 |
Mesh Oriented datABase
(version 5.4.1)
Array-based unstructured mesh datastructure
|
|
Mesh Oriented datABase
(version 5.4.1)
Array-based unstructured mesh datastructure
|
#include <ParCommGraph.hpp>
Collaboration diagram for moab::ParCommGraph:Public Types | |
| enum | TypeGraph { INITIAL_MIGRATE, COVERAGE, DOF_BASED } |
Public Member Functions | |
| virtual | ~ParCommGraph () |
| ParCommGraph (MPI_Comm joincomm, MPI_Group group1, MPI_Group group2, int coid1, int coid2) | |
| collective constructor, will be called on all sender tasks and receiver tasks | |
| ParCommGraph (const ParCommGraph &) | |
| copy constructor will copy only the senders, receivers, compid1, etc | |
| ErrorCode | compute_trivial_partition (std::vector< int > &numElemsPerTaskInGroup1) |
| Based on the number of elements on each task in group 1, partition for group 2, trivially. | |
| ErrorCode | pack_receivers_graph (std::vector< int > &packed_recv_array) |
| pack information about receivers view of the graph, for future sending to receiver root | |
| bool | is_root_sender () |
| bool | is_root_receiver () |
| int | sender (int index) |
| int | receiver (int index) |
| int | get_component_id1 () |
| int | get_component_id2 () |
| int | get_context_id () |
| void | set_context_id (int other_id) |
| EntityHandle | get_cover_set () |
| void | set_cover_set (EntityHandle cover) |
| ErrorCode | split_owned_range (int sender_rank, Range &owned) |
| ErrorCode | split_owned_range (Range &owned) |
| ErrorCode | send_graph (MPI_Comm jcomm, std::vector< char > &zBuff) |
| ErrorCode | send_graph_partition (ParallelComm *pco, MPI_Comm jcomm, std::vector< char > &zoltanBuffer) |
| ErrorCode | send_mesh_parts (MPI_Comm jcomm, ParallelComm *pco, Range &owned) |
| ErrorCode | receive_comm_graph (MPI_Comm jcomm, ParallelComm *pco, std::vector< int > &pack_array, std::vector< char > &zoltanBuffer) |
| ErrorCode | receive_mesh (MPI_Comm jcomm, ParallelComm *pco, EntityHandle local_set, std::vector< int > &senders_local) |
| ErrorCode | release_send_buffers () |
| ErrorCode | send_tag_values (MPI_Comm jcomm, ParallelComm *pco, Range &owned, std::vector< Tag > &tag_handles) |
| ErrorCode | receive_tag_values (MPI_Comm jcomm, ParallelComm *pco, Range &owned, std::vector< Tag > &tag_handles) |
| const std::vector< int > & | senders () |
| const std::vector< int > & | receivers () |
| ErrorCode | settle_send_graph (TupleList &TLcovIDs) |
| void | SetReceivingAfterCoverage (std::map< int, std::set< int > > &idsFromProcs) |
| void | settle_comm_by_ids (int comp, TupleList &TLBackToComp, std::vector< int > &valuesComp) |
| ErrorCode | set_split_ranges (int comp, TupleList &TLBackToComp1, std::vector< int > &valuesComp1, int lenTag, Range &ents_of_interest, int type) |
| ErrorCode | form_tuples_to_migrate_mesh (Interface *mb, TupleList &TLv, TupleList &TLc, int type, int lenTagType1) |
| ErrorCode | form_mesh_from_tuples (Interface *mb, TupleList &TLv, TupleList &TLc, int type, int lenTagType1, EntityHandle fset, Range &primary_ents, std::vector< int > &values_entities) |
| ErrorCode | compute_partition (ParallelComm *pco, Range &owned, int met, std::vector< char > &zoltanBuffer) |
| ErrorCode | dump_comm_information (const std::string &prefix, int is_send, int verbose) |
Private Member Functions | |
| void | find_group_ranks (MPI_Group group, MPI_Comm join, std::vector< int > &ranks) |
| find ranks of a group with respect to an encompassing communicator | |
Private Attributes | |
| MPI_Comm | comm |
| std::vector< int > | senderTasks |
| std::vector< int > | receiverTasks |
| bool | rootSender |
| bool | rootReceiver |
| int | rankInGroup1 |
| int | rankInGroup2 |
| int | rankInJoin |
| int | joinSize |
| int | compid1 |
| int | compid2 |
| int | context_id |
| EntityHandle | cover_set |
| std::map< int, std::vector< int > > | recv_graph |
| std::map< int, std::vector< int > > | recv_sizes |
| std::map< int, std::vector< int > > | sender_graph |
| std::map< int, std::vector< int > > | sender_sizes |
| std::vector < ParallelComm::Buffer * > | localSendBuffs |
| std::vector< int > | comm_graph |
| std::vector< char > | zBuff |
| std::map< int, Range > | split_ranges |
| std::vector< MPI_Request > | sendReqs |
| std::vector< int > | corr_tasks |
| std::vector< int > | corr_sizes |
| TypeGraph | graph_type |
| std::map< int, std::vector< int > > | involved_IDs_map |
| std::map< int, std::vector< int > > | map_index |
| std::map< int, std::vector< int > > | map_ptr |
Definition at line 55 of file ParCommGraph.hpp.
Definition at line 58 of file ParCommGraph.hpp.
{
INITIAL_MIGRATE,
COVERAGE,
DOF_BASED
};
| moab::ParCommGraph::~ParCommGraph | ( | ) | [virtual] |
Definition at line 71 of file ParCommGraph.cpp.
{
// TODO Auto-generated destructor stub
}
| moab::ParCommGraph::ParCommGraph | ( | MPI_Comm | joincomm, |
| MPI_Group | group1, | ||
| MPI_Group | group2, | ||
| int | coid1, | ||
| int | coid2 | ||
| ) |
collective constructor, will be called on all sender tasks and receiver tasks
| [in] | joincomm | joint MPI communicator that covers both sender and receiver MPI groups |
| [in] | group1 | MPI group formed with sender tasks; (sender usually loads the mesh in a migrate scenario) |
| [in] | group2 | MPI group formed with receiver tasks; (receiver usually receives the mesh in a migrate scenario) |
| [in] | coid1 | sender component unique identifier in a coupled application (in climate simulations could be the Atmosphere Comp id = 5 or Ocean Comp ID , 17) |
| [in] | coid2 | receiver component unique identifier in a coupled application (it is usually the coupler, 2, in E3SM) |
this graph will be formed on sender and receiver tasks, and, in principle, will hold info about how the local entities are distributed on the other side
Its major role is to help in migration of data, from component to the coupler and vice-versa; Each local entity has a corresponding task (or tasks) on the other side, to where the data needs to be sent
important data stored in ParCommGraph, immediately it is created
Definition at line 20 of file ParCommGraph.cpp.
References comm, context_id, cover_set, find_group_ranks(), graph_type, INITIAL_MIGRATE, joinSize, rankInGroup1, rankInGroup2, rankInJoin, receiverTasks, rootReceiver, rootSender, and senderTasks.
: comm( joincomm ), compid1( coid1 ), compid2( coid2 )
{
// find out the tasks from each group, in the joint communicator
find_group_ranks( group1, comm, senderTasks );
find_group_ranks( group2, comm, receiverTasks );
rootSender = rootReceiver = false;
rankInGroup1 = rankInGroup2 = rankInJoin = -1; // not initialized, or not part of the group
int mpierr = MPI_Group_rank( group1, &rankInGroup1 );
if( MPI_SUCCESS != mpierr || rankInGroup1 == MPI_UNDEFINED ) rankInGroup1 = -1;
mpierr = MPI_Group_rank( group2, &rankInGroup2 );
if( MPI_SUCCESS != mpierr || rankInGroup2 == MPI_UNDEFINED ) rankInGroup2 = -1;
mpierr = MPI_Comm_rank( comm, &rankInJoin );
if( MPI_SUCCESS != mpierr ) // it should be a fatal error
rankInJoin = -1;
mpierr = MPI_Comm_size( comm, &joinSize );
if( MPI_SUCCESS != mpierr ) // it should be a fatal error
joinSize = -1;
if( 0 == rankInGroup1 ) rootSender = true;
if( 0 == rankInGroup2 ) rootReceiver = true;
graph_type = INITIAL_MIGRATE; // 0
context_id = -1;
cover_set = 0; // refers to nothing yet
}
| moab::ParCommGraph::ParCommGraph | ( | const ParCommGraph & | src | ) |
copy constructor will copy only the senders, receivers, compid1, etc
Definition at line 52 of file ParCommGraph.cpp.
References comm, compid1, compid2, context_id, cover_set, graph_type, joinSize, rankInGroup1, rankInGroup2, rankInJoin, receiverTasks, rootReceiver, rootSender, and senderTasks.
{
comm = src.comm;
senderTasks = src.senderTasks; // these are the sender tasks in joint comm
receiverTasks = src.receiverTasks; // these are all the receiver tasks in joint comm
rootSender = src.rootSender;
rootReceiver = src.rootReceiver;
rankInGroup1 = src.rankInGroup1;
rankInGroup2 = src.rankInGroup2; // group 1 is sender, 2 is receiver
rankInJoin = src.rankInJoin;
joinSize = src.joinSize;
compid1 = src.compid1;
compid2 = src.compid2;
graph_type = src.graph_type;
context_id = src.context_id;
cover_set = src.cover_set;
return;
}
| ErrorCode moab::ParCommGraph::compute_partition | ( | ParallelComm * | pco, |
| Range & | owned, | ||
| int | met, | ||
| std::vector< char > & | zoltanBuffer | ||
| ) |
Definition at line 1163 of file ParCommGraph.cpp.
References moab::Range::begin(), moab::ProcConfig::crystal_router(), moab::Core::dimension_from_handle(), moab::Range::empty(), moab::TupleList::enableWriteAccess(), moab::Range::end(), ErrorCode, moab::Core::get_adjacencies(), moab::ParallelComm::get_moab(), moab::TupleList::get_n(), moab::ParallelComm::get_shared_entities(), moab::ParallelComm::get_sharing_data(), moab::Core::globalId_tag(), moab::TupleList::inc_n(), moab::TupleList::initialize(), MAX_SHARING_PROCS, mb, MB_CHK_ERR, MB_SUCCESS, ZoltanPartitioner::partition_owned_cells(), moab::TupleList::print_to_file(), moab::ParallelComm::proc_config(), moab::ParallelComm::rank(), moab::Range::rbegin(), receiverTasks, rootSender, moab::Range::size(), split_ranges, moab::Range::subset_by_dimension(), moab::Core::tag_get_data(), moab::TupleList::vi_rd, moab::TupleList::vi_wr, moab::TupleList::vul_rd, and moab::TupleList::vul_wr.
{
// we are on a task on sender, and need to compute a new partition;
// primary cells need to be distributed to nb receivers tasks
// first, we will use graph partitioner, with zoltan;
// in the graph that we need to build, the first layer of ghosts is needed;
// can we avoid that ? For example, we can find out from each boundary edge/face what is the
// other cell (on the other side), then form the global graph, and call zoltan in parallel met 1
// would be a geometric partitioner, and met 2 would be a graph partitioner for method 1 we do
// not need any ghost exchange
// find first edges that are shared
if( owned.empty() )
return MB_SUCCESS; // nothing to do? empty partition is not allowed, maybe we should return
// error?
Core* mb = (Core*)pco->get_moab();
double t1, t2, t3;
t1 = MPI_Wtime();
int primaryDim = mb->dimension_from_handle( *owned.rbegin() );
int interfaceDim = primaryDim - 1; // should be 1 or 2
Range sharedEdges;
ErrorCode rval;
std::vector< int > shprocs( MAX_SHARING_PROCS );
std::vector< EntityHandle > shhandles( MAX_SHARING_PROCS );
Tag gidTag = mb->globalId_tag();
int np;
unsigned char pstatus;
std::multimap< int, int > extraGraphEdges;
// std::map adjCellsId;
std::map< int, int > extraCellsProc;
// if method is 2, no need to do the exchange for adjacent cells across partition boundary
// these maps above will be empty for method 2 (geometry)
if( 1 == met )
{
rval = pco->get_shared_entities( /*int other_proc*/ -1, sharedEdges, interfaceDim,
/*const bool iface*/ true );MB_CHK_ERR( rval );
#ifdef VERBOSE
std::cout << " on sender task " << pco->rank() << " number of shared interface cells " << sharedEdges.size()
<< "\n";
#endif
// find to what processors we need to send the ghost info about the edge
// first determine the local graph; what elements are adjacent to each cell in owned range
// cells that are sharing a partition interface edge, are identified first, and form a map
TupleList TLe; // tuple list for cells
TLe.initialize( 2, 0, 1, 0, sharedEdges.size() ); // send to, id of adj cell, remote edge
TLe.enableWriteAccess();
std::map< EntityHandle, int > edgeToCell; // from local boundary edge to adjacent cell id
// will be changed after
for( Range::iterator eit = sharedEdges.begin(); eit != sharedEdges.end(); eit++ )
{
EntityHandle edge = *eit;
// get the adjacent cell
Range adjEnts;
rval = mb->get_adjacencies( &edge, 1, primaryDim, false, adjEnts );MB_CHK_ERR( rval );
if( adjEnts.size() > 0 )
{
EntityHandle adjCell = adjEnts[0];
int gid;
rval = mb->tag_get_data( gidTag, &adjCell, 1, &gid );MB_CHK_ERR( rval );
rval = pco->get_sharing_data( edge, &shprocs[0], &shhandles[0], pstatus, np );MB_CHK_ERR( rval );
int n = TLe.get_n();
TLe.vi_wr[2 * n] = shprocs[0];
TLe.vi_wr[2 * n + 1] = gid;
TLe.vul_wr[n] = shhandles[0]; // the remote edge corresponding to shared edge
edgeToCell[edge] = gid; // store the map between edge and local id of adj cell
TLe.inc_n();
}
}
#ifdef VERBOSE
std::stringstream ff2;
ff2 << "TLe_" << pco->rank() << ".txt";
TLe.print_to_file( ff2.str().c_str() );
#endif
// send the data to the other processors:
( pco->proc_config().crystal_router() )->gs_transfer( 1, TLe, 0 );
// on receiver side, each local edge will have the remote cell adjacent to it!
int ne = TLe.get_n();
for( int i = 0; i < ne; i++ )
{
int sharedProc = TLe.vi_rd[2 * i]; // this info is coming from here, originally
int remoteCellID = TLe.vi_rd[2 * i + 1]; // this is the id of the remote cell, on sharedProc
EntityHandle localCell = TLe.vul_rd[i]; // this is now local edge/face on this proc
int localCellId = edgeToCell[localCell]; // this is the local cell adjacent to edge/face
// now, we will need to add to the graph the pair
std::pair< int, int > extraAdj = std::make_pair( localCellId, remoteCellID );
extraGraphEdges.insert( extraAdj );
// adjCellsId [edgeToCell[localCell]] = remoteCellID;
extraCellsProc[remoteCellID] = sharedProc;
#ifdef VERBOSE
std::cout << "local ID " << edgeToCell[localCell] << " remote cell ID: " << remoteCellID << "\n";
#endif
}
}
t2 = MPI_Wtime();
if( rootSender ) std::cout << " time preparing the input for Zoltan:" << t2 - t1 << " seconds. \n";
// so adj cells ids; need to call zoltan for parallel partition
#ifdef MOAB_HAVE_ZOLTAN
ZoltanPartitioner* mbZTool = new ZoltanPartitioner( mb, pco );
if( 1 <= met ) // partition in zoltan, either graph or geometric partitioner
{
std::map< int, Range > distribution; // how to distribute owned elements by processors in receiving groups
// in how many tasks do we want to be distributed?
int numNewPartitions = (int)receiverTasks.size();
Range primaryCells = owned.subset_by_dimension( primaryDim );
rval = mbZTool->partition_owned_cells( primaryCells, extraGraphEdges, extraCellsProc, numNewPartitions,
distribution, met, zoltanBuffer );MB_CHK_ERR( rval );
for( std::map< int, Range >::iterator mit = distribution.begin(); mit != distribution.end(); mit++ )
{
int part_index = mit->first;
assert( part_index < numNewPartitions );
split_ranges[receiverTasks[part_index]] = mit->second;
}
}
// delete now the partitioner
delete mbZTool;
#endif
t3 = MPI_Wtime();
if( rootSender ) std::cout << " time spent by Zoltan " << t3 - t2 << " seconds. \n";
return MB_SUCCESS;
}
| ErrorCode moab::ParCommGraph::compute_trivial_partition | ( | std::vector< int > & | numElemsPerTaskInGroup1 | ) |
Based on the number of elements on each task in group 1, partition for group 2, trivially.
Operations: it is called on every receiver task; decides how are all elements distributed
Note: establish how many elements are sent from each task in group 1 to tasks in group 2 This call is usually made on a root / master process, and will construct local maps that are member data, which contain the communication graph, in both directions Also, number of elements migrated/exchanged between each sender/receiver
| [in] | numElemsPerTaskInGroup1 | (std::vector<int> &) number of elements on each sender task |
Definition at line 98 of file ParCommGraph.cpp.
References MB_SUCCESS, receiverTasks, recv_graph, recv_sizes, sender_graph, sender_sizes, and senderTasks.
{
recv_graph.clear();
recv_sizes.clear();
sender_graph.clear();
sender_sizes.clear();
if( numElemsPerTaskInGroup1.size() != senderTasks.size() )
return MB_FAILURE; // each sender has a number of elements that it owns
// first find out total number of elements to be sent from all senders
int total_elems = 0;
std::vector< int > accum;
accum.push_back( 0 );
int num_senders = (int)senderTasks.size();
for( size_t k = 0; k < numElemsPerTaskInGroup1.size(); k++ )
{
total_elems += numElemsPerTaskInGroup1[k];
accum.push_back( total_elems );
}
int num_recv = ( (int)receiverTasks.size() );
// in trivial partition, every receiver should get about total_elems/num_receivers elements
int num_per_receiver = (int)( total_elems / num_recv );
int leftover = total_elems - num_per_receiver * num_recv;
// so receiver k will receive [starts[k], starts[k+1] ) interval
std::vector< int > starts;
starts.resize( num_recv + 1 );
starts[0] = 0;
for( int k = 0; k < num_recv; k++ )
{
starts[k + 1] = starts[k] + num_per_receiver;
if( k < leftover ) starts[k + 1]++;
}
// each sender will send to a number of receivers, based on how the
// arrays starts[0:num_recv] and accum[0:sendr] overlap
int lastUsedReceiverRank = 0; // first receiver was not treated yet
for( int j = 0; j < num_senders; j++ )
{
// we could start the receiver loop with the latest receiver that received from previous
// sender
for( int k = lastUsedReceiverRank; k < num_recv; k++ )
{
// if overlap:
if( starts[k] < accum[j + 1] && starts[k + 1] > accum[j] )
{
recv_graph[receiverTasks[k]].push_back( senderTasks[j] );
sender_graph[senderTasks[j]].push_back( receiverTasks[k] );
// we still need to decide what is the overlap
int sizeOverlap = 1; // at least 1, for sure
// 1
if( starts[k] >= accum[j] ) // one end is starts[k]
{
if( starts[k + 1] >= accum[j + 1] ) // the other end is accum[j+1]
sizeOverlap = accum[j + 1] - starts[k];
else //
sizeOverlap = starts[k + 1] - starts[k];
}
else // one end is accum[j]
{
if( starts[k + 1] >= accum[j + 1] ) // the other end is accum[j+1]
sizeOverlap = accum[j + 1] - accum[j];
else
sizeOverlap = starts[k + 1] - accum[j];
}
recv_sizes[receiverTasks[k]].push_back( sizeOverlap ); // basically, task k will receive from
// sender j, sizeOverlap elems
sender_sizes[senderTasks[j]].push_back( sizeOverlap );
if( starts[k] > accum[j + 1] )
{
lastUsedReceiverRank = k - 1; // so next k loop will start a little higher, we
// probably finished with first few receivers (up
// to receiver lastUsedReceiverRank)
break; // break the k loop, we distributed all elements from sender j to some
// receivers
}
}
}
}
return MB_SUCCESS;
}
| ErrorCode moab::ParCommGraph::dump_comm_information | ( | const std::string & | prefix, |
| int | is_send, | ||
| int | verbose | ||
| ) |
Definition at line 1635 of file ParCommGraph.cpp.
References COVERAGE, DOF_BASED, graph_type, INITIAL_MIGRATE, involved_IDs_map, MB_SUCCESS, rankInGroup1, rankInGroup2, rankInJoin, moab::Range::size(), and split_ranges.
{
//
if( -1 != rankInGroup1 && 1 == is_send ) // it is a sender task
{
std::ofstream dbfile;
std::stringstream outf;
outf << prefix << "_sender_" << rankInGroup1 << "_joint" << rankInJoin << "_type_" << (int)graph_type << ".txt";
dbfile.open( outf.str().c_str() );
if( graph_type == COVERAGE )
{
for( std::map< int, std::vector< int > >::iterator mit = involved_IDs_map.begin();
mit != involved_IDs_map.end(); mit++ )
{
int receiver_proc = mit->first;
std::vector< int >& eids = mit->second;
dbfile << "receiver: " << receiver_proc << " size:" << eids.size() << "\n";
if( verbose >= 1 )
{
for( size_t i = 0; i < eids.size(); i++ )
{
dbfile << eids[i] << " ";
if( i % 20 == 19 ) dbfile << "\n";
}
dbfile << "\n";
}
}
}
else if( graph_type == INITIAL_MIGRATE ) // just after migration
{
for( std::map< int, Range >::iterator mit = split_ranges.begin(); mit != split_ranges.end(); mit++ )
{
int receiver_proc = mit->first;
Range& eids = mit->second;
dbfile << "receiver: " << receiver_proc << " size:" << eids.size() << "\n";
}
}
else if( graph_type == DOF_BASED ) // just after migration, or from computeGraph
{
for( std::map< int, std::vector< int > >::iterator mit = involved_IDs_map.begin();
mit != involved_IDs_map.end(); mit++ )
{
int receiver_proc = mit->first;
dbfile << "receiver: " << receiver_proc << " size:" << mit->second.size() << "\n";
}
}
dbfile.close();
}
if( -1 != rankInGroup2 && 0 == is_send ) // it is a receiver task
{
std::ofstream dbfile;
std::stringstream outf;
outf << prefix << "_receiver_" << rankInGroup2 << "_joint" << rankInJoin << "_type_" << (int)graph_type
<< ".txt";
dbfile.open( outf.str().c_str() );
if( graph_type == COVERAGE )
{
for( std::map< int, std::vector< int > >::iterator mit = involved_IDs_map.begin();
mit != involved_IDs_map.end(); mit++ )
{
int sender_proc = mit->first;
std::vector< int >& eids = mit->second;
dbfile << "sender: " << sender_proc << " size:" << eids.size() << "\n";
if( verbose >= 1 )
{
for( size_t i = 0; i < eids.size(); i++ )
{
dbfile << eids[i] << " ";
if( i % 20 == 19 ) dbfile << "\n";
}
dbfile << "\n";
}
}
}
else if( graph_type == INITIAL_MIGRATE ) // just after migration
{
for( std::map< int, Range >::iterator mit = split_ranges.begin(); mit != split_ranges.end(); mit++ )
{
int sender_proc = mit->first;
Range& eids = mit->second;
dbfile << "sender: " << sender_proc << " size:" << eids.size() << "\n";
}
}
else if( graph_type == DOF_BASED ) // just after migration
{
for( std::map< int, std::vector< int > >::iterator mit = involved_IDs_map.begin();
mit != involved_IDs_map.end(); mit++ )
{
int sender_proc = mit->first;
dbfile << "receiver: " << sender_proc << " size:" << mit->second.size() << "\n";
}
}
dbfile.close();
}
return MB_SUCCESS;
}
| void moab::ParCommGraph::find_group_ranks | ( | MPI_Group | group, |
| MPI_Comm | join, | ||
| std::vector< int > & | ranks | ||
| ) | [private] |
find ranks of a group with respect to an encompassing communicator
Operations: Local, usually called on root process of the group
| [in] | joincomm | (MPI_Comm) |
| [in] | group | (MPI_Group) |
| [out] | ranks | ( std::vector<int>) ranks with respect to the joint communicator |
Definition at line 79 of file ParCommGraph.cpp.
Referenced by ParCommGraph().
{
MPI_Group global_grp;
MPI_Comm_group( joincomm, &global_grp );
int grp_size;
MPI_Group_size( group, &grp_size );
std::vector< int > rks( grp_size );
ranks.resize( grp_size );
for( int i = 0; i < grp_size; i++ )
rks[i] = i;
MPI_Group_translate_ranks( group, grp_size, &rks[0], global_grp, &ranks[0] );
MPI_Group_free( &global_grp );
return;
}
| ErrorCode moab::ParCommGraph::form_mesh_from_tuples | ( | Interface * | mb, |
| TupleList & | TLv, | ||
| TupleList & | TLc, | ||
| int | type, | ||
| int | lenTagType1, | ||
| EntityHandle | fset, | ||
| Range & | primary_ents, | ||
| std::vector< int > & | values_entities | ||
| ) |
Definition at line 1425 of file ParCommGraph.cpp.
References moab::Interface::add_entities(), moab::Interface::create_element(), moab::Interface::create_vertex(), ErrorCode, moab::TupleList::get_n(), moab::Interface::globalId_tag(), moab::Range::insert(), MB_CHK_ERR, MB_CHK_SET_ERR, MB_SUCCESS, MB_TAG_CREAT, MB_TAG_DENSE, MB_TYPE_INTEGER, MBPOLYGON, MBQUAD, MBTRI, moab::Range::size(), split_ranges, moab::Interface::tag_get_data(), moab::Interface::tag_get_handle(), moab::Interface::tag_set_data(), moab::TupleList::vi_rd, and moab::TupleList::vr_rd.
{
// might need to fill also the split_range things
// we will always need GlobalID tag
Tag gidtag = mb->globalId_tag();
// for Type1, we need GLOBAL_DOFS tag;
Tag gds;
ErrorCode rval;
std::vector< int > def_val( lenTagType1, 0 );
if( type == 1 )
{
// we may need to create this tag
rval = mb->tag_get_handle( "GLOBAL_DOFS", lenTagType1, MB_TYPE_INTEGER, gds, MB_TAG_CREAT | MB_TAG_DENSE,
&def_val[0] );MB_CHK_ERR( rval );
}
std::map< int, EntityHandle > vertexMap; //
Range verts;
// always form vertices and add them to the fset;
int n = TLv.get_n();
EntityHandle vertex;
for( int i = 0; i < n; i++ )
{
int gid = TLv.vi_rd[2 * i + 1];
if( vertexMap.find( gid ) == vertexMap.end() )
{
// need to form this vertex
rval = mb->create_vertex( &( TLv.vr_rd[3 * i] ), vertex );MB_CHK_ERR( rval );
vertexMap[gid] = vertex;
verts.insert( vertex );
rval = mb->tag_set_data( gidtag, &vertex, 1, &gid );MB_CHK_ERR( rval );
// if point cloud,
}
if( 2 == type ) // point cloud, add it to the split_ranges ?
{
split_ranges[TLv.vi_rd[2 * i]].insert( vertexMap[gid] );
}
// todo : when to add the values_entities ?
}
rval = mb->add_entities( fset, verts );MB_CHK_ERR( rval );
if( 2 == type )
{
primary_ents = verts;
values_entities.resize( verts.size() ); // just get the ids of vertices
rval = mb->tag_get_data( gidtag, verts, &values_entities[0] );MB_CHK_ERR( rval );
return MB_SUCCESS;
}
n = TLc.get_n();
int size_tuple = 2 + ( ( type != 1 ) ? 0 : lenTagType1 ) + 1 + 10; // 10 is the max number of vertices in cell
EntityHandle new_element;
Range cells;
std::map< int, EntityHandle > cellMap; // do no tcreate one if it already exists, maybe from other processes
for( int i = 0; i < n; i++ )
{
int from_proc = TLc.vi_rd[size_tuple * i];
int globalIdEl = TLc.vi_rd[size_tuple * i + 1];
if( cellMap.find( globalIdEl ) == cellMap.end() ) // need to create the cell
{
int current_index = 2;
if( 1 == type ) current_index += lenTagType1;
int nnodes = TLc.vi_rd[size_tuple * i + current_index];
std::vector< EntityHandle > conn;
conn.resize( nnodes );
for( int j = 0; j < nnodes; j++ )
{
conn[j] = vertexMap[TLc.vi_rd[size_tuple * i + current_index + j + 1]];
}
//
EntityType entType = MBQUAD;
if( nnodes > 4 ) entType = MBPOLYGON;
if( nnodes < 4 ) entType = MBTRI;
rval = mb->create_element( entType, &conn[0], nnodes, new_element );MB_CHK_SET_ERR( rval, "can't create new element " );
cells.insert( new_element );
cellMap[globalIdEl] = new_element;
rval = mb->tag_set_data( gidtag, &new_element, 1, &globalIdEl );MB_CHK_SET_ERR( rval, "can't set global id tag on cell " );
if( 1 == type )
{
// set the gds tag
rval = mb->tag_set_data( gds, &new_element, 1, &( TLc.vi_rd[size_tuple * i + 2] ) );MB_CHK_SET_ERR( rval, "can't set gds tag on cell " );
}
}
split_ranges[from_proc].insert( cellMap[globalIdEl] );
}
rval = mb->add_entities( fset, cells );MB_CHK_ERR( rval );
primary_ents = cells;
if( 1 == type )
{
values_entities.resize( lenTagType1 * primary_ents.size() );
rval = mb->tag_get_data( gds, primary_ents, &values_entities[0] );MB_CHK_ERR( rval );
}
else // type == 3
{
values_entities.resize( primary_ents.size() ); // just get the ids !
rval = mb->tag_get_data( gidtag, primary_ents, &values_entities[0] );MB_CHK_ERR( rval );
}
return MB_SUCCESS;
}
| ErrorCode moab::ParCommGraph::form_tuples_to_migrate_mesh | ( | Interface * | mb, |
| TupleList & | TLv, | ||
| TupleList & | TLc, | ||
| int | type, | ||
| int | lenTagType1 | ||
| ) |
Definition at line 1338 of file ParCommGraph.cpp.
References moab::Range::begin(), moab::TupleList::enableWriteAccess(), moab::Range::end(), ErrorCode, moab::Interface::get_connectivity(), moab::Interface::get_coords(), moab::TupleList::get_n(), moab::Interface::globalId_tag(), moab::TupleList::inc_n(), moab::TupleList::initialize(), MB_CHK_ERR, MB_SUCCESS, moab::Range::size(), split_ranges, moab::Interface::tag_get_data(), moab::Interface::tag_get_handle(), moab::TupleList::vi_wr, and moab::TupleList::vr_wr.
{
// we will always need GlobalID tag
Tag gidtag = mb->globalId_tag();
// for Type1, we need GLOBAL_DOFS tag;
Tag gds;
ErrorCode rval;
if( type == 1 )
{
rval = mb->tag_get_handle( "GLOBAL_DOFS", gds );
}
// find vertices to be sent, for each of the split_ranges procs
std::map< int, Range > verts_to_proc;
int numv = 0, numc = 0;
for( auto it = split_ranges.begin(); it != split_ranges.end(); it++ )
{
int to_proc = it->first;
Range verts;
if( type != 2 )
{
rval = mb->get_connectivity( it->second, verts );MB_CHK_ERR( rval );
numc += (int)it->second.size();
}
else
verts = it->second;
verts_to_proc[to_proc] = verts;
numv += (int)verts.size();
}
// first vertices:
TLv.initialize( 2, 0, 0, 3, numv ); // to proc, GLOBAL ID, 3 real coordinates
TLv.enableWriteAccess();
// use the global id of vertices for connectivity
for( auto it = verts_to_proc.begin(); it != verts_to_proc.end(); it++ )
{
int to_proc = it->first;
Range& verts = it->second;
for( Range::iterator vit = verts.begin(); vit != verts.end(); ++vit )
{
EntityHandle v = *vit;
int n = TLv.get_n(); // current size of tuple list
TLv.vi_wr[2 * n] = to_proc; // send to processor
rval = mb->tag_get_data( gidtag, &v, 1, &( TLv.vi_wr[2 * n + 1] ) );MB_CHK_ERR( rval );
rval = mb->get_coords( &v, 1, &( TLv.vr_wr[3 * n] ) );MB_CHK_ERR( rval );
TLv.inc_n(); // increment tuple list size
}
}
if( type == 2 ) return MB_SUCCESS; // no need to fill TLc
// to proc, ID cell, gdstag, nbv, id conn,
int size_tuple = 2 + ( ( type != 1 ) ? 0 : lenTagType1 ) + 1 + 10; // 10 is the max number of vertices in cell
std::vector< int > gdvals;
TLc.initialize( size_tuple, 0, 0, 0, numc ); // to proc, GLOBAL ID, 3 real coordinates
TLc.enableWriteAccess();
for( auto it = split_ranges.begin(); it != split_ranges.end(); it++ )
{
int to_proc = it->first;
Range& cells = it->second;
for( Range::iterator cit = cells.begin(); cit != cells.end(); ++cit )
{
EntityHandle cell = *cit;
int n = TLc.get_n(); // current size of tuple list
TLc.vi_wr[size_tuple * n] = to_proc;
int current_index = 2;
rval = mb->tag_get_data( gidtag, &cell, 1, &( TLc.vi_wr[size_tuple * n + 1] ) );MB_CHK_ERR( rval );
if( 1 == type )
{
rval = mb->tag_get_data( gds, &cell, 1, &( TLc.vi_wr[size_tuple * n + current_index] ) );MB_CHK_ERR( rval );
current_index += lenTagType1;
}
// now get connectivity
const EntityHandle* conn = NULL;
int nnodes = 0;
rval = mb->get_connectivity( cell, conn, nnodes );MB_CHK_ERR( rval );
// fill nnodes:
TLc.vi_wr[size_tuple * n + current_index] = nnodes;
rval = mb->tag_get_data( gidtag, conn, nnodes, &( TLc.vi_wr[size_tuple * n + current_index + 1] ) );MB_CHK_ERR( rval );
TLc.inc_n(); // increment tuple list size
}
}
return MB_SUCCESS;
}
| int moab::ParCommGraph::get_component_id1 | ( | ) | [inline] |
| int moab::ParCommGraph::get_component_id2 | ( | ) | [inline] |
| int moab::ParCommGraph::get_context_id | ( | ) | [inline] |
| EntityHandle moab::ParCommGraph::get_cover_set | ( | ) | [inline] |
| bool moab::ParCommGraph::is_root_receiver | ( | ) | [inline] |
| bool moab::ParCommGraph::is_root_sender | ( | ) | [inline] |
Definition at line 133 of file ParCommGraph.hpp.
References rootSender.
Referenced by send_graph(), send_graph_partition(), and send_mesh_parts().
{
return rootSender;
}
| ErrorCode moab::ParCommGraph::pack_receivers_graph | ( | std::vector< int > & | packed_recv_array | ) |
pack information about receivers view of the graph, for future sending to receiver root
Operations: Local, called on root process of the senders group
| [out] | packed_recv_array | packed data will be sent to the root of receivers, and distributed from there, and will have this information, for each receiver, concatenated receiver 1 task, number of senders for receiver 1, then sender tasks for receiver 1, receiver 2 task, number of senders for receiver 2, sender tasks for receiver 2, etc Note: only the root of senders will compute this, and send it over to the receiver root, which will distribute it over each receiver; We do not pack the sizes of data to be sent, only the senders for each of the receivers (could be of size O(n^2) , where n is the number of tasks ; but in general, it should be more like O(n) ). Each sender sends to a "finite" number of receivers, and each receiver receives from a finite number of senders). We need this info to decide how to set up the send/receive waiting game for non-blocking communication ) |
Definition at line 187 of file ParCommGraph.cpp.
References MB_SUCCESS, receiverTasks, recv_graph, and senders().
Referenced by send_graph().
{
// it will basically look at local data, to pack communication graph, each receiver task will
// have to post receives for each sender task that will send data to it; the array will be
// communicated to root receiver, and eventually distributed to receiver tasks
/*
* packed_array will have receiver, number of senders, then senders, etc
*/
if( recv_graph.size() < receiverTasks.size() )
{
// big problem, we have empty partitions in receive
std::cout << " WARNING: empty partitions, some receiver tasks will receive nothing.\n";
}
for( std::map< int, std::vector< int > >::iterator it = recv_graph.begin(); it != recv_graph.end(); it++ )
{
int recv = it->first;
std::vector< int >& senders = it->second;
packed_recv_array.push_back( recv );
packed_recv_array.push_back( (int)senders.size() );
for( int k = 0; k < (int)senders.size(); k++ )
packed_recv_array.push_back( senders[k] );
}
return MB_SUCCESS;
}
| ErrorCode moab::ParCommGraph::receive_comm_graph | ( | MPI_Comm | jcomm, |
| ParallelComm * | pco, | ||
| std::vector< int > & | pack_array, | ||
| std::vector< char > & | zoltanBuffer | ||
| ) |
Definition at line 370 of file ParCommGraph.cpp.
References moab::ParallelComm::comm(), MB_SUCCESS, rootReceiver, and sender().
{
// first, receive from sender_rank 0, the communication graph (matrix), so each receiver
// knows what data to expect
MPI_Comm receive = pco->comm();
int size_pack_array, ierr;
MPI_Status status;
if( rootReceiver )
{
ierr = MPI_Probe( sender( 0 ), 20, jcomm, &status );
if( 0 != ierr )
{
std::cout << " MPI_Probe failure: " << ierr << "\n";
return MB_FAILURE;
}
// get the count of data received from the MPI_Status structure
ierr = MPI_Get_count( &status, MPI_INT, &size_pack_array );
if( 0 != ierr )
{
std::cout << " MPI_Get_count failure: " << ierr << "\n";
return MB_FAILURE;
}
#ifdef VERBOSE
std::cout << " receive comm graph size: " << size_pack_array << "\n";
#endif
pack_array.resize( size_pack_array );
ierr = MPI_Recv( &pack_array[0], size_pack_array, MPI_INT, sender( 0 ), 20, jcomm, &status );
if( 0 != ierr ) return MB_FAILURE;
#ifdef VERBOSE
std::cout << " receive comm graph ";
for( int k = 0; k < (int)pack_array.size(); k++ )
std::cout << " " << pack_array[k];
std::cout << "\n";
#endif
// the last int tells if we have another receive to do or not (for zoltan buffer)
// look at the last value, to see if we receive zoltan buffer or not
int semaphore = pack_array[size_pack_array - 1];
if( 1 == semaphore )
{
// expect zoltanBuffer, the difference is the tag; we still need the joint comm
// the buffer was sent with a nonblocking send, from the root sender
ierr = MPI_Probe( sender( 0 ), 30, jcomm, &status ); // blocking call, to get size
if( 0 != ierr )
{
std::cout << " MPI_Probe failure: " << ierr << "\n";
return MB_FAILURE;
}
int incoming_msg_size;
MPI_Get_count( &status, MPI_CHAR, &incoming_msg_size );
zoltanBuffer.resize( incoming_msg_size );
ierr = MPI_Recv( &zoltanBuffer[0], incoming_msg_size, MPI_CHAR, sender( 0 ), 30, jcomm, &status );
if( 0 != ierr )
{
std::cout << " MPI_Recv failure: " << ierr << "\n";
return MB_FAILURE;
}
}
}
// now broadcast this whole array to all receivers, so they know what to expect
ierr = MPI_Bcast( &size_pack_array, 1, MPI_INT, 0, receive );
if( 0 != ierr ) return MB_FAILURE;
pack_array.resize( size_pack_array );
ierr = MPI_Bcast( &pack_array[0], size_pack_array, MPI_INT, 0, receive );
if( 0 != ierr ) return MB_FAILURE;
return MB_SUCCESS;
}
| ErrorCode moab::ParCommGraph::receive_mesh | ( | MPI_Comm | jcomm, |
| ParallelComm * | pco, | ||
| EntityHandle | local_set, | ||
| std::vector< int > & | senders_local | ||
| ) |
Definition at line 441 of file ParCommGraph.cpp.
References moab::Core::a_entity_factory(), moab::Interface::add_entities(), moab::Range::begin(), moab::ParallelComm::Buffer::buff_ptr, buffer, corr_sizes, corr_tasks, moab::AEntityFactory::create_vert_elem_adjacencies(), moab::Range::empty(), moab::Range::end(), entities, ErrorCode, moab::Core::get_connectivity(), moab::ParallelComm::get_moab(), mb, MB_CHK_SET_ERR, MB_SUCCESS, MB_TAG_CREAT, MB_TAG_DENSE, MB_TYPE_INTEGER, MBVERTEX, moab::ParallelComm::Buffer::mem_ptr, moab::Range::merge(), moab::AEntityFactory::notify_create_entity(), rankInGroup2, rankInJoin, moab::ParallelComm::Buffer::reset_ptr(), moab::Range::size(), split_ranges, moab::Range::subset_by_dimension(), moab::Range::subset_by_type(), moab::subtract(), moab::Interface::tag_get_handle(), moab::Interface::tag_set_data(), moab::ParallelComm::unpack_buffer(), moab::AEntityFactory::vert_elem_adjacencies(), and moab::Interface::write_file().
{
ErrorCode rval;
int ierr;
MPI_Status status;
// we also need to fill corresponding mesh info on the other side
corr_tasks = senders_local;
Range newEnts;
Tag orgSendProcTag; // this will be a tag set on the received mesh, with info about from what
// task / PE the
// primary element came from, in the joint communicator ; this will be forwarded by coverage
// mesh
int defaultInt = -1; // no processor, so it was not migrated from somewhere else
rval = pco->get_moab()->tag_get_handle( "orig_sending_processor", 1, MB_TYPE_INTEGER, orgSendProcTag,
MB_TAG_DENSE | MB_TAG_CREAT, &defaultInt );MB_CHK_SET_ERR( rval, "can't create original sending processor tag" );
if( !senders_local.empty() )
{
for( size_t k = 0; k < senders_local.size(); k++ )
{
int sender1 = senders_local[k];
// first receive the size of the buffer using probe
/*
* MPI_Probe(
int source,
int tag,
MPI_Comm comm,
MPI_Status* status)
*
*/
ierr = MPI_Probe( sender1, 2, jcomm, &status );
if( 0 != ierr )
{
std::cout << " MPI_Probe failure in ParCommGraph::receive_mesh " << ierr << "\n";
return MB_FAILURE;
}
// get the count of data received from the MPI_Status structure
int size_pack;
ierr = MPI_Get_count( &status, MPI_CHAR, &size_pack );
if( 0 != ierr )
{
std::cout << " MPI_Get_count failure in ParCommGraph::receive_mesh " << ierr << "\n";
return MB_FAILURE;
}
/* ierr = MPI_Recv (&size_pack, 1, MPI_INT, sender1, 1, jcomm, &status);
if (0!=ierr) return MB_FAILURE;*/
// now resize the buffer, then receive it
ParallelComm::Buffer* buffer = new ParallelComm::Buffer( size_pack );
// buffer->reserve(size_pack);
ierr = MPI_Recv( buffer->mem_ptr, size_pack, MPI_CHAR, sender1, 2, jcomm, &status );
if( 0 != ierr )
{
std::cout << " MPI_Recv failure in ParCommGraph::receive_mesh " << ierr << "\n";
return MB_FAILURE;
}
// now unpack the buffer we just received
Range entities;
std::vector< std::vector< EntityHandle > > L1hloc, L1hrem;
std::vector< std::vector< int > > L1p;
std::vector< EntityHandle > L2hloc, L2hrem;
std::vector< unsigned int > L2p;
buffer->reset_ptr( sizeof( int ) );
std::vector< EntityHandle > entities_vec( entities.size() );
std::copy( entities.begin(), entities.end(), entities_vec.begin() );
rval = pco->unpack_buffer( buffer->buff_ptr, false, -1, -1, L1hloc, L1hrem, L1p, L2hloc, L2hrem, L2p,
entities_vec );
delete buffer;
if( MB_SUCCESS != rval ) return rval;
std::copy( entities_vec.begin(), entities_vec.end(), range_inserter( entities ) );
// we have to add them to the local set
rval = pco->get_moab()->add_entities( local_set, entities );
if( MB_SUCCESS != rval ) return rval;
// corr_sizes is the size of primary entities received
Range verts = entities.subset_by_dimension( 0 );
Range local_primary_ents = subtract( entities, verts );
if( local_primary_ents.empty() )
{
// it is possible that all ents sent were vertices (point cloud)
// then consider primary entities the vertices
local_primary_ents = verts;
}
else
{
// set a tag with the original sender for the primary entity
// will be used later for coverage mesh
std::vector< int > orig_senders( local_primary_ents.size(), sender1 );
rval = pco->get_moab()->tag_set_data( orgSendProcTag, local_primary_ents, &orig_senders[0] );
}
corr_sizes.push_back( (int)local_primary_ents.size() );
newEnts.merge( entities );
// make these in split ranges
split_ranges[sender1] = local_primary_ents;
#ifdef VERBOSE
std::ostringstream partial_outFile;
partial_outFile << "part_send_" << sender1 << "."
<< "recv" << rankInJoin << ".vtk";
// the mesh contains ghosts too, but they are not part of mat/neumann set
// write in serial the file, to see what tags are missing
std::cout << " writing from receiver " << rankInJoin << " from sender " << sender1
<< " entities: " << entities.size() << std::endl;
rval = pco->get_moab()->write_file( partial_outFile.str().c_str(), 0, 0, &local_set,
1 ); // everything on local set received
if( MB_SUCCESS != rval ) return rval;
#endif
}
}
// make sure adjacencies are updated on the new elements
if( newEnts.empty() )
{
std::cout << "task:" << rankInGroup2 << " in receiver did not receive any entities \n";
}
else
{
// in order for the merging to work, we need to be sure that the adjacencies are updated
// (created)
Range local_verts = newEnts.subset_by_type( MBVERTEX );
newEnts = subtract( newEnts, local_verts );
Core* mb = (Core*)pco->get_moab();
AEntityFactory* adj_fact = mb->a_entity_factory();
if( !adj_fact->vert_elem_adjacencies() )
adj_fact->create_vert_elem_adjacencies();
else
{
for( Range::iterator it = newEnts.begin(); it != newEnts.end(); ++it )
{
EntityHandle eh = *it;
const EntityHandle* conn = NULL;
int num_nodes = 0;
rval = mb->get_connectivity( eh, conn, num_nodes );
if( MB_SUCCESS != rval ) return rval;
adj_fact->notify_create_entity( eh, conn, num_nodes );
}
}
}
return MB_SUCCESS;
}
| ErrorCode moab::ParCommGraph::receive_tag_values | ( | MPI_Comm | jcomm, |
| ParallelComm * | pco, | ||
| Range & | owned, | ||
| std::vector< Tag > & | tag_handles | ||
| ) |
Get the size of the specified tag in bytes
Definition at line 817 of file ParCommGraph.cpp.
References moab::Range::begin(), moab::ParallelComm::Buffer::buff_ptr, buffer, COVERAGE, DOF_BASED, moab::Range::end(), ErrorCode, moab::ParallelComm::get_moab(), moab::Core::globalId_tag(), graph_type, moab::Core::id_from_handle(), INITIAL_MIGRATE, involved_IDs_map, map_index, map_ptr, mb, MB_CHK_ERR, MB_SUCCESS, moab::ParallelComm::Buffer::mem_ptr, rankInJoin, moab::ParallelComm::Buffer::reset_ptr(), moab::Range::size(), split_ranges, moab::Core::tag_get_bytes(), moab::Core::tag_get_data(), moab::Core::tag_get_length(), and moab::Core::tag_set_data().
{
// opposite to sending, we will use blocking receives
int ierr;
MPI_Status status;
// basically, owned.size() needs to be equal to sum(corr_sizes)
// get info about the tag size, type, etc
Core* mb = (Core*)pco->get_moab();
// get info about the tag
//! Get the size of the specified tag in bytes
ErrorCode rval;
int total_bytes_per_entity = 0;
std::vector< int > vect_bytes_per_tag;
#ifdef VERBOSE
std::vector< int > tag_sizes;
#endif
for( size_t i = 0; i < tag_handles.size(); i++ )
{
int bytes_per_tag;
rval = mb->tag_get_bytes( tag_handles[i], bytes_per_tag );MB_CHK_ERR( rval );
total_bytes_per_entity += bytes_per_tag;
vect_bytes_per_tag.push_back( bytes_per_tag );
#ifdef VERBOSE
int tag_size;
rval = mb->tag_get_length( tag_handles[i], tag_size );MB_CHK_ERR( rval );
tag_sizes.push_back( tag_size );
#endif
}
if( graph_type == INITIAL_MIGRATE )
{
// std::map split_ranges;
// rval = split_owned_range ( owned);MB_CHK_ERR ( rval );
// use the buffers data structure to allocate memory for receiving the tags
for( std::map< int, Range >::iterator it = split_ranges.begin(); it != split_ranges.end(); it++ )
{
int sender_proc = it->first;
Range ents = it->second; // primary entities, with the tag data, we will receive
int size_buffer = 4 + total_bytes_per_entity *
(int)ents.size(); // hopefully, below 2B; if more, we have a big problem ...
ParallelComm::Buffer* buffer = new ParallelComm::Buffer( size_buffer );
buffer->reset_ptr( sizeof( int ) );
*( (int*)buffer->mem_ptr ) = size_buffer;
// int size_pack = buffer->get_current_size(); // debug check
ierr = MPI_Recv( buffer->mem_ptr, size_buffer, MPI_CHAR, sender_proc, 222, jcomm, &status );
if( ierr != 0 ) return MB_FAILURE;
// now set the tag
// copy to tag
for( size_t i = 0; i < tag_handles.size(); i++ )
{
rval = mb->tag_set_data( tag_handles[i], ents, (void*)( buffer->buff_ptr ) );
buffer->buff_ptr += vect_bytes_per_tag[i] * ents.size();
}
delete buffer; // no need for it afterwards
MB_CHK_ERR( rval );
}
}
else if( graph_type == COVERAGE ) // receive buffer, then extract tag data, in a loop
{
// we know that we will need to receive some tag data in a specific order (by ids stored)
// first, get the ids of the local elements, from owned Range; unpack the buffer in order
Tag gidTag = mb->globalId_tag();
std::vector< int > gids;
gids.resize( owned.size() );
rval = mb->tag_get_data( gidTag, owned, &gids[0] );MB_CHK_ERR( rval );
std::map< int, EntityHandle > gidToHandle;
size_t i = 0;
for( Range::iterator it = owned.begin(); it != owned.end(); it++ )
{
EntityHandle eh = *it;
gidToHandle[gids[i++]] = eh;
}
//
// now, unpack the data and set it to the tag
for( std::map< int, std::vector< int > >::iterator mit = involved_IDs_map.begin();
mit != involved_IDs_map.end(); mit++ )
{
int sender_proc = mit->first;
std::vector< int >& eids = mit->second;
int size_buffer = 4 + total_bytes_per_entity *
(int)eids.size(); // hopefully, below 2B; if more, we have a big problem ...
ParallelComm::Buffer* buffer = new ParallelComm::Buffer( size_buffer );
buffer->reset_ptr( sizeof( int ) );
*( (int*)buffer->mem_ptr ) = size_buffer; // this is really not necessary, it should receive this too
// receive the buffer
ierr = MPI_Recv( buffer->mem_ptr, size_buffer, MPI_CHAR, sender_proc, 222, jcomm, &status );
if( ierr != 0 ) return MB_FAILURE;
// start copy
#ifdef VERBOSE
std::ofstream dbfile;
std::stringstream outf;
outf << "recvFrom_" << sender_proc << "_on_proc_" << rankInJoin << ".txt";
dbfile.open( outf.str().c_str() );
dbfile << "recvFrom_" << sender_proc << " on proc " << rankInJoin << "\n";
#endif
// copy tag data from buffer->buff_ptr
// data is arranged by tag , and repeat the loop for each entity ()
// maybe it should be arranged by entity now, not by tag (so one loop for entities,
// outside)
for( std::vector< int >::iterator it = eids.begin(); it != eids.end(); it++ )
{
int eID = *it;
std::map< int, EntityHandle >::iterator mit2 = gidToHandle.find( eID );
if( mit2 == gidToHandle.end() )
{
std::cout << " on rank: " << rankInJoin << " cannot find entity handle with global ID " << eID
<< "\n";
return MB_FAILURE;
}
EntityHandle eh = mit2->second;
for( i = 0; i < tag_handles.size(); i++ )
{
rval = mb->tag_set_data( tag_handles[i], &eh, 1, (void*)( buffer->buff_ptr ) );MB_CHK_ERR( rval );
#ifdef VERBOSE
dbfile << "global ID " << eID << " local handle " << mb->id_from_handle( eh ) << " vals: ";
double* vals = (double*)( buffer->buff_ptr );
for( int kk = 0; kk < tag_sizes[i]; kk++ )
{
dbfile << " " << *vals;
vals++;
}
dbfile << "\n";
#endif
buffer->buff_ptr += vect_bytes_per_tag[i];
}
}
// delete receive buffer
delete buffer;
#ifdef VERBOSE
dbfile.close();
#endif
}
}
else if( graph_type == DOF_BASED )
{
// need to fill up the values for each tag, in the order desired, from the buffer received
//
// get all the tags, for all owned entities, and pack the buffers accordingly
// we do not want to get the tags by entity, it may be too expensive
std::vector< std::vector< double > > valuesTags;
valuesTags.resize( tag_handles.size() );
for( size_t i = 0; i < tag_handles.size(); i++ )
{
int bytes_per_tag;
rval = mb->tag_get_bytes( tag_handles[i], bytes_per_tag );MB_CHK_ERR( rval );
valuesTags[i].resize( owned.size() * bytes_per_tag / sizeof( double ) );
// fill the whole array, we will pick up from here
// we will fill this array, using data from received buffer
// rval = mb->tag_get_data(owned, (void*)( &(valuesTags[i][0])) );MB_CHK_ERR ( rval );
}
// now, unpack the data and set the tags
for( std::map< int, std::vector< int > >::iterator mit = involved_IDs_map.begin();
mit != involved_IDs_map.end(); mit++ )
{
int sender_proc = mit->first;
std::vector< int >& eids = mit->second;
std::vector< int >& index_in_values = map_index[sender_proc];
std::vector< int >& index_ptr = map_ptr[sender_proc]; // this is eids.size()+1;
int size_buffer = 4 + total_bytes_per_entity *
(int)eids.size(); // hopefully, below 2B; if more, we have a big problem ...
ParallelComm::Buffer* buffer = new ParallelComm::Buffer( size_buffer );
buffer->reset_ptr( sizeof( int ) );
// receive the buffer
ierr = MPI_Recv( buffer->mem_ptr, size_buffer, MPI_CHAR, sender_proc, 222, jcomm, &status );
if( ierr != 0 ) return MB_FAILURE;
// use the values in buffer to populate valuesTag arrays, fill it up!
int j = 0;
for( std::vector< int >::iterator it = eids.begin(); it != eids.end(); it++, j++ )
{
for( size_t i = 0; i < tag_handles.size(); i++ )
{
// right now, move just doubles; but it could be any type of tag
double val = *( (double*)( buffer->buff_ptr ) );
buffer->buff_ptr += 8; // we know we are working with doubles only !!!
for( int k = index_ptr[j]; k < index_ptr[j + 1]; k++ )
valuesTags[i][index_in_values[k]] = val;
}
}
// we are done with the buffer in which we received tags, release / delete it
delete buffer;
}
// now we populated the values for all tags; set now the tags!
for( size_t i = 0; i < tag_handles.size(); i++ )
{
// we will fill this array, using data from received buffer
rval = mb->tag_set_data( tag_handles[i], owned, (void*)( &( valuesTags[i][0] ) ) );MB_CHK_ERR( rval );
}
}
return MB_SUCCESS;
}
| int moab::ParCommGraph::receiver | ( | int | index | ) | [inline] |
Definition at line 148 of file ParCommGraph.hpp.
References receiverTasks.
Referenced by send_graph().
{
return receiverTasks[index];
}
| const std::vector< int >& moab::ParCommGraph::receivers | ( | ) | [inline] |
Definition at line 213 of file ParCommGraph.hpp.
References receiverTasks.
Referenced by split_owned_range().
{
return receiverTasks;
}
Definition at line 591 of file ParCommGraph.cpp.
References comm_graph, localSendBuffs, MB_SUCCESS, sendReqs, and zBuff.
{
int ierr, nsize = (int)sendReqs.size();
std::vector< MPI_Status > mult_status;
mult_status.resize( sendReqs.size() );
ierr = MPI_Waitall( nsize, &sendReqs[0], &mult_status[0] );
if( ierr != 0 ) return MB_FAILURE;
// now we can free all buffers
comm_graph.clear();
zBuff.clear(); // this is for zoltan buffer, it will be used only when sending the
// the RCB tree from component (sender) root to coupler (receiver) root
std::vector< ParallelComm::Buffer* >::iterator vit;
for( vit = localSendBuffs.begin(); vit != localSendBuffs.end(); ++vit )
delete( *vit );
localSendBuffs.clear();
return MB_SUCCESS;
}
| ErrorCode moab::ParCommGraph::send_graph | ( | MPI_Comm | jcomm, |
| std::vector< char > & | zBuff | ||
| ) |
Definition at line 263 of file ParCommGraph.cpp.
References comm_graph, ErrorCode, is_root_sender(), MB_SUCCESS, pack_receivers_graph(), receiver(), sendReqs, and zBuff.
Referenced by send_graph_partition().
{
if( is_root_sender() )
{
int ierr;
// will need to build a communication graph, because each sender knows now to which receiver
// to send data the receivers need to post receives for each sender that will send data to
// them will need to gather on rank 0 on the sender comm, global ranks of sender with
// receivers to send build communication matrix, each receiver will receive from what sender
std::vector< int > packed_recv_array;
ErrorCode rval = pack_receivers_graph( packed_recv_array );
if( MB_SUCCESS != rval ) return rval;
int size_pack_array = (int)packed_recv_array.size() + 1;
// the last integer
// will signal if we have to send zoltan buffer too, in a separate message 0 for no, 1 for yes
comm_graph = packed_recv_array;
comm_graph.resize( size_pack_array ); // bigger by 1, to store the semaphore about zBuff
// will add 1 or 2 requests; first one with comm graph, second with zoltan buffer if needed
if( zoltanBuffer.size() > 0 )
{
sendReqs.resize( 2 );
comm_graph[size_pack_array - 1] = 1; // send zoltanBuffer too :)
zBuff = zoltanBuffer; // do a deep copy here, because the zoltanBuffer will go out of scope, and
// we need to keep the sent buffer, after the non-blocking sent is executed; thanks Karen Devine !
}
else
{
sendReqs.resize( 1 );
comm_graph[size_pack_array - 1] = 0; // do not send zoltan buffer
}
// we have to use global communicator if (ierr!=0) return MB_FAILURE;*/
ierr = MPI_Isend( &comm_graph[0], size_pack_array, MPI_INT, receiver( 0 ), 20, jcomm,
&sendReqs[0] ); // we have to use global communicator
if( ierr != 0 ) return MB_FAILURE;
if( zBuff.size() > 0 )
{
ierr = MPI_Isend( &zBuff[0], (int)zBuff.size(), MPI_CHAR, receiver( 0 ), 30, jcomm,
&sendReqs[1] ); // we have to use global communicator
if( ierr != 0 ) return MB_FAILURE;
}
}
return MB_SUCCESS;
}
| ErrorCode moab::ParCommGraph::send_graph_partition | ( | ParallelComm * | pco, |
| MPI_Comm | jcomm, | ||
| std::vector< char > & | zoltanBuffer | ||
| ) |
Definition at line 1534 of file ParCommGraph.cpp.
References buffer, moab::ParallelComm::comm(), compid1, compid2, ErrorCode, is_root_sender(), MB_CHK_ERR, MB_SUCCESS, recv_graph, send_graph(), senders(), senderTasks, and split_ranges.
{
// first, accumulate the info to root of sender; use gatherv
// first, accumulate number of receivers from each sender, to the root receiver
int numberReceivers =
(int)split_ranges.size(); // these are ranges of elements to be sent to each receiver, from this task
int nSenders = (int)senderTasks.size(); //
// this sender will have to send to this many receivers
std::vector< int > displs( 1 ); // displacements for gatherv
std::vector< int > counts( 1 );
if( is_root_sender() )
{
displs.resize( nSenders + 1 );
counts.resize( nSenders );
}
int ierr = MPI_Gather( &numberReceivers, 1, MPI_INT, &counts[0], 1, MPI_INT, 0, pco->comm() );
if( ierr != MPI_SUCCESS ) return MB_FAILURE;
// compute now displacements
if( is_root_sender() )
{
displs[0] = 0;
for( int k = 0; k < nSenders; k++ )
{
displs[k + 1] = displs[k] + counts[k];
}
}
std::vector< int > buffer;
if( is_root_sender() ) buffer.resize( displs[nSenders] ); // the last one will have the total count now
std::vector< int > recvs;
for( std::map< int, Range >::iterator mit = split_ranges.begin(); mit != split_ranges.end(); mit++ )
{
recvs.push_back( mit->first );
}
ierr =
MPI_Gatherv( &recvs[0], numberReceivers, MPI_INT, &buffer[0], &counts[0], &displs[0], MPI_INT, 0, pco->comm() );
if( ierr != MPI_SUCCESS ) return MB_FAILURE;
// now form recv_graph map; points from the
// now form the graph to be sent to the other side; only on root
if( is_root_sender() )
{
#ifdef GRAPH_INFO
std::ofstream dbfileSender;
std::stringstream outf;
outf << "S_" << compid1 << "_R_" << compid2 << "_SenderGraph.txt";
dbfileSender.open( outf.str().c_str() );
dbfileSender << " number senders: " << nSenders << "\n";
dbfileSender << " senderRank \treceivers \n";
for( int k = 0; k < nSenders; k++ )
{
int indexInBuff = displs[k];
int senderTask = senderTasks[k];
dbfileSender << senderTask << "\t\t";
for( int j = 0; j < counts[k]; j++ )
{
int recvTask = buffer[indexInBuff + j];
dbfileSender << recvTask << " ";
}
dbfileSender << "\n";
}
dbfileSender.close();
#endif
for( int k = 0; k < nSenders; k++ )
{
int indexInBuff = displs[k];
int senderTask = senderTasks[k];
for( int j = 0; j < counts[k]; j++ )
{
int recvTask = buffer[indexInBuff + j];
recv_graph[recvTask].push_back( senderTask ); // this will be packed and sent to root receiver, with
// nonblocking send
}
}
#ifdef GRAPH_INFO
std::ofstream dbfile;
std::stringstream outf2;
outf2 << "S_" << compid1 << "_R_" << compid2 << "_RecvGraph.txt";
dbfile.open( outf2.str().c_str() );
dbfile << " number receivers: " << recv_graph.size() << "\n";
dbfile << " receiverRank \tsenders \n";
for( std::map< int, std::vector< int > >::iterator mit = recv_graph.begin(); mit != recv_graph.end(); mit++ )
{
int recvTask = mit->first;
std::vector< int >& senders = mit->second;
dbfile << recvTask << "\t\t";
for( std::vector< int >::iterator vit = senders.begin(); vit != senders.end(); vit++ )
dbfile << *vit << " ";
dbfile << "\n";
}
dbfile.close();
#endif
// this is the same as trivial partition
ErrorCode rval = send_graph( jcomm, zoltanBuffer );MB_CHK_ERR( rval );
}
return MB_SUCCESS;
}
| ErrorCode moab::ParCommGraph::send_mesh_parts | ( | MPI_Comm | jcomm, |
| ParallelComm * | pco, | ||
| Range & | owned | ||
| ) |
not anymore !
Definition at line 311 of file ParCommGraph.cpp.
References buffer, corr_sizes, corr_tasks, ErrorCode, moab::Interface::get_adjacencies(), moab::ParallelComm::Buffer::get_current_size(), moab::ParallelComm::get_moab(), moab::ParallelComm::INITIAL_BUFF_SIZE, is_root_sender(), localSendBuffs, MB_SUCCESS, moab::ParallelComm::Buffer::mem_ptr, moab::Range::merge(), moab::ParallelComm::pack_buffer(), rankInGroup1, moab::ParallelComm::Buffer::reset_ptr(), sender_graph, sender_sizes, senderTasks, sendReqs, split_owned_range(), split_ranges, and moab::Interface::UNION.
{
ErrorCode rval;
if( split_ranges.empty() ) // in trivial partition
{
rval = split_owned_range( rankInGroup1, owned );
if( rval != MB_SUCCESS ) return rval;
// we know this on the sender side:
corr_tasks = sender_graph[senderTasks[rankInGroup1]]; // copy
corr_sizes = sender_sizes[senderTasks[rankInGroup1]]; // another copy
}
int indexReq = 0;
int ierr; // MPI error
if( is_root_sender() ) indexReq = (int)sendReqs.size(); // we could have 1 or 2 MPI_Request's already
sendReqs.resize( indexReq + split_ranges.size() );
for( std::map< int, Range >::iterator it = split_ranges.begin(); it != split_ranges.end(); it++ )
{
int receiver_proc = it->first;
Range ents = it->second;
// add necessary vertices too
Range verts;
rval = pco->get_moab()->get_adjacencies( ents, 0, false, verts, Interface::UNION );
if( rval != MB_SUCCESS )
{
std::cout << " can't get adjacencies. for entities to send\n";
return rval;
}
ents.merge( verts );
ParallelComm::Buffer* buffer = new ParallelComm::Buffer( ParallelComm::INITIAL_BUFF_SIZE );
buffer->reset_ptr( sizeof( int ) );
rval = pco->pack_buffer( ents, false, true, false, -1, buffer );
if( rval != MB_SUCCESS )
{
std::cout << " can't pack buffer for entities to send\n";
return rval;
}
int size_pack = buffer->get_current_size();
// TODO there could be an issue with endian things; check !!!!!
// we are sending the size of the buffer first as an int!!!
/// not anymore !
/* ierr = MPI_Isend(buffer->mem_ptr, 1, MPI_INT, receiver_proc, 1, jcomm,
&sendReqs[indexReq]); // we have to use global communicator if (ierr!=0) return MB_FAILURE;
indexReq++;*/
ierr = MPI_Isend( buffer->mem_ptr, size_pack, MPI_CHAR, receiver_proc, 2, jcomm,
&sendReqs[indexReq] ); // we have to use global communicator
if( ierr != 0 ) return MB_FAILURE;
indexReq++;
localSendBuffs.push_back(
buffer ); // these buffers will be cleared only after all MPI_Request's have been waited upon
}
return MB_SUCCESS;
}
| ErrorCode moab::ParCommGraph::send_tag_values | ( | MPI_Comm | jcomm, |
| ParallelComm * | pco, | ||
| Range & | owned, | ||
| std::vector< Tag > & | tag_handles | ||
| ) |
Get the size of the specified tag in bytes
Definition at line 612 of file ParCommGraph.cpp.
References moab::Range::begin(), moab::ParallelComm::Buffer::buff_ptr, buffer, COVERAGE, DOF_BASED, moab::Range::end(), ErrorCode, moab::ParallelComm::get_moab(), moab::Core::globalId_tag(), graph_type, moab::Core::id_from_handle(), INITIAL_MIGRATE, involved_IDs_map, localSendBuffs, map_index, map_ptr, mb, MB_CHK_ERR, MB_SET_ERR, MB_SUCCESS, moab::ParallelComm::Buffer::mem_ptr, rankInJoin, moab::ParallelComm::Buffer::reset_ptr(), sendReqs, moab::Range::size(), split_ranges, moab::Core::tag_get_bytes(), moab::Core::tag_get_data(), and moab::Core::tag_get_length().
{
// basically, owned.size() needs to be equal to sum(corr_sizes)
// get info about the tag size, type, etc
int ierr;
Core* mb = (Core*)pco->get_moab();
// get info about the tag
//! Get the size of the specified tag in bytes
int total_bytes_per_entity = 0; // we need to know, to allocate buffers
ErrorCode rval;
std::vector< int > vect_bytes_per_tag;
#ifdef VERBOSE
std::vector< int > tag_sizes;
#endif
for( size_t i = 0; i < tag_handles.size(); i++ )
{
int bytes_per_tag;
rval = mb->tag_get_bytes( tag_handles[i], bytes_per_tag );MB_CHK_ERR( rval );
int tag_size1; // length
rval = mb->tag_get_length( tag_handles[i], tag_size1 );MB_CHK_ERR( rval );
if( graph_type == DOF_BASED )
bytes_per_tag = bytes_per_tag / tag_size1; // we know we have one double per tag , per ID sent;
// could be 8 for double, 4 for int, etc
total_bytes_per_entity += bytes_per_tag;
vect_bytes_per_tag.push_back( bytes_per_tag );
#ifdef VERBOSE
int tag_size;
rval = mb->tag_get_length( tag_handles[i], tag_size );MB_CHK_ERR( rval );
tag_sizes.push_back( tag_size );
#endif
}
int indexReq = 0;
if( graph_type == INITIAL_MIGRATE ) // original send
{
// use the buffers data structure to allocate memory for sending the tags
sendReqs.resize( split_ranges.size() );
for( std::map< int, Range >::iterator it = split_ranges.begin(); it != split_ranges.end(); it++ )
{
int receiver_proc = it->first;
Range ents = it->second; // primary entities, with the tag data
int size_buffer = 4 + total_bytes_per_entity *
(int)ents.size(); // hopefully, below 2B; if more, we have a big problem ...
ParallelComm::Buffer* buffer = new ParallelComm::Buffer( size_buffer );
buffer->reset_ptr( sizeof( int ) );
for( size_t i = 0; i < tag_handles.size(); i++ )
{
// copy tag data to buffer->buff_ptr, and send the buffer (we could have used
// regular char arrays)
rval = mb->tag_get_data( tag_handles[i], ents, (void*)( buffer->buff_ptr ) );MB_CHK_ERR( rval );
// advance the butter
buffer->buff_ptr += vect_bytes_per_tag[i] * ents.size();
}
*( (int*)buffer->mem_ptr ) = size_buffer;
// int size_pack = buffer->get_current_size(); // debug check
ierr = MPI_Isend( buffer->mem_ptr, size_buffer, MPI_CHAR, receiver_proc, 222, jcomm,
&sendReqs[indexReq] ); // we have to use global communicator
if( ierr != 0 ) return MB_FAILURE;
indexReq++;
localSendBuffs.push_back( buffer ); // we will release them after nonblocking sends are completed
}
}
else if( graph_type == COVERAGE )
{
// we know that we will need to send some tag data in a specific order
// first, get the ids of the local elements, from owned Range; arrange the buffer in order
// of increasing global id
Tag gidTag = mb->globalId_tag();
std::vector< int > gids;
gids.resize( owned.size() );
rval = mb->tag_get_data( gidTag, owned, &gids[0] );MB_CHK_ERR( rval );
std::map< int, EntityHandle > gidToHandle;
size_t i = 0;
for( Range::iterator it = owned.begin(); it != owned.end(); it++ )
{
EntityHandle eh = *it;
gidToHandle[gids[i++]] = eh;
}
// now, pack the data and send it
sendReqs.resize( involved_IDs_map.size() );
for( std::map< int, std::vector< int > >::iterator mit = involved_IDs_map.begin();
mit != involved_IDs_map.end(); mit++ )
{
int receiver_proc = mit->first;
std::vector< int >& eids = mit->second;
int size_buffer = 4 + total_bytes_per_entity *
(int)eids.size(); // hopefully, below 2B; if more, we have a big problem ...
ParallelComm::Buffer* buffer = new ParallelComm::Buffer( size_buffer );
buffer->reset_ptr( sizeof( int ) );
#ifdef VERBOSE
std::ofstream dbfile;
std::stringstream outf;
outf << "from_" << rankInJoin << "_send_to_" << receiver_proc << ".txt";
dbfile.open( outf.str().c_str() );
dbfile << "from " << rankInJoin << " send to " << receiver_proc << "\n";
#endif
// copy tag data to buffer->buff_ptr, and send the buffer (we could have used regular
// char arrays) pack data by tag, to be consistent with above, even though we loop
// through the entities for each tag
for( std::vector< int >::iterator it = eids.begin(); it != eids.end(); it++ )
{
int eID = *it;
EntityHandle eh = gidToHandle[eID];
for( i = 0; i < tag_handles.size(); i++ )
{
rval = mb->tag_get_data( tag_handles[i], &eh, 1, (void*)( buffer->buff_ptr ) );
if( rval != MB_SUCCESS )
{
delete buffer; // free parallel comm buffer first
MB_SET_ERR( rval, "Tag get data failed" );
}
#ifdef VERBOSE
dbfile << "global ID " << eID << " local handle " << mb->id_from_handle( eh ) << " vals: ";
double* vals = (double*)( buffer->buff_ptr );
for( int kk = 0; kk < tag_sizes[i]; kk++ )
{
dbfile << " " << *vals;
vals++;
}
dbfile << "\n";
#endif
buffer->buff_ptr += vect_bytes_per_tag[i];
}
}
#ifdef VERBOSE
dbfile.close();
#endif
*( (int*)buffer->mem_ptr ) = size_buffer;
// int size_pack = buffer->get_current_size(); // debug check
ierr = MPI_Isend( buffer->mem_ptr, size_buffer, MPI_CHAR, receiver_proc, 222, jcomm,
&sendReqs[indexReq] ); // we have to use global communicator
if( ierr != 0 ) return MB_FAILURE;
indexReq++;
localSendBuffs.push_back( buffer ); // we will release them after nonblocking sends are completed
}
}
else if( graph_type == DOF_BASED )
{
// need to fill up the buffer, in the order desired, send it
// get all the tags, for all owned entities, and pack the buffers accordingly
// we do not want to get the tags by entity, it may be too expensive
std::vector< std::vector< double > > valuesTags;
valuesTags.resize( tag_handles.size() );
for( size_t i = 0; i < tag_handles.size(); i++ )
{
int bytes_per_tag;
rval = mb->tag_get_bytes( tag_handles[i], bytes_per_tag );MB_CHK_ERR( rval );
valuesTags[i].resize( owned.size() * bytes_per_tag / sizeof( double ) );
// fill the whole array, we will pick up from here
rval = mb->tag_get_data( tag_handles[i], owned, (void*)( &( valuesTags[i][0] ) ) );MB_CHK_ERR( rval );
}
// now, pack the data and send it
sendReqs.resize( involved_IDs_map.size() );
for( std::map< int, std::vector< int > >::iterator mit = involved_IDs_map.begin();
mit != involved_IDs_map.end(); mit++ )
{
int receiver_proc = mit->first;
std::vector< int >& eids = mit->second;
std::vector< int >& index_in_values = map_index[receiver_proc];
std::vector< int >& index_ptr = map_ptr[receiver_proc]; // this is eids.size()+1;
int size_buffer = 4 + total_bytes_per_entity *
(int)eids.size(); // hopefully, below 2B; if more, we have a big problem ...
ParallelComm::Buffer* buffer = new ParallelComm::Buffer( size_buffer );
buffer->reset_ptr( sizeof( int ) );
#ifdef VERBOSE
std::ofstream dbfile;
std::stringstream outf;
outf << "from_" << rankInJoin << "_send_to_" << receiver_proc << ".txt";
dbfile.open( outf.str().c_str() );
dbfile << "from " << rankInJoin << " send to " << receiver_proc << "\n";
#endif
// copy tag data to buffer->buff_ptr, and send the buffer
// pack data by tag, to be consistent with above
int j = 0;
for( std::vector< int >::iterator it = eids.begin(); it != eids.end(); it++, j++ )
{
int index_in_v = index_in_values[index_ptr[j]];
for( size_t i = 0; i < tag_handles.size(); i++ )
{
// right now, move just doubles; but it could be any type of tag
*( (double*)( buffer->buff_ptr ) ) = valuesTags[i][index_in_v];
buffer->buff_ptr += 8; // we know we are working with doubles only !!!
}
};
*( (int*)buffer->mem_ptr ) = size_buffer;
// int size_pack = buffer->get_current_size(); // debug check
ierr = MPI_Isend( buffer->mem_ptr, size_buffer, MPI_CHAR, receiver_proc, 222, jcomm,
&sendReqs[indexReq] ); // we have to use global communicator
if( ierr != 0 ) return MB_FAILURE;
indexReq++;
localSendBuffs.push_back( buffer ); // we will release them after nonblocking sends are completed
}
}
return MB_SUCCESS;
}
| int moab::ParCommGraph::sender | ( | int | index | ) | [inline] |
Definition at line 143 of file ParCommGraph.hpp.
References senderTasks.
Referenced by receive_comm_graph().
{
return senderTasks[index];
}
| const std::vector< int >& moab::ParCommGraph::senders | ( | ) | [inline] |
Definition at line 209 of file ParCommGraph.hpp.
References senderTasks.
Referenced by pack_receivers_graph(), and send_graph_partition().
{
return senderTasks;
} // reference copy; refers to sender tasks in joint comm
| void moab::ParCommGraph::set_context_id | ( | int | other_id | ) | [inline] |
| void moab::ParCommGraph::set_cover_set | ( | EntityHandle | cover | ) | [inline] |
| ErrorCode moab::ParCommGraph::set_split_ranges | ( | int | comp, |
| TupleList & | TLBackToComp1, | ||
| std::vector< int > & | valuesComp1, | ||
| int | lenTag, | ||
| Range & | ents_of_interest, | ||
| int | type | ||
| ) |
Definition at line 1293 of file ParCommGraph.cpp.
References moab::TupleList::get_n(), MB_SUCCESS, rootSender, moab::Range::size(), split_ranges, and moab::TupleList::vi_wr.
{
// settle split_ranges // same role as partitioning
if( rootSender ) std::cout << " find split_ranges on component " << comp << " according to read map \n";
// Vector to store element
// with respective present index
int n = TLBackToComp1.get_n();
// third_method = true; // do not rely only on involved_IDs_map.size(); this can be 0 in some
// cases
std::map< int, std::set< int > > uniqueIDs;
for( int i = 0; i < n; i++ )
{
int to_proc = TLBackToComp1.vi_wr[3 * i + 2];
int globalId = TLBackToComp1.vi_wr[3 * i + 1];
uniqueIDs[to_proc].insert( globalId );
}
for( int i = 0; i < (int)ents_of_interest.size(); i++ )
{
EntityHandle ent = ents_of_interest[i];
for( int j = 0; j < lenTag; j++ )
{
int marker = valuesComp1[i * lenTag + j];
for( auto mit = uniqueIDs.begin(); mit != uniqueIDs.end(); mit++ )
{
int proc = mit->first;
std::set< int >& setIds = mit->second;
if( setIds.find( marker ) != setIds.end() )
{
split_ranges[proc].insert( ent );
}
}
}
}
return MB_SUCCESS;
}
| void moab::ParCommGraph::SetReceivingAfterCoverage | ( | std::map< int, std::set< int > > & | idsFromProcs | ) |
Definition at line 1051 of file ParCommGraph.cpp.
References COVERAGE, graph_type, and involved_IDs_map.
{
for( std::map< int, std::set< int > >::iterator mt = idsFromProcs.begin(); mt != idsFromProcs.end(); mt++ )
{
int fromProc = mt->first;
std::set< int >& setIds = mt->second;
involved_IDs_map[fromProc].resize( setIds.size() );
std::vector< int >& listIDs = involved_IDs_map[fromProc];
size_t indx = 0;
for( std::set< int >::iterator st = setIds.begin(); st != setIds.end(); st++ )
{
int valueID = *st;
listIDs[indx++] = valueID;
}
}
graph_type = COVERAGE;
return;
}
| void moab::ParCommGraph::settle_comm_by_ids | ( | int | comp, |
| TupleList & | TLBackToComp, | ||
| std::vector< int > & | valuesComp | ||
| ) |
Definition at line 1071 of file ParCommGraph.cpp.
References DOF_BASED, moab::GeomUtil::first(), moab::TupleList::get_n(), graph_type, involved_IDs_map, map_index, map_ptr, rankInJoin, rootReceiver, rootSender, and moab::TupleList::vi_wr.
{
// settle comm graph on comp
if( rootSender || rootReceiver ) std::cout << " settle comm graph by id on component " << comp << "\n";
int n = TLBackToComp.get_n();
// third_method = true; // do not rely only on involved_IDs_map.size(); this can be 0 in some
// cases
std::map< int, std::set< int > > uniqueIDs;
for( int i = 0; i < n; i++ )
{
int to_proc = TLBackToComp.vi_wr[3 * i + 2];
int globalId = TLBackToComp.vi_wr[3 * i + 1];
uniqueIDs[to_proc].insert( globalId );
}
// Vector to store element
// with respective present index
std::vector< std::pair< int, int > > vp;
vp.reserve( valuesComp.size() );
// Inserting element in pair vector
// to keep track of previous indexes in valuesComp
for( int i = 0; i < (int)valuesComp.size(); ++i )
{
vp.push_back( std::make_pair( valuesComp[i], i ) );
}
// Sorting pair vector
sort( vp.begin(), vp.end() );
// vp[i].first, second
// count now how many times some value appears in ordered (so in valuesComp)
for( std::map< int, std::set< int > >::iterator it = uniqueIDs.begin(); it != uniqueIDs.end(); it++ )
{
int procId = it->first;
std::set< int >& nums = it->second;
std::vector< int >& indx = map_ptr[procId];
std::vector< int >& indices = map_index[procId];
indx.resize( nums.size() + 1 );
int indexInVp = 0;
int indexVal = 0;
indx[0] = 0; // start from 0
for( std::set< int >::iterator sst = nums.begin(); sst != nums.end(); sst++, indexVal++ )
{
int val = *sst;
involved_IDs_map[procId].push_back( val );
indx[indexVal + 1] = indx[indexVal];
while( ( indexInVp < (int)valuesComp.size() ) && ( vp[indexInVp].first <= val ) ) // should be equal !
{
if( vp[indexInVp].first == val )
{
indx[indexVal + 1]++;
indices.push_back( vp[indexInVp].second );
}
indexInVp++;
}
}
}
#ifdef VERBOSE
std::stringstream f1;
std::ofstream dbfile;
f1 << "Involve_" << comp << "_" << rankInJoin << ".txt";
dbfile.open( f1.str().c_str() );
for( std::map< int, std::vector< int > >::iterator mit = involved_IDs_map.begin(); mit != involved_IDs_map.end();
mit++ )
{
int corrTask = mit->first;
std::vector< int >& corrIds = mit->second;
std::vector< int >& indx = map_ptr[corrTask];
std::vector< int >& indices = map_index[corrTask];
dbfile << " towards proc " << corrTask << " \n";
for( int i = 0; i < (int)corrIds.size(); i++ )
{
dbfile << corrIds[i] << " [" << indx[i] << "," << indx[i + 1] << ") : ";
for( int j = indx[i]; j < indx[i + 1]; j++ )
dbfile << indices[j] << " ";
dbfile << "\n";
}
dbfile << " \n";
}
dbfile.close();
#endif
graph_type = DOF_BASED;
// now we need to fill back and forth information, needed to fill the arrays
// for example, from spectral to involved_IDs_map, in case we want to send data from
// spectral to phys
}
| ErrorCode moab::ParCommGraph::settle_send_graph | ( | TupleList & | TLcovIDs | ) |
Definition at line 1023 of file ParCommGraph.cpp.
References COVERAGE, moab::TupleList::get_n(), graph_type, involved_IDs_map, MB_SUCCESS, and moab::TupleList::vi_wr.
{
// fill involved_IDs_map with data
// will have "receiving proc" and global id of element
int n = TLcovIDs.get_n();
graph_type = COVERAGE; // do not rely only on involved_IDs_map.size(); this can be 0 in some cases
for( int i = 0; i < n; i++ )
{
int to_proc = TLcovIDs.vi_wr[2 * i];
int globalIdElem = TLcovIDs.vi_wr[2 * i + 1];
involved_IDs_map[to_proc].push_back( globalIdElem );
}
#ifdef VERBOSE
for( std::map< int, std::vector< int > >::iterator mit = involved_IDs_map.begin(); mit != involved_IDs_map.end();
mit++ )
{
std::cout << " towards task " << mit->first << " send: " << mit->second.size() << " cells " << std::endl;
for( size_t i = 0; i < mit->second.size(); i++ )
{
std::cout << " " << mit->second[i];
}
std::cout << std::endl;
}
#endif
return MB_SUCCESS;
}
| ErrorCode moab::ParCommGraph::split_owned_range | ( | int | sender_rank, |
| Range & | owned | ||
| ) |
Definition at line 215 of file ParCommGraph.cpp.
References moab::Range::begin(), moab::Range::insert(), MB_SUCCESS, receivers(), sender_graph, sender_sizes, senderTasks, split_ranges, and moab::subtract().
Referenced by send_mesh_parts().
{
int senderTask = senderTasks[sender_rank];
std::vector< int >& distribution = sender_sizes[senderTask];
std::vector< int >& receivers = sender_graph[senderTask];
if( distribution.size() != receivers.size() ) //
return MB_FAILURE;
Range current = owned; // get the full range first, then we will subtract stuff, for
// the following ranges
Range rleftover = current;
for( size_t k = 0; k < receivers.size(); k++ )
{
Range newr;
newr.insert( current.begin(), current.begin() + distribution[k] );
split_ranges[receivers[k]] = newr;
rleftover = subtract( current, newr );
current = rleftover;
}
return MB_SUCCESS;
}
| ErrorCode moab::ParCommGraph::split_owned_range | ( | Range & | owned | ) |
Definition at line 241 of file ParCommGraph.cpp.
References moab::Range::begin(), corr_sizes, corr_tasks, moab::Range::insert(), MB_SUCCESS, split_ranges, and moab::subtract().
{
if( corr_tasks.size() != corr_sizes.size() ) //
return MB_FAILURE;
Range current = owned; // get the full range first, then we will subtract stuff, for
// the following ranges
Range rleftover = current;
for( size_t k = 0; k < corr_tasks.size(); k++ )
{
Range newr;
newr.insert( current.begin(), current.begin() + corr_sizes[k] );
split_ranges[corr_tasks[k]] = newr;
rleftover = subtract( current, newr );
current = rleftover;
}
return MB_SUCCESS;
}
MPI_Comm moab::ParCommGraph::comm [private] |
Definition at line 266 of file ParCommGraph.hpp.
Referenced by ParCommGraph().
std::vector< int > moab::ParCommGraph::comm_graph [private] |
Definition at line 291 of file ParCommGraph.hpp.
Referenced by release_send_buffers(), and send_graph().
int moab::ParCommGraph::compid1 [private] |
Definition at line 273 of file ParCommGraph.hpp.
Referenced by get_component_id1(), ParCommGraph(), and send_graph_partition().
int moab::ParCommGraph::compid2 [private] |
Definition at line 273 of file ParCommGraph.hpp.
Referenced by get_component_id2(), ParCommGraph(), and send_graph_partition().
int moab::ParCommGraph::context_id [private] |
Definition at line 274 of file ParCommGraph.hpp.
Referenced by get_context_id(), ParCommGraph(), and set_context_id().
std::vector< int > moab::ParCommGraph::corr_sizes [private] |
Definition at line 309 of file ParCommGraph.hpp.
Referenced by receive_mesh(), send_mesh_parts(), and split_owned_range().
std::vector< int > moab::ParCommGraph::corr_tasks [private] |
Definition at line 307 of file ParCommGraph.hpp.
Referenced by receive_mesh(), send_mesh_parts(), and split_owned_range().
EntityHandle moab::ParCommGraph::cover_set [private] |
Definition at line 275 of file ParCommGraph.hpp.
Referenced by get_cover_set(), ParCommGraph(), and set_cover_set().
TypeGraph moab::ParCommGraph::graph_type [private] |
Definition at line 315 of file ParCommGraph.hpp.
Referenced by dump_comm_information(), ParCommGraph(), receive_tag_values(), send_tag_values(), SetReceivingAfterCoverage(), settle_comm_by_ids(), and settle_send_graph().
std::map< int, std::vector< int > > moab::ParCommGraph::involved_IDs_map [private] |
Definition at line 316 of file ParCommGraph.hpp.
Referenced by dump_comm_information(), receive_tag_values(), send_tag_values(), SetReceivingAfterCoverage(), settle_comm_by_ids(), and settle_send_graph().
int moab::ParCommGraph::joinSize [private] |
Definition at line 272 of file ParCommGraph.hpp.
Referenced by ParCommGraph().
std::vector< ParallelComm::Buffer* > moab::ParCommGraph::localSendBuffs [private] |
Definition at line 288 of file ParCommGraph.hpp.
Referenced by release_send_buffers(), send_mesh_parts(), and send_tag_values().
std::map< int, std::vector< int > > moab::ParCommGraph::map_index [private] |
Definition at line 319 of file ParCommGraph.hpp.
Referenced by receive_tag_values(), send_tag_values(), and settle_comm_by_ids().
std::map< int, std::vector< int > > moab::ParCommGraph::map_ptr [private] |
Definition at line 320 of file ParCommGraph.hpp.
Referenced by receive_tag_values(), send_tag_values(), and settle_comm_by_ids().
int moab::ParCommGraph::rankInGroup1 [private] |
Definition at line 271 of file ParCommGraph.hpp.
Referenced by dump_comm_information(), ParCommGraph(), and send_mesh_parts().
int moab::ParCommGraph::rankInGroup2 [private] |
Definition at line 271 of file ParCommGraph.hpp.
Referenced by dump_comm_information(), ParCommGraph(), and receive_mesh().
int moab::ParCommGraph::rankInJoin [private] |
Definition at line 272 of file ParCommGraph.hpp.
Referenced by dump_comm_information(), ParCommGraph(), receive_mesh(), receive_tag_values(), send_tag_values(), and settle_comm_by_ids().
std::vector< int > moab::ParCommGraph::receiverTasks [private] |
Definition at line 268 of file ParCommGraph.hpp.
Referenced by compute_partition(), compute_trivial_partition(), pack_receivers_graph(), ParCommGraph(), receiver(), and receivers().
std::map< int, std::vector< int > > moab::ParCommGraph::recv_graph [private] |
Definition at line 280 of file ParCommGraph.hpp.
Referenced by compute_trivial_partition(), pack_receivers_graph(), and send_graph_partition().
std::map< int, std::vector< int > > moab::ParCommGraph::recv_sizes [private] |
Definition at line 282 of file ParCommGraph.hpp.
Referenced by compute_trivial_partition().
bool moab::ParCommGraph::rootReceiver [private] |
Definition at line 270 of file ParCommGraph.hpp.
Referenced by is_root_receiver(), ParCommGraph(), receive_comm_graph(), and settle_comm_by_ids().
bool moab::ParCommGraph::rootSender [private] |
Definition at line 269 of file ParCommGraph.hpp.
Referenced by compute_partition(), is_root_sender(), ParCommGraph(), set_split_ranges(), and settle_comm_by_ids().
std::map< int, std::vector< int > > moab::ParCommGraph::sender_graph [private] |
Definition at line 284 of file ParCommGraph.hpp.
Referenced by compute_trivial_partition(), send_mesh_parts(), and split_owned_range().
std::map< int, std::vector< int > > moab::ParCommGraph::sender_sizes [private] |
Definition at line 286 of file ParCommGraph.hpp.
Referenced by compute_trivial_partition(), send_mesh_parts(), and split_owned_range().
std::vector< int > moab::ParCommGraph::senderTasks [private] |
Definition at line 267 of file ParCommGraph.hpp.
Referenced by compute_trivial_partition(), ParCommGraph(), send_graph_partition(), send_mesh_parts(), sender(), senders(), and split_owned_range().
std::vector< MPI_Request > moab::ParCommGraph::sendReqs [private] |
Definition at line 303 of file ParCommGraph.hpp.
Referenced by release_send_buffers(), send_graph(), send_mesh_parts(), and send_tag_values().
std::map< int, Range > moab::ParCommGraph::split_ranges [private] |
Definition at line 301 of file ParCommGraph.hpp.
Referenced by compute_partition(), dump_comm_information(), form_mesh_from_tuples(), form_tuples_to_migrate_mesh(), receive_mesh(), receive_tag_values(), send_graph_partition(), send_mesh_parts(), send_tag_values(), set_split_ranges(), and split_owned_range().
std::vector< char > moab::ParCommGraph::zBuff [private] |
Definition at line 296 of file ParCommGraph.hpp.
Referenced by release_send_buffers(), and send_graph().
1.7.6.1.
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