 |
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 <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 | |
| 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 | |
| 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. | |
| virtual | ~ReadParallel () |
| Destructor. | |
| ErrorCode | delete_nonlocal_entities (std::string &ptag_name, std::vector< int > &ptag_vals, bool distribute, EntityHandle file_set) |
| PUBLIC TO ALLOW TESTING. | |
| 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 |
Definition at line 17 of file ReadParallel.hpp.
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
};
Definition at line 85 of file ReadParallel.hpp.
{
POPT_NONE = 0,
POPT_BCAST,
POPT_BCAST_DELETE,
POPT_READ_DELETE,
POPT_READ_PART,
POPT_DEFAULT
};
| moab::ReadParallel::ReadParallel | ( | Interface * | impl = NULL, |
| ParallelComm * | pc = NULL |
||
| ) |
Constructor.
Definition at line 39 of file ReadParallel.cpp.
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().
: 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 );
}
| virtual moab::ReadParallel::~ReadParallel | ( | ) | [inline, virtual] |
| ErrorCode moab::ReadParallel::create_partition_sets | ( | std::string & | ptag_name, |
| EntityHandle | file_set | ||
| ) | [protected] |
Definition at line 720 of file ReadParallel.cpp.
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(), moab::Range::size(), moab::Interface::tag_delete_data(), moab::Interface::tag_get_handle(), and moab::Interface::tag_set_data().
Referenced by load_file().
{
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;
}
| 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.
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().
{
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;
}
Definition at line 758 of file ReadParallel.cpp.
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().
{
// 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;
}
| static ReaderIface* moab::ReadParallel::factory | ( | Interface * | ) | [static] |
| 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.
Referenced by load_file(), and moab::Core::load_file().
{
return load_file( &file_name, 1, file_set, opts, subset_list, file_id_tag );
}
| 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.
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().
{
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;
}
| 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.
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::Range::clear(), 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::Range::subset_by_dimension(), 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().
{
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;
}
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().
Error* moab::ReadParallel::mError [private] |
Definition at line 114 of file ReadParallel.hpp.
Referenced by ReadParallel().
DebugOutput moab::ReadParallel::myDebug [private] |
Definition at line 112 of file ReadParallel.hpp.
Referenced by delete_nonlocal_entities(), load_file(), and ReadParallel().
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().
const char * moab::ReadParallel::ParallelActionsNames [static] |
{ "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().
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().
1.7.6.1.
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