1 2 /* 3 Defines projective product routines where A is a MPIAIJ matrix 4 C = P^T * A * P 5 */ 6 7 #include <../src/mat/impls/aij/seq/aij.h> /*I "petscmat.h" I*/ 8 #include <../src/mat/utils/freespace.h> 9 #include <../src/mat/impls/aij/mpi/mpiaij.h> 10 #include <petscbt.h> 11 #include <petsctime.h> 12 13 /* #define PTAP_PROFILE */ 14 15 extern PetscErrorCode MatDestroy_MPIAIJ(Mat); 16 #undef __FUNCT__ 17 #define __FUNCT__ "MatDestroy_MPIAIJ_PtAP" 18 PetscErrorCode MatDestroy_MPIAIJ_PtAP(Mat A) 19 { 20 PetscErrorCode ierr; 21 Mat_MPIAIJ *a=(Mat_MPIAIJ*)A->data; 22 Mat_PtAPMPI *ptap=a->ptap; 23 24 PetscFunctionBegin; 25 if (ptap) { 26 Mat_Merge_SeqsToMPI *merge=ptap->merge; 27 ierr = PetscFree2(ptap->startsj_s,ptap->startsj_r);CHKERRQ(ierr); 28 ierr = PetscFree(ptap->bufa);CHKERRQ(ierr); 29 ierr = MatDestroy(&ptap->P_loc);CHKERRQ(ierr); 30 ierr = MatDestroy(&ptap->P_oth);CHKERRQ(ierr); 31 ierr = MatDestroy(&ptap->A_loc);CHKERRQ(ierr); /* used by MatTransposeMatMult() */ 32 ierr = MatDestroy(&ptap->Rd);CHKERRQ(ierr); 33 ierr = MatDestroy(&ptap->Ro);CHKERRQ(ierr); 34 if (ptap->AP_loc) { /* used by alg_rap */ 35 Mat_SeqAIJ *ap = (Mat_SeqAIJ*)(ptap->AP_loc)->data; 36 ierr = PetscFree(ap->i);CHKERRQ(ierr); 37 ierr = PetscFree2(ap->j,ap->a);CHKERRQ(ierr); 38 ierr = MatDestroy(&ptap->AP_loc);CHKERRQ(ierr); 39 } else { /* used by alg_ptap */ 40 ierr = PetscFree(ptap->api);CHKERRQ(ierr); 41 ierr = PetscFree(ptap->apj);CHKERRQ(ierr); 42 } 43 ierr = MatDestroy(&ptap->C_loc);CHKERRQ(ierr); 44 ierr = MatDestroy(&ptap->C_oth);CHKERRQ(ierr); 45 if (ptap->apa) {ierr = PetscFree(ptap->apa);CHKERRQ(ierr);} 46 if (merge) { /* used by alg_ptap */ 47 ierr = PetscFree(merge->id_r);CHKERRQ(ierr); 48 ierr = PetscFree(merge->len_s);CHKERRQ(ierr); 49 ierr = PetscFree(merge->len_r);CHKERRQ(ierr); 50 ierr = PetscFree(merge->bi);CHKERRQ(ierr); 51 ierr = PetscFree(merge->bj);CHKERRQ(ierr); 52 ierr = PetscFree(merge->buf_ri[0]);CHKERRQ(ierr); 53 ierr = PetscFree(merge->buf_ri);CHKERRQ(ierr); 54 ierr = PetscFree(merge->buf_rj[0]);CHKERRQ(ierr); 55 ierr = PetscFree(merge->buf_rj);CHKERRQ(ierr); 56 ierr = PetscFree(merge->coi);CHKERRQ(ierr); 57 ierr = PetscFree(merge->coj);CHKERRQ(ierr); 58 ierr = PetscFree(merge->owners_co);CHKERRQ(ierr); 59 ierr = PetscLayoutDestroy(&merge->rowmap);CHKERRQ(ierr); 60 ierr = merge->destroy(A);CHKERRQ(ierr); 61 ierr = PetscFree(ptap->merge);CHKERRQ(ierr); 62 } else { 63 ierr = MatDestroy_MPIAIJ(A);CHKERRQ(ierr); 64 } 65 ierr = PetscFree(ptap);CHKERRQ(ierr); 66 } 67 PetscFunctionReturn(0); 68 } 69 70 #undef __FUNCT__ 71 #define __FUNCT__ "MatDuplicate_MPIAIJ_MatPtAP" 72 PetscErrorCode MatDuplicate_MPIAIJ_MatPtAP(Mat A, MatDuplicateOption op, Mat *M) 73 { 74 PetscErrorCode ierr; 75 Mat_MPIAIJ *a = (Mat_MPIAIJ*)A->data; 76 Mat_PtAPMPI *ptap = a->ptap; 77 78 PetscFunctionBegin; 79 ierr = (*ptap->duplicate)(A,op,M);CHKERRQ(ierr); 80 (*M)->ops->destroy = ptap->destroy; 81 (*M)->ops->duplicate = ptap->duplicate; 82 PetscFunctionReturn(0); 83 } 84 85 #undef __FUNCT__ 86 #define __FUNCT__ "MatPtAP_MPIAIJ_MPIAIJ" 87 PetscErrorCode MatPtAP_MPIAIJ_MPIAIJ(Mat A,Mat P,MatReuse scall,PetscReal fill,Mat *C) 88 { 89 PetscErrorCode ierr; 90 PetscBool rap=PETSC_TRUE; /* do R=P^T locally, then C=R*A*P */ 91 MPI_Comm comm; 92 93 PetscFunctionBegin; 94 /* check if matrix local sizes are compatible */ 95 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 96 if (A->rmap->rstart != P->rmap->rstart || A->rmap->rend != P->rmap->rend) { 97 SETERRQ4(comm,PETSC_ERR_ARG_SIZ,"Matrix local dimensions are incompatible, Arow (%D, %D) != Prow (%D,%D)",A->rmap->rstart,A->rmap->rend,P->rmap->rstart,P->rmap->rend); 98 } 99 if (A->cmap->rstart != P->rmap->rstart || A->cmap->rend != P->rmap->rend) { 100 SETERRQ4(comm,PETSC_ERR_ARG_SIZ,"Matrix local dimensions are incompatible, Acol (%D, %D) != Prow (%D,%D)",A->cmap->rstart,A->cmap->rend,P->rmap->rstart,P->rmap->rend); 101 } 102 103 ierr = PetscOptionsGetBool(NULL,"-matrap",&rap,NULL);CHKERRQ(ierr); 104 if (scall == MAT_INITIAL_MATRIX) { 105 ierr = PetscLogEventBegin(MAT_PtAPSymbolic,A,P,0,0);CHKERRQ(ierr); 106 if (rap) { /* do R=P^T locally, then C=R*A*P */ 107 ierr = MatPtAPSymbolic_MPIAIJ_MPIAIJ(A,P,fill,C);CHKERRQ(ierr); 108 } else { /* do P^T*A*P */ 109 ierr = MatPtAPSymbolic_MPIAIJ_MPIAIJ_ptap(A,P,fill,C);CHKERRQ(ierr); 110 } 111 ierr = PetscLogEventEnd(MAT_PtAPSymbolic,A,P,0,0);CHKERRQ(ierr); 112 } 113 ierr = PetscLogEventBegin(MAT_PtAPNumeric,A,P,0,0);CHKERRQ(ierr); 114 ierr = (*(*C)->ops->ptapnumeric)(A,P,*C);CHKERRQ(ierr); 115 ierr = PetscLogEventEnd(MAT_PtAPNumeric,A,P,0,0);CHKERRQ(ierr); 116 PetscFunctionReturn(0); 117 } 118 119 /* requires array of size pN, thus nonscalable version */ 120 #undef __FUNCT__ 121 #define __FUNCT__ "MatPtAPSymbolic_MPIAIJ_MPIAIJ" 122 PetscErrorCode MatPtAPSymbolic_MPIAIJ_MPIAIJ(Mat A,Mat P,PetscReal fill,Mat *C) 123 { 124 PetscErrorCode ierr; 125 Mat_PtAPMPI *ptap; 126 Mat_MPIAIJ *a=(Mat_MPIAIJ*)A->data,*p=(Mat_MPIAIJ*)P->data,*c; 127 MPI_Comm comm; 128 PetscMPIInt size,rank; 129 Mat Cmpi; 130 PetscFreeSpaceList free_space=NULL,current_space=NULL; 131 PetscInt am=A->rmap->n,pm=P->rmap->n; 132 PetscInt *lnk,i,k,pnz,row,nnz; 133 PetscInt pN=P->cmap->N,pn=P->cmap->n; 134 PetscBT lnkbt; 135 PetscMPIInt tagi,tagj,*len_si,*len_s,*len_ri,icompleted=0,nrecv; 136 PetscInt **buf_rj,**buf_ri,**buf_ri_k; 137 PetscInt len,proc,*dnz,*onz,*owners; 138 PetscInt nzi,nspacedouble; 139 PetscInt nrows,*buf_s,*buf_si,*buf_si_i,**nextrow,**nextci; 140 MPI_Request *swaits,*rwaits; 141 MPI_Status *sstatus,rstatus; 142 PetscLayout rowmap; 143 PetscInt *owners_co,*coi,*coj; /* i and j array of (p->B)^T*A*P - used in the communication */ 144 PetscInt nsend; 145 PetscMPIInt *len_r,*id_r; /* array of length of comm->size, store send/recv matrix values */ 146 PetscInt *api,*apj,*Jptr,apnz,*prmap=p->garray,con,j,ap_rmax=0,Prmax,APrmax; 147 PetscInt rmax,*aj,*ai,*pi; 148 Mat_SeqAIJ *p_loc,*p_oth,*ad=(Mat_SeqAIJ*)(a->A)->data,*ao=(Mat_SeqAIJ*)(a->B)->data,*c_loc,*c_oth; 149 PetscScalar *apv; 150 PetscTable ta,Cta; 151 #if defined(PETSC_USE_INFO) 152 PetscReal apfill; 153 #endif 154 #if defined(PTAP_PROFILE) 155 PetscLogDouble t0,t1,t11,t12,t2,t3,t4; 156 #endif 157 158 PetscFunctionBegin; 159 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 160 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 161 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 162 #if defined(PTAP_PROFILE) 163 ierr = PetscTime(&t0);CHKERRQ(ierr); 164 #endif 165 166 /* create struct Mat_PtAPMPI and attached it to C later */ 167 ierr = PetscNew(&ptap);CHKERRQ(ierr); 168 ptap->reuse = MAT_INITIAL_MATRIX; 169 170 /* get P_oth by taking rows of P (= non-zero cols of local A) from other processors */ 171 ierr = MatGetBrowsOfAoCols_MPIAIJ(A,P,MAT_INITIAL_MATRIX,&ptap->startsj_s,&ptap->startsj_r,&ptap->bufa,&ptap->P_oth);CHKERRQ(ierr); 172 /* get P_loc by taking all local rows of P */ 173 ierr = MatMPIAIJGetLocalMat(P,MAT_INITIAL_MATRIX,&ptap->P_loc);CHKERRQ(ierr); 174 175 /* (0) compute Rd = Pd^T, Ro = Po^T */ 176 /* --------------------------------- */ 177 ierr = MatTranspose_SeqAIJ(p->A,MAT_INITIAL_MATRIX,&ptap->Rd);CHKERRQ(ierr); 178 ierr = MatTranspose_SeqAIJ(p->B,MAT_INITIAL_MATRIX,&ptap->Ro);CHKERRQ(ierr); 179 #if defined(PTAP_PROFILE) 180 ierr = PetscTime(&t11);CHKERRQ(ierr); 181 #endif 182 183 /* (1) compute symbolic AP = A_loc*P = Ad*P_loc + Ao*P_oth (api,apj) */ 184 /* ----------------------------------------------------------------- */ 185 p_loc = (Mat_SeqAIJ*)(ptap->P_loc)->data; 186 p_oth = (Mat_SeqAIJ*)(ptap->P_oth)->data; 187 188 /* create and initialize a linked list */ 189 Prmax = p_loc->rmax+p_oth->rmax; 190 #if 0 191 printf("[%d] p_loc->rmax %d + p_oth->rmax %d = %d\n",rank,p_loc->rmax, p_oth->rmax,Prmax); 192 #endif 193 ierr = PetscTableCreate(2*Prmax,pN,&ta);CHKERRQ(ierr); /* for compute AP_loc */ 194 ierr = PetscTableCreate(2*Prmax,pN,&Cta);CHKERRQ(ierr);/* for compute Cmpi */ 195 for (row=0; row<ptap->P_loc->rmap->N; row++) { 196 nzi = p_loc->i[row+1] - p_loc->i[row]; 197 for (j=0; j<nzi; j++) { 198 Jptr = j + p_loc->j + p_loc->i[row]; 199 ierr = PetscTableAdd(ta,*Jptr+1,1,INSERT_VALUES);CHKERRQ(ierr); /* key must be >0 */ 200 } 201 } 202 for (row=0; row<ptap->P_oth->rmap->N; row++) { 203 nzi = p_oth->i[row+1] - p_oth->i[row]; 204 for (j=0; j<nzi; j++) { 205 Jptr = j + p_oth->j + p_oth->i[row]; 206 ierr = PetscTableAdd(ta,*Jptr+1,1,INSERT_VALUES);CHKERRQ(ierr); /* key must be >0 */ 207 } 208 } 209 ierr = PetscTableGetCount(ta,&Prmax);CHKERRQ(ierr); /* Prmax = nnz(sum of Prows) */ 210 ierr = PetscTableDestroy(&ta);CHKERRQ(ierr); 211 #if 0 212 //printf("[%d] Prmax %d, pN %d\n",rank,Prmax,pN); 213 printf("[%d] p_loc->rmax %d + p_oth->rmax %d = %d; Prmax %d\n",rank,p_loc->rmax, p_oth->rmax,p_loc->rmax+p_oth->rmax,Prmax); 214 #endif 215 ierr = PetscLLCondensedCreate(Prmax,pN,&lnk,&lnkbt);CHKERRQ(ierr); 216 217 /* Initial FreeSpace size is fill*(nnz(A) + nnz(P)) */ 218 ierr = PetscFreeSpaceGet((PetscInt)(fill*(ad->i[am]+ao->i[am]+p_loc->i[pm])),&free_space);CHKERRQ(ierr); 219 current_space = free_space; 220 nspacedouble = 0; 221 222 ierr = PetscMalloc1(am+1,&api);CHKERRQ(ierr); 223 api[0] = 0; 224 for (i=0; i<am; i++) { 225 /* diagonal portion: Ad[i,:]*P */ 226 ai = ad->i; pi = p_loc->i; 227 nzi = ai[i+1] - ai[i]; 228 aj = ad->j + ai[i]; 229 for (j=0; j<nzi; j++) { 230 row = aj[j]; 231 pnz = pi[row+1] - pi[row]; 232 Jptr = p_loc->j + pi[row]; 233 /* add non-zero cols of P into the sorted linked list lnk */ 234 ierr = PetscLLCondensedAddSorted(pnz,Jptr,lnk,lnkbt);CHKERRQ(ierr); 235 } 236 /* off-diagonal portion: Ao[i,:]*P */ 237 ai = ao->i; pi = p_oth->i; 238 nzi = ai[i+1] - ai[i]; 239 aj = ao->j + ai[i]; 240 for (j=0; j<nzi; j++) { 241 row = aj[j]; 242 pnz = pi[row+1] - pi[row]; 243 Jptr = p_oth->j + pi[row]; 244 ierr = PetscLLCondensedAddSorted(pnz,Jptr,lnk,lnkbt);CHKERRQ(ierr); 245 } 246 apnz = lnk[0]; 247 api[i+1] = api[i] + apnz; 248 if (ap_rmax < apnz) ap_rmax = apnz; 249 250 /* if free space is not available, double the total space in the list */ 251 if (current_space->local_remaining<apnz) { 252 ierr = PetscFreeSpaceGet(apnz+current_space->total_array_size,¤t_space);CHKERRQ(ierr); 253 nspacedouble++; 254 } 255 256 /* Copy data into free space, then initialize lnk */ 257 ierr = PetscLLCondensedClean(pN,apnz,current_space->array,lnk,lnkbt);CHKERRQ(ierr); 258 259 /* add column indices into Cta */ 260 for (j=0; j<apnz; j++) { 261 ierr = PetscTableAdd(Cta,current_space->array[j]+1,1,INSERT_VALUES);CHKERRQ(ierr); /* key must be >0 */ 262 } 263 264 current_space->array += apnz; 265 current_space->local_used += apnz; 266 current_space->local_remaining -= apnz; 267 } 268 /* Allocate space for apj and apv, initialize apj, and */ 269 /* destroy list of free space and other temporary array(s) */ 270 ierr = PetscMalloc2(api[am],&apj,api[am],&apv);CHKERRQ(ierr); 271 ierr = PetscFreeSpaceContiguous(&free_space,apj);CHKERRQ(ierr); 272 ierr = PetscLLDestroy(lnk,lnkbt);CHKERRQ(ierr); 273 274 ierr = PetscLLCondensedCreate(pN,pN,&lnk,&lnkbt);CHKERRQ(ierr); /* rm later! */ 275 276 /* Create AP_loc for reuse */ 277 ierr = MatCreateSeqAIJWithArrays(PETSC_COMM_SELF,am,pN,api,apj,apv,&ptap->AP_loc);CHKERRQ(ierr); 278 #if 0 279 Mat_SeqAIJ *ap_loc = (Mat_SeqAIJ*)(ptap->AP_loc)->data; 280 if (rank==1) printf("[%d] pN %d, AP_loc->rmax %d\n",rank,pN,ap_loc->rmax); 281 if (ap_loc->rmax == 0) { 282 printf("[%d] ap_loc->rmax == 0, empty AP_loc?, Prmax %d\n",rank,Prmax); 283 } 284 #endif 285 286 #if defined(PETSC_USE_INFO) 287 apfill = (PetscReal)api[am]/(ad->i[am]+ao->i[am]+p_loc->i[pm]+1); 288 ptap->AP_loc->info.mallocs = nspacedouble; 289 ptap->AP_loc->info.fill_ratio_given = fill; 290 ptap->AP_loc->info.fill_ratio_needed = apfill; 291 292 if (api[am]) { 293 ierr = PetscInfo3(ptap->AP_loc,"AP_loc reallocs %D; Fill ratio: given %g needed %g.\n",nspacedouble,(double)fill,(double)apfill);CHKERRQ(ierr); 294 ierr = PetscInfo1(ptap->AP_loc,"Use MatPtAP(A,B,MatReuse,%g,&C) for best AP_loc performance.;\n",(double)apfill);CHKERRQ(ierr); 295 } else { 296 ierr = PetscInfo(ptap->AP_loc,"AP_loc is empty \n");CHKERRQ(ierr); 297 } 298 #endif 299 300 #if defined(PTAP_PROFILE) 301 ierr = PetscTime(&t12);CHKERRQ(ierr); 302 #endif 303 304 /* (2-1) compute symbolic Co = Ro*AP_loc */ 305 /* ------------------------------------ */ 306 ierr = MatMatMultSymbolic_SeqAIJ_SeqAIJ(ptap->Ro,ptap->AP_loc,fill,&ptap->C_oth);CHKERRQ(ierr); 307 c_oth = (Mat_SeqAIJ*)ptap->C_oth->data; 308 #if defined(PTAP_PROFILE) 309 ierr = PetscTime(&t1);CHKERRQ(ierr); 310 #endif 311 312 /* (3) send coj of C_oth to other processors */ 313 /* ------------------------------------------ */ 314 /* determine row ownership */ 315 ierr = PetscLayoutCreate(comm,&rowmap);CHKERRQ(ierr); 316 rowmap->n = pn; 317 rowmap->bs = 1; 318 ierr = PetscLayoutSetUp(rowmap);CHKERRQ(ierr); 319 owners = rowmap->range; 320 321 /* determine the number of messages to send, their lengths */ 322 ierr = PetscMalloc4(size,&len_s,size,&len_si,size,&sstatus,size+2,&owners_co);CHKERRQ(ierr); 323 ierr = PetscMemzero(len_s,size*sizeof(PetscMPIInt));CHKERRQ(ierr); 324 ierr = PetscMemzero(len_si,size*sizeof(PetscMPIInt));CHKERRQ(ierr); 325 326 c_oth = (Mat_SeqAIJ*)ptap->C_oth->data; 327 coi = c_oth->i; coj = c_oth->j; 328 con = ptap->C_oth->rmap->n; 329 proc = 0; 330 for (i=0; i<con; i++) { 331 while (prmap[i] >= owners[proc+1]) proc++; 332 len_si[proc]++; /* num of rows in Co(=Pt*AP) to be sent to [proc] */ 333 len_s[proc] += coi[i+1] - coi[i]; /* num of nonzeros in Co to be sent to [proc] */ 334 } 335 336 len = 0; /* max length of buf_si[], see (4) */ 337 owners_co[0] = 0; 338 nsend = 0; 339 for (proc=0; proc<size; proc++) { 340 owners_co[proc+1] = owners_co[proc] + len_si[proc]; 341 if (len_s[proc]) { 342 nsend++; 343 len_si[proc] = 2*(len_si[proc] + 1); /* length of buf_si to be sent to [proc] */ 344 len += len_si[proc]; 345 } 346 } 347 348 /* determine the number and length of messages to receive for coi and coj */ 349 ierr = PetscGatherNumberOfMessages(comm,NULL,len_s,&nrecv);CHKERRQ(ierr); 350 ierr = PetscGatherMessageLengths2(comm,nsend,nrecv,len_s,len_si,&id_r,&len_r,&len_ri);CHKERRQ(ierr); 351 352 /* post the Irecv and Isend of coj */ 353 ierr = PetscCommGetNewTag(comm,&tagj);CHKERRQ(ierr); 354 ierr = PetscPostIrecvInt(comm,tagj,nrecv,id_r,len_r,&buf_rj,&rwaits);CHKERRQ(ierr); 355 ierr = PetscMalloc1(nsend+1,&swaits);CHKERRQ(ierr); 356 for (proc=0, k=0; proc<size; proc++) { 357 if (!len_s[proc]) continue; 358 i = owners_co[proc]; 359 ierr = MPI_Isend(coj+coi[i],len_s[proc],MPIU_INT,proc,tagj,comm,swaits+k);CHKERRQ(ierr); 360 k++; 361 } 362 363 /* (2-2) compute symbolic C_loc = Rd*AP_loc */ 364 /* ---------------------------------------- */ 365 ierr = MatMatMultSymbolic_SeqAIJ_SeqAIJ(ptap->Rd,ptap->AP_loc,fill,&ptap->C_loc);CHKERRQ(ierr); 366 c_loc = (Mat_SeqAIJ*)ptap->C_loc->data; 367 368 /* receives coj are complete */ 369 for (i=0; i<nrecv; i++) { 370 ierr = MPI_Waitany(nrecv,rwaits,&icompleted,&rstatus);CHKERRQ(ierr); 371 } 372 ierr = PetscFree(rwaits);CHKERRQ(ierr); 373 if (nsend) {ierr = MPI_Waitall(nsend,swaits,sstatus);CHKERRQ(ierr);} 374 375 ierr = PetscTableGetCount(Cta,&APrmax);CHKERRQ(ierr); /* Prmax = nnz(sum of Prows) */ 376 /* printf("[%d] APrmax %d, pN %d\n",rank,APrmax,pN); */ 377 378 /* (4) send and recv coi */ 379 /*-----------------------*/ 380 ierr = PetscCommGetNewTag(comm,&tagi);CHKERRQ(ierr); 381 ierr = PetscPostIrecvInt(comm,tagi,nrecv,id_r,len_ri,&buf_ri,&rwaits);CHKERRQ(ierr); 382 ierr = PetscMalloc1(len+1,&buf_s);CHKERRQ(ierr); 383 buf_si = buf_s; /* points to the beginning of k-th msg to be sent */ 384 for (proc=0,k=0; proc<size; proc++) { 385 if (!len_s[proc]) continue; 386 /* form outgoing message for i-structure: 387 buf_si[0]: nrows to be sent 388 [1:nrows]: row index (global) 389 [nrows+1:2*nrows+1]: i-structure index 390 */ 391 /*-------------------------------------------*/ 392 nrows = len_si[proc]/2 - 1; /* num of rows in Co to be sent to [proc] */ 393 buf_si_i = buf_si + nrows+1; 394 buf_si[0] = nrows; 395 buf_si_i[0] = 0; 396 nrows = 0; 397 for (i=owners_co[proc]; i<owners_co[proc+1]; i++) { 398 nzi = coi[i+1] - coi[i]; 399 buf_si_i[nrows+1] = buf_si_i[nrows] + nzi; /* i-structure */ 400 buf_si[nrows+1] = prmap[i] -owners[proc]; /* local row index */ 401 nrows++; 402 } 403 ierr = MPI_Isend(buf_si,len_si[proc],MPIU_INT,proc,tagi,comm,swaits+k);CHKERRQ(ierr); 404 k++; 405 buf_si += len_si[proc]; 406 } 407 for (i=0; i<nrecv; i++) { 408 ierr = MPI_Waitany(nrecv,rwaits,&icompleted,&rstatus);CHKERRQ(ierr); 409 } 410 ierr = PetscFree(rwaits);CHKERRQ(ierr); 411 if (nsend) {ierr = MPI_Waitall(nsend,swaits,sstatus);CHKERRQ(ierr);} 412 413 ierr = PetscFree4(len_s,len_si,sstatus,owners_co);CHKERRQ(ierr); 414 ierr = PetscFree(len_ri);CHKERRQ(ierr); 415 ierr = PetscFree(swaits);CHKERRQ(ierr); 416 ierr = PetscFree(buf_s);CHKERRQ(ierr); 417 #if defined(PTAP_PROFILE) 418 ierr = PetscTime(&t2);CHKERRQ(ierr); 419 #endif 420 /* (5) compute the local portion of Cmpi */ 421 /* ------------------------------------------ */ 422 ierr = PetscTableDestroy(&Cta);CHKERRQ(ierr); 423 424 /* set initial free space to be pN */ 425 ierr = PetscFreeSpaceGet(pN,&free_space);CHKERRQ(ierr); /* non-scalable version */ 426 current_space = free_space; 427 428 ierr = PetscMalloc3(nrecv,&buf_ri_k,nrecv,&nextrow,nrecv,&nextci);CHKERRQ(ierr); 429 for (k=0; k<nrecv; k++) { 430 buf_ri_k[k] = buf_ri[k]; /* beginning of k-th recved i-structure */ 431 nrows = *buf_ri_k[k]; 432 nextrow[k] = buf_ri_k[k] + 1; /* next row number of k-th recved i-structure */ 433 nextci[k] = buf_ri_k[k] + (nrows + 1); /* poins to the next i-structure of k-th recved i-structure */ 434 } 435 ierr = MatPreallocateInitialize(comm,pn,pn,dnz,onz);CHKERRQ(ierr); 436 437 rmax = 0; 438 for (i=0; i<pn; i++) { 439 /* add C_loc into Cmpi */ 440 nzi = c_loc->i[i+1] - c_loc->i[i]; 441 Jptr = c_loc->j + c_loc->i[i]; 442 ierr = PetscLLCondensedAddSorted(nzi,Jptr,lnk,lnkbt);CHKERRQ(ierr); 443 444 /* add received col data into lnk */ 445 for (k=0; k<nrecv; k++) { /* k-th received message */ 446 if (i == *nextrow[k]) { /* i-th row */ 447 nzi = *(nextci[k]+1) - *nextci[k]; 448 Jptr = buf_rj[k] + *nextci[k]; 449 ierr = PetscLLCondensedAddSorted(nzi,Jptr,lnk,lnkbt);CHKERRQ(ierr); 450 nextrow[k]++; nextci[k]++; 451 } 452 } 453 nnz = lnk[0]; 454 455 /* copy data into free space, then initialize lnk */ 456 ierr = PetscLLCondensedClean(pN,nnz,current_space->array,lnk,lnkbt);CHKERRQ(ierr); 457 ierr = MatPreallocateSet(i+owners[rank],nnz,current_space->array,dnz,onz);CHKERRQ(ierr); 458 if (nnz > rmax) rmax = nnz; 459 } 460 ierr = PetscFree3(buf_ri_k,nextrow,nextci);CHKERRQ(ierr); 461 ierr = PetscLLDestroy(lnk,lnkbt);CHKERRQ(ierr); 462 ierr = PetscFreeSpaceDestroy(free_space);CHKERRQ(ierr); 463 #if defined(PTAP_PROFILE) 464 ierr = PetscTime(&t3);CHKERRQ(ierr); 465 #endif 466 467 /* (6) create symbolic parallel matrix Cmpi */ 468 /*------------------------------------------*/ 469 ierr = MatCreate(comm,&Cmpi);CHKERRQ(ierr); 470 ierr = MatSetSizes(Cmpi,pn,pn,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 471 ierr = MatSetBlockSizes(Cmpi,PetscAbs(P->cmap->bs),PetscAbs(P->cmap->bs));CHKERRQ(ierr); 472 ierr = MatSetType(Cmpi,MATMPIAIJ);CHKERRQ(ierr); 473 ierr = MatMPIAIJSetPreallocation(Cmpi,0,dnz,0,onz);CHKERRQ(ierr); 474 ierr = MatPreallocateFinalize(dnz,onz);CHKERRQ(ierr); 475 476 /* members in merge */ 477 ierr = PetscFree(id_r);CHKERRQ(ierr); 478 ierr = PetscFree(len_r);CHKERRQ(ierr); 479 ierr = PetscFree(buf_ri[0]);CHKERRQ(ierr); 480 ierr = PetscFree(buf_ri);CHKERRQ(ierr); 481 ierr = PetscFree(buf_rj[0]);CHKERRQ(ierr); 482 ierr = PetscFree(buf_rj);CHKERRQ(ierr); 483 ierr = PetscLayoutDestroy(&rowmap);CHKERRQ(ierr); 484 485 /* attach the supporting struct to Cmpi for reuse */ 486 c = (Mat_MPIAIJ*)Cmpi->data; 487 c->ptap = ptap; 488 ptap->rmax = ap_rmax; 489 ptap->duplicate = Cmpi->ops->duplicate; 490 ptap->destroy = Cmpi->ops->destroy; 491 492 /* Do dense axpy in MatPtAPNumeric_MPIAIJ_MPIAIJ_new() */ 493 ierr = PetscCalloc1(pN,&ptap->apa);CHKERRQ(ierr); 494 495 496 /* Cmpi is not ready for use - assembly will be done by MatPtAPNumeric() */ 497 Cmpi->assembled = PETSC_FALSE; 498 Cmpi->ops->destroy = MatDestroy_MPIAIJ_PtAP; 499 Cmpi->ops->duplicate = MatDuplicate_MPIAIJ_MatPtAP; 500 Cmpi->ops->ptapnumeric = MatPtAPNumeric_MPIAIJ_MPIAIJ; 501 *C = Cmpi; 502 503 #if defined(PTAP_PROFILE) 504 ierr = PetscTime(&t4);CHKERRQ(ierr); 505 if (rank == 1) { 506 printf("PtAPSym: %g + %g + %g + %g + %g + %g = %g\n",t11-t0,t1-t11,t12-t11,t2-t2,t3-t2,t4-t3,t4-t0); 507 } 508 #endif 509 PetscFunctionReturn(0); 510 } 511 512 #undef __FUNCT__ 513 #define __FUNCT__ "MatPtAPNumeric_MPIAIJ_MPIAIJ" 514 PetscErrorCode MatPtAPNumeric_MPIAIJ_MPIAIJ(Mat A,Mat P,Mat C) 515 { 516 PetscErrorCode ierr; 517 Mat_MPIAIJ *a=(Mat_MPIAIJ*)A->data,*p=(Mat_MPIAIJ*)P->data,*c=(Mat_MPIAIJ*)C->data; 518 Mat_SeqAIJ *ad=(Mat_SeqAIJ*)(a->A)->data,*ao=(Mat_SeqAIJ*)(a->B)->data; 519 Mat_SeqAIJ *ap,*p_loc,*p_oth,*c_seq; 520 Mat_PtAPMPI *ptap = c->ptap; 521 Mat AP_loc,C_loc,C_oth; 522 PetscInt i,rstart,rend,cm,ncols,row; 523 PetscInt *api,*apj,am = A->rmap->n,j,col,apnz; 524 PetscScalar *apa; 525 const PetscInt *cols; 526 const PetscScalar *vals; 527 #if defined(PTAP_PROFILE) 528 PetscMPIInt rank; 529 MPI_Comm comm; 530 PetscLogDouble t0,t1,t2,t3,t4,eR,eAP,eCseq,eCmpi; 531 #endif 532 533 PetscFunctionBegin; 534 ierr = MatZeroEntries(C);CHKERRQ(ierr); 535 536 /* 1) get R = Pd^T,Ro = Po^T */ 537 #if defined(PTAP_PROFILE) 538 ierr = PetscTime(&t0);CHKERRQ(ierr); 539 #endif 540 if (ptap->reuse == MAT_REUSE_MATRIX) { 541 ierr = MatTranspose_SeqAIJ(p->A,MAT_REUSE_MATRIX,&ptap->Rd);CHKERRQ(ierr); 542 ierr = MatTranspose_SeqAIJ(p->B,MAT_REUSE_MATRIX,&ptap->Ro);CHKERRQ(ierr); 543 } 544 #if defined(PTAP_PROFILE) 545 ierr = PetscTime(&t1);CHKERRQ(ierr); 546 eR = t1 - t0; 547 #endif 548 549 /* 2) get AP_loc */ 550 AP_loc = ptap->AP_loc; 551 ap = (Mat_SeqAIJ*)AP_loc->data; 552 553 /* 2-1) get P_oth = ptap->P_oth and P_loc = ptap->P_loc */ 554 /*-----------------------------------------------------*/ 555 if (ptap->reuse == MAT_REUSE_MATRIX) { 556 /* P_oth and P_loc are obtained in MatPtASymbolic() when reuse == MAT_INITIAL_MATRIX */ 557 ierr = MatGetBrowsOfAoCols_MPIAIJ(A,P,MAT_REUSE_MATRIX,&ptap->startsj_s,&ptap->startsj_r,&ptap->bufa,&ptap->P_oth);CHKERRQ(ierr); 558 ierr = MatMPIAIJGetLocalMat(P,MAT_REUSE_MATRIX,&ptap->P_loc);CHKERRQ(ierr); 559 } 560 561 /* 2-2) compute numeric A_loc*P - dominating part */ 562 /* ---------------------------------------------- */ 563 /* get data from symbolic products */ 564 p_loc = (Mat_SeqAIJ*)(ptap->P_loc)->data; 565 p_oth = (Mat_SeqAIJ*)(ptap->P_oth)->data; 566 apa = ptap->apa; 567 api = ap->i; 568 apj = ap->j; 569 for (i=0; i<am; i++) { 570 /* AP[i,:] = A[i,:]*P = Ad*P_loc Ao*P_oth */ 571 AProw_nonscalable(i,ad,ao,p_loc,p_oth,apa); 572 apnz = api[i+1] - api[i]; 573 for (j=0; j<apnz; j++) { 574 col = apj[j+api[i]]; 575 ap->a[j+ap->i[i]] = apa[col]; 576 apa[col] = 0.0; 577 } 578 ierr = PetscLogFlops(2.0*apnz);CHKERRQ(ierr); 579 } 580 #if defined(PTAP_PROFILE) 581 ierr = PetscTime(&t2);CHKERRQ(ierr); 582 eAP = t2 - t1; 583 #endif 584 585 /* 3) C_loc = Rd*AP_loc, C_oth = Ro*AP_loc */ 586 ierr = ((ptap->C_loc)->ops->matmultnumeric)(ptap->Rd,AP_loc,ptap->C_loc);CHKERRQ(ierr); 587 ierr = ((ptap->C_oth)->ops->matmultnumeric)(ptap->Ro,AP_loc,ptap->C_oth);CHKERRQ(ierr); 588 C_loc = ptap->C_loc; 589 C_oth = ptap->C_oth; 590 #if defined(PTAP_PROFILE) 591 ierr = PetscTime(&t3);CHKERRQ(ierr); 592 eCseq = t3 - t2; 593 #endif 594 595 /* add C_loc and Co to to C */ 596 ierr = MatGetOwnershipRange(C,&rstart,&rend);CHKERRQ(ierr); 597 598 /* C_loc -> C */ 599 cm = C_loc->rmap->N; 600 c_seq = (Mat_SeqAIJ*)C_loc->data; 601 cols = c_seq->j; 602 vals = c_seq->a; 603 for (i=0; i<cm; i++) { 604 ncols = c_seq->i[i+1] - c_seq->i[i]; 605 row = rstart + i; 606 ierr = MatSetValues(C,1,&row,ncols,cols,vals,ADD_VALUES);CHKERRQ(ierr); 607 cols += ncols; vals += ncols; 608 } 609 610 /* Co -> C, off-processor part */ 611 cm = C_oth->rmap->N; 612 c_seq = (Mat_SeqAIJ*)C_oth->data; 613 cols = c_seq->j; 614 vals = c_seq->a; 615 for (i=0; i<cm; i++) { 616 ncols = c_seq->i[i+1] - c_seq->i[i]; 617 row = p->garray[i]; 618 ierr = MatSetValues(C,1,&row,ncols,cols,vals,ADD_VALUES);CHKERRQ(ierr); 619 cols += ncols; vals += ncols; 620 } 621 ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 622 ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 623 #if defined(PTAP_PROFILE) 624 ierr = PetscTime(&t4);CHKERRQ(ierr); 625 eCmpi = t4 - t3; 626 627 ierr = PetscObjectGetComm((PetscObject)C,&comm);CHKERRQ(ierr); 628 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 629 if (rank==1) { 630 ierr = PetscPrintf(MPI_COMM_SELF," R %g, AP %g, Cseq %g, Cmpi %g = %g\n", eR,eAP,eCseq,eCmpi,eR+eAP+eCseq+eCmpi);CHKERRQ(ierr); 631 } 632 #endif 633 ptap->reuse = MAT_REUSE_MATRIX; 634 PetscFunctionReturn(0); 635 } 636 637 #undef __FUNCT__ 638 #define __FUNCT__ "MatPtAPSymbolic_MPIAIJ_MPIAIJ_ptap" 639 PetscErrorCode MatPtAPSymbolic_MPIAIJ_MPIAIJ_ptap(Mat A,Mat P,PetscReal fill,Mat *C) 640 { 641 PetscErrorCode ierr; 642 Mat Cmpi; 643 Mat_PtAPMPI *ptap; 644 PetscFreeSpaceList free_space=NULL,current_space=NULL; 645 Mat_MPIAIJ *a =(Mat_MPIAIJ*)A->data,*p=(Mat_MPIAIJ*)P->data,*c; 646 Mat_SeqAIJ *ad =(Mat_SeqAIJ*)(a->A)->data,*ao=(Mat_SeqAIJ*)(a->B)->data; 647 Mat_SeqAIJ *p_loc,*p_oth; 648 PetscInt *pi_loc,*pj_loc,*pi_oth,*pj_oth,*pdti,*pdtj,*poti,*potj,*ptJ; 649 PetscInt *adi=ad->i,*aj,*aoi=ao->i,nnz; 650 PetscInt *lnk,*owners_co,*coi,*coj,i,k,pnz,row; 651 PetscInt am=A->rmap->n,pN=P->cmap->N,pm=P->rmap->n,pn=P->cmap->n; 652 PetscBT lnkbt; 653 MPI_Comm comm; 654 PetscMPIInt size,rank,tagi,tagj,*len_si,*len_s,*len_ri,icompleted=0; 655 PetscInt **buf_rj,**buf_ri,**buf_ri_k; 656 PetscInt len,proc,*dnz,*onz,*owners; 657 PetscInt nzi,*pti,*ptj; 658 PetscInt nrows,*buf_s,*buf_si,*buf_si_i,**nextrow,**nextci; 659 MPI_Request *swaits,*rwaits; 660 MPI_Status *sstatus,rstatus; 661 Mat_Merge_SeqsToMPI *merge; 662 PetscInt *api,*apj,*Jptr,apnz,*prmap=p->garray,pon,nspacedouble=0,j,ap_rmax=0; 663 PetscReal afill=1.0,afill_tmp; 664 PetscInt rmax; 665 666 PetscFunctionBegin; 667 ierr = PetscObjectGetComm((PetscObject)A,&comm);CHKERRQ(ierr); 668 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 669 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 670 671 /* create struct Mat_PtAPMPI and attached it to C later */ 672 ierr = PetscNew(&ptap);CHKERRQ(ierr); 673 ierr = PetscNew(&merge);CHKERRQ(ierr); 674 ptap->merge = merge; 675 ptap->reuse = MAT_INITIAL_MATRIX; 676 677 /* get P_oth by taking rows of P (= non-zero cols of local A) from other processors */ 678 ierr = MatGetBrowsOfAoCols_MPIAIJ(A,P,MAT_INITIAL_MATRIX,&ptap->startsj_s,&ptap->startsj_r,&ptap->bufa,&ptap->P_oth);CHKERRQ(ierr); 679 680 /* get P_loc by taking all local rows of P */ 681 ierr = MatMPIAIJGetLocalMat(P,MAT_INITIAL_MATRIX,&ptap->P_loc);CHKERRQ(ierr); 682 683 p_loc = (Mat_SeqAIJ*)(ptap->P_loc)->data; 684 p_oth = (Mat_SeqAIJ*)(ptap->P_oth)->data; 685 pi_loc = p_loc->i; pj_loc = p_loc->j; 686 pi_oth = p_oth->i; pj_oth = p_oth->j; 687 688 /* (1) compute symbolic AP = A_loc*P = A_diag*P_loc + A_off*P_oth (api,apj) */ 689 /*--------------------------------------------------------------------------*/ 690 ierr = PetscMalloc1(am+1,&api);CHKERRQ(ierr); 691 api[0] = 0; 692 693 /* create and initialize a linked list */ 694 ierr = PetscLLCondensedCreate(pN,pN,&lnk,&lnkbt);CHKERRQ(ierr); 695 696 /* Initial FreeSpace size is fill*(nnz(A) + nnz(P)) -OOM for ex56, np=8k on Intrepid! */ 697 ierr = PetscFreeSpaceGet((PetscInt)(fill*(adi[am]+aoi[am]+pi_loc[pm])),&free_space);CHKERRQ(ierr); 698 current_space = free_space; 699 700 for (i=0; i<am; i++) { 701 /* diagonal portion of A */ 702 nzi = adi[i+1] - adi[i]; 703 aj = ad->j + adi[i]; 704 for (j=0; j<nzi; j++) { 705 row = aj[j]; 706 pnz = pi_loc[row+1] - pi_loc[row]; 707 Jptr = pj_loc + pi_loc[row]; 708 /* add non-zero cols of P into the sorted linked list lnk */ 709 ierr = PetscLLCondensedAddSorted(pnz,Jptr,lnk,lnkbt);CHKERRQ(ierr); 710 } 711 /* off-diagonal portion of A */ 712 nzi = aoi[i+1] - aoi[i]; 713 aj = ao->j + aoi[i]; 714 for (j=0; j<nzi; j++) { 715 row = aj[j]; 716 pnz = pi_oth[row+1] - pi_oth[row]; 717 Jptr = pj_oth + pi_oth[row]; 718 ierr = PetscLLCondensedAddSorted(pnz,Jptr,lnk,lnkbt);CHKERRQ(ierr); 719 } 720 apnz = lnk[0]; 721 api[i+1] = api[i] + apnz; 722 if (ap_rmax < apnz) ap_rmax = apnz; 723 724 /* if free space is not available, double the total space in the list */ 725 if (current_space->local_remaining<apnz) { 726 ierr = PetscFreeSpaceGet(apnz+current_space->total_array_size,¤t_space);CHKERRQ(ierr); 727 nspacedouble++; 728 } 729 730 /* Copy data into free space, then initialize lnk */ 731 ierr = PetscLLCondensedClean(pN,apnz,current_space->array,lnk,lnkbt);CHKERRQ(ierr); 732 733 current_space->array += apnz; 734 current_space->local_used += apnz; 735 current_space->local_remaining -= apnz; 736 } 737 738 /* Allocate space for apj, initialize apj, and */ 739 /* destroy list of free space and other temporary array(s) */ 740 ierr = PetscMalloc1(api[am]+1,&apj);CHKERRQ(ierr); 741 ierr = PetscFreeSpaceContiguous(&free_space,apj);CHKERRQ(ierr); 742 afill_tmp = (PetscReal)api[am]/(adi[am]+aoi[am]+pi_loc[pm]+1); 743 if (afill_tmp > afill) afill = afill_tmp; 744 745 /* (2) determine symbolic Co=(p->B)^T*AP - send to others (coi,coj)*/ 746 /*-----------------------------------------------------------------*/ 747 ierr = MatGetSymbolicTranspose_SeqAIJ(p->B,&poti,&potj);CHKERRQ(ierr); 748 749 /* then, compute symbolic Co = (p->B)^T*AP */ 750 pon = (p->B)->cmap->n; /* total num of rows to be sent to other processors 751 >= (num of nonzero rows of C_seq) - pn */ 752 ierr = PetscMalloc1(pon+1,&coi);CHKERRQ(ierr); 753 coi[0] = 0; 754 755 /* set initial free space to be fill*(nnz(p->B) + nnz(AP)) */ 756 nnz = fill*(poti[pon] + api[am]); 757 ierr = PetscFreeSpaceGet(nnz,&free_space);CHKERRQ(ierr); 758 current_space = free_space; 759 760 for (i=0; i<pon; i++) { 761 pnz = poti[i+1] - poti[i]; 762 ptJ = potj + poti[i]; 763 for (j=0; j<pnz; j++) { 764 row = ptJ[j]; /* row of AP == col of Pot */ 765 apnz = api[row+1] - api[row]; 766 Jptr = apj + api[row]; 767 /* add non-zero cols of AP into the sorted linked list lnk */ 768 ierr = PetscLLCondensedAddSorted(apnz,Jptr,lnk,lnkbt);CHKERRQ(ierr); 769 } 770 nnz = lnk[0]; 771 772 /* If free space is not available, double the total space in the list */ 773 if (current_space->local_remaining<nnz) { 774 ierr = PetscFreeSpaceGet(nnz+current_space->total_array_size,¤t_space);CHKERRQ(ierr); 775 nspacedouble++; 776 } 777 778 /* Copy data into free space, and zero out denserows */ 779 ierr = PetscLLCondensedClean(pN,nnz,current_space->array,lnk,lnkbt);CHKERRQ(ierr); 780 781 current_space->array += nnz; 782 current_space->local_used += nnz; 783 current_space->local_remaining -= nnz; 784 785 coi[i+1] = coi[i] + nnz; 786 } 787 788 ierr = PetscMalloc1(coi[pon],&coj);CHKERRQ(ierr); 789 ierr = PetscFreeSpaceContiguous(&free_space,coj);CHKERRQ(ierr); 790 afill_tmp = (PetscReal)coi[pon]/(poti[pon] + api[am]+1); 791 if (afill_tmp > afill) afill = afill_tmp; 792 ierr = MatRestoreSymbolicTranspose_SeqAIJ(p->B,&poti,&potj);CHKERRQ(ierr); 793 794 /* (3) send j-array (coj) of Co to other processors */ 795 /*--------------------------------------------------*/ 796 ierr = PetscCalloc1(size,&merge->len_s);CHKERRQ(ierr); 797 len_s = merge->len_s; 798 merge->nsend = 0; 799 800 801 /* determine row ownership */ 802 ierr = PetscLayoutCreate(comm,&merge->rowmap);CHKERRQ(ierr); 803 merge->rowmap->n = pn; 804 merge->rowmap->bs = 1; 805 806 ierr = PetscLayoutSetUp(merge->rowmap);CHKERRQ(ierr); 807 owners = merge->rowmap->range; 808 809 /* determine the number of messages to send, their lengths */ 810 ierr = PetscMalloc2(size,&len_si,size,&sstatus);CHKERRQ(ierr); 811 ierr = PetscMemzero(len_si,size*sizeof(PetscMPIInt));CHKERRQ(ierr); 812 ierr = PetscMalloc1(size+2,&owners_co);CHKERRQ(ierr); 813 814 proc = 0; 815 for (i=0; i<pon; i++) { 816 while (prmap[i] >= owners[proc+1]) proc++; 817 len_si[proc]++; /* num of rows in Co(=Pt*AP) to be sent to [proc] */ 818 len_s[proc] += coi[i+1] - coi[i]; /* num of nonzeros in Co to be sent to [proc] */ 819 } 820 821 len = 0; /* max length of buf_si[], see (4) */ 822 owners_co[0] = 0; 823 for (proc=0; proc<size; proc++) { 824 owners_co[proc+1] = owners_co[proc] + len_si[proc]; 825 if (len_s[proc]) { 826 merge->nsend++; 827 len_si[proc] = 2*(len_si[proc] + 1); /* length of buf_si to be sent to [proc] */ 828 len += len_si[proc]; 829 } 830 } 831 832 /* determine the number and length of messages to receive for coi and coj */ 833 ierr = PetscGatherNumberOfMessages(comm,NULL,len_s,&merge->nrecv);CHKERRQ(ierr); 834 ierr = PetscGatherMessageLengths2(comm,merge->nsend,merge->nrecv,len_s,len_si,&merge->id_r,&merge->len_r,&len_ri);CHKERRQ(ierr); 835 836 /* post the Irecv and Isend of coj */ 837 ierr = PetscCommGetNewTag(comm,&tagj);CHKERRQ(ierr); 838 ierr = PetscPostIrecvInt(comm,tagj,merge->nrecv,merge->id_r,merge->len_r,&buf_rj,&rwaits);CHKERRQ(ierr); 839 ierr = PetscMalloc1(merge->nsend+1,&swaits);CHKERRQ(ierr); 840 for (proc=0, k=0; proc<size; proc++) { 841 if (!len_s[proc]) continue; 842 i = owners_co[proc]; 843 ierr = MPI_Isend(coj+coi[i],len_s[proc],MPIU_INT,proc,tagj,comm,swaits+k);CHKERRQ(ierr); 844 k++; 845 } 846 847 /* receives and sends of coj are complete */ 848 for (i=0; i<merge->nrecv; i++) { 849 ierr = MPI_Waitany(merge->nrecv,rwaits,&icompleted,&rstatus);CHKERRQ(ierr); 850 } 851 ierr = PetscFree(rwaits);CHKERRQ(ierr); 852 if (merge->nsend) {ierr = MPI_Waitall(merge->nsend,swaits,sstatus);CHKERRQ(ierr);} 853 854 /* (4) send and recv coi */ 855 /*-----------------------*/ 856 ierr = PetscCommGetNewTag(comm,&tagi);CHKERRQ(ierr); 857 ierr = PetscPostIrecvInt(comm,tagi,merge->nrecv,merge->id_r,len_ri,&buf_ri,&rwaits);CHKERRQ(ierr); 858 ierr = PetscMalloc1(len+1,&buf_s);CHKERRQ(ierr); 859 buf_si = buf_s; /* points to the beginning of k-th msg to be sent */ 860 for (proc=0,k=0; proc<size; proc++) { 861 if (!len_s[proc]) continue; 862 /* form outgoing message for i-structure: 863 buf_si[0]: nrows to be sent 864 [1:nrows]: row index (global) 865 [nrows+1:2*nrows+1]: i-structure index 866 */ 867 /*-------------------------------------------*/ 868 nrows = len_si[proc]/2 - 1; /* num of rows in Co to be sent to [proc] */ 869 buf_si_i = buf_si + nrows+1; 870 buf_si[0] = nrows; 871 buf_si_i[0] = 0; 872 nrows = 0; 873 for (i=owners_co[proc]; i<owners_co[proc+1]; i++) { 874 nzi = coi[i+1] - coi[i]; 875 buf_si_i[nrows+1] = buf_si_i[nrows] + nzi; /* i-structure */ 876 buf_si[nrows+1] = prmap[i] -owners[proc]; /* local row index */ 877 nrows++; 878 } 879 ierr = MPI_Isend(buf_si,len_si[proc],MPIU_INT,proc,tagi,comm,swaits+k);CHKERRQ(ierr); 880 k++; 881 buf_si += len_si[proc]; 882 } 883 i = merge->nrecv; 884 while (i--) { 885 ierr = MPI_Waitany(merge->nrecv,rwaits,&icompleted,&rstatus);CHKERRQ(ierr); 886 } 887 ierr = PetscFree(rwaits);CHKERRQ(ierr); 888 if (merge->nsend) {ierr = MPI_Waitall(merge->nsend,swaits,sstatus);CHKERRQ(ierr);} 889 890 ierr = PetscFree2(len_si,sstatus);CHKERRQ(ierr); 891 ierr = PetscFree(len_ri);CHKERRQ(ierr); 892 ierr = PetscFree(swaits);CHKERRQ(ierr); 893 ierr = PetscFree(buf_s);CHKERRQ(ierr); 894 895 /* (5) compute the local portion of C (mpi mat) */ 896 /*----------------------------------------------*/ 897 ierr = MatGetSymbolicTranspose_SeqAIJ(p->A,&pdti,&pdtj);CHKERRQ(ierr); 898 899 /* allocate pti array and free space for accumulating nonzero column info */ 900 ierr = PetscMalloc1(pn+1,&pti);CHKERRQ(ierr); 901 pti[0] = 0; 902 903 /* set initial free space to be fill*(nnz(P) + nnz(AP)) */ 904 nnz = fill*(pi_loc[pm] + api[am]); 905 ierr = PetscFreeSpaceGet(nnz,&free_space);CHKERRQ(ierr); 906 current_space = free_space; 907 908 ierr = PetscMalloc3(merge->nrecv,&buf_ri_k,merge->nrecv,&nextrow,merge->nrecv,&nextci);CHKERRQ(ierr); 909 for (k=0; k<merge->nrecv; k++) { 910 buf_ri_k[k] = buf_ri[k]; /* beginning of k-th recved i-structure */ 911 nrows = *buf_ri_k[k]; 912 nextrow[k] = buf_ri_k[k] + 1; /* next row number of k-th recved i-structure */ 913 nextci[k] = buf_ri_k[k] + (nrows + 1); /* poins to the next i-structure of k-th recved i-structure */ 914 } 915 ierr = MatPreallocateInitialize(comm,pn,pn,dnz,onz);CHKERRQ(ierr); 916 rmax = 0; 917 for (i=0; i<pn; i++) { 918 /* add pdt[i,:]*AP into lnk */ 919 pnz = pdti[i+1] - pdti[i]; 920 ptJ = pdtj + pdti[i]; 921 for (j=0; j<pnz; j++) { 922 row = ptJ[j]; /* row of AP == col of Pt */ 923 apnz = api[row+1] - api[row]; 924 Jptr = apj + api[row]; 925 /* add non-zero cols of AP into the sorted linked list lnk */ 926 ierr = PetscLLCondensedAddSorted(apnz,Jptr,lnk,lnkbt);CHKERRQ(ierr); 927 } 928 929 /* add received col data into lnk */ 930 for (k=0; k<merge->nrecv; k++) { /* k-th received message */ 931 if (i == *nextrow[k]) { /* i-th row */ 932 nzi = *(nextci[k]+1) - *nextci[k]; 933 Jptr = buf_rj[k] + *nextci[k]; 934 ierr = PetscLLCondensedAddSorted(nzi,Jptr,lnk,lnkbt);CHKERRQ(ierr); 935 nextrow[k]++; nextci[k]++; 936 } 937 } 938 nnz = lnk[0]; 939 940 /* if free space is not available, make more free space */ 941 if (current_space->local_remaining<nnz) { 942 ierr = PetscFreeSpaceGet(nnz+current_space->total_array_size,¤t_space);CHKERRQ(ierr); 943 nspacedouble++; 944 } 945 /* copy data into free space, then initialize lnk */ 946 ierr = PetscLLCondensedClean(pN,nnz,current_space->array,lnk,lnkbt);CHKERRQ(ierr); 947 ierr = MatPreallocateSet(i+owners[rank],nnz,current_space->array,dnz,onz);CHKERRQ(ierr); 948 949 current_space->array += nnz; 950 current_space->local_used += nnz; 951 current_space->local_remaining -= nnz; 952 953 pti[i+1] = pti[i] + nnz; 954 if (nnz > rmax) rmax = nnz; 955 } 956 ierr = MatRestoreSymbolicTranspose_SeqAIJ(p->A,&pdti,&pdtj);CHKERRQ(ierr); 957 ierr = PetscFree3(buf_ri_k,nextrow,nextci);CHKERRQ(ierr); 958 959 ierr = PetscMalloc1(pti[pn]+1,&ptj);CHKERRQ(ierr); 960 ierr = PetscFreeSpaceContiguous(&free_space,ptj);CHKERRQ(ierr); 961 afill_tmp = (PetscReal)pti[pn]/(pi_loc[pm] + api[am]+1); 962 if (afill_tmp > afill) afill = afill_tmp; 963 ierr = PetscLLDestroy(lnk,lnkbt);CHKERRQ(ierr); 964 965 /* (6) create symbolic parallel matrix Cmpi */ 966 /*------------------------------------------*/ 967 ierr = MatCreate(comm,&Cmpi);CHKERRQ(ierr); 968 ierr = MatSetSizes(Cmpi,pn,pn,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 969 ierr = MatSetBlockSizes(Cmpi,PetscAbs(P->cmap->bs),PetscAbs(P->cmap->bs));CHKERRQ(ierr); 970 ierr = MatSetType(Cmpi,MATMPIAIJ);CHKERRQ(ierr); 971 ierr = MatMPIAIJSetPreallocation(Cmpi,0,dnz,0,onz);CHKERRQ(ierr); 972 ierr = MatPreallocateFinalize(dnz,onz);CHKERRQ(ierr); 973 974 merge->bi = pti; /* Cseq->i */ 975 merge->bj = ptj; /* Cseq->j */ 976 merge->coi = coi; /* Co->i */ 977 merge->coj = coj; /* Co->j */ 978 merge->buf_ri = buf_ri; 979 merge->buf_rj = buf_rj; 980 merge->owners_co = owners_co; 981 merge->destroy = Cmpi->ops->destroy; 982 983 /* attach the supporting struct to Cmpi for reuse */ 984 c = (Mat_MPIAIJ*)Cmpi->data; 985 c->ptap = ptap; 986 ptap->api = api; 987 ptap->apj = apj; 988 ptap->rmax = ap_rmax; 989 ptap->duplicate = Cmpi->ops->duplicate; 990 ptap->destroy = Cmpi->ops->destroy; 991 992 /* Cmpi is not ready for use - assembly will be done by MatPtAPNumeric() */ 993 Cmpi->assembled = PETSC_FALSE; 994 Cmpi->ops->destroy = MatDestroy_MPIAIJ_PtAP; 995 Cmpi->ops->duplicate = MatDuplicate_MPIAIJ_MatPtAP; 996 Cmpi->ops->ptapnumeric = MatPtAPNumeric_MPIAIJ_MPIAIJ_ptap; 997 *C = Cmpi; 998 999 /* flag 'scalable' determines which implementations to be used: 1000 0: do dense axpy in MatPtAPNumeric() - fast, but requires storage of a nonscalable dense array apa; 1001 1: do sparse axpy in MatPtAPNumeric() - might slow, uses a sparse array apa */ 1002 /* set default scalable */ 1003 ptap->scalable = PETSC_FALSE; /* PETSC_TRUE; */ 1004 1005 ierr = PetscOptionsGetBool(((PetscObject)Cmpi)->prefix,"-matptap_scalable",&ptap->scalable,NULL);CHKERRQ(ierr); 1006 if (!ptap->scalable) { /* Do dense axpy */ 1007 ierr = PetscCalloc1(pN,&ptap->apa);CHKERRQ(ierr); 1008 } else { 1009 ierr = PetscCalloc1(ap_rmax+1,&ptap->apa);CHKERRQ(ierr); 1010 } 1011 1012 #if defined(PETSC_USE_INFO) 1013 if (pti[pn] != 0) { 1014 ierr = PetscInfo3(Cmpi,"Reallocs %D; Fill ratio: given %g needed %g.\n",nspacedouble,(double)fill,(double)afill);CHKERRQ(ierr); 1015 ierr = PetscInfo1(Cmpi,"Use MatPtAP(A,P,MatReuse,%g,&C) for best performance.\n",(double)afill);CHKERRQ(ierr); 1016 } else { 1017 ierr = PetscInfo(Cmpi,"Empty matrix product\n");CHKERRQ(ierr); 1018 } 1019 #endif 1020 PetscFunctionReturn(0); 1021 } 1022 1023 #undef __FUNCT__ 1024 #define __FUNCT__ "MatPtAPNumeric_MPIAIJ_MPIAIJ_ptap" 1025 PetscErrorCode MatPtAPNumeric_MPIAIJ_MPIAIJ_ptap(Mat A,Mat P,Mat C) 1026 { 1027 PetscErrorCode ierr; 1028 Mat_MPIAIJ *a =(Mat_MPIAIJ*)A->data,*p=(Mat_MPIAIJ*)P->data,*c=(Mat_MPIAIJ*)C->data; 1029 Mat_SeqAIJ *ad=(Mat_SeqAIJ*)(a->A)->data,*ao=(Mat_SeqAIJ*)(a->B)->data; 1030 Mat_SeqAIJ *pd=(Mat_SeqAIJ*)(p->A)->data,*po=(Mat_SeqAIJ*)(p->B)->data; 1031 Mat_SeqAIJ *p_loc,*p_oth; 1032 Mat_PtAPMPI *ptap; 1033 Mat_Merge_SeqsToMPI *merge; 1034 PetscInt *adi=ad->i,*aoi=ao->i,*adj,*aoj,*apJ,nextp; 1035 PetscInt *pi_loc,*pj_loc,*pi_oth,*pj_oth,*pJ,*pj; 1036 PetscInt i,j,k,anz,pnz,apnz,nextap,row,*cj; 1037 MatScalar *ada,*aoa,*apa,*pa,*ca,*pa_loc,*pa_oth,valtmp; 1038 PetscInt am =A->rmap->n,cm=C->rmap->n,pon=(p->B)->cmap->n; 1039 MPI_Comm comm; 1040 PetscMPIInt size,rank,taga,*len_s; 1041 PetscInt *owners,proc,nrows,**buf_ri_k,**nextrow,**nextci; 1042 PetscInt **buf_ri,**buf_rj; 1043 PetscInt cnz=0,*bj_i,*bi,*bj,bnz,nextcj; /* bi,bj,ba: local array of C(mpi mat) */ 1044 MPI_Request *s_waits,*r_waits; 1045 MPI_Status *status; 1046 MatScalar **abuf_r,*ba_i,*pA,*coa,*ba; 1047 PetscInt *api,*apj,*coi,*coj; 1048 PetscInt *poJ=po->j,*pdJ=pd->j,pcstart=P->cmap->rstart,pcend=P->cmap->rend; 1049 PetscBool scalable; 1050 #if defined(PTAP_PROFILE) 1051 PetscLogDouble t0,t1,t2,eP,t3,t4,et2_AP=0.0,ePtAP=0.0,t2_0,t2_1,t2_2; 1052 #endif 1053 1054 PetscFunctionBegin; 1055 ierr = PetscObjectGetComm((PetscObject)C,&comm);CHKERRQ(ierr); 1056 #if defined(PTAP_PROFILE) 1057 ierr = PetscTime(&t0);CHKERRQ(ierr); 1058 #endif 1059 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 1060 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 1061 1062 ptap = c->ptap; 1063 if (!ptap) SETERRQ(PetscObjectComm((PetscObject)C),PETSC_ERR_ARG_INCOMP,"MatPtAP() has not been called to create matrix C yet, cannot use MAT_REUSE_MATRIX"); 1064 merge = ptap->merge; 1065 apa = ptap->apa; 1066 scalable = ptap->scalable; 1067 1068 /* 1) get P_oth = ptap->P_oth and P_loc = ptap->P_loc */ 1069 /*-----------------------------------------------------*/ 1070 if (ptap->reuse == MAT_INITIAL_MATRIX) { 1071 /* P_oth and P_loc are obtained in MatPtASymbolic(), skip calling MatGetBrowsOfAoCols() and MatMPIAIJGetLocalMat() */ 1072 ptap->reuse = MAT_REUSE_MATRIX; 1073 } else { /* update numerical values of P_oth and P_loc */ 1074 ierr = MatGetBrowsOfAoCols_MPIAIJ(A,P,MAT_REUSE_MATRIX,&ptap->startsj_s,&ptap->startsj_r,&ptap->bufa,&ptap->P_oth);CHKERRQ(ierr); 1075 ierr = MatMPIAIJGetLocalMat(P,MAT_REUSE_MATRIX,&ptap->P_loc);CHKERRQ(ierr); 1076 } 1077 #if defined(PTAP_PROFILE) 1078 ierr = PetscTime(&t1);CHKERRQ(ierr); 1079 eP = t1-t0; 1080 #endif 1081 /* 1082 printf("[%d] Ad: %d, %d; Ao: %d, %d; P_loc: %d, %d; P_oth %d, %d;\n",rank, 1083 a->A->rmap->N,a->A->cmap->N,a->B->rmap->N,a->B->cmap->N, 1084 ptap->P_loc->rmap->N,ptap->P_loc->cmap->N, 1085 ptap->P_oth->rmap->N,ptap->P_oth->cmap->N); 1086 */ 1087 1088 /* 2) compute numeric C_seq = P_loc^T*A_loc*P - dominating part */ 1089 /*--------------------------------------------------------------*/ 1090 /* get data from symbolic products */ 1091 p_loc = (Mat_SeqAIJ*)(ptap->P_loc)->data; 1092 p_oth = (Mat_SeqAIJ*)(ptap->P_oth)->data; 1093 pi_loc=p_loc->i; pj_loc=p_loc->j; pJ=pj_loc; pa_loc=p_loc->a; 1094 pi_oth=p_oth->i; pj_oth=p_oth->j; pa_oth=p_oth->a; 1095 1096 coi = merge->coi; coj = merge->coj; 1097 ierr = PetscCalloc1(coi[pon]+1,&coa);CHKERRQ(ierr); 1098 1099 bi = merge->bi; bj = merge->bj; 1100 owners = merge->rowmap->range; 1101 ierr = PetscCalloc1(bi[cm]+1,&ba);CHKERRQ(ierr); /* ba: Cseq->a */ 1102 1103 api = ptap->api; apj = ptap->apj; 1104 1105 if (!scalable) { /* Do dense axpy on apa (length of pN, stores A[i,:]*P) - nonscalable, but faster (could take 1/3 scalable time) */ 1106 ierr = PetscInfo(C,"Using non-scalable dense axpy\n");CHKERRQ(ierr); 1107 #if defined(PTAP_PROFILE) 1108 ierr = PetscTime(&t1);CHKERRQ(ierr); 1109 #endif 1110 for (i=0; i<am; i++) { 1111 #if defined(PTAP_PROFILE) 1112 ierr = PetscTime(&t2_0);CHKERRQ(ierr); 1113 #endif 1114 /* 2-a) form i-th sparse row of A_loc*P = Ad*P_loc + Ao*P_oth */ 1115 /*------------------------------------------------------------*/ 1116 apJ = apj + api[i]; 1117 1118 /* diagonal portion of A */ 1119 anz = adi[i+1] - adi[i]; 1120 adj = ad->j + adi[i]; 1121 ada = ad->a + adi[i]; 1122 for (j=0; j<anz; j++) { 1123 row = adj[j]; 1124 pnz = pi_loc[row+1] - pi_loc[row]; 1125 pj = pj_loc + pi_loc[row]; 1126 pa = pa_loc + pi_loc[row]; 1127 1128 /* perform dense axpy */ 1129 valtmp = ada[j]; 1130 for (k=0; k<pnz; k++) { 1131 apa[pj[k]] += valtmp*pa[k]; 1132 } 1133 ierr = PetscLogFlops(2.0*pnz);CHKERRQ(ierr); 1134 } 1135 1136 /* off-diagonal portion of A */ 1137 anz = aoi[i+1] - aoi[i]; 1138 aoj = ao->j + aoi[i]; 1139 aoa = ao->a + aoi[i]; 1140 for (j=0; j<anz; j++) { 1141 row = aoj[j]; 1142 pnz = pi_oth[row+1] - pi_oth[row]; 1143 pj = pj_oth + pi_oth[row]; 1144 pa = pa_oth + pi_oth[row]; 1145 1146 /* perform dense axpy */ 1147 valtmp = aoa[j]; 1148 for (k=0; k<pnz; k++) { 1149 apa[pj[k]] += valtmp*pa[k]; 1150 } 1151 ierr = PetscLogFlops(2.0*pnz);CHKERRQ(ierr); 1152 } 1153 #if defined(PTAP_PROFILE) 1154 ierr = PetscTime(&t2_1);CHKERRQ(ierr); 1155 et2_AP += t2_1 - t2_0; 1156 #endif 1157 1158 /* 2-b) Compute Cseq = P_loc[i,:]^T*AP[i,:] using outer product */ 1159 /*--------------------------------------------------------------*/ 1160 apnz = api[i+1] - api[i]; 1161 /* put the value into Co=(p->B)^T*AP (off-diagonal part, send to others) */ 1162 pnz = po->i[i+1] - po->i[i]; 1163 poJ = po->j + po->i[i]; 1164 pA = po->a + po->i[i]; 1165 for (j=0; j<pnz; j++) { 1166 row = poJ[j]; 1167 cnz = coi[row+1] - coi[row]; 1168 cj = coj + coi[row]; 1169 ca = coa + coi[row]; 1170 /* perform dense axpy */ 1171 valtmp = pA[j]; 1172 for (k=0; k<cnz; k++) { 1173 ca[k] += valtmp*apa[cj[k]]; 1174 } 1175 ierr = PetscLogFlops(2.0*cnz);CHKERRQ(ierr); 1176 } 1177 /* put the value into Cd (diagonal part) */ 1178 pnz = pd->i[i+1] - pd->i[i]; 1179 pdJ = pd->j + pd->i[i]; 1180 pA = pd->a + pd->i[i]; 1181 for (j=0; j<pnz; j++) { 1182 row = pdJ[j]; 1183 cnz = bi[row+1] - bi[row]; 1184 cj = bj + bi[row]; 1185 ca = ba + bi[row]; 1186 /* perform dense axpy */ 1187 valtmp = pA[j]; 1188 for (k=0; k<cnz; k++) { 1189 ca[k] += valtmp*apa[cj[k]]; 1190 } 1191 ierr = PetscLogFlops(2.0*cnz);CHKERRQ(ierr); 1192 } 1193 1194 /* zero the current row of A*P */ 1195 for (k=0; k<apnz; k++) apa[apJ[k]] = 0.0; 1196 #if defined(PTAP_PROFILE) 1197 ierr = PetscTime(&t2_2);CHKERRQ(ierr); 1198 ePtAP += t2_2 - t2_1; 1199 #endif 1200 } 1201 } else { /* Do sparse axpy on apa (length of ap_rmax, stores A[i,:]*P) - scalable, but slower */ 1202 ierr = PetscInfo(C,"Using scalable sparse axpy\n");CHKERRQ(ierr); 1203 /*-----------------------------------------------------------------------------------------*/ 1204 pA=pa_loc; 1205 for (i=0; i<am; i++) { 1206 #if defined(PTAP_PROFILE) 1207 ierr = PetscTime(&t2_0);CHKERRQ(ierr); 1208 #endif 1209 /* form i-th sparse row of A*P */ 1210 apnz = api[i+1] - api[i]; 1211 apJ = apj + api[i]; 1212 /* diagonal portion of A */ 1213 anz = adi[i+1] - adi[i]; 1214 adj = ad->j + adi[i]; 1215 ada = ad->a + adi[i]; 1216 for (j=0; j<anz; j++) { 1217 row = adj[j]; 1218 pnz = pi_loc[row+1] - pi_loc[row]; 1219 pj = pj_loc + pi_loc[row]; 1220 pa = pa_loc + pi_loc[row]; 1221 valtmp = ada[j]; 1222 nextp = 0; 1223 for (k=0; nextp<pnz; k++) { 1224 if (apJ[k] == pj[nextp]) { /* col of AP == col of P */ 1225 apa[k] += valtmp*pa[nextp++]; 1226 } 1227 } 1228 ierr = PetscLogFlops(2.0*pnz);CHKERRQ(ierr); 1229 } 1230 /* off-diagonal portion of A */ 1231 anz = aoi[i+1] - aoi[i]; 1232 aoj = ao->j + aoi[i]; 1233 aoa = ao->a + aoi[i]; 1234 for (j=0; j<anz; j++) { 1235 row = aoj[j]; 1236 pnz = pi_oth[row+1] - pi_oth[row]; 1237 pj = pj_oth + pi_oth[row]; 1238 pa = pa_oth + pi_oth[row]; 1239 valtmp = aoa[j]; 1240 nextp = 0; 1241 for (k=0; nextp<pnz; k++) { 1242 if (apJ[k] == pj[nextp]) { /* col of AP == col of P */ 1243 apa[k] += valtmp*pa[nextp++]; 1244 } 1245 } 1246 ierr = PetscLogFlops(2.0*pnz);CHKERRQ(ierr); 1247 } 1248 #if defined(PTAP_PROFILE) 1249 ierr = PetscTime(&t2_1);CHKERRQ(ierr); 1250 et2_AP += t2_1 - t2_0; 1251 #endif 1252 1253 /* 2-b) Compute Cseq = P_loc[i,:]^T*AP[i,:] using outer product */ 1254 /*--------------------------------------------------------------*/ 1255 pnz = pi_loc[i+1] - pi_loc[i]; 1256 pJ = pj_loc + pi_loc[i]; 1257 for (j=0; j<pnz; j++) { 1258 nextap = 0; 1259 row = pJ[j]; /* global index */ 1260 if (row < pcstart || row >=pcend) { /* put the value into Co */ 1261 row = *poJ; 1262 cj = coj + coi[row]; 1263 ca = coa + coi[row]; poJ++; 1264 } else { /* put the value into Cd */ 1265 row = *pdJ; 1266 cj = bj + bi[row]; 1267 ca = ba + bi[row]; pdJ++; 1268 } 1269 valtmp = pA[j]; 1270 for (k=0; nextap<apnz; k++) { 1271 if (cj[k]==apJ[nextap]) ca[k] += valtmp*apa[nextap++]; 1272 } 1273 ierr = PetscLogFlops(2.0*apnz);CHKERRQ(ierr); 1274 } 1275 pA += pnz; 1276 /* zero the current row info for A*P */ 1277 ierr = PetscMemzero(apa,apnz*sizeof(MatScalar));CHKERRQ(ierr); 1278 #if defined(PTAP_PROFILE) 1279 ierr = PetscTime(&t2_2);CHKERRQ(ierr); 1280 ePtAP += t2_2 - t2_1; 1281 #endif 1282 } 1283 } 1284 #if defined(PTAP_PROFILE) 1285 ierr = PetscTime(&t2);CHKERRQ(ierr); 1286 #endif 1287 1288 /* 3) send and recv matrix values coa */ 1289 /*------------------------------------*/ 1290 buf_ri = merge->buf_ri; 1291 buf_rj = merge->buf_rj; 1292 len_s = merge->len_s; 1293 ierr = PetscCommGetNewTag(comm,&taga);CHKERRQ(ierr); 1294 ierr = PetscPostIrecvScalar(comm,taga,merge->nrecv,merge->id_r,merge->len_r,&abuf_r,&r_waits);CHKERRQ(ierr); 1295 1296 ierr = PetscMalloc2(merge->nsend+1,&s_waits,size,&status);CHKERRQ(ierr); 1297 for (proc=0,k=0; proc<size; proc++) { 1298 if (!len_s[proc]) continue; 1299 i = merge->owners_co[proc]; 1300 ierr = MPI_Isend(coa+coi[i],len_s[proc],MPIU_MATSCALAR,proc,taga,comm,s_waits+k);CHKERRQ(ierr); 1301 k++; 1302 } 1303 if (merge->nrecv) {ierr = MPI_Waitall(merge->nrecv,r_waits,status);CHKERRQ(ierr);} 1304 if (merge->nsend) {ierr = MPI_Waitall(merge->nsend,s_waits,status);CHKERRQ(ierr);} 1305 1306 ierr = PetscFree2(s_waits,status);CHKERRQ(ierr); 1307 ierr = PetscFree(r_waits);CHKERRQ(ierr); 1308 ierr = PetscFree(coa);CHKERRQ(ierr); 1309 #if defined(PTAP_PROFILE) 1310 ierr = PetscTime(&t3);CHKERRQ(ierr); 1311 #endif 1312 1313 /* 4) insert local Cseq and received values into Cmpi */ 1314 /*------------------------------------------------------*/ 1315 ierr = PetscMalloc3(merge->nrecv,&buf_ri_k,merge->nrecv,&nextrow,merge->nrecv,&nextci);CHKERRQ(ierr); 1316 for (k=0; k<merge->nrecv; k++) { 1317 buf_ri_k[k] = buf_ri[k]; /* beginning of k-th recved i-structure */ 1318 nrows = *(buf_ri_k[k]); 1319 nextrow[k] = buf_ri_k[k]+1; /* next row number of k-th recved i-structure */ 1320 nextci[k] = buf_ri_k[k] + (nrows + 1); /* poins to the next i-structure of k-th recved i-structure */ 1321 } 1322 1323 for (i=0; i<cm; i++) { 1324 row = owners[rank] + i; /* global row index of C_seq */ 1325 bj_i = bj + bi[i]; /* col indices of the i-th row of C */ 1326 ba_i = ba + bi[i]; 1327 bnz = bi[i+1] - bi[i]; 1328 /* add received vals into ba */ 1329 for (k=0; k<merge->nrecv; k++) { /* k-th received message */ 1330 /* i-th row */ 1331 if (i == *nextrow[k]) { 1332 cnz = *(nextci[k]+1) - *nextci[k]; 1333 cj = buf_rj[k] + *(nextci[k]); 1334 ca = abuf_r[k] + *(nextci[k]); 1335 nextcj = 0; 1336 for (j=0; nextcj<cnz; j++) { 1337 if (bj_i[j] == cj[nextcj]) { /* bcol == ccol */ 1338 ba_i[j] += ca[nextcj++]; 1339 } 1340 } 1341 nextrow[k]++; nextci[k]++; 1342 ierr = PetscLogFlops(2.0*cnz);CHKERRQ(ierr); 1343 } 1344 } 1345 ierr = MatSetValues(C,1,&row,bnz,bj_i,ba_i,INSERT_VALUES);CHKERRQ(ierr); 1346 } 1347 ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1348 ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1349 1350 ierr = PetscFree(ba);CHKERRQ(ierr); 1351 ierr = PetscFree(abuf_r[0]);CHKERRQ(ierr); 1352 ierr = PetscFree(abuf_r);CHKERRQ(ierr); 1353 ierr = PetscFree3(buf_ri_k,nextrow,nextci);CHKERRQ(ierr); 1354 #if defined(PTAP_PROFILE) 1355 ierr = PetscTime(&t4);CHKERRQ(ierr); 1356 if (rank==1) { 1357 ierr = PetscPrintf(MPI_COMM_SELF," [%d] PtAPNum %g/P + %g/PtAP( %g/A*P + %g/Pt*AP ) + %g/comm + %g/Cloc = %g\n\n",rank,eP,t2-t1,et2_AP,ePtAP,t3-t2,t4-t3,t4-t0);CHKERRQ(ierr); 1358 } 1359 #endif 1360 PetscFunctionReturn(0); 1361 } 1362