Date: 2016-07-24T16:49:19+00:00

Actual source code: vecstash.c
petsc-3.7.3 2016-07-24
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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: */
     22: PetscErrorCode VecStashCreate_Private(MPI_Comm comm,PetscInt bs,VecStash *stash)
     23: {
     25:   PetscInt       max,*opt,nopt;
     26:   PetscBool      flg;

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

     36:   nopt = stash->size;
     37:   PetscMalloc1(nopt,&opt);
     38:   PetscOptionsGetIntArray(NULL,NULL,"-vecstash_initial_size",opt,&nopt,&flg);
     39:   if (flg) {
     40:     if (nopt == 1)                max = opt[0];
     41:     else if (nopt == stash->size) max = opt[stash->rank];
     42:     else if (stash->rank < nopt)  max = opt[stash->rank];
     43:     else                          max = 0; /* use default */
     44:     stash->umax = max;
     45:   } else {
     46:     stash->umax = 0;
     47:   }
     48:   PetscFree(opt);

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

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

     60:   stash->send_waits   = 0;
     61:   stash->recv_waits   = 0;
     62:   stash->send_status  = 0;
     63:   stash->nsends       = 0;
     64:   stash->nrecvs       = 0;
     65:   stash->svalues      = 0;
     66:   stash->rvalues      = 0;
     67:   stash->rmax         = 0;
     68:   stash->nprocs       = 0;
     69:   stash->nprocessed   = 0;
     70:   stash->donotstash   = PETSC_FALSE;
     71:   stash->ignorenegidx = PETSC_FALSE;
     72:   return(0);
     73: }

     75: /*
     76:    VecStashDestroy_Private - Destroy the stash
     77: */
     80: PetscErrorCode VecStashDestroy_Private(VecStash *stash)
     81: {

     85:   PetscFree2(stash->array,stash->idx);
     86:   PetscFree(stash->bowners);
     87:   return(0);
     88: }

     90: /*
     91:    VecStashScatterEnd_Private - This is called as the fial stage of
     92:    scatter. The final stages of message passing is done here, and
     93:    all the memory used for message passing is cleanedu up. This
     94:    routine also resets the stash, and deallocates the memory used
     95:    for the stash. It also keeps track of the current memory usage
     96:    so that the same value can be used the next time through.
     97: */
    100: PetscErrorCode VecStashScatterEnd_Private(VecStash *stash)
    101: {
    103:   PetscInt       nsends=stash->nsends,oldnmax;
    104:   MPI_Status     *send_status;

    107:   /* wait on sends */
    108:   if (nsends) {
    109:     PetscMalloc1(2*nsends,&send_status);
    110:     MPI_Waitall(2*nsends,stash->send_waits,send_status);
    111:     PetscFree(send_status);
    112:   }

    114:   /* Now update nmaxold to be app 10% more than max n, this way the
    115:      wastage of space is reduced the next time this stash is used.
    116:      Also update the oldmax, only if it increases */
    117:   if (stash->n) {
    118:     oldnmax = ((PetscInt)(stash->n * 1.1) + 5)*stash->bs;
    119:     if (oldnmax > stash->oldnmax) stash->oldnmax = oldnmax;
    120:   }

    122:   stash->nmax       = 0;
    123:   stash->n          = 0;
    124:   stash->reallocs   = -1;
    125:   stash->rmax       = 0;
    126:   stash->nprocessed = 0;

    128:   PetscFree2(stash->array,stash->idx);
    129:   stash->array = 0;
    130:   stash->idx   = 0;
    131:   PetscFree(stash->send_waits);
    132:   PetscFree(stash->recv_waits);
    133:   PetscFree2(stash->svalues,stash->sindices);
    134:   PetscFree2(stash->rvalues,stash->rindices);
    135:   PetscFree(stash->nprocs);
    136:   return(0);
    137: }

    139: /*
    140:    VecStashGetInfo_Private - Gets the relavant statistics of the stash

    142:    Input Parameters:
    143:    stash    - the stash
    144:    nstash   - the size of the stash
    145:    reallocs - the number of additional mallocs incurred.

    147: */
    150: PetscErrorCode VecStashGetInfo_Private(VecStash *stash,PetscInt *nstash,PetscInt *reallocs)
    151: {
    153:   if (nstash) *nstash = stash->n*stash->bs;
    154:   if (reallocs) {
    155:     if (stash->reallocs < 0) *reallocs = 0;
    156:     else                     *reallocs = stash->reallocs;
    157:   }
    158:   return(0);
    159: }

    162: /*
    163:    VecStashSetInitialSize_Private - Sets the initial size of the stash

    165:    Input Parameters:
    166:    stash  - the stash
    167:    max    - the value that is used as the max size of the stash.
    168:             this value is used while allocating memory. It specifies
    169:             the number of vals stored, even with the block-stash
    170: */
    173: PetscErrorCode VecStashSetInitialSize_Private(VecStash *stash,PetscInt max)
    174: {
    176:   stash->umax = max;
    177:   return(0);
    178: }

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

    184:    Input Parameters:
    185:    stash - the stash
    186:    incr  - the minimum increase requested

    188:    Notes:
    189:    This routine doubles the currently used memory.
    190: */
    193: PetscErrorCode VecStashExpand_Private(VecStash *stash,PetscInt incr)
    194: {
    196:   PetscInt       *n_idx,newnmax,bs=stash->bs;
    197:   PetscScalar    *n_array;

    200:   /* allocate a larger stash. */
    201:   if (!stash->oldnmax && !stash->nmax) { /* new stash */
    202:     if (stash->umax)                  newnmax = stash->umax/bs;
    203:     else                              newnmax = DEFAULT_STASH_SIZE/bs;
    204:   } else if (!stash->nmax) { /* resuing stash */
    205:     if (stash->umax > stash->oldnmax) newnmax = stash->umax/bs;
    206:     else                              newnmax = stash->oldnmax/bs;
    207:   } else                              newnmax = stash->nmax*2;

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

    211:   PetscMalloc2(bs*newnmax,&n_array,newnmax,&n_idx);
    212:   PetscMemcpy(n_array,stash->array,bs*stash->nmax*sizeof(PetscScalar));
    213:   PetscMemcpy(n_idx,stash->idx,stash->nmax*sizeof(PetscInt));
    214:   PetscFree2(stash->array,stash->idx);

    216:   stash->array = n_array;
    217:   stash->idx   = n_idx;
    218:   stash->nmax  = newnmax;
    219:   stash->reallocs++;
    220:   return(0);
    221: }
    222: /*
    223:   VecStashScatterBegin_Private - Initiates the transfer of values to the
    224:   correct owners. This function goes through the stash, and check the
    225:   owners of each stashed value, and sends the values off to the owner
    226:   processors.

    228:   Input Parameters:
    229:   stash  - the stash
    230:   owners - an array of size 'no-of-procs' which gives the ownership range
    231:            for each node.

    233:   Notes: The 'owners' array in the cased of the blocked-stash has the
    234:   ranges specified blocked global indices, and for the regular stash in
    235:   the proper global indices.
    236: */
    239: PetscErrorCode VecStashScatterBegin_Private(VecStash *stash,PetscInt *owners)
    240: {
    242:   PetscMPIInt    size = stash->size,tag1=stash->tag1,tag2=stash->tag2;
    243:   PetscInt       *owner,*start,*nprocs,nsends,nreceives;
    244:   PetscInt       nmax,count,*sindices,*rindices,i,j,idx,bs=stash->bs,lastidx;
    245:   PetscScalar    *rvalues,*svalues;
    246:   MPI_Comm       comm = stash->comm;
    247:   MPI_Request    *send_waits,*recv_waits;

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

    254:   j       = 0;
    255:   lastidx = -1;
    256:   for (i=0; i<stash->n; i++) {
    257:     /* if indices are NOT locally sorted, need to start search at the beginning */
    258:     if (lastidx > (idx = stash->idx[i])) j = 0;
    259:     lastidx = idx;
    260:     for (; j<size; j++) {
    261:       if (idx >= owners[j] && idx < owners[j+1]) {
    262:         nprocs[2*j]++; nprocs[2*j+1] = 1; owner[i] = j; break;
    263:       }
    264:     }
    265:   }
    266:   nsends = 0;
    267:   for (i=0; i<size; i++) nsends += nprocs[2*i+1];

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

    272:   /* post receives:
    273:      since we don't know how long each individual message is we
    274:      allocate the largest needed buffer for each receive. Potentially
    275:      this is a lot of wasted space.
    276:   */
    277:   PetscMalloc2(nreceives*nmax*bs,&rvalues,nreceives*nmax,&rindices);
    278:   PetscMalloc1(2*nreceives,&recv_waits);
    279:   for (i=0,count=0; i<nreceives; i++) {
    280:     MPI_Irecv(rvalues+bs*nmax*i,bs*nmax,MPIU_SCALAR,MPI_ANY_SOURCE,tag1,comm,recv_waits+count++);
    281:     MPI_Irecv(rindices+nmax*i,nmax,MPIU_INT,MPI_ANY_SOURCE,tag2,comm,recv_waits+count++);
    282:   }

    284:   /* do sends:
    285:       1) starts[i] gives the starting index in svalues for stuff going to
    286:          the ith processor
    287:   */
    288:   PetscMalloc2(stash->n*bs,&svalues,stash->n,&sindices);
    289:   PetscMalloc1(2*nsends,&send_waits);
    290:   PetscMalloc1(size,&start);
    291:   /* use 2 sends the first with all_v, the next with all_i */
    292:   start[0] = 0;
    293:   for (i=1; i<size; i++) start[i] = start[i-1] + nprocs[2*i-2];

    295:   for (i=0; i<stash->n; i++) {
    296:     j = owner[i];
    297:     if (bs == 1) svalues[start[j]] = stash->array[i];
    298:     else {
    299:       PetscMemcpy(svalues+bs*start[j],stash->array+bs*i,bs*sizeof(PetscScalar));
    300:     }
    301:     sindices[start[j]] = stash->idx[i];
    302:     start[j]++;
    303:   }
    304:   start[0] = 0;
    305:   for (i=1; i<size; i++) start[i] = start[i-1] + nprocs[2*i-2];

    307:   for (i=0,count=0; i<size; i++) {
    308:     if (nprocs[2*i+1]) {
    309:       MPI_Isend(svalues+bs*start[i],bs*nprocs[2*i],MPIU_SCALAR,i,tag1,comm,send_waits+count++);
    310:       MPI_Isend(sindices+start[i],nprocs[2*i],MPIU_INT,i,tag2,comm,send_waits+count++);
    311:     }
    312:   }
    313:   PetscFree(owner);
    314:   PetscFree(start);
    315:   /* This memory is reused in scatter end  for a different purpose*/
    316:   for (i=0; i<2*size; i++) nprocs[i] = -1;

    318:   stash->nprocs     = nprocs;
    319:   stash->svalues    = svalues;
    320:   stash->sindices   = sindices;
    321:   stash->rvalues    = rvalues;
    322:   stash->rindices   = rindices;
    323:   stash->nsends     = nsends;
    324:   stash->nrecvs     = nreceives;
    325:   stash->send_waits = send_waits;
    326:   stash->recv_waits = recv_waits;
    327:   stash->rmax       = nmax;
    328:   return(0);
    329: }

    331: /*
    332:    VecStashScatterGetMesg_Private - This function waits on the receives posted
    333:    in the function VecStashScatterBegin_Private() and returns one message at
    334:    a time to the calling function. If no messages are left, it indicates this
    335:    by setting flg = 0, else it sets flg = 1.

    337:    Input Parameters:
    338:    stash - the stash

    340:    Output Parameters:
    341:    nvals - the number of entries in the current message.
    342:    rows  - an array of row indices (or blocked indices) corresponding to the values
    343:    cols  - an array of columnindices (or blocked indices) corresponding to the values
    344:    vals  - the values
    345:    flg   - 0 indicates no more message left, and the current call has no values associated.
    346:            1 indicates that the current call successfully received a message, and the
    347:              other output parameters nvals,rows,cols,vals are set appropriately.
    348: */
    351: PetscErrorCode VecStashScatterGetMesg_Private(VecStash *stash,PetscMPIInt *nvals,PetscInt **rows,PetscScalar **vals,PetscInt *flg)
    352: {
    354:   PetscMPIInt    i = 0; /* dummy value so MPI-Uni doesn't think it is not set */
    355:   PetscInt       *flg_v;
    356:   PetscInt       i1,i2,bs=stash->bs;
    357:   MPI_Status     recv_status;
    358:   PetscBool      match_found = PETSC_FALSE;

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

    365:   flg_v = stash->nprocs;
    366:   /* If a matching pair of receives are found, process them, and return the data to
    367:      the calling function. Until then keep receiving messages */
    368:   while (!match_found) {
    369:     MPI_Waitany(2*stash->nrecvs,stash->recv_waits,&i,&recv_status);
    370:     /* Now pack the received message into a structure which is useable by others */
    371:     if (i % 2) {
    372:       MPI_Get_count(&recv_status,MPIU_INT,nvals);
    373:       flg_v[2*recv_status.MPI_SOURCE+1] = i/2;
    374:     } else {
    375:       MPI_Get_count(&recv_status,MPIU_SCALAR,nvals);
    376:       flg_v[2*recv_status.MPI_SOURCE] = i/2;
    377:       *nvals = *nvals/bs;
    378:     }

    380:     /* Check if we have both the messages from this proc */
    381:     i1 = flg_v[2*recv_status.MPI_SOURCE];
    382:     i2 = flg_v[2*recv_status.MPI_SOURCE+1];
    383:     if (i1 != -1 && i2 != -1) {
    384:       *rows = stash->rindices + i2*stash->rmax;
    385:       *vals = stash->rvalues + i1*bs*stash->rmax;
    386:       *flg  = 1;
    387:       stash->nprocessed++;
    388:       match_found = PETSC_TRUE;
    389:     }
    390:   }
    391:   return(0);
    392: }

    396: /*
    397:  * Sort the stash, removing duplicates (combining as appropriate).
    398:  */
    399: PetscErrorCode VecStashSortCompress_Private(VecStash *stash)
    400: {
    402:   PetscInt i,j,bs = stash->bs;

    405:   if (!stash->n) return(0);
    406:   if (bs == 1) {
    407:     PetscSortIntWithScalarArray(stash->n,stash->idx,stash->array);
    408:     for (i=1,j=0; i<stash->n; i++) {
    409:       if (stash->idx[i] == stash->idx[j]) {
    410:         switch (stash->insertmode) {
    411:         case ADD_VALUES:
    412:           stash->array[j] += stash->array[i];
    413:           break;
    414:         case INSERT_VALUES:
    415:           stash->array[j] = stash->array[i];
    416:           break;
    417:         default: SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP,"Insert mode not supported 0x%x",stash->insertmode);
    418:         }
    419:       } else {
    420:         j++;
    421:         stash->idx[j]   = stash->idx[i];
    422:         stash->array[j] = stash->array[i];
    423:       }
    424:     }
    425:     stash->n = j + 1;
    426:   } else {                      /* block stash */
    427:     PetscInt *perm = NULL;
    428:     PetscScalar *arr;
    429:     PetscMalloc2(stash->n,&perm,stash->n*bs,&arr);
    430:     for (i=0; i<stash->n; i++) perm[i] = i;
    431:     PetscSortIntWithArray(stash->n,stash->idx,perm);

    433:     /* Out-of-place copy of arr */
    434:     PetscMemcpy(arr,stash->array,bs*sizeof(PetscScalar));
    435:     for (i=1,j=0; i<stash->n; i++) {
    436:       PetscInt k;
    437:       if (stash->idx[i] == stash->idx[j]) {
    438:         switch (stash->insertmode) {
    439:         case ADD_VALUES:
    440:           for (k=0; k<bs; k++) arr[j*bs+k] += stash->array[perm[i]*bs+k];
    441:           break;
    442:         case INSERT_VALUES:
    443:           for (k=0; k<bs; k++) arr[j*bs+k] = stash->array[perm[i]*bs+k];
    444:           break;
    445:         default: SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP,"Insert mode not supported 0x%x",stash->insertmode);
    446:         }
    447:       } else {
    448:         j++;
    449:         stash->idx[j] = stash->idx[i];
    450:         for (k=0; k<bs; k++) arr[j*bs+k] = stash->array[perm[i]*bs+k];
    451:       }
    452:     }
    453:     stash->n = j + 1;
    454:     PetscMemcpy(stash->array,arr,stash->n*bs*sizeof(PetscScalar));
    455:     PetscFree2(perm,arr);
    456:   }
    457:   return(0);
    458: }

    462: PetscErrorCode VecStashGetOwnerList_Private(VecStash *stash,PetscLayout map,PetscMPIInt *nowners,PetscMPIInt **owners)
    463: {
    465:   PetscInt i,bs = stash->bs,r;
    466:   PetscSegBuffer seg;

    469:   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);
    470:   PetscSegBufferCreate(sizeof(PetscMPIInt),50,&seg);
    471:   *nowners = 0;
    472:   for (i=0,r=-1; i<stash->n; i++) {
    473:     if (stash->idx[i]*bs >= map->range[r+1]) {
    474:       PetscMPIInt *rank;
    475:       PetscSegBufferGet(seg,1,&rank);
    476:       PetscLayoutFindOwner(map,stash->idx[i]*bs,&r);
    477:       *rank = r;
    478:       (*nowners)++;
    479:     }
    480:   }
    481:   PetscSegBufferExtractAlloc(seg,owners);
    482:   PetscSegBufferDestroy(&seg);
    483:   return(0);
    484: }