1 /*$Id: baijov.c,v 1.38 1999/10/13 20:37:30 bsmith Exp bsmith $*/ 2 3 /* 4 Routines to compute overlapping regions of a parallel MPI matrix 5 and to find submatrices that were shared across processors. 6 */ 7 #include "src/mat/impls/baij/mpi/mpibaij.h" 8 #include "bitarray.h" 9 10 static int MatIncreaseOverlap_MPIBAIJ_Once(Mat, int, IS *); 11 static int MatIncreaseOverlap_MPIBAIJ_Local(Mat , int , char **,int*, int**); 12 static int MatIncreaseOverlap_MPIBAIJ_Receive(Mat , int, int **, int**, int* ); 13 extern int MatGetRow_MPIBAIJ(Mat,int,int*,int**,Scalar**); 14 extern int MatRestoreRow_MPIBAIJ(Mat,int,int*,int**,Scalar**); 15 16 #undef __FUNC__ 17 #define __FUNC__ "MatCompressIndicesGeneral_MPIBAIJ" 18 static int MatCompressIndicesGeneral_MPIBAIJ(Mat C, int imax, IS *is_in, IS *is_out) 19 { 20 Mat_MPIBAIJ *baij = (Mat_MPIBAIJ *) C->data; 21 int ierr,isz,bs = baij->bs,Nbs,n,i,j,*idx,*nidx,ival; 22 BTPetsc table; 23 24 PetscFunctionBegin; 25 Nbs = baij->Nbs; 26 nidx = (int *) PetscMalloc((Nbs+1)*sizeof(int));CHKPTRQ(nidx); 27 ierr = PetscBTCreate(Nbs,table);CHKERRQ(ierr); 28 29 for (i=0; i<imax; i++) { 30 isz = 0; 31 ierr = PetscBTMemzero(Nbs,table);CHKERRQ(ierr); 32 ierr = ISGetIndices(is_in[i],&idx);CHKERRQ(ierr); 33 ierr = ISGetSize(is_in[i],&n);CHKERRQ(ierr); 34 for (j=0; j<n ; j++) { 35 ival = idx[j]/bs; /* convert the indices into block indices */ 36 if (ival>Nbs) SETERRQ(PETSC_ERR_ARG_OUTOFRANGE,0,"index greater than mat-dim"); 37 if(!PetscBTLoopupSet(table, ival)) { nidx[isz++] = ival;} 38 } 39 ierr = ISRestoreIndices(is_in[i],&idx);CHKERRQ(ierr); 40 ierr = ISCreateGeneral(PETSC_COMM_SELF, isz, nidx, (is_out+i));CHKERRQ(ierr); 41 } 42 ierr = PetscBTDestroy(table);CHKERRQ(ierr); 43 ierr = PetscFree(nidx);CHKERRQ(ierr); 44 PetscFunctionReturn(0); 45 } 46 47 #undef __FUNC__ 48 #define __FUNC__ "MatCompressIndicesSorted_MPIBAIJ" 49 static int MatCompressIndicesSorted_MPIBAIJ(Mat C, int imax, IS *is_in, IS *is_out) 50 { 51 Mat_MPIBAIJ *baij = (Mat_MPIBAIJ *) C->data; 52 int ierr,bs=baij->bs,i,j,k,val,n,*idx,*nidx,Nbs=baij->Nbs,*idx_local; 53 PetscTruth flg; 54 55 PetscFunctionBegin; 56 for (i=0; i<imax; i++) { 57 ierr = ISSorted(is_in[i],&flg);CHKERRQ(ierr); 58 if (!flg) SETERRQ(PETSC_ERR_ARG_WRONGSTATE,0,"Indices are not sorted"); 59 } 60 nidx = (int *) PetscMalloc((Nbs+1)*sizeof(int));CHKPTRQ(nidx); 61 /* Now check if the indices are in block order */ 62 for (i=0; i<imax; i++) { 63 ierr = ISGetIndices(is_in[i],&idx);CHKERRQ(ierr); 64 ierr = ISGetSize(is_in[i],&n);CHKERRQ(ierr); 65 if ( n%bs !=0 ) SETERRA(1,0,"Indices are not block ordered"); 66 67 n = n/bs; /* The reduced index size */ 68 idx_local = idx; 69 for (j=0; j<n ; j++) { 70 val = idx_local[0]; 71 if (val%bs != 0) SETERRA(1,0,"Indices are not block ordered"); 72 for (k=0; k<bs; k++) { 73 if ( val+k != idx_local[k]) SETERRA(1,0,"Indices are not block ordered"); 74 } 75 nidx[j] = val/bs; 76 idx_local +=bs; 77 } 78 ierr = ISRestoreIndices(is_in[i],&idx);CHKERRQ(ierr); 79 ierr = ISCreateGeneral(PETSC_COMM_SELF,n,nidx,(is_out+i));CHKERRQ(ierr); 80 } 81 ierr = PetscFree(nidx);CHKERRQ(ierr); 82 PetscFunctionReturn(0); 83 } 84 85 #undef __FUNC__ 86 #define __FUNC__ "MatExpandIndices_MPIBAIJ" 87 static int MatExpandIndices_MPIBAIJ(Mat C, int imax, IS *is_in, IS *is_out) 88 { 89 Mat_MPIBAIJ *baij = (Mat_MPIBAIJ *) C->data; 90 int ierr,bs = baij->bs,Nbs,n,i,j,k,*idx,*nidx; 91 92 PetscFunctionBegin; 93 Nbs = baij->Nbs; 94 95 nidx = (int *) PetscMalloc((Nbs*bs+1)*sizeof(int));CHKPTRQ(nidx); 96 97 for ( i=0; i<imax; i++ ) { 98 ierr = ISGetIndices(is_in[i],&idx);CHKERRQ(ierr); 99 ierr = ISGetSize(is_in[i],&n);CHKERRQ(ierr); 100 for (j=0; j<n ; ++j){ 101 for (k=0; k<bs; k++) 102 nidx[j*bs+k] = idx[j]*bs+k; 103 } 104 ierr = ISRestoreIndices(is_in[i],&idx);CHKERRQ(ierr); 105 ierr = ISCreateGeneral(PETSC_COMM_SELF, n*bs, nidx, (is_out+i));CHKERRQ(ierr); 106 } 107 ierr = PetscFree(nidx);CHKERRQ(ierr); 108 PetscFunctionReturn(0); 109 } 110 111 112 #undef __FUNC__ 113 #define __FUNC__ "MatIncreaseOverlap_MPIBAIJ" 114 int MatIncreaseOverlap_MPIBAIJ(Mat C, int imax, IS *is, int ov) 115 { 116 int i, ierr; 117 IS *is_new; 118 119 PetscFunctionBegin; 120 is_new = (IS *)PetscMalloc(imax*sizeof(IS));CHKPTRQ(is_new); 121 /* Convert the indices into block format */ 122 ierr = MatCompressIndicesGeneral_MPIBAIJ(C, imax, is,is_new);CHKERRQ(ierr); 123 if (ov < 0){ SETERRQ(PETSC_ERR_ARG_OUTOFRANGE,0,"Negative overlap specified\n");} 124 for (i=0; i<ov; ++i) { 125 ierr = MatIncreaseOverlap_MPIBAIJ_Once(C, imax, is_new);CHKERRQ(ierr); 126 } 127 for (i=0; i<imax; i++) {ierr = ISDestroy(is[i]);CHKERRQ(ierr);} 128 ierr = MatExpandIndices_MPIBAIJ(C, imax, is_new,is);CHKERRQ(ierr); 129 for (i=0; i<imax; i++) {ierr = ISDestroy(is_new[i]);CHKERRQ(ierr);} 130 ierr = PetscFree(is_new);CHKERRQ(ierr); 131 PetscFunctionReturn(0); 132 } 133 134 /* 135 Sample message format: 136 If a processor A wants processor B to process some elements corresponding 137 to index sets 1s[1], is[5] 138 mesg [0] = 2 ( no of index sets in the mesg) 139 ----------- 140 mesg [1] = 1 => is[1] 141 mesg [2] = sizeof(is[1]); 142 ----------- 143 mesg [5] = 5 => is[5] 144 mesg [6] = sizeof(is[5]); 145 ----------- 146 mesg [7] 147 mesg [n] datas[1] 148 ----------- 149 mesg[n+1] 150 mesg[m] data(is[5]) 151 ----------- 152 153 Notes: 154 nrqs - no of requests sent (or to be sent out) 155 nrqr - no of requests recieved (which have to be or which have been processed 156 */ 157 #undef __FUNC__ 158 #define __FUNC__ "MatIncreaseOverlap_MPIBAIJ_Once" 159 static int MatIncreaseOverlap_MPIBAIJ_Once(Mat C, int imax, IS *is) 160 { 161 Mat_MPIBAIJ *c = (Mat_MPIBAIJ *) C->data; 162 int **idx, *n, *w1, *w2, *w3, *w4, *rtable,**data,len,*idx_i; 163 int size,rank,Mbs,i,j,k,ierr,**rbuf,row,proc,nrqs,msz,**outdat,**ptr; 164 int *ctr,*pa,tag,*tmp,bsz,nrqr,*isz,*isz1,**xdata,bsz1,**rbuf2; 165 BTPetsc *table; 166 MPI_Comm comm; 167 MPI_Request *s_waits1,*r_waits1,*s_waits2,*r_waits2; 168 MPI_Status *s_status,*recv_status; 169 170 PetscFunctionBegin; 171 comm = C->comm; 172 tag = C->tag; 173 size = c->size; 174 rank = c->rank; 175 Mbs = c->Mbs; 176 177 len = (imax+1)*sizeof(int *) + (imax + Mbs)*sizeof(int); 178 idx = (int **) PetscMalloc(len);CHKPTRQ(idx); 179 n = (int *) (idx + imax); 180 rtable = n + imax; 181 182 for (i=0; i<imax; i++) { 183 ierr = ISGetIndices(is[i],&idx[i]);CHKERRQ(ierr); 184 ierr = ISGetSize(is[i],&n[i]);CHKERRQ(ierr); 185 } 186 187 /* Create hash table for the mapping :row -> proc*/ 188 for (i=0,j=0; i<size; i++) { 189 len = c->rowners[i+1]; 190 for (; j<len; j++) { 191 rtable[j] = i; 192 } 193 } 194 195 /* evaluate communication - mesg to who, length of mesg, and buffer space 196 required. Based on this, buffers are allocated, and data copied into them*/ 197 w1 = (int *)PetscMalloc(size*4*sizeof(int));CHKPTRQ(w1);/* mesg size */ 198 w2 = w1 + size; /* if w2[i] marked, then a message to proc i*/ 199 w3 = w2 + size; /* no of IS that needs to be sent to proc i */ 200 w4 = w3 + size; /* temp work space used in determining w1, w2, w3 */ 201 ierr = PetscMemzero(w1,size*3*sizeof(int));CHKERRQ(ierr); /* initialise work vector*/ 202 for (i=0; i<imax; i++) { 203 ierr = PetscMemzero(w4,size*sizeof(int));CHKERRQ(ierr); /* initialise work vector*/ 204 idx_i = idx[i]; 205 len = n[i]; 206 for (j=0; j<len; j++) { 207 row = idx_i[j]; 208 if (row < 0) { 209 SETERRQ(1,1,"Index set cannot have negative entries"); 210 } 211 proc = rtable[row]; 212 w4[proc]++; 213 } 214 for (j=0; j<size; j++){ 215 if (w4[j]) { w1[j] += w4[j]; w3[j]++;} 216 } 217 } 218 219 nrqs = 0; /* no of outgoing messages */ 220 msz = 0; /* total mesg length (for all proc */ 221 w1[rank] = 0; /* no mesg sent to intself */ 222 w3[rank] = 0; 223 for ( i=0; i<size; i++) { 224 if (w1[i]) {w2[i] = 1; nrqs++;} /* there exists a message to proc i */ 225 } 226 /* pa - is list of processors to communicate with */ 227 pa = (int *)PetscMalloc((nrqs+1)*sizeof(int));CHKPTRQ(pa); 228 for (i=0,j=0; i<size; i++) { 229 if (w1[i]) {pa[j] = i; j++;} 230 } 231 232 /* Each message would have a header = 1 + 2*(no of IS) + data */ 233 for (i=0; i<nrqs; i++) { 234 j = pa[i]; 235 w1[j] += w2[j] + 2*w3[j]; 236 msz += w1[j]; 237 } 238 239 240 /* Do a global reduction to determine how many messages to expect*/ 241 { 242 int *rw1; 243 rw1 = (int *) PetscMalloc(2*size*sizeof(int));CHKPTRQ(rw1); 244 ierr = MPI_Allreduce(w1, rw1, 2*size, MPI_INT, PetscMaxSum_Op, comm);CHKERRQ(ierr); 245 bsz = rw1[rank]; 246 nrqr = rw1[size+rank]; 247 ierr = PetscFree(rw1);CHKERRQ(ierr); 248 } 249 250 /* Allocate memory for recv buffers . Prob none if nrqr = 0 ???? */ 251 len = (nrqr+1)*sizeof(int*) + nrqr*bsz*sizeof(int); 252 rbuf = (int**) PetscMalloc(len);CHKPTRQ(rbuf); 253 rbuf[0] = (int *) (rbuf + nrqr); 254 for (i=1; i<nrqr; ++i) rbuf[i] = rbuf[i-1] + bsz; 255 256 /* Post the receives */ 257 r_waits1 = (MPI_Request *) PetscMalloc((nrqr+1)*sizeof(MPI_Request));CHKPTRQ(r_waits1); 258 for (i=0; i<nrqr; ++i) { 259 ierr = MPI_Irecv(rbuf[i],bsz,MPI_INT,MPI_ANY_SOURCE,tag,comm,r_waits1+i);CHKERRQ(ierr); 260 } 261 262 /* Allocate Memory for outgoing messages */ 263 len = 2*size*sizeof(int*) + (size+msz)*sizeof(int); 264 outdat = (int **)PetscMalloc(len);CHKPTRQ(outdat); 265 ptr = outdat + size; /* Pointers to the data in outgoing buffers */ 266 ierr = PetscMemzero(outdat,2*size*sizeof(int*));CHKERRQ(ierr); 267 tmp = (int *) (outdat + 2*size); 268 ctr = tmp + msz; 269 270 { 271 int *iptr = tmp,ict = 0; 272 for (i=0; i<nrqs; i++) { 273 j = pa[i]; 274 iptr += ict; 275 outdat[j] = iptr; 276 ict = w1[j]; 277 } 278 } 279 280 /* Form the outgoing messages */ 281 /*plug in the headers*/ 282 for (i=0; i<nrqs; i++) { 283 j = pa[i]; 284 outdat[j][0] = 0; 285 ierr = PetscMemzero(outdat[j]+1,2*w3[j]*sizeof(int));CHKERRQ(ierr); 286 ptr[j] = outdat[j] + 2*w3[j] + 1; 287 } 288 289 /* Memory for doing local proc's work*/ 290 { 291 int *d_p; 292 char *t_p; 293 294 len = (imax)*(sizeof(BTPetsc) + sizeof(int *) + sizeof(int)) + 295 (Mbs)*imax*sizeof(int) + (Mbs/BITSPERBYTE+1)*imax*sizeof(char) + 1; 296 table = (BTPetsc *)PetscMalloc(len);CHKPTRQ(table); 297 ierr = PetscMemzero(table,len);CHKERRQ(ierr); 298 data = (int **)(table + imax); 299 isz = (int *)(data + imax); 300 d_p = (int *)(isz + imax); 301 t_p = (char *)(d_p + Mbs*imax); 302 for (i=0; i<imax; i++) { 303 table[i] = t_p + (Mbs/BITSPERBYTE+1)*i; 304 data[i] = d_p + (Mbs)*i; 305 } 306 } 307 308 /* Parse the IS and update local tables and the outgoing buf with the data*/ 309 { 310 int n_i,*data_i,isz_i,*outdat_j,ctr_j; 311 BTPetsc table_i; 312 313 for (i=0; i<imax; i++) { 314 ierr = PetscMemzero(ctr,size*sizeof(int));CHKERRQ(ierr); 315 n_i = n[i]; 316 table_i = table[i]; 317 idx_i = idx[i]; 318 data_i = data[i]; 319 isz_i = isz[i]; 320 for (j=0; j<n_i; j++) { /* parse the indices of each IS */ 321 row = idx_i[j]; 322 proc = rtable[row]; 323 if (proc != rank) { /* copy to the outgoing buffer */ 324 ctr[proc]++; 325 *ptr[proc] = row; 326 ptr[proc]++; 327 } 328 else { /* Update the local table */ 329 if (!PetscBTLoopupSet(table_i,row)) { data_i[isz_i++] = row;} 330 } 331 } 332 /* Update the headers for the current IS */ 333 for (j=0; j<size; j++) { /* Can Optimise this loop by using pa[] */ 334 if ((ctr_j = ctr[j])) { 335 outdat_j = outdat[j]; 336 k = ++outdat_j[0]; 337 outdat_j[2*k] = ctr_j; 338 outdat_j[2*k-1] = i; 339 } 340 } 341 isz[i] = isz_i; 342 } 343 } 344 345 346 347 /* Now post the sends */ 348 s_waits1 = (MPI_Request *) PetscMalloc((nrqs+1)*sizeof(MPI_Request));CHKPTRQ(s_waits1); 349 for (i=0; i<nrqs; ++i) { 350 j = pa[i]; 351 ierr = MPI_Isend(outdat[j], w1[j], MPI_INT, j, tag, comm, s_waits1+i);CHKERRQ(ierr); 352 } 353 354 /* No longer need the original indices*/ 355 for (i=0; i<imax; ++i) { 356 ierr = ISRestoreIndices(is[i], idx+i);CHKERRQ(ierr); 357 } 358 ierr = PetscFree(idx);CHKERRQ(ierr); 359 360 for (i=0; i<imax; ++i) { 361 ierr = ISDestroy(is[i]);CHKERRQ(ierr); 362 } 363 364 /* Do Local work*/ 365 ierr = MatIncreaseOverlap_MPIBAIJ_Local(C,imax,table,isz,data);CHKERRQ(ierr); 366 367 /* Receive messages*/ 368 { 369 int index; 370 371 recv_status = (MPI_Status *) PetscMalloc((nrqr+1)*sizeof(MPI_Status));CHKPTRQ(recv_status); 372 for (i=0; i<nrqr; ++i) { 373 ierr = MPI_Waitany(nrqr, r_waits1, &index, recv_status+i);CHKERRQ(ierr); 374 } 375 376 s_status = (MPI_Status *) PetscMalloc((nrqs+1)*sizeof(MPI_Status));CHKPTRQ(s_status); 377 ierr = MPI_Waitall(nrqs,s_waits1,s_status);CHKERRQ(ierr); 378 } 379 380 /* Phase 1 sends are complete - deallocate buffers */ 381 ierr = PetscFree(outdat);CHKERRQ(ierr); 382 ierr = PetscFree(w1);CHKERRQ(ierr); 383 384 xdata = (int **)PetscMalloc((nrqr+1)*sizeof(int *));CHKPTRQ(xdata); 385 isz1 = (int *)PetscMalloc((nrqr+1)*sizeof(int));CHKPTRQ(isz1); 386 ierr = MatIncreaseOverlap_MPIBAIJ_Receive(C,nrqr,rbuf,xdata,isz1);CHKERRQ(ierr); 387 ierr = PetscFree(rbuf);CHKERRQ(ierr); 388 389 /* Send the data back*/ 390 /* Do a global reduction to know the buffer space req for incoming messages*/ 391 { 392 int *rw1, *rw2; 393 394 rw1 = (int *)PetscMalloc(2*size*sizeof(int));CHKPTRQ(rw1); 395 ierr = PetscMemzero(rw1,2*size*sizeof(int));CHKERRQ(ierr); 396 rw2 = rw1+size; 397 for (i=0; i<nrqr; ++i) { 398 proc = recv_status[i].MPI_SOURCE; 399 rw1[proc] = isz1[i]; 400 } 401 402 ierr = MPI_Allreduce(rw1, rw2, size, MPI_INT, MPI_MAX, comm);CHKERRQ(ierr); 403 bsz1 = rw2[rank]; 404 ierr = PetscFree(rw1);CHKERRQ(ierr); 405 } 406 407 /* Allocate buffers*/ 408 409 /* Allocate memory for recv buffers. Prob none if nrqr = 0 ???? */ 410 len = (nrqs+1)*sizeof(int*) + nrqs*bsz1*sizeof(int); 411 rbuf2 = (int**) PetscMalloc(len);CHKPTRQ(rbuf2); 412 rbuf2[0] = (int *) (rbuf2 + nrqs); 413 for (i=1; i<nrqs; ++i) rbuf2[i] = rbuf2[i-1] + bsz1; 414 415 /* Post the receives */ 416 r_waits2 = (MPI_Request *)PetscMalloc((nrqs+1)*sizeof(MPI_Request));CHKPTRQ(r_waits2); 417 for (i=0; i<nrqs; ++i) { 418 ierr = MPI_Irecv(rbuf2[i], bsz1, MPI_INT, MPI_ANY_SOURCE, tag, comm, r_waits2+i);CHKERRQ(ierr); 419 } 420 421 /* Now post the sends */ 422 s_waits2 = (MPI_Request *) PetscMalloc((nrqr+1)*sizeof(MPI_Request));CHKPTRQ(s_waits2); 423 for (i=0; i<nrqr; ++i) { 424 j = recv_status[i].MPI_SOURCE; 425 ierr = MPI_Isend( xdata[i], isz1[i], MPI_INT, j, tag, comm, s_waits2+i);CHKERRQ(ierr); 426 } 427 428 /* receive work done on other processors*/ 429 { 430 int index, is_no, ct1, max,*rbuf2_i,isz_i,*data_i,jmax; 431 BTPetsc table_i; 432 MPI_Status *status2; 433 434 status2 = (MPI_Status *) PetscMalloc((nrqs+1)*sizeof(MPI_Status));CHKPTRQ(status2); 435 436 for (i=0; i<nrqs; ++i) { 437 ierr = MPI_Waitany(nrqs, r_waits2, &index, status2+i);CHKERRQ(ierr); 438 /* Process the message*/ 439 rbuf2_i = rbuf2[index]; 440 ct1 = 2*rbuf2_i[0]+1; 441 jmax = rbuf2[index][0]; 442 for (j=1; j<=jmax; j++) { 443 max = rbuf2_i[2*j]; 444 is_no = rbuf2_i[2*j-1]; 445 isz_i = isz[is_no]; 446 data_i = data[is_no]; 447 table_i = table[is_no]; 448 for (k=0; k<max; k++,ct1++) { 449 row = rbuf2_i[ct1]; 450 if (!PetscBTLoopupSet(table_i,row)) { data_i[isz_i++] = row;} 451 } 452 isz[is_no] = isz_i; 453 } 454 } 455 ierr = MPI_Waitall(nrqr,s_waits2,status2);CHKERRQ(ierr); 456 ierr = PetscFree(status2); CHKERRQ(ierr); 457 } 458 459 for (i=0; i<imax; ++i) { 460 ierr = ISCreateGeneral(PETSC_COMM_SELF, isz[i], data[i], is+i);CHKERRQ(ierr); 461 } 462 463 ierr = PetscFree(pa);CHKERRQ(ierr); 464 ierr = PetscFree(rbuf2);CHKERRQ(ierr); 465 ierr = PetscFree(s_waits1);CHKERRQ(ierr); 466 ierr = PetscFree(r_waits1);CHKERRQ(ierr); 467 ierr = PetscFree(s_waits2);CHKERRQ(ierr); 468 ierr = PetscFree(r_waits2);CHKERRQ(ierr); 469 ierr = PetscFree(table);CHKERRQ(ierr); 470 ierr = PetscFree(s_status);CHKERRQ(ierr); 471 ierr = PetscFree(recv_status);CHKERRQ(ierr); 472 ierr = PetscFree(xdata[0]);CHKERRQ(ierr); 473 ierr = PetscFree(xdata);CHKERRQ(ierr); 474 ierr = PetscFree(isz1);CHKERRQ(ierr); 475 PetscFunctionReturn(0); 476 } 477 478 #undef __FUNC__ 479 #define __FUNC__ "MatIncreaseOverlap_MPIBAIJ_Local" 480 /* 481 MatIncreaseOverlap_MPIBAIJ_Local - Called by MatincreaseOverlap, to do 482 the work on the local processor. 483 484 Inputs: 485 C - MAT_MPIBAIJ; 486 imax - total no of index sets processed at a time; 487 table - an array of char - size = Mbs bits. 488 489 Output: 490 isz - array containing the count of the solution elements correspondign 491 to each index set; 492 data - pointer to the solutions 493 */ 494 static int MatIncreaseOverlap_MPIBAIJ_Local(Mat C,int imax,BTPetsc *table,int *isz,int **data) 495 { 496 Mat_MPIBAIJ *c = (Mat_MPIBAIJ *) C->data; 497 Mat A = c->A, B = c->B; 498 Mat_SeqBAIJ *a = (Mat_SeqBAIJ*)A->data,*b = (Mat_SeqBAIJ*)B->data; 499 int start, end, val, max, rstart,cstart,*ai, *aj; 500 int *bi, *bj, *garray, i, j, k, row,*data_i,isz_i; 501 BTPetsc table_i; 502 503 PetscFunctionBegin; 504 rstart = c->rstart; 505 cstart = c->cstart; 506 ai = a->i; 507 aj = a->j; 508 bi = b->i; 509 bj = b->j; 510 garray = c->garray; 511 512 513 for (i=0; i<imax; i++) { 514 data_i = data[i]; 515 table_i = table[i]; 516 isz_i = isz[i]; 517 for (j=0, max=isz[i]; j<max; j++) { 518 row = data_i[j] - rstart; 519 start = ai[row]; 520 end = ai[row+1]; 521 for (k=start; k<end; k++) { /* Amat */ 522 val = aj[k] + cstart; 523 if (!PetscBTLoopupSet(table_i,val)) { data_i[isz_i++] = val;} 524 } 525 start = bi[row]; 526 end = bi[row+1]; 527 for (k=start; k<end; k++) { /* Bmat */ 528 val = garray[bj[k]]; 529 if (!PetscBTLoopupSet(table_i,val)) { data_i[isz_i++] = val;} 530 } 531 } 532 isz[i] = isz_i; 533 } 534 PetscFunctionReturn(0); 535 } 536 #undef __FUNC__ 537 #define __FUNC__ "MatIncreaseOverlap_MPIBAIJ_Receive" 538 /* 539 MatIncreaseOverlap_MPIBAIJ_Receive - Process the recieved messages, 540 and return the output 541 542 Input: 543 C - the matrix 544 nrqr - no of messages being processed. 545 rbuf - an array of pointers to the recieved requests 546 547 Output: 548 xdata - array of messages to be sent back 549 isz1 - size of each message 550 551 For better efficiency perhaps we should malloc seperately each xdata[i], 552 then if a remalloc is required we need only copy the data for that one row 553 rather then all previous rows as it is now where a single large chunck of 554 memory is used. 555 556 */ 557 static int MatIncreaseOverlap_MPIBAIJ_Receive(Mat C,int nrqr,int **rbuf,int **xdata, int * isz1) 558 { 559 Mat_MPIBAIJ *c = (Mat_MPIBAIJ *) C->data; 560 Mat A = c->A, B = c->B; 561 Mat_SeqBAIJ *a = (Mat_SeqBAIJ*)A->data,*b = (Mat_SeqBAIJ*)B->data; 562 int rstart,cstart,*ai, *aj, *bi, *bj, *garray, i, j, k; 563 int row,total_sz,ct, ct1, ct2, ct3,mem_estimate, oct2, l, start, end; 564 int val, max1, max2, rank, Mbs, no_malloc =0, *tmp, new_estimate, ctr; 565 int *rbuf_i,kmax,rbuf_0,ierr; 566 BTPetsc xtable; 567 568 PetscFunctionBegin; 569 rank = c->rank; 570 Mbs = c->Mbs; 571 rstart = c->rstart; 572 cstart = c->cstart; 573 ai = a->i; 574 aj = a->j; 575 bi = b->i; 576 bj = b->j; 577 garray = c->garray; 578 579 580 for (i=0,ct=0,total_sz=0; i<nrqr; ++i) { 581 rbuf_i = rbuf[i]; 582 rbuf_0 = rbuf_i[0]; 583 ct += rbuf_0; 584 for (j=1; j<=rbuf_0; j++) { total_sz += rbuf_i[2*j]; } 585 } 586 587 if (c->Mbs) max1 = ct*(a->nz +b->nz)/c->Mbs; 588 else max1 = 1; 589 mem_estimate = 3*((total_sz > max1 ? total_sz : max1)+1); 590 xdata[0] = (int *) PetscMalloc(mem_estimate*sizeof(int));CHKPTRQ(xdata[0]); 591 ++no_malloc; 592 ierr = PetscBTCreate(Mbs,xtable);CHKERRQ(ierr); 593 ierr = PetscMemzero(isz1,nrqr*sizeof(int));CHKERRQ(ierr); 594 595 ct3 = 0; 596 for (i=0; i<nrqr; i++) { /* for easch mesg from proc i */ 597 rbuf_i = rbuf[i]; 598 rbuf_0 = rbuf_i[0]; 599 ct1 = 2*rbuf_0+1; 600 ct2 = ct1; 601 ct3 += ct1; 602 for (j=1; j<=rbuf_0; j++) { /* for each IS from proc i*/ 603 ierr = PetscBTMemzero(Mbs,xtable);CHKERRQ(ierr); 604 oct2 = ct2; 605 kmax = rbuf_i[2*j]; 606 for (k=0; k<kmax; k++, ct1++) { 607 row = rbuf_i[ct1]; 608 if (!PetscBTLoopupSet(xtable,row)) { 609 if (!(ct3 < mem_estimate)) { 610 new_estimate = (int)(1.5*mem_estimate)+1; 611 tmp = (int*) PetscMalloc(new_estimate * sizeof(int));CHKPTRQ(tmp); 612 ierr = PetscMemcpy(tmp,xdata[0],mem_estimate*sizeof(int));CHKERRQ(ierr); 613 ierr = PetscFree(xdata[0]);CHKERRQ(ierr); 614 xdata[0] = tmp; 615 mem_estimate = new_estimate; ++no_malloc; 616 for (ctr=1; ctr<=i; ctr++) { xdata[ctr] = xdata[ctr-1] + isz1[ctr-1];} 617 } 618 xdata[i][ct2++] = row; 619 ct3++; 620 } 621 } 622 for (k=oct2,max2=ct2; k<max2; k++) { 623 row = xdata[i][k] - rstart; 624 start = ai[row]; 625 end = ai[row+1]; 626 for (l=start; l<end; l++) { 627 val = aj[l] + cstart; 628 if (!PetscBTLoopupSet(xtable,val)) { 629 if (!(ct3 < mem_estimate)) { 630 new_estimate = (int)(1.5*mem_estimate)+1; 631 tmp = (int*) PetscMalloc(new_estimate * sizeof(int));CHKPTRQ(tmp); 632 ierr = PetscMemcpy(tmp,xdata[0],mem_estimate*sizeof(int));CHKERRQ(ierr); 633 ierr = PetscFree(xdata[0]);CHKERRQ(ierr); 634 xdata[0] = tmp; 635 mem_estimate = new_estimate; ++no_malloc; 636 for (ctr=1; ctr<=i; ctr++) { xdata[ctr] = xdata[ctr-1] + isz1[ctr-1];} 637 } 638 xdata[i][ct2++] = val; 639 ct3++; 640 } 641 } 642 start = bi[row]; 643 end = bi[row+1]; 644 for (l=start; l<end; l++) { 645 val = garray[bj[l]]; 646 if (!PetscBTLoopupSet(xtable,val)) { 647 if (!(ct3 < mem_estimate)) { 648 new_estimate = (int)(1.5*mem_estimate)+1; 649 tmp = (int*) PetscMalloc(new_estimate * sizeof(int));CHKPTRQ(tmp); 650 ierr = PetscMemcpy(tmp,xdata[0],mem_estimate*sizeof(int));CHKERRQ(ierr); 651 ierr = PetscFree(xdata[0]);CHKERRQ(ierr); 652 xdata[0] = tmp; 653 mem_estimate = new_estimate; ++no_malloc; 654 for (ctr =1; ctr <=i; ctr++) { xdata[ctr] = xdata[ctr-1] + isz1[ctr-1];} 655 } 656 xdata[i][ct2++] = val; 657 ct3++; 658 } 659 } 660 } 661 /* Update the header*/ 662 xdata[i][2*j] = ct2 - oct2; /* Undo the vector isz1 and use only a var*/ 663 xdata[i][2*j-1] = rbuf_i[2*j-1]; 664 } 665 xdata[i][0] = rbuf_0; 666 xdata[i+1] = xdata[i] + ct2; 667 isz1[i] = ct2; /* size of each message */ 668 } 669 ierr = PetscBTDestroy(xtable);CHKERRQ(ierr); 670 PLogInfo(0,"MatIncreaseOverlap_MPIBAIJ:[%d] Allocated %d bytes, required %d, no of mallocs = %d\n",rank,mem_estimate,ct3,no_malloc); 671 PetscFunctionReturn(0); 672 } 673 674 static int MatGetSubMatrices_MPIBAIJ_local(Mat,int,IS *,IS *,MatReuse,Mat *); 675 676 #undef __FUNC__ 677 #define __FUNC__ "MatGetSubMatrices_MPIBAIJ" 678 int MatGetSubMatrices_MPIBAIJ(Mat C,int ismax,IS *isrow,IS *iscol, 679 MatReuse scall,Mat **submat) 680 { 681 IS *isrow_new,*iscol_new; 682 Mat_MPIBAIJ *c = (Mat_MPIBAIJ *) C->data; 683 int nmax,nstages_local,nstages,i,pos,max_no,ierr; 684 685 PetscFunctionBegin; 686 /* The compression and expansion should be avoided. Does'nt point 687 out errors might change the indices hence buggey */ 688 689 isrow_new = (IS *)PetscMalloc(2*(ismax+1)*sizeof(IS));CHKPTRQ(isrow_new); 690 iscol_new = isrow_new + ismax; 691 ierr = MatCompressIndicesSorted_MPIBAIJ(C, ismax, isrow,isrow_new);CHKERRQ(ierr); 692 ierr = MatCompressIndicesSorted_MPIBAIJ(C, ismax, iscol,iscol_new);CHKERRQ(ierr); 693 694 /* Allocate memory to hold all the submatrices */ 695 if (scall != MAT_REUSE_MATRIX) { 696 *submat = (Mat *)PetscMalloc((ismax+1)*sizeof(Mat));CHKPTRQ(*submat); 697 } 698 /* Determine the number of stages through which submatrices are done */ 699 nmax = 20*1000000 / (c->Nbs * sizeof(int)); 700 if (nmax == 0) nmax = 1; 701 nstages_local = ismax/nmax + ((ismax % nmax)?1:0); 702 703 /* Make sure every porcessor loops through the nstages */ 704 ierr = MPI_Allreduce(&nstages_local,&nstages,1,MPI_INT,MPI_MAX,C->comm);CHKERRQ(ierr); 705 706 for ( i=0,pos=0; i<nstages; i++ ) { 707 if (pos+nmax <= ismax) max_no = nmax; 708 else if (pos == ismax) max_no = 0; 709 else max_no = ismax-pos; 710 ierr = MatGetSubMatrices_MPIBAIJ_local(C,max_no,isrow_new+pos,iscol_new+pos,scall,*submat+pos);CHKERRQ(ierr); 711 pos += max_no; 712 } 713 714 for (i=0; i<ismax; i++) { 715 ierr = ISDestroy(isrow_new[i]);CHKERRQ(ierr); 716 ierr = ISDestroy(iscol_new[i]);CHKERRQ(ierr); 717 } 718 ierr = PetscFree(isrow_new);CHKERRQ(ierr); 719 PetscFunctionReturn(0); 720 } 721 722 /* -------------------------------------------------------------------------*/ 723 #undef __FUNC__ 724 #define __FUNC__ "MatGetSubMatrices_MPIBAIJ_local" 725 static int MatGetSubMatrices_MPIBAIJ_local(Mat C,int ismax,IS *isrow,IS *iscol, 726 MatReuse scall,Mat *submats) 727 { 728 Mat_MPIBAIJ *c = (Mat_MPIBAIJ *) C->data; 729 Mat A = c->A; 730 Mat_SeqBAIJ *a = (Mat_SeqBAIJ*)A->data, *b = (Mat_SeqBAIJ*)c->B->data, *mat; 731 int **irow,**icol,*nrow,*ncol,*w1,*w2,*w3,*w4,*rtable,start,end,size; 732 int **sbuf1,**sbuf2, rank, Mbs,i,j,k,l,ct1,ct2,ierr, **rbuf1,row,proc; 733 int nrqs, msz, **ptr,index,*req_size,*ctr,*pa,*tmp,tcol,bsz,nrqr; 734 int **rbuf3,*req_source,**sbuf_aj, **rbuf2, max1,max2,**rmap; 735 int **cmap,**lens,is_no,ncols,*cols,mat_i,*mat_j,tmp2,jmax,*irow_i; 736 int len,ctr_j,*sbuf1_j,*sbuf_aj_i,*rbuf1_i,kmax,*cmap_i,*lens_i; 737 int *rmap_i,bs=c->bs,bs2=c->bs2,*a_j=a->j,*b_j=b->j,*cworkA, *cworkB; 738 int cstart = c->cstart,nzA,nzB,*a_i=a->i,*b_i=b->i,imark; 739 int *bmap = c->garray,ctmp,rstart=c->rstart,tag0,tag1,tag2,tag3; 740 MPI_Request *s_waits1,*r_waits1,*s_waits2,*r_waits2,*r_waits3; 741 MPI_Request *r_waits4,*s_waits3,*s_waits4; 742 MPI_Status *r_status1,*r_status2,*s_status1,*s_status3,*s_status2; 743 MPI_Status *r_status3,*r_status4,*s_status4; 744 MPI_Comm comm; 745 Scalar **rbuf4,**sbuf_aa,*vals,*mat_a,*sbuf_aa_i,*vworkA,*vworkB; 746 Scalar *a_a=a->a,*b_a=b->a; 747 PetscTruth flag; 748 749 PetscFunctionBegin; 750 comm = C->comm; 751 tag0 = C->tag; 752 size = c->size; 753 rank = c->rank; 754 Mbs = c->Mbs; 755 756 /* Get some new tags to keep the communication clean */ 757 ierr = PetscObjectGetNewTag((PetscObject)C,&tag1);CHKERRQ(ierr); 758 ierr = PetscObjectGetNewTag((PetscObject)C,&tag2);CHKERRQ(ierr); 759 ierr = PetscObjectGetNewTag((PetscObject)C,&tag3);CHKERRQ(ierr); 760 761 /* Check if the col indices are sorted */ 762 for (i=0; i<ismax; i++) { 763 ierr = ISSorted(iscol[i],(PetscTruth*)&j);CHKERRQ(ierr); 764 if (!j) SETERRQ(PETSC_ERR_ARG_WRONGSTATE,0,"IS is not sorted"); 765 } 766 767 len = (2*ismax+1)*(sizeof(int *) + sizeof(int)) + (Mbs+1)*sizeof(int); 768 irow = (int **)PetscMalloc(len);CHKPTRQ(irow); 769 icol = irow + ismax; 770 nrow = (int *) (icol + ismax); 771 ncol = nrow + ismax; 772 rtable = ncol + ismax; 773 774 for (i=0; i<ismax; i++) { 775 ierr = ISGetIndices(isrow[i],&irow[i]);CHKERRQ(ierr); 776 ierr = ISGetIndices(iscol[i],&icol[i]);CHKERRQ(ierr); 777 ierr = ISGetSize(isrow[i],&nrow[i]);CHKERRQ(ierr); 778 ierr = ISGetSize(iscol[i],&ncol[i]);CHKERRQ(ierr); 779 } 780 781 /* Create hash table for the mapping :row -> proc*/ 782 for (i=0,j=0; i<size; i++) { 783 jmax = c->rowners[i+1]; 784 for (; j<jmax; j++) { 785 rtable[j] = i; 786 } 787 } 788 789 /* evaluate communication - mesg to who, length of mesg, and buffer space 790 required. Based on this, buffers are allocated, and data copied into them*/ 791 w1 = (int *)PetscMalloc(size*4*sizeof(int));CHKPTRQ(w1); /* mesg size */ 792 w2 = w1 + size; /* if w2[i] marked, then a message to proc i*/ 793 w3 = w2 + size; /* no of IS that needs to be sent to proc i */ 794 w4 = w3 + size; /* temp work space used in determining w1, w2, w3 */ 795 ierr = PetscMemzero(w1,size*3*sizeof(int));CHKERRQ(ierr); /* initialise work vector*/ 796 for (i=0; i<ismax; i++) { 797 ierr = PetscMemzero(w4,size*sizeof(int));CHKERRQ(ierr); /* initialise work vector*/ 798 jmax = nrow[i]; 799 irow_i = irow[i]; 800 for (j=0; j<jmax; j++) { 801 row = irow_i[j]; 802 proc = rtable[row]; 803 w4[proc]++; 804 } 805 for (j=0; j<size; j++) { 806 if (w4[j]) { w1[j] += w4[j]; w3[j]++;} 807 } 808 } 809 810 nrqs = 0; /* no of outgoing messages */ 811 msz = 0; /* total mesg length for all proc */ 812 w1[rank] = 0; /* no mesg sent to intself */ 813 w3[rank] = 0; 814 for (i=0; i<size; i++) { 815 if (w1[i]) { w2[i] = 1; nrqs++;} /* there exists a message to proc i */ 816 } 817 pa = (int *)PetscMalloc((nrqs+1)*sizeof(int));CHKPTRQ(pa); /*(proc -array)*/ 818 for (i=0, j=0; i<size; i++) { 819 if (w1[i]) { pa[j] = i; j++; } 820 } 821 822 /* Each message would have a header = 1 + 2*(no of IS) + data */ 823 for (i=0; i<nrqs; i++) { 824 j = pa[i]; 825 w1[j] += w2[j] + 2* w3[j]; 826 msz += w1[j]; 827 } 828 /* Do a global reduction to determine how many messages to expect*/ 829 { 830 int *rw1; 831 rw1 = (int *)PetscMalloc(2*size*sizeof(int));CHKPTRQ(rw1); 832 ierr = MPI_Allreduce(w1, rw1, 2*size, MPI_INT, PetscMaxSum_Op, comm);CHKERRQ(ierr); 833 bsz = rw1[rank]; 834 nrqr = rw1[size+rank]; 835 ierr = PetscFree(rw1);CHKERRQ(ierr); 836 } 837 838 /* Allocate memory for recv buffers . Prob none if nrqr = 0 ???? */ 839 len = (nrqr+1)*sizeof(int*) + nrqr*bsz*sizeof(int); 840 rbuf1 = (int**) PetscMalloc(len);CHKPTRQ(rbuf1); 841 rbuf1[0] = (int *) (rbuf1 + nrqr); 842 for (i=1; i<nrqr; ++i) rbuf1[i] = rbuf1[i-1] + bsz; 843 844 /* Post the receives */ 845 r_waits1 = (MPI_Request *) PetscMalloc((nrqr+1)*sizeof(MPI_Request));CHKPTRQ(r_waits1); 846 for (i=0; i<nrqr; ++i) { 847 ierr = MPI_Irecv(rbuf1[i],bsz,MPI_INT,MPI_ANY_SOURCE,tag0,comm,r_waits1+i);CHKERRQ(ierr); 848 } 849 850 /* Allocate Memory for outgoing messages */ 851 len = 2*size*sizeof(int*) + 2*msz*sizeof(int) + size*sizeof(int); 852 sbuf1 = (int **)PetscMalloc(len);CHKPTRQ(sbuf1); 853 ptr = sbuf1 + size; /* Pointers to the data in outgoing buffers */ 854 ierr = PetscMemzero(sbuf1,2*size*sizeof(int*));CHKERRQ(ierr); 855 /* allocate memory for outgoing data + buf to receive the first reply */ 856 tmp = (int *) (ptr + size); 857 ctr = tmp + 2*msz; 858 859 { 860 int *iptr = tmp,ict = 0; 861 for (i=0; i<nrqs; i++) { 862 j = pa[i]; 863 iptr += ict; 864 sbuf1[j] = iptr; 865 ict = w1[j]; 866 } 867 } 868 869 /* Form the outgoing messages */ 870 /* Initialise the header space */ 871 for (i=0; i<nrqs; i++) { 872 j = pa[i]; 873 sbuf1[j][0] = 0; 874 ierr = PetscMemzero(sbuf1[j]+1, 2*w3[j]*sizeof(int));CHKERRQ(ierr); 875 ptr[j] = sbuf1[j] + 2*w3[j] + 1; 876 } 877 878 /* Parse the isrow and copy data into outbuf */ 879 for (i=0; i<ismax; i++) { 880 ierr = PetscMemzero(ctr,size*sizeof(int));CHKERRQ(ierr); 881 irow_i = irow[i]; 882 jmax = nrow[i]; 883 for (j=0; j<jmax; j++) { /* parse the indices of each IS */ 884 row = irow_i[j]; 885 proc = rtable[row]; 886 if (proc != rank) { /* copy to the outgoing buf*/ 887 ctr[proc]++; 888 *ptr[proc] = row; 889 ptr[proc]++; 890 } 891 } 892 /* Update the headers for the current IS */ 893 for (j=0; j<size; j++) { /* Can Optimise this loop too */ 894 if ((ctr_j = ctr[j])) { 895 sbuf1_j = sbuf1[j]; 896 k = ++sbuf1_j[0]; 897 sbuf1_j[2*k] = ctr_j; 898 sbuf1_j[2*k-1] = i; 899 } 900 } 901 } 902 903 /* Now post the sends */ 904 s_waits1 = (MPI_Request *) PetscMalloc((nrqs+1)*sizeof(MPI_Request));CHKPTRQ(s_waits1); 905 for (i=0; i<nrqs; ++i) { 906 j = pa[i]; 907 ierr = MPI_Isend( sbuf1[j], w1[j], MPI_INT, j, tag0, comm, s_waits1+i);CHKERRQ(ierr); 908 } 909 910 /* Post Recieves to capture the buffer size */ 911 r_waits2 = (MPI_Request *) PetscMalloc((nrqs+1)*sizeof(MPI_Request));CHKPTRQ(r_waits2); 912 rbuf2 = (int**)PetscMalloc((nrqs+1)*sizeof(int *));CHKPTRQ(rbuf2); 913 rbuf2[0] = tmp + msz; 914 for (i=1; i<nrqs; ++i) { 915 j = pa[i]; 916 rbuf2[i] = rbuf2[i-1]+w1[pa[i-1]]; 917 } 918 for (i=0; i<nrqs; ++i) { 919 j = pa[i]; 920 ierr = MPI_Irecv( rbuf2[i], w1[j], MPI_INT, j, tag1, comm, r_waits2+i);CHKERRQ(ierr); 921 } 922 923 /* Send to other procs the buf size they should allocate */ 924 925 926 /* Receive messages*/ 927 s_waits2 = (MPI_Request *) PetscMalloc((nrqr+1)*sizeof(MPI_Request));CHKPTRQ(s_waits2); 928 r_status1 = (MPI_Status *) PetscMalloc((nrqr+1)*sizeof(MPI_Status));CHKPTRQ(r_status1); 929 len = 2*nrqr*sizeof(int) + (nrqr+1)*sizeof(int*); 930 sbuf2 = (int**) PetscMalloc(len);CHKPTRQ(sbuf2); 931 req_size = (int *) (sbuf2 + nrqr); 932 req_source = req_size + nrqr; 933 934 { 935 Mat_SeqBAIJ *sA = (Mat_SeqBAIJ*) c->A->data, *sB = (Mat_SeqBAIJ*) c->B->data; 936 int *sAi = sA->i, *sBi = sB->i, id, *sbuf2_i; 937 938 for (i=0; i<nrqr; ++i) { 939 ierr = MPI_Waitany(nrqr, r_waits1, &index, r_status1+i);CHKERRQ(ierr); 940 req_size[index] = 0; 941 rbuf1_i = rbuf1[index]; 942 start = 2*rbuf1_i[0] + 1; 943 ierr = MPI_Get_count(r_status1+i,MPI_INT, &end);CHKERRQ(ierr); 944 sbuf2[index] = (int *)PetscMalloc(end*sizeof(int));CHKPTRQ(sbuf2[index]); 945 sbuf2_i = sbuf2[index]; 946 for (j=start; j<end; j++) { 947 id = rbuf1_i[j] - rstart; 948 ncols = sAi[id+1] - sAi[id] + sBi[id+1] - sBi[id]; 949 sbuf2_i[j] = ncols; 950 req_size[index] += ncols; 951 } 952 req_source[index] = r_status1[i].MPI_SOURCE; 953 /* form the header */ 954 sbuf2_i[0] = req_size[index]; 955 for (j=1; j<start; j++) { sbuf2_i[j] = rbuf1_i[j]; } 956 ierr = MPI_Isend(sbuf2_i,end,MPI_INT,req_source[index],tag1,comm,s_waits2+i);CHKERRQ(ierr); 957 } 958 } 959 ierr = PetscFree(r_status1);CHKERRQ(ierr); 960 ierr = PetscFree(r_waits1);CHKERRQ(ierr); 961 962 /* recv buffer sizes */ 963 /* Receive messages*/ 964 965 rbuf3 = (int**)PetscMalloc((nrqs+1)*sizeof(int*));CHKPTRQ(rbuf3); 966 rbuf4 = (Scalar**)PetscMalloc((nrqs+1)*sizeof(Scalar*));CHKPTRQ(rbuf4); 967 r_waits3 = (MPI_Request *) PetscMalloc((nrqs+1)*sizeof(MPI_Request));CHKPTRQ(r_waits3); 968 r_waits4 = (MPI_Request *) PetscMalloc((nrqs+1)*sizeof(MPI_Request));CHKPTRQ(r_waits4); 969 r_status2 = (MPI_Status *) PetscMalloc((nrqs+1)*sizeof(MPI_Status));CHKPTRQ(r_status2); 970 971 for (i=0; i<nrqs; ++i) { 972 ierr = MPI_Waitany(nrqs, r_waits2, &index, r_status2+i);CHKERRQ(ierr); 973 rbuf3[index] = (int *)PetscMalloc(rbuf2[index][0]*sizeof(int));CHKPTRQ(rbuf3[index]); 974 rbuf4[index] = (Scalar *)PetscMalloc(rbuf2[index][0]*bs2*sizeof(Scalar));CHKPTRQ(rbuf4[index]); 975 ierr = MPI_Irecv(rbuf3[index],rbuf2[index][0], MPI_INT, 976 r_status2[i].MPI_SOURCE, tag2, comm, r_waits3+index);CHKERRQ(ierr); 977 ierr = MPI_Irecv(rbuf4[index],rbuf2[index][0]*bs2, MPIU_SCALAR, 978 r_status2[i].MPI_SOURCE, tag3, comm, r_waits4+index);CHKERRQ(ierr); 979 } 980 ierr = PetscFree(r_status2);CHKERRQ(ierr); 981 ierr = PetscFree(r_waits2);CHKERRQ(ierr); 982 983 /* Wait on sends1 and sends2 */ 984 s_status1 = (MPI_Status *) PetscMalloc((nrqs+1)*sizeof(MPI_Status));CHKPTRQ(s_status1); 985 s_status2 = (MPI_Status *) PetscMalloc((nrqr+1)*sizeof(MPI_Status));CHKPTRQ(s_status2); 986 987 ierr = MPI_Waitall(nrqs,s_waits1,s_status1);CHKERRQ(ierr); 988 ierr = MPI_Waitall(nrqr,s_waits2,s_status2);CHKERRQ(ierr); 989 ierr = PetscFree(s_status1);CHKERRQ(ierr); 990 ierr = PetscFree(s_status2);CHKERRQ(ierr); 991 ierr = PetscFree(s_waits1);CHKERRQ(ierr); 992 ierr = PetscFree(s_waits2);CHKERRQ(ierr); 993 994 /* Now allocate buffers for a->j, and send them off */ 995 sbuf_aj = (int **)PetscMalloc((nrqr+1)*sizeof(int *));CHKPTRQ(sbuf_aj); 996 for (i=0,j=0; i<nrqr; i++) j += req_size[i]; 997 sbuf_aj[0] = (int*) PetscMalloc((j+1)*sizeof(int));CHKPTRQ(sbuf_aj[0]); 998 for (i=1; i<nrqr; i++) sbuf_aj[i] = sbuf_aj[i-1] + req_size[i-1]; 999 1000 s_waits3 = (MPI_Request *) PetscMalloc((nrqr+1)*sizeof(MPI_Request));CHKPTRQ(s_waits3); 1001 { 1002 for (i=0; i<nrqr; i++) { 1003 rbuf1_i = rbuf1[i]; 1004 sbuf_aj_i = sbuf_aj[i]; 1005 ct1 = 2*rbuf1_i[0] + 1; 1006 ct2 = 0; 1007 for (j=1,max1=rbuf1_i[0]; j<=max1; j++) { 1008 kmax = rbuf1[i][2*j]; 1009 for (k=0; k<kmax; k++,ct1++) { 1010 row = rbuf1_i[ct1] - rstart; 1011 nzA = a_i[row+1] - a_i[row]; nzB = b_i[row+1] - b_i[row]; 1012 ncols = nzA + nzB; 1013 cworkA = a_j + a_i[row]; cworkB = b_j + b_i[row]; 1014 1015 /* load the column indices for this row into cols*/ 1016 cols = sbuf_aj_i + ct2; 1017 for (l=0; l<nzB; l++) { 1018 if ((ctmp = bmap[cworkB[l]]) < cstart) cols[l] = ctmp; 1019 else break; 1020 } 1021 imark = l; 1022 for (l=0; l<nzA; l++) cols[imark+l] = cstart + cworkA[l]; 1023 for (l=imark; l<nzB; l++) cols[nzA+l] = bmap[cworkB[l]]; 1024 ct2 += ncols; 1025 } 1026 } 1027 ierr = MPI_Isend(sbuf_aj_i,req_size[i],MPI_INT,req_source[i],tag2,comm,s_waits3+i);CHKERRQ(ierr); 1028 } 1029 } 1030 r_status3 = (MPI_Status *) PetscMalloc((nrqs+1)*sizeof(MPI_Status));CHKPTRQ(r_status3); 1031 s_status3 = (MPI_Status *) PetscMalloc((nrqr+1)*sizeof(MPI_Status));CHKPTRQ(s_status3); 1032 1033 /* Allocate buffers for a->a, and send them off */ 1034 sbuf_aa = (Scalar **)PetscMalloc((nrqr+1)*sizeof(Scalar *));CHKPTRQ(sbuf_aa); 1035 for (i=0,j=0; i<nrqr; i++) j += req_size[i]; 1036 sbuf_aa[0] = (Scalar*) PetscMalloc((j+1)*bs2*sizeof(Scalar));CHKPTRQ(sbuf_aa[0]); 1037 for (i=1; i<nrqr; i++) sbuf_aa[i] = sbuf_aa[i-1] + req_size[i-1]*bs2; 1038 1039 s_waits4 = (MPI_Request *) PetscMalloc((nrqr+1)*sizeof(MPI_Request));CHKPTRQ(s_waits4); 1040 { 1041 for (i=0; i<nrqr; i++) { 1042 rbuf1_i = rbuf1[i]; 1043 sbuf_aa_i = sbuf_aa[i]; 1044 ct1 = 2*rbuf1_i[0]+1; 1045 ct2 = 0; 1046 for (j=1,max1=rbuf1_i[0]; j<=max1; j++) { 1047 kmax = rbuf1_i[2*j]; 1048 for (k=0; k<kmax; k++,ct1++) { 1049 row = rbuf1_i[ct1] - rstart; 1050 nzA = a_i[row+1] - a_i[row]; nzB = b_i[row+1] - b_i[row]; 1051 ncols = nzA + nzB; 1052 cworkA = a_j + a_i[row]; cworkB = b_j + b_i[row]; 1053 vworkA = a_a + a_i[row]*bs2; vworkB = b_a + b_i[row]*bs2; 1054 1055 /* load the column values for this row into vals*/ 1056 vals = sbuf_aa_i+ct2*bs2; 1057 for (l=0; l<nzB; l++) { 1058 if ((bmap[cworkB[l]]) < cstart) { 1059 ierr = PetscMemcpy(vals+l*bs2,vworkB+l*bs2,bs2*sizeof(Scalar));CHKERRQ(ierr); 1060 } 1061 else break; 1062 } 1063 imark = l; 1064 for (l=0; l<nzA; l++) { 1065 ierr = PetscMemcpy(vals+(imark+l)*bs2,vworkA+l*bs2,bs2*sizeof(Scalar));CHKERRQ(ierr); 1066 } 1067 for (l=imark; l<nzB; l++) { 1068 ierr = PetscMemcpy(vals+(nzA+l)*bs2,vworkB+l*bs2,bs2*sizeof(Scalar));CHKERRQ(ierr); 1069 } 1070 ct2 += ncols; 1071 } 1072 } 1073 ierr = MPI_Isend(sbuf_aa_i,req_size[i]*bs2,MPIU_SCALAR,req_source[i],tag3,comm,s_waits4+i);CHKERRQ(ierr); 1074 } 1075 } 1076 r_status4 = (MPI_Status *) PetscMalloc((nrqs+1)*sizeof(MPI_Status));CHKPTRQ(r_status4); 1077 s_status4 = (MPI_Status *) PetscMalloc((nrqr+1)*sizeof(MPI_Status));CHKPTRQ(s_status4); 1078 ierr = PetscFree(rbuf1);CHKERRQ(ierr); 1079 1080 /* Form the matrix */ 1081 /* create col map */ 1082 { 1083 int *icol_i; 1084 1085 len = (1+ismax)*sizeof(int *) + ismax*c->Nbs*sizeof(int); 1086 cmap = (int **)PetscMalloc(len);CHKPTRQ(cmap); 1087 cmap[0] = (int *)(cmap + ismax); 1088 ierr = PetscMemzero(cmap[0],(1+ismax*c->Nbs)*sizeof(int));CHKERRQ(ierr); 1089 for (i=1; i<ismax; i++) { cmap[i] = cmap[i-1] + c->Nbs; } 1090 for (i=0; i<ismax; i++) { 1091 jmax = ncol[i]; 1092 icol_i = icol[i]; 1093 cmap_i = cmap[i]; 1094 for (j=0; j<jmax; j++) { 1095 cmap_i[icol_i[j]] = j+1; 1096 } 1097 } 1098 } 1099 1100 1101 /* Create lens which is required for MatCreate... */ 1102 for (i=0,j=0; i<ismax; i++) { j += nrow[i]; } 1103 len = (1+ismax)*sizeof(int *) + j*sizeof(int); 1104 lens = (int **)PetscMalloc(len);CHKPTRQ(lens); 1105 lens[0] = (int *)(lens + ismax); 1106 ierr = PetscMemzero(lens[0], j*sizeof(int));CHKERRQ(ierr); 1107 for (i=1; i<ismax; i++) { lens[i] = lens[i-1] + nrow[i-1]; } 1108 1109 /* Update lens from local data */ 1110 for (i=0; i<ismax; i++) { 1111 jmax = nrow[i]; 1112 cmap_i = cmap[i]; 1113 irow_i = irow[i]; 1114 lens_i = lens[i]; 1115 for (j=0; j<jmax; j++) { 1116 row = irow_i[j]; 1117 proc = rtable[row]; 1118 if (proc == rank) { 1119 /* Get indices from matA and then from matB */ 1120 row = row - rstart; 1121 nzA = a_i[row+1] - a_i[row]; nzB = b_i[row+1] - b_i[row]; 1122 cworkA = a_j + a_i[row]; cworkB = b_j + b_i[row]; 1123 for (k=0; k<nzA; k++) { 1124 if (cmap_i[cstart + cworkA[k]]) { lens_i[j]++;} 1125 } 1126 for (k=0; k<nzB; k++) { 1127 if (cmap_i[bmap[cworkB[k]]]) { lens_i[j]++;} 1128 } 1129 } 1130 } 1131 } 1132 1133 /* Create row map*/ 1134 len = (1+ismax)*sizeof(int *) + ismax*c->Mbs*sizeof(int); 1135 rmap = (int **)PetscMalloc(len);CHKPTRQ(rmap); 1136 rmap[0] = (int *)(rmap + ismax); 1137 ierr = PetscMemzero(rmap[0],ismax*c->Mbs*sizeof(int));CHKERRQ(ierr); 1138 for (i=1; i<ismax; i++) { rmap[i] = rmap[i-1] + c->Mbs;} 1139 for (i=0; i<ismax; i++) { 1140 rmap_i = rmap[i]; 1141 irow_i = irow[i]; 1142 jmax = nrow[i]; 1143 for (j=0; j<jmax; j++) { 1144 rmap_i[irow_i[j]] = j; 1145 } 1146 } 1147 1148 /* Update lens from offproc data */ 1149 { 1150 int *rbuf2_i, *rbuf3_i, *sbuf1_i; 1151 1152 for (tmp2=0; tmp2<nrqs; tmp2++) { 1153 ierr = MPI_Waitany(nrqs, r_waits3, &i, r_status3+tmp2);CHKERRQ(ierr); 1154 index = pa[i]; 1155 sbuf1_i = sbuf1[index]; 1156 jmax = sbuf1_i[0]; 1157 ct1 = 2*jmax+1; 1158 ct2 = 0; 1159 rbuf2_i = rbuf2[i]; 1160 rbuf3_i = rbuf3[i]; 1161 for (j=1; j<=jmax; j++) { 1162 is_no = sbuf1_i[2*j-1]; 1163 max1 = sbuf1_i[2*j]; 1164 lens_i = lens[is_no]; 1165 cmap_i = cmap[is_no]; 1166 rmap_i = rmap[is_no]; 1167 for (k=0; k<max1; k++,ct1++) { 1168 row = rmap_i[sbuf1_i[ct1]]; /* the val in the new matrix to be */ 1169 max2 = rbuf2_i[ct1]; 1170 for (l=0; l<max2; l++,ct2++) { 1171 if (cmap_i[rbuf3_i[ct2]]) { 1172 lens_i[row]++; 1173 } 1174 } 1175 } 1176 } 1177 } 1178 } 1179 ierr = PetscFree(r_status3);CHKERRQ(ierr); 1180 ierr = PetscFree(r_waits3);CHKERRQ(ierr); 1181 ierr = MPI_Waitall(nrqr,s_waits3,s_status3);CHKERRQ(ierr); 1182 ierr = PetscFree(s_status3);CHKERRQ(ierr); 1183 ierr = PetscFree(s_waits3);CHKERRQ(ierr); 1184 1185 /* Create the submatrices */ 1186 if (scall == MAT_REUSE_MATRIX) { 1187 /* 1188 Assumes new rows are same length as the old rows, hence bug! 1189 */ 1190 for (i=0; i<ismax; i++) { 1191 mat = (Mat_SeqBAIJ *)(submats[i]->data); 1192 if ((mat->mbs != nrow[i]) || (mat->nbs != ncol[i] || mat->bs != bs)) { 1193 SETERRQ(PETSC_ERR_ARG_SIZ,0,"Cannot reuse matrix. wrong size"); 1194 } 1195 ierr = PetscMemcmp(mat->ilen,lens[i], mat->mbs *sizeof(int),&flag);CHKERRQ(ierr); 1196 if (flag == PETSC_FALSE) { 1197 SETERRQ(PETSC_ERR_ARG_INCOMP,0,"Cannot reuse matrix. wrong no of nonzeros"); 1198 } 1199 /* Initial matrix as if empty */ 1200 ierr = PetscMemzero(mat->ilen,mat->mbs*sizeof(int));CHKERRQ(ierr); 1201 submats[i]->factor = C->factor; 1202 } 1203 } else { 1204 for (i=0; i<ismax; i++) { 1205 ierr = MatCreateSeqBAIJ(PETSC_COMM_SELF,a->bs,nrow[i]*bs,ncol[i]*bs,0,lens[i],submats+i);CHKERRQ(ierr); 1206 } 1207 } 1208 1209 /* Assemble the matrices */ 1210 /* First assemble the local rows */ 1211 { 1212 int ilen_row,*imat_ilen, *imat_j, *imat_i; 1213 Scalar *imat_a; 1214 1215 for (i=0; i<ismax; i++) { 1216 mat = (Mat_SeqBAIJ *) submats[i]->data; 1217 imat_ilen = mat->ilen; 1218 imat_j = mat->j; 1219 imat_i = mat->i; 1220 imat_a = mat->a; 1221 cmap_i = cmap[i]; 1222 rmap_i = rmap[i]; 1223 irow_i = irow[i]; 1224 jmax = nrow[i]; 1225 for (j=0; j<jmax; j++) { 1226 row = irow_i[j]; 1227 proc = rtable[row]; 1228 if (proc == rank) { 1229 row = row - rstart; 1230 nzA = a_i[row+1] - a_i[row]; 1231 nzB = b_i[row+1] - b_i[row]; 1232 cworkA = a_j + a_i[row]; 1233 cworkB = b_j + b_i[row]; 1234 vworkA = a_a + a_i[row]*bs2; 1235 vworkB = b_a + b_i[row]*bs2; 1236 1237 row = rmap_i[row + rstart]; 1238 mat_i = imat_i[row]; 1239 mat_a = imat_a + mat_i*bs2; 1240 mat_j = imat_j + mat_i; 1241 ilen_row = imat_ilen[row]; 1242 1243 /* load the column indices for this row into cols*/ 1244 for (l=0; l<nzB; l++) { 1245 if ((ctmp = bmap[cworkB[l]]) < cstart) { 1246 if ((tcol = cmap_i[ctmp])) { 1247 *mat_j++ = tcol - 1; 1248 ierr = PetscMemcpy(mat_a,vworkB+l*bs2,bs2*sizeof(Scalar));CHKERRQ(ierr); 1249 mat_a += bs2; 1250 ilen_row++; 1251 } 1252 } else break; 1253 } 1254 imark = l; 1255 for (l=0; l<nzA; l++) { 1256 if ((tcol = cmap_i[cstart + cworkA[l]])) { 1257 *mat_j++ = tcol - 1; 1258 ierr = PetscMemcpy(mat_a,vworkA+l*bs2,bs2*sizeof(Scalar));CHKERRQ(ierr); 1259 mat_a += bs2; 1260 ilen_row++; 1261 } 1262 } 1263 for (l=imark; l<nzB; l++) { 1264 if ((tcol = cmap_i[bmap[cworkB[l]]])) { 1265 *mat_j++ = tcol - 1; 1266 ierr = PetscMemcpy(mat_a,vworkB+l*bs2,bs2*sizeof(Scalar));CHKERRQ(ierr); 1267 mat_a += bs2; 1268 ilen_row++; 1269 } 1270 } 1271 imat_ilen[row] = ilen_row; 1272 } 1273 } 1274 1275 } 1276 } 1277 1278 /* Now assemble the off proc rows*/ 1279 { 1280 int *sbuf1_i,*rbuf2_i,*rbuf3_i,*imat_ilen,ilen; 1281 int *imat_j,*imat_i; 1282 Scalar *imat_a,*rbuf4_i; 1283 1284 for (tmp2=0; tmp2<nrqs; tmp2++) { 1285 ierr = MPI_Waitany(nrqs, r_waits4, &i, r_status4+tmp2);CHKERRQ(ierr); 1286 index = pa[i]; 1287 sbuf1_i = sbuf1[index]; 1288 jmax = sbuf1_i[0]; 1289 ct1 = 2*jmax + 1; 1290 ct2 = 0; 1291 rbuf2_i = rbuf2[i]; 1292 rbuf3_i = rbuf3[i]; 1293 rbuf4_i = rbuf4[i]; 1294 for (j=1; j<=jmax; j++) { 1295 is_no = sbuf1_i[2*j-1]; 1296 rmap_i = rmap[is_no]; 1297 cmap_i = cmap[is_no]; 1298 mat = (Mat_SeqBAIJ *) submats[is_no]->data; 1299 imat_ilen = mat->ilen; 1300 imat_j = mat->j; 1301 imat_i = mat->i; 1302 imat_a = mat->a; 1303 max1 = sbuf1_i[2*j]; 1304 for (k=0; k<max1; k++, ct1++) { 1305 row = sbuf1_i[ct1]; 1306 row = rmap_i[row]; 1307 ilen = imat_ilen[row]; 1308 mat_i = imat_i[row]; 1309 mat_a = imat_a + mat_i*bs2; 1310 mat_j = imat_j + mat_i; 1311 max2 = rbuf2_i[ct1]; 1312 for (l=0; l<max2; l++,ct2++) { 1313 if ((tcol = cmap_i[rbuf3_i[ct2]])) { 1314 *mat_j++ = tcol - 1; 1315 /* *mat_a++= rbuf4_i[ct2]; */ 1316 ierr = PetscMemcpy(mat_a,rbuf4_i+ct2*bs2,bs2*sizeof(Scalar));CHKERRQ(ierr); 1317 mat_a += bs2; 1318 ilen++; 1319 } 1320 } 1321 imat_ilen[row] = ilen; 1322 } 1323 } 1324 } 1325 } 1326 ierr = PetscFree(r_status4);CHKERRQ(ierr); 1327 ierr = PetscFree(r_waits4);CHKERRQ(ierr); 1328 ierr = MPI_Waitall(nrqr,s_waits4,s_status4);CHKERRQ(ierr); 1329 ierr = PetscFree(s_waits4);CHKERRQ(ierr); 1330 ierr = PetscFree(s_status4);CHKERRQ(ierr); 1331 1332 /* Restore the indices */ 1333 for (i=0; i<ismax; i++) { 1334 ierr = ISRestoreIndices(isrow[i], irow+i);CHKERRQ(ierr); 1335 ierr = ISRestoreIndices(iscol[i], icol+i);CHKERRQ(ierr); 1336 } 1337 1338 /* Destroy allocated memory */ 1339 ierr = PetscFree(irow);CHKERRQ(ierr); 1340 ierr = PetscFree(w1);CHKERRQ(ierr); 1341 ierr = PetscFree(pa);CHKERRQ(ierr); 1342 1343 ierr = PetscFree(sbuf1);CHKERRQ(ierr); 1344 ierr = PetscFree(rbuf2);CHKERRQ(ierr); 1345 for (i=0; i<nrqr; ++i) { 1346 ierr = PetscFree(sbuf2[i]);CHKERRQ(ierr); 1347 } 1348 for (i=0; i<nrqs; ++i) { 1349 ierr = PetscFree(rbuf3[i]);CHKERRQ(ierr); 1350 ierr = PetscFree(rbuf4[i]);CHKERRQ(ierr); 1351 } 1352 1353 ierr = PetscFree(sbuf2);CHKERRQ(ierr); 1354 ierr = PetscFree(rbuf3);CHKERRQ(ierr); 1355 ierr = PetscFree(rbuf4 );CHKERRQ(ierr); 1356 ierr = PetscFree(sbuf_aj[0]);CHKERRQ(ierr); 1357 ierr = PetscFree(sbuf_aj);CHKERRQ(ierr); 1358 ierr = PetscFree(sbuf_aa[0]);CHKERRQ(ierr); 1359 ierr = PetscFree(sbuf_aa);CHKERRQ(ierr); 1360 1361 ierr = PetscFree(cmap);CHKERRQ(ierr); 1362 ierr = PetscFree(rmap);CHKERRQ(ierr); 1363 ierr = PetscFree(lens);CHKERRQ(ierr); 1364 1365 for (i=0; i<ismax; i++) { 1366 ierr = MatAssemblyBegin(submats[i], MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1367 ierr = MatAssemblyEnd(submats[i], MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1368 } 1369 1370 ierr = PetscObjectRestoreNewTag((PetscObject)C,&tag3);CHKERRQ(ierr); 1371 ierr = PetscObjectRestoreNewTag((PetscObject)C,&tag2);CHKERRQ(ierr); 1372 ierr = PetscObjectRestoreNewTag((PetscObject)C,&tag1);CHKERRQ(ierr); 1373 1374 PetscFunctionReturn(0); 1375 } 1376 1377 1378