示例#1
0
/*@
   ISExpand - Computes the union of two index sets, by concatenating 2 lists and
   removing duplicates.

   Collective on IS

   Input Parameter:
+  is1 - first index set
-  is2 - index values to be added

   Output Parameters:
.  isout - is1 + is2 The index set is2 is appended to is1 removing duplicates

   Notes:
   Negative values are removed from the lists. This requires O(imax-imin)
   memory and O(imax-imin) work, where imin and imax are the bounds on the
   indices in is1 and is2.

   The IS's do not need to be sorted.

   Level: intermediate

.seealso: ISDestroy(), ISView(), ISDifference(), ISSum()

   Concepts: index sets^difference
   Concepts: IS^difference

@*/
PetscErrorCode ISExpand(IS is1,IS is2,IS *isout)
{
  PetscErrorCode ierr;
  PetscInt       i,n1,n2,imin,imax,nout,*iout;
  const PetscInt *i1,*i2;
  PetscBT        mask;
  MPI_Comm       comm;

  PetscFunctionBegin;
  PetscValidHeaderSpecific(is1,IS_CLASSID,1);
  PetscValidHeaderSpecific(is2,IS_CLASSID,2);
  PetscValidPointer(isout,3);

  ierr = ISGetIndices(is1,&i1);CHKERRQ(ierr);
  ierr = ISGetLocalSize(is1,&n1);CHKERRQ(ierr);
  ierr = ISGetIndices(is2,&i2);CHKERRQ(ierr);
  ierr = ISGetLocalSize(is2,&n2);CHKERRQ(ierr);

  /* Create a bit mask array to contain required values */
  if (n1 || n2) {
    imin = PETSC_MAX_INT;
    imax = 0;
    for (i=0; i<n1; i++) {
      if (i1[i] < 0) continue;
      imin = PetscMin(imin,i1[i]);
      imax = PetscMax(imax,i1[i]);
    }
    for (i=0; i<n2; i++) {
      if (i2[i] < 0) continue;
      imin = PetscMin(imin,i2[i]);
      imax = PetscMax(imax,i2[i]);
    }
  } else imin = imax = 0;

  ierr = PetscMalloc1(n1+n2,&iout);CHKERRQ(ierr);
  nout = 0;
  ierr = PetscBTCreate(imax-imin,&mask);CHKERRQ(ierr);
  /* Put the values from is1 */
  for (i=0; i<n1; i++) {
    if (i1[i] < 0) continue;
    if (!PetscBTLookupSet(mask,i1[i] - imin)) iout[nout++] = i1[i];
  }
  ierr = ISRestoreIndices(is1,&i1);CHKERRQ(ierr);
  /* Put the values from is2 */
  for (i=0; i<n2; i++) {
    if (i2[i] < 0) continue;
    if (!PetscBTLookupSet(mask,i2[i] - imin)) iout[nout++] = i2[i];
  }
  ierr = ISRestoreIndices(is2,&i2);CHKERRQ(ierr);

  /* create the new IS containing the sum */
  ierr = PetscObjectGetComm((PetscObject)is1,&comm);CHKERRQ(ierr);
  ierr = ISCreateGeneral(comm,nout,iout,PETSC_OWN_POINTER,isout);CHKERRQ(ierr);

  ierr = PetscBTDestroy(&mask);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}
示例#2
0
static PetscErrorCode MatIncreaseOverlap_MPISBAIJ_Once(Mat C,PetscInt is_max,IS is[])
{
  Mat_MPISBAIJ  *c = (Mat_MPISBAIJ*)C->data;
  PetscErrorCode ierr;
  PetscMPIInt    size,rank,tag1,tag2,*len_s,nrqr,nrqs,*id_r1,*len_r1,flag,len;
  const PetscInt *idx_i;
  PetscInt       idx,isz,col,*n,*data1,**data1_start,*data2,*data2_i,*data,*data_i,
                 Mbs,i,j,k,*odata1,*odata2,
                 proc_id,**odata2_ptr,*ctable=0,*btable,len_max,len_est;
  PetscInt       proc_end=0,*iwork,len_unused,nodata2;
  PetscInt       ois_max; /* max no of is[] in each of processor */
  char           *t_p;
  MPI_Comm       comm;
  MPI_Request    *s_waits1,*s_waits2,r_req;
  MPI_Status     *s_status,r_status;
  PetscBT        *table;  /* mark indices of this processor's is[] */
  PetscBT        table_i;
  PetscBT        otable; /* mark indices of other processors' is[] */ 
  PetscInt       bs=C->rmap->bs,Bn = c->B->cmap->n,Bnbs = Bn/bs,*Bowners;  
  IS             garray_local,garray_gl;

  PetscFunctionBegin;
  comm = ((PetscObject)C)->comm;
  size = c->size;
  rank = c->rank;
  Mbs  = c->Mbs;

  ierr = PetscObjectGetNewTag((PetscObject)C,&tag1);CHKERRQ(ierr);
  ierr = PetscObjectGetNewTag((PetscObject)C,&tag2);CHKERRQ(ierr);

  /* create tables used in
     step 1: table[i] - mark c->garray of proc [i]
     step 3: table[i] - mark indices of is[i] when whose=MINE     
             table[0] - mark incideces of is[] when whose=OTHER */
  len = PetscMax(is_max, size);CHKERRQ(ierr);
  ierr = PetscMalloc2(len,PetscBT,&table,(Mbs/PETSC_BITS_PER_BYTE+1)*len,char,&t_p);CHKERRQ(ierr);
  for (i=0; i<len; i++) {
    table[i]  = t_p  + (Mbs/PETSC_BITS_PER_BYTE+1)*i; 
  }

  ierr = MPI_Allreduce(&is_max,&ois_max,1,MPIU_INT,MPI_MAX,comm);CHKERRQ(ierr);
  
  /* 1. Send this processor's is[] to other processors */
  /*---------------------------------------------------*/
  /* allocate spaces */
  ierr = PetscMalloc(is_max*sizeof(PetscInt),&n);CHKERRQ(ierr);
  len = 0;
  for (i=0; i<is_max; i++) {
    ierr = ISGetLocalSize(is[i],&n[i]);CHKERRQ(ierr);
    len += n[i]; 
  }
  if (!len) { 
    is_max = 0;
  } else {
    len += 1 + is_max; /* max length of data1 for one processor */
  }

 
  ierr = PetscMalloc((size*len+1)*sizeof(PetscInt),&data1);CHKERRQ(ierr);
  ierr = PetscMalloc(size*sizeof(PetscInt*),&data1_start);CHKERRQ(ierr);
  for (i=0; i<size; i++) data1_start[i] = data1 + i*len;

  ierr = PetscMalloc4(size,PetscInt,&len_s,size,PetscInt,&btable,size,PetscInt,&iwork,size+1,PetscInt,&Bowners);CHKERRQ(ierr);

  /* gather c->garray from all processors */
  ierr = ISCreateGeneral(comm,Bnbs,c->garray,&garray_local);CHKERRQ(ierr);
  ierr = ISAllGather(garray_local, &garray_gl);CHKERRQ(ierr);
  ierr = ISDestroy(garray_local);CHKERRQ(ierr);
  ierr = MPI_Allgather(&Bnbs,1,MPIU_INT,Bowners+1,1,MPIU_INT,comm);CHKERRQ(ierr);
  Bowners[0] = 0;
  for (i=0; i<size; i++) Bowners[i+1] += Bowners[i];
  
  if (is_max){ 
    /* hash table ctable which maps c->row to proc_id) */
    ierr = PetscMalloc(Mbs*sizeof(PetscInt),&ctable);CHKERRQ(ierr);
    for (proc_id=0,j=0; proc_id<size; proc_id++) {
      for (; j<C->rmap->range[proc_id+1]/bs; j++) {
        ctable[j] = proc_id;
      }
    }

    /* hash tables marking c->garray */
    ierr = ISGetIndices(garray_gl,&idx_i);
    for (i=0; i<size; i++){
      table_i = table[i]; 
      ierr    = PetscBTMemzero(Mbs,table_i);CHKERRQ(ierr);
      for (j = Bowners[i]; j<Bowners[i+1]; j++){ /* go through B cols of proc[i]*/
        ierr = PetscBTSet(table_i,idx_i[j]);CHKERRQ(ierr);
      }
    }
    ierr = ISRestoreIndices(garray_gl,&idx_i);CHKERRQ(ierr);
  }  /* if (is_max) */
  ierr = ISDestroy(garray_gl);CHKERRQ(ierr); 

  /* evaluate communication - mesg to who, length, and buffer space */
  for (i=0; i<size; i++) len_s[i] = 0;
  
  /* header of data1 */
  for (proc_id=0; proc_id<size; proc_id++){
    iwork[proc_id] = 0;
    *data1_start[proc_id] = is_max; 
    data1_start[proc_id]++;
    for (j=0; j<is_max; j++) { 
      if (proc_id == rank){
        *data1_start[proc_id] = n[j]; 
      } else {
        *data1_start[proc_id] = 0;  
      }
      data1_start[proc_id]++;
    }
  }
  
  for (i=0; i<is_max; i++) { 
    ierr = ISGetIndices(is[i],&idx_i);CHKERRQ(ierr); 
    for (j=0; j<n[i]; j++){
      idx = idx_i[j];
      *data1_start[rank] = idx; data1_start[rank]++; /* for local proccessing */
      proc_end = ctable[idx];
      for (proc_id=0;  proc_id<=proc_end; proc_id++){ /* for others to process */
        if (proc_id == rank ) continue; /* done before this loop */
        if (proc_id < proc_end && !PetscBTLookup(table[proc_id],idx)) 
          continue;   /* no need for sending idx to [proc_id] */
        *data1_start[proc_id] = idx; data1_start[proc_id]++;
        len_s[proc_id]++;
      }
    } 
    /* update header data */
    for (proc_id=0; proc_id<size; proc_id++){ 
      if (proc_id== rank) continue;
      *(data1 + proc_id*len + 1 + i) = len_s[proc_id] - iwork[proc_id];
      iwork[proc_id] = len_s[proc_id] ;
    } 
    ierr = ISRestoreIndices(is[i],&idx_i);CHKERRQ(ierr);
  } 

  nrqs = 0; nrqr = 0;
  for (i=0; i<size; i++){
    data1_start[i] = data1 + i*len;
    if (len_s[i]){
      nrqs++;
      len_s[i] += 1 + is_max; /* add no. of header msg */
    }
  }

  for (i=0; i<is_max; i++) { 
    ierr = ISDestroy(is[i]);CHKERRQ(ierr); 
  }
  ierr = PetscFree(n);CHKERRQ(ierr);
  ierr = PetscFree(ctable);CHKERRQ(ierr);

  /* Determine the number of messages to expect, their lengths, from from-ids */
  ierr = PetscGatherNumberOfMessages(comm,PETSC_NULL,len_s,&nrqr);CHKERRQ(ierr);
  ierr = PetscGatherMessageLengths(comm,nrqs,nrqr,len_s,&id_r1,&len_r1);CHKERRQ(ierr); 
  
  /*  Now  post the sends */
  ierr = PetscMalloc2(size,MPI_Request,&s_waits1,size,MPI_Request,&s_waits2);CHKERRQ(ierr);
  k = 0;
  for (proc_id=0; proc_id<size; proc_id++){  /* send data1 to processor [proc_id] */
    if (len_s[proc_id]){
      ierr = MPI_Isend(data1_start[proc_id],len_s[proc_id],MPIU_INT,proc_id,tag1,comm,s_waits1+k);CHKERRQ(ierr);
      k++;
    }
  }

  /* 2. Receive other's is[] and process. Then send back */
  /*-----------------------------------------------------*/
  len = 0;
  for (i=0; i<nrqr; i++){
    if (len_r1[i] > len)len = len_r1[i];
  }
  ierr = PetscFree(len_r1);CHKERRQ(ierr);
  ierr = PetscFree(id_r1);CHKERRQ(ierr);

  for (proc_id=0; proc_id<size; proc_id++)
    len_s[proc_id] = iwork[proc_id] = 0;
  
  ierr = PetscMalloc((len+1)*sizeof(PetscInt),&odata1);CHKERRQ(ierr);
  ierr = PetscMalloc(size*sizeof(PetscInt**),&odata2_ptr);CHKERRQ(ierr); 
  ierr = PetscBTCreate(Mbs,otable);CHKERRQ(ierr);

  len_max = ois_max*(Mbs+1);  /* max space storing all is[] for each receive */
  len_est = 2*len_max; /* estimated space of storing is[] for all receiving messages */
  ierr = PetscMalloc((len_est+1)*sizeof(PetscInt),&odata2);CHKERRQ(ierr);
  nodata2 = 0;       /* nodata2+1: num of PetscMalloc(,&odata2_ptr[]) called */
  odata2_ptr[nodata2] = odata2;
  len_unused = len_est; /* unused space in the array odata2_ptr[nodata2]-- needs to be >= len_max  */
  
  k = 0;
  while (k < nrqr){
    /* Receive messages */
    ierr = MPI_Iprobe(MPI_ANY_SOURCE,tag1,comm,&flag,&r_status);CHKERRQ(ierr);
    if (flag){ 
      ierr = MPI_Get_count(&r_status,MPIU_INT,&len);CHKERRQ(ierr); 
      proc_id = r_status.MPI_SOURCE;
      ierr = MPI_Irecv(odata1,len,MPIU_INT,proc_id,r_status.MPI_TAG,comm,&r_req);CHKERRQ(ierr);
      ierr = MPI_Wait(&r_req,&r_status);CHKERRQ(ierr);

      /*  Process messages */
      /*  make sure there is enough unused space in odata2 array */
      if (len_unused < len_max){ /* allocate more space for odata2 */
        ierr = PetscMalloc((len_est+1)*sizeof(PetscInt),&odata2);CHKERRQ(ierr);
        odata2_ptr[++nodata2] = odata2;
        len_unused = len_est;
      }

      ierr = MatIncreaseOverlap_MPISBAIJ_Local(C,odata1,OTHER,odata2,&otable);CHKERRQ(ierr);
      len = 1 + odata2[0];
      for (i=0; i<odata2[0]; i++){
        len += odata2[1 + i];
      }

      /* Send messages back */
      ierr = MPI_Isend(odata2,len,MPIU_INT,proc_id,tag2,comm,s_waits2+k);CHKERRQ(ierr);
      k++;
      odata2     += len;
      len_unused -= len;
      len_s[proc_id] = len; /* num of messages sending back to [proc_id] by this proc */
    } 
  } 
  ierr = PetscFree(odata1);CHKERRQ(ierr); 
  ierr = PetscBTDestroy(otable);CHKERRQ(ierr); 

  /* 3. Do local work on this processor's is[] */
  /*-------------------------------------------*/
  /* make sure there is enough unused space in odata2(=data) array */
  len_max = is_max*(Mbs+1); /* max space storing all is[] for this processor */
  if (len_unused < len_max){ /* allocate more space for odata2 */
    ierr = PetscMalloc((len_est+1)*sizeof(PetscInt),&odata2);CHKERRQ(ierr);
    odata2_ptr[++nodata2] = odata2;
    len_unused = len_est;
  }

  data = odata2;
  ierr = MatIncreaseOverlap_MPISBAIJ_Local(C,data1_start[rank],MINE,data,table);CHKERRQ(ierr);
  ierr = PetscFree(data1_start);CHKERRQ(ierr);

  /* 4. Receive work done on other processors, then merge */
  /*------------------------------------------------------*/
  /* get max number of messages that this processor expects to recv */
  ierr = MPI_Allreduce(len_s,iwork,size,MPIU_INT,MPI_MAX,comm);CHKERRQ(ierr);
  ierr = PetscMalloc((iwork[rank]+1)*sizeof(PetscInt),&data2);CHKERRQ(ierr);
  ierr = PetscFree4(len_s,btable,iwork,Bowners);CHKERRQ(ierr);

  k = 0;
  while (k < nrqs){
    /* Receive messages */
    ierr = MPI_Iprobe(MPI_ANY_SOURCE,tag2,comm,&flag,&r_status);
    if (flag){
      ierr = MPI_Get_count(&r_status,MPIU_INT,&len);CHKERRQ(ierr);
      proc_id = r_status.MPI_SOURCE;
      ierr = MPI_Irecv(data2,len,MPIU_INT,proc_id,r_status.MPI_TAG,comm,&r_req);CHKERRQ(ierr);
      ierr = MPI_Wait(&r_req,&r_status);CHKERRQ(ierr);
      if (len > 1+is_max){ /* Add data2 into data */
        data2_i = data2 + 1 + is_max;
        for (i=0; i<is_max; i++){
          table_i = table[i];
          data_i  = data + 1 + is_max + Mbs*i;
          isz     = data[1+i]; 
          for (j=0; j<data2[1+i]; j++){
            col = data2_i[j];
            if (!PetscBTLookupSet(table_i,col)) {data_i[isz++] = col;}
          }
          data[1+i] = isz;
          if (i < is_max - 1) data2_i += data2[1+i]; 
        } 
      } 
      k++;
    } 
  } 
  ierr = PetscFree(data2);CHKERRQ(ierr);
  ierr = PetscFree2(table,t_p);CHKERRQ(ierr);

  /* phase 1 sends are complete */
  ierr = PetscMalloc(size*sizeof(MPI_Status),&s_status);CHKERRQ(ierr);
  if (nrqs) {ierr = MPI_Waitall(nrqs,s_waits1,s_status);CHKERRQ(ierr);}
  ierr = PetscFree(data1);CHKERRQ(ierr); 
       
  /* phase 2 sends are complete */
  if (nrqr){ierr = MPI_Waitall(nrqr,s_waits2,s_status);CHKERRQ(ierr);}
  ierr = PetscFree2(s_waits1,s_waits2);CHKERRQ(ierr);
  ierr = PetscFree(s_status);CHKERRQ(ierr); 

  /* 5. Create new is[] */
  /*--------------------*/ 
  for (i=0; i<is_max; i++) {
    data_i = data + 1 + is_max + Mbs*i;
    ierr = ISCreateGeneral(PETSC_COMM_SELF,data[1+i],data_i,is+i);CHKERRQ(ierr);
  }
  for (k=0; k<=nodata2; k++){
    ierr = PetscFree(odata2_ptr[k]);CHKERRQ(ierr); 
  }
  ierr = PetscFree(odata2_ptr);CHKERRQ(ierr);

  PetscFunctionReturn(0);
}
示例#3
0
/* Would computation be reduced by swapping the loop 'for each is' and 'for each row'? */
static PetscErrorCode MatIncreaseOverlap_MPISBAIJ_Local(Mat C,PetscInt *data,PetscInt whose,PetscInt *nidx,PetscBT *table)
{
  Mat_MPISBAIJ   *c = (Mat_MPISBAIJ*)C->data;
  Mat_SeqSBAIJ   *a = (Mat_SeqSBAIJ*)(c->A)->data;
  Mat_SeqBAIJ    *b = (Mat_SeqBAIJ*)(c->B)->data;
  PetscErrorCode ierr;
  PetscInt       row,mbs,Mbs,*nidx_i,col,col_max,isz,isz0,*ai,*aj,*bi,*bj,*garray,rstart,l;
  PetscInt       a_start,a_end,b_start,b_end,i,j,k,is_max,*idx_i,n;
  PetscBT        table0;  /* mark the indices of input is[] for look up */
  PetscBT        table_i; /* poits to i-th table. When whose=OTHER, a single table is used for all is[] */
  
  PetscFunctionBegin;
  Mbs = c->Mbs; mbs = a->mbs; 
  ai = a->i; aj = a->j;
  bi = b->i; bj = b->j;
  garray = c->garray;
  rstart = c->rstartbs;
  is_max = data[0];

  ierr = PetscBTCreate(Mbs,table0);CHKERRQ(ierr);
  
  nidx[0] = is_max; 
  idx_i   = data + is_max + 1; /* ptr to input is[0] array */
  nidx_i  = nidx + is_max + 1; /* ptr to output is[0] array */
  for (i=0; i<is_max; i++) { /* for each is */
    isz  = 0;
    n = data[1+i]; /* size of input is[i] */

    /* initialize and set table_i(mark idx and nidx) and table0(only mark idx) */
    if (whose == MINE){ /* process this processor's is[] */
      table_i = table[i];
      nidx_i  = nidx + 1+ is_max + Mbs*i;
    } else {            /* process other processor's is[] - only use one temp table */
      table_i = table[0];
    }
    ierr = PetscBTMemzero(Mbs,table_i);CHKERRQ(ierr);
    ierr = PetscBTMemzero(Mbs,table0);CHKERRQ(ierr);
    if (n==0) {
       nidx[1+i] = 0; /* size of new is[i] */
       continue; 
    }

    isz0 = 0; col_max = 0;
    for (j=0; j<n; j++){
      col = idx_i[j]; 
      if (col >= Mbs) SETERRQ2(PETSC_ERR_ARG_OUTOFRANGE,"index col %D >= Mbs %D",col,Mbs);
      if(!PetscBTLookupSet(table_i,col)) { 
        ierr = PetscBTSet(table0,col);CHKERRQ(ierr);
        if (whose == MINE) {nidx_i[isz0] = col;}
        if (col_max < col) col_max = col;
        isz0++;
      }
    }
      
    if (whose == MINE) {isz = isz0;}
    k = 0;  /* no. of indices from input is[i] that have been examined */
    for (row=0; row<mbs; row++){ 
      a_start = ai[row]; a_end = ai[row+1];
      b_start = bi[row]; b_end = bi[row+1];
      if (PetscBTLookup(table0,row+rstart)){ /* row is on input is[i]:
                                                do row search: collect all col in this row */
        for (l = a_start; l<a_end ; l++){ /* Amat */
          col = aj[l] + rstart;
          if (!PetscBTLookupSet(table_i,col)) {nidx_i[isz++] = col;}
        }
        for (l = b_start; l<b_end ; l++){ /* Bmat */
          col = garray[bj[l]];
          if (!PetscBTLookupSet(table_i,col)) {nidx_i[isz++] = col;}
        }
        k++;
        if (k >= isz0) break; /* for (row=0; row<mbs; row++) */
      } else { /* row is not on input is[i]:
                  do col serach: add row onto nidx_i if there is a col in nidx_i */
        for (l = a_start; l<a_end ; l++){ /* Amat */
          col = aj[l] + rstart;
          if (col > col_max) break; 
          if (PetscBTLookup(table0,col)){
            if (!PetscBTLookupSet(table_i,row+rstart)) {nidx_i[isz++] = row+rstart;}
            break; /* for l = start; l<end ; l++) */
          }
        } 
        for (l = b_start; l<b_end ; l++){ /* Bmat */
          col = garray[bj[l]];
          if (col > col_max) break; 
          if (PetscBTLookup(table0,col)){
            if (!PetscBTLookupSet(table_i,row+rstart)) {nidx_i[isz++] = row+rstart;}
            break; /* for l = start; l<end ; l++) */
          }
        } 
      }
    } 
    
    if (i < is_max - 1){
      idx_i  += n;   /* ptr to input is[i+1] array */
      nidx_i += isz; /* ptr to output is[i+1] array */
    }
    nidx[1+i] = isz; /* size of new is[i] */
  } /* for each is */
  ierr = PetscBTDestroy(table0);CHKERRQ(ierr); 
  
  PetscFunctionReturn(0);
}
示例#4
0
/*@
   ISCompressIndicesGeneral - convert the indices into block indices
   Input Parameters:
+  n - maximum possible length of the index set
.  nkeys - expected number of keys when PETSC_USE_CTABLE
.  bs - the size of block
.  imax - the number of index sets
-  is_in - the non-blocked array of index sets

   Output Parameter:
.  is_out - the blocked new index set

   Level: intermediate

.seealso: ISExpandIndicesGeneral()
@*/
PetscErrorCode  ISCompressIndicesGeneral(PetscInt n,PetscInt nkeys,PetscInt bs,PetscInt imax,const IS is_in[],IS is_out[])
{
  PetscErrorCode ierr;
  PetscInt       isz,len,i,j,ival,Nbs;
  const PetscInt *idx;
#if defined(PETSC_USE_CTABLE)
  PetscTable         gid1_lid1;
  PetscInt           tt, gid1, *nidx,Nkbs;
  PetscTablePosition tpos;
#else
  PetscInt *nidx;
  PetscBT  table;
#endif

  PetscFunctionBegin;
  Nbs =n/bs;
#if defined(PETSC_USE_CTABLE)
  Nkbs = nkeys/bs;
  ierr = PetscTableCreate(Nkbs,Nbs,&gid1_lid1);CHKERRQ(ierr);
#else
  ierr = PetscMalloc1(Nbs,&nidx);CHKERRQ(ierr);
  ierr = PetscBTCreate(Nbs,&table);CHKERRQ(ierr);
#endif
  for (i=0; i<imax; i++) {
    isz = 0;
#if defined(PETSC_USE_CTABLE)
    ierr = PetscTableRemoveAll(gid1_lid1);CHKERRQ(ierr);
#else
    ierr = PetscBTMemzero(Nbs,table);CHKERRQ(ierr);
#endif
    ierr = ISGetIndices(is_in[i],&idx);CHKERRQ(ierr);
    ierr = ISGetLocalSize(is_in[i],&len);CHKERRQ(ierr);
    for (j=0; j<len; j++) {
      ival = idx[j]/bs; /* convert the indices into block indices */
#if defined(PETSC_USE_CTABLE)
      ierr = PetscTableFind(gid1_lid1,ival+1,&tt);CHKERRQ(ierr);
      if (!tt) {
        ierr = PetscTableAdd(gid1_lid1,ival+1,isz+1,INSERT_VALUES);CHKERRQ(ierr);
        isz++;
      }
#else
      if (ival>Nbs) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"index greater than mat-dim");
      if (!PetscBTLookupSet(table,ival)) nidx[isz++] = ival;
#endif
    }
    ierr = ISRestoreIndices(is_in[i],&idx);CHKERRQ(ierr);

#if defined(PETSC_USE_CTABLE)
    ierr = PetscMalloc1(isz,&nidx);CHKERRQ(ierr);
    ierr = PetscTableGetHeadPosition(gid1_lid1,&tpos);CHKERRQ(ierr);
    j    = 0;
    while (tpos) {
      ierr = PetscTableGetNext(gid1_lid1,&tpos,&gid1,&tt);CHKERRQ(ierr);
      if (tt-- > isz) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"index greater than array-dim");
      nidx[tt] = gid1 - 1;
      j++;
    }
    if (j != isz) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"table error: jj != isz");
    ierr = ISCreateGeneral(PETSC_COMM_SELF,isz,nidx,PETSC_OWN_POINTER,(is_out+i));CHKERRQ(ierr);
#else
    ierr = ISCreateGeneral(PETSC_COMM_SELF,isz,nidx,PETSC_COPY_VALUES,(is_out+i));CHKERRQ(ierr);
#endif
  }
#if defined(PETSC_USE_CTABLE)
  ierr = PetscTableDestroy(&gid1_lid1);CHKERRQ(ierr);
#else
  ierr = PetscBTDestroy(&table);CHKERRQ(ierr);
  ierr = PetscFree(nidx);CHKERRQ(ierr);
#endif
  PetscFunctionReturn(0);
}
示例#5
0
文件: sbaijov.c 项目: petsc/petsc
PetscErrorCode MatIncreaseOverlap_MPISBAIJ(Mat C,PetscInt is_max,IS is[],PetscInt ov)
{
    PetscErrorCode ierr;
    PetscInt       i,N=C->cmap->N, bs=C->rmap->bs,M=C->rmap->N,Mbs=M/bs,*nidx,isz,iov;
    IS             *is_new,*is_row;
    Mat            *submats;
    Mat_MPISBAIJ   *c=(Mat_MPISBAIJ*)C->data;
    Mat_SeqSBAIJ   *asub_i;
    PetscBT        table;
    PetscInt       *ai,brow,nz,nis,l,nmax,nstages_local,nstages,max_no,pos;
    const PetscInt *idx;
    PetscBool      flg,*allcolumns,*allrows;

    PetscFunctionBegin;
    ierr = PetscMalloc1(is_max,&is_new);
    CHKERRQ(ierr);
    /* Convert the indices into block format */
    ierr = ISCompressIndicesGeneral(N,C->rmap->n,bs,is_max,is,is_new);
    CHKERRQ(ierr);
    if (ov < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Negative overlap specified\n");

    /* ----- previous non-scalable implementation ----- */
    flg  = PETSC_FALSE;
    ierr = PetscOptionsHasName(NULL,NULL, "-IncreaseOverlap_old", &flg);
    CHKERRQ(ierr);
    if (flg) { /* previous non-scalable implementation */
        printf("use previous non-scalable implementation...\n");
        for (i=0; i<ov; ++i) {
            ierr = MatIncreaseOverlap_MPISBAIJ_Once(C,is_max,is_new);
            CHKERRQ(ierr);
        }
    } else { /* implementation using modified BAIJ routines */

        ierr = PetscMalloc1(Mbs+1,&nidx);
        CHKERRQ(ierr);
        ierr = PetscBTCreate(Mbs,&table);
        CHKERRQ(ierr); /* for column search */
        ierr = PetscMalloc2(is_max+1,&allcolumns,is_max+1,&allrows);
        CHKERRQ(ierr);

        /* Create is_row */
        ierr = PetscMalloc1(is_max,&is_row);
        CHKERRQ(ierr);
        ierr = ISCreateStride(PETSC_COMM_SELF,Mbs,0,1,&is_row[0]);
        CHKERRQ(ierr);

        allrows[0] = PETSC_TRUE;
        for (i=1; i<is_max; i++) {
            is_row[i]  = is_row[0]; /* reuse is_row[0] */
            allrows[i] = PETSC_TRUE;
        }

        /* Allocate memory to hold all the submatrices - Modified from MatGetSubMatrices_MPIBAIJ() */
        ierr = PetscMalloc1(is_max+1,&submats);
        CHKERRQ(ierr);

        /* Check for special case: each processor gets entire matrix columns */
        for (i=0; i<is_max; i++) {
            ierr = ISIdentity(is_new[i],&flg);
            CHKERRQ(ierr);
            ierr = ISGetLocalSize(is_new[i],&isz);
            CHKERRQ(ierr);
            if (flg && isz == Mbs) {
                allcolumns[i] = PETSC_TRUE;
            } else {
                allcolumns[i] = PETSC_FALSE;
            }
        }

        /* Determine the number of stages through which submatrices are done */
        nmax = 20*1000000 / (c->Nbs * sizeof(PetscInt));
        if (!nmax) nmax = 1;
        nstages_local = is_max/nmax + ((is_max % nmax) ? 1 : 0);

        /* Make sure every processor loops through the nstages */
        ierr = MPIU_Allreduce(&nstages_local,&nstages,1,MPIU_INT,MPI_MAX,PetscObjectComm((PetscObject)C));
        CHKERRQ(ierr);

        for (iov=0; iov<ov; ++iov) {
            /* 1) Get submats for column search */
            for (i=0,pos=0; i<nstages; i++) {
                if (pos+nmax <= is_max) max_no = nmax;
                else if (pos == is_max) max_no = 0;
                else                    max_no = is_max-pos;
                c->ijonly = PETSC_TRUE;
                ierr      = MatGetSubMatrices_MPIBAIJ_local(C,max_no,is_row+pos,is_new+pos,MAT_INITIAL_MATRIX,allrows+pos,allcolumns+pos,submats+pos);
                CHKERRQ(ierr);
                pos      += max_no;
            }

            /* 2) Row search */
            ierr = MatIncreaseOverlap_MPIBAIJ_Once(C,is_max,is_new);
            CHKERRQ(ierr);

            /* 3) Column search */
            for (i=0; i<is_max; i++) {
                asub_i = (Mat_SeqSBAIJ*)submats[i]->data;
                ai     = asub_i->i;;

                /* put is_new obtained from MatIncreaseOverlap_MPIBAIJ() to table */
                ierr = PetscBTMemzero(Mbs,table);
                CHKERRQ(ierr);

                ierr = ISGetIndices(is_new[i],&idx);
                CHKERRQ(ierr);
                ierr = ISGetLocalSize(is_new[i],&nis);
                CHKERRQ(ierr);
                for (l=0; l<nis; l++) {
                    ierr    = PetscBTSet(table,idx[l]);
                    CHKERRQ(ierr);
                    nidx[l] = idx[l];
                }
                isz = nis;

                /* add column entries to table */
                for (brow=0; brow<Mbs; brow++) {
                    nz = ai[brow+1] - ai[brow];
                    if (nz) {
                        if (!PetscBTLookupSet(table,brow)) nidx[isz++] = brow;
                    }
                }
                ierr = ISRestoreIndices(is_new[i],&idx);
                CHKERRQ(ierr);
                ierr = ISDestroy(&is_new[i]);
                CHKERRQ(ierr);

                /* create updated is_new */
                ierr = ISCreateGeneral(PETSC_COMM_SELF,isz,nidx,PETSC_COPY_VALUES,is_new+i);
                CHKERRQ(ierr);
            }

            /* Free tmp spaces */
            for (i=0; i<is_max; i++) {
                ierr = MatDestroy(&submats[i]);
                CHKERRQ(ierr);
            }
        }
        ierr = PetscFree2(allcolumns,allrows);
        CHKERRQ(ierr);
        ierr = PetscBTDestroy(&table);
        CHKERRQ(ierr);
        ierr = PetscFree(submats);
        CHKERRQ(ierr);
        ierr = ISDestroy(&is_row[0]);
        CHKERRQ(ierr);
        ierr = PetscFree(is_row);
        CHKERRQ(ierr);
        ierr = PetscFree(nidx);
        CHKERRQ(ierr);

    }

    for (i=0; i<is_max; i++) {
        ierr = ISDestroy(&is[i]);
        CHKERRQ(ierr);
    }
    ierr = ISExpandIndicesGeneral(N,N,bs,is_max,is_new,is);
    CHKERRQ(ierr);

    for (i=0; i<is_max; i++) {
        ierr = ISDestroy(&is_new[i]);
        CHKERRQ(ierr);
    }
    ierr = PetscFree(is_new);
    CHKERRQ(ierr);
    PetscFunctionReturn(0);
}