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MOAB: Mesh Oriented datABase
(version 5.4.1)
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MOAB: Mesh Oriented datABase
(version 5.4.1)
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#include "moab/Core.hpp"#include "moab/ProgOptions.hpp"#include "moab/ReorderTool.hpp"#include <iostream>#include <sstream>#include <cmath>#include <cstdlib>#include <list>#include <ctime>#include "moab/IntxMesh/IntxUtils.hpp"
Include dependency graph for mbpart.cpp:Go to the source code of this file.
Typedefs | |
| typedef int | PartType |
Functions | |
| int | main (int argc, char *argv[]) |
Variables | |
| std::string | DEFAULT_TAGGEDSETS_TAG = "PARALLEL_PARTITION" |
| const char | DEFAULT_ZOLTAN_METHOD [] = "RCB" |
| const char | METIS_DEFAULT_METHOD [] = "ML_KWAY" |
| const char | BRIEF_DESC [] = "Use Zoltan or Metis to partition MOAB meshes for use on parallel computers" |
| std::ostringstream | LONG_DESC |
| typedef int PartType |
Definition at line 23 of file mbpart.cpp.
| int main | ( | int | argc, |
| char * | argv[] | ||
| ) |
Definition at line 51 of file mbpart.cpp.
References ProgOptions::addOpt(), BRIEF_DESC, moab::Interface::create_meshset(), DEFAULT_TAGGEDSETS_TAG, DEFAULT_ZOLTAN_METHOD, dim, ErrorCode, moab::Interface::get_coords(), moab::Interface::get_entities_by_dimension(), moab::Interface::get_entities_by_type_and_tag(), moab::Interface::get_number_entities_by_dimension(), moab::ReorderTool::handle_order_from_int_tag(), moab::ReorderTool::handle_order_from_sets_and_adj(), ZoltanPartitioner::include_closure(), input_file, ProgOptions::int_flag, moab::Interface::load_file(), moab::Interface::load_mesh(), LONG_DESC, mb, MB_CHK_ERR, MB_CHK_SET_ERR, MB_SET_ERR, MB_SUCCESS, MB_TYPE_INTEGER, MBENTITYSET, MESHSET_SET, METIS_DEFAULT_METHOD, ZoltanPartitioner::partition_inferred_mesh(), MetisPartitioner::partition_mesh(), ZoltanPartitioner::partition_mesh_and_geometry(), print_time(), moab::ReorderTool::reorder_entities(), moab::IntxUtils::ScaleToRadius(), PartitionerBase< T >::set_global_id_option(), moab::Range::size(), t, moab::Interface::tag_delete(), moab::Interface::tag_get_handle(), and moab::Interface::write_file().
{
#ifdef MOAB_HAVE_MPI
int err = MPI_Init( &argc, &argv );
if( err )
{
std::cerr << "MPI_Init failed. Aborting." << std::endl;
return 3;
}
#endif
Core moab;
Interface& mb = moab;
std::vector< int > set_l;
#ifdef MOAB_HAVE_ZOLTAN
bool moab_use_zoltan = false;
#endif
#ifdef MOAB_HAVE_METIS
bool moab_use_metis = false;
#endif
LONG_DESC << "This utility invokes the ZoltanPartitioner or MetisPartitioner component of MOAB/CGM "
"to partition a mesh/geometry."
<< std::endl
<< "If no partitioning method is specified, the defaults are: "
<< "for Zoltan=\"" << DEFAULT_ZOLTAN_METHOD << "\" and Metis=\"" << METIS_DEFAULT_METHOD << " method"
<< std::endl;
ProgOptions opts( LONG_DESC.str(), BRIEF_DESC );
int part_dim = 3;
opts.addOpt< int >( "dimension",
"Specify dimension of entities to partition."
" Default is largest in file.",
&part_dim, ProgOptions::int_flag );
std::string zoltan_method, parm_method, oct_method, metis_method;
#ifdef MOAB_HAVE_ZOLTAN
opts.addOpt< std::string >( "zoltan,z",
"(Zoltan) Specify Zoltan partition method. "
"One of RR, RCB, RIB, HFSC, PHG, or Hypergraph (PHG and Hypergraph "
"are synonymous).",
&zoltan_method );
#ifdef MOAB_HAVE_PARMETIS
opts.addOpt< std::string >( "parmetis,p", "(Zoltan+PARMetis) Specify PARMetis partition method.", &parm_method );
#endif // MOAB_HAVE_PARMETIS
opts.addOpt< std::string >( "octpart,o", "(Zoltan) Specify OctPart partition method.", &oct_method );
bool incl_closure = false;
opts.addOpt< void >( "include_closure,c", "Include element closure for part sets.", &incl_closure );
bool recompute_box_rcb = false;
opts.addOpt< void >( "recompute_rcb_box,b", "recompute box in rcb cuts", &recompute_box_rcb );
#endif // MOAB_HAVE_ZOLTAN
double imbal_tol = 1.03;
opts.addOpt< double >( "imbalance,i", "Imbalance tolerance (used in PHG/Hypergraph method)", &imbal_tol );
#ifdef MOAB_HAVE_METIS
opts.addOpt< std::string >( "metis,m", "(Metis) Specify Metis partition method. One of ML_RB or ML_KWAY.",
&metis_method );
#endif // MOAB_HAVE_METIS
bool write_sets = true, write_tags = false;
opts.addOpt< void >( "sets,s", "Write partition as tagged sets (Default)", &write_sets );
opts.addOpt< void >( "tags,t", "Write partition by tagging entities", &write_tags );
int power = -1;
opts.addOpt< int >( "power,M", "Generate multiple partitions, in powers of 2, up to 2^(pow)", &power );
bool reorder = false;
opts.addOpt< void >( "reorder,R", "Reorder mesh to group entities by partition", &reorder );
double part_geom_mesh_size = -1.0;
#ifdef MOAB_HAVE_ZOLTAN
bool part_surf = false;
#ifdef MOAB_HAVE_CGM
opts.addOpt< double >( "geom,g", "(CGM) If partition geometry, specify mesh size.", &part_geom_mesh_size );
opts.addOpt< void >( "surf,f", "(CGM) Specify if partition geometry surface.", &part_surf );
#endif // MOAB_HAVE_CGM
bool ghost = false;
opts.addOpt< void >( "ghost,H", "(Zoltan) Specify if partition ghost geometry body." );
int obj_weight = 0;
opts.addOpt< int >( "vertex_w,v", "(Zoltan) Number of weights associated with a graph vertex." );
int edge_weight = 0;
opts.addOpt< int >( "edge_w,e", "(Zoltan) Number of weights associated with an edge." );
bool moab_partition_slave = false;
std::string slave_file_name = "";
opts.addOpt< std::string >( "inferred",
"(Zoltan) Specify inferred slave mesh file name to impose "
"partition based on cuts computed for original master mesh.",
&slave_file_name );
bool rescale_spherical_radius = false;
opts.addOpt< void >( "scale_sphere",
"(Zoltan) If the meshes are defined on a sphere, rescale radius as needed "
"(in combination with --inferred)",
&rescale_spherical_radius );
#endif // MOAB_HAVE_ZOLTAN
long num_parts;
opts.addOpt< std::vector< int > >( "set_l,l",
"Load material set(s) with specified ids (comma separated) for partition" );
opts.addRequiredArg< int >( "#parts", "Number of parts in partition" );
std::string input_file, output_file;
opts.addRequiredArg< std::string >( "input_file", "Mesh/geometry to partition", &input_file );
opts.addRequiredArg< std::string >( "output_file", "File to which to write partitioned mesh/geometry",
&output_file );
bool print_time = false;
opts.addOpt< void >( ",T", "Print CPU time for each phase.", &print_time );
int projection_type = 0;
opts.addOpt< int >( "project_on_sphere,p",
"use spherical coordinates (1) or gnomonic projection (2) for partitioning ",
&projection_type );
#ifdef MOAB_HAVE_METIS
bool partition_tagged_sets = false;
opts.addOpt< void >( "taggedsets,x", "(Metis) Partition tagged sets.", &partition_tagged_sets );
bool partition_tagged_ents = false;
opts.addOpt< void >( "taggedents,y", "(Metis) Partition tagged ents.", &partition_tagged_ents );
std::string aggregating_tag;
opts.addOpt< std::string >( "aggregatingtag,a",
"(Metis) Specify aggregating tag to partion tagged sets or tagged entities.",
&aggregating_tag );
std::string aggregating_bc_tag;
opts.addOpt< std::string >( "aggregatingBCtag,B",
"(Metis) Specify boundary id tag name used to group cells with same boundary ids.",
&aggregating_bc_tag );
std::string boundaryIds;
std::vector< int > BCids;
opts.addOpt< std::string >( "aggregatingBCids,I",
" (Metis) Specify id or ids of boundaries to be aggregated before "
"partitioning (all elements with same boundary id will be in the "
"same partition). Comma separated e.g. -I 1,2,5 ",
&boundaryIds );
#endif // MOAB_HAVE_METIS
bool assign_global_ids = false;
opts.addOpt< void >( "globalIds,j", "Assign GLOBAL_ID tag to entities", &assign_global_ids );
opts.parseCommandLine( argc, argv );
#ifdef MOAB_HAVE_ZOLTAN
if( !zoltan_method.empty() )
moab_use_zoltan = true;
else
#endif
#ifdef MOAB_HAVE_METIS
if( !metis_method.empty() )
moab_use_metis = true;
else
#endif
MB_SET_ERR( MB_FAILURE, "Specify either Zoltan or Metis partitioner type" );
#ifdef MOAB_HAVE_ZOLTAN
ZoltanPartitioner* zoltan_tool = NULL;
// check if partition geometry, if it is, should get mesh size for the geometry
if( part_geom_mesh_size != -1.0 && part_geom_mesh_size <= 0.0 )
{
std::cerr << part_geom_mesh_size << ": invalid geometry partition mesh size." << std::endl << std::endl;
opts.printHelp();
return EXIT_FAILURE;
}
if( slave_file_name.size() ) moab_partition_slave = true;
if( moab_use_zoltan )
{
if( part_geom_mesh_size < 0. )
{
// partition mesh we have no ParallelComm here, so we will create one later
zoltan_tool = new ZoltanPartitioner( &mb, NULL, false, argc, argv );
}
else
{
// partition geometry
#ifdef MOAB_HAVE_CGM
CubitStatus status = InitCGMA::initialize_cgma();
if( CUBIT_SUCCESS != status )
{
std::cerr << "CGM couldn't be initialized." << std::endl << std::endl;
opts.printHelp();
return EXIT_FAILURE;
}
GeometryQueryTool* gti = GeometryQueryTool::instance();
// no ParallelComm so far
zoltan_tool = new ZoltanPartitioner( &mb, NULL, false, argc, argv, gti );
#else
std::cerr << "CGM should be configured to partition geometry." << std::endl << std::endl;
opts.printHelp();
return EXIT_FAILURE;
#endif // MOAB_HAVE_CGM
}
zoltan_tool->set_global_id_option( assign_global_ids );
}
if( zoltan_method.empty() && parm_method.empty() && oct_method.empty() ) zoltan_method = DEFAULT_ZOLTAN_METHOD;
if( !parm_method.empty() ) zoltan_method = ZOLTAN_PARMETIS_METHOD;
if( !oct_method.empty() ) zoltan_method = ZOLTAN_OCTPART_METHOD;
#endif // MOAB_HAVE_ZOLTAN
#ifdef MOAB_HAVE_METIS
MetisPartitioner* metis_tool = NULL;
if( moab_use_metis && !metis_tool )
{
metis_tool = new MetisPartitioner( &mb, false );
metis_tool->set_global_id_option( assign_global_ids );
}
if( ( aggregating_tag.empty() && partition_tagged_sets ) || ( aggregating_tag.empty() && partition_tagged_ents ) )
aggregating_tag = DEFAULT_TAGGEDSETS_TAG;
if( !write_sets && !write_tags ) write_sets = true;
if( !boundaryIds.empty() )
{
std::vector< std::string > ids;
std::stringstream ss( boundaryIds );
std::string item;
while( std::getline( ss, item, ',' ) )
{
ids.push_back( item );
}
for( unsigned int i = 0; i < ids.size(); i++ )
BCids.push_back( std::atoi( ids[i].c_str() ) );
}
if( metis_method.empty() )
{
metis_method = METIS_DEFAULT_METHOD;
}
#endif // MOAB_HAVE_METIS
if( !write_sets && !write_tags ) write_sets = true;
if( -1 == power )
{
num_parts = opts.getReqArg< int >( "#parts" );
power = 1;
}
else if( power < 1 || power > 18 )
{
std::cerr << power << ": invalid power for multiple partitions. Expected value in [1,18]" << std::endl
<< std::endl;
opts.printHelp();
return EXIT_FAILURE;
}
else
{
num_parts = 2;
}
if( part_dim < 0 || part_dim > 3 )
{
std::cerr << part_dim << " : invalid dimension" << std::endl << std::endl;
opts.printHelp();
return EXIT_FAILURE;
}
if( imbal_tol < 0.0 )
{
std::cerr << imbal_tol << ": invalid imbalance tolerance" << std::endl << std::endl;
opts.printHelp();
return EXIT_FAILURE;
}
bool load_msets = false;
if( opts.getOpt( "set_l,l", &set_l ) )
{
load_msets = true;
if( set_l.size() <= 0 )
{
std::cerr << " No material set id's to load" << std::endl << std::endl;
opts.printHelp();
return EXIT_FAILURE;
}
}
if( num_parts <= 1 )
{
std::cerr << "** Please specify #parts = " << num_parts << " to be greater than 1." << std::endl << std::endl;
opts.printHelp();
return EXIT_FAILURE;
}
clock_t t = clock();
const char* options = NULL;
ErrorCode rval;
#ifdef MOAB_HAVE_ZOLTAN
if( part_geom_mesh_size > 0. ) options = "FACET_DISTANCE_TOLERANCE=0.1";
#endif // MOAB_HAVE_ZOLTAN
std::cout << "Loading file " << input_file << "..." << std::endl;
if( load_msets == false )
{
rval = mb.load_file( input_file.c_str(), 0, options );MB_CHK_SET_ERR( rval, "Failed to load input file: " + input_file );
}
else // load the material set(s)
{
rval = mb.load_mesh( input_file.c_str(), &set_l[0], (int)set_l.size() );MB_CHK_SET_ERR( rval, "Failed to load input mesh: " + input_file );
}
if( print_time )
std::cout << "Read input file in " << ( clock() - t ) / (double)CLOCKS_PER_SEC << " seconds" << std::endl;
for( int dim = part_dim; dim >= 0; --dim )
{
int n;
rval = mb.get_number_entities_by_dimension( 0, dim, n );
if( MB_SUCCESS == rval && 0 != n )
{
part_dim = dim;
break;
}
}
if( part_dim < 0 )
{
std::cerr << input_file << " : file does not contain any mesh entities" << std::endl;
return 2;
}
ReorderTool reorder_tool( &moab );
for( int p = 0; p < power; p++ )
{
t = clock();
#ifdef MOAB_HAVE_ZOLTAN
if( moab_use_zoltan )
{
rval = zoltan_tool->partition_mesh_and_geometry(
part_geom_mesh_size, num_parts, zoltan_method.c_str(),
( !parm_method.empty() ? parm_method.c_str() : oct_method.c_str() ), imbal_tol, part_dim, write_sets,
write_tags, obj_weight, edge_weight, part_surf, ghost, projection_type, recompute_box_rcb, print_time );MB_CHK_SET_ERR( rval, "Zoltan partitioner failed." );
}
#endif
#ifdef MOAB_HAVE_METIS
if( moab_use_metis )
{
rval = metis_tool->partition_mesh( num_parts, metis_method.c_str(), part_dim, write_sets, write_tags,
partition_tagged_sets, partition_tagged_ents, aggregating_tag.c_str(),
print_time );MB_CHK_SET_ERR( rval, "Metis partitioner failed." );
}
#endif
if( print_time )
std::cout << "Generated " << num_parts << " part partitioning in "
<< ( clock() - t ) / (double)CLOCKS_PER_SEC << " seconds" << std::endl;
if( reorder && part_geom_mesh_size < 0. )
{
std::cout << "Reordering mesh for partition..." << std::endl;
Tag tag, order;
rval = mb.tag_get_handle( DEFAULT_TAGGEDSETS_TAG.c_str(), 1, MB_TYPE_INTEGER, tag );MB_CHK_SET_ERR( rval, "Partitioner did not create " + DEFAULT_TAGGEDSETS_TAG + " tag" );
t = clock();
if( write_sets )
{
Range sets;
mb.get_entities_by_type_and_tag( 0, MBENTITYSET, &tag, 0, 1, sets );
rval = reorder_tool.handle_order_from_sets_and_adj( sets, order );MB_CHK_SET_ERR( rval, "Failed to calculate reordering." );
}
else
{
rval = reorder_tool.handle_order_from_int_tag( tag, -1, order );MB_CHK_SET_ERR( rval, "Failed to calculate reordering." );
}
rval = reorder_tool.reorder_entities( order );MB_CHK_SET_ERR( rval, "Failed to perform reordering." );
rval = mb.tag_delete( order );MB_CHK_SET_ERR( rval, "Failed to delete tag." );
if( print_time )
std::cout << "Reordered mesh in " << ( clock() - t ) / (double)CLOCKS_PER_SEC << " seconds"
<< std::endl;
}
#ifdef MOAB_HAVE_ZOLTAN
if( incl_closure )
{
rval = zoltan_tool->include_closure();MB_CHK_SET_ERR( rval, "Closure inclusion failed." );
}
#endif
std::ostringstream tmp_output_file;
if( power > 1 )
{
// append num_parts to output filename
std::string::size_type idx = output_file.find_last_of( "." );
if( idx == std::string::npos )
{
tmp_output_file << output_file << "_" << num_parts;
if( part_geom_mesh_size < 0. )
tmp_output_file << ".h5m";
else
{
std::cerr << "output file type is not specified." << std::endl;
return 1;
}
}
else
{
tmp_output_file << output_file.substr( 0, idx ) << "_" << num_parts << output_file.substr( idx );
}
}
else
tmp_output_file << output_file;
t = clock();
std::cout << "Saving file to " << output_file << "..." << std::endl;
if( part_geom_mesh_size < 0. )
{
rval = mb.write_file( tmp_output_file.str().c_str() );MB_CHK_SET_ERR( rval, tmp_output_file.str() << " : failed to write file." << std::endl );
}
#ifdef MOAB_HAVE_ZOLTAN
#ifdef MOAB_HAVE_CGM
else
{
std::string::size_type idx = output_file.find_last_of( "." );
int c_size = output_file.length() - idx;
const char* file_type = NULL;
if( output_file.compare( idx, c_size, ".occ" ) == 0 || output_file.compare( idx, c_size, ".OCC" ) == 0 )
file_type = "OCC";
else if( output_file.compare( idx, c_size, ".sab" ) == 0 )
file_type = "ACIS_SAB";
else if( output_file.compare( idx, c_size, ".sat" ) == 0 )
file_type = "ACIS_SAT";
else
{
std::cerr << "File type for " << output_file.c_str() << " not supported." << std::endl;
return 1;
}
int num_ents_exported = 0;
DLIList< RefEntity* > ref_entity_list;
CubitStatus status =
CubitCompat_export_solid_model( ref_entity_list, tmp_output_file.str().c_str(), file_type,
num_ents_exported, CubitString( __FILE__ ) );
if( CUBIT_SUCCESS != status )
{
std::cerr << "CGM couldn't export models." << std::endl;
return 1;
}
}
#endif
#endif
if( print_time )
std::cout << "Wrote \"" << tmp_output_file.str() << "\" in " << ( clock() - t ) / (double)CLOCKS_PER_SEC
<< " seconds" << std::endl;
#ifdef MOAB_HAVE_ZOLTAN
if( moab_use_zoltan && moab_partition_slave && p == 0 )
{
t = clock();
double master_radius, slave_radius;
if( rescale_spherical_radius )
{
EntityHandle rootset = 0;
Range masterverts;
rval = mb.get_entities_by_dimension( rootset, 0, masterverts );MB_CHK_SET_ERR( rval, "Can't create vertices on master set" );
double points[6];
EntityHandle mfrontback[2] = { masterverts[0], masterverts[masterverts.size() - 1] };
rval = mb.get_coords( &mfrontback[0], 2, points );MB_CHK_ERR( rval );
const double mr1 = std::sqrt( points[0] * points[0] + points[1] * points[1] + points[2] * points[2] );
const double mr2 = std::sqrt( points[3] * points[3] + points[4] * points[4] + points[5] * points[5] );
master_radius = 0.5 * ( mr1 + mr2 );
}
EntityHandle slaveset;
rval = mb.create_meshset( moab::MESHSET_SET, slaveset );MB_CHK_SET_ERR( rval, "Can't create new set" );
rval = mb.load_file( slave_file_name.c_str(), &slaveset, options );MB_CHK_SET_ERR( rval, "Can't load slave mesh" );
if( rescale_spherical_radius )
{
double points[6];
Range slaveverts;
rval = mb.get_entities_by_dimension( slaveset, 0, slaveverts );MB_CHK_SET_ERR( rval, "Can't create vertices on master set" );
EntityHandle sfrontback[2] = { slaveverts[0], slaveverts[slaveverts.size() - 1] };
rval = mb.get_coords( &sfrontback[0], 2, points );MB_CHK_ERR( rval );
const double sr1 = std::sqrt( points[0] * points[0] + points[1] * points[1] + points[2] * points[2] );
const double sr2 = std::sqrt( points[3] * points[3] + points[4] * points[4] + points[5] * points[5] );
slave_radius = 0.5 * ( sr1 + sr2 );
// Let us rescale both master and slave meshes to a unit sphere
rval = moab::IntxUtils::ScaleToRadius( &mb, slaveset, master_radius );MB_CHK_ERR( rval );
}
rval = zoltan_tool->partition_inferred_mesh( slaveset, num_parts, part_dim, write_sets, projection_type );MB_CHK_ERR( rval );
if( rescale_spherical_radius )
{
// rescale the slave mesh back to its original radius
rval = moab::IntxUtils::ScaleToRadius( &mb, slaveset, slave_radius );MB_CHK_ERR( rval );
}
if( print_time )
{
std::cout << "Time taken to infer slave mesh partitions = " << ( clock() - t ) / (double)CLOCKS_PER_SEC
<< " seconds" << std::endl;
}
size_t lastindex = slave_file_name.find_last_of( "." );
std::string inferred_output_file = slave_file_name.substr( 0, lastindex ) + "_inferred" +
slave_file_name.substr( lastindex, slave_file_name.size() );
// Save the resulting mesh
std::cout << "Saving inferred file to " << inferred_output_file << "..." << std::endl;
rval = mb.write_file( inferred_output_file.c_str(), 0, 0, &slaveset, 1 );MB_CHK_SET_ERR( rval, inferred_output_file << " : failed to write file." << std::endl );
}
#endif
num_parts *= 2;
}
#ifdef MOAB_HAVE_ZOLTAN
delete zoltan_tool;
#endif
#ifdef MOAB_HAVE_METIS
delete metis_tool;
#endif
#ifdef MOAB_HAVE_MPI
err = MPI_Finalize();
assert( MPI_SUCCESS == err );
#endif
return 0;
}
| const char BRIEF_DESC[] = "Use Zoltan or Metis to partition MOAB meshes for use on parallel computers" |
Definition at line 48 of file mbpart.cpp.
| std::string DEFAULT_TAGGEDSETS_TAG = "PARALLEL_PARTITION" |
Definition at line 37 of file mbpart.cpp.
Referenced by main().
| const char DEFAULT_ZOLTAN_METHOD[] = "RCB" |
Definition at line 39 of file mbpart.cpp.
Referenced by main().
| std::ostringstream LONG_DESC |
Definition at line 49 of file mbpart.cpp.
| const char METIS_DEFAULT_METHOD[] = "ML_KWAY" |
Definition at line 45 of file mbpart.cpp.
Referenced by main().
1.7.6.1