ierr = PetscFree(olengths1);CHKERRQ(ierr); 256 257 /* Determine the number of messages to expect, their lengths, from from-ids */ 258 ierr = PetscGatherMessageLengths(comm,nrqr,nrqs,rw1,&onodes2,&olengths2);CHKERRQ(ierr); 259 ierr = PetscFree(rw1);CHKERRQ(ierr); 260 } 261 /* Now post the Irecvs corresponding to these messages */ 262 ierr = PetscPostIrecvInt(comm,tag2,nrqs,onodes2,olengths2,&rbuf2,&r_waits2);CHKERRQ(ierr); 263 264 /* Now post the sends */ 265 ierr = PetscMalloc1(nrqr+1,&s_waits2);CHKERRQ(ierr); 266 for (i=0; i<nrqr; ++i) { 267 j = recv_status[i].MPI_SOURCE; 268 ierr = MPI_Isend(xdata[i],isz1[i],MPIU_INT,j,tag2,comm,s_waits2+i);CHKERRQ(ierr); 269 } 270 271 /* receive work done on other processors*/ 272 { 273 PetscMPIInt idex; 274 PetscInt is_no,ct1,max,*rbuf2_i,isz_i,*data_i,jmax; 275 PetscBT table_i; 276 MPI_Status *status2; 277 278 ierr = PetscMalloc1(PetscMax(nrqr,nrqs)+1,&status2);CHKERRQ(ierr); 279 for (i=0; i<nrqs; ++i) { 280 ierr = MPI_Waitany(nrqs,r_waits2,&idex,status2+i);CHKERRQ(ierr); 281 /* Process the message*/ 282 rbuf2_i = rbuf2[idex]; 283 ct1 = 2*rbuf2_i[0]+1; 284 jmax = rbuf2[idex][0]; 285 for (j=1; j<=jmax; j++) { 286 max = rbuf2_i[2*j]; 287 is_no = rbuf2_i[2*j-1]; 288 isz_i = isz[is_no]; 289 data_i = data[is_no]; 290 table_i = table[is_no]; 291 for (k=0; k<max; k++,ct1++) { 292 row = rbuf2_i[ct1]; 293 if (!PetscBTLookupSet(table_i,row)) data_i[isz_i++] = row; 294 } 295 isz[is_no] = isz_i; 296 } 297 } 298 if (nrqr) {ierr = MPI_Waitall(nrqr,s_waits2,status2);CHKERRQ(ierr);} 299 ierr = PetscFree(status2);CHKERRQ(ierr); 300 } 301 302 for (i=0; i<imax; ++i) { 303 ierr = ISCreateGeneral(PETSC_COMM_SELF,isz[i],data[i],PETSC_COPY_VALUES,is+i);CHKERRQ(ierr); 304 } 305 306 307 ierr = PetscFree(onodes2);CHKERRQ(ierr); 308 ierr = PetscFree(olengths2);CHKERRQ(ierr); 309 310 ierr = PetscFree(pa);CHKERRQ(ierr); 311 ierr = PetscFree(rbuf2[0]);CHKERRQ(ierr); 312 ierr = PetscFree(rbuf2);CHKERRQ(ierr); 313 ierr = PetscFree(s_waits1);CHKERRQ(ierr); 314 ierr = PetscFree(r_waits1);CHKERRQ(ierr); 315 ierr = PetscFree(s_waits2);CHKERRQ(ierr); 316 ierr = PetscFree(r_waits2);CHKERRQ(ierr); 317 ierr = PetscFree5(table,data,isz,d_p,t_p);CHKERRQ(ierr); 318 ierr = PetscFree(s_status);CHKERRQ(ierr); 319 ierr = PetscFree(recv_status);CHKERRQ(ierr); 320 ierr = PetscFree(xdata[0]);CHKERRQ(ierr); 321 ierr = PetscFree(xdata);CHKERRQ(ierr); 322 ierr = PetscFree(isz1);CHKERRQ(ierr); 323 PetscFunctionReturn(0); 324 } 325 326 /* 327 MatIncreaseOverlap_MPIBAIJ_Local - Called by MatincreaseOverlap, to do 328 the work on the local processor. 329 330 Inputs: 331 C - MAT_MPIBAIJ; 332 imax - total no of index sets processed at a time; 333 table - an array of char - size = Mbs bits. 334 335 Output: 336 isz - array containing the count of the solution elements corresponding 337 to each index set; 338 data - pointer to the solutions 339 */ 340 static PetscErrorCode MatIncreaseOverlap_MPIBAIJ_Local(Mat C,PetscInt imax,PetscBT *table,PetscInt *isz,PetscInt **data) 341 { 342 Mat_MPIBAIJ *c = (Mat_MPIBAIJ*)C->data; 343 Mat A = c->A,B = c->B; 344 Mat_SeqBAIJ *a = (Mat_SeqBAIJ*)A->data,*b = (Mat_SeqBAIJ*)B->data; 345 PetscInt start,end,val,max,rstart,cstart,*ai,*aj; 346 PetscInt *bi,*bj,*garray,i,j,k,row,*data_i,isz_i; 347 PetscBT table_i; 348 349 PetscFunctionBegin; 350 rstart = c->rstartbs; 351 cstart = c->cstartbs; 352 ai = a->i; 353 aj = a->j; 354 bi = b->i; 355 bj = b->j; 356 garray = c->garray; 357 358 359 for (i=0; i<imax; i++) { 360 data_i = data[i]; 361 table_i = table[i]; 362 isz_i = isz[i]; 363 for (j=0,max=isz[i]; j<max; j++) { 364 row = data_i[j] - rstart; 365 start = ai[row]; 366 end = ai[row+1]; 367 for (k=start; k<end; k++) { /* Amat */ 368 val = aj[k] + cstart; 369 if (!PetscBTLookupSet(table_i,val)) data_i[isz_i++] = val; 370 } 371 start = bi[row]; 372 end = bi[row+1]; 373 for (k=start; k<end; k++) { /* Bmat */ 374 val = garray[bj[k]]; 375 if (!PetscBTLookupSet(table_i,val)) data_i[isz_i++] = val; 376 } 377 } 378 isz[i] = isz_i; 379 } 380 PetscFunctionReturn(0); 381 } 382 /* 383 MatIncreaseOverlap_MPIBAIJ_Receive - Process the recieved messages, 384 and return the output 385 386 Input: 387 C - the matrix 388 nrqr - no of messages being processed. 389 rbuf - an array of pointers to the recieved requests 390 391 Output: 392 xdata - array of messages to be sent back 393 isz1 - size of each message 394 395 For better efficiency perhaps we should malloc separately each xdata[i], 396 then if a remalloc is required we need only copy the data for that one row 397 rather than all previous rows as it is now where a single large chunck of 398 memory is used. 399 400 */ 401 static PetscErrorCode MatIncreaseOverlap_MPIBAIJ_Receive(Mat C,PetscInt nrqr,PetscInt **rbuf,PetscInt **xdata,PetscInt * isz1) 402 { 403 Mat_MPIBAIJ *c = (Mat_MPIBAIJ*)C->data; 404 Mat A = c->A,B = c->B; 405 Mat_SeqBAIJ *a = (Mat_SeqBAIJ*)A->data,*b = (Mat_SeqBAIJ*)B->data; 406 PetscErrorCode ierr; 407 PetscInt rstart,cstart,*ai,*aj,*bi,*bj,*garray,i,j,k; 408 PetscInt row,total_sz,ct,ct1,ct2,ct3,mem_estimate,oct2,l,start,end; 409 PetscInt val,max1,max2,Mbs,no_malloc =0,*tmp,new_estimate,ctr; 410 PetscInt *rbuf_i,kmax,rbuf_0; 411 PetscBT xtable; 412 413 PetscFunctionBegin; 414 Mbs = c->Mbs; 415 rstart = c->rstartbs; 416 cstart = c->cstartbs; 417 ai = a->i; 418 aj = a->j; 419 bi = b->i; 420 bj = b->j; 421 garray = c->garray; 422 423 424 for (i=0,ct=0,total_sz=0; i<nrqr; ++i) { 425 rbuf_i = rbuf[i]; 426 rbuf_0 = rbuf_i[0]; 427 ct += rbuf_0; 428 for (j=1; j<=rbuf_0; j++) total_sz += rbuf_i[2*j]; 429 } 430 431 if (c->Mbs) max1 = ct*(a->nz +b->nz)/c->Mbs; 432 else max1 = 1; 433 mem_estimate = 3*((total_sz > max1 ? total_sz : max1)+1); 434 ierr = PetscMalloc1(mem_estimate,&xdata[0]);CHKERRQ(ierr); 435 ++no_malloc; 436 ierr = PetscBTCreate(Mbs,&xtable);CHKERRQ(ierr); 437 ierr = PetscMemzero(isz1,nrqr*sizeof(PetscInt));CHKERRQ(ierr); 438 439 ct3 = 0; 440 for (i=0; i<nrqr; i++) { /* for easch mesg from proc i */ 441 rbuf_i = rbuf[i]; 442 rbuf_0 = rbuf_i[0]; 443 ct1 = 2*rbuf_0+1; 444 ct2 = ct1; 445 ct3 += ct1; 446 for (j=1; j<=rbuf_0; j++) { /* for each IS from proc i*/ 447 ierr = PetscBTMemzero(Mbs,xtable);CHKERRQ(ierr); 448 oct2 = ct2; 449 kmax = rbuf_i[2*j]; 450 for (k=0; k<kmax; k++,ct1++) { 451 row = rbuf_i[ct1]; 452 if (!PetscBTLookupSet(xtable,row)) { 453 if (!(ct3 < mem_estimate)) { 454 new_estimate = (PetscInt)(1.5*mem_estimate)+1; 455 ierr = PetscMalloc1(new_estimate,&tmp);CHKERRQ(ierr); 456 ierr = PetscMemcpy(tmp,xdata[0],mem_estimate*sizeof(PetscInt));CHKERRQ(ierr); 457 ierr = PetscFree(xdata[0]);CHKERRQ(ierr); 458 xdata[0] = tmp; 459 mem_estimate = new_estimate; ++no_malloc; 460 for (ctr=1; ctr<=i; ctr++) xdata[ctr] = xdata[ctr-1] + isz1[ctr-1]; 461 } 462 xdata[i][ct2++] = row; 463 ct3++; 464 } 465 } 466 for (k=oct2,max2=ct2; k<max2; k++) { 467 row = xdata[i][k] - rstart; 468 start = ai[row]; 469 end = ai[row+1]; 470 for (l=start; l<end; l++) { 471 val = aj[l] + cstart; 472 if (!PetscBTLookupSet(xtable,val)) { 473 if (!(ct3 < mem_estimate)) { 474 new_estimate = (PetscInt)(1.5*mem_estimate)+1; 475 ierr = PetscMalloc1(new_estimate,&tmp);CHKERRQ(ierr); 476 ierr = PetscMemcpy(tmp,xdata[0],mem_estimate*sizeof(PetscInt));CHKERRQ(ierr); 477 ierr = PetscFree(xdata[0]);CHKERRQ(ierr); 478 xdata[0] = tmp; 479 mem_estimate = new_estimate; ++no_malloc; 480 for (ctr=1; ctr<=i; ctr++) xdata[ctr] = xdata[ctr-1] + isz1[ctr-1]; 481 } 482 xdata[i][ct2++] = val; 483 ct3++; 484 } 485 } 486 start = bi[row]; 487 end = bi[row+1]; 488 for (l=start; l<end; l++) { 489 val = garray[bj[l]]; 490 if (!PetscBTLookupSet(xtable,val)) { 491 if (!(ct3 < mem_estimate)) { 492 new_estimate = (PetscInt)(1.5*mem_estimate)+1; 493 ierr = PetscMalloc1(new_estimate,&tmp);CHKERRQ(ierr); 494 ierr = PetscMemcpy(tmp,xdata[0],mem_estimate*sizeof(PetscInt));CHKERRQ(ierr); 495 ierr = PetscFree(xdata[0]);CHKERRQ(ierr); 496 xdata[0] = tmp; 497 mem_estimate = new_estimate; ++no_malloc; 498 for (ctr =1; ctr <=i; ctr++) xdata[ctr] = xdata[ctr-1] + isz1[ctr-1]; 499 } 500 xdata[i][ct2++] = val; 501 ct3++; 502 } 503 } 504 } 505 /* Update the header*/ 506 xdata[i][2*j] = ct2 - oct2; /* Undo the vector isz1 and use only a var*/ 507 xdata[i][2*j-1] = rbuf_i[2*j-1]; 508 } 509 xdata[i][0] = rbuf_0; 510 xdata[i+1] = xdata[i] + ct2; 511 isz1[i] = ct2; /* size of each message */ 512 } 513 ierr = PetscBTDestroy(&xtable);CHKERRQ(ierr); 514 ierr = PetscInfo3(C,"Allocated %D bytes, required %D, no of mallocs = %D\n",mem_estimate,ct3,no_malloc);CHKERRQ(ierr); 515 PetscFunctionReturn(0); 516 } 517 518 PetscErrorCode MatGetSubMatrices_MPIBAIJ(Mat C,PetscInt ismax,const IS isrow[],const IS iscol[],MatReuse scall,Mat *submat[]) 519 { 520 IS *isrow_block,*iscol_block; 521 Mat_MPIBAIJ *c = (Mat_MPIBAIJ*)C->data; 522 PetscErrorCode ierr; 523 PetscInt nmax,nstages_local,nstages,i,pos,max_no,N=C->cmap->N,bs=C->rmap->bs; 524 525 PetscFunctionBegin; 526 /* The compression and expansion should be avoided. Doesn't point 527 out errors, might change the indices, hence buggey */ 528 ierr = PetscMalloc2(ismax+1,&isrow_block,ismax+1,&iscol_block);CHKERRQ(ierr); 529 ierr = ISCompressIndicesGeneral(N,C->rmap->n,bs,ismax,isrow,isrow_block);CHKERRQ(ierr); 530 ierr = ISCompressIndicesGeneral(N,C->cmap->n,bs,ismax,iscol,iscol_block);CHKERRQ(ierr); 531 532 /* Allocate memory to hold all the submatrices */ 533 if (scall == MAT_INITIAL_MATRIX) { 534 ierr = PetscMalloc1(ismax+1,submat);CHKERRQ(ierr); 535 } 536 /* Determine the number of stages through which submatrices are done */ 537 nmax = 20*1000000 / (c->Nbs * sizeof(PetscInt)); 538 if (!nmax) nmax = 1; 539 nstages_local = ismax/nmax + ((ismax % nmax) ? 1 : 0); 540 541 /* Make sure every processor loops through the nstages */ 542 ierr = MPIU_Allreduce(&nstages_local,&nstages,1,MPIU_INT,MPI_MAX,PetscObjectComm((PetscObject)C));CHKERRQ(ierr); 543 for (i=0,pos=0; i<nstages; i++) { 544 if (pos+nmax <= ismax) max_no = nmax; 545 else if (pos == ismax) max_no = 0; 546 else max_no = ismax-pos; 547 548 ierr = MatGetSubMatrices_MPIBAIJ_local(C,max_no,isrow_block+pos,iscol_block+pos,scall,*submat+pos);CHKERRQ(ierr); 549 pos += max_no; 550 } 551 552 for (i=0; i<ismax; i++) { 553 ierr = ISDestroy(&isrow_block[i]);CHKERRQ(ierr); 554 ierr = ISDestroy(&iscol_block[i]);CHKERRQ(ierr); 555 } 556 ierr = PetscFree2(isrow_block,iscol_block);CHKERRQ(ierr); 557 PetscFunctionReturn(0); 558 } 559 560 #if defined(PETSC_USE_CTABLE) 561 PetscErrorCode PetscGetProc(const PetscInt row, const PetscMPIInt size, const PetscInt proc_gnode[], PetscMPIInt *rank) 562 { 563 PetscInt nGlobalNd = proc_gnode[size]; 564 PetscMPIInt fproc; 565 PetscErrorCode ierr; 566 567 PetscFunctionBegin; 568 ierr = PetscMPIIntCast((PetscInt)(((float)row * (float)size / (float)nGlobalNd + 0.5)),&fproc);CHKERRQ(ierr); 569 if (fproc > size) fproc = size; 570 while (row < proc_gnode[fproc] || row >= proc_gnode[fproc+1]) { 571 if (row < proc_gnode[fproc]) fproc--; 572 else fproc++; 573 } 574 *rank = fproc; 575 PetscFunctionReturn(0); 576 } 577 #endif 578 579 /* -------------------------------------------------------------------------*/ 580 /* This code is used for BAIJ and SBAIJ matrices (unfortunate dependency) */ 581 582 PetscErrorCode MatDestroy_MPIBAIJ_MatGetSubmatrices(Mat C) 583 { 584 PetscErrorCode ierr; 585 Mat_SeqBAIJ *c = (Mat_SeqBAIJ*)C->data; 586 Mat_SubMat *submatj = c->submatis1; 587 PetscInt i; 588 589 PetscFunctionBegin; 590 if (!submatj->id) { /* delete data that are linked only to submats[id=0] */ 591 ierr = PetscFree4(submatj->sbuf1,submatj->ptr,submatj->tmp,submatj->ctr);CHKERRQ(ierr); 592 593 for (i=0; i<submatj->nrqr; ++i) { 594 ierr = PetscFree(submatj->sbuf2[i]);CHKERRQ(ierr); 595 } 596 ierr = PetscFree3(submatj->sbuf2,submatj->req_size,submatj->req_source1);CHKERRQ(ierr); 597 598 if (submatj->rbuf1) { 599 ierr = PetscFree(submatj->rbuf1[0]);CHKERRQ(ierr); 600 ierr = PetscFree(submatj->rbuf1);CHKERRQ(ierr); 601 } 602 603 for (i=0; i<submatj->nrqs; ++i) { 604 ierr = PetscFree(submatj->rbuf3[i]);CHKERRQ(ierr); 605 } 606 ierr = PetscFree3(submatj->req_source2,submatj->rbuf2,submatj->rbuf3);CHKERRQ(ierr); 607 ierr = PetscFree(submatj->pa);CHKERRQ(ierr); 608 } 609 610 #if defined(PETSC_USE_CTABLE) 611 ierr = PetscTableDestroy((PetscTable*)&submatj->rmap);CHKERRQ(ierr); 612 if (submatj->cmap_loc) {ierr = PetscFree(submatj->cmap_loc);CHKERRQ(ierr);} 613 ierr = PetscFree(submatj->rmap_loc);CHKERRQ(ierr); 614 #else 615 ierr = PetscFree(submatj->rmap);CHKERRQ(ierr); 616 #endif 617 618 if (!submatj->allcolumns) { 619 #if defined(PETSC_USE_CTABLE) 620 ierr = PetscTableDestroy((PetscTable*)&submatj->cmap);CHKERRQ(ierr); 621 #else 622 ierr = PetscFree(submatj->cmap);CHKERRQ(ierr); 623 #endif 624 } 625 ierr = submatj->destroy(C);CHKERRQ(ierr); 626 ierr = PetscFree(submatj->row2proc);CHKERRQ(ierr); 627 628 ierr = PetscFree(submatj);CHKERRQ(ierr); 629 PetscFunctionReturn(0); 630 } 631 632 PetscErrorCode MatGetSubMatrices_MPIBAIJ_local(Mat C,PetscInt ismax,const IS isrow[],const IS iscol[],MatReuse scall,Mat *submats) 633 { 634 Mat_MPIBAIJ *c = (Mat_MPIBAIJ*)C->data; 635 Mat A = c->A; 636 Mat_SeqBAIJ *a = (Mat_SeqBAIJ*)A->data,*b = (Mat_SeqBAIJ*)c->B->data,*subc; 637 const PetscInt **icol,**irow; 638 PetscInt *nrow,*ncol,start; 639 PetscErrorCode ierr; 640 PetscMPIInt rank,size,tag0,tag2,tag3,tag4,*w1,*w2,*w3,*w4,nrqr; 641 PetscInt **sbuf1,**sbuf2,i,j,k,l,ct1,ct2,**rbuf1,row,proc=-1; 642 PetscInt nrqs=0,msz,**ptr=NULL,*req_size=NULL,*ctr=NULL,*pa,*tmp=NULL,tcol; 643 PetscInt **rbuf3=NULL,*req_source1=NULL,*req_source2,**sbuf_aj,**rbuf2=NULL,max1,max2; 644 PetscInt **lens,is_no,ncols,*cols,mat_i,*mat_j,tmp2,jmax; 645 #if defined(PETSC_USE_CTABLE) 646 PetscTable *cmap,cmap_i=NULL,*rmap,rmap_i; 647 #else 648 PetscInt **cmap,*cmap_i=NULL,**rmap,*rmap_i; 649 #endif 650 const PetscInt *irow_i; 651 PetscInt ctr_j,*sbuf1_j,*sbuf_aj_i,*rbuf1_i,kmax,*lens_i; 652 MPI_Request *s_waits1,*r_waits1,*s_waits2,*r_waits2,*r_waits3; 653 MPI_Request *r_waits4,*s_waits3,*s_waits4; 654 MPI_Status *r_status1,*r_status2,*s_status1,*s_status3,*s_status2; 655 MPI_Status *r_status3,*r_status4,*s_status4; 656 MPI_Comm comm; 657 PetscScalar **rbuf4,*rbuf4_i,**sbuf_aa,*vals,*mat_a,*imat_a,*sbuf_aa_i; 658 PetscMPIInt *onodes1,*olengths1,end; 659 PetscInt **row2proc,*row2proc_i,*imat_ilen,*imat_j,*imat_i; 660 Mat_SubMat **smats,*smat_i; 661 PetscBool *issorted,colflag,iscsorted=PETSC_TRUE; 662 PetscInt *sbuf1_i,*rbuf2_i,*rbuf3_i,ilen; 663 PetscInt bs=C->rmap->bs,bs2=c->bs2,rstart = c->rstartbs; 664 PetscBool ijonly=c->ijonly; /* private flag indicates only matrix data structures are requested */ 665 PetscInt nzA,nzB,*a_i=a->i,*b_i=b->i,*a_j = a->j,*b_j = b->j,ctmp,imark,*cworkA,*cworkB; 666 PetscScalar *vworkA,*vworkB,*a_a = a->a,*b_a = b->a; 667 PetscInt cstart = c->cstartbs,*bmap = c->garray; 668 PetscBool *allrows,*allcolumns; 669 670 PetscFunctionBegin; 671 ierr = PetscObjectGetComm((PetscObject)C,&comm);CHKERRQ(ierr); 672 size = c->size; 673 rank = c->rank; 674 675 ierr = PetscMalloc6(ismax,&smats,ismax,&row2proc,ismax,&cmap,ismax,&rmap,ismax,&allcolumns,ismax,&allrows);CHKERRQ(ierr); 676 ierr = PetscMalloc5(ismax,&irow,ismax,&icol,ismax,&nrow,ismax,&ncol,ismax,&issorted);CHKERRQ(ierr); 677 678 for (i=0; i<ismax; i++) { 679 ierr = ISSorted(iscol[i],&issorted[i]);CHKERRQ(ierr); 680 if (!issorted[i]) iscsorted = issorted[i]; /* columns are not sorted! */ 681 ierr = ISSorted(isrow[i],&issorted[i]);CHKERRQ(ierr); 682 683 /* Check for special case: allcolumns */ 684 ierr = ISIdentity(iscol[i],&colflag);CHKERRQ(ierr); 685 ierr = ISGetLocalSize(iscol[i],&ncol[i]);CHKERRQ(ierr); 686 687 if (colflag && ncol[i] == c->Nbs) { 688 allcolumns[i] = PETSC_TRUE; 689 icol[i] = NULL; 690 } else { 691 allcolumns[i] = PETSC_FALSE; 692 ierr = ISGetIndices(iscol[i],&icol[i]);CHKERRQ(ierr); 693 } 694 695 /* Check for special case: allrows */ 696 ierr = ISIdentity(isrow[i],&colflag);CHKERRQ(ierr); 697 ierr = ISGetLocalSize(isrow[i],&nrow[i]);CHKERRQ(ierr); 698 if (colflag && nrow[i] == c->Mbs) { 699 allrows[i] = PETSC_TRUE; 700 irow[i] = NULL; 701 } else { 702 allrows[i] = PETSC_FALSE; 703 ierr = ISGetIndices(isrow[i],&irow[i]);CHKERRQ(ierr); 704 } 705 } 706 707 if (scall == MAT_REUSE_MATRIX) { 708 /* Assumes new rows are same length as the old rows */ 709 for (i=0; i<ismax; i++) { 710 subc = (Mat_SeqBAIJ*)(submats[i]->data); 711 if (subc->mbs != nrow[i] || subc->nbs != ncol[i]) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Cannot reuse matrix. wrong size"); 712 713 /* Initial matrix as if empty */ 714 ierr = PetscMemzero(subc->ilen,subc->mbs*sizeof(PetscInt));CHKERRQ(ierr); 715 716 /* Initial matrix as if empty */ 717 submats[i]->factortype = C->factortype; 718 719 smat_i = subc->submatis1; 720 smats[i] = smat_i; 721 722 nrqs = smat_i->nrqs; 723 nrqr = smat_i->nrqr; 724 rbuf1 = smat_i->rbuf1; 725 rbuf2 = smat_i->rbuf2; 726 rbuf3 = smat_i->rbuf3; 727 req_source2 = smat_i->req_source2; 728 729 sbuf1 = smat_i->sbuf1; 730 sbuf2 = smat_i->sbuf2; 731 ptr = smat_i->ptr; 732 tmp = smat_i->tmp; 733 ctr = smat_i->ctr; 734 735 pa = smat_i->pa; 736 req_size = smat_i->req_size; 737 req_source1 = smat_i->req_source1; 738 739 allcolumns[i] = smat_i->allcolumns; 740 allrows[i] = smat_i->allrows; 741 row2proc[i] = smat_i->row2proc; 742 rmap[i] = smat_i->rmap; 743 cmap[i] = smat_i->cmap; 744 } 745 } else { /* scall == MAT_INITIAL_MATRIX */ 746 /* Get some new tags to keep the communication clean */ 747 ierr = PetscObjectGetNewTag((PetscObject)C,&tag2);CHKERRQ(ierr); 748 ierr = PetscObjectGetNewTag((PetscObject)C,&tag3);CHKERRQ(ierr); 749 750 /* evaluate communication - mesg to who, length of mesg, and buffer space 751 required. Based on this, buffers are allocated, and data copied into them*/ 752 ierr = PetscCalloc4(size,&w1,size,&w2,size,&w3,size,&w4);CHKERRQ(ierr); /* mesg size, initialize work vectors */ 753 754 for (i=0; i<ismax; i++) { 755 jmax = nrow[i]; 756 irow_i = irow[i]; 757 758 ierr = PetscMalloc1(jmax,&row2proc_i);CHKERRQ(ierr); 759 row2proc[i] = row2proc_i; 760 761 if (issorted[i]) proc = 0; 762 for (j=0; j<jmax; j++) { 763 if (!issorted[i]) proc = 0; 764 if (allrows[i]) row = j; 765 else row = irow_i[j]; 766 767 while (row >= c->rangebs[proc+1]) proc++; 768 w4[proc]++; 769 row2proc_i[j] = proc; /* map row index to proc */ 770 } 771 for (j=0; j<size; j++) { 772 if (w4[j]) { w1[j] += w4[j]; w3[j]++; w4[j] = 0;} 773 } 774 } 775 776 nrqs = 0; /* no of outgoing messages */ 777 msz = 0; /* total mesg length (for all procs) */ 778 w1[rank] = 0; /* no mesg sent to self */ 779 w3[rank] = 0; 780 for (i=0; i<size; i++) { 781 if (w1[i]) { w2[i] = 1; nrqs++;} /* there exists a message to proc i */ 782 } 783 ierr = PetscMalloc1(nrqs+1,&pa);CHKERRQ(ierr); /*(proc -array)*/ 784 for (i=0,j=0; i<size; i++) { 785 if (w1[i]) { pa[j] = i; j++; } 786 } 787 788 /* Each message would have a header = 1 + 2*(no of IS) + data */ 789 for (i=0; i<nrqs; i++) { 790 j = pa[i]; 791 w1[j] += w2[j] + 2* w3[j]; 792 msz += w1[j]; 793 } 794 ierr = PetscInfo2(0,"Number of outgoing messages %D Total message length %D\n",nrqs,msz);CHKERRQ(ierr); 795 796 /* Determine the number of messages to expect, their lengths, from from-ids */ 797 ierr = PetscGatherNumberOfMessages(comm,w2,w1,&nrqr);CHKERRQ(ierr); 798 ierr = PetscGatherMessageLengths(comm,nrqs,nrqr,w1,&onodes1,&olengths1);CHKERRQ(ierr); 799 800 /* Now post the Irecvs corresponding to these messages */ 801 tag0 = ((PetscObject)C)->tag; 802 ierr = PetscPostIrecvInt(comm,tag0,nrqr,onodes1,olengths1,&rbuf1,&r_waits1);CHKERRQ(ierr); 803 804 ierr = PetscFree(onodes1);CHKERRQ(ierr); 805 ierr = PetscFree(olengths1);CHKERRQ(ierr); 806 807 /* Allocate Memory for outgoing messages */ 808 ierr = PetscMalloc4(size,&sbuf1,size,&ptr,2*msz,&tmp,size,&ctr);CHKERRQ(ierr); 809 ierr = PetscMemzero(sbuf1,size*sizeof(PetscInt*));CHKERRQ(ierr); 810 ierr = PetscMemzero(ptr,size*sizeof(PetscInt*));CHKERRQ(ierr); 811 812 { 813 PetscInt *iptr = tmp; 814 k = 0; 815 for (i=0; i<nrqs; i++) { 816 j = pa[i]; 817 iptr += k; 818 sbuf1[j] = iptr; 819 k = w1[j]; 820 } 821 } 822 823 /* Form the outgoing messages. Initialize the header space */ 824 for (i=0; i<nrqs; i++) { 825 j = pa[i]; 826 sbuf1[j][0] = 0; 827 ierr = PetscMemzero(sbuf1[j]+1,2*w3[j]*sizeof(PetscInt));CHKERRQ(ierr); 828 ptr[j] = sbuf1[j] + 2*w3[j] + 1; 829 } 830 831 /* Parse the isrow and copy data into outbuf */ 832 for (i=0; i<ismax; i++) { 833 row2proc_i = row2proc[i]; 834 ierr = PetscMemzero(ctr,size*sizeof(PetscInt));CHKERRQ(ierr); 835 irow_i = irow[i]; 836 jmax = nrow[i]; 837 for (j=0; j<jmax; j++) { /* parse the indices of each IS */ 838 proc = row2proc_i[j]; 839 if (allrows[i]) row = j; 840 else row = irow_i[j]; 841 842 if (proc != rank) { /* copy to the outgoing buf*/ 843 ctr[proc]++; 844 *ptr[proc] = row; 845 ptr[proc]++; 846 } 847 } 848 /* Update the headers for the current IS */ 849 for (j=0; j<size; j++) { /* Can Optimise this loop too */ 850 if ((ctr_j = ctr[j])) { 851 sbuf1_j = sbuf1[j]; 852 k = ++sbuf1_j[0]; 853 sbuf1_j[2*k] = ctr_j; 854 sbuf1_j[2*k-1] = i; 855 } 856 } 857 } 858 859 /* Now post the sends */ 860 ierr = PetscMalloc1(nrqs+1,&s_waits1);CHKERRQ(ierr); 861 for (i=0; i<nrqs; ++i) { 862 j = pa[i]; 863 ierr = MPI_Isend(sbuf1[j],w1[j],MPIU_INT,j,tag0,comm,s_waits1+i);CHKERRQ(ierr); 864 } 865 866 /* Post Receives to capture the buffer size */ 867 ierr = PetscMalloc1(nrqs+1,&r_waits2);CHKERRQ(ierr); 868 ierr = PetscMalloc3(nrqs+1,&req_source2,nrqs+1,&rbuf2,nrqs+1,&rbuf3);CHKERRQ(ierr); 869 rbuf2[0] = tmp + msz; 870 for (i=1; i<nrqs; ++i) { 871 rbuf2[i] = rbuf2[i-1]+w1[pa[i-1]]; 872 } 873 for (i=0; i<nrqs; ++i) { 874 j = pa[i]; 875 ierr = MPI_Irecv(rbuf2[i],w1[j],MPIU_INT,j,tag2,comm,r_waits2+i);CHKERRQ(ierr); 876 } 877 878 /* Send to other procs the buf size they should allocate */ 879 /* Receive messages*/ 880 ierr = PetscMalloc1(nrqr+1,&s_waits2);CHKERRQ(ierr); 881 ierr = PetscMalloc1(nrqr+1,&r_status1);CHKERRQ(ierr); 882 ierr = PetscMalloc3(nrqr,&sbuf2,nrqr,&req_size,nrqr,&req_source1);CHKERRQ(ierr); 883 { 884 PetscInt *sAi = a->i,*sBi = b->i,id; 885 PetscInt *sbuf2_i; 886 887 ierr = MPI_Waitall(nrqr,r_waits1,r_status1);CHKERRQ(ierr); 888 for (i=0; i<nrqr; ++i) { 889 req_size[i] = 0; 890 rbuf1_i = rbuf1[i]; 891 start = 2*rbuf1_i[0] + 1; 892 ierr = MPI_Get_count(r_status1+i,MPIU_INT,&end);CHKERRQ(ierr); 893 ierr = PetscMalloc1(end+1,&sbuf2[i]);CHKERRQ(ierr); 894 sbuf2_i = sbuf2[i]; 895 for (j=start; j<end; j++) { 896 id = rbuf1_i[j] - rstart; 897 ncols = sAi[id+1] - sAi[id] + sBi[id+1] - sBi[id]; 898 sbuf2_i[j] = ncols; 899 req_size[i] += ncols; 900 } 901 req_source1[i] = r_status1[i].MPI_SOURCE; 902 /* form the header */ 903 sbuf2_i[0] = req_size[i]; 904 for (j=1; j<start; j++) sbuf2_i[j] = rbuf1_i[j]; 905 906 ierr = MPI_Isend(sbuf2_i,end,MPIU_INT,req_source1[i],tag2,comm,s_waits2+i);CHKERRQ(ierr); 907 } 908 } 909 ierr = PetscFree(r_status1);CHKERRQ(ierr); 910 ierr = PetscFree(r_waits1);CHKERRQ(ierr); 911 ierr = PetscFree4(w1,w2,w3,w4);CHKERRQ(ierr); 912 913 /* Receive messages*/ 914 ierr = PetscMalloc1(nrqs+1,&r_waits3);CHKERRQ(ierr); 915 ierr = PetscMalloc1(nrqs+1,&r_status2);CHKERRQ(ierr); 916 917 ierr = MPI_Waitall(nrqs,r_waits2,r_status2);CHKERRQ(ierr); 918 for (i=0; i<nrqs; ++i) { 919 ierr = PetscMalloc1(rbuf2[i][0]+1,&rbuf3[i]);CHKERRQ(ierr); 920 req_source2[i] = r_status2[i].MPI_SOURCE; 921 ierr = MPI_Irecv(rbuf3[i],rbuf2[i][0],MPIU_INT,req_source2[i],tag3,comm,r_waits3+i);CHKERRQ(ierr); 922 } 923 ierr = PetscFree(r_status2);CHKERRQ(ierr); 924 ierr = PetscFree(r_waits2);CHKERRQ(ierr); 925 926 /* Wait on sends1 and sends2 */ 927 ierr = PetscMalloc1(nrqs+1,&s_status1);CHKERRQ(ierr); 928 ierr = PetscMalloc1(nrqr+1,&s_status2);CHKERRQ(ierr); 929 930 if (nrqs) {ierr = MPI_Waitall(nrqs,s_waits1,s_status1);CHKERRQ(ierr);} 931 if (nrqr) {ierr = MPI_Waitall(nrqr,s_waits2,s_status2);CHKERRQ(ierr);} 932 ierr = PetscFree(s_status1);CHKERRQ(ierr); 933 ierr = PetscFree(s_status2);CHKERRQ(ierr); 934 ierr = PetscFree(s_waits1);CHKERRQ(ierr); 935 ierr = PetscFree(s_waits2);CHKERRQ(ierr); 936 937 /* Now allocate sending buffers for a->j, and send them off */ 938 ierr = PetscMalloc1(nrqr+1,&sbuf_aj);CHKERRQ(ierr); 939 for (i=0,j=0; i<nrqr; i++) j += req_size[i]; 940 ierr = PetscMalloc1(j+1,&sbuf_aj[0]);CHKERRQ(ierr); 941 for (i=1; i<nrqr; i++) sbuf_aj[i] = sbuf_aj[i-1] + req_size[i-1]; 942 943 ierr = PetscMalloc1(nrqr+1,&s_waits3);CHKERRQ(ierr); 944 { 945 946 for (i=0; i<nrqr; i++) { 947 rbuf1_i = rbuf1[i]; 948 sbuf_aj_i = sbuf_aj[i]; 949 ct1 = 2*rbuf1_i[0] + 1; 950 ct2 = 0; 951 for (j=1,max1=rbuf1_i[0]; j<=max1; j++) { 952 kmax = rbuf1[i][2*j]; 953 for (k=0; k<kmax; k++,ct1++) { 954 row = rbuf1_i[ct1] - rstart; 955 nzA = a_i[row+1] - a_i[row]; nzB = b_i[row+1] - b_i[row]; 956 ncols = nzA + nzB; 957 cworkA = a_j + a_i[row]; cworkB = 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 ierr = MPI_Isend(sbuf_aj_i,req_size[i],MPIU_INT,req_source1[i],tag3,comm,s_waits3+i);CHKERRQ(ierr); 972 } 973 } 974 ierr = PetscMalloc2(nrqs+1,&r_status3,nrqr+1,&s_status3);CHKERRQ(ierr); 975 976 /* create col map: global col of C -> local col of submatrices */ 977 const PetscInt *icol_i; 978 #if defined(PETSC_USE_CTABLE) 979 for (i=0; i<ismax; i++) { 980 if (!allcolumns[i]) { 981 ierr = PetscTableCreate(ncol[i]+1,c->Nbs+1,&cmap[i]);CHKERRQ(ierr); 982 983 jmax = ncol[i]; 984 icol_i = icol[i]; 985 cmap_i = cmap[i]; 986 for (j=0; j<jmax; j++) { 987 ierr = PetscTableAdd(cmap[i],icol_i[j]+1,j+1,INSERT_VALUES);CHKERRQ(ierr); 988 } 989 } else cmap[i] = NULL; 990 } 991 #else 992 for (i=0; i<ismax; i++) { 993 if (!allcolumns[i]) { 994 ierr = PetscCalloc1(c->Nbs,&cmap[i]);CHKERRQ(ierr); 995 jmax = ncol[i]; 996 icol_i = icol[i]; 997 cmap_i = cmap[i]; 998 for (j=0; j<jmax; j++) cmap_i[icol_i[j]] = j+1; 999 } else cmap[i] = NULL; 1000 } 1001 #endif 1002 1003 /* Create lens which is required for MatCreate... */ 1004 for (i=0,j=0; i<ismax; i++) j += nrow[i]; 1005 ierr = PetscMalloc1(ismax,&lens);CHKERRQ(ierr); 1006 1007 if (ismax) { 1008 ierr = PetscCalloc1(j,&lens[0]);CHKERRQ(ierr); 1009 } 1010 for (i=1; i<ismax; i++) lens[i] = lens[i-1] + nrow[i-1]; 1011 1012 /* Update lens from local data */ 1013 for (i=0; i<ismax; i++) { 1014 row2proc_i = row2proc[i]; 1015 jmax = nrow[i]; 1016 if (!allcolumns[i]) cmap_i = cmap[i]; 1017 irow_i = irow[i]; 1018 lens_i = lens[i]; 1019 for (j=0; j<jmax; j++) { 1020 if (allrows[i]) row = j; 1021 else row = irow_i[j]; /* global blocked row of C */ 1022 1023 proc = row2proc_i[j]; 1024 if (proc == rank) { 1025 /* Get indices from matA and then from matB */ 1026 #if defined(PETSC_USE_CTABLE) 1027 PetscInt tt; 1028 #endif 1029 row = row - rstart; 1030 nzA = a_i[row+1] - a_i[row]; 1031 nzB = b_i[row+1] - b_i[row]; 1032 cworkA = a_j + a_i[row]; 1033 cworkB = b_j + b_i[row]; 1034 1035 if (!allcolumns[i]) { 1036 #if defined(PETSC_USE_CTABLE) 1037 for (k=0; k<nzA; k++) { 1038 ierr = PetscTableFind(cmap_i,cstart+cworkA[k]+1,&tt);CHKERRQ(ierr); 1039 if (tt) lens_i[j]++; 1040 } 1041 for (k=0; k<nzB; k++) { 1042 ierr = PetscTableFind(cmap_i,bmap[cworkB[k]]+1,&tt);CHKERRQ(ierr); 1043 if (tt) lens_i[j]++; 1044 } 1045 1046 #else 1047 for (k=0; k<nzA; k++) { 1048 if (cmap_i[cstart + cworkA[k]]) lens_i[j]++; 1049 } 1050 for (k=0; k<nzB; k++) { 1051 if (cmap_i[bmap[cworkB[k]]]) lens_i[j]++; 1052 } 1053 #endif 1054 } else { /* allcolumns */ 1055 lens_i[j] = nzA + nzB; 1056 } 1057 } 1058 } 1059 } 1060 1061 /* Create row map: global row of C -> local row of submatrices */ 1062 #if defined(PETSC_USE_CTABLE) 1063 for (i=0; i<ismax; i++) { 1064 ierr = PetscTableCreate(nrow[i]+1,c->Mbs+1,&rmap[i]);CHKERRQ(ierr); 1065 irow_i = irow[i]; 1066 jmax = nrow[i]; 1067 for (j=0; j<jmax; j++) { 1068 if (allrows[i]) { 1069 ierr = PetscTableAdd(rmap[i],j+1,j+1,INSERT_VALUES);CHKERRQ(ierr); 1070 } else { 1071 ierr = PetscTableAdd(rmap[i],irow_i[j]+1,j+1,INSERT_VALUES);CHKERRQ(ierr); 1072 } 1073 } 1074 } 1075 #else 1076 for (i=0; i<ismax; i++) { 1077 ierr = PetscCalloc1(c->Mbs,&rmap[i]);CHKERRQ(ierr); 1078 rmap_i = rmap[i]; 1079 irow_i = irow[i]; 1080 jmax = nrow[i]; 1081 for (j=0; j<jmax; j++) { 1082 if (allrows[i]) rmap_i[j] = j; 1083 else rmap_i[irow_i[j]] = j; 1084 } 1085 } 1086 #endif 1087 1088 /* Update lens from offproc data */ 1089 { 1090 PetscInt *rbuf2_i,*rbuf3_i,*sbuf1_i; 1091 1092 ierr = MPI_Waitall(nrqs,r_waits3,r_status3);CHKERRQ(ierr); 1093 for (tmp2=0; tmp2<nrqs; tmp2++) { 1094 sbuf1_i = sbuf1[pa[tmp2]]; 1095 jmax = sbuf1_i[0]; 1096 ct1 = 2*jmax+1; 1097 ct2 = 0; 1098 rbuf2_i = rbuf2[tmp2]; 1099 rbuf3_i = rbuf3[tmp2]; 1100 for (j=1; j<=jmax; j++) { 1101 is_no = sbuf1_i[2*j-1]; 1102 max1 = sbuf1_i[2*j]; 1103 lens_i = lens[is_no]; 1104 if (!allcolumns[is_no]) cmap_i = cmap[is_no]; 1105 rmap_i = rmap[is_no]; 1106 for (k=0; k<max1; k++,ct1++) { 1107 #if defined(PETSC_USE_CTABLE) 1108 ierr = PetscTableFind(rmap_i,sbuf1_i[ct1]+1,&row);CHKERRQ(ierr); 1109 row--; 1110 if (allrows[is_no] && sbuf1_i[ct1] != row) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"sbuf1_i[ct1] %d != row %d",sbuf1_i[ct1],row); 1111 1112 if (row < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"row not found in table"); 1113 #else 1114 row = rmap_i[sbuf1_i[ct1]]; /* the val in the new matrix to be */ 1115 #endif 1116 max2 = rbuf2_i[ct1]; 1117 for (l=0; l<max2; l++,ct2++) { 1118 if (!allcolumns[is_no]) { 1119 #if defined(PETSC_USE_CTABLE) 1120 ierr = PetscTableFind(cmap_i,rbuf3_i[ct2]+1,&tcol);CHKERRQ(ierr); 1121 #else 1122 tcol = cmap_i[rbuf3_i[ct2]]; 1123 #endif 1124 if (tcol) lens_i[row]++; 1125 } else { /* allcolumns */ 1126 lens_i[row]++; /* lens_i[row] += max2 ? */ 1127 } 1128 } 1129 } 1130 } 1131 } 1132 } 1133 ierr = PetscFree(r_waits3);CHKERRQ(ierr); 1134 if (nrqr) {ierr = MPI_Waitall(nrqr,s_waits3,s_status3);CHKERRQ(ierr);} 1135 ierr = PetscFree2(r_status3,s_status3);CHKERRQ(ierr); 1136 ierr = PetscFree(s_waits3);CHKERRQ(ierr); 1137 1138 /* Create the submatrices */ 1139 for (i=0; i<ismax; i++) { 1140 PetscInt bs_tmp; 1141 if (ijonly) bs_tmp = 1; 1142 else bs_tmp = bs; 1143 1144 ierr = MatCreate(PETSC_COMM_SELF,submats+i);CHKERRQ(ierr); 1145 ierr = MatSetSizes(submats[i],nrow[i]*bs_tmp,ncol[i]*bs_tmp,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 1146 1147 ierr = MatSetType(submats[i],((PetscObject)A)->type_name);CHKERRQ(ierr); 1148 ierr = MatSeqBAIJSetPreallocation(submats[i],bs_tmp,0,lens[i]);CHKERRQ(ierr); 1149 ierr = MatSeqSBAIJSetPreallocation(submats[i],bs_tmp,0,lens[i]);CHKERRQ(ierr); /* this subroutine is used by SBAIJ routines */ 1150 1151 /* create struct Mat_SubMat and attached it to submat */ 1152 ierr = PetscNew(&smat_i);CHKERRQ(ierr); 1153 subc = (Mat_SeqBAIJ*)submats[i]->data; 1154 subc->submatis1 = smat_i; 1155 smats[i] = smat_i; 1156 1157 smat_i->destroy = submats[i]->ops->destroy; 1158 submats[i]->ops->destroy = MatDestroy_MPIBAIJ_MatGetSubmatrices; 1159 submats[i]->factortype = C->factortype; 1160 1161 smat_i->id = i; 1162 smat_i->nrqs = nrqs; 1163 smat_i->nrqr = nrqr; 1164 smat_i->rbuf1 = rbuf1; 1165 smat_i->rbuf2 = rbuf2; 1166 smat_i->rbuf3 = rbuf3; 1167 smat_i->sbuf2 = sbuf2; 1168 smat_i->req_source2 = req_source2; 1169 1170 smat_i->sbuf1 = sbuf1; 1171 smat_i->ptr = ptr; 1172 smat_i->tmp = tmp; 1173 smat_i->ctr = ctr; 1174 1175 smat_i->pa = pa; 1176 smat_i->req_size = req_size; 1177 smat_i->req_source1 = req_source1; 1178 1179 smat_i->allcolumns = allcolumns[i]; 1180 smat_i->allrows = allrows[i]; 1181 smat_i->singleis = PETSC_FALSE; 1182 smat_i->row2proc = row2proc[i]; 1183 smat_i->rmap = rmap[i]; 1184 smat_i->cmap = cmap[i]; 1185 } 1186 1187 if (ismax) {ierr = PetscFree(lens[0]);CHKERRQ(ierr);} 1188 ierr = PetscFree(lens);CHKERRQ(ierr); 1189 ierr = PetscFree(sbuf_aj[0]);CHKERRQ(ierr); 1190 ierr = PetscFree(sbuf_aj);CHKERRQ(ierr); 1191 1192 } /* endof scall == MAT_INITIAL_MATRIX */ 1193 1194 /* Post recv matrix values */ 1195 if (!ijonly) { 1196 ierr = PetscObjectGetNewTag((PetscObject)C,&tag4);CHKERRQ(ierr); 1197 ierr = PetscMalloc1(nrqs+1,&rbuf4);CHKERRQ(ierr); 1198 ierr = PetscMalloc1(nrqs+1,&r_waits4);CHKERRQ(ierr); 1199 ierr = PetscMalloc1(nrqs+1,&r_status4);CHKERRQ(ierr); 1200 ierr = PetscMalloc1(nrqr+1,&s_status4);CHKERRQ(ierr); 1201 for (i=0; i<nrqs; ++i) { 1202 ierr = PetscMalloc1(rbuf2[i][0]*bs2,&rbuf4[i]);CHKERRQ(ierr); 1203 ierr = MPI_Irecv(rbuf4[i],rbuf2[i][0]*bs2,MPIU_SCALAR,req_source2[i],tag4,comm,r_waits4+i);CHKERRQ(ierr); 1204 } 1205 1206 /* Allocate sending buffers for a->a, and send them off */ 1207 ierr = PetscMalloc1(nrqr+1,&sbuf_aa);CHKERRQ(ierr); 1208 for (i=0,j=0; i<nrqr; i++) j += req_size[i]; 1209 1210 ierr = PetscMalloc1((j+1)*bs2,&sbuf_aa[0]);CHKERRQ(ierr); 1211 for (i=1; i<nrqr; i++) sbuf_aa[i] = sbuf_aa[i-1] + req_size[i-1]*bs2; 1212 1213 ierr = PetscMalloc1(nrqr+1,&s_waits4);CHKERRQ(ierr); 1214 1215 for (i=0; i<nrqr; i++) { 1216 rbuf1_i = rbuf1[i]; 1217 sbuf_aa_i = sbuf_aa[i]; 1218 ct1 = 2*rbuf1_i[0]+1; 1219 ct2 = 0; 1220 for (j=1,max1=rbuf1_i[0]; j<=max1; j++) { 1221 kmax = rbuf1_i[2*j]; 1222 for (k=0; k<kmax; k++,ct1++) { 1223 row = rbuf1_i[ct1] - rstart; 1224 nzA = a_i[row+1] - a_i[row]; 1225 nzB = b_i[row+1] - b_i[row]; 1226 ncols = nzA + nzB; 1227 cworkB = b_j + b_i[row]; 1228 vworkA = a_a + a_i[row]*bs2; 1229 vworkB = b_a + b_i[row]*bs2; 1230 1231 /* load the column values for this row into vals*/ 1232 vals = sbuf_aa_i+ct2*bs2; 1233 for (l=0; l<nzB; l++) { 1234 if ((bmap[cworkB[l]]) < cstart) { 1235 ierr = PetscMemcpy(vals+l*bs2,vworkB+l*bs2,bs2*sizeof(MatScalar));CHKERRQ(ierr); 1236 } else break; 1237 } 1238 imark = l; 1239 for (l=0; l<nzA; l++) { 1240 ierr = PetscMemcpy(vals+(imark+l)*bs2,vworkA+l*bs2,bs2*sizeof(MatScalar));CHKERRQ(ierr); 1241 } 1242 for (l=imark; l<nzB; l++) { 1243 ierr = PetscMemcpy(vals+(nzA+l)*bs2,vworkB+l*bs2,bs2*sizeof(MatScalar));CHKERRQ(ierr); 1244 } 1245 1246 ct2 += ncols; 1247 } 1248 } 1249 ierr = MPI_Isend(sbuf_aa_i,req_size[i]*bs2,MPIU_SCALAR,req_source1[i],tag4,comm,s_waits4+i);CHKERRQ(ierr); 1250 } 1251 } 1252 1253 if (!ismax) { 1254 ierr = PetscFree(rbuf1[0]);CHKERRQ(ierr); 1255 ierr = PetscFree(rbuf1);CHKERRQ(ierr); 1256 } 1257 1258 /* Assemble the matrices */ 1259 /* First assemble the local rows */ 1260 for (i=0; i<ismax; i++) { 1261 row2proc_i = row2proc[i]; 1262 subc = (Mat_SeqBAIJ*)submats[i]->data; 1263 imat_ilen = subc->ilen; 1264 imat_j = subc->j; 1265 imat_i = subc->i; 1266 imat_a = subc->a; 1267 1268 if (!allcolumns[i]) cmap_i = cmap[i]; 1269 rmap_i = rmap[i]; 1270 irow_i = irow[i]; 1271 jmax = nrow[i]; 1272 for (j=0; j<jmax; j++) { 1273 if (allrows[i]) row = j; 1274 else row = irow_i[j]; 1275 proc = row2proc_i[j]; 1276 1277 if (proc == rank) { 1278 1279 row = row - rstart; 1280 nzA = a_i[row+1] - a_i[row]; 1281 nzB = b_i[row+1] - b_i[row]; 1282 cworkA = a_j + a_i[row]; 1283 cworkB = b_j + b_i[row]; 1284 if (!ijonly) { 1285 vworkA = a_a + a_i[row]*bs2; 1286 vworkB = b_a + b_i[row]*bs2; 1287 } 1288 #if defined(PETSC_USE_CTABLE) 1289 PetscInt Crow = row+rstart; 1290 ierr = PetscTableFind(rmap_i,row+rstart+1,&row);CHKERRQ(ierr); 1291 row--; 1292 if (allrows[i] && Crow != row) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Crow %d != row %d",Crow,row); 1293 1294 if (row < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"row not found in table"); 1295 #else 1296 row = rmap_i[row + rstart]; 1297 #endif 1298 mat_i = imat_i[row]; 1299 if (!ijonly) mat_a = imat_a + mat_i*bs2; 1300 mat_j = imat_j + mat_i; 1301 ilen = imat_ilen[row]; 1302 1303 /* load the column indices for this row into cols*/ 1304 if (!allcolumns[i]) { 1305 for (l=0; l<nzB; l++) { 1306 if ((ctmp = bmap[cworkB[l]]) < cstart) { 1307 #if defined(PETSC_USE_CTABLE) 1308 ierr = PetscTableFind(cmap_i,ctmp+1,&tcol);CHKERRQ(ierr); 1309 if (tcol) { 1310 #else 1311 if ((tcol = cmap_i[ctmp])) { 1312 #endif 1313 *mat_j++ = tcol - 1; 1314 ierr = PetscMemcpy(mat_a,vworkB+l*bs2,bs2*sizeof(MatScalar));CHKERRQ(ierr); 1315 mat_a += bs2; 1316 ilen++; 1317 } 1318 } else break; 1319 } 1320 imark = l; 1321 for (l=0; l<nzA; l++) { 1322 #if defined(PETSC_USE_CTABLE) 1323 ierr = PetscTableFind(cmap_i,cstart+cworkA[l]+1,&tcol);CHKERRQ(ierr); 1324 if (tcol) { 1325 #else 1326 if ((tcol = cmap_i[cstart + cworkA[l]])) { 1327 #endif 1328 *mat_j++ = tcol - 1; 1329 if (!ijonly) { 1330 ierr = PetscMemcpy(mat_a,vworkA+l*bs2,bs2*sizeof(MatScalar));CHKERRQ(ierr); 1331 mat_a += bs2; 1332 } 1333 ilen++; 1334 } 1335 } 1336 for (l=imark; l<nzB; l++) { 1337 #if defined(PETSC_USE_CTABLE) 1338 ierr = PetscTableFind(cmap_i,bmap[cworkB[l]]+1,&tcol);CHKERRQ(ierr); 1339 if (tcol) { 1340 #else 1341 if ((tcol = cmap_i[bmap[cworkB[l]]])) { 1342 #endif 1343 *mat_j++ = tcol - 1; 1344 if (!ijonly) { 1345 ierr = PetscMemcpy(mat_a,vworkB+l*bs2,bs2*sizeof(MatScalar));CHKERRQ(ierr); 1346 mat_a += bs2; 1347 } 1348 ilen++; 1349 } 1350 } 1351 } else { /* allcolumns */ 1352 for (l=0; l<nzB; l++) { 1353 if ((ctmp = bmap[cworkB[l]]) < cstart) { 1354 *mat_j++ = ctmp; 1355 ierr = PetscMemcpy(mat_a,vworkB+l*bs2,bs2*sizeof(MatScalar));CHKERRQ(ierr); 1356 mat_a += bs2; 1357 ilen++; 1358 } else break; 1359 } 1360 imark = l; 1361 for (l=0; l<nzA; l++) { 1362 *mat_j++ = cstart+cworkA[l]; 1363 if (!ijonly) { 1364 ierr = PetscMemcpy(mat_a,vworkA+l*bs2,bs2*sizeof(MatScalar));CHKERRQ(ierr); 1365 mat_a += bs2; 1366 } 1367 ilen++; 1368 } 1369 for (l=imark; l<nzB; l++) { 1370 *mat_j++ = bmap[cworkB[l]]; 1371 if (!ijonly) { 1372 ierr = PetscMemcpy(mat_a,vworkB+l*bs2,bs2*sizeof(MatScalar));CHKERRQ(ierr); 1373 mat_a += bs2; 1374 } 1375 ilen++; 1376 } 1377 } 1378 imat_ilen[row] = ilen; 1379 } 1380 } 1381 } 1382 1383 /* Now assemble the off proc rows */ 1384 if (!ijonly) { 1385 ierr = MPI_Waitall(nrqs,r_waits4,r_status4);CHKERRQ(ierr); 1386 } 1387 for (tmp2=0; tmp2<nrqs; tmp2++) { 1388 sbuf1_i = sbuf1[pa[tmp2]]; 1389 jmax = sbuf1_i[0]; 1390 ct1 = 2*jmax + 1; 1391 ct2 = 0; 1392 rbuf2_i = rbuf2[tmp2]; 1393 rbuf3_i = rbuf3[tmp2]; 1394 if (!ijonly) rbuf4_i = rbuf4[tmp2]; 1395 for (j=1; j<=jmax; j++) { 1396 is_no = sbuf1_i[2*j-1]; 1397 rmap_i = rmap[is_no]; 1398 if (!allcolumns[is_no]) cmap_i = cmap[is_no]; 1399 subc = (Mat_SeqBAIJ*)submats[is_no]->data; 1400 imat_ilen = subc->ilen; 1401 imat_j = subc->j; 1402 imat_i = subc->i; 1403 if (!ijonly) imat_a = subc->a; 1404 max1 = sbuf1_i[2*j]; 1405 for (k=0; k<max1; k++,ct1++) { /* for each recved block row */ 1406 row = sbuf1_i[ct1]; 1407 #if defined(PETSC_USE_CTABLE) 1408 PetscInt Crow = row; 1409 ierr = PetscTableFind(rmap_i,row+1,&row);CHKERRQ(ierr); 1410 row--; 1411 if (row < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"row not found in table"); 1412 1413 if (allrows[is_no] && Crow != row) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"Crow %d != row %d",Crow,row); 1414 #else 1415 row = rmap_i[row]; 1416 #endif 1417 ilen = imat_ilen[row]; 1418 mat_i = imat_i[row]; 1419 if (!ijonly) mat_a = imat_a + mat_i*bs2; 1420 mat_j = imat_j + mat_i; 1421 max2 = rbuf2_i[ct1]; 1422 if (!allcolumns[is_no]) { 1423 for (l=0; l<max2; l++,ct2++) { 1424 #if defined(PETSC_USE_CTABLE) 1425 ierr = PetscTableFind(cmap_i,rbuf3_i[ct2]+1,&tcol);CHKERRQ(ierr); 1426 #else 1427 tcol = cmap_i[rbuf3_i[ct2]]; 1428 #endif 1429 if (tcol) { 1430 *mat_j++ = tcol - 1; 1431 if (!ijonly) { 1432 ierr = PetscMemcpy(mat_a,rbuf4_i+ct2*bs2,bs2*sizeof(MatScalar));CHKERRQ(ierr); 1433 mat_a += bs2; 1434 } 1435 ilen++; 1436 } 1437 } 1438 } else { /* allcolumns */ 1439 for (l=0; l<max2; l++,ct2++) { 1440 *mat_j++ = rbuf3_i[ct2]; /* same global column index of C */ 1441 if (!ijonly) { 1442 ierr = PetscMemcpy(mat_a,rbuf4_i+ct2*bs2,bs2*sizeof(MatScalar));CHKERRQ(ierr); 1443 mat_a += bs2; 1444 } 1445 ilen++; 1446 } 1447 } 1448 imat_ilen[row] = ilen; 1449 } 1450 } 1451 } 1452 1453 if (!iscsorted) { /* sort column indices of the rows */ 1454 MatScalar *work; 1455 1456 ierr = PetscMalloc1(bs2,&work);CHKERRQ(ierr); 1457 for (i=0; i<ismax; i++) { 1458 subc = (Mat_SeqBAIJ*)submats[i]->data; 1459 imat_ilen = subc->ilen; 1460 imat_j = subc->j; 1461 imat_i = subc->i; 1462 if (ijonly) imat_a = subc->a; 1463 1464 if (allcolumns[i]) continue; 1465 jmax = nrow[i]; 1466 for (j=0; j<jmax; j++) { 1467 ilen = imat_ilen[j]; 1468 mat_i = imat_i[j]; 1469 mat_j = imat_j + mat_i; 1470 if (ijonly) { 1471 ierr = PetscSortInt(ilen,mat_j);CHKERRQ(ierr); 1472 } else { 1473 mat_a = imat_a + mat_i; 1474 ierr = PetscSortIntWithDataArray(ilen,mat_j,mat_a,bs2*sizeof(MatScalar),work);CHKERRQ(ierr); 1475 } 1476 } 1477 } 1478 ierr = PetscFree(work);CHKERRQ(ierr); 1479 } 1480 1481 if (!ijonly) { 1482 ierr = PetscFree(r_status4);CHKERRQ(ierr); 1483 ierr = PetscFree(r_waits4);CHKERRQ(ierr); 1484 if (nrqr) {ierr = MPI_Waitall(nrqr,s_waits4,s_status4);CHKERRQ(ierr);} 1485 ierr = PetscFree(s_waits4);CHKERRQ(ierr); 1486 ierr = PetscFree(s_status4);CHKERRQ(ierr); 1487 } 1488 1489 /* Restore the indices */ 1490 for (i=0; i<ismax; i++) { 1491 if (!allrows[i]) { 1492 ierr = ISRestoreIndices(isrow[i],irow+i);CHKERRQ(ierr); 1493 } 1494 if (!allcolumns[i]) { 1495 ierr = ISRestoreIndices(iscol[i],icol+i);CHKERRQ(ierr); 1496 } 1497 } 1498 1499 for (i=0; i<ismax; i++) { 1500 ierr = MatAssemblyBegin(submats[i],MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1501 ierr = MatAssemblyEnd(submats[i],MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1502 } 1503 1504 /* Destroy allocated memory */ 1505 if (!ismax) { 1506 ierr = PetscFree(pa);CHKERRQ(ierr); 1507 ierr = PetscFree4(sbuf1,ptr,tmp,ctr);CHKERRQ(ierr); 1508 for (i=0; i<nrqr; ++i) { 1509 ierr = PetscFree(sbuf2[i]);CHKERRQ(ierr); 1510 } 1511 for (i=0; i<nrqs; ++i) { 1512 ierr = PetscFree(rbuf3[i]);CHKERRQ(ierr); 1513 } 1514 1515 ierr = PetscFree3(sbuf2,req_size,req_source1);CHKERRQ(ierr); 1516 ierr = PetscFree3(req_source2,rbuf2,rbuf3);CHKERRQ(ierr); 1517 } 1518 ierr = PetscFree5(irow,icol,nrow,ncol,issorted);CHKERRQ(ierr); 1519 ierr = PetscFree6(smats,row2proc,cmap,rmap,allcolumns,allrows);CHKERRQ(ierr); 1520 1521 if (!ijonly) { 1522 ierr = PetscFree(sbuf_aa[0]);CHKERRQ(ierr); 1523 ierr = PetscFree(sbuf_aa);CHKERRQ(ierr); 1524 1525 for (i=0; i<nrqs; ++i) { 1526 ierr = PetscFree(rbuf4[i]);CHKERRQ(ierr); 1527 } 1528 ierr = PetscFree(rbuf4);CHKERRQ(ierr); 1529 } 1530 c->ijonly = PETSC_FALSE; /* set back to the default */ 1531 PetscFunctionReturn(0); 1532 } 1533