Date: 2016-07-24T16:53:55+00:00

Actual source code: mpiptap.c
petsc-3.7.3 2016-07-24
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      2: /*
      3:   Defines projective product routines where A is a MPIAIJ matrix
      4:           C = P^T * A * P
      5: */

      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>

     13: /* #define PTAP_PROFILE */

     15: extern PetscErrorCode MatDestroy_MPIAIJ(Mat);
     18: PetscErrorCode MatDestroy_MPIAIJ_PtAP(Mat A)
     19: {
     21:   Mat_MPIAIJ     *a=(Mat_MPIAIJ*)A->data;
     22:   Mat_PtAPMPI    *ptap=a->ptap;

     25:   if (ptap) {
     26:     Mat_Merge_SeqsToMPI *merge=ptap->merge;
     27:     PetscFree2(ptap->startsj_s,ptap->startsj_r);
     28:     PetscFree(ptap->bufa);
     29:     MatDestroy(&ptap->P_loc);
     30:     MatDestroy(&ptap->P_oth);
     31:     MatDestroy(&ptap->A_loc); /* used by MatTransposeMatMult() */
     32:     MatDestroy(&ptap->Rd);
     33:     MatDestroy(&ptap->Ro);
     34:     if (ptap->AP_loc) { /* used by alg_rap */
     35:       Mat_SeqAIJ *ap = (Mat_SeqAIJ*)(ptap->AP_loc)->data;
     36:       PetscFree(ap->i);
     37:       PetscFree2(ap->j,ap->a);
     38:       MatDestroy(&ptap->AP_loc);
     39:     } else { /* used by alg_ptap */
     40:       PetscFree(ptap->api);
     41:       PetscFree(ptap->apj);
     42:     }
     43:     MatDestroy(&ptap->C_loc);
     44:     MatDestroy(&ptap->C_oth);
     45:     if (ptap->apa) {PetscFree(ptap->apa);}

     47:     if (merge) { /* used by alg_ptap */
     48:       PetscFree(merge->id_r);
     49:       PetscFree(merge->len_s);
     50:       PetscFree(merge->len_r);
     51:       PetscFree(merge->bi);
     52:       PetscFree(merge->bj);
     53:       PetscFree(merge->buf_ri[0]);
     54:       PetscFree(merge->buf_ri);
     55:       PetscFree(merge->buf_rj[0]);
     56:       PetscFree(merge->buf_rj);
     57:       PetscFree(merge->coi);
     58:       PetscFree(merge->coj);
     59:       PetscFree(merge->owners_co);
     60:       PetscLayoutDestroy(&merge->rowmap);
     61:       PetscFree(ptap->merge);
     62:     }
     63:
     64:     ptap->destroy(A);
     65:     PetscFree(ptap);
     66:   }
     67:   return(0);
     68: }

     72: PetscErrorCode MatDuplicate_MPIAIJ_MatPtAP(Mat A, MatDuplicateOption op, Mat *M)
     73: {
     75:   Mat_MPIAIJ     *a     = (Mat_MPIAIJ*)A->data;
     76:   Mat_PtAPMPI    *ptap  = a->ptap;

     79:   (*ptap->duplicate)(A,op,M);
     80:   (*M)->ops->destroy   = ptap->destroy;
     81:   (*M)->ops->duplicate = ptap->duplicate;
     82:   return(0);
     83: }

     87: PETSC_INTERN PetscErrorCode MatPtAP_MPIAIJ_MPIAIJ(Mat A,Mat P,MatReuse scall,PetscReal fill,Mat *C)
     88: {
     90:   PetscBool      rap=PETSC_TRUE; /* do R=P^T locally, then C=R*A*P */
     91:   MPI_Comm       comm;

     94:   /* check if matrix local sizes are compatible */
     95:   PetscObjectGetComm((PetscObject)A,&comm);
     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);

     99:   PetscOptionsGetBool(NULL,NULL,"-matrap",&rap,NULL);
    100:   if (scall == MAT_INITIAL_MATRIX) {
    101:     PetscLogEventBegin(MAT_PtAPSymbolic,A,P,0,0);
    102:     if (rap) { /* do R=P^T locally, then C=R*A*P */
    103:       MatPtAPSymbolic_MPIAIJ_MPIAIJ(A,P,fill,C);
    104:     } else {       /* do P^T*A*P */
    105:       MatPtAPSymbolic_MPIAIJ_MPIAIJ_ptap(A,P,fill,C);
    106:     }
    107:     PetscLogEventEnd(MAT_PtAPSymbolic,A,P,0,0);
    108:   }
    109:   PetscLogEventBegin(MAT_PtAPNumeric,A,P,0,0);
    110:   (*(*C)->ops->ptapnumeric)(A,P,*C);
    111:   PetscLogEventEnd(MAT_PtAPNumeric,A,P,0,0);
    112:   return(0);
    113: }

    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

    152:   PetscObjectGetComm((PetscObject)A,&comm);
    153:   MPI_Comm_size(comm,&size);
    154:   MPI_Comm_rank(comm,&rank);
    155: #if defined(PTAP_PROFILE)
    156:   PetscTime(&t0);
    157: #endif

    159:   /* create struct Mat_PtAPMPI and attached it to C later */
    160:   PetscNew(&ptap);
    161:   ptap->reuse = MAT_INITIAL_MATRIX;

    163:   /* get P_oth by taking rows of P (= non-zero cols of local A) from other processors */
    164:   MatGetBrowsOfAoCols_MPIAIJ(A,P,MAT_INITIAL_MATRIX,&ptap->startsj_s,&ptap->startsj_r,&ptap->bufa,&ptap->P_oth);
    165:   /* get P_loc by taking all local rows of P */
    166:   MatMPIAIJGetLocalMat(P,MAT_INITIAL_MATRIX,&ptap->P_loc);

    168:   /* (0) compute Rd = Pd^T, Ro = Po^T  */
    169:   /* --------------------------------- */
    170:   MatTranspose_SeqAIJ(p->A,MAT_INITIAL_MATRIX,&ptap->Rd);
    171:   MatTranspose_SeqAIJ(p->B,MAT_INITIAL_MATRIX,&ptap->Ro);
    172: #if defined(PTAP_PROFILE)
    173:   PetscTime(&t11);
    174: #endif

    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;

    181:   /* create and initialize a linked list */
    182:   PetscTableCreate(pN,pN,&ta); /* for compute AP_loc and Cmpi */
    183:   MatRowMergeMax_SeqAIJ(p_loc,ptap->P_loc->rmap->N,ta);
    184:   MatRowMergeMax_SeqAIJ(p_oth,ptap->P_oth->rmap->N,ta);
    185:   PetscTableGetCount(ta,&Crmax); /* Crmax = nnz(sum of Prows) */
    186:   /* printf("[%d] est %d, Crmax %d; pN %d\n",rank,5*(p_loc->rmax+p_oth->rmax + (PetscInt)(1.e-2*pN)),Crmax,pN); */

    188:   PetscLLCondensedCreate(Crmax,pN,&lnk,&lnkbt);

    190:   /* Initial FreeSpace size is fill*(nnz(A) + nnz(P)) */
    191:   PetscFreeSpaceGet(PetscRealIntMultTruncate(fill,PetscIntSumTruncate(ad->i[am],PetscIntSumTruncate(ao->i[am],p_loc->i[pm]))),&free_space);
    192:   current_space = free_space;
    193:   nspacedouble  = 0;

    195:   PetscMalloc1(am+1,&api);
    196:   api[0] = 0;
    197:   for (i=0; i<am; i++) {
    198:     /* diagonal portion: Ad[i,:]*P */
    199:     ai = ad->i; pi = p_loc->i;
    200:     nzi = ai[i+1] - ai[i];
    201:     aj  = ad->j + ai[i];
    202:     for (j=0; j<nzi; j++) {
    203:       row  = aj[j];
    204:       pnz  = pi[row+1] - pi[row];
    205:       Jptr = p_loc->j + pi[row];
    206:       /* add non-zero cols of P into the sorted linked list lnk */
    207:       PetscLLCondensedAddSorted(pnz,Jptr,lnk,lnkbt);
    208:     }
    209:     /* off-diagonal portion: Ao[i,:]*P */
    210:     ai = ao->i; pi = p_oth->i;
    211:     nzi = ai[i+1] - ai[i];
    212:     aj  = ao->j + ai[i];
    213:     for (j=0; j<nzi; j++) {
    214:       row  = aj[j];
    215:       pnz  = pi[row+1] - pi[row];
    216:       Jptr = p_oth->j + pi[row];
    217:       PetscLLCondensedAddSorted(pnz,Jptr,lnk,lnkbt);
    218:     }
    219:     apnz     = lnk[0];
    220:     api[i+1] = api[i] + apnz;
    221:     if (ap_rmax < apnz) ap_rmax = apnz;

    223:     /* if free space is not available, double the total space in the list */
    224:     if (current_space->local_remaining<apnz) {
    225:       PetscFreeSpaceGet(PetscIntSumTruncate(apnz,current_space->total_array_size),&current_space);
    226:       nspacedouble++;
    227:     }

    229:     /* Copy data into free space, then initialize lnk */
    230:     PetscLLCondensedClean(pN,apnz,current_space->array,lnk,lnkbt);

    232:     current_space->array           += apnz;
    233:     current_space->local_used      += apnz;
    234:     current_space->local_remaining -= apnz;
    235:   }
    236:   /* Allocate space for apj and apv, initialize apj, and */
    237:   /* destroy list of free space and other temporary array(s) */
    238:   PetscMalloc2(api[am],&apj,api[am],&apv);
    239:   PetscFreeSpaceContiguous(&free_space,apj);
    240:   PetscLLDestroy(lnk,lnkbt);

    242:   /* Create AP_loc for reuse */
    243:   MatCreateSeqAIJWithArrays(PETSC_COMM_SELF,am,pN,api,apj,apv,&ptap->AP_loc);

    245: #if defined(PETSC_USE_INFO)
    246:   apfill = (PetscReal)api[am]/(ad->i[am]+ao->i[am]+p_loc->i[pm]+1);
    247:   ptap->AP_loc->info.mallocs           = nspacedouble;
    248:   ptap->AP_loc->info.fill_ratio_given  = fill;
    249:   ptap->AP_loc->info.fill_ratio_needed = apfill;

    251:   if (api[am]) {
    252:     PetscInfo3(ptap->AP_loc,"AP_loc reallocs %D; Fill ratio: given %g needed %g.\n",nspacedouble,(double)fill,(double)apfill);
    253:     PetscInfo1(ptap->AP_loc,"Use MatPtAP(A,B,MatReuse,%g,&C) for best AP_loc performance.;\n",(double)apfill);
    254:   } else {
    255:     PetscInfo(ptap->AP_loc,"AP_loc is empty \n");
    256:   }
    257: #endif

    259: #if defined(PTAP_PROFILE)
    260:   PetscTime(&t12);
    261: #endif

    263:   /* (2-1) compute symbolic Co = Ro*AP_loc  */
    264:   /* ------------------------------------ */
    265:   MatMatMultSymbolic_SeqAIJ_SeqAIJ(ptap->Ro,ptap->AP_loc,fill,&ptap->C_oth);
    266: #if defined(PTAP_PROFILE)
    267:   PetscTime(&t1);
    268: #endif
    269:
    270:   /* (3) send coj of C_oth to other processors  */
    271:   /* ------------------------------------------ */
    272:   /* determine row ownership */
    273:   PetscLayoutCreate(comm,&rowmap);
    274:   rowmap->n  = pn;
    275:   rowmap->bs = 1;
    276:   PetscLayoutSetUp(rowmap);
    277:   owners = rowmap->range;

    279:   /* determine the number of messages to send, their lengths */
    280:   PetscMalloc4(size,&len_s,size,&len_si,size,&sstatus,size+2,&owners_co);
    281:   PetscMemzero(len_s,size*sizeof(PetscMPIInt));
    282:   PetscMemzero(len_si,size*sizeof(PetscMPIInt));

    284:   c_oth = (Mat_SeqAIJ*)ptap->C_oth->data;
    285:   coi   = c_oth->i; coj = c_oth->j;
    286:   con   = ptap->C_oth->rmap->n;
    287:   proc  = 0;
    288:   for (i=0; i<con; i++) {
    289:     while (prmap[i] >= owners[proc+1]) proc++;
    290:     len_si[proc]++;               /* num of rows in Co(=Pt*AP) to be sent to [proc] */
    291:     len_s[proc] += coi[i+1] - coi[i]; /* num of nonzeros in Co to be sent to [proc] */
    292:   }

    294:   len          = 0; /* max length of buf_si[], see (4) */
    295:   owners_co[0] = 0;
    296:   nsend        = 0;
    297:   for (proc=0; proc<size; proc++) {
    298:     owners_co[proc+1] = owners_co[proc] + len_si[proc];
    299:     if (len_s[proc]) {
    300:       nsend++;
    301:       len_si[proc] = 2*(len_si[proc] + 1); /* length of buf_si to be sent to [proc] */
    302:       len         += len_si[proc];
    303:     }
    304:   }

    306:   /* determine the number and length of messages to receive for coi and coj  */
    307:   PetscGatherNumberOfMessages(comm,NULL,len_s,&nrecv);
    308:   PetscGatherMessageLengths2(comm,nsend,nrecv,len_s,len_si,&id_r,&len_r,&len_ri);

    310:   /* post the Irecv and Isend of coj */
    311:   PetscCommGetNewTag(comm,&tagj);
    312:   PetscPostIrecvInt(comm,tagj,nrecv,id_r,len_r,&buf_rj,&rwaits);
    313:   PetscMalloc1(nsend+1,&swaits);
    314:   for (proc=0, k=0; proc<size; proc++) {
    315:     if (!len_s[proc]) continue;
    316:     i    = owners_co[proc];
    317:     MPI_Isend(coj+coi[i],len_s[proc],MPIU_INT,proc,tagj,comm,swaits+k);
    318:     k++;
    319:   }

    321:   /* (2-2) compute symbolic C_loc = Rd*AP_loc */
    322:   /* ---------------------------------------- */
    323:   MatMatMultSymbolic_SeqAIJ_SeqAIJ(ptap->Rd,ptap->AP_loc,fill,&ptap->C_loc);
    324:   c_loc = (Mat_SeqAIJ*)ptap->C_loc->data;

    326:   /* receives coj are complete */
    327:   for (i=0; i<nrecv; i++) {
    328:     MPI_Waitany(nrecv,rwaits,&icompleted,&rstatus);
    329:   }
    330:   PetscFree(rwaits);
    331:   if (nsend) {MPI_Waitall(nsend,swaits,sstatus);}

    333:   /* add received column indices into ta to update Crmax */
    334:   for (k=0; k<nrecv; k++) {/* k-th received message */
    335:     Jptr = buf_rj[k];
    336:     for (j=0; j<len_r[k]; j++) {
    337:       PetscTableAdd(ta,*(Jptr+j)+1,1,INSERT_VALUES);
    338:     }
    339:   }
    340:   PetscTableGetCount(ta,&Crmax);
    341:   PetscTableDestroy(&ta);

    343:   /* (4) send and recv coi */
    344:   /*-----------------------*/
    345:   PetscCommGetNewTag(comm,&tagi);
    346:   PetscPostIrecvInt(comm,tagi,nrecv,id_r,len_ri,&buf_ri,&rwaits);
    347:   PetscMalloc1(len+1,&buf_s);
    348:   buf_si = buf_s;  /* points to the beginning of k-th msg to be sent */
    349:   for (proc=0,k=0; proc<size; proc++) {
    350:     if (!len_s[proc]) continue;
    351:     /* form outgoing message for i-structure:
    352:          buf_si[0]:                 nrows to be sent
    353:                [1:nrows]:           row index (global)
    354:                [nrows+1:2*nrows+1]: i-structure index
    355:     */
    356:     /*-------------------------------------------*/
    357:     nrows       = len_si[proc]/2 - 1; /* num of rows in Co to be sent to [proc] */
    358:     buf_si_i    = buf_si + nrows+1;
    359:     buf_si[0]   = nrows;
    360:     buf_si_i[0] = 0;
    361:     nrows       = 0;
    362:     for (i=owners_co[proc]; i<owners_co[proc+1]; i++) {
    363:       nzi = coi[i+1] - coi[i];
    364:       buf_si_i[nrows+1] = buf_si_i[nrows] + nzi;  /* i-structure */
    365:       buf_si[nrows+1]   = prmap[i] -owners[proc]; /* local row index */
    366:       nrows++;
    367:     }
    368:     MPI_Isend(buf_si,len_si[proc],MPIU_INT,proc,tagi,comm,swaits+k);
    369:     k++;
    370:     buf_si += len_si[proc];
    371:   }
    372:   for (i=0; i<nrecv; i++) {
    373:     MPI_Waitany(nrecv,rwaits,&icompleted,&rstatus);
    374:   }
    375:   PetscFree(rwaits);
    376:   if (nsend) {MPI_Waitall(nsend,swaits,sstatus);}

    378:   PetscFree4(len_s,len_si,sstatus,owners_co);
    379:   PetscFree(len_ri);
    380:   PetscFree(swaits);
    381:   PetscFree(buf_s);
    382: #if defined(PTAP_PROFILE)
    383:   PetscTime(&t2);
    384: #endif
    385:   /* (5) compute the local portion of Cmpi      */
    386:   /* ------------------------------------------ */
    387:   /* set initial free space to be Crmax, sufficient for holding nozeros in each row of Cmpi */
    388:   PetscFreeSpaceGet(Crmax,&free_space);
    389:   current_space = free_space;

    391:   PetscMalloc3(nrecv,&buf_ri_k,nrecv,&nextrow,nrecv,&nextci);
    392:   for (k=0; k<nrecv; k++) {
    393:     buf_ri_k[k] = buf_ri[k]; /* beginning of k-th recved i-structure */
    394:     nrows       = *buf_ri_k[k];
    395:     nextrow[k]  = buf_ri_k[k] + 1;  /* next row number of k-th recved i-structure */
    396:     nextci[k]   = buf_ri_k[k] + (nrows + 1); /* poins to the next i-structure of k-th recved i-structure  */
    397:   }

    399:   MatPreallocateInitialize(comm,pn,pn,dnz,onz);
    400:   PetscLLCondensedCreate(Crmax,pN,&lnk,&lnkbt);
    401:   for (i=0; i<pn; i++) {
    402:     /* add C_loc into Cmpi */
    403:     nzi  = c_loc->i[i+1] - c_loc->i[i];
    404:     Jptr = c_loc->j + c_loc->i[i];
    405:     PetscLLCondensedAddSorted(nzi,Jptr,lnk,lnkbt);

    407:     /* add received col data into lnk */
    408:     for (k=0; k<nrecv; k++) { /* k-th received message */
    409:       if (i == *nextrow[k]) { /* i-th row */
    410:         nzi  = *(nextci[k]+1) - *nextci[k];
    411:         Jptr = buf_rj[k] + *nextci[k];
    412:         PetscLLCondensedAddSorted(nzi,Jptr,lnk,lnkbt);
    413:         nextrow[k]++; nextci[k]++;
    414:       }
    415:     }
    416:     nzi = lnk[0];

    418:     /* copy data into free space, then initialize lnk */
    419:     PetscLLCondensedClean(pN,nzi,current_space->array,lnk,lnkbt);
    420:     MatPreallocateSet(i+owners[rank],nzi,current_space->array,dnz,onz);
    421:   }
    422:   PetscFree3(buf_ri_k,nextrow,nextci);
    423:   PetscLLDestroy(lnk,lnkbt);
    424:   PetscFreeSpaceDestroy(free_space);
    425: #if defined(PTAP_PROFILE)
    426:   PetscTime(&t3);
    427: #endif

    429:   /* (6) create symbolic parallel matrix Cmpi */
    430:   /*------------------------------------------*/
    431:   MatCreate(comm,&Cmpi);
    432:   MatSetSizes(Cmpi,pn,pn,PETSC_DETERMINE,PETSC_DETERMINE);
    433:   MatSetBlockSizes(Cmpi,PetscAbs(P->cmap->bs),PetscAbs(P->cmap->bs));
    434:   MatSetType(Cmpi,MATMPIAIJ);
    435:   MatMPIAIJSetPreallocation(Cmpi,0,dnz,0,onz);
    436:   MatPreallocateFinalize(dnz,onz);

    438:   /* members in merge */
    439:   PetscFree(id_r);
    440:   PetscFree(len_r);
    441:   PetscFree(buf_ri[0]);
    442:   PetscFree(buf_ri);
    443:   PetscFree(buf_rj[0]);
    444:   PetscFree(buf_rj);
    445:   PetscLayoutDestroy(&rowmap);

    447:   /* attach the supporting struct to Cmpi for reuse */
    448:   c = (Mat_MPIAIJ*)Cmpi->data;
    449:   c->ptap         = ptap;
    450:   ptap->duplicate = Cmpi->ops->duplicate;
    451:   ptap->destroy   = Cmpi->ops->destroy;

    453:   PetscObjectOptionsBegin((PetscObject)A);
    454:   PetscOptionsEList("-matptap_via","Algorithmic approach","MatPtAP",algTypes,2,algTypes[1],&alg,NULL);
    455:   PetscOptionsEnd();

    457:   if (alg == 1) {
    458:     /* Do dense axpy in MatPtAPNumeric_MPIAIJ_MPIAIJ() */
    459:     PetscCalloc1(pN,&ptap->apa);
    460:     Cmpi->ops->ptapnumeric = MatPtAPNumeric_MPIAIJ_MPIAIJ;
    461:   } else {
    462:     Cmpi->ops->ptapnumeric = 0; /* not done yet */
    463:     SETERRQ(comm,PETSC_ERR_ARG_SIZ,"Not done yet");
    464:   }

    467:   /* Cmpi is not ready for use - assembly will be done by MatPtAPNumeric() */
    468:   Cmpi->assembled        = PETSC_FALSE;
    469:   Cmpi->ops->destroy     = MatDestroy_MPIAIJ_PtAP;
    470:   Cmpi->ops->duplicate   = MatDuplicate_MPIAIJ_MatPtAP;
    471:   *C                     = Cmpi;

    473: #if defined(PTAP_PROFILE)
    474:   PetscTime(&t4);
    475:   if (rank == 1) {
    476:     printf("PtAPSym: %g + %g + %g + %g + %g + %g = %g\n",t11-t0,t1-t11,t12-t11,t2-t2,t3-t2,t4-t3,t4-t0);
    477:   }
    478: #endif
    479:   return(0);
    480: }

    484: PetscErrorCode MatPtAPNumeric_MPIAIJ_MPIAIJ(Mat A,Mat P,Mat C)
    485: {
    486:   PetscErrorCode    ierr;
    487:   Mat_MPIAIJ        *a=(Mat_MPIAIJ*)A->data,*p=(Mat_MPIAIJ*)P->data,*c=(Mat_MPIAIJ*)C->data;
    488:   Mat_SeqAIJ        *ad=(Mat_SeqAIJ*)(a->A)->data,*ao=(Mat_SeqAIJ*)(a->B)->data;
    489:   Mat_SeqAIJ        *ap,*p_loc,*p_oth,*c_seq;
    490:   Mat_PtAPMPI       *ptap = c->ptap;
    491:   Mat               AP_loc,C_loc,C_oth;
    492:   PetscInt          i,rstart,rend,cm,ncols,row;
    493:   PetscInt          *api,*apj,am = A->rmap->n,j,col,apnz;
    494:   PetscScalar       *apa;
    495:   const PetscInt    *cols;
    496:   const PetscScalar *vals;
    497: #if defined(PTAP_PROFILE)
    498:   PetscMPIInt       rank;
    499:   MPI_Comm          comm;
    500:   PetscLogDouble    t0,t1,t2,t3,t4,eR,eAP,eCseq,eCmpi;
    501: #endif

    504:   MatZeroEntries(C);

    506:   /* 1) get R = Pd^T,Ro = Po^T */
    507: #if defined(PTAP_PROFILE)
    508:   PetscTime(&t0);
    509: #endif
    510:   if (ptap->reuse == MAT_REUSE_MATRIX) {
    511:     MatTranspose_SeqAIJ(p->A,MAT_REUSE_MATRIX,&ptap->Rd);
    512:     MatTranspose_SeqAIJ(p->B,MAT_REUSE_MATRIX,&ptap->Ro);
    513:   }
    514: #if defined(PTAP_PROFILE)
    515:   PetscTime(&t1);
    516:   eR = t1 - t0;
    517: #endif

    519:   /* 2) get AP_loc */
    520:   AP_loc = ptap->AP_loc;
    521:   ap = (Mat_SeqAIJ*)AP_loc->data;

    523:   /* 2-1) get P_oth = ptap->P_oth  and P_loc = ptap->P_loc */
    524:   /*-----------------------------------------------------*/
    525:   if (ptap->reuse == MAT_REUSE_MATRIX) {
    526:     /* P_oth and P_loc are obtained in MatPtASymbolic() when reuse == MAT_INITIAL_MATRIX */
    527:     MatGetBrowsOfAoCols_MPIAIJ(A,P,MAT_REUSE_MATRIX,&ptap->startsj_s,&ptap->startsj_r,&ptap->bufa,&ptap->P_oth);
    528:     MatMPIAIJGetLocalMat(P,MAT_REUSE_MATRIX,&ptap->P_loc);
    529:   }
    530:
    531:   /* 2-2) compute numeric A_loc*P - dominating part */
    532:   /* ---------------------------------------------- */
    533:   /* get data from symbolic products */
    534:   p_loc = (Mat_SeqAIJ*)(ptap->P_loc)->data;
    535:   p_oth = (Mat_SeqAIJ*)(ptap->P_oth)->data;
    536:   apa   = ptap->apa;
    537:   api   = ap->i;
    538:   apj   = ap->j;
    539:   for (i=0; i<am; i++) {
    540:     /* AP[i,:] = A[i,:]*P = Ad*P_loc Ao*P_oth */
    541:     AProw_nonscalable(i,ad,ao,p_loc,p_oth,apa);
    542:     apnz = api[i+1] - api[i];
    543:     for (j=0; j<apnz; j++) {
    544:       col = apj[j+api[i]];
    545:       ap->a[j+ap->i[i]] = apa[col];
    546:       apa[col] = 0.0;
    547:     }
    548:     PetscLogFlops(2.0*apnz);
    549:   }
    550: #if defined(PTAP_PROFILE)
    551:   PetscTime(&t2);
    552:   eAP = t2 - t1;
    553: #endif
    554:
    555:   /* 3) C_loc = Rd*AP_loc, C_oth = Ro*AP_loc */
    556:   ((ptap->C_loc)->ops->matmultnumeric)(ptap->Rd,AP_loc,ptap->C_loc);
    557:   ((ptap->C_oth)->ops->matmultnumeric)(ptap->Ro,AP_loc,ptap->C_oth);
    558:   C_loc = ptap->C_loc;
    559:   C_oth = ptap->C_oth;
    560: #if defined(PTAP_PROFILE)
    561:   PetscTime(&t3);
    562:   eCseq = t3 - t2;
    563: #endif

    565:   /* add C_loc and Co to to C */
    566:   MatGetOwnershipRange(C,&rstart,&rend);
    567:
    568:   /* C_loc -> C */
    569:   cm    = C_loc->rmap->N;
    570:   c_seq = (Mat_SeqAIJ*)C_loc->data;
    571:   cols = c_seq->j;
    572:   vals = c_seq->a;
    573:   for (i=0; i<cm; i++) {
    574:     ncols = c_seq->i[i+1] - c_seq->i[i];
    575:     row = rstart + i;
    576:     MatSetValues(C,1,&row,ncols,cols,vals,ADD_VALUES);
    577:     cols += ncols; vals += ncols;
    578:   }
    579:
    580:   /* Co -> C, off-processor part */
    581:   cm = C_oth->rmap->N;
    582:   c_seq = (Mat_SeqAIJ*)C_oth->data;
    583:   cols = c_seq->j;
    584:   vals = c_seq->a;
    585:   for (i=0; i<cm; i++) {
    586:     ncols = c_seq->i[i+1] - c_seq->i[i];
    587:     row = p->garray[i];
    588:     MatSetValues(C,1,&row,ncols,cols,vals,ADD_VALUES);
    589:     cols += ncols; vals += ncols;
    590:   }
    591:   MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);
    592:   MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);
    593: #if defined(PTAP_PROFILE)
    594:   PetscTime(&t4);
    595:   eCmpi = t4 - t3;

    597:   PetscObjectGetComm((PetscObject)C,&comm);
    598:   MPI_Comm_rank(comm,&rank);
    599:   if (rank==1) {
    600:     PetscPrintf(MPI_COMM_SELF," R %g, AP %g, Cseq %g, Cmpi %g = %g\n", eR,eAP,eCseq,eCmpi,eR+eAP+eCseq+eCmpi);
    601:   }
    602: #endif
    603:   ptap->reuse = MAT_REUSE_MATRIX;
    604:   return(0);
    605: }

    609: PetscErrorCode MatPtAPSymbolic_MPIAIJ_MPIAIJ_ptap(Mat A,Mat P,PetscReal fill,Mat *C)
    610: {
    611:   PetscErrorCode      ierr;
    612:   Mat                 Cmpi;
    613:   Mat_PtAPMPI         *ptap;
    614:   PetscFreeSpaceList  free_space=NULL,current_space=NULL;
    615:   Mat_MPIAIJ          *a        =(Mat_MPIAIJ*)A->data,*p=(Mat_MPIAIJ*)P->data,*c;
    616:   Mat_SeqAIJ          *ad       =(Mat_SeqAIJ*)(a->A)->data,*ao=(Mat_SeqAIJ*)(a->B)->data;
    617:   Mat_SeqAIJ          *p_loc,*p_oth;
    618:   PetscInt            *pi_loc,*pj_loc,*pi_oth,*pj_oth,*pdti,*pdtj,*poti,*potj,*ptJ;
    619:   PetscInt            *adi=ad->i,*aj,*aoi=ao->i,nnz;
    620:   PetscInt            *lnk,*owners_co,*coi,*coj,i,k,pnz,row;
    621:   PetscInt            am=A->rmap->n,pN=P->cmap->N,pm=P->rmap->n,pn=P->cmap->n;
    622:   PetscBT             lnkbt;
    623:   MPI_Comm            comm;
    624:   PetscMPIInt         size,rank,tagi,tagj,*len_si,*len_s,*len_ri,icompleted=0;
    625:   PetscInt            **buf_rj,**buf_ri,**buf_ri_k;
    626:   PetscInt            len,proc,*dnz,*onz,*owners;
    627:   PetscInt            nzi,*pti,*ptj;
    628:   PetscInt            nrows,*buf_s,*buf_si,*buf_si_i,**nextrow,**nextci;
    629:   MPI_Request         *swaits,*rwaits;
    630:   MPI_Status          *sstatus,rstatus;
    631:   Mat_Merge_SeqsToMPI *merge;
    632:   PetscInt            *api,*apj,*Jptr,apnz,*prmap=p->garray,pon,nspacedouble=0,j,ap_rmax=0;
    633:   PetscReal           afill=1.0,afill_tmp;

    636:   PetscObjectGetComm((PetscObject)A,&comm);
    637:   MPI_Comm_size(comm,&size);
    638:   MPI_Comm_rank(comm,&rank);

    640:   /* create struct Mat_PtAPMPI and attached it to C later */
    641:   PetscNew(&ptap);
    642:   PetscNew(&merge);
    643:   ptap->merge = merge;
    644:   ptap->reuse = MAT_INITIAL_MATRIX;

    646:   /* get P_oth by taking rows of P (= non-zero cols of local A) from other processors */
    647:   MatGetBrowsOfAoCols_MPIAIJ(A,P,MAT_INITIAL_MATRIX,&ptap->startsj_s,&ptap->startsj_r,&ptap->bufa,&ptap->P_oth);

    649:   /* get P_loc by taking all local rows of P */
    650:   MatMPIAIJGetLocalMat(P,MAT_INITIAL_MATRIX,&ptap->P_loc);

    652:   p_loc  = (Mat_SeqAIJ*)(ptap->P_loc)->data;
    653:   p_oth  = (Mat_SeqAIJ*)(ptap->P_oth)->data;
    654:   pi_loc = p_loc->i; pj_loc = p_loc->j;
    655:   pi_oth = p_oth->i; pj_oth = p_oth->j;

    657:   /* (1) compute symbolic AP = A_loc*P = A_diag*P_loc + A_off*P_oth (api,apj) */
    658:   /*--------------------------------------------------------------------------*/
    659:   PetscMalloc1(am+1,&api);
    660:   api[0] = 0;

    662:   /* create and initialize a linked list */
    663:   PetscLLCondensedCreate(pN,pN,&lnk,&lnkbt);

    665:   /* Initial FreeSpace size is fill*(nnz(A) + nnz(P)) -OOM for ex56, np=8k on Intrepid! */
    666:   PetscFreeSpaceGet(PetscRealIntMultTruncate(fill,PetscIntSumTruncate(adi[am],PetscIntSumTruncate(aoi[am],pi_loc[pm]))),&free_space);
    667:   current_space = free_space;

    669:   for (i=0; i<am; i++) {
    670:     /* diagonal portion of A */
    671:     nzi = adi[i+1] - adi[i];
    672:     aj  = ad->j + adi[i];
    673:     for (j=0; j<nzi; j++) {
    674:       row  = aj[j];
    675:       pnz  = pi_loc[row+1] - pi_loc[row];
    676:       Jptr = pj_loc + pi_loc[row];
    677:       /* add non-zero cols of P into the sorted linked list lnk */
    678:       PetscLLCondensedAddSorted(pnz,Jptr,lnk,lnkbt);
    679:     }
    680:     /* off-diagonal portion of A */
    681:     nzi = aoi[i+1] - aoi[i];
    682:     aj  = ao->j + aoi[i];
    683:     for (j=0; j<nzi; j++) {
    684:       row  = aj[j];
    685:       pnz  = pi_oth[row+1] - pi_oth[row];
    686:       Jptr = pj_oth + pi_oth[row];
    687:       PetscLLCondensedAddSorted(pnz,Jptr,lnk,lnkbt);
    688:     }
    689:     apnz     = lnk[0];
    690:     api[i+1] = api[i] + apnz;
    691:     if (ap_rmax < apnz) ap_rmax = apnz;

    693:     /* if free space is not available, double the total space in the list */
    694:     if (current_space->local_remaining<apnz) {
    695:       PetscFreeSpaceGet(PetscIntSumTruncate(apnz,current_space->total_array_size),&current_space);
    696:       nspacedouble++;
    697:     }

    699:     /* Copy data into free space, then initialize lnk */
    700:     PetscLLCondensedClean(pN,apnz,current_space->array,lnk,lnkbt);

    702:     current_space->array           += apnz;
    703:     current_space->local_used      += apnz;
    704:     current_space->local_remaining -= apnz;
    705:   }

    707:   /* Allocate space for apj, initialize apj, and */
    708:   /* destroy list of free space and other temporary array(s) */
    709:   PetscMalloc1(api[am]+1,&apj);
    710:   PetscFreeSpaceContiguous(&free_space,apj);
    711:   afill_tmp = (PetscReal)api[am]/(adi[am]+aoi[am]+pi_loc[pm]+1);
    712:   if (afill_tmp > afill) afill = afill_tmp;

    714:   /* (2) determine symbolic Co=(p->B)^T*AP - send to others (coi,coj)*/
    715:   /*-----------------------------------------------------------------*/
    716:   MatGetSymbolicTranspose_SeqAIJ(p->B,&poti,&potj);

    718:   /* then, compute symbolic Co = (p->B)^T*AP */
    719:   pon    = (p->B)->cmap->n; /* total num of rows to be sent to other processors
    720:                          >= (num of nonzero rows of C_seq) - pn */
    721:   PetscMalloc1(pon+1,&coi);
    722:   coi[0] = 0;

    724:   /* set initial free space to be fill*(nnz(p->B) + nnz(AP)) */
    725:   nnz           = PetscRealIntMultTruncate(fill,PetscIntSumTruncate(poti[pon],api[am]));
    726:   PetscFreeSpaceGet(nnz,&free_space);
    727:   current_space = free_space;

    729:   for (i=0; i<pon; i++) {
    730:     pnz = poti[i+1] - poti[i];
    731:     ptJ = potj + poti[i];
    732:     for (j=0; j<pnz; j++) {
    733:       row  = ptJ[j]; /* row of AP == col of Pot */
    734:       apnz = api[row+1] - api[row];
    735:       Jptr = apj + api[row];
    736:       /* add non-zero cols of AP into the sorted linked list lnk */
    737:       PetscLLCondensedAddSorted(apnz,Jptr,lnk,lnkbt);
    738:     }
    739:     nnz = lnk[0];

    741:     /* If free space is not available, double the total space in the list */
    742:     if (current_space->local_remaining<nnz) {
    743:       PetscFreeSpaceGet(PetscIntSumTruncate(nnz,current_space->total_array_size),&current_space);
    744:       nspacedouble++;
    745:     }

    747:     /* Copy data into free space, and zero out denserows */
    748:     PetscLLCondensedClean(pN,nnz,current_space->array,lnk,lnkbt);

    750:     current_space->array           += nnz;
    751:     current_space->local_used      += nnz;
    752:     current_space->local_remaining -= nnz;

    754:     coi[i+1] = coi[i] + nnz;
    755:   }
    756:
    757:   PetscMalloc1(coi[pon],&coj);
    758:   PetscFreeSpaceContiguous(&free_space,coj);
    759:   afill_tmp = (PetscReal)coi[pon]/(poti[pon] + api[am]+1);
    760:   if (afill_tmp > afill) afill = afill_tmp;
    761:   MatRestoreSymbolicTranspose_SeqAIJ(p->B,&poti,&potj);

    763:   /* (3) send j-array (coj) of Co to other processors */
    764:   /*--------------------------------------------------*/
    765:   PetscCalloc1(size,&merge->len_s);
    766:   len_s        = merge->len_s;
    767:   merge->nsend = 0;

    770:   /* determine row ownership */
    771:   PetscLayoutCreate(comm,&merge->rowmap);
    772:   merge->rowmap->n  = pn;
    773:   merge->rowmap->bs = 1;

    775:   PetscLayoutSetUp(merge->rowmap);
    776:   owners = merge->rowmap->range;

    778:   /* determine the number of messages to send, their lengths */
    779:   PetscMalloc2(size,&len_si,size,&sstatus);
    780:   PetscMemzero(len_si,size*sizeof(PetscMPIInt));
    781:   PetscMalloc1(size+2,&owners_co);

    783:   proc = 0;
    784:   for (i=0; i<pon; i++) {
    785:     while (prmap[i] >= owners[proc+1]) proc++;
    786:     len_si[proc]++;               /* num of rows in Co(=Pt*AP) to be sent to [proc] */
    787:     len_s[proc] += coi[i+1] - coi[i]; /* num of nonzeros in Co to be sent to [proc] */
    788:   }

    790:   len          = 0; /* max length of buf_si[], see (4) */
    791:   owners_co[0] = 0;
    792:   for (proc=0; proc<size; proc++) {
    793:     owners_co[proc+1] = owners_co[proc] + len_si[proc];
    794:     if (len_s[proc]) {
    795:       merge->nsend++;
    796:       len_si[proc] = 2*(len_si[proc] + 1); /* length of buf_si to be sent to [proc] */
    797:       len         += len_si[proc];
    798:     }
    799:   }

    801:   /* determine the number and length of messages to receive for coi and coj  */
    802:   PetscGatherNumberOfMessages(comm,NULL,len_s,&merge->nrecv);
    803:   PetscGatherMessageLengths2(comm,merge->nsend,merge->nrecv,len_s,len_si,&merge->id_r,&merge->len_r,&len_ri);

    805:   /* post the Irecv and Isend of coj */
    806:   PetscCommGetNewTag(comm,&tagj);
    807:   PetscPostIrecvInt(comm,tagj,merge->nrecv,merge->id_r,merge->len_r,&buf_rj,&rwaits);
    808:   PetscMalloc1(merge->nsend+1,&swaits);
    809:   for (proc=0, k=0; proc<size; proc++) {
    810:     if (!len_s[proc]) continue;
    811:     i    = owners_co[proc];
    812:     MPI_Isend(coj+coi[i],len_s[proc],MPIU_INT,proc,tagj,comm,swaits+k);
    813:     k++;
    814:   }

    816:   /* receives and sends of coj are complete */
    817:   for (i=0; i<merge->nrecv; i++) {
    818:     MPI_Waitany(merge->nrecv,rwaits,&icompleted,&rstatus);
    819:   }
    820:   PetscFree(rwaits);
    821:   if (merge->nsend) {MPI_Waitall(merge->nsend,swaits,sstatus);}

    823:   /* (4) send and recv coi */
    824:   /*-----------------------*/
    825:   PetscCommGetNewTag(comm,&tagi);
    826:   PetscPostIrecvInt(comm,tagi,merge->nrecv,merge->id_r,len_ri,&buf_ri,&rwaits);
    827:   PetscMalloc1(len+1,&buf_s);
    828:   buf_si = buf_s;  /* points to the beginning of k-th msg to be sent */
    829:   for (proc=0,k=0; proc<size; proc++) {
    830:     if (!len_s[proc]) continue;
    831:     /* form outgoing message for i-structure:
    832:          buf_si[0]:                 nrows to be sent
    833:                [1:nrows]:           row index (global)
    834:                [nrows+1:2*nrows+1]: i-structure index
    835:     */
    836:     /*-------------------------------------------*/
    837:     nrows       = len_si[proc]/2 - 1; /* num of rows in Co to be sent to [proc] */
    838:     buf_si_i    = buf_si + nrows+1;
    839:     buf_si[0]   = nrows;
    840:     buf_si_i[0] = 0;
    841:     nrows       = 0;
    842:     for (i=owners_co[proc]; i<owners_co[proc+1]; i++) {
    843:       nzi = coi[i+1] - coi[i];
    844:       buf_si_i[nrows+1] = buf_si_i[nrows] + nzi;  /* i-structure */
    845:       buf_si[nrows+1]   = prmap[i] -owners[proc]; /* local row index */
    846:       nrows++;
    847:     }
    848:     MPI_Isend(buf_si,len_si[proc],MPIU_INT,proc,tagi,comm,swaits+k);
    849:     k++;
    850:     buf_si += len_si[proc];
    851:   }
    852:   i = merge->nrecv;
    853:   while (i--) {
    854:     MPI_Waitany(merge->nrecv,rwaits,&icompleted,&rstatus);
    855:   }
    856:   PetscFree(rwaits);
    857:   if (merge->nsend) {MPI_Waitall(merge->nsend,swaits,sstatus);}

    859:   PetscFree2(len_si,sstatus);
    860:   PetscFree(len_ri);
    861:   PetscFree(swaits);
    862:   PetscFree(buf_s);

    864:   /* (5) compute the local portion of C (mpi mat) */
    865:   /*----------------------------------------------*/
    866:   MatGetSymbolicTranspose_SeqAIJ(p->A,&pdti,&pdtj);

    868:   /* allocate pti array and free space for accumulating nonzero column info */
    869:   PetscMalloc1(pn+1,&pti);
    870:   pti[0] = 0;

    872:   /* set initial free space to be fill*(nnz(P) + nnz(AP)) */
    873:   nnz           = PetscRealIntMultTruncate(fill,PetscIntSumTruncate(pi_loc[pm],api[am]));
    874:   PetscFreeSpaceGet(nnz,&free_space);
    875:   current_space = free_space;

    877:   PetscMalloc3(merge->nrecv,&buf_ri_k,merge->nrecv,&nextrow,merge->nrecv,&nextci);
    878:   for (k=0; k<merge->nrecv; k++) {
    879:     buf_ri_k[k] = buf_ri[k]; /* beginning of k-th recved i-structure */
    880:     nrows       = *buf_ri_k[k];
    881:     nextrow[k]  = buf_ri_k[k] + 1;  /* next row number of k-th recved i-structure */
    882:     nextci[k]   = buf_ri_k[k] + (nrows + 1); /* poins to the next i-structure of k-th recved i-structure  */
    883:   }
    884:   MatPreallocateInitialize(comm,pn,pn,dnz,onz);
    885:
    886:   for (i=0; i<pn; i++) {
    887:     /* add pdt[i,:]*AP into lnk */
    888:     pnz = pdti[i+1] - pdti[i];
    889:     ptJ = pdtj + pdti[i];
    890:     for (j=0; j<pnz; j++) {
    891:       row  = ptJ[j];  /* row of AP == col of Pt */
    892:       apnz = api[row+1] - api[row];
    893:       Jptr = apj + api[row];
    894:       /* add non-zero cols of AP into the sorted linked list lnk */
    895:       PetscLLCondensedAddSorted(apnz,Jptr,lnk,lnkbt);
    896:     }

    898:     /* add received col data into lnk */
    899:     for (k=0; k<merge->nrecv; k++) { /* k-th received message */
    900:       if (i == *nextrow[k]) { /* i-th row */
    901:         nzi  = *(nextci[k]+1) - *nextci[k];
    902:         Jptr = buf_rj[k] + *nextci[k];
    903:         PetscLLCondensedAddSorted(nzi,Jptr,lnk,lnkbt);
    904:         nextrow[k]++; nextci[k]++;
    905:       }
    906:     }
    907:     nnz = lnk[0];

    909:     /* if free space is not available, make more free space */
    910:     if (current_space->local_remaining<nnz) {
    911:       PetscFreeSpaceGet(PetscIntSumTruncate(nnz,current_space->total_array_size),&current_space);
    912:       nspacedouble++;
    913:     }
    914:     /* copy data into free space, then initialize lnk */
    915:     PetscLLCondensedClean(pN,nnz,current_space->array,lnk,lnkbt);
    916:     MatPreallocateSet(i+owners[rank],nnz,current_space->array,dnz,onz);

    918:     current_space->array           += nnz;
    919:     current_space->local_used      += nnz;
    920:     current_space->local_remaining -= nnz;

    922:     pti[i+1] = pti[i] + nnz;
    923:   }
    924:   MatRestoreSymbolicTranspose_SeqAIJ(p->A,&pdti,&pdtj);
    925:   PetscFree3(buf_ri_k,nextrow,nextci);

    927:   PetscMalloc1(pti[pn]+1,&ptj);
    928:   PetscFreeSpaceContiguous(&free_space,ptj);
    929:   afill_tmp = (PetscReal)pti[pn]/(pi_loc[pm] + api[am]+1);
    930:   if (afill_tmp > afill) afill = afill_tmp;
    931:   PetscLLDestroy(lnk,lnkbt);

    933:   /* (6) create symbolic parallel matrix Cmpi */
    934:   /*------------------------------------------*/
    935:   MatCreate(comm,&Cmpi);
    936:   MatSetSizes(Cmpi,pn,pn,PETSC_DETERMINE,PETSC_DETERMINE);
    937:   MatSetBlockSizes(Cmpi,PetscAbs(P->cmap->bs),PetscAbs(P->cmap->bs));
    938:   MatSetType(Cmpi,MATMPIAIJ);
    939:   MatMPIAIJSetPreallocation(Cmpi,0,dnz,0,onz);
    940:   MatPreallocateFinalize(dnz,onz);

    942:   merge->bi        = pti;      /* Cseq->i */
    943:   merge->bj        = ptj;      /* Cseq->j */
    944:   merge->coi       = coi;      /* Co->i   */
    945:   merge->coj       = coj;      /* Co->j   */
    946:   merge->buf_ri    = buf_ri;
    947:   merge->buf_rj    = buf_rj;
    948:   merge->owners_co = owners_co;
    949:   merge->destroy   = Cmpi->ops->destroy;

    951:   /* attach the supporting struct to Cmpi for reuse */
    952:   c           = (Mat_MPIAIJ*)Cmpi->data;
    953:   c->ptap     = ptap;
    954:   ptap->api   = api;
    955:   ptap->apj   = apj;
    956:   ptap->duplicate = Cmpi->ops->duplicate;
    957:   ptap->destroy   = Cmpi->ops->destroy;

    959:   /* Cmpi is not ready for use - assembly will be done by MatPtAPNumeric() */
    960:   Cmpi->assembled        = PETSC_FALSE;
    961:   Cmpi->ops->destroy     = MatDestroy_MPIAIJ_PtAP;
    962:   Cmpi->ops->duplicate   = MatDuplicate_MPIAIJ_MatPtAP;
    963:   Cmpi->ops->ptapnumeric = MatPtAPNumeric_MPIAIJ_MPIAIJ_ptap;
    964:   *C                     = Cmpi;

    966:   /* flag 'scalable' determines which implementations to be used:
    967:        0: do dense axpy in MatPtAPNumeric() - fast, but requires storage of a nonscalable dense array apa;
    968:        1: do sparse axpy in MatPtAPNumeric() - might slow, uses a sparse array apa */
    969:   /* set default scalable */
    970:   ptap->scalable = PETSC_FALSE; /* PETSC_TRUE; */

    972:   PetscOptionsGetBool(((PetscObject)Cmpi)->options,((PetscObject)Cmpi)->prefix,"-matptap_scalable",&ptap->scalable,NULL);
    973:   if (!ptap->scalable) {  /* Do dense axpy */
    974:     PetscCalloc1(pN,&ptap->apa);
    975:   } else {
    976:     PetscCalloc1(ap_rmax+1,&ptap->apa);
    977:   }

    979: #if defined(PETSC_USE_INFO)
    980:   if (pti[pn] != 0) {
    981:     PetscInfo3(Cmpi,"Reallocs %D; Fill ratio: given %g needed %g.\n",nspacedouble,(double)fill,(double)afill);
    982:     PetscInfo1(Cmpi,"Use MatPtAP(A,P,MatReuse,%g,&C) for best performance.\n",(double)afill);
    983:   } else {
    984:     PetscInfo(Cmpi,"Empty matrix product\n");
    985:   }
    986: #endif
    987:   return(0);
    988: }

    992: PetscErrorCode MatPtAPNumeric_MPIAIJ_MPIAIJ_ptap(Mat A,Mat P,Mat C)
    993: {
    994:   PetscErrorCode      ierr;
    995:   Mat_MPIAIJ          *a =(Mat_MPIAIJ*)A->data,*p=(Mat_MPIAIJ*)P->data,*c=(Mat_MPIAIJ*)C->data;
    996:   Mat_SeqAIJ          *ad=(Mat_SeqAIJ*)(a->A)->data,*ao=(Mat_SeqAIJ*)(a->B)->data;
    997:   Mat_SeqAIJ          *pd=(Mat_SeqAIJ*)(p->A)->data,*po=(Mat_SeqAIJ*)(p->B)->data;
    998:   Mat_SeqAIJ          *p_loc,*p_oth;
    999:   Mat_PtAPMPI         *ptap;
    1000:   Mat_Merge_SeqsToMPI *merge;
    1001:   PetscInt            *adi=ad->i,*aoi=ao->i,*adj,*aoj,*apJ,nextp;
    1002:   PetscInt            *pi_loc,*pj_loc,*pi_oth,*pj_oth,*pJ,*pj;
    1003:   PetscInt            i,j,k,anz,pnz,apnz,nextap,row,*cj;
    1004:   MatScalar           *ada,*aoa,*apa,*pa,*ca,*pa_loc,*pa_oth,valtmp;
    1005:   PetscInt            am  =A->rmap->n,cm=C->rmap->n,pon=(p->B)->cmap->n;
    1006:   MPI_Comm            comm;
    1007:   PetscMPIInt         size,rank,taga,*len_s;
    1008:   PetscInt            *owners,proc,nrows,**buf_ri_k,**nextrow,**nextci;
    1009:   PetscInt            **buf_ri,**buf_rj;
    1010:   PetscInt            cnz=0,*bj_i,*bi,*bj,bnz,nextcj;  /* bi,bj,ba: local array of C(mpi mat) */
    1011:   MPI_Request         *s_waits,*r_waits;
    1012:   MPI_Status          *status;
    1013:   MatScalar           **abuf_r,*ba_i,*pA,*coa,*ba;
    1014:   PetscInt            *api,*apj,*coi,*coj;
    1015:   PetscInt            *poJ=po->j,*pdJ=pd->j,pcstart=P->cmap->rstart,pcend=P->cmap->rend;
    1016:   PetscBool           scalable;
    1017: #if defined(PTAP_PROFILE)
    1018:   PetscLogDouble t0,t1,t2,eP,t3,t4,et2_AP=0.0,ePtAP=0.0,t2_0,t2_1,t2_2;
    1019: #endif

    1022:   PetscObjectGetComm((PetscObject)C,&comm);
    1023: #if defined(PTAP_PROFILE)
    1024:   PetscTime(&t0);
    1025: #endif
    1026:   MPI_Comm_size(comm,&size);
    1027:   MPI_Comm_rank(comm,&rank);

    1029:   ptap = c->ptap;
    1030:   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");
    1031:   merge    = ptap->merge;
    1032:   apa      = ptap->apa;
    1033:   scalable = ptap->scalable;

    1035:   /* 1) get P_oth = ptap->P_oth  and P_loc = ptap->P_loc */
    1036:   /*-----------------------------------------------------*/
    1037:   if (ptap->reuse == MAT_INITIAL_MATRIX) {
    1038:     /* P_oth and P_loc are obtained in MatPtASymbolic(), skip calling MatGetBrowsOfAoCols() and MatMPIAIJGetLocalMat() */
    1039:     ptap->reuse = MAT_REUSE_MATRIX;
    1040:   } else { /* update numerical values of P_oth and P_loc */
    1041:     MatGetBrowsOfAoCols_MPIAIJ(A,P,MAT_REUSE_MATRIX,&ptap->startsj_s,&ptap->startsj_r,&ptap->bufa,&ptap->P_oth);
    1042:     MatMPIAIJGetLocalMat(P,MAT_REUSE_MATRIX,&ptap->P_loc);
    1043:   }
    1044: #if defined(PTAP_PROFILE)
    1045:   PetscTime(&t1);
    1046:   eP = t1-t0;
    1047: #endif
    1048:   /*
    1049:   printf("[%d] Ad: %d, %d; Ao: %d, %d; P_loc: %d, %d; P_oth %d, %d;\n",rank,
    1050:          a->A->rmap->N,a->A->cmap->N,a->B->rmap->N,a->B->cmap->N,
    1051:          ptap->P_loc->rmap->N,ptap->P_loc->cmap->N,
    1052:          ptap->P_oth->rmap->N,ptap->P_oth->cmap->N);
    1053:    */

    1055:   /* 2) compute numeric C_seq = P_loc^T*A_loc*P - dominating part */
    1056:   /*--------------------------------------------------------------*/
    1057:   /* get data from symbolic products */
    1058:   p_loc = (Mat_SeqAIJ*)(ptap->P_loc)->data;
    1059:   p_oth = (Mat_SeqAIJ*)(ptap->P_oth)->data;
    1060:   pi_loc=p_loc->i; pj_loc=p_loc->j; pa_loc=p_loc->a;
    1061:   pi_oth=p_oth->i; pj_oth=p_oth->j; pa_oth=p_oth->a;

    1063:   coi  = merge->coi; coj = merge->coj;
    1064:   PetscCalloc1(coi[pon]+1,&coa);

    1066:   bi     = merge->bi; bj = merge->bj;
    1067:   owners = merge->rowmap->range;
    1068:   PetscCalloc1(bi[cm]+1,&ba);  /* ba: Cseq->a */

    1070:   api = ptap->api; apj = ptap->apj;

    1072:   if (!scalable) { /* Do dense axpy on apa (length of pN, stores A[i,:]*P) - nonscalable, but faster (could take 1/3 scalable time) */
    1073:     PetscInfo(C,"Using non-scalable dense axpy\n");
    1074: #if defined(PTAP_PROFILE)
    1075:     PetscTime(&t1);
    1076: #endif
    1077:     for (i=0; i<am; i++) {
    1078: #if defined(PTAP_PROFILE)
    1079:       PetscTime(&t2_0);
    1080: #endif
    1081:       /* 2-a) form i-th sparse row of A_loc*P = Ad*P_loc + Ao*P_oth */
    1082:       /*------------------------------------------------------------*/
    1083:       apJ = apj + api[i];

    1085:       /* diagonal portion of A */
    1086:       anz = adi[i+1] - adi[i];
    1087:       adj = ad->j + adi[i];
    1088:       ada = ad->a + adi[i];
    1089:       for (j=0; j<anz; j++) {
    1090:         row = adj[j];
    1091:         pnz = pi_loc[row+1] - pi_loc[row];
    1092:         pj  = pj_loc + pi_loc[row];
    1093:         pa  = pa_loc + pi_loc[row];

    1095:         /* perform dense axpy */
    1096:         valtmp = ada[j];
    1097:         for (k=0; k<pnz; k++) {
    1098:           apa[pj[k]] += valtmp*pa[k];
    1099:         }
    1100:         PetscLogFlops(2.0*pnz);
    1101:       }

    1103:       /* off-diagonal portion of A */
    1104:       anz = aoi[i+1] - aoi[i];
    1105:       aoj = ao->j + aoi[i];
    1106:       aoa = ao->a + aoi[i];
    1107:       for (j=0; j<anz; j++) {
    1108:         row = aoj[j];
    1109:         pnz = pi_oth[row+1] - pi_oth[row];
    1110:         pj  = pj_oth + pi_oth[row];
    1111:         pa  = pa_oth + pi_oth[row];

    1113:         /* perform dense axpy */
    1114:         valtmp = aoa[j];
    1115:         for (k=0; k<pnz; k++) {
    1116:           apa[pj[k]] += valtmp*pa[k];
    1117:         }
    1118:         PetscLogFlops(2.0*pnz);
    1119:       }
    1120: #if defined(PTAP_PROFILE)
    1121:       PetscTime(&t2_1);
    1122:       et2_AP += t2_1 - t2_0;
    1123: #endif

    1125:       /* 2-b) Compute Cseq = P_loc[i,:]^T*AP[i,:] using outer product */
    1126:       /*--------------------------------------------------------------*/
    1127:       apnz = api[i+1] - api[i];
    1128:       /* put the value into Co=(p->B)^T*AP (off-diagonal part, send to others) */
    1129:       pnz = po->i[i+1] - po->i[i];
    1130:       poJ = po->j + po->i[i];
    1131:       pA  = po->a + po->i[i];
    1132:       for (j=0; j<pnz; j++) {
    1133:         row = poJ[j];
    1134:         cnz = coi[row+1] - coi[row];
    1135:         cj  = coj + coi[row];
    1136:         ca  = coa + coi[row];
    1137:         /* perform dense axpy */
    1138:         valtmp = pA[j];
    1139:         for (k=0; k<cnz; k++) {
    1140:           ca[k] += valtmp*apa[cj[k]];
    1141:         }
    1142:         PetscLogFlops(2.0*cnz);
    1143:       }
    1144:       /* put the value into Cd (diagonal part) */
    1145:       pnz = pd->i[i+1] - pd->i[i];
    1146:       pdJ = pd->j + pd->i[i];
    1147:       pA  = pd->a + pd->i[i];
    1148:       for (j=0; j<pnz; j++) {
    1149:         row = pdJ[j];
    1150:         cnz = bi[row+1] - bi[row];
    1151:         cj  = bj + bi[row];
    1152:         ca  = ba + bi[row];
    1153:         /* perform dense axpy */
    1154:         valtmp = pA[j];
    1155:         for (k=0; k<cnz; k++) {
    1156:           ca[k] += valtmp*apa[cj[k]];
    1157:         }
    1158:         PetscLogFlops(2.0*cnz);
    1159:       }
    1160:
    1161:       /* zero the current row of A*P */
    1162:       for (k=0; k<apnz; k++) apa[apJ[k]] = 0.0;
    1163: #if defined(PTAP_PROFILE)
    1164:       PetscTime(&t2_2);
    1165:       ePtAP += t2_2 - t2_1;
    1166: #endif
    1167:     }
    1168:   } else { /* Do sparse axpy on apa (length of ap_rmax, stores A[i,:]*P) - scalable, but slower */
    1169:     PetscInfo(C,"Using scalable sparse axpy\n");
    1170:     /*-----------------------------------------------------------------------------------------*/
    1171:     pA=pa_loc;
    1172:     for (i=0; i<am; i++) {
    1173: #if defined(PTAP_PROFILE)
    1174:       PetscTime(&t2_0);
    1175: #endif
    1176:       /* form i-th sparse row of A*P */
    1177:       apnz = api[i+1] - api[i];
    1178:       apJ  = apj + api[i];
    1179:       /* diagonal portion of A */
    1180:       anz = adi[i+1] - adi[i];
    1181:       adj = ad->j + adi[i];
    1182:       ada = ad->a + adi[i];
    1183:       for (j=0; j<anz; j++) {
    1184:         row    = adj[j];
    1185:         pnz    = pi_loc[row+1] - pi_loc[row];
    1186:         pj     = pj_loc + pi_loc[row];
    1187:         pa     = pa_loc + pi_loc[row];
    1188:         valtmp = ada[j];
    1189:         nextp  = 0;
    1190:         for (k=0; nextp<pnz; k++) {
    1191:           if (apJ[k] == pj[nextp]) { /* col of AP == col of P */
    1192:             apa[k] += valtmp*pa[nextp++];
    1193:           }
    1194:         }
    1195:         PetscLogFlops(2.0*pnz);
    1196:       }
    1197:       /* off-diagonal portion of A */
    1198:       anz = aoi[i+1] - aoi[i];
    1199:       aoj = ao->j + aoi[i];
    1200:       aoa = ao->a + aoi[i];
    1201:       for (j=0; j<anz; j++) {
    1202:         row    = aoj[j];
    1203:         pnz    = pi_oth[row+1] - pi_oth[row];
    1204:         pj     = pj_oth + pi_oth[row];
    1205:         pa     = pa_oth + pi_oth[row];
    1206:         valtmp = aoa[j];
    1207:         nextp  = 0;
    1208:         for (k=0; nextp<pnz; k++) {
    1209:           if (apJ[k] == pj[nextp]) { /* col of AP == col of P */
    1210:             apa[k] += valtmp*pa[nextp++];
    1211:           }
    1212:         }
    1213:         PetscLogFlops(2.0*pnz);
    1214:       }
    1215: #if defined(PTAP_PROFILE)
    1216:       PetscTime(&t2_1);
    1217:       et2_AP += t2_1 - t2_0;
    1218: #endif

    1220:       /* 2-b) Compute Cseq = P_loc[i,:]^T*AP[i,:] using outer product */
    1221:       /*--------------------------------------------------------------*/
    1222:       pnz = pi_loc[i+1] - pi_loc[i];
    1223:       pJ  = pj_loc + pi_loc[i];
    1224:       for (j=0; j<pnz; j++) {
    1225:         nextap = 0;
    1226:         row    = pJ[j]; /* global index */
    1227:         if (row < pcstart || row >=pcend) { /* put the value into Co */
    1228:           row = *poJ;
    1229:           cj  = coj + coi[row];
    1230:           ca  = coa + coi[row]; poJ++;
    1231:         } else {                            /* put the value into Cd */
    1232:           row = *pdJ;
    1233:           cj  = bj + bi[row];
    1234:           ca  = ba + bi[row]; pdJ++;
    1235:         }
    1236:         valtmp = pA[j];
    1237:         for (k=0; nextap<apnz; k++) {
    1238:           if (cj[k]==apJ[nextap]) ca[k] += valtmp*apa[nextap++];
    1239:         }
    1240:         PetscLogFlops(2.0*apnz);
    1241:       }
    1242:       pA += pnz;
    1243:       /* zero the current row info for A*P */
    1244:       PetscMemzero(apa,apnz*sizeof(MatScalar));
    1245: #if defined(PTAP_PROFILE)
    1246:       PetscTime(&t2_2);
    1247:       ePtAP += t2_2 - t2_1;
    1248: #endif
    1249:     }
    1250:   }
    1251: #if defined(PTAP_PROFILE)
    1252:   PetscTime(&t2);
    1253: #endif

    1255:   /* 3) send and recv matrix values coa */
    1256:   /*------------------------------------*/
    1257:   buf_ri = merge->buf_ri;
    1258:   buf_rj = merge->buf_rj;
    1259:   len_s  = merge->len_s;
    1260:   PetscCommGetNewTag(comm,&taga);
    1261:   PetscPostIrecvScalar(comm,taga,merge->nrecv,merge->id_r,merge->len_r,&abuf_r,&r_waits);

    1263:   PetscMalloc2(merge->nsend+1,&s_waits,size,&status);
    1264:   for (proc=0,k=0; proc<size; proc++) {
    1265:     if (!len_s[proc]) continue;
    1266:     i    = merge->owners_co[proc];
    1267:     MPI_Isend(coa+coi[i],len_s[proc],MPIU_MATSCALAR,proc,taga,comm,s_waits+k);
    1268:     k++;
    1269:   }
    1270:   if (merge->nrecv) {MPI_Waitall(merge->nrecv,r_waits,status);}
    1271:   if (merge->nsend) {MPI_Waitall(merge->nsend,s_waits,status);}

    1273:   PetscFree2(s_waits,status);
    1274:   PetscFree(r_waits);
    1275:   PetscFree(coa);
    1276: #if defined(PTAP_PROFILE)
    1277:   PetscTime(&t3);
    1278: #endif

    1280:   /* 4) insert local Cseq and received values into Cmpi */
    1281:   /*------------------------------------------------------*/
    1282:   PetscMalloc3(merge->nrecv,&buf_ri_k,merge->nrecv,&nextrow,merge->nrecv,&nextci);
    1283:   for (k=0; k<merge->nrecv; k++) {
    1284:     buf_ri_k[k] = buf_ri[k]; /* beginning of k-th recved i-structure */
    1285:     nrows       = *(buf_ri_k[k]);
    1286:     nextrow[k]  = buf_ri_k[k]+1;  /* next row number of k-th recved i-structure */
    1287:     nextci[k]   = buf_ri_k[k] + (nrows + 1); /* poins to the next i-structure of k-th recved i-structure  */
    1288:   }

    1290:   for (i=0; i<cm; i++) {
    1291:     row  = owners[rank] + i; /* global row index of C_seq */
    1292:     bj_i = bj + bi[i];  /* col indices of the i-th row of C */
    1293:     ba_i = ba + bi[i];
    1294:     bnz  = bi[i+1] - bi[i];
    1295:     /* add received vals into ba */
    1296:     for (k=0; k<merge->nrecv; k++) { /* k-th received message */
    1297:       /* i-th row */
    1298:       if (i == *nextrow[k]) {
    1299:         cnz    = *(nextci[k]+1) - *nextci[k];
    1300:         cj     = buf_rj[k] + *(nextci[k]);
    1301:         ca     = abuf_r[k] + *(nextci[k]);
    1302:         nextcj = 0;
    1303:         for (j=0; nextcj<cnz; j++) {
    1304:           if (bj_i[j] == cj[nextcj]) { /* bcol == ccol */
    1305:             ba_i[j] += ca[nextcj++];
    1306:           }
    1307:         }
    1308:         nextrow[k]++; nextci[k]++;
    1309:         PetscLogFlops(2.0*cnz);
    1310:       }
    1311:     }
    1312:     MatSetValues(C,1,&row,bnz,bj_i,ba_i,INSERT_VALUES);
    1313:   }
    1314:   MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);
    1315:   MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);

    1317:   PetscFree(ba);
    1318:   PetscFree(abuf_r[0]);
    1319:   PetscFree(abuf_r);
    1320:   PetscFree3(buf_ri_k,nextrow,nextci);
    1321: #if defined(PTAP_PROFILE)
    1322:   PetscTime(&t4);
    1323:   if (rank==1) {
    1324:     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);
    1325:   }
    1326: #endif
    1327:   return(0);
    1328: }