Date: 2013-07-02T14:39:48+00:00

Actual source code: vecstash.c
petsc-3.4.2 2013-07-02

      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:   PetscMalloc(nopt*sizeof(PetscInt),&opt);
     38:   PetscOptionsGetIntArray(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:     PetscMalloc(2*nsends*sizeof(MPI_Status),&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,PetscScalar,&n_array,newnmax,PetscInt,&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:   PetscMalloc(2*size*sizeof(PetscInt),&nprocs);
    252:   PetscMemzero(nprocs,2*size*sizeof(PetscInt));
    253:   PetscMalloc(stash->n*sizeof(PetscInt),&owner);

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

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

    273:   /* post receives:
    274:      since we don't know how long each individual message is we
    275:      allocate the largest needed buffer for each receive. Potentially
    276:      this is a lot of wasted space.
    277:   */
    278:   PetscMalloc2(nreceives*nmax*bs,PetscScalar,&rvalues,nreceives*nmax,PetscInt,&rindices);
    279:   PetscMalloc(2*nreceives*sizeof(MPI_Request),&recv_waits);
    280:   for (i=0,count=0; i<nreceives; i++) {
    281:     MPI_Irecv(rvalues+bs*nmax*i,bs*nmax,MPIU_SCALAR,MPI_ANY_SOURCE,tag1,comm,recv_waits+count++);
    282:     MPI_Irecv(rindices+nmax*i,nmax,MPIU_INT,MPI_ANY_SOURCE,tag2,comm,recv_waits+count++);
    283:   }

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

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

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

    319:   stash->nprocs     = nprocs;
    320:   stash->svalues    = svalues;
    321:   stash->sindices   = sindices;
    322:   stash->rvalues    = rvalues;
    323:   stash->rindices   = rindices;
    324:   stash->nsends     = nsends;
    325:   stash->nrecvs     = nreceives;
    326:   stash->send_waits = send_waits;
    327:   stash->recv_waits = recv_waits;
    328:   stash->rmax       = nmax;
    329:   return(0);
    330: }

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

    338:    Input Parameters:
    339:    stash - the stash

    341:    Output Parameters:
    342:    nvals - the number of entries in the current message.
    343:    rows  - an array of row indices (or blocked indices) corresponding to the values
    344:    cols  - an array of columnindices (or blocked indices) corresponding to the values
    345:    vals  - the values
    346:    flg   - 0 indicates no more message left, and the current call has no values associated.
    347:            1 indicates that the current call successfully received a message, and the
    348:              other output parameters nvals,rows,cols,vals are set appropriately.
    349: */
    352: PetscErrorCode VecStashScatterGetMesg_Private(VecStash *stash,PetscMPIInt *nvals,PetscInt **rows,PetscScalar **vals,PetscInt *flg)
    353: {
    355:   PetscMPIInt    i = 0; /* dummy value so MPI-Uni doesn't think it is not set */
    356:   PetscInt       *flg_v;
    357:   PetscInt       i1,i2,bs=stash->bs;
    358:   MPI_Status     recv_status;
    359:   PetscBool      match_found = PETSC_FALSE;

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

    366:   flg_v = stash->nprocs;
    367:   /* If a matching pair of receieves are found, process them, and return the data to
    368:      the calling function. Until then keep receiving messages */
    369:   while (!match_found) {
    370:     MPI_Waitany(2*stash->nrecvs,stash->recv_waits,&i,&recv_status);
    371:     /* Now pack the received message into a structure which is useable by others */
    372:     if (i % 2) {
    373:       MPI_Get_count(&recv_status,MPIU_INT,nvals);
    374:       flg_v[2*recv_status.MPI_SOURCE+1] = i/2;
    375:     } else {
    376:       MPI_Get_count(&recv_status,MPIU_SCALAR,nvals);
    377:       flg_v[2*recv_status.MPI_SOURCE] = i/2;
    378:       *nvals = *nvals/bs;
    379:     }

    381:     /* Check if we have both the messages from this proc */
    382:     i1 = flg_v[2*recv_status.MPI_SOURCE];
    383:     i2 = flg_v[2*recv_status.MPI_SOURCE+1];
    384:     if (i1 != -1 && i2 != -1) {
    385:       *rows = stash->rindices + i2*stash->rmax;
    386:       *vals = stash->rvalues + i1*bs*stash->rmax;
    387:       *flg  = 1;
    388:       stash->nprocessed++;
    389:       match_found = PETSC_TRUE;
    390:     }
    391:   }
    392:   return(0);
    393: }