mbslavepart.cpp

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//
// Usage:
// tools/mbslavepart -d 2 -m mpas/x1.2562.grid.h5m -s mpas/x1.10242.grid.h5m -o mpas_slave.h5m -e
// 1e-8 -b 1e-6 -O
//
#include <iostream>
#include <exception>
#include <cmath>
#include <vector>
#include <string>
 
#include "moab/ProgOptions.hpp"
#include "moab/Core.hpp"
#include "moab/AdaptiveKDTree.hpp"
#include "moab/BVHTree.hpp"
 
#include "moab/IntxMesh/IntxUtils.hpp"
 
#ifdef MOAB_HAVE_MPI
#include "moab_mpi.h"
#include "moab/ParallelComm.hpp"
#include "MBParallelConventions.h"
#endif
 
using namespace moab;
 
// A function to get the non-default value from a std::map
template < typename K, typename V >
static V get_map_value( const std::map< K, V >& m, const K& key, const V& defval )
{
 typename std::map< K, V >::const_iterator it = m.find( key );
 if( it == m.end() )
 {
 return defval;
 }
 else
 {
 return it->second;
 }
}
 
int main( int argc, char* argv[] )
{
 int nprocs = 1, dimension = 3;
#ifdef MOAB_HAVE_MPI
 int proc_id = 0;
 MPI_Init( &argc, &argv );
 MPI_Comm_rank( MPI_COMM_WORLD, &proc_id );
 MPI_Comm_size( MPI_COMM_WORLD, &nprocs );
#endif
 
 int defaultpart = 0;
 double tolerance = 1e-2, treetolerance = 1e-13, btolerance = 1e-4;
 std::string masterfile, slavefile, outfile( "slavemesh.h5m" );
 bool keepsparts = false;
 bool use_spherical = false;
 ProgOptions opts;
 
 opts.addOpt< std::string >( "master,m", "Master mesh filename", &masterfile );
 opts.addOpt< std::string >( "slave,s", "Slave mesh filename", &slavefile );
 opts.addOpt< std::string >( "output,o", "Output partitioned mesh filename", &outfile );
 opts.addOpt< int >( "dim,d", "Dimension of entities to use for partitioning", &dimension );
 opts.addOpt< int >( "defaultpart,p", "Default partition number if target element is not found on source grid",
 &defaultpart );
 opts.addOpt< double >( "eps,e", "Tolerance for the point search", &tolerance );
 opts.addOpt< double >( "beps,b", "Tolerance for the bounding box search", &btolerance );
 opts.addOpt< void >( "keep,K",
 "Keep the existing partitions in the slave mesh (use PARALLEL_PARTITION_SLAVE instead)",
 &keepsparts );
 opts.addOpt< void >( "spherical", "Hint that the meshes are defined on a spherical surface (Climate problems)",
 &use_spherical );
 opts.parseCommandLine( argc, argv );
 
 if( masterfile.empty() || slavefile.empty() )
 {
 opts.printHelp();
#ifdef MOAB_HAVE_MPI
 MPI_Finalize();
#endif
 exit( 1 );
 }
 
 ErrorCode error;
 Core* mbCore = new Core();
 
 // Set the read options for parallel file loading
 const std::string partition_set_name = "PARALLEL_PARTITION";
 const std::string global_id_name = "GLOBAL_ID";
 std::vector< std::string > read_opts, write_opts;
 std::string read_options( "" ), write_options( "" );
 
 if( nprocs > 1 )
 {
 read_options = "PARALLEL=READ_PART;PARTITION=" + partition_set_name + ";PARALLEL_RESOLVE_SHARED_ENTS";
 write_options = "PARALLEL=WRITE_PART";
 }
 
 EntityHandle masterfileset, slavefileset;
 error = mbCore->create_meshset( moab::MESHSET_TRACK_OWNER | moab::MESHSET_SET, masterfileset );MB_CHK_ERR( error );
 error = mbCore->create_meshset( moab::MESHSET_TRACK_OWNER | moab::MESHSET_SET, slavefileset );MB_CHK_ERR( error );
 
 // Load file
 error = mbCore->load_file( masterfile.c_str(), &masterfileset, read_options.c_str() );MB_CHK_ERR( error );
 error = mbCore->load_file( slavefile.c_str(), &slavefileset, read_options.c_str() );MB_CHK_ERR( error );
 // if (error != MB_SUCCESS && size > 1)
 // {
 // std::string newread_options = "PARALLEL=BCAST_DELETE;PARALLEL_RESOLVE_SHARED_ENTS";
 // error = mbCore->load_file(slavefile.c_str(), &slavefileset, newread_options.c_str());
 // }
 // else MB_CHK_ERR(error);
 
 Tag gidtag = 0, parttag = 0, sparttag = 0;
 int dum_id = -1;
 error = mbCore->tag_get_handle( partition_set_name.c_str(), 1, MB_TYPE_INTEGER, parttag,
 MB_TAG_SPARSE | MB_TAG_CREAT, &dum_id );MB_CHK_ERR( error );
 gidtag = mbCore->globalId_tag();
 if( keepsparts )
 {
 error = mbCore->tag_get_handle( std::string( partition_set_name + "_SLAVE" ).c_str(), 1, MB_TYPE_INTEGER,
 sparttag, MB_TAG_CREAT | MB_TAG_SPARSE, &dum_id );MB_CHK_ERR( error );
 }
 
 Range melems, msets, selems, ssets;
 
 // Get the partition sets on the master mesh
 std::map< int, int > mpartvals;
 error = mbCore->get_entities_by_type_and_tag( masterfileset, MBENTITYSET, &parttag, NULL, 1, msets,
 moab::Interface::UNION, true );MB_CHK_ERR( error );
 if( msets.size() == 0 )
 {
 std::cout << "No partition sets found in the master mesh. Quitting..." << std::endl;
 exit( 1 );
 }
 
 for( unsigned i = 0; i < msets.size(); ++i )
 {
 EntityHandle mset = msets[i];
 
 moab::Range msetelems;
 error = mbCore->get_entities_by_dimension( mset, dimension, msetelems );MB_CHK_ERR( error );
 melems.merge( msetelems );
 
 int partID;
 error = mbCore->tag_get_data( parttag, &mset, 1, &partID );MB_CHK_ERR( error );
 
 // Get the global ID and use that as the indicator
 std::vector< int > gidMelems( msetelems.size() );
 error = mbCore->tag_get_data( gidtag, msetelems, gidMelems.data() );MB_CHK_ERR( error );
 
 for( unsigned j = 0; j < msetelems.size(); ++j )
 mpartvals[gidMelems[j]] = partID;
 // mpartvals[msetelems[j]]=partID;
#ifdef VERBOSE
 std::cout << "Part " << partID << " has " << msetelems.size() << " elements." << std::endl;
#endif
 }
 
 // Get information about the slave file set
 error = mbCore->get_entities_by_type_and_tag( slavefileset, MBENTITYSET, &parttag, NULL, 1, ssets,
 moab::Interface::UNION );MB_CHK_ERR( error );
 // TODO: expand and add other dimensional elements
 error = mbCore->get_entities_by_dimension( slavefileset, dimension, selems );MB_CHK_ERR( error );
 
 std::cout << "Master (elements, parts) : (" << melems.size() << ", " << msets.size()
 << "), Slave (elements, parts) : (" << selems.size() << ", " << ssets.size() << ")" << std::endl;
 
 double master_radius = 1.0, slave_radius = 1.0;
 std::vector< double > mastercoords;
 Range masterverts, slaveverts;
 {
 error = mbCore->get_entities_by_dimension( masterfileset, 0, masterverts );MB_CHK_ERR( error );
 error = mbCore->get_entities_by_dimension( slavefileset, 0, slaveverts );MB_CHK_ERR( error );
 }
 if( use_spherical )
 {
 double points[6];
 EntityHandle mfrontback[2] = { masterverts[0], masterverts[masterverts.size() - 1] };
 error = mbCore->get_coords( &mfrontback[0], 2, points );MB_CHK_ERR( error );
 master_radius = 0.5 * ( std::sqrt( points[0] * points[0] + points[1] * points[1] + points[2] * points[2] ) +
 std::sqrt( points[3] * points[3] + points[4] * points[4] + points[5] * points[5] ) );
 EntityHandle sfrontback[2] = { slaveverts[0], slaveverts[slaveverts.size() - 1] };
 error = mbCore->get_coords( &sfrontback[0], 2, points );MB_CHK_ERR( error );
 slave_radius = 0.5 * ( std::sqrt( points[0] * points[0] + points[1] * points[1] + points[2] * points[2] ) +
 std::sqrt( points[3] * points[3] + points[4] * points[4] + points[5] * points[5] ) );
 // Let us rescale both master and slave meshes to a unit sphere
 error = moab::IntxUtils::ScaleToRadius( mbCore, masterfileset, 1.0 );MB_CHK_ERR( error );
 error = moab::IntxUtils::ScaleToRadius( mbCore, slavefileset, 1.0 );MB_CHK_ERR( error );
 }
 
 try
 {
 std::map< int, moab::Range > spartvals;
 int npoints_notfound = 0;
 {
 FileOptions fopts( ( use_spherical ? "SPHERICAL" : "" ) );
 moab::EntityHandle tree_root = masterfileset;
 
 moab::AdaptiveKDTree tree( mbCore );
 error = tree.build_tree( melems, &tree_root, &fopts );
 
 // moab::BVHTree tree(mbCore);
 // error = tree.build_tree(melems, &tree_root);MB_CHK_ERR(error);
 
 for( size_t ie = 0; ie < selems.size(); ie++ )
 {
 moab::EntityHandle selem, leaf;
 double point[3];
 selem = selems[ie];
 
 // Get the element centroid to be queried
 error = mbCore->get_coords( &selem, 1, point );MB_CHK_ERR( error );
 
 std::vector< moab::EntityHandle > leaf_elems;
 
 // Search for the closest source element in the master mesh corresponding
 // to the target element centroid in the slave mesh
 error = tree.point_search( point, leaf, treetolerance, btolerance );MB_CHK_ERR( error );
 
 // We only care about the dimension that the user specified.
 // MOAB partitions are ordered by elements anyway.
 error = mbCore->get_entities_by_dimension( leaf, dimension, leaf_elems, true );MB_CHK_ERR( error );
 
 if( leaf != 0 && leaf_elems.size() )
 {
 
 // Now get the master element centroids so that we can compute
 // the minimum distance to the target point
 std::vector< double > centroids( leaf_elems.size() * 3 );
 error = mbCore->get_coords( &leaf_elems[0], leaf_elems.size(), &centroids[0] );MB_CHK_ERR( error );
 
 if( !leaf_elems.size() )
 std::cout << ie << ": "
 << " No leaf elements found." << std::endl;
 // else std::cout << ie << " found " << leaf_elems.size() << " leaves for
 // current point " << std::endl;
 
 double dist = 1e10;
 int pinelem = -1;
 for( size_t il = 0; il < leaf_elems.size(); ++il )
 {
 const double* centroid = &centroids[il * 3];
 const double locdist = std::pow( point[0] - centroid[0], 2 ) +
 std::pow( point[1] - centroid[1], 2 ) +
 std::pow( point[2] - centroid[2], 2 );
 if( locdist < dist && locdist < 1.0E-2 )
 {
 dist = locdist;
 pinelem = il;
 
#ifdef VERBOSE
 int gidMelem;
 error = mbCore->tag_get_data( gidtag, &leaf_elems[il], 1, &gidMelem );MB_CHK_ERR( error );
 std::cout << "\t Trial leaf " << il << " set " << gidMelem
 << " and part = " << get_map_value( mpartvals, gidMelem, -1 )
 << " with distance = " << locdist << std::endl;
#endif
 }
 }
 
 if( pinelem < 0 )
 {
#ifdef VERBOSE
 std::cout << ie
 << ": [Error] - Could not find a minimum distance within the "
 "leaf nodes."
 << std::endl;
#endif
 npoints_notfound++;
 spartvals[defaultpart].insert( selems[ie] );
 }
 else
 {
 int gidMelem;
 error = mbCore->tag_get_data( gidtag, &leaf_elems[pinelem], 1, &gidMelem );MB_CHK_ERR( error );
 
 int mpartid = get_map_value( mpartvals, gidMelem, -1 );
 if( mpartid < 0 )
 std::cout << "[WARNING]: Part number for element " << leaf_elems[pinelem]
 << " with global ID = " << gidMelem << " not found.\n";
 
#ifdef VERBOSE
 std::cout << "Adding element " << ie << " set " << mpartid << " with distance = " << dist
 << std::endl;
#endif
 spartvals[mpartid].insert( selems[ie] );
 }
 }
 else
 {
#ifdef VERBOSE
 std::cout << "[WARNING]: Adding element " << ie << " to default (part) set " << defaultpart
 << std::endl;
#endif
 spartvals[defaultpart].insert( selems[ie] );
 }
 }
 error = tree.reset_tree();MB_CHK_ERR( error );
 }
 if( npoints_notfound )
 std::cout << "Could not find " << npoints_notfound
 << " points in the master mesh. Added to defaultpart set = " << defaultpart << std::endl;
 
 if( use_spherical )
 {
 error = moab::IntxUtils::ScaleToRadius( mbCore, slavefileset, slave_radius );MB_CHK_ERR( error );
 }
 
 error = mbCore->delete_entities( &masterfileset, 1 );MB_CHK_ERR( error );
 // Find parallel partition sets in the slave mesh - and delete it since we are going to
 // overwrite the sets
 if( !keepsparts )
 {
 std::cout << "Deleting " << ssets.size() << " sets in the slave mesh" << std::endl;
 error = mbCore->remove_entities( slavefileset, ssets );MB_CHK_ERR( error );
 ssets.clear();
 }
 
 size_t ntotslave_elems = 0, ntotslave_parts = 0;
 for( std::map< int, moab::Range >::iterator it = spartvals.begin(); it != spartvals.end(); ++it )
 {
 int partID = it->first;
 moab::EntityHandle pset;
 error = mbCore->create_meshset( moab::MESHSET_SET, pset );MB_CHK_ERR( error );
 error = mbCore->add_entities( pset, it->second );MB_CHK_ERR( error );
 error = mbCore->add_parent_child( slavefileset, pset );MB_CHK_ERR( error );
 
#ifdef VERBOSE
 std::cout << "Slave Part " << partID << " has " << it->second.size() << " elements." << std::endl;
#endif
 ntotslave_elems += it->second.size();
 ntotslave_parts++;
 
 if( keepsparts )
 {
 error = mbCore->tag_set_data( sparttag, &pset, 1, &partID );MB_CHK_ERR( error );
 }
 else
 {
 error = mbCore->tag_set_data( parttag, &pset, 1, &partID );MB_CHK_ERR( error );
 }
 }
 std::cout << "Slave mesh: given " << selems.size() << " elements, and assigned " << ntotslave_elems
 << " elements to " << ntotslave_parts << " parts.\n";
 assert( ntotslave_elems == selems.size() );
 
 // mbCore->print_database();
 
 // Write the re-partitioned slave mesh to disk
 if( nprocs == 1 )
 {
 error = mbCore->write_file( "slavemesh.vtk", "VTK", NULL, &slavefileset, 1 );MB_CHK_ERR( error );
 }
 error = mbCore->write_file( outfile.c_str(), NULL, write_options.c_str(), &slavefileset, 1 );MB_CHK_ERR( error );
 // error = mbCore->write_file(outfile.c_str(), NULL,
 // write_options.c_str());MB_CHK_ERR(error);
 }
 catch( std::exception& e )
 {
 std::cout << " exception caught during tree initialization " << e.what() << std::endl;
 }
 delete mbCore;
 
#ifdef MOAB_HAVE_MPI
 MPI_Finalize();
#endif
 exit( 0 );
}