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 received (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,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 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,(PetscInt***)&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 = PetscArrayzero(w4,size);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 = PetscArrayzero(outdat,size);CHKERRQ(ierr); 138 ierr = PetscArrayzero(ptr,size);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 = PetscArrayzero(outdat[j]+1,2*w3[j]);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 = PetscArrayzero(ctr,size);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);CHKERRMPI(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(*(PetscInt***)&idx,n);CHKERRQ(ierr); 216 217 ierr = PetscMalloc1(imax,&iscomms);CHKERRQ(ierr); 218 for (i=0; i<imax; ++i) { 219 ierr = PetscCommDuplicate(PetscObjectComm((PetscObject)is[i]),&iscomms[i],NULL);CHKERRQ(ierr); 220 ierr = ISDestroy(&is[i]);CHKERRQ(ierr); 221 } 222 223 /* Do Local work*/ 224 ierr = MatIncreaseOverlap_MPIBAIJ_Local(C,imax,table,isz,data);CHKERRQ(ierr); 225 226 /* Receive messages*/ 227 ierr = PetscMalloc1(nrqr+1,&recv_status);CHKERRQ(ierr); 228 if (nrqr) {ierr = MPI_Waitall(nrqr,r_waits1,recv_status);CHKERRMPI(ierr);} 229 230 ierr = PetscMalloc1(nrqs+1,&s_status);CHKERRQ(ierr); 231 if (nrqs) {ierr = MPI_Waitall(nrqs,s_waits1,s_status);CHKERRMPI(ierr);} 232 233 /* Phase 1 sends are complete - deallocate buffers */ 234 ierr = PetscFree4(outdat,ptr,tmp,ctr);CHKERRQ(ierr); 235 ierr = PetscFree4(w1,w2,w3,w4);CHKERRQ(ierr); 236 237 ierr = PetscMalloc1(nrqr+1,&xdata);CHKERRQ(ierr); 238 ierr = PetscMalloc1(nrqr+1,&isz1);CHKERRQ(ierr); 239 ierr = MatIncreaseOverlap_MPIBAIJ_Receive(C,nrqr,rbuf,xdata,isz1);CHKERRQ(ierr); 240 ierr = PetscFree(rbuf[0]);CHKERRQ(ierr); 241 ierr = PetscFree(rbuf);CHKERRQ(ierr); 242 243 /* Send the data back*/ 244 /* Do a global reduction to know the buffer space req for incoming messages*/ 245 { 246 PetscMPIInt *rw1; 247 248 ierr = PetscCalloc1(size,&rw1);CHKERRQ(ierr); 249 250 for (i=0; i<nrqr; ++i) { 251 proc = recv_status[i].MPI_SOURCE; 252 if (proc != onodes1[i]) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"MPI_SOURCE mismatch"); 253 rw1[proc] = isz1[i]; 254 } 255 256 ierr = PetscFree(onodes1);CHKERRQ(ierr); 257 ierr = PetscFree(olengths1);CHKERRQ(ierr); 258 259 /* Determine the number of messages to expect, their lengths, from from-ids */ 260 ierr = PetscGatherMessageLengths(comm,nrqr,nrqs,rw1,&onodes2,&olengths2);CHKERRQ(ierr); 261 ierr = PetscFree(rw1);CHKERRQ(ierr); 262 } 263 /* Now post the Irecvs corresponding to these messages */ 264 ierr = PetscPostIrecvInt(comm,tag2,nrqs,onodes2,olengths2,&rbuf2,&r_waits2);CHKERRQ(ierr); 265 266 /* Now post the sends */ 267 ierr = PetscMalloc1(nrqr+1,&s_waits2);CHKERRQ(ierr); 268 for (i=0; i<nrqr; ++i) { 269 j = recv_status[i].MPI_SOURCE; 270 ierr = MPI_Isend(xdata[i],isz1[i],MPIU_INT,j,tag2,comm,s_waits2+i);CHKERRMPI(ierr); 271 } 272 273 /* receive work done on other processors*/ 274 { 275 PetscMPIInt idex; 276 PetscInt is_no,ct1,max,*rbuf2_i,isz_i,*data_i,jmax; 277 PetscBT table_i; 278 MPI_Status *status2; 279 280 ierr = PetscMalloc1(PetscMax(nrqr,nrqs)+1,&status2);CHKERRQ(ierr); 281 for (i=0; i<nrqs; ++i) { 282 ierr = MPI_Waitany(nrqs,r_waits2,&idex,status2+i);CHKERRMPI(ierr); 283 /* Process the message*/ 284 rbuf2_i = rbuf2[idex]; 285 ct1 = 2*rbuf2_i[0]+1; 286 jmax = rbuf2[idex][0]; 287 for (j=1; j<=jmax; j++) { 288 max = rbuf2_i[2*j]; 289 is_no = rbuf2_i[2*j-1]; 290 isz_i = isz[is_no]; 291 data_i = data[is_no]; 292 table_i = table[is_no]; 293 for (k=0; k<max; k++,ct1++) { 294 row = rbuf2_i[ct1]; 295 if (!PetscBTLookupSet(table_i,row)) data_i[isz_i++] = row; 296 } 297 isz[is_no] = isz_i; 298 } 299 } 300 if (nrqr) {ierr = MPI_Waitall(nrqr,s_waits2,status2);CHKERRMPI(ierr);} 301 ierr = PetscFree(status2);CHKERRQ(ierr); 302 } 303 304 for (i=0; i<imax; ++i) { 305 ierr = ISCreateGeneral(iscomms[i],isz[i],data[i],PETSC_COPY_VALUES,is+i);CHKERRQ(ierr); 306 ierr = PetscCommDestroy(&iscomms[i]);CHKERRQ(ierr); 307 } 308 309 ierr = PetscFree(iscomms);CHKERRQ(ierr); 310 ierr = PetscFree(onodes2);CHKERRQ(ierr); 311 ierr = PetscFree(olengths2);CHKERRQ(ierr); 312 313 ierr = PetscFree(pa);CHKERRQ(ierr); 314 ierr = PetscFree(rbuf2[0]);CHKERRQ(ierr); 315 ierr = PetscFree(rbuf2);CHKERRQ(ierr); 316 ierr = PetscFree(s_waits1);CHKERRQ(ierr); 317 ierr = PetscFree(r_waits1);CHKERRQ(ierr); 318 ierr = PetscFree(s_waits2);CHKERRQ(ierr); 319 ierr = PetscFree(r_waits2);CHKERRQ(ierr); 320 ierr = PetscFree5(table,data,isz,d_p,t_p);CHKERRQ(ierr); 321 ierr = PetscFree(s_status);CHKERRQ(ierr); 322 ierr = PetscFree(recv_status);CHKERRQ(ierr); 323 ierr = PetscFree(xdata[0]);CHKERRQ(ierr); 324 ierr = PetscFree(xdata);CHKERRQ(ierr); 325 ierr = PetscFree(isz1);CHKERRQ(ierr); 326 PetscFunctionReturn(0); 327 } 328 329 /* 330 MatIncreaseOverlap_MPIBAIJ_Local - Called by MatincreaseOverlap, to do 331 the work on the local processor. 332 333 Inputs: 334 C - MAT_MPIBAIJ; 335 imax - total no of index sets processed at a time; 336 table - an array of char - size = Mbs bits. 337 338 Output: 339 isz - array containing the count of the solution elements corresponding 340 to each index set; 341 data - pointer to the solutions 342 */ 343 static PetscErrorCode MatIncreaseOverlap_MPIBAIJ_Local(Mat C,PetscInt imax,PetscBT *table,PetscInt *isz,PetscInt **data) 344 { 345 Mat_MPIBAIJ *c = (Mat_MPIBAIJ*)C->data; 346 Mat A = c->A,B = c->B; 347 Mat_SeqBAIJ *a = (Mat_SeqBAIJ*)A->data,*b = (Mat_SeqBAIJ*)B->data; 348 PetscInt start,end,val,max,rstart,cstart,*ai,*aj; 349 PetscInt *bi,*bj,*garray,i,j,k,row,*data_i,isz_i; 350 PetscBT table_i; 351 352 PetscFunctionBegin; 353 rstart = c->rstartbs; 354 cstart = c->cstartbs; 355 ai = a->i; 356 aj = a->j; 357 bi = b->i; 358 bj = b->j; 359 garray = c->garray; 360 361 for (i=0; i<imax; i++) { 362 data_i = data[i]; 363 table_i = table[i]; 364 isz_i = isz[i]; 365 for (j=0,max=isz[i]; j<max; j++) { 366 row = data_i[j] - rstart; 367 start = ai[row]; 368 end = ai[row+1]; 369 for (k=start; k<end; k++) { /* Amat */ 370 val = aj[k] + cstart; 371 if (!PetscBTLookupSet(table_i,val)) data_i[isz_i++] = val; 372 } 373 start = bi[row]; 374 end = bi[row+1]; 375 for (k=start; k<end; k++) { /* Bmat */ 376 val = garray[bj[k]]; 377 if (!PetscBTLookupSet(table_i,val)) data_i[isz_i++] = val; 378 } 379 } 380 isz[i] = isz_i; 381 } 382 PetscFunctionReturn(0); 383 } 384 /* 385 MatIncreaseOverlap_MPIBAIJ_Receive - Process the received messages, 386 and return the output 387 388 Input: 389 C - the matrix 390 nrqr - no of messages being processed. 391 rbuf - an array of pointers to the received requests 392 393 Output: 394 xdata - array of messages to be sent back 395 isz1 - size of each message 396 397 For better efficiency perhaps we should malloc separately each xdata[i], 398 then if a remalloc is required we need only copy the data for that one row 399 rather than all previous rows as it is now where a single large chunck of 400 memory is used. 401 402 */ 403 static PetscErrorCode MatIncreaseOverlap_MPIBAIJ_Receive(Mat C,PetscInt nrqr,PetscInt **rbuf,PetscInt **xdata,PetscInt * isz1) 404 { 405 Mat_MPIBAIJ *c = (Mat_MPIBAIJ*)C->data; 406 Mat A = c->A,B = c->B; 407 Mat_SeqBAIJ *a = (Mat_SeqBAIJ*)A->data,*b = (Mat_SeqBAIJ*)B->data; 408 PetscErrorCode ierr; 409 PetscInt rstart,cstart,*ai,*aj,*bi,*bj,*garray,i,j,k; 410 PetscInt row,total_sz,ct,ct1,ct2,ct3,mem_estimate,oct2,l,start,end; 411 PetscInt val,max1,max2,Mbs,no_malloc =0,*tmp,new_estimate,ctr; 412 PetscInt *rbuf_i,kmax,rbuf_0; 413 PetscBT xtable; 414 415 PetscFunctionBegin; 416 Mbs = c->Mbs; 417 rstart = c->rstartbs; 418 cstart = c->cstartbs; 419 ai = a->i; 420 aj = a->j; 421 bi = b->i; 422 bj = b->j; 423 garray = c->garray; 424 425 for (i=0,ct=0,total_sz=0; i<nrqr; ++i) { 426 rbuf_i = rbuf[i]; 427 rbuf_0 = rbuf_i[0]; 428 ct += rbuf_0; 429 for (j=1; j<=rbuf_0; j++) total_sz += rbuf_i[2*j]; 430 } 431 432 if (c->Mbs) max1 = ct*(a->nz +b->nz)/c->Mbs; 433 else max1 = 1; 434 mem_estimate = 3*((total_sz > max1 ? total_sz : max1)+1); 435 ierr = PetscMalloc1(mem_estimate,&xdata[0]);CHKERRQ(ierr); 436 ++no_malloc; 437 ierr = PetscBTCreate(Mbs,&xtable);CHKERRQ(ierr); 438 ierr = PetscArrayzero(isz1,nrqr);CHKERRQ(ierr); 439 440 ct3 = 0; 441 for (i=0; i<nrqr; i++) { /* for easch mesg from proc i */ 442 rbuf_i = rbuf[i]; 443 rbuf_0 = rbuf_i[0]; 444 ct1 = 2*rbuf_0+1; 445 ct2 = ct1; 446 ct3 += ct1; 447 for (j=1; j<=rbuf_0; j++) { /* for each IS from proc i*/ 448 ierr = PetscBTMemzero(Mbs,xtable);CHKERRQ(ierr); 449 oct2 = ct2; 450 kmax = rbuf_i[2*j]; 451 for (k=0; k<kmax; k++,ct1++) { 452 row = rbuf_i[ct1]; 453 if (!PetscBTLookupSet(xtable,row)) { 454 if (!(ct3 < mem_estimate)) { 455 new_estimate = (PetscInt)(1.5*mem_estimate)+1; 456 ierr = PetscMalloc1(new_estimate,&tmp);CHKERRQ(ierr); 457 ierr = PetscArraycpy(tmp,xdata[0],mem_estimate);CHKERRQ(ierr); 458 ierr = PetscFree(xdata[0]);CHKERRQ(ierr); 459 xdata[0] = tmp; 460 mem_estimate = new_estimate; ++no_malloc; 461 for (ctr=1; ctr<=i; ctr++) xdata[ctr] = xdata[ctr-1] + isz1[ctr-1]; 462 } 463 xdata[i][ct2++] = row; 464 ct3++; 465 } 466 } 467 for (k=oct2,max2=ct2; k<max2; k++) { 468 row = xdata[i][k] - rstart; 469 start = ai[row]; 470 end = ai[row+1]; 471 for (l=start; l<end; l++) { 472 val = aj[l] + cstart; 473 if (!PetscBTLookupSet(xtable,val)) { 474 if (!(ct3 < mem_estimate)) { 475 new_estimate = (PetscInt)(1.5*mem_estimate)+1; 476 ierr = PetscMalloc1(new_estimate,&tmp);CHKERRQ(ierr); 477 ierr = PetscArraycpy(tmp,xdata[0],mem_estimate);CHKERRQ(ierr); 478 ierr = PetscFree(xdata[0]);CHKERRQ(ierr); 479 xdata[0] = tmp; 480 mem_estimate = new_estimate; ++no_malloc; 481 for (ctr=1; ctr<=i; ctr++) xdata[ctr] = xdata[ctr-1] + isz1[ctr-1]; 482 } 483 xdata[i][ct2++] = val; 484 ct3++; 485 } 486 } 487 start = bi[row]; 488 end = bi[row+1]; 489 for (l=start; l<end; l++) { 490 val = garray[bj[l]]; 491 if (!PetscBTLookupSet(xtable,val)) { 492 if (!(ct3 < mem_estimate)) { 493 new_estimate = (PetscInt)(1.5*mem_estimate)+1; 494 ierr = PetscMalloc1(new_estimate,&tmp);CHKERRQ(ierr); 495 ierr = PetscArraycpy(tmp,xdata[0],mem_estimate);CHKERRQ(ierr); 496 ierr = PetscFree(xdata[0]);CHKERRQ(ierr); 497 xdata[0] = tmp; 498 mem_estimate = new_estimate; ++no_malloc; 499 for (ctr =1; ctr <=i; ctr++) xdata[ctr] = xdata[ctr-1] + isz1[ctr-1]; 500 } 501 xdata[i][ct2++] = val; 502 ct3++; 503 } 504 } 505 } 506 /* Update the header*/ 507 xdata[i][2*j] = ct2 - oct2; /* Undo the vector isz1 and use only a var*/ 508 xdata[i][2*j-1] = rbuf_i[2*j-1]; 509 } 510 xdata[i][0] = rbuf_0; 511 xdata[i+1] = xdata[i] + ct2; 512 isz1[i] = ct2; /* size of each message */ 513 } 514 ierr = PetscBTDestroy(&xtable);CHKERRQ(ierr); 515 ierr = PetscInfo3(C,"Allocated %D bytes, required %D, no of mallocs = %D\n",mem_estimate,ct3,no_malloc);CHKERRQ(ierr); 516 PetscFunctionReturn(0); 517 } 518 519 PetscErrorCode MatCreateSubMatrices_MPIBAIJ(Mat C,PetscInt ismax,const IS isrow[],const IS iscol[],MatReuse scall,Mat *submat[]) 520 { 521 IS *isrow_block,*iscol_block; 522 Mat_MPIBAIJ *c = (Mat_MPIBAIJ*)C->data; 523 PetscErrorCode ierr; 524 PetscInt nmax,nstages_local,nstages,i,pos,max_no,N=C->cmap->N,bs=C->rmap->bs; 525 Mat_SeqBAIJ *subc; 526 Mat_SubSppt *smat; 527 528 PetscFunctionBegin; 529 /* The compression and expansion should be avoided. Doesn't point 530 out errors, might change the indices, hence buggey */ 531 ierr = PetscMalloc2(ismax+1,&isrow_block,ismax+1,&iscol_block);CHKERRQ(ierr); 532 ierr = ISCompressIndicesGeneral(N,C->rmap->n,bs,ismax,isrow,isrow_block);CHKERRQ(ierr); 533 ierr = ISCompressIndicesGeneral(N,C->cmap->n,bs,ismax,iscol,iscol_block);CHKERRQ(ierr); 534 535 /* Determine the number of stages through which submatrices are done */ 536 if (!C->cmap->N) nmax=20*1000000/sizeof(PetscInt); 537 else nmax = 20*1000000 / (c->Nbs * sizeof(PetscInt)); 538 if (!nmax) nmax = 1; 539 540 if (scall == MAT_INITIAL_MATRIX) { 541 nstages_local = ismax/nmax + ((ismax % nmax) ? 1 : 0); /* local nstages */ 542 543 /* Make sure every processor loops through the nstages */ 544 ierr = MPIU_Allreduce(&nstages_local,&nstages,1,MPIU_INT,MPI_MAX,PetscObjectComm((PetscObject)C));CHKERRMPI(ierr); 545 546 /* Allocate memory to hold all the submatrices and dummy submatrices */ 547 ierr = PetscCalloc1(ismax+nstages,submat);CHKERRQ(ierr); 548 } else { /* MAT_REUSE_MATRIX */ 549 if (ismax) { 550 subc = (Mat_SeqBAIJ*)((*submat)[0]->data); 551 smat = subc->submatis1; 552 } else { /* (*submat)[0] is a dummy matrix */ 553 smat = (Mat_SubSppt*)(*submat)[0]->data; 554 } 555 if (!smat) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_NULL,"MatCreateSubMatrices(...,MAT_REUSE_MATRIX,...) requires submat"); 556 nstages = smat->nstages; 557 } 558 559 for (i=0,pos=0; i<nstages; i++) { 560 if (pos+nmax <= ismax) max_no = nmax; 561 else if (pos >= ismax) max_no = 0; 562 else max_no = ismax-pos; 563 564 ierr = MatCreateSubMatrices_MPIBAIJ_local(C,max_no,isrow_block+pos,iscol_block+pos,scall,*submat+pos);CHKERRQ(ierr); 565 if (!max_no) { 566 if (scall == MAT_INITIAL_MATRIX) { /* submat[pos] is a dummy matrix */ 567 smat = (Mat_SubSppt*)(*submat)[pos]->data; 568 smat->nstages = nstages; 569 } 570 pos++; /* advance to next dummy matrix if any */ 571 } else pos += max_no; 572 } 573 574 if (scall == MAT_INITIAL_MATRIX && ismax) { 575 /* save nstages for reuse */ 576 subc = (Mat_SeqBAIJ*)((*submat)[0]->data); 577 smat = subc->submatis1; 578 smat->nstages = nstages; 579 } 580 581 for (i=0; i<ismax; i++) { 582 ierr = ISDestroy(&isrow_block[i]);CHKERRQ(ierr); 583 ierr = ISDestroy(&iscol_block[i]);CHKERRQ(ierr); 584 } 585 ierr = PetscFree2(isrow_block,iscol_block);CHKERRQ(ierr); 586 PetscFunctionReturn(0); 587 } 588 589 #if defined(PETSC_USE_CTABLE) 590 PetscErrorCode PetscGetProc(const PetscInt row, const PetscMPIInt size, const PetscInt proc_gnode[], PetscMPIInt *rank) 591 { 592 PetscInt nGlobalNd = proc_gnode[size]; 593 PetscMPIInt fproc; 594 PetscErrorCode ierr; 595 596 PetscFunctionBegin; 597 ierr = PetscMPIIntCast((PetscInt)(((float)row * (float)size / (float)nGlobalNd + 0.5)),&fproc);CHKERRQ(ierr); 598 if (fproc > size) fproc = size; 599 while (row < proc_gnode[fproc] || row >= proc_gnode[fproc+1]) { 600 if (row < proc_gnode[fproc]) fproc--; 601 else fproc++; 602 } 603 *rank = fproc; 604 PetscFunctionReturn(0); 605 } 606 #endif 607 608 /* -------------------------------------------------------------------------*/ 609 /* This code is used for BAIJ and SBAIJ matrices (unfortunate dependency) */ 610 PetscErrorCode MatCreateSubMatrices_MPIBAIJ_local(Mat C,PetscInt ismax,const IS isrow[],const IS iscol[],MatReuse scall,Mat *submats) 611 { 612 Mat_MPIBAIJ *c = (Mat_MPIBAIJ*)C->data; 613 Mat A = c->A; 614 Mat_SeqBAIJ *a = (Mat_SeqBAIJ*)A->data,*b = (Mat_SeqBAIJ*)c->B->data,*subc; 615 const PetscInt **icol,**irow; 616 PetscInt *nrow,*ncol,start; 617 PetscErrorCode ierr; 618 PetscMPIInt rank,size,tag0,tag2,tag3,tag4,*w1,*w2,*w3,*w4,nrqr; 619 PetscInt **sbuf1,**sbuf2,*sbuf2_i,i,j,k,l,ct1,ct2,**rbuf1,row,proc=-1; 620 PetscInt nrqs=0,msz,**ptr=NULL,*req_size=NULL,*ctr=NULL,*pa,*tmp=NULL,tcol; 621 PetscInt **rbuf3=NULL,*req_source1=NULL,*req_source2,**sbuf_aj,**rbuf2=NULL,max1,max2; 622 PetscInt **lens,is_no,ncols,*cols,mat_i,*mat_j,tmp2,jmax; 623 #if defined(PETSC_USE_CTABLE) 624 PetscTable *cmap,cmap_i=NULL,*rmap,rmap_i; 625 #else 626 PetscInt **cmap,*cmap_i=NULL,**rmap,*rmap_i; 627 #endif 628 const PetscInt *irow_i,*icol_i; 629 PetscInt ctr_j,*sbuf1_j,*sbuf_aj_i,*rbuf1_i,kmax,*lens_i; 630 MPI_Request *s_waits1,*r_waits1,*s_waits2,*r_waits2,*r_waits3; 631 MPI_Request *r_waits4,*s_waits3,*s_waits4; 632 MPI_Status *r_status1,*r_status2,*s_status1,*s_status3,*s_status2; 633 MPI_Status *r_status3,*r_status4,*s_status4; 634 MPI_Comm comm; 635 PetscScalar **rbuf4,*rbuf4_i=NULL,**sbuf_aa,*vals,*mat_a=NULL,*imat_a=NULL,*sbuf_aa_i; 636 PetscMPIInt *onodes1,*olengths1,end; 637 PetscInt **row2proc,*row2proc_i,*imat_ilen,*imat_j,*imat_i; 638 Mat_SubSppt *smat_i; 639 PetscBool *issorted,colflag,iscsorted=PETSC_TRUE; 640 PetscInt *sbuf1_i,*rbuf2_i,*rbuf3_i,ilen; 641 PetscInt bs=C->rmap->bs,bs2=c->bs2,rstart = c->rstartbs; 642 PetscBool ijonly=c->ijonly; /* private flag indicates only matrix data structures are requested */ 643 PetscInt nzA,nzB,*a_i=a->i,*b_i=b->i,*a_j = a->j,*b_j = b->j,ctmp,imark,*cworkA,*cworkB; 644 PetscScalar *vworkA=NULL,*vworkB=NULL,*a_a = a->a,*b_a = b->a; 645 PetscInt cstart = c->cstartbs,*bmap = c->garray; 646 PetscBool *allrows,*allcolumns; 647 648 PetscFunctionBegin; 649 ierr = PetscObjectGetComm((PetscObject)C,&comm);CHKERRQ(ierr); 650 size = c->size; 651 rank = c->rank; 652 653 ierr = PetscMalloc5(ismax,&row2proc,ismax,&cmap,ismax,&rmap,ismax+1,&allcolumns,ismax,&allrows);CHKERRQ(ierr); 654 ierr = PetscMalloc5(ismax,(PetscInt***)&irow,ismax,(PetscInt***)&icol,ismax,&nrow,ismax,&ncol,ismax,&issorted);CHKERRQ(ierr); 655 656 for (i=0; i<ismax; i++) { 657 ierr = ISSorted(iscol[i],&issorted[i]);CHKERRQ(ierr); 658 if (!issorted[i]) iscsorted = issorted[i]; /* columns are not sorted! */ 659 ierr = ISSorted(isrow[i],&issorted[i]);CHKERRQ(ierr); 660 661 /* Check for special case: allcolumns */ 662 ierr = ISIdentity(iscol[i],&colflag);CHKERRQ(ierr); 663 ierr = ISGetLocalSize(iscol[i],&ncol[i]);CHKERRQ(ierr); 664 665 if (colflag && ncol[i] == c->Nbs) { 666 allcolumns[i] = PETSC_TRUE; 667 icol[i] = NULL; 668 } else { 669 allcolumns[i] = PETSC_FALSE; 670 ierr = ISGetIndices(iscol[i],&icol[i]);CHKERRQ(ierr); 671 } 672 673 /* Check for special case: allrows */ 674 ierr = ISIdentity(isrow[i],&colflag);CHKERRQ(ierr); 675 ierr = ISGetLocalSize(isrow[i],&nrow[i]);CHKERRQ(ierr); 676 if (colflag && nrow[i] == c->Mbs) { 677 allrows[i] = PETSC_TRUE; 678 irow[i] = NULL; 679 } else { 680 allrows[i] = PETSC_FALSE; 681 ierr = ISGetIndices(isrow[i],&irow[i]);CHKERRQ(ierr); 682 } 683 } 684 685 if (scall == MAT_REUSE_MATRIX) { 686 /* Assumes new rows are same length as the old rows */ 687 for (i=0; i<ismax; i++) { 688 subc = (Mat_SeqBAIJ*)(submats[i]->data); 689 if (subc->mbs != nrow[i] || subc->nbs != ncol[i]) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Cannot reuse matrix. wrong size"); 690 691 /* Initial matrix as if empty */ 692 ierr = PetscArrayzero(subc->ilen,subc->mbs);CHKERRQ(ierr); 693 694 /* Initial matrix as if empty */ 695 submats[i]->factortype = C->factortype; 696 697 smat_i = subc->submatis1; 698 699 nrqs = smat_i->nrqs; 700 nrqr = smat_i->nrqr; 701 rbuf1 = smat_i->rbuf1; 702 rbuf2 = smat_i->rbuf2; 703 rbuf3 = smat_i->rbuf3; 704 req_source2 = smat_i->req_source2; 705 706 sbuf1 = smat_i->sbuf1; 707 sbuf2 = smat_i->sbuf2; 708 ptr = smat_i->ptr; 709 tmp = smat_i->tmp; 710 ctr = smat_i->ctr; 711 712 pa = smat_i->pa; 713 req_size = smat_i->req_size; 714 req_source1 = smat_i->req_source1; 715 716 allcolumns[i] = smat_i->allcolumns; 717 allrows[i] = smat_i->allrows; 718 row2proc[i] = smat_i->row2proc; 719 rmap[i] = smat_i->rmap; 720 cmap[i] = smat_i->cmap; 721 } 722 723 if (!ismax){ /* Get dummy submatrices and retrieve struct submatis1 */ 724 if (!submats[0]) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_NULL,"submats are null, cannot reuse"); 725 smat_i = (Mat_SubSppt*)submats[0]->data; 726 727 nrqs = smat_i->nrqs; 728 nrqr = smat_i->nrqr; 729 rbuf1 = smat_i->rbuf1; 730 rbuf2 = smat_i->rbuf2; 731 rbuf3 = smat_i->rbuf3; 732 req_source2 = smat_i->req_source2; 733 734 sbuf1 = smat_i->sbuf1; 735 sbuf2 = smat_i->sbuf2; 736 ptr = smat_i->ptr; 737 tmp = smat_i->tmp; 738 ctr = smat_i->ctr; 739 740 pa = smat_i->pa; 741 req_size = smat_i->req_size; 742 req_source1 = smat_i->req_source1; 743 744 allcolumns[0] = PETSC_FALSE; 745 } 746 } else { /* scall == MAT_INITIAL_MATRIX */ 747 /* Get some new tags to keep the communication clean */ 748 ierr = PetscObjectGetNewTag((PetscObject)C,&tag2);CHKERRQ(ierr); 749 ierr = PetscObjectGetNewTag((PetscObject)C,&tag3);CHKERRQ(ierr); 750 751 /* evaluate communication - mesg to who, length of mesg, and buffer space 752 required. Based on this, buffers are allocated, and data copied into them*/ 753 ierr = PetscCalloc4(size,&w1,size,&w2,size,&w3,size,&w4);CHKERRQ(ierr); /* mesg size, initialize work vectors */ 754 755 for (i=0; i<ismax; i++) { 756 jmax = nrow[i]; 757 irow_i = irow[i]; 758 759 ierr = PetscMalloc1(jmax,&row2proc_i);CHKERRQ(ierr); 760 row2proc[i] = row2proc_i; 761 762 if (issorted[i]) proc = 0; 763 for (j=0; j<jmax; j++) { 764 if (!issorted[i]) proc = 0; 765 if (allrows[i]) row = j; 766 else row = irow_i[j]; 767 768 while (row >= c->rangebs[proc+1]) proc++; 769 w4[proc]++; 770 row2proc_i[j] = proc; /* map row index to proc */ 771 } 772 for (j=0; j<size; j++) { 773 if (w4[j]) { w1[j] += w4[j]; w3[j]++; w4[j] = 0;} 774 } 775 } 776 777 nrqs = 0; /* no of outgoing messages */ 778 msz = 0; /* total mesg length (for all procs) */ 779 w1[rank] = 0; /* no mesg sent to self */ 780 w3[rank] = 0; 781 for (i=0; i<size; i++) { 782 if (w1[i]) { w2[i] = 1; nrqs++;} /* there exists a message to proc i */ 783 } 784 ierr = PetscMalloc1(nrqs+1,&pa);CHKERRQ(ierr); /*(proc -array)*/ 785 for (i=0,j=0; i<size; i++) { 786 if (w1[i]) { pa[j] = i; j++; } 787 } 788 789 /* Each message would have a header = 1 + 2*(no of IS) + data */ 790 for (i=0; i<nrqs; i++) { 791 j = pa[i]; 792 w1[j] += w2[j] + 2* w3[j]; 793 msz += w1[j]; 794 } 795 ierr = PetscInfo2(0,"Number of outgoing messages %D Total message length %D\n",nrqs,msz);CHKERRQ(ierr); 796 797 /* Determine the number of messages to expect, their lengths, from from-ids */ 798 ierr = PetscGatherNumberOfMessages(comm,w2,w1,&nrqr);CHKERRQ(ierr); 799 ierr = PetscGatherMessageLengths(comm,nrqs,nrqr,w1,&onodes1,&olengths1);CHKERRQ(ierr); 800 801 /* Now post the Irecvs corresponding to these messages */ 802 tag0 = ((PetscObject)C)->tag; 803 ierr = PetscPostIrecvInt(comm,tag0,nrqr,onodes1,olengths1,&rbuf1,&r_waits1);CHKERRQ(ierr); 804 805 ierr = PetscFree(onodes1);CHKERRQ(ierr); 806 ierr = PetscFree(olengths1);CHKERRQ(ierr); 807 808 /* Allocate Memory for outgoing messages */ 809 ierr = PetscMalloc4(size,&sbuf1,size,&ptr,2*msz,&tmp,size,&ctr);CHKERRQ(ierr); 810 ierr = PetscArrayzero(sbuf1,size);CHKERRQ(ierr); 811 ierr = PetscArrayzero(ptr,size);CHKERRQ(ierr); 812 813 { 814 PetscInt *iptr = tmp; 815 k = 0; 816 for (i=0; i<nrqs; i++) { 817 j = pa[i]; 818 iptr += k; 819 sbuf1[j] = iptr; 820 k = w1[j]; 821 } 822 } 823 824 /* Form the outgoing messages. Initialize the header space */ 825 for (i=0; i<nrqs; i++) { 826 j = pa[i]; 827 sbuf1[j][0] = 0; 828 ierr = PetscArrayzero(sbuf1[j]+1,2*w3[j]);CHKERRQ(ierr); 829 ptr[j] = sbuf1[j] + 2*w3[j] + 1; 830 } 831 832 /* Parse the isrow and copy data into outbuf */ 833 for (i=0; i<ismax; i++) { 834 row2proc_i = row2proc[i]; 835 ierr = PetscArrayzero(ctr,size);CHKERRQ(ierr); 836 irow_i = irow[i]; 837 jmax = nrow[i]; 838 for (j=0; j<jmax; j++) { /* parse the indices of each IS */ 839 proc = row2proc_i[j]; 840 if (allrows[i]) row = j; 841 else row = irow_i[j]; 842 843 if (proc != rank) { /* copy to the outgoing buf*/ 844 ctr[proc]++; 845 *ptr[proc] = row; 846 ptr[proc]++; 847 } 848 } 849 /* Update the headers for the current IS */ 850 for (j=0; j<size; j++) { /* Can Optimise this loop too */ 851 if ((ctr_j = ctr[j])) { 852 sbuf1_j = sbuf1[j]; 853 k = ++sbuf1_j[0]; 854 sbuf1_j[2*k] = ctr_j; 855 sbuf1_j[2*k-1] = i; 856 } 857 } 858 } 859 860 /* Now post the sends */ 861 ierr = PetscMalloc1(nrqs+1,&s_waits1);CHKERRQ(ierr); 862 for (i=0; i<nrqs; ++i) { 863 j = pa[i]; 864 ierr = MPI_Isend(sbuf1[j],w1[j],MPIU_INT,j,tag0,comm,s_waits1+i);CHKERRMPI(ierr); 865 } 866 867 /* Post Receives to capture the buffer size */ 868 ierr = PetscMalloc1(nrqs+1,&r_waits2);CHKERRQ(ierr); 869 ierr = PetscMalloc3(nrqs+1,&req_source2,nrqs+1,&rbuf2,nrqs+1,&rbuf3);CHKERRQ(ierr); 870 rbuf2[0] = tmp + msz; 871 for (i=1; i<nrqs; ++i) { 872 rbuf2[i] = rbuf2[i-1]+w1[pa[i-1]]; 873 } 874 for (i=0; i<nrqs; ++i) { 875 j = pa[i]; 876 ierr = MPI_Irecv(rbuf2[i],w1[j],MPIU_INT,j,tag2,comm,r_waits2+i);CHKERRMPI(ierr); 877 } 878 879 /* Send to other procs the buf size they should allocate */ 880 /* Receive messages*/ 881 ierr = PetscMalloc1(nrqr+1,&s_waits2);CHKERRQ(ierr); 882 ierr = PetscMalloc1(nrqr+1,&r_status1);CHKERRQ(ierr); 883 ierr = PetscMalloc3(nrqr,&sbuf2,nrqr,&req_size,nrqr,&req_source1);CHKERRQ(ierr); 884 885 ierr = MPI_Waitall(nrqr,r_waits1,r_status1);CHKERRMPI(ierr); 886 for (i=0; i<nrqr; ++i) { 887 req_size[i] = 0; 888 rbuf1_i = rbuf1[i]; 889 start = 2*rbuf1_i[0] + 1; 890 ierr = MPI_Get_count(r_status1+i,MPIU_INT,&end);CHKERRMPI(ierr); 891 ierr = PetscMalloc1(end+1,&sbuf2[i]);CHKERRQ(ierr); 892 sbuf2_i = sbuf2[i]; 893 for (j=start; j<end; j++) { 894 row = rbuf1_i[j] - rstart; 895 ncols = a_i[row+1] - a_i[row] + b_i[row+1] - b_i[row]; 896 sbuf2_i[j] = ncols; 897 req_size[i] += ncols; 898 } 899 req_source1[i] = r_status1[i].MPI_SOURCE; 900 /* form the header */ 901 sbuf2_i[0] = req_size[i]; 902 for (j=1; j<start; j++) sbuf2_i[j] = rbuf1_i[j]; 903 904 ierr = MPI_Isend(sbuf2_i,end,MPIU_INT,req_source1[i],tag2,comm,s_waits2+i);CHKERRMPI(ierr); 905 } 906 907 ierr = PetscFree(r_status1);CHKERRQ(ierr); 908 ierr = PetscFree(r_waits1);CHKERRQ(ierr); 909 ierr = PetscFree4(w1,w2,w3,w4);CHKERRQ(ierr); 910 911 /* Receive messages*/ 912 ierr = PetscMalloc1(nrqs+1,&r_waits3);CHKERRQ(ierr); 913 ierr = PetscMalloc1(nrqs+1,&r_status2);CHKERRQ(ierr); 914 915 ierr = MPI_Waitall(nrqs,r_waits2,r_status2);CHKERRMPI(ierr); 916 for (i=0; i<nrqs; ++i) { 917 ierr = PetscMalloc1(rbuf2[i][0]+1,&rbuf3[i]);CHKERRQ(ierr); 918 req_source2[i] = r_status2[i].MPI_SOURCE; 919 ierr = MPI_Irecv(rbuf3[i],rbuf2[i][0],MPIU_INT,req_source2[i],tag3,comm,r_waits3+i);CHKERRMPI(ierr); 920 } 921 ierr = PetscFree(r_status2);CHKERRQ(ierr); 922 ierr = PetscFree(r_waits2);CHKERRQ(ierr); 923 924 /* Wait on sends1 and sends2 */ 925 ierr = PetscMalloc1(nrqs+1,&s_status1);CHKERRQ(ierr); 926 ierr = PetscMalloc1(nrqr+1,&s_status2);CHKERRQ(ierr); 927 928 if (nrqs) {ierr = MPI_Waitall(nrqs,s_waits1,s_status1);CHKERRMPI(ierr);} 929 if (nrqr) {ierr = MPI_Waitall(nrqr,s_waits2,s_status2);CHKERRMPI(ierr);} 930 ierr = PetscFree(s_status1);CHKERRQ(ierr); 931 ierr = PetscFree(s_status2);CHKERRQ(ierr); 932 ierr = PetscFree(s_waits1);CHKERRQ(ierr); 933 ierr = PetscFree(s_waits2);CHKERRQ(ierr); 934 935 /* Now allocate sending buffers for a->j, and send them off */ 936 ierr = PetscMalloc1(nrqr+1,&sbuf_aj);CHKERRQ(ierr); 937 for (i=0,j=0; i<nrqr; i++) j += req_size[i]; 938 ierr = PetscMalloc1(j+1,&sbuf_aj[0]);CHKERRQ(ierr); 939 for (i=1; i<nrqr; i++) sbuf_aj[i] = sbuf_aj[i-1] + req_size[i-1]; 940 941 ierr = PetscMalloc1(nrqr+1,&s_waits3);CHKERRQ(ierr); 942 { 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]; nzB = b_i[row+1] - b_i[row]; 954 ncols = nzA + nzB; 955 cworkA = a_j + a_i[row]; cworkB = b_j + b_i[row]; 956 957 /* load the column indices for this row into cols */ 958 cols = sbuf_aj_i + ct2; 959 for (l=0; l<nzB; l++) { 960 if ((ctmp = bmap[cworkB[l]]) < cstart) cols[l] = ctmp; 961 else break; 962 } 963 imark = l; 964 for (l=0; l<nzA; l++) {cols[imark+l] = cstart + cworkA[l];} 965 for (l=imark; l<nzB; l++) cols[nzA+l] = bmap[cworkB[l]]; 966 ct2 += ncols; 967 } 968 } 969 ierr = MPI_Isend(sbuf_aj_i,req_size[i],MPIU_INT,req_source1[i],tag3,comm,s_waits3+i);CHKERRMPI(ierr); 970 } 971 } 972 ierr = PetscMalloc2(nrqs+1,&r_status3,nrqr+1,&s_status3);CHKERRQ(ierr); 973 974 /* create col map: global col of C -> local col of submatrices */ 975 #if defined(PETSC_USE_CTABLE) 976 for (i=0; i<ismax; i++) { 977 if (!allcolumns[i]) { 978 ierr = PetscTableCreate(ncol[i]+1,c->Nbs+1,&cmap[i]);CHKERRQ(ierr); 979 980 jmax = ncol[i]; 981 icol_i = icol[i]; 982 cmap_i = cmap[i]; 983 for (j=0; j<jmax; j++) { 984 ierr = PetscTableAdd(cmap[i],icol_i[j]+1,j+1,INSERT_VALUES);CHKERRQ(ierr); 985 } 986 } else cmap[i] = NULL; 987 } 988 #else 989 for (i=0; i<ismax; i++) { 990 if (!allcolumns[i]) { 991 ierr = PetscCalloc1(c->Nbs,&cmap[i]);CHKERRQ(ierr); 992 jmax = ncol[i]; 993 icol_i = icol[i]; 994 cmap_i = cmap[i]; 995 for (j=0; j<jmax; j++) cmap_i[icol_i[j]] = j+1; 996 } else cmap[i] = NULL; 997 } 998 #endif 999 1000 /* Create lens which is required for MatCreate... */ 1001 for (i=0,j=0; i<ismax; i++) j += nrow[i]; 1002 ierr = PetscMalloc1(ismax,&lens);CHKERRQ(ierr); 1003 1004 if (ismax) { 1005 ierr = PetscCalloc1(j,&lens[0]);CHKERRQ(ierr); 1006 } 1007 for (i=1; i<ismax; i++) lens[i] = lens[i-1] + nrow[i-1]; 1008 1009 /* Update lens from local data */ 1010 for (i=0; i<ismax; i++) { 1011 row2proc_i = row2proc[i]; 1012 jmax = nrow[i]; 1013 if (!allcolumns[i]) cmap_i = cmap[i]; 1014 irow_i = irow[i]; 1015 lens_i = lens[i]; 1016 for (j=0; j<jmax; j++) { 1017 if (allrows[i]) row = j; 1018 else row = irow_i[j]; /* global blocked row of C */ 1019 1020 proc = row2proc_i[j]; 1021 if (proc == rank) { 1022 /* Get indices from matA and then from matB */ 1023 #if defined(PETSC_USE_CTABLE) 1024 PetscInt tt; 1025 #endif 1026 row = row - rstart; 1027 nzA = a_i[row+1] - a_i[row]; 1028 nzB = b_i[row+1] - b_i[row]; 1029 cworkA = a_j + a_i[row]; 1030 cworkB = b_j + b_i[row]; 1031 1032 if (!allcolumns[i]) { 1033 #if defined(PETSC_USE_CTABLE) 1034 for (k=0; k<nzA; k++) { 1035 ierr = PetscTableFind(cmap_i,cstart+cworkA[k]+1,&tt);CHKERRQ(ierr); 1036 if (tt) lens_i[j]++; 1037 } 1038 for (k=0; k<nzB; k++) { 1039 ierr = PetscTableFind(cmap_i,bmap[cworkB[k]]+1,&tt);CHKERRQ(ierr); 1040 if (tt) lens_i[j]++; 1041 } 1042 1043 #else 1044 for (k=0; k<nzA; k++) { 1045 if (cmap_i[cstart + cworkA[k]]) lens_i[j]++; 1046 } 1047 for (k=0; k<nzB; k++) { 1048 if (cmap_i[bmap[cworkB[k]]]) lens_i[j]++; 1049 } 1050 #endif 1051 } else { /* allcolumns */ 1052 lens_i[j] = nzA + nzB; 1053 } 1054 } 1055 } 1056 } 1057 1058 /* Create row map: global row of C -> local row of submatrices */ 1059 for (i=0; i<ismax; i++) { 1060 if (!allrows[i]) { 1061 #if defined(PETSC_USE_CTABLE) 1062 ierr = PetscTableCreate(nrow[i]+1,c->Mbs+1,&rmap[i]);CHKERRQ(ierr); 1063 irow_i = irow[i]; 1064 jmax = nrow[i]; 1065 for (j=0; j<jmax; j++) { 1066 if (allrows[i]) { 1067 ierr = PetscTableAdd(rmap[i],j+1,j+1,INSERT_VALUES);CHKERRQ(ierr); 1068 } else { 1069 ierr = PetscTableAdd(rmap[i],irow_i[j]+1,j+1,INSERT_VALUES);CHKERRQ(ierr); 1070 } 1071 } 1072 #else 1073 ierr = PetscCalloc1(c->Mbs,&rmap[i]);CHKERRQ(ierr); 1074 rmap_i = rmap[i]; 1075 irow_i = irow[i]; 1076 jmax = nrow[i]; 1077 for (j=0; j<jmax; j++) { 1078 if (allrows[i]) rmap_i[j] = j; 1079 else rmap_i[irow_i[j]] = j; 1080 } 1081 #endif 1082 } else rmap[i] = NULL; 1083 } 1084 1085 /* Update lens from offproc data */ 1086 { 1087 PetscInt *rbuf2_i,*rbuf3_i,*sbuf1_i; 1088 1089 ierr = MPI_Waitall(nrqs,r_waits3,r_status3);CHKERRMPI(ierr); 1090 for (tmp2=0; tmp2<nrqs; tmp2++) { 1091 sbuf1_i = sbuf1[pa[tmp2]]; 1092 jmax = sbuf1_i[0]; 1093 ct1 = 2*jmax+1; 1094 ct2 = 0; 1095 rbuf2_i = rbuf2[tmp2]; 1096 rbuf3_i = rbuf3[tmp2]; 1097 for (j=1; j<=jmax; j++) { 1098 is_no = sbuf1_i[2*j-1]; 1099 max1 = sbuf1_i[2*j]; 1100 lens_i = lens[is_no]; 1101 if (!allcolumns[is_no]) cmap_i = cmap[is_no]; 1102 rmap_i = rmap[is_no]; 1103 for (k=0; k<max1; k++,ct1++) { 1104 if (allrows[is_no]) { 1105 row = sbuf1_i[ct1]; 1106 } else { 1107 #if defined(PETSC_USE_CTABLE) 1108 ierr = PetscTableFind(rmap_i,sbuf1_i[ct1]+1,&row);CHKERRQ(ierr); 1109 row--; 1110 if (row < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"row not found in table"); 1111 #else 1112 row = rmap_i[sbuf1_i[ct1]]; /* the val in the new matrix to be */ 1113 #endif 1114 } 1115 max2 = rbuf2_i[ct1]; 1116 for (l=0; l<max2; l++,ct2++) { 1117 if (!allcolumns[is_no]) { 1118 #if defined(PETSC_USE_CTABLE) 1119 ierr = PetscTableFind(cmap_i,rbuf3_i[ct2]+1,&tcol);CHKERRQ(ierr); 1120 #else 1121 tcol = cmap_i[rbuf3_i[ct2]]; 1122 #endif 1123 if (tcol) lens_i[row]++; 1124 } else { /* allcolumns */ 1125 lens_i[row]++; /* lens_i[row] += max2 ? */ 1126 } 1127 } 1128 } 1129 } 1130 } 1131 } 1132 ierr = PetscFree(r_waits3);CHKERRQ(ierr); 1133 if (nrqr) {ierr = MPI_Waitall(nrqr,s_waits3,s_status3);CHKERRMPI(ierr);} 1134 ierr = PetscFree2(r_status3,s_status3);CHKERRQ(ierr); 1135 ierr = PetscFree(s_waits3);CHKERRQ(ierr); 1136 1137 /* Create the submatrices */ 1138 for (i=0; i<ismax; i++) { 1139 PetscInt bs_tmp; 1140 if (ijonly) bs_tmp = 1; 1141 else bs_tmp = bs; 1142 1143 ierr = MatCreate(PETSC_COMM_SELF,submats+i);CHKERRQ(ierr); 1144 ierr = MatSetSizes(submats[i],nrow[i]*bs_tmp,ncol[i]*bs_tmp,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 1145 1146 ierr = MatSetType(submats[i],((PetscObject)A)->type_name);CHKERRQ(ierr); 1147 ierr = MatSeqBAIJSetPreallocation(submats[i],bs_tmp,0,lens[i]);CHKERRQ(ierr); 1148 ierr = MatSeqSBAIJSetPreallocation(submats[i],bs_tmp,0,lens[i]);CHKERRQ(ierr); /* this subroutine is used by SBAIJ routines */ 1149 1150 /* create struct Mat_SubSppt and attached it to submat */ 1151 ierr = PetscNew(&smat_i);CHKERRQ(ierr); 1152 subc = (Mat_SeqBAIJ*)submats[i]->data; 1153 subc->submatis1 = smat_i; 1154 1155 smat_i->destroy = submats[i]->ops->destroy; 1156 submats[i]->ops->destroy = MatDestroySubMatrix_SeqBAIJ; 1157 submats[i]->factortype = C->factortype; 1158 1159 smat_i->id = i; 1160 smat_i->nrqs = nrqs; 1161 smat_i->nrqr = nrqr; 1162 smat_i->rbuf1 = rbuf1; 1163 smat_i->rbuf2 = rbuf2; 1164 smat_i->rbuf3 = rbuf3; 1165 smat_i->sbuf2 = sbuf2; 1166 smat_i->req_source2 = req_source2; 1167 1168 smat_i->sbuf1 = sbuf1; 1169 smat_i->ptr = ptr; 1170 smat_i->tmp = tmp; 1171 smat_i->ctr = ctr; 1172 1173 smat_i->pa = pa; 1174 smat_i->req_size = req_size; 1175 smat_i->req_source1 = req_source1; 1176 1177 smat_i->allcolumns = allcolumns[i]; 1178 smat_i->allrows = allrows[i]; 1179 smat_i->singleis = PETSC_FALSE; 1180 smat_i->row2proc = row2proc[i]; 1181 smat_i->rmap = rmap[i]; 1182 smat_i->cmap = cmap[i]; 1183 } 1184 1185 if (!ismax) { /* Create dummy submats[0] for reuse struct subc */ 1186 ierr = MatCreate(PETSC_COMM_SELF,&submats[0]);CHKERRQ(ierr); 1187 ierr = MatSetSizes(submats[0],0,0,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 1188 ierr = MatSetType(submats[0],MATDUMMY);CHKERRQ(ierr); 1189 1190 /* create struct Mat_SubSppt and attached it to submat */ 1191 ierr = PetscNewLog(submats[0],&smat_i);CHKERRQ(ierr); 1192 submats[0]->data = (void*)smat_i; 1193 1194 smat_i->destroy = submats[0]->ops->destroy; 1195 submats[0]->ops->destroy = MatDestroySubMatrix_Dummy; 1196 submats[0]->factortype = C->factortype; 1197 1198 smat_i->id = 0; 1199 smat_i->nrqs = nrqs; 1200 smat_i->nrqr = nrqr; 1201 smat_i->rbuf1 = rbuf1; 1202 smat_i->rbuf2 = rbuf2; 1203 smat_i->rbuf3 = rbuf3; 1204 smat_i->sbuf2 = sbuf2; 1205 smat_i->req_source2 = req_source2; 1206 1207 smat_i->sbuf1 = sbuf1; 1208 smat_i->ptr = ptr; 1209 smat_i->tmp = tmp; 1210 smat_i->ctr = ctr; 1211 1212 smat_i->pa = pa; 1213 smat_i->req_size = req_size; 1214 smat_i->req_source1 = req_source1; 1215 1216 smat_i->allcolumns = PETSC_FALSE; 1217 smat_i->singleis = PETSC_FALSE; 1218 smat_i->row2proc = NULL; 1219 smat_i->rmap = NULL; 1220 smat_i->cmap = NULL; 1221 } 1222 1223 if (ismax) {ierr = PetscFree(lens[0]);CHKERRQ(ierr);} 1224 ierr = PetscFree(lens);CHKERRQ(ierr); 1225 ierr = PetscFree(sbuf_aj[0]);CHKERRQ(ierr); 1226 ierr = PetscFree(sbuf_aj);CHKERRQ(ierr); 1227 1228 } /* endof scall == MAT_INITIAL_MATRIX */ 1229 1230 /* Post recv matrix values */ 1231 if (!ijonly) { 1232 ierr = PetscObjectGetNewTag((PetscObject)C,&tag4);CHKERRQ(ierr); 1233 ierr = PetscMalloc1(nrqs+1,&rbuf4);CHKERRQ(ierr); 1234 ierr = PetscMalloc1(nrqs+1,&r_waits4);CHKERRQ(ierr); 1235 ierr = PetscMalloc1(nrqs+1,&r_status4);CHKERRQ(ierr); 1236 ierr = PetscMalloc1(nrqr+1,&s_status4);CHKERRQ(ierr); 1237 for (i=0; i<nrqs; ++i) { 1238 ierr = PetscMalloc1(rbuf2[i][0]*bs2,&rbuf4[i]);CHKERRQ(ierr); 1239 ierr = MPI_Irecv(rbuf4[i],rbuf2[i][0]*bs2,MPIU_SCALAR,req_source2[i],tag4,comm,r_waits4+i);CHKERRMPI(ierr); 1240 } 1241 1242 /* Allocate sending buffers for a->a, and send them off */ 1243 ierr = PetscMalloc1(nrqr+1,&sbuf_aa);CHKERRQ(ierr); 1244 for (i=0,j=0; i<nrqr; i++) j += req_size[i]; 1245 1246 ierr = PetscMalloc1((j+1)*bs2,&sbuf_aa[0]);CHKERRQ(ierr); 1247 for (i=1; i<nrqr; i++) sbuf_aa[i] = sbuf_aa[i-1] + req_size[i-1]*bs2; 1248 1249 ierr = PetscMalloc1(nrqr+1,&s_waits4);CHKERRQ(ierr); 1250 1251 for (i=0; i<nrqr; i++) { 1252 rbuf1_i = rbuf1[i]; 1253 sbuf_aa_i = sbuf_aa[i]; 1254 ct1 = 2*rbuf1_i[0]+1; 1255 ct2 = 0; 1256 for (j=1,max1=rbuf1_i[0]; j<=max1; j++) { 1257 kmax = rbuf1_i[2*j]; 1258 for (k=0; k<kmax; k++,ct1++) { 1259 row = rbuf1_i[ct1] - rstart; 1260 nzA = a_i[row+1] - a_i[row]; 1261 nzB = b_i[row+1] - b_i[row]; 1262 ncols = nzA + nzB; 1263 cworkB = b_j + b_i[row]; 1264 vworkA = a_a + a_i[row]*bs2; 1265 vworkB = b_a + b_i[row]*bs2; 1266 1267 /* load the column values for this row into vals*/ 1268 vals = sbuf_aa_i+ct2*bs2; 1269 for (l=0; l<nzB; l++) { 1270 if ((bmap[cworkB[l]]) < cstart) { 1271 ierr = PetscArraycpy(vals+l*bs2,vworkB+l*bs2,bs2);CHKERRQ(ierr); 1272 } else break; 1273 } 1274 imark = l; 1275 for (l=0; l<nzA; l++) { 1276 ierr = PetscArraycpy(vals+(imark+l)*bs2,vworkA+l*bs2,bs2);CHKERRQ(ierr); 1277 } 1278 for (l=imark; l<nzB; l++) { 1279 ierr = PetscArraycpy(vals+(nzA+l)*bs2,vworkB+l*bs2,bs2);CHKERRQ(ierr); 1280 } 1281 1282 ct2 += ncols; 1283 } 1284 } 1285 ierr = MPI_Isend(sbuf_aa_i,req_size[i]*bs2,MPIU_SCALAR,req_source1[i],tag4,comm,s_waits4+i);CHKERRMPI(ierr); 1286 } 1287 } 1288 1289 /* Assemble the matrices */ 1290 /* First assemble the local rows */ 1291 for (i=0; i<ismax; i++) { 1292 row2proc_i = row2proc[i]; 1293 subc = (Mat_SeqBAIJ*)submats[i]->data; 1294 imat_ilen = subc->ilen; 1295 imat_j = subc->j; 1296 imat_i = subc->i; 1297 imat_a = subc->a; 1298 1299 if (!allcolumns[i]) cmap_i = cmap[i]; 1300 rmap_i = rmap[i]; 1301 irow_i = irow[i]; 1302 jmax = nrow[i]; 1303 for (j=0; j<jmax; j++) { 1304 if (allrows[i]) row = j; 1305 else row = irow_i[j]; 1306 proc = row2proc_i[j]; 1307 1308 if (proc == rank) { 1309 1310 row = row - rstart; 1311 nzA = a_i[row+1] - a_i[row]; 1312 nzB = b_i[row+1] - b_i[row]; 1313 cworkA = a_j + a_i[row]; 1314 cworkB = b_j + b_i[row]; 1315 if (!ijonly) { 1316 vworkA = a_a + a_i[row]*bs2; 1317 vworkB = b_a + b_i[row]*bs2; 1318 } 1319 1320 if (allrows[i]) { 1321 row = row+rstart; 1322 } else { 1323 #if defined(PETSC_USE_CTABLE) 1324 ierr = PetscTableFind(rmap_i,row+rstart+1,&row);CHKERRQ(ierr); 1325 row--; 1326 1327 if (row < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"row not found in table"); 1328 #else 1329 row = rmap_i[row + rstart]; 1330 #endif 1331 } 1332 mat_i = imat_i[row]; 1333 if (!ijonly) mat_a = imat_a + mat_i*bs2; 1334 mat_j = imat_j + mat_i; 1335 ilen = imat_ilen[row]; 1336 1337 /* load the column indices for this row into cols*/ 1338 if (!allcolumns[i]) { 1339 for (l=0; l<nzB; l++) { 1340 if ((ctmp = bmap[cworkB[l]]) < cstart) { 1341 #if defined(PETSC_USE_CTABLE) 1342 ierr = PetscTableFind(cmap_i,ctmp+1,&tcol);CHKERRQ(ierr); 1343 if (tcol) { 1344 #else 1345 if ((tcol = cmap_i[ctmp])) { 1346 #endif 1347 *mat_j++ = tcol - 1; 1348 ierr = PetscArraycpy(mat_a,vworkB+l*bs2,bs2);CHKERRQ(ierr); 1349 mat_a += bs2; 1350 ilen++; 1351 } 1352 } else break; 1353 } 1354 imark = l; 1355 for (l=0; l<nzA; l++) { 1356 #if defined(PETSC_USE_CTABLE) 1357 ierr = PetscTableFind(cmap_i,cstart+cworkA[l]+1,&tcol);CHKERRQ(ierr); 1358 if (tcol) { 1359 #else 1360 if ((tcol = cmap_i[cstart + cworkA[l]])) { 1361 #endif 1362 *mat_j++ = tcol - 1; 1363 if (!ijonly) { 1364 ierr = PetscArraycpy(mat_a,vworkA+l*bs2,bs2);CHKERRQ(ierr); 1365 mat_a += bs2; 1366 } 1367 ilen++; 1368 } 1369 } 1370 for (l=imark; l<nzB; l++) { 1371 #if defined(PETSC_USE_CTABLE) 1372 ierr = PetscTableFind(cmap_i,bmap[cworkB[l]]+1,&tcol);CHKERRQ(ierr); 1373 if (tcol) { 1374 #else 1375 if ((tcol = cmap_i[bmap[cworkB[l]]])) { 1376 #endif 1377 *mat_j++ = tcol - 1; 1378 if (!ijonly) { 1379 ierr = PetscArraycpy(mat_a,vworkB+l*bs2,bs2);CHKERRQ(ierr); 1380 mat_a += bs2; 1381 } 1382 ilen++; 1383 } 1384 } 1385 } else { /* allcolumns */ 1386 for (l=0; l<nzB; l++) { 1387 if ((ctmp = bmap[cworkB[l]]) < cstart) { 1388 *mat_j++ = ctmp; 1389 ierr = PetscArraycpy(mat_a,vworkB+l*bs2,bs2);CHKERRQ(ierr); 1390 mat_a += bs2; 1391 ilen++; 1392 } else break; 1393 } 1394 imark = l; 1395 for (l=0; l<nzA; l++) { 1396 *mat_j++ = cstart+cworkA[l]; 1397 if (!ijonly) { 1398 ierr = PetscArraycpy(mat_a,vworkA+l*bs2,bs2);CHKERRQ(ierr); 1399 mat_a += bs2; 1400 } 1401 ilen++; 1402 } 1403 for (l=imark; l<nzB; l++) { 1404 *mat_j++ = bmap[cworkB[l]]; 1405 if (!ijonly) { 1406 ierr = PetscArraycpy(mat_a,vworkB+l*bs2,bs2);CHKERRQ(ierr); 1407 mat_a += bs2; 1408 } 1409 ilen++; 1410 } 1411 } 1412 imat_ilen[row] = ilen; 1413 } 1414 } 1415 } 1416 1417 /* Now assemble the off proc rows */ 1418 if (!ijonly) { 1419 ierr = MPI_Waitall(nrqs,r_waits4,r_status4);CHKERRMPI(ierr); 1420 } 1421 for (tmp2=0; tmp2<nrqs; tmp2++) { 1422 sbuf1_i = sbuf1[pa[tmp2]]; 1423 jmax = sbuf1_i[0]; 1424 ct1 = 2*jmax + 1; 1425 ct2 = 0; 1426 rbuf2_i = rbuf2[tmp2]; 1427 rbuf3_i = rbuf3[tmp2]; 1428 if (!ijonly) rbuf4_i = rbuf4[tmp2]; 1429 for (j=1; j<=jmax; j++) { 1430 is_no = sbuf1_i[2*j-1]; 1431 rmap_i = rmap[is_no]; 1432 if (!allcolumns[is_no]) cmap_i = cmap[is_no]; 1433 subc = (Mat_SeqBAIJ*)submats[is_no]->data; 1434 imat_ilen = subc->ilen; 1435 imat_j = subc->j; 1436 imat_i = subc->i; 1437 if (!ijonly) imat_a = subc->a; 1438 max1 = sbuf1_i[2*j]; 1439 for (k=0; k<max1; k++,ct1++) { /* for each recved block row */ 1440 row = sbuf1_i[ct1]; 1441 1442 if (allrows[is_no]) { 1443 row = sbuf1_i[ct1]; 1444 } else { 1445 #if defined(PETSC_USE_CTABLE) 1446 ierr = PetscTableFind(rmap_i,row+1,&row);CHKERRQ(ierr); 1447 row--; 1448 if (row < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"row not found in table"); 1449 #else 1450 row = rmap_i[row]; 1451 #endif 1452 } 1453 ilen = imat_ilen[row]; 1454 mat_i = imat_i[row]; 1455 if (!ijonly) mat_a = imat_a + mat_i*bs2; 1456 mat_j = imat_j + mat_i; 1457 max2 = rbuf2_i[ct1]; 1458 if (!allcolumns[is_no]) { 1459 for (l=0; l<max2; l++,ct2++) { 1460 #if defined(PETSC_USE_CTABLE) 1461 ierr = PetscTableFind(cmap_i,rbuf3_i[ct2]+1,&tcol);CHKERRQ(ierr); 1462 #else 1463 tcol = cmap_i[rbuf3_i[ct2]]; 1464 #endif 1465 if (tcol) { 1466 *mat_j++ = tcol - 1; 1467 if (!ijonly) { 1468 ierr = PetscArraycpy(mat_a,rbuf4_i+ct2*bs2,bs2);CHKERRQ(ierr); 1469 mat_a += bs2; 1470 } 1471 ilen++; 1472 } 1473 } 1474 } else { /* allcolumns */ 1475 for (l=0; l<max2; l++,ct2++) { 1476 *mat_j++ = rbuf3_i[ct2]; /* same global column index of C */ 1477 if (!ijonly) { 1478 ierr = PetscArraycpy(mat_a,rbuf4_i+ct2*bs2,bs2);CHKERRQ(ierr); 1479 mat_a += bs2; 1480 } 1481 ilen++; 1482 } 1483 } 1484 imat_ilen[row] = ilen; 1485 } 1486 } 1487 } 1488 1489 if (!iscsorted) { /* sort column indices of the rows */ 1490 MatScalar *work; 1491 1492 ierr = PetscMalloc1(bs2,&work);CHKERRQ(ierr); 1493 for (i=0; i<ismax; i++) { 1494 subc = (Mat_SeqBAIJ*)submats[i]->data; 1495 imat_ilen = subc->ilen; 1496 imat_j = subc->j; 1497 imat_i = subc->i; 1498 if (!ijonly) imat_a = subc->a; 1499 if (allcolumns[i]) continue; 1500 1501 jmax = nrow[i]; 1502 for (j=0; j<jmax; j++) { 1503 mat_i = imat_i[j]; 1504 mat_j = imat_j + mat_i; 1505 ilen = imat_ilen[j]; 1506 if (ijonly) { 1507 ierr = PetscSortInt(ilen,mat_j);CHKERRQ(ierr); 1508 } else { 1509 mat_a = imat_a + mat_i*bs2; 1510 ierr = PetscSortIntWithDataArray(ilen,mat_j,mat_a,bs2*sizeof(MatScalar),work);CHKERRQ(ierr); 1511 } 1512 } 1513 } 1514 ierr = PetscFree(work);CHKERRQ(ierr); 1515 } 1516 1517 if (!ijonly) { 1518 ierr = PetscFree(r_status4);CHKERRQ(ierr); 1519 ierr = PetscFree(r_waits4);CHKERRQ(ierr); 1520 if (nrqr) {ierr = MPI_Waitall(nrqr,s_waits4,s_status4);CHKERRMPI(ierr);} 1521 ierr = PetscFree(s_waits4);CHKERRQ(ierr); 1522 ierr = PetscFree(s_status4);CHKERRQ(ierr); 1523 } 1524 1525 /* Restore the indices */ 1526 for (i=0; i<ismax; i++) { 1527 if (!allrows[i]) { 1528 ierr = ISRestoreIndices(isrow[i],irow+i);CHKERRQ(ierr); 1529 } 1530 if (!allcolumns[i]) { 1531 ierr = ISRestoreIndices(iscol[i],icol+i);CHKERRQ(ierr); 1532 } 1533 } 1534 1535 for (i=0; i<ismax; i++) { 1536 ierr = MatAssemblyBegin(submats[i],MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1537 ierr = MatAssemblyEnd(submats[i],MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1538 } 1539 1540 ierr = PetscFree5(*(PetscInt***)&irow,*(PetscInt***)&icol,nrow,ncol,issorted);CHKERRQ(ierr); 1541 ierr = PetscFree5(row2proc,cmap,rmap,allcolumns,allrows);CHKERRQ(ierr); 1542 1543 if (!ijonly) { 1544 ierr = PetscFree(sbuf_aa[0]);CHKERRQ(ierr); 1545 ierr = PetscFree(sbuf_aa);CHKERRQ(ierr); 1546 1547 for (i=0; i<nrqs; ++i) { 1548 ierr = PetscFree(rbuf4[i]);CHKERRQ(ierr); 1549 } 1550 ierr = PetscFree(rbuf4);CHKERRQ(ierr); 1551 } 1552 c->ijonly = PETSC_FALSE; /* set back to the default */ 1553 PetscFunctionReturn(0); 1554 } 1555