Actual source code: vecstash.c
petsc-3.10.5 2019-03-28
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      2:  #include <petsc/private/vecimpl.h>

      4: #define DEFAULT_STASH_SIZE   100

      6: /*
      7:   VecStashCreate_Private - Creates a stash,currently used for all the parallel
      8:   matrix implementations. The stash is where elements of a matrix destined
      9:   to be stored on other processors are kept until matrix assembly is done.

     11:   This is a simple minded stash. Simply adds entries to end of stash.

     13:   Input Parameters:
     14:   comm - communicator, required for scatters.
     15:   bs   - stash block size. used when stashing blocks of values

     17:   Output Parameters:
     18:   stash    - the newly created stash
     19: */
     20: PetscErrorCode VecStashCreate_Private(MPI_Comm comm,PetscInt bs,VecStash *stash)
     21: {
     23:   PetscInt       max,*opt,nopt;
     24:   PetscBool      flg;

     27:   /* Require 2 tags, get the second using PetscCommGetNewTag() */
     28:   stash->comm = comm;
     29:   PetscCommGetNewTag(stash->comm,&stash->tag1);
     30:   PetscCommGetNewTag(stash->comm,&stash->tag2);
     31:   MPI_Comm_size(stash->comm,&stash->size);
     32:   MPI_Comm_rank(stash->comm,&stash->rank);

     34:   nopt = stash->size;
     35:   PetscMalloc1(nopt,&opt);
     36:   PetscOptionsGetIntArray(NULL,NULL,"-vecstash_initial_size",opt,&nopt,&flg);
     37:   if (flg) {
     38:     if (nopt == 1)                max = opt[0];
     39:     else if (nopt == stash->size) max = opt[stash->rank];
     40:     else if (stash->rank < nopt)  max = opt[stash->rank];
     41:     else                          max = 0; /* use default */
     42:     stash->umax = max;
     43:   } else {
     44:     stash->umax = 0;
     45:   }
     46:   PetscFree(opt);

     48:   if (bs <= 0) bs = 1;

     50:   stash->bs       = bs;
     51:   stash->nmax     = 0;
     52:   stash->oldnmax  = 0;
     53:   stash->n        = 0;
     54:   stash->reallocs = -1;
     55:   stash->idx      = 0;
     56:   stash->array    = 0;

     58:   stash->send_waits   = 0;
     59:   stash->recv_waits   = 0;
     60:   stash->send_status  = 0;
     61:   stash->nsends       = 0;
     62:   stash->nrecvs       = 0;
     63:   stash->svalues      = 0;
     64:   stash->rvalues      = 0;
     65:   stash->rmax         = 0;
     66:   stash->nprocs       = 0;
     67:   stash->nprocessed   = 0;
     68:   stash->donotstash   = PETSC_FALSE;
     69:   stash->ignorenegidx = PETSC_FALSE;
     70:   return(0);
     71: }

     73: /*
     74:    VecStashDestroy_Private - Destroy the stash
     75: */
     76: PetscErrorCode VecStashDestroy_Private(VecStash *stash)
     77: {

     81:   PetscFree2(stash->array,stash->idx);
     82:   PetscFree(stash->bowners);
     83:   return(0);
     84: }

     86: /*
     87:    VecStashScatterEnd_Private - This is called as the fial stage of
     88:    scatter. The final stages of message passing is done here, and
     89:    all the memory used for message passing is cleanedu up. This
     90:    routine also resets the stash, and deallocates the memory used
     91:    for the stash. It also keeps track of the current memory usage
     92:    so that the same value can be used the next time through.
     93: */
     94: PetscErrorCode VecStashScatterEnd_Private(VecStash *stash)
     95: {
     97:   PetscInt       nsends=stash->nsends,oldnmax;
     98:   MPI_Status     *send_status;

    101:   /* wait on sends */
    102:   if (nsends) {
    103:     PetscMalloc1(2*nsends,&send_status);
    104:     MPI_Waitall(2*nsends,stash->send_waits,send_status);
    105:     PetscFree(send_status);
    106:   }

    108:   /* Now update nmaxold to be app 10% more than max n, this way the
    109:      wastage of space is reduced the next time this stash is used.
    110:      Also update the oldmax, only if it increases */
    111:   if (stash->n) {
    112:     oldnmax = ((PetscInt)(stash->n * 1.1) + 5)*stash->bs;
    113:     if (oldnmax > stash->oldnmax) stash->oldnmax = oldnmax;
    114:   }

    116:   stash->nmax       = 0;
    117:   stash->n          = 0;
    118:   stash->reallocs   = -1;
    119:   stash->rmax       = 0;
    120:   stash->nprocessed = 0;

    122:   PetscFree2(stash->array,stash->idx);
    123:   stash->array = 0;
    124:   stash->idx   = 0;
    125:   PetscFree(stash->send_waits);
    126:   PetscFree(stash->recv_waits);
    127:   PetscFree2(stash->svalues,stash->sindices);
    128:   PetscFree2(stash->rvalues,stash->rindices);
    129:   PetscFree(stash->nprocs);
    130:   return(0);
    131: }

    133: /*
    134:    VecStashGetInfo_Private - Gets the relavant statistics of the stash

    136:    Input Parameters:
    137:    stash    - the stash
    138:    nstash   - the size of the stash
    139:    reallocs - the number of additional mallocs incurred.

    141: */
    142: PetscErrorCode VecStashGetInfo_Private(VecStash *stash,PetscInt *nstash,PetscInt *reallocs)
    143: {
    145:   if (nstash) *nstash = stash->n*stash->bs;
    146:   if (reallocs) {
    147:     if (stash->reallocs < 0) *reallocs = 0;
    148:     else                     *reallocs = stash->reallocs;
    149:   }
    150:   return(0);
    151: }

    154: /*
    155:    VecStashSetInitialSize_Private - Sets the initial size of the stash

    157:    Input Parameters:
    158:    stash  - the stash
    159:    max    - the value that is used as the max size of the stash.
    160:             this value is used while allocating memory. It specifies
    161:             the number of vals stored, even with the block-stash
    162: */
    163: PetscErrorCode VecStashSetInitialSize_Private(VecStash *stash,PetscInt max)
    164: {
    166:   stash->umax = max;
    167:   return(0);
    168: }

    170: /* VecStashExpand_Private - Expand the stash. This function is called
    171:    when the space in the stash is not sufficient to add the new values
    172:    being inserted into the stash.

    174:    Input Parameters:
    175:    stash - the stash
    176:    incr  - the minimum increase requested

    178:    Notes:
    179:    This routine doubles the currently used memory.
    180: */
    181: PetscErrorCode VecStashExpand_Private(VecStash *stash,PetscInt incr)
    182: {
    184:   PetscInt       *n_idx,newnmax,bs=stash->bs;
    185:   PetscScalar    *n_array;

    188:   /* allocate a larger stash. */
    189:   if (!stash->oldnmax && !stash->nmax) { /* new stash */
    190:     if (stash->umax)                  newnmax = stash->umax/bs;
    191:     else                              newnmax = DEFAULT_STASH_SIZE/bs;
    192:   } else if (!stash->nmax) { /* resuing stash */
    193:     if (stash->umax > stash->oldnmax) newnmax = stash->umax/bs;
    194:     else                              newnmax = stash->oldnmax/bs;
    195:   } else                              newnmax = stash->nmax*2;

    197:   if (newnmax  < (stash->nmax + incr)) newnmax += 2*incr;

    199:   PetscMalloc2(bs*newnmax,&n_array,newnmax,&n_idx);
    200:   PetscMemcpy(n_array,stash->array,bs*stash->nmax*sizeof(PetscScalar));
    201:   PetscMemcpy(n_idx,stash->idx,stash->nmax*sizeof(PetscInt));
    202:   PetscFree2(stash->array,stash->idx);

    204:   stash->array = n_array;
    205:   stash->idx   = n_idx;
    206:   stash->nmax  = newnmax;
    207:   stash->reallocs++;
    208:   return(0);
    209: }
    210: /*
    211:   VecStashScatterBegin_Private - Initiates the transfer of values to the
    212:   correct owners. This function goes through the stash, and check the
    213:   owners of each stashed value, and sends the values off to the owner
    214:   processors.

    216:   Input Parameters:
    217:   stash  - the stash
    218:   owners - an array of size 'no-of-procs' which gives the ownership range
    219:            for each node.

    221:   Notes:
    222:     The 'owners' array in the cased of the blocked-stash has the
    223:   ranges specified blocked global indices, and for the regular stash in
    224:   the proper global indices.
    225: */
    226: PetscErrorCode VecStashScatterBegin_Private(VecStash *stash,PetscInt *owners)
    227: {
    229:   PetscMPIInt    size = stash->size,tag1=stash->tag1,tag2=stash->tag2;
    230:   PetscInt       *owner,*start,*nprocs,nsends,nreceives;
    231:   PetscInt       nmax,count,*sindices,*rindices,i,j,idx,bs=stash->bs,lastidx;
    232:   PetscScalar    *rvalues,*svalues;
    233:   MPI_Comm       comm = stash->comm;
    234:   MPI_Request    *send_waits,*recv_waits;

    237:   /*  first count number of contributors to each processor */
    238:   PetscCalloc1(2*size,&nprocs);
    239:   PetscMalloc1(stash->n,&owner);

    241:   j       = 0;
    242:   lastidx = -1;
    243:   for (i=0; i<stash->n; i++) {
    244:     /* if indices are NOT locally sorted, need to start search at the beginning */
    245:     if (lastidx > (idx = stash->idx[i])) j = 0;
    246:     lastidx = idx;
    247:     for (; j<size; j++) {
    248:       if (idx >= owners[j] && idx < owners[j+1]) {
    249:         nprocs[2*j]++; nprocs[2*j+1] = 1; owner[i] = j; break;
    250:       }
    251:     }
    252:   }
    253:   nsends = 0;
    254:   for (i=0; i<size; i++) nsends += nprocs[2*i+1];

    256:   /* inform other processors of number of messages and max length*/
    257:   PetscMaxSum(comm,nprocs,&nmax,&nreceives);

    259:   /* post receives:
    260:      since we don't know how long each individual message is we
    261:      allocate the largest needed buffer for each receive. Potentially
    262:      this is a lot of wasted space.
    263:   */
    264:   PetscMalloc2(nreceives*nmax*bs,&rvalues,nreceives*nmax,&rindices);
    265:   PetscMalloc1(2*nreceives,&recv_waits);
    266:   for (i=0,count=0; i<nreceives; i++) {
    267:     MPI_Irecv(rvalues+bs*nmax*i,bs*nmax,MPIU_SCALAR,MPI_ANY_SOURCE,tag1,comm,recv_waits+count++);
    268:     MPI_Irecv(rindices+nmax*i,nmax,MPIU_INT,MPI_ANY_SOURCE,tag2,comm,recv_waits+count++);
    269:   }

    271:   /* do sends:
    272:       1) starts[i] gives the starting index in svalues for stuff going to
    273:          the ith processor
    274:   */
    275:   PetscMalloc2(stash->n*bs,&svalues,stash->n,&sindices);
    276:   PetscMalloc1(2*nsends,&send_waits);
    277:   PetscMalloc1(size,&start);
    278:   /* use 2 sends the first with all_v, the next with all_i */
    279:   start[0] = 0;
    280:   for (i=1; i<size; i++) start[i] = start[i-1] + nprocs[2*i-2];

    282:   for (i=0; i<stash->n; i++) {
    283:     j = owner[i];
    284:     if (bs == 1) svalues[start[j]] = stash->array[i];
    285:     else {
    286:       PetscMemcpy(svalues+bs*start[j],stash->array+bs*i,bs*sizeof(PetscScalar));
    287:     }
    288:     sindices[start[j]] = stash->idx[i];
    289:     start[j]++;
    290:   }
    291:   start[0] = 0;
    292:   for (i=1; i<size; i++) start[i] = start[i-1] + nprocs[2*i-2];

    294:   for (i=0,count=0; i<size; i++) {
    295:     if (nprocs[2*i+1]) {
    296:       MPI_Isend(svalues+bs*start[i],bs*nprocs[2*i],MPIU_SCALAR,i,tag1,comm,send_waits+count++);
    297:       MPI_Isend(sindices+start[i],nprocs[2*i],MPIU_INT,i,tag2,comm,send_waits+count++);
    298:     }
    299:   }
    300:   PetscFree(owner);
    301:   PetscFree(start);
    302:   /* This memory is reused in scatter end  for a different purpose*/
    303:   for (i=0; i<2*size; i++) nprocs[i] = -1;

    305:   stash->nprocs     = nprocs;
    306:   stash->svalues    = svalues;
    307:   stash->sindices   = sindices;
    308:   stash->rvalues    = rvalues;
    309:   stash->rindices   = rindices;
    310:   stash->nsends     = nsends;
    311:   stash->nrecvs     = nreceives;
    312:   stash->send_waits = send_waits;
    313:   stash->recv_waits = recv_waits;
    314:   stash->rmax       = nmax;
    315:   return(0);
    316: }

    318: /*
    319:    VecStashScatterGetMesg_Private - This function waits on the receives posted
    320:    in the function VecStashScatterBegin_Private() and returns one message at
    321:    a time to the calling function. If no messages are left, it indicates this
    322:    by setting flg = 0, else it sets flg = 1.

    324:    Input Parameters:
    325:    stash - the stash

    327:    Output Parameters:
    328:    nvals - the number of entries in the current message.
    329:    rows  - an array of row indices (or blocked indices) corresponding to the values
    330:    cols  - an array of columnindices (or blocked indices) corresponding to the values
    331:    vals  - the values
    332:    flg   - 0 indicates no more message left, and the current call has no values associated.
    333:            1 indicates that the current call successfully received a message, and the
    334:              other output parameters nvals,rows,cols,vals are set appropriately.
    335: */
    336: PetscErrorCode VecStashScatterGetMesg_Private(VecStash *stash,PetscMPIInt *nvals,PetscInt **rows,PetscScalar **vals,PetscInt *flg)
    337: {
    339:   PetscMPIInt    i = 0; /* dummy value so MPI-Uni doesn't think it is not set */
    340:   PetscInt       *flg_v;
    341:   PetscInt       i1,i2,bs=stash->bs;
    342:   MPI_Status     recv_status;
    343:   PetscBool      match_found = PETSC_FALSE;

    346:   *flg = 0; /* When a message is discovered this is reset to 1 */
    347:   /* Return if no more messages to process */
    348:   if (stash->nprocessed == stash->nrecvs) return(0);

    350:   flg_v = stash->nprocs;
    351:   /* If a matching pair of receives are found, process them, and return the data to
    352:      the calling function. Until then keep receiving messages */
    353:   while (!match_found) {
    354:     MPI_Waitany(2*stash->nrecvs,stash->recv_waits,&i,&recv_status);
    355:     /* Now pack the received message into a structure which is useable by others */
    356:     if (i % 2) {
    357:       MPI_Get_count(&recv_status,MPIU_INT,nvals);
    358:       flg_v[2*recv_status.MPI_SOURCE+1] = i/2;
    359:     } else {
    360:       MPI_Get_count(&recv_status,MPIU_SCALAR,nvals);
    361:       flg_v[2*recv_status.MPI_SOURCE] = i/2;
    362:       *nvals = *nvals/bs;
    363:     }

    365:     /* Check if we have both the messages from this proc */
    366:     i1 = flg_v[2*recv_status.MPI_SOURCE];
    367:     i2 = flg_v[2*recv_status.MPI_SOURCE+1];
    368:     if (i1 != -1 && i2 != -1) {
    369:       *rows = stash->rindices + i2*stash->rmax;
    370:       *vals = stash->rvalues + i1*bs*stash->rmax;
    371:       *flg  = 1;
    372:       stash->nprocessed++;
    373:       match_found = PETSC_TRUE;
    374:     }
    375:   }
    376:   return(0);
    377: }

    379: /*
    380:  * Sort the stash, removing duplicates (combining as appropriate).
    381:  */
    382: PetscErrorCode VecStashSortCompress_Private(VecStash *stash)
    383: {
    385:   PetscInt i,j,bs = stash->bs;

    388:   if (!stash->n) return(0);
    389:   if (bs == 1) {
    390:     PetscSortIntWithScalarArray(stash->n,stash->idx,stash->array);
    391:     for (i=1,j=0; i<stash->n; i++) {
    392:       if (stash->idx[i] == stash->idx[j]) {
    393:         switch (stash->insertmode) {
    394:         case ADD_VALUES:
    395:           stash->array[j] += stash->array[i];
    396:           break;
    397:         case INSERT_VALUES:
    398:           stash->array[j] = stash->array[i];
    399:           break;
    400:         default: SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP,"Insert mode not supported 0x%x",stash->insertmode);
    401:         }
    402:       } else {
    403:         j++;
    404:         stash->idx[j]   = stash->idx[i];
    405:         stash->array[j] = stash->array[i];
    406:       }
    407:     }
    408:     stash->n = j + 1;
    409:   } else {                      /* block stash */
    410:     PetscInt *perm = NULL;
    411:     PetscScalar *arr;
    412:     PetscMalloc2(stash->n,&perm,stash->n*bs,&arr);
    413:     for (i=0; i<stash->n; i++) perm[i] = i;
    414:     PetscSortIntWithArray(stash->n,stash->idx,perm);

    416:     /* Out-of-place copy of arr */
    417:     PetscMemcpy(arr,stash->array+perm[0]*bs,bs*sizeof(PetscScalar));
    418:     for (i=1,j=0; i<stash->n; i++) {
    419:       PetscInt k;
    420:       if (stash->idx[i] == stash->idx[j]) {
    421:         switch (stash->insertmode) {
    422:         case ADD_VALUES:
    423:           for (k=0; k<bs; k++) arr[j*bs+k] += stash->array[perm[i]*bs+k];
    424:           break;
    425:         case INSERT_VALUES:
    426:           for (k=0; k<bs; k++) arr[j*bs+k] = stash->array[perm[i]*bs+k];
    427:           break;
    428:         default: SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP,"Insert mode not supported 0x%x",stash->insertmode);
    429:         }
    430:       } else {
    431:         j++;
    432:         stash->idx[j] = stash->idx[i];
    433:         for (k=0; k<bs; k++) arr[j*bs+k] = stash->array[perm[i]*bs+k];
    434:       }
    435:     }
    436:     stash->n = j + 1;
    437:     PetscMemcpy(stash->array,arr,stash->n*bs*sizeof(PetscScalar));
    438:     PetscFree2(perm,arr);
    439:   }
    440:   return(0);
    441: }

    443: PetscErrorCode VecStashGetOwnerList_Private(VecStash *stash,PetscLayout map,PetscMPIInt *nowners,PetscMPIInt **owners)
    444: {
    446:   PetscInt i,bs = stash->bs,r;
    447:   PetscSegBuffer seg;

    450:   if (bs != 1 && bs != map->bs) SETERRQ2(map->comm,PETSC_ERR_PLIB,"Stash block size %D does not match layout block size %D",bs,map->bs);
    451:   PetscSegBufferCreate(sizeof(PetscMPIInt),50,&seg);
    452:   *nowners = 0;
    453:   for (i=0,r=-1; i<stash->n; i++) {
    454:     if (stash->idx[i]*bs >= map->range[r+1]) {
    455:       PetscMPIInt *rank;
    456:       PetscSegBufferGet(seg,1,&rank);
    457:       PetscLayoutFindOwner(map,stash->idx[i]*bs,&r);
    458:       *rank = r;
    459:       (*nowners)++;
    460:     }
    461:   }
    462:   PetscSegBufferExtractAlloc(seg,owners);
    463:   PetscSegBufferDestroy(&seg);
    464:   return(0);
    465: }