moab::ReadParallel Class Reference

#include <ReadParallel.hpp>

Collaboration diagram for moab::ReadParallel:

Public Types
enum	ParallelActions {   PA_READ = 0 , PA_READ_PART = 1 , PA_BROADCAST = 2 , PA_DELETE_NONLOCAL = 3 ,   PA_CHECK_GIDS_SERIAL = 4 , PA_GET_FILESET_ENTS = 5 , PA_RESOLVE_SHARED_ENTS = 6 , PA_EXCHANGE_GHOSTS = 7 ,   PA_RESOLVE_SHARED_SETS = 8 , PA_AUGMENT_SETS_WITH_GHOSTS = 9 , PA_PRINT_PARALLEL = 10 , PA_CREATE_TRIVIAL_PARTITION = 11 ,   PA_CORRECT_THIN_GHOSTS = 12 }
enum	ParallelOpts {   POPT_NONE = 0 , POPT_BCAST , POPT_BCAST_DELETE , POPT_READ_DELETE ,   POPT_READ_PART , POPT_DEFAULT }

Public Member Functions
ErrorCode	load_file (const char *file_name, const EntityHandle *file_set, const FileOptions &opts, const ReaderIface::SubsetList *subset_list=0, const Tag *file_id_tag=0)
	load a file More...
ErrorCode	load_file (const char **file_names, const int num_files, const EntityHandle *file_set, const FileOptions &opts, const ReaderIface::SubsetList *subset_list=0, const Tag *file_id_tag=0)
	load multiple files More...
ErrorCode	load_file (const char **file_names, const int num_files, const EntityHandle *file_set, int parallel_mode, std::string &partition_tag_name, std::vector< int > &partition_tag_vals, bool distrib, bool partition_by_rank, std::vector< int > &pa_vec, const FileOptions &opts, const ReaderIface::SubsetList *subset_list, const Tag *file_id_tag, const int reader_rank, const bool cputime, const int resolve_dim, const int shared_dim, const int ghost_dim, const int bridge_dim, const int num_layers, const int addl_ents)
	ReadParallel (Interface *impl=NULL, ParallelComm *pc=NULL)
	Constructor. More...
virtual	~ReadParallel ()
	Destructor. More...
ErrorCode	delete_nonlocal_entities (std::string &ptag_name, std::vector< int > &ptag_vals, bool distribute, EntityHandle file_set)
	PUBLIC TO ALLOW TESTING. More...
ErrorCode	delete_nonlocal_entities (EntityHandle file_set)

Static Public Member Functions
static ReaderIface *	factory (Interface *)

Static Public Attributes
static const char *	parallelOptsNames [] = { "NONE", "BCAST", "BCAST_DELETE", "READ_DELETE", "READ_PART", "", 0 }
static const char *	ParallelActionsNames []

Protected Member Functions
ErrorCode	create_partition_sets (std::string &ptag_name, EntityHandle file_set)

Private Attributes
Interface *	mbImpl
ParallelComm *	myPcomm
DebugOutput	myDebug
Error *	mError

Detailed Description

Definition at line 17 of file ReadParallel.hpp.

Member Enumeration Documentation

ParallelActions

enum moab::ReadParallel::ParallelActions

Enumerator
PA_READ
PA_READ_PART
PA_BROADCAST
PA_DELETE_NONLOCAL
PA_CHECK_GIDS_SERIAL
PA_GET_FILESET_ENTS
PA_RESOLVE_SHARED_ENTS
PA_EXCHANGE_GHOSTS
PA_RESOLVE_SHARED_SETS
PA_AUGMENT_SETS_WITH_GHOSTS
PA_PRINT_PARALLEL
PA_CREATE_TRIVIAL_PARTITION
PA_CORRECT_THIN_GHOSTS

Definition at line 66 of file ReadParallel.hpp.

 {
 PA_READ = 0,
 PA_READ_PART = 1,
 PA_BROADCAST = 2,
 PA_DELETE_NONLOCAL = 3,
 PA_CHECK_GIDS_SERIAL = 4,
 PA_GET_FILESET_ENTS = 5,
 PA_RESOLVE_SHARED_ENTS = 6,
 PA_EXCHANGE_GHOSTS = 7,
 PA_RESOLVE_SHARED_SETS = 8,
 PA_AUGMENT_SETS_WITH_GHOSTS = 9,
 PA_PRINT_PARALLEL = 10,
 PA_CREATE_TRIVIAL_PARTITION = 11,
 PA_CORRECT_THIN_GHOSTS = 12
 };

ParallelOpts

enum moab::ReadParallel::ParallelOpts

Enumerator
POPT_NONE
POPT_BCAST
POPT_BCAST_DELETE
POPT_READ_DELETE
POPT_READ_PART
POPT_DEFAULT

Definition at line 85 of file ReadParallel.hpp.

 {
 POPT_NONE = 0,
 POPT_BCAST,
 POPT_BCAST_DELETE,
 POPT_READ_DELETE,
 POPT_READ_PART,
 POPT_DEFAULT
 };

Constructor & Destructor Documentation

ReadParallel()

moab::ReadParallel::ReadParallel	(	Interface *	impl = NULL,
		ParallelComm *	pc = NULL
	)

Constructor.

Definition at line 39 of file ReadParallel.cpp.

 : mbImpl( impl ), myPcomm( pc ), myDebug( "ReadPara", std::cerr )
{
 if( !myPcomm )
 {
 myPcomm = ParallelComm::get_pcomm( mbImpl, 0 );
 if( NULL == myPcomm ) myPcomm = new ParallelComm( mbImpl, MPI_COMM_WORLD );
 }
 myDebug.set_rank( myPcomm->proc_config().proc_rank() );
 if( debug ) // For backwards compatibility, enable all debug output if constant is true
 myDebug.set_verbosity( 10 );
 
 impl->query_interface( mError );
}

References moab::debug, moab::ParallelComm::get_pcomm(), mbImpl, mError, myDebug, myPcomm, moab::ParallelComm::proc_config(), moab::ProcConfig::proc_rank(), moab::Interface::query_interface(), moab::DebugOutput::set_rank(), and moab::DebugOutput::set_verbosity().

~ReadParallel()

virtual moab::ReadParallel::~ReadParallel ( )

inlinevirtual

Destructor.

Definition at line 62 of file ReadParallel.hpp.

{}

Member Function Documentation

create_partition_sets()

ErrorCode moab::ReadParallel::create_partition_sets ( std::string &  ptag_name, EntityHandle  file_set  )

protected

Definition at line 720 of file ReadParallel.cpp.

{
 int proc_rk = myPcomm->proc_config().proc_rank();
 ErrorCode result = MB_SUCCESS;
 
 Tag ptag;
 
 // Tag the partition sets with a standard tag name
 if( ptag_name.empty() ) ptag_name = PARALLEL_PARTITION_TAG_NAME;
 bool tag_created = false;
 result = mbImpl->tag_get_handle( ptag_name.c_str(), 1, MB_TYPE_INTEGER, ptag, MB_TAG_SPARSE | MB_TAG_CREAT, 0,
 &tag_created );MB_CHK_SET_ERR( result, "Trouble getting PARALLEL_PARTITION tag" );
 
 if( !tag_created )
 {
 // This tag already exists; better check to see that tagged sets
 // agree with this partition
 Range tagged_sets;
 int* proc_rk_ptr = &proc_rk;
 result = mbImpl->get_entities_by_type_and_tag( file_set, MBENTITYSET, &ptag, (const void* const*)&proc_rk_ptr,
 1, tagged_sets );MB_CHK_SET_ERR( result, "Trouble getting tagged sets" );
 if( !tagged_sets.empty() && tagged_sets != myPcomm->partition_sets() )
 {
 result = mbImpl->tag_delete_data( ptag, tagged_sets );MB_CHK_SET_ERR( result, "Trouble deleting data of PARALLEL_PARTITION tag" );
 }
 else if( tagged_sets == myPcomm->partition_sets() )
 return MB_SUCCESS;
 }
 
 // If we get here, we need to assign the tag
 std::vector< int > values( myPcomm->partition_sets().size() );
 for( unsigned int i = 0; i < myPcomm->partition_sets().size(); i++ )
 values[i] = proc_rk;
 result = mbImpl->tag_set_data( ptag, myPcomm->partition_sets(), &values[0] );MB_CHK_SET_ERR( result, "Trouble setting data to PARALLEL_PARTITION tag" );
 
 return MB_SUCCESS;
}

References moab::Range::empty(), ErrorCode, moab::Interface::get_entities_by_type_and_tag(), MB_CHK_SET_ERR, MB_SUCCESS, MB_TAG_CREAT, MB_TAG_SPARSE, MB_TYPE_INTEGER, MBENTITYSET, mbImpl, myPcomm, PARALLEL_PARTITION_TAG_NAME, moab::ParallelComm::partition_sets(), moab::ParallelComm::proc_config(), moab::ProcConfig::proc_rank(), size, moab::Range::size(), moab::Interface::tag_delete_data(), moab::Interface::tag_get_handle(), and moab::Interface::tag_set_data().

Referenced by load_file().

delete_nonlocal_entities() [1/2]

ErrorCode moab::ReadParallel::delete_nonlocal_entities

(

EntityHandle

file_set

)

Definition at line 758 of file ReadParallel.cpp.

{
 // Get partition entities and ents related to/used by those
 // get ents in the partition
 ReadUtilIface* read_iface;
 mbImpl->query_interface( read_iface );
 Range partition_ents, all_sets;
 
 myDebug.tprint( 2, "Gathering related entities.\n" );
 
 ErrorCode result = read_iface->gather_related_ents( myPcomm->partition_sets(), partition_ents, &file_set );MB_CHK_SET_ERR( result, "Failure gathering related entities" );
 
 // Get pre-existing entities
 Range file_ents;
 result = mbImpl->get_entities_by_handle( file_set, file_ents );MB_CHK_SET_ERR( result, "Couldn't get pre-existing entities" );
 
 if( 0 == myPcomm->proc_config().proc_rank() )
 {
 myDebug.print( 2, "File entities: ", file_ents );
 }
 
 // Get deletable entities by subtracting partition ents from file ents
 Range deletable_ents = subtract( file_ents, partition_ents );
 
 // Cache deletable vs. keepable sets
 Range deletable_sets = deletable_ents.subset_by_type( MBENTITYSET );
 Range keepable_sets = subtract( file_ents.subset_by_type( MBENTITYSET ), deletable_sets );
 
 myDebug.tprint( 2, "Removing deletable entities from keepable sets.\n" );
 
 // Remove deletable ents from all keepable sets
 for( Range::iterator rit = keepable_sets.begin(); rit != keepable_sets.end(); ++rit )
 {
 result = mbImpl->remove_entities( *rit, deletable_ents );MB_CHK_SET_ERR( result, "Failure removing deletable entities" );
 }
 result = mbImpl->remove_entities( file_set, deletable_ents );MB_CHK_SET_ERR( result, "Failure removing deletable entities" );
 
 myDebug.tprint( 2, "Deleting deletable entities.\n" );
 
 if( 0 == myPcomm->proc_config().proc_rank() )
 {
 myDebug.print( 2, "Deletable sets: ", deletable_sets );
 }
 
 // Delete sets, then ents
 if( !deletable_sets.empty() )
 {
 result = mbImpl->delete_entities( deletable_sets );MB_CHK_SET_ERR( result, "Failure deleting sets in delete_nonlocal_entities" );
 }
 
 deletable_ents -= deletable_sets;
 
 if( 0 == myPcomm->proc_config().proc_rank() )
 {
 myDebug.print( 2, "Deletable entities: ", deletable_ents );
 }
 
 if( !deletable_ents.empty() )
 {
 result = mbImpl->delete_entities( deletable_ents );MB_CHK_SET_ERR( result, "Failure deleting entities in delete_nonlocal_entities" );
 }
 
 return MB_SUCCESS;
}

References moab::Range::begin(), moab::Interface::delete_entities(), moab::Range::empty(), moab::Range::end(), ErrorCode, moab::ReadUtilIface::gather_related_ents(), moab::Interface::get_entities_by_handle(), MB_CHK_SET_ERR, MB_SUCCESS, MBENTITYSET, mbImpl, myDebug, myPcomm, moab::ParallelComm::partition_sets(), moab::DebugOutput::print(), moab::ParallelComm::proc_config(), moab::ProcConfig::proc_rank(), moab::Interface::query_interface(), moab::Interface::remove_entities(), moab::Range::subset_by_type(), moab::subtract(), and moab::DebugOutput::tprint().

delete_nonlocal_entities() [2/2]

ErrorCode moab::ReadParallel::delete_nonlocal_entities	(	std::string &	ptag_name,
		std::vector< int > &	ptag_vals,
		bool	distribute,
		EntityHandle	file_set
	)

PUBLIC TO ALLOW TESTING.

Definition at line 654 of file ReadParallel.cpp.

{
 Range partition_sets;
 
 Tag ptag;
 ErrorCode result = mbImpl->tag_get_handle( ptag_name.c_str(), 1, MB_TYPE_INTEGER, ptag );MB_CHK_SET_ERR( result, "Failed getting tag handle in delete_nonlocal_entities" );
 
 result = mbImpl->get_entities_by_type_and_tag( file_set, MBENTITYSET, &ptag, NULL, 1, myPcomm->partition_sets() );MB_CHK_SET_ERR( result, "Failed to get sets with partition-type tag" );
 
 int proc_sz = myPcomm->proc_config().proc_size();
 int proc_rk = myPcomm->proc_config().proc_rank();
 
 if( !ptag_vals.empty() )
 {
 // Values input, get sets with those values
 Range tmp_sets;
 std::vector< int > tag_vals( myPcomm->partition_sets().size() );
 result = mbImpl->tag_get_data( ptag, myPcomm->partition_sets(), &tag_vals[0] );MB_CHK_SET_ERR( result, "Failed to get tag data for partition vals tag" );
 for( std::vector< int >::iterator pit = tag_vals.begin(); pit != tag_vals.end(); ++pit )
 {
 std::vector< int >::iterator pit2 = std::find( ptag_vals.begin(), ptag_vals.end(), *pit );
 if( pit2 != ptag_vals.end() ) tmp_sets.insert( myPcomm->partition_sets()[pit - tag_vals.begin()] );
 }
 
 myPcomm->partition_sets().swap( tmp_sets );
 }
 
 if( distribute )
 {
 // For now, require that number of partition sets be greater
 // than number of procs
 if( myPcomm->partition_sets().size() < (unsigned int)proc_sz )
 {
 MB_SET_ERR( MB_FAILURE, "Too few parts; P = " << proc_rk << ", tag = " << ptag
 << ", # sets = " << myPcomm->partition_sets().size() );
 }
 
 Range tmp_sets;
 // Distribute the partition sets
 unsigned int num_sets = myPcomm->partition_sets().size() / proc_sz;
 unsigned int num_leftover = myPcomm->partition_sets().size() % proc_sz;
 int begin_set = 0;
 if( proc_rk < (int)num_leftover )
 {
 num_sets++;
 begin_set = num_sets * proc_rk;
 }
 else
 begin_set = proc_rk * num_sets + num_leftover;
 
 for( unsigned int i = 0; i < num_sets; i++ )
 tmp_sets.insert( myPcomm->partition_sets()[begin_set + i] );
 
 myPcomm->partition_sets().swap( tmp_sets );
 }
 
 myDebug.print( 1, "My partition sets: ", myPcomm->partition_sets() );
 
 result = delete_nonlocal_entities( file_set );MB_CHK_ERR( result );
 
 return MB_SUCCESS;
}

References ErrorCode, moab::Interface::get_entities_by_type_and_tag(), moab::Range::insert(), MB_CHK_ERR, MB_CHK_SET_ERR, MB_SET_ERR, MB_SUCCESS, MB_TYPE_INTEGER, MBENTITYSET, mbImpl, myDebug, myPcomm, moab::ParallelComm::partition_sets(), moab::DebugOutput::print(), moab::ParallelComm::proc_config(), moab::ProcConfig::proc_rank(), moab::ProcConfig::proc_size(), moab::Range::size(), moab::Range::swap(), moab::Interface::tag_get_data(), and moab::Interface::tag_get_handle().

Referenced by load_file().

factory()

static ReaderIface* moab::ReadParallel::factory ( Interface *  )

static

load_file() [1/3]

ErrorCode moab::ReadParallel::load_file	(	const char **	file_names,
		const int	num_files,
		const EntityHandle *	file_set,
		const FileOptions &	opts,
		const ReaderIface::SubsetList *	subset_list = 0,
		const Tag *	file_id_tag = 0
	)

load multiple files

Definition at line 54 of file ReadParallel.cpp.

{
 int tmpval;
 if( MB_SUCCESS == opts.get_int_option( "DEBUG_PIO", 1, tmpval ) )
 {
 myDebug.set_verbosity( tmpval );
 myPcomm->set_debug_verbosity( tmpval );
 }
 myDebug.tprint( 1, "Setting up...\n" );
 
 // Get parallel settings
 int parallel_mode;
 ErrorCode result = opts.match_option( "PARALLEL", parallelOptsNames, parallel_mode );
 if( MB_FAILURE == result )
 {
 MB_SET_ERR( MB_FAILURE, "Unexpected value for 'PARALLEL' option" );
 }
 else if( MB_ENTITY_NOT_FOUND == result )
 {
 parallel_mode = 0;
 }
 
 // Get partition setting
 bool distrib;
 std::string partition_tag_name;
 result = opts.get_option( "PARTITION", partition_tag_name );
 if( MB_ENTITY_NOT_FOUND == result )
 {
 distrib = false;
 partition_tag_name = "";
 }
 else
 {
 distrib = true;
 if( partition_tag_name.empty() ) partition_tag_name = PARALLEL_PARTITION_TAG_NAME;
 
 // Also get deprecated PARTITION_DISTRIBUTE option
 // so that higher-level code doesn't return an error
 // due to an unrecognized option
 opts.get_null_option( "PARTITION_DISTRIBUTE" );
 }
 
 // Get partition tag value(s), if any, and whether they're to be
 // distributed or assigned
 std::vector< int > partition_tag_vals;
 opts.get_ints_option( "PARTITION_VAL", partition_tag_vals );
 
 // see if partition tag name is "TRIVIAL", if the tag exists
 bool create_trivial_partition = false;
 if( partition_tag_name == std::string( "TRIVIAL" ) )
 {
 Tag ttag; // see if the trivial tag exists
 result = mbImpl->tag_get_handle( partition_tag_name.c_str(), ttag );
 if( MB_TAG_NOT_FOUND == result ) create_trivial_partition = true;
 }
 // See if we need to report times
 bool cputime = false;
 result = opts.get_null_option( "CPUTIME" );
 if( MB_SUCCESS == result ) cputime = true;
 
 // See if we need to report times
 bool print_parallel = false;
 result = opts.get_null_option( "PRINT_PARALLEL" );
 if( MB_SUCCESS == result ) print_parallel = true;
 
 // Get ghosting options
 std::string ghost_str;
 int bridge_dim, ghost_dim = -1, num_layers, addl_ents = 0;
 result = opts.get_str_option( "PARALLEL_GHOSTS", ghost_str );
 if( MB_TYPE_OUT_OF_RANGE == result )
 {
 ghost_dim = 3;
 bridge_dim = 0;
 num_layers = 1;
 }
 else if( MB_SUCCESS == result )
 {
 int num_fields = sscanf( ghost_str.c_str(), "%d.%d.%d.%d", &ghost_dim, &bridge_dim, &num_layers, &addl_ents );
 if( 3 > num_fields )
 {
 MB_SET_ERR( MB_FAILURE, "Didn't read 3 fields from PARALLEL_GHOSTS string" );
 }
 }
 
 // Get resolve_shared_ents option
 std::string shared_str;
 int resolve_dim = -2, shared_dim = -1;
 result = opts.get_str_option( "PARALLEL_RESOLVE_SHARED_ENTS", shared_str );
 if( MB_TYPE_OUT_OF_RANGE == result )
 {
 resolve_dim = -1;
 shared_dim = -1;
 }
 else if( MB_SUCCESS == result )
 {
 int num_fields = sscanf( shared_str.c_str(), "%d.%d", &resolve_dim, &shared_dim );
 if( 2 != num_fields )
 {
 MB_SET_ERR( MB_FAILURE, "Didn't read 2 fields from PARALLEL_RESOLVE_SHARED_ENTS string" );
 }
 }
 
 // Get skip augmenting with ghosts option
 bool skip_augment = false;
 result = opts.get_null_option( "SKIP_AUGMENT_WITH_GHOSTS" );
 if( MB_SUCCESS == result ) skip_augment = true;
 
 bool correct_thin_ghosts = false;
 result = opts.get_null_option( "PARALLEL_THIN_GHOST_LAYER" );
 if( MB_SUCCESS == result ) correct_thin_ghosts = true;
 
 // Get MPI IO processor rank
 int reader_rank;
 result = opts.get_int_option( "MPI_IO_RANK", reader_rank );
 if( MB_ENTITY_NOT_FOUND == result )
 reader_rank = 0;
 else if( MB_SUCCESS != result )
 {
 MB_SET_ERR( MB_FAILURE, "Unexpected value for 'MPI_IO_RANK' option" );
 }
 
 // Now that we've parsed all the parallel options, make an instruction queue
 std::vector< int > pa_vec;
 bool is_reader = ( reader_rank == (int)myPcomm->proc_config().proc_rank() );
 
 bool partition_by_rank = false;
 if( MB_SUCCESS == opts.get_null_option( "PARTITION_BY_RANK" ) )
 {
 partition_by_rank = true;
 if( !partition_tag_vals.empty() )
 {
 MB_SET_ERR( MB_FAILURE, "Cannot specify both PARTITION_VALS and PARTITION_BY_RANK" );
 }
 }
 
 double factor_seq;
 if( MB_SUCCESS == opts.get_real_option( "PARALLEL_SEQUENCE_FACTOR", factor_seq ) )
 {
 if( factor_seq < 1. ) MB_SET_ERR( MB_FAILURE, "cannot have sequence factor less than 1." );
 mbImpl->set_sequence_multiplier( factor_seq );
 }
 switch( parallel_mode )
 {
 case POPT_BCAST:
 myDebug.print( 1, "Read mode is BCAST\n" );
 if( is_reader )
 {
 pa_vec.push_back( PA_READ );
 pa_vec.push_back( PA_CHECK_GIDS_SERIAL );
 pa_vec.push_back( PA_GET_FILESET_ENTS );
 }
 pa_vec.push_back( PA_BROADCAST );
 if( !is_reader ) pa_vec.push_back( PA_GET_FILESET_ENTS );
 break;
 
 case POPT_BCAST_DELETE:
 myDebug.print( 1, "Read mode is BCAST_DELETE\n" );
 if( is_reader )
 {
 pa_vec.push_back( PA_READ );
 pa_vec.push_back( PA_CHECK_GIDS_SERIAL );
 pa_vec.push_back( PA_GET_FILESET_ENTS );
 if( create_trivial_partition ) pa_vec.push_back( PA_CREATE_TRIVIAL_PARTITION );
 }
 pa_vec.push_back( PA_BROADCAST );
 if( !is_reader ) pa_vec.push_back( PA_GET_FILESET_ENTS );
 pa_vec.push_back( PA_DELETE_NONLOCAL );
 break;
 
 case POPT_DEFAULT:
 case POPT_READ_DELETE:
 myDebug.print( 1, "Read mode is READ_DELETE\n" );
 pa_vec.push_back( PA_READ );
 pa_vec.push_back( PA_CHECK_GIDS_SERIAL );
 pa_vec.push_back( PA_GET_FILESET_ENTS );
 pa_vec.push_back( PA_DELETE_NONLOCAL );
 break;
 
 case POPT_READ_PART:
 myDebug.print( 1, "Read mode is READ_PART\n" );
 pa_vec.push_back( PA_READ_PART );
 break;
 
 default:
 MB_SET_ERR( MB_FAILURE, "Unexpected parallel read mode" );
 }
 
 if( -2 != resolve_dim ) pa_vec.push_back( PA_RESOLVE_SHARED_ENTS );
 
 if( -1 != ghost_dim ) pa_vec.push_back( PA_EXCHANGE_GHOSTS );
 
 if( -2 != resolve_dim )
 {
 pa_vec.push_back( PA_RESOLVE_SHARED_SETS );
 if( -1 != ghost_dim && !skip_augment ) pa_vec.push_back( PA_AUGMENT_SETS_WITH_GHOSTS );
 if( -1 != ghost_dim && correct_thin_ghosts ) pa_vec.push_back( PA_CORRECT_THIN_GHOSTS );
 }
 
 if( print_parallel ) pa_vec.push_back( PA_PRINT_PARALLEL );
 
 result = load_file( file_names, num_files, file_set, parallel_mode, partition_tag_name, partition_tag_vals, distrib,
 partition_by_rank, pa_vec, opts, subset_list, file_id_tag, reader_rank, cputime, resolve_dim,
 shared_dim, ghost_dim, bridge_dim, num_layers, addl_ents );MB_CHK_ERR( result );
 
 if( parallel_mode == POPT_BCAST_DELETE && !is_reader ) opts.mark_all_seen();
 
 return MB_SUCCESS;
}

References ErrorCode, moab::FileOptions::get_int_option(), moab::FileOptions::get_ints_option(), moab::FileOptions::get_null_option(), moab::FileOptions::get_option(), moab::FileOptions::get_real_option(), moab::FileOptions::get_str_option(), load_file(), moab::FileOptions::mark_all_seen(), moab::FileOptions::match_option(), MB_CHK_ERR, MB_ENTITY_NOT_FOUND, MB_SET_ERR, MB_SUCCESS, MB_TAG_NOT_FOUND, MB_TYPE_OUT_OF_RANGE, mbImpl, myDebug, myPcomm, PA_AUGMENT_SETS_WITH_GHOSTS, PA_BROADCAST, PA_CHECK_GIDS_SERIAL, PA_CORRECT_THIN_GHOSTS, PA_CREATE_TRIVIAL_PARTITION, PA_DELETE_NONLOCAL, PA_EXCHANGE_GHOSTS, PA_GET_FILESET_ENTS, PA_PRINT_PARALLEL, PA_READ, PA_READ_PART, PA_RESOLVE_SHARED_ENTS, PA_RESOLVE_SHARED_SETS, PARALLEL_PARTITION_TAG_NAME, parallelOptsNames, POPT_BCAST, POPT_BCAST_DELETE, POPT_DEFAULT, POPT_READ_DELETE, POPT_READ_PART, moab::DebugOutput::print(), moab::ParallelComm::proc_config(), moab::ProcConfig::proc_rank(), moab::ParallelComm::set_debug_verbosity(), moab::Interface::set_sequence_multiplier(), moab::DebugOutput::set_verbosity(), moab::Interface::tag_get_handle(), and moab::DebugOutput::tprint().

load_file() [2/3]

ErrorCode moab::ReadParallel::load_file	(	const char **	file_names,
		const int	num_files,
		const EntityHandle *	file_set,
		int	parallel_mode,
		std::string &	partition_tag_name,
		std::vector< int > &	partition_tag_vals,
		bool	distrib,
		bool	partition_by_rank,
		std::vector< int > &	pa_vec,
		const FileOptions &	opts,
		const ReaderIface::SubsetList *	subset_list,
		const Tag *	file_id_tag,
		const int	reader_rank,
		const bool	cputime,
		const int	resolve_dim,
		const int	shared_dim,
		const int	ghost_dim,
		const int	bridge_dim,
		const int	num_layers,
		const int	addl_ents
	)

Definition at line 268 of file ReadParallel.cpp.

{
 ErrorCode result = MB_SUCCESS;
 if( myPcomm == NULL ) myPcomm = new ParallelComm( mbImpl, MPI_COMM_WORLD );
 
 Range entities;
 Tag file_set_tag = 0;
 int other_sets = 0;
 ReaderWriterSet::iterator iter;
 Range other_file_sets, file_sets;
 Core* impl = dynamic_cast< Core* >( mbImpl );
 
 std::vector< double > act_times( pa_vec.size() + 1 );
 std::vector< int >::iterator vit;
 int i, j;
 act_times[0] = MPI_Wtime();
 
 // Make a new set for the parallel read
 EntityHandle file_set;
 if( !file_set_ptr || !( *file_set_ptr ) )
 {
 result = mbImpl->create_meshset( MESHSET_SET, file_set );MB_CHK_SET_ERR( result, "Trouble creating file set" );
 }
 else
 file_set = *file_set_ptr;
 
 bool i_read = false;
 Tag id_tag = 0;
 bool use_id_tag = false;
 Range ents;
 
 for( i = 1, vit = pa_vec.begin(); vit != pa_vec.end(); ++vit, i++ )
 {
 ErrorCode tmp_result = MB_SUCCESS;
 switch( *vit )
 {
 //==================
 case PA_READ:
 i_read = true;
 
 for( j = 0; j < num_files; j++ )
 {
 myDebug.tprintf( 1, "Reading file: \"%s\"\n", file_names[j] );
 
 EntityHandle new_file_set;
 result = mbImpl->create_meshset( MESHSET_SET, new_file_set );MB_CHK_SET_ERR( result, "Trouble creating file set" );
 tmp_result = impl->serial_load_file( file_names[j], &new_file_set, opts, subset_list, file_id_tag );
 if( MB_SUCCESS != tmp_result ) break;
 
 // Put the contents of each file set for the reader into the
 // file set for the parallel read
 assert( 0 != new_file_set );
 Range all_ents;
 tmp_result = mbImpl->get_entities_by_handle( new_file_set, all_ents );
 if( MB_SUCCESS != tmp_result ) break;
 all_ents.insert( new_file_set );
 tmp_result = mbImpl->add_entities( file_set, all_ents );
 if( MB_SUCCESS != tmp_result ) break;
 }
 if( MB_SUCCESS != tmp_result ) break;
 
 // Mark the file set for this parallel reader
 tmp_result = mbImpl->tag_get_handle( "__file_set", 1, MB_TYPE_INTEGER, file_set_tag,
 MB_TAG_SPARSE | MB_TAG_CREAT );
 if( MB_SUCCESS != tmp_result ) break;
 
 tmp_result = mbImpl->tag_set_data( file_set_tag, &file_set, 1, &other_sets );
 break;
 
 //==================
 case PA_READ_PART: {
 myDebug.tprintf( 1, "Reading file: \"%s\"\n", file_names[0] );
 
 i_read = true;
 if( num_files != 1 )
 {
 MB_SET_ERR( MB_NOT_IMPLEMENTED, "Multiple file read not supported for READ_PART" );
 }
 
 // If we're going to resolve shared entities, then we need
 // to ask the file reader to populate a tag with unique ids
 // (typically file ids/indices/whatever.)
 if( std::find( pa_vec.begin(), pa_vec.end(), PA_RESOLVE_SHARED_ENTS ) != pa_vec.end() )
 {
 use_id_tag = true;
 if( !file_id_tag )
 {
 // This tag is really used for resolving shared entities with crystal router
 // In the end, this is an identifier that gets converted to long
 // In hdf5 file reader, we also convert from hdf5 file id type to long
 tmp_result = mbImpl->tag_get_handle( "", sizeof( long ), MB_TYPE_OPAQUE, id_tag,
 MB_TAG_DENSE | MB_TAG_CREAT );
 if( MB_SUCCESS != tmp_result ) break;
 file_id_tag = &id_tag;
 }
 }
 
 ReaderIface::IDTag parts = { partition_tag_name.c_str(), 0, 0 };
 ReaderIface::SubsetList sl;
 sl.num_parts = 0;
 int rank = myPcomm->rank();
 if( partition_by_rank )
 {
 assert( partition_tag_vals.empty() );
 parts.tag_values = &rank;
 parts.num_tag_values = 1;
 }
 else
 {
 sl.num_parts = myPcomm->size();
 sl.part_number = myPcomm->rank();
 if( !partition_tag_vals.empty() )
 {
 parts.tag_values = &partition_tag_vals[0];
 parts.num_tag_values = partition_tag_vals.size();
 }
 }
 std::vector< ReaderIface::IDTag > subset;
 if( subset_list )
 {
 std::vector< ReaderIface::IDTag > tmplist( subset_list->tag_list,
 subset_list->tag_list + subset_list->tag_list_length );
 tmplist.push_back( parts );
 subset.swap( tmplist );
 sl.tag_list = &subset[0];
 sl.tag_list_length = subset.size();
 }
 else
 {
 sl.tag_list = &parts;
 sl.tag_list_length = 1;
 }
 tmp_result = impl->serial_load_file( *file_names, &file_set, opts, &sl, file_id_tag );
 if( MB_SUCCESS != tmp_result ) break;
 
 if( !partition_tag_name.empty() )
 {
 Tag part_tag;
 tmp_result = impl->tag_get_handle( partition_tag_name.c_str(), 1, MB_TYPE_INTEGER, part_tag );
 if( MB_SUCCESS != tmp_result ) break;
 
 tmp_result = impl->get_entities_by_type_and_tag( file_set, MBENTITYSET, &part_tag, 0, 1,
 myPcomm->partition_sets() );
 }
 }
 break;
 
 //==================
 case PA_GET_FILESET_ENTS:
 myDebug.tprint( 1, "Getting fileset entities.\n" );
 
 // Get entities in the file set, and add actual file set to it;
 // mark the file set to make sure any receiving procs know which it is
 tmp_result = mbImpl->get_entities_by_handle( file_set, entities );
 if( MB_SUCCESS != tmp_result )
 {
 entities.clear();
 break;
 }
 
 // Add actual file set to entities too
 entities.insert( file_set );
 break;
 //==================
 case PA_CREATE_TRIVIAL_PARTITION: {
 myDebug.tprint( 1, "create trivial partition, for higher dim entities.\n" );
 // get high dim entities (2 or 3)
 Range hi_dim_ents = entities.subset_by_dimension( 3 );
 if( hi_dim_ents.empty() ) hi_dim_ents = entities.subset_by_dimension( 2 );
 if( hi_dim_ents.empty() ) hi_dim_ents = entities.subset_by_dimension( 1 );
 if( hi_dim_ents.empty() ) MB_SET_ERR( MB_FAILURE, "there are no elements of dim 1-3" );
 
 size_t num_hi_ents = hi_dim_ents.size();
 unsigned int num_parts = myPcomm->size();
 
 // create first the trivial partition tag
 int dum_id = -1;
 Tag ttag; // trivial tag
 tmp_result = mbImpl->tag_get_handle( partition_tag_name.c_str(), 1, MB_TYPE_INTEGER, ttag,
 MB_TAG_CREAT | MB_TAG_SPARSE, &dum_id );MB_CHK_SET_ERR( tmp_result, "Can't create trivial partition tag" );
 
 // Compute the number of high dim entities on each part
 size_t nPartEnts = num_hi_ents / num_parts;
 
 // Number of extra entities after equal split over parts
 int iextra = num_hi_ents % num_parts;
 Range::iterator itr = hi_dim_ents.begin();
 for( int k = 0; k < (int)num_parts; k++ )
 {
 // create a mesh set, insert a subrange of entities
 EntityHandle part_set;
 tmp_result = mbImpl->create_meshset( MESHSET_SET, part_set );MB_CHK_SET_ERR( tmp_result, "Can't create part set" );
 entities.insert( part_set );
 
 tmp_result = mbImpl->tag_set_data( ttag, &part_set, 1, &k );MB_CHK_SET_ERR( tmp_result, "Can't set trivial partition tag" );
 Range subrange;
 size_t num_ents_in_part = nPartEnts;
 if( i < iextra ) num_ents_in_part++;
 for( size_t i1 = 0; i1 < num_ents_in_part; i1++, itr++ )
 subrange.insert( *itr );
 tmp_result = mbImpl->add_entities( part_set, subrange );MB_CHK_SET_ERR( tmp_result, "Can't add entities to trivial part " << k );
 myDebug.tprintf( 1, "create trivial part %d with %lu entities \n", k, num_ents_in_part );
 tmp_result = mbImpl->add_entities( file_set, &part_set, 1 );MB_CHK_SET_ERR( tmp_result, "Can't add trivial part to file set " << k );
 }
 }
 
 break;
 //==================
 case PA_BROADCAST:
 // Do the actual broadcast; if single-processor, ignore error
 myDebug.tprint( 1, "Broadcasting mesh.\n" );
 
 if( myPcomm->proc_config().proc_size() > 1 )
 {
 tmp_result = myPcomm->broadcast_entities( reader_rank, entities );
 if( MB_SUCCESS != tmp_result ) break;
 }
 
 if( debug )
 {
 std::cerr << "Bcast done; entities:" << std::endl;
 mbImpl->list_entities( 0, 0 );
 }
 
 // Add the received entities to this fileset if I wasn't the reader
 if( !i_read && MB_SUCCESS == tmp_result ) tmp_result = mbImpl->add_entities( file_set, entities );
 
 break;
 
 //==================
 case PA_DELETE_NONLOCAL:
 myDebug.tprint( 1, "Deleting nonlocal entities.\n" );
 
 tmp_result = delete_nonlocal_entities( partition_tag_name, partition_tag_vals, distrib, file_set );
 if( debug )
 {
 std::cerr << "Delete nonlocal done; entities:" << std::endl;
 mbImpl->list_entities( 0, 0 );
 }
 
 if( MB_SUCCESS == tmp_result ) tmp_result = create_partition_sets( partition_tag_name, file_set );
 
 break;
 
 //==================
 case PA_CHECK_GIDS_SERIAL:
 myDebug.tprint( 1, "Checking global IDs.\n" );
 
 tmp_result = myPcomm->check_global_ids( file_set, 0, 1, true, false );
 break;
 
 //==================
 case PA_RESOLVE_SHARED_ENTS:
 myDebug.tprint( 1, "Resolving shared entities.\n" );
 
 if( 1 == myPcomm->size() )
 tmp_result = MB_SUCCESS;
 else
 tmp_result =
 myPcomm->resolve_shared_ents( file_set, resolve_dim, shared_dim, use_id_tag ? file_id_tag : 0 );
 if( MB_SUCCESS != tmp_result ) break;
 
#ifndef NDEBUG
 // check number of owned vertices through pcomm's public interface
 tmp_result = mbImpl->get_entities_by_type( 0, MBVERTEX, ents );
 if( MB_SUCCESS == tmp_result )
 tmp_result = myPcomm->filter_pstatus( ents, PSTATUS_NOT_OWNED, PSTATUS_NOT );
 if( MB_SUCCESS == tmp_result )
 myDebug.tprintf( 1, "Proc %u reports %lu owned vertices.\n", myPcomm->proc_config().proc_rank(),
 ents.size() );
#endif
 break;
 
 //==================
 case PA_EXCHANGE_GHOSTS:
 myDebug.tprint( 1, "Exchanging ghost entities.\n" );
 
 tmp_result = myPcomm->exchange_ghost_cells( ghost_dim, bridge_dim, num_layers, addl_ents, true, true,
 &file_set );
 break;
 
 //==================
 case PA_RESOLVE_SHARED_SETS:
 myDebug.tprint( 1, "Resolving shared sets.\n" );
 
 if( 1 == myPcomm->size() )
 tmp_result = MB_SUCCESS;
 else
 tmp_result = myPcomm->resolve_shared_sets( file_set, use_id_tag ? file_id_tag : 0 );
 break;
 
 //==================
 case PA_AUGMENT_SETS_WITH_GHOSTS:
 myDebug.tprint( 1, "Augmenting sets with ghost entities.\n" );
 
 if( 1 == myPcomm->size() )
 tmp_result = MB_SUCCESS;
 else
 tmp_result = myPcomm->augment_default_sets_with_ghosts( file_set );
 break;
 //==================
 case PA_CORRECT_THIN_GHOSTS:
 myDebug.tprint( 1, "correcting thin ghost layers.\n" );
 if( 2 >= myPcomm->size() ) // it is a problem only for multi-shared entities
 tmp_result = MB_SUCCESS;
 else
 tmp_result = myPcomm->correct_thin_ghost_layers();
 break;
 case PA_PRINT_PARALLEL:
 myDebug.tprint( 1, "Printing parallel information.\n" );
 
 tmp_result = myPcomm->list_entities( 0, -1 );
 break;
 
 //==================
 default:
 MB_SET_ERR( MB_FAILURE, "Unexpected parallel action" );
 } // switch (*vit)
 
 if( MB_SUCCESS != tmp_result )
 {
 MB_SET_ERR( MB_FAILURE, "Failed in step " << ParallelActionsNames[*vit] );
 }
 
 if( cputime ) act_times[i] = MPI_Wtime();
 } // for (i = 1, vit = pa_vec.begin(); vit != pa_vec.end(); ++vit, i++)
 
 if( use_id_tag )
 {
 result = mbImpl->tag_delete( id_tag );MB_CHK_SET_ERR( result, "Trouble deleting id tag" );
 }
 
 if( cputime )
 {
 for( i = pa_vec.size(); i > 0; i-- )
 act_times[i] -= act_times[i - 1];
 
 // Replace initial time with overall time
 act_times[0] = MPI_Wtime() - act_times[0];
 // Get the maximum over all procs
 if( 0 != myPcomm->proc_config().proc_rank() )
 {
 MPI_Reduce( &act_times[0], 0, pa_vec.size() + 1, MPI_DOUBLE, MPI_MAX, 0,
 myPcomm->proc_config().proc_comm() );
 }
 else
 {
#if( MPI_VERSION >= 2 )
 MPI_Reduce( MPI_IN_PLACE, &act_times[0], pa_vec.size() + 1, MPI_DOUBLE, MPI_MAX, 0,
 myPcomm->proc_config().proc_comm() );
#else
 // Note, extra comm-size allocation is required
 std::vector< double > act_times_tmp( pa_vec.size() + 1 );
 MPI_Reduce( &act_times[0], &act_times_tmp[0], pa_vec.size() + 1, MPI_DOUBLE, MPI_MAX, 0,
 myPcomm->proc_config().proc_comm() );
 act_times = act_times_tmp; // extra copy here too
#endif
 std::cout << "Parallel Read times: " << std::endl;
 for( i = 1, vit = pa_vec.begin(); vit != pa_vec.end(); ++vit, i++ )
 std::cout << " " << act_times[i] << " " << ParallelActionsNames[*vit] << std::endl;
 std::cout << " " << act_times[0] << " PARALLEL TOTAL" << std::endl;
 }
 }
 
 return MB_SUCCESS;
}

References moab::Interface::add_entities(), moab::ParallelComm::augment_default_sets_with_ghosts(), moab::Range::begin(), moab::ParallelComm::broadcast_entities(), moab::ParallelComm::check_global_ids(), moab::ParallelComm::correct_thin_ghost_layers(), moab::Interface::create_meshset(), create_partition_sets(), moab::debug, delete_nonlocal_entities(), moab::Range::empty(), entities, ErrorCode, moab::ParallelComm::exchange_ghost_cells(), moab::ParallelComm::filter_pstatus(), moab::Interface::get_entities_by_handle(), moab::Interface::get_entities_by_type(), moab::Core::get_entities_by_type_and_tag(), moab::Range::insert(), moab::ParallelComm::list_entities(), moab::Interface::list_entities(), MB_CHK_SET_ERR, MB_NOT_IMPLEMENTED, MB_SET_ERR, MB_SUCCESS, MB_TAG_CREAT, MB_TAG_DENSE, MB_TAG_SPARSE, MB_TYPE_INTEGER, MB_TYPE_OPAQUE, MBENTITYSET, mbImpl, MBVERTEX, MESHSET_SET, myDebug, myPcomm, moab::ReaderIface::SubsetList::num_parts, moab::ReaderIface::IDTag::num_tag_values, PA_AUGMENT_SETS_WITH_GHOSTS, PA_BROADCAST, PA_CHECK_GIDS_SERIAL, PA_CORRECT_THIN_GHOSTS, PA_CREATE_TRIVIAL_PARTITION, PA_DELETE_NONLOCAL, PA_EXCHANGE_GHOSTS, PA_GET_FILESET_ENTS, PA_PRINT_PARALLEL, PA_READ, PA_READ_PART, PA_RESOLVE_SHARED_ENTS, PA_RESOLVE_SHARED_SETS, ParallelActionsNames, moab::ReaderIface::SubsetList::part_number, moab::ParallelComm::partition_sets(), moab::ProcConfig::proc_comm(), moab::ParallelComm::proc_config(), moab::ProcConfig::proc_rank(), moab::ProcConfig::proc_size(), PSTATUS_NOT, PSTATUS_NOT_OWNED, moab::ParallelComm::rank(), moab::ParallelComm::resolve_shared_ents(), moab::ParallelComm::resolve_shared_sets(), moab::Core::serial_load_file(), moab::Range::size(), moab::ParallelComm::size(), moab::Interface::tag_delete(), moab::Core::tag_get_handle(), moab::Interface::tag_get_handle(), moab::ReaderIface::SubsetList::tag_list, moab::ReaderIface::SubsetList::tag_list_length, moab::Interface::tag_set_data(), moab::ReaderIface::IDTag::tag_values, moab::DebugOutput::tprint(), and moab::DebugOutput::tprintf().

load_file() [3/3]

ErrorCode moab::ReadParallel::load_file ( const char *  file_name, const EntityHandle *  file_set, const FileOptions &  opts, const ReaderIface::SubsetList *  subset_list = 0, const Tag *  file_id_tag = 0  )

inline

load a file

Definition at line 117 of file ReadParallel.hpp.

{
 return load_file( &file_name, 1, file_set, opts, subset_list, file_id_tag );
}

Referenced by load_file(), and moab::Core::load_file().

Member Data Documentation

mbImpl

Interface* moab::ReadParallel::mbImpl

private

Definition at line 107 of file ReadParallel.hpp.

Referenced by create_partition_sets(), delete_nonlocal_entities(), load_file(), and ReadParallel().

mError

Error* moab::ReadParallel::mError

private

Definition at line 114 of file ReadParallel.hpp.

Referenced by ReadParallel().

myDebug

DebugOutput moab::ReadParallel::myDebug

private

Definition at line 112 of file ReadParallel.hpp.

Referenced by delete_nonlocal_entities(), load_file(), and ReadParallel().

myPcomm

ParallelComm* moab::ReadParallel::myPcomm

private

Definition at line 110 of file ReadParallel.hpp.

Referenced by create_partition_sets(), delete_nonlocal_entities(), load_file(), and ReadParallel().

ParallelActionsNames

const char * moab::ReadParallel::ParallelActionsNames

static

Initial value:

= { "PARALLEL READ",
 "PARALLEL READ PART",
 "PARALLEL BROADCAST",
 "PARALLEL DELETE NONLOCAL",
 "PARALLEL CHECK_GIDS_SERIAL",
 "PARALLEL GET_FILESET_ENTS",
 "PARALLEL RESOLVE_SHARED_ENTS",
 "PARALLEL EXCHANGE_GHOSTS",
 "PARALLEL RESOLVE_SHARED_SETS",
 "PARALLEL_AUGMENT_SETS_WITH_GHOSTS",
 "PARALLEL PRINT_PARALLEL",
 "PARALLEL_CREATE_TRIVIAL_PARTITION",
 "PARALLEL_CORRECT_THIN_GHOST_LAYERS" }

Definition at line 83 of file ReadParallel.hpp.

Referenced by load_file().

parallelOptsNames

const char * moab::ReadParallel::parallelOptsNames = { "NONE", "BCAST", "BCAST_DELETE", "READ_DELETE", "READ_PART", "", 0 }

static

Definition at line 64 of file ReadParallel.hpp.

Referenced by load_file().

---

The documentation for this class was generated from the following files:

• ReadParallel.hpp
• ReadParallel.cpp