/*@
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);
}
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);
}
/* 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);
}
/*@
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);
}
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);
}