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Adding initial code to map bubble ids between timesteps

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This commit is contained in:
Mark Berrill
2015-07-16 22:08:43 -04:00
parent 5d86abf774
commit f4a2f22f57
4 changed files with 388 additions and 25 deletions
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154
analysis/analysis.cpp
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@@ -736,4 +736,158 @@ int ComputeGlobalPhaseComponent( int nx, int ny, int nz, RankInfoStruct rank_inf
}
/******************************************************************
* Compute the mapping of blob ids between timesteps *
******************************************************************/
void gatherSet( std::set<int>& set )
{
int nprocs;
MPI_Comm_size(MPI_COMM_WORLD,&nprocs);
std::vector<int> send_data(set.begin(),set.end());
int send_count = send_data.size();
std::vector<int> recv_count(nprocs,0), recv_disp(nprocs,0);
MPI_Allgather(&send_count,1,MPI_INT,getPtr(recv_count),1,MPI_INT,MPI_COMM_WORLD);
for (int i=1; i<nprocs; i++)
recv_disp[i] = recv_disp[i-1] + recv_count[i-1];
std::vector<int> recv_data(recv_disp[nprocs-1]+recv_count[nprocs-1]);
MPI_Allgatherv(getPtr(send_data),send_count,MPI_INT,
getPtr(recv_data),getPtr(recv_count),getPtr(recv_disp),MPI_INT,
MPI_COMM_WORLD);
for (size_t i=0; i<recv_data.size(); i++)
set.insert(recv_data[i]);
}
void gatherSrcIDMap( std::map<int,std::set<int> >& src_map )
{
int nprocs;
MPI_Comm_size(MPI_COMM_WORLD,&nprocs);
std::vector<int> send_data;
for (std::map<int,std::set<int> >::const_iterator it=src_map.begin(); it!=src_map.end(); ++it) {
int id = it->first;
const std::set<int>& src_ids = it->second;
send_data.push_back(id);
send_data.push_back(src_ids.size());
for (std::set<int>::const_iterator it2=src_ids.begin(); it2!=src_ids.end(); ++it2)
send_data.push_back(*it2);
}
int send_count = send_data.size();
std::vector<int> recv_count(nprocs,0), recv_disp(nprocs,0);
MPI_Allgather(&send_count,1,MPI_INT,getPtr(recv_count),1,MPI_INT,MPI_COMM_WORLD);
for (int i=1; i<nprocs; i++)
recv_disp[i] = recv_disp[i-1] + recv_count[i-1];
std::vector<int> recv_data(recv_disp[nprocs-1]+recv_count[nprocs-1]);
MPI_Allgatherv(getPtr(send_data),send_count,MPI_INT,
getPtr(recv_data),getPtr(recv_count),getPtr(recv_disp),MPI_INT,
MPI_COMM_WORLD);
size_t i=0;
while ( i < recv_data.size() ) {
int id = recv_data[i];
int count = recv_data[i+1];
i += 2;
std::set<int>& src_ids = src_map[id];
for (int j=0; j<count; j++,i++)
src_ids.insert(recv_data[i]);
}
}
void addSrcDstIDs( int src_id, std::map<int,std::set<int> >& src_map,
std::map<int,std::set<int> >& dst_map, std::set<int>& src, std::set<int>& dst )
{
src.insert(src_id);
const std::set<int>& dst_ids = dst_map[src_id];
for (std::set<int>::const_iterator it=dst_ids.begin(); it!=dst_ids.end(); ++it) {
if ( dst.find(*it)==dst.end() )
addSrcDstIDs(*it,dst_map,src_map,dst,src);
}
}
ID_map_struct computeIDMap( const IntArray& ID1, const IntArray& ID2 )
{
ASSERT(ID1.size(0)==ID2.size(0)&&ID1.size(1)==ID2.size(1)&&ID1.size(2)==ID2.size(2));
PROFILE_START("computeIDMap");
// Get a global list of all src/dst ids and the src map for each local blob
std::set<int> src_set, dst_set;
std::map<int,std::set<int> > src_map; // Map of the src ids for each dst id
for (size_t i=0; i<ID1.length(); i++) {
if ( ID1(i)>=0 )
src_set.insert(ID1(i));
if ( ID2(i)>=0 )
dst_set.insert(ID2(i));
if ( ID2(i)>=0 && ID1(i)>=0 ) {
std::set<int>& src_ids = src_map[ID2(i)];
src_ids.insert(ID1(i));
}
}
// Communicate the src/dst ids and src id map to all processors and reduce
gatherSet( src_set );
gatherSet( dst_set );
gatherSrcIDMap( src_map );
// Compute the dst id map
std::map<int,std::set<int> > dst_map; // Map of the dst ids for each src id
for (std::map<int,std::set<int> >::const_iterator it=src_map.begin(); it!=src_map.end(); ++it) {
int id = it->first;
const std::set<int>& src_ids = it->second;
for (std::set<int>::const_iterator it2=src_ids.begin(); it2!=src_ids.end(); ++it2) {
std::set<int>& dst_ids = dst_map[*it2];
dst_ids.insert(id);
}
}
// Perform the mapping of ids
ID_map_struct id_map;
// Find new blobs
for (std::set<int>::const_iterator it=dst_set.begin(); it!=dst_set.end(); ++it) {
if ( src_map.find(*it)==src_map.end() )
id_map.created.push_back(*it);
}
// Fine blobs that disappeared
for (std::set<int>::const_iterator it=src_set.begin(); it!=src_set.end(); ++it) {
if ( dst_map.find(*it)==dst_map.end() )
id_map.destroyed.push_back(*it);
}
// Find blobs with a 1-to-1 mapping
std::vector<int> dst_list;
dst_list.reserve(src_map.size());
for (std::map<int,std::set<int> >::const_iterator it=src_map.begin(); it!=src_map.end(); ++it)
dst_list.push_back(it->first);
for (size_t i=0; i<dst_list.size(); i++) {
int dst_id = dst_list[i];
const std::set<int>& src_ids = src_map[dst_id];
if ( src_ids.size()==1 ) {
int src_id = *src_ids.begin();
const std::set<int>& dst_ids = dst_map[src_id];
if ( dst_ids.size()==1 ) {
ASSERT(*dst_ids.begin()==dst_id);
src_map.erase(dst_id);
dst_map.erase(src_id);
id_map.src_dst.push_back(std::pair<int,int>(src_id,dst_id));
}
}
}
// Handle merge/splits
while ( !dst_map.empty() ) {
// Get a lit of the src-dst ids
std::set<int> src, dst;
addSrcDstIDs( dst_map.begin()->first, src_map, dst_map, src, dst );
for (std::set<int>::const_iterator it=src.begin(); it!=src.end(); ++it)
dst_map.erase(*it);
for (std::set<int>::const_iterator it=dst.begin(); it!=dst.end(); ++it)
src_map.erase(*it);
if ( src.size()==1 ) {
// Bubble split
id_map.split.push_back( BlobIDSplitStruct(*src.begin(),std::vector<int>(dst.begin(),dst.end())) );
} else if ( dst.size()==1 ) {
// Bubble merge
id_map.merge.push_back( BlobIDMergeStruct(std::vector<int>(src.begin(),src.end()),*dst.begin()) );
} else {
// Bubble split/merge
id_map.merge_split.push_back( BlobIDMergeSplitStruct(
std::vector<int>(src.begin(),src.end()), std::vector<int>(dst.begin(),dst.end() ) ) );
}
}
ASSERT(src_map.empty());
PROFILE_STOP("computeIDMap");
return id_map;
}