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