void PETSC_STDCALL petscsortmpiintwitharray_(PetscMPIInt *n,PetscMPIInt i[],PetscMPIInt Ii[], int *__ierr ){
*__ierr = PetscSortMPIIntWithArray(*n,i,Ii);
}
static PetscErrorCode PCSetUp_Redistribute(PC pc)
{
PC_Redistribute *red = (PC_Redistribute*)pc->data;
PetscErrorCode ierr;
MPI_Comm comm;
PetscInt rstart,rend,i,nz,cnt,*rows,ncnt,dcnt,*drows;
PetscLayout map,nmap;
PetscMPIInt size,imdex,tag,n;
PetscInt *source = PETSC_NULL;
PetscMPIInt *nprocs = PETSC_NULL,nrecvs;
PetscInt j,nsends;
PetscInt *owner = PETSC_NULL,*starts = PETSC_NULL,count,slen;
PetscInt *rvalues,*svalues,recvtotal;
PetscMPIInt *onodes1,*olengths1;
MPI_Request *send_waits = PETSC_NULL,*recv_waits = PETSC_NULL;
MPI_Status recv_status,*send_status;
Vec tvec,diag;
Mat tmat;
const PetscScalar *d;
PetscFunctionBegin;
if (pc->setupcalled) {
ierr = KSPGetOperators(red->ksp,PETSC_NULL,&tmat,PETSC_NULL);CHKERRQ(ierr);
ierr = MatGetSubMatrix(pc->pmat,red->is,red->is,MAT_REUSE_MATRIX,&tmat);CHKERRQ(ierr);
ierr = KSPSetOperators(red->ksp,tmat,tmat,SAME_NONZERO_PATTERN);CHKERRQ(ierr);
} else {
PetscInt NN;
ierr = PetscObjectGetComm((PetscObject)pc,&comm);CHKERRQ(ierr);
ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr);
ierr = PetscObjectGetNewTag((PetscObject)pc,&tag);CHKERRQ(ierr);
/* count non-diagonal rows on process */
ierr = MatGetOwnershipRange(pc->mat,&rstart,&rend);CHKERRQ(ierr);
cnt = 0;
for (i=rstart; i<rend; i++) {
ierr = MatGetRow(pc->mat,i,&nz,PETSC_NULL,PETSC_NULL);CHKERRQ(ierr);
if (nz > 1) cnt++;
ierr = MatRestoreRow(pc->mat,i,&nz,PETSC_NULL,PETSC_NULL);CHKERRQ(ierr);
}
ierr = PetscMalloc(cnt*sizeof(PetscInt),&rows);CHKERRQ(ierr);
ierr = PetscMalloc((rend - rstart - cnt)*sizeof(PetscInt),&drows);CHKERRQ(ierr);
/* list non-diagonal rows on process */
cnt = 0; dcnt = 0;
for (i=rstart; i<rend; i++) {
ierr = MatGetRow(pc->mat,i,&nz,PETSC_NULL,PETSC_NULL);CHKERRQ(ierr);
if (nz > 1) rows[cnt++] = i;
else drows[dcnt++] = i - rstart;
ierr = MatRestoreRow(pc->mat,i,&nz,PETSC_NULL,PETSC_NULL);CHKERRQ(ierr);
}
/* create PetscLayout for non-diagonal rows on each process */
ierr = PetscLayoutCreate(comm,&map);CHKERRQ(ierr);
ierr = PetscLayoutSetLocalSize(map,cnt);CHKERRQ(ierr);
ierr = PetscLayoutSetBlockSize(map,1);CHKERRQ(ierr);
ierr = PetscLayoutSetUp(map);CHKERRQ(ierr);
rstart = map->rstart;
rend = map->rend;
/* create PetscLayout for load-balanced non-diagonal rows on each process */
ierr = PetscLayoutCreate(comm,&nmap);CHKERRQ(ierr);
ierr = MPI_Allreduce(&cnt,&ncnt,1,MPIU_INT,MPI_SUM,comm);CHKERRQ(ierr);
ierr = PetscLayoutSetSize(nmap,ncnt);CHKERRQ(ierr);
ierr = PetscLayoutSetBlockSize(nmap,1);CHKERRQ(ierr);
ierr = PetscLayoutSetUp(nmap);CHKERRQ(ierr);
ierr = MatGetSize(pc->pmat,&NN,PETSC_NULL);CHKERRQ(ierr);
ierr = PetscInfo2(pc,"Number of diagonal rows eliminated %d, percentage eliminated %g\n",NN-ncnt,((PetscReal)(NN-ncnt))/((PetscReal)(NN)));CHKERRQ(ierr);
/*
this code is taken from VecScatterCreate_PtoS()
Determines what rows need to be moved where to
load balance the non-diagonal rows
*/
/* count number of contributors to each processor */
ierr = PetscMalloc2(size,PetscMPIInt,&nprocs,cnt,PetscInt,&owner);CHKERRQ(ierr);
ierr = PetscMemzero(nprocs,size*sizeof(PetscMPIInt));CHKERRQ(ierr);
j = 0;
nsends = 0;
for (i=rstart; i<rend; i++) {
if (i < nmap->range[j]) j = 0;
for (; j<size; j++) {
if (i < nmap->range[j+1]) {
if (!nprocs[j]++) nsends++;
owner[i-rstart] = j;
break;
}
}
}
/* inform other processors of number of messages and max length*/
ierr = PetscGatherNumberOfMessages(comm,PETSC_NULL,nprocs,&nrecvs);CHKERRQ(ierr);
ierr = PetscGatherMessageLengths(comm,nsends,nrecvs,nprocs,&onodes1,&olengths1);CHKERRQ(ierr);
ierr = PetscSortMPIIntWithArray(nrecvs,onodes1,olengths1);CHKERRQ(ierr);
recvtotal = 0; for (i=0; i<nrecvs; i++) recvtotal += olengths1[i];
/* post receives: rvalues - rows I will own; count - nu */
ierr = PetscMalloc3(recvtotal,PetscInt,&rvalues,nrecvs,PetscInt,&source,nrecvs,MPI_Request,&recv_waits);CHKERRQ(ierr);
count = 0;
for (i=0; i<nrecvs; i++) {
ierr = MPI_Irecv((rvalues+count),olengths1[i],MPIU_INT,onodes1[i],tag,comm,recv_waits+i);CHKERRQ(ierr);
count += olengths1[i];
}
/* do sends:
1) starts[i] gives the starting index in svalues for stuff going to
the ith processor
*/
ierr = PetscMalloc3(cnt,PetscInt,&svalues,nsends,MPI_Request,&send_waits,size,PetscInt,&starts);CHKERRQ(ierr);
starts[0] = 0;
for (i=1; i<size; i++) { starts[i] = starts[i-1] + nprocs[i-1];}
for (i=0; i<cnt; i++) {
svalues[starts[owner[i]]++] = rows[i];
}
for (i=0; i<cnt; i++) rows[i] = rows[i] - rstart;
red->drows = drows;
red->dcnt = dcnt;
ierr = PetscFree(rows);CHKERRQ(ierr);
starts[0] = 0;
for (i=1; i<size; i++) { starts[i] = starts[i-1] + nprocs[i-1];}
count = 0;
for (i=0; i<size; i++) {
if (nprocs[i]) {
ierr = MPI_Isend(svalues+starts[i],nprocs[i],MPIU_INT,i,tag,comm,send_waits+count++);CHKERRQ(ierr);
}
}
/* wait on receives */
count = nrecvs;
slen = 0;
while (count) {
ierr = MPI_Waitany(nrecvs,recv_waits,&imdex,&recv_status);CHKERRQ(ierr);
/* unpack receives into our local space */
ierr = MPI_Get_count(&recv_status,MPIU_INT,&n);CHKERRQ(ierr);
slen += n;
count--;
}
if (slen != recvtotal) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Total message lengths %D not expected %D",slen,recvtotal);
ierr = ISCreateGeneral(comm,slen,rvalues,PETSC_COPY_VALUES,&red->is);CHKERRQ(ierr);
/* free up all work space */
ierr = PetscFree(olengths1);CHKERRQ(ierr);
ierr = PetscFree(onodes1);CHKERRQ(ierr);
ierr = PetscFree3(rvalues,source,recv_waits);CHKERRQ(ierr);
ierr = PetscFree2(nprocs,owner);CHKERRQ(ierr);
if (nsends) { /* wait on sends */
ierr = PetscMalloc(nsends*sizeof(MPI_Status),&send_status);CHKERRQ(ierr);
ierr = MPI_Waitall(nsends,send_waits,send_status);CHKERRQ(ierr);
ierr = PetscFree(send_status);CHKERRQ(ierr);
}
ierr = PetscFree3(svalues,send_waits,starts);CHKERRQ(ierr);
ierr = PetscLayoutDestroy(&map);CHKERRQ(ierr);
ierr = PetscLayoutDestroy(&nmap);CHKERRQ(ierr);
ierr = VecCreateMPI(comm,slen,PETSC_DETERMINE,&red->b);CHKERRQ(ierr);
ierr = VecDuplicate(red->b,&red->x);CHKERRQ(ierr);
ierr = MatGetVecs(pc->pmat,&tvec,PETSC_NULL);CHKERRQ(ierr);
ierr = VecScatterCreate(tvec,red->is,red->b,PETSC_NULL,&red->scatter);CHKERRQ(ierr);
ierr = VecDestroy(&tvec);CHKERRQ(ierr);
ierr = MatGetSubMatrix(pc->pmat,red->is,red->is,MAT_INITIAL_MATRIX,&tmat);CHKERRQ(ierr);
ierr = KSPSetOperators(red->ksp,tmat,tmat,SAME_NONZERO_PATTERN);CHKERRQ(ierr);
ierr = MatDestroy(&tmat);CHKERRQ(ierr);
}
/* get diagonal portion of matrix */
ierr = PetscMalloc(red->dcnt*sizeof(PetscScalar),&red->diag);CHKERRQ(ierr);
ierr = MatGetVecs(pc->pmat,&diag,PETSC_NULL);CHKERRQ(ierr);
ierr = MatGetDiagonal(pc->pmat,diag);CHKERRQ(ierr);
ierr = VecGetArrayRead(diag,&d);CHKERRQ(ierr);
for (i=0; i<red->dcnt; i++) {
red->diag[i] = 1.0/d[red->drows[i]];
}
ierr = VecRestoreArrayRead(diag,&d);CHKERRQ(ierr);
ierr = VecDestroy(&diag);CHKERRQ(ierr);
ierr = KSPSetUp(red->ksp);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/*@
ISBuildTwoSided - Takes an IS that describes where we will go. Generates an IS that contains new numbers from remote or local
on the IS.
Collective on IS
Input Parameters
. to - an IS describes where we will go. Negative target rank will be ignored
. toindx - an IS describes what indices should send. NULL means sending natural numbering
Output Parameter:
. rows - contains new numbers from remote or local
Level: advanced
.seealso: MatPartitioningCreate(), ISPartitioningToNumbering(), ISPartitioningCount()
@*/
PetscErrorCode ISBuildTwoSided(IS ito,IS toindx, IS *rows)
{
const PetscInt *ito_indices,*toindx_indices;
PetscInt *send_indices,rstart,*recv_indices,nrecvs,nsends;
PetscInt *tosizes,*fromsizes,i,j,*tosizes_tmp,*tooffsets_tmp,ito_ln;
PetscMPIInt *toranks,*fromranks,size,target_rank,*fromperm_newtoold,nto,nfrom;
PetscLayout isrmap;
MPI_Comm comm;
PetscSF sf;
PetscSFNode *iremote;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = PetscObjectGetComm((PetscObject)ito,&comm);CHKERRQ(ierr);
ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr);
ierr = ISGetLocalSize(ito,&ito_ln);CHKERRQ(ierr);
/* why we do not have ISGetLayout? */
isrmap = ito->map;
ierr = PetscLayoutGetRange(isrmap,&rstart,NULL);CHKERRQ(ierr);
ierr = ISGetIndices(ito,&ito_indices);CHKERRQ(ierr);
ierr = PetscCalloc2(size,&tosizes_tmp,size+1,&tooffsets_tmp);CHKERRQ(ierr);
for(i=0; i<ito_ln; i++){
if(ito_indices[i]<0) continue;
#if defined(PETSC_USE_DEBUG)
if(ito_indices[i]>=size) SETERRQ2(comm,PETSC_ERR_ARG_OUTOFRANGE,"target rank %d is larger than communicator size %d ",ito_indices[i],size);
#endif
tosizes_tmp[ito_indices[i]]++;
}
nto = 0;
for(i=0; i<size; i++){
tooffsets_tmp[i+1] = tooffsets_tmp[i]+tosizes_tmp[i];
if(tosizes_tmp[i]>0) nto++;
}
ierr = PetscCalloc2(nto,&toranks,2*nto,&tosizes);CHKERRQ(ierr);
nto = 0;
for(i=0; i<size; i++){
if(tosizes_tmp[i]>0){
toranks[nto] = i;
tosizes[2*nto] = tosizes_tmp[i];/* size */
tosizes[2*nto+1] = tooffsets_tmp[i];/* offset */
nto++;
}
}
nsends = tooffsets_tmp[size];
ierr = PetscCalloc1(nsends,&send_indices);CHKERRQ(ierr);
if(toindx){
ierr = ISGetIndices(toindx,&toindx_indices);CHKERRQ(ierr);
}
for(i=0; i<ito_ln; i++){
if(ito_indices[i]<0) continue;
target_rank = ito_indices[i];
send_indices[tooffsets_tmp[target_rank]] = toindx? toindx_indices[i]:(i+rstart);
tooffsets_tmp[target_rank]++;
}
if(toindx){
ierr = ISRestoreIndices(toindx,&toindx_indices);CHKERRQ(ierr);
}
ierr = ISRestoreIndices(ito,&ito_indices);CHKERRQ(ierr);
ierr = PetscFree2(tosizes_tmp,tooffsets_tmp);CHKERRQ(ierr);
ierr = PetscCommBuildTwoSided(comm,2,MPIU_INT,nto,toranks,tosizes,&nfrom,&fromranks,&fromsizes);CHKERRQ(ierr);
ierr = PetscFree2(toranks,tosizes);CHKERRQ(ierr);
ierr = PetscCalloc1(nfrom,&fromperm_newtoold);CHKERRQ(ierr);
for(i=0; i<nfrom; i++){
fromperm_newtoold[i] = i;
}
ierr = PetscSortMPIIntWithArray(nfrom,fromranks,fromperm_newtoold);CHKERRQ(ierr);
nrecvs = 0;
for(i=0; i<nfrom; i++){
nrecvs += fromsizes[i*2];
}
ierr = PetscCalloc1(nrecvs,&recv_indices);CHKERRQ(ierr);
ierr = PetscCalloc1(nrecvs,&iremote);CHKERRQ(ierr);
nrecvs = 0;
for(i=0; i<nfrom; i++){
for(j=0; j<fromsizes[2*fromperm_newtoold[i]]; j++){
iremote[nrecvs].rank = fromranks[i];
iremote[nrecvs++].index = fromsizes[2*fromperm_newtoold[i]+1]+j;
}
}
ierr = PetscSFCreate(comm,&sf);CHKERRQ(ierr);
ierr = PetscSFSetGraph(sf,nsends,nrecvs,NULL,PETSC_OWN_POINTER,iremote,PETSC_OWN_POINTER);CHKERRQ(ierr);
ierr = PetscSFSetType(sf,PETSCSFBASIC);CHKERRQ(ierr);
/* how to put a prefix ? */
ierr = PetscSFSetFromOptions(sf);CHKERRQ(ierr);
ierr = PetscSFBcastBegin(sf,MPIU_INT,send_indices,recv_indices);CHKERRQ(ierr);
ierr = PetscSFBcastEnd(sf,MPIU_INT,send_indices,recv_indices);CHKERRQ(ierr);
ierr = PetscSFDestroy(&sf);CHKERRQ(ierr);
ierr = PetscFree(fromranks);CHKERRQ(ierr);
ierr = PetscFree(fromsizes);CHKERRQ(ierr);
ierr = PetscFree(fromperm_newtoold);CHKERRQ(ierr);
ierr = PetscFree(send_indices);CHKERRQ(ierr);
if(rows){
ierr = PetscSortInt(nrecvs,recv_indices);CHKERRQ(ierr);
ierr = ISCreateGeneral(comm, nrecvs,recv_indices,PETSC_OWN_POINTER,rows);CHKERRQ(ierr);
}else{
ierr = PetscFree(recv_indices);CHKERRQ(ierr);
}
PetscFunctionReturn(0);
}
