mbpart.cpp File Reference

#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 Documentation

PartType

typedef int PartType

Definition at line 18 of file mbpart.cpp.

Function Documentation

main()

int main	(	int	argc,
		char *	argv[]
	)

Definition at line 46 of file mbpart.cpp.

{
#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"
                 "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
    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
            MB_CHK_SET_ERR( MB_FAILURE, "Geometry will not be partitioned.\n" );
        }
        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, 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 );
        }
        else
        {
          MB_CHK_SET_ERR( MB_FAILURE, "Geometry will not be partitioned.\n" );
        }
 
        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;
}

References ProgOptions::addOpt(), ProgOptions::addRequiredArg(), BRIEF_DESC, moab::Core::create_meshset(), DEFAULT_TAGGEDSETS_TAG, DEFAULT_ZOLTAN_METHOD, dim, ErrorCode, moab::Core::get_coords(), moab::Core::get_entities_by_dimension(), moab::Core::get_entities_by_type_and_tag(), moab::Core::get_number_entities_by_dimension(), ProgOptions::getOpt(), ProgOptions::getReqArg(), moab::ReorderTool::handle_order_from_int_tag(), moab::ReorderTool::handle_order_from_sets_and_adj(), ZoltanPartitioner::include_closure(), input_file, ProgOptions::int_flag, moab::Core::load_file(), moab::Core::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, ProgOptions::parseCommandLine(), ZoltanPartitioner::partition_inferred_mesh(), MetisPartitioner::partition_mesh(), ZoltanPartitioner::partition_mesh_and_geometry(), print_time(), ProgOptions::printHelp(), moab::ReorderTool::reorder_entities(), moab::IntxUtils::ScaleToRadius(), PartitionerBase< T >::set_global_id_option(), moab::Range::size(), moab::Core::tag_delete(), moab::Core::tag_get_handle(), and moab::Core::write_file().

Variable Documentation

BRIEF_DESC

const char BRIEF_DESC[] = "Use Zoltan or Metis to partition MOAB meshes for use on parallel computers"

Definition at line 43 of file mbpart.cpp.

Referenced by main().

DEFAULT_TAGGEDSETS_TAG

std::string DEFAULT_TAGGEDSETS_TAG = "PARALLEL_PARTITION"

Definition at line 32 of file mbpart.cpp.

Referenced by main().

DEFAULT_ZOLTAN_METHOD

const char DEFAULT_ZOLTAN_METHOD[] = "RCB"

Definition at line 34 of file mbpart.cpp.

Referenced by main().

LONG_DESC

std::ostringstream LONG_DESC

Definition at line 44 of file mbpart.cpp.

Referenced by main().

METIS_DEFAULT_METHOD

const char METIS_DEFAULT_METHOD[] = "ML_KWAY"

Definition at line 40 of file mbpart.cpp.

Referenced by main().