#include <HDF5ParallelReader.h>
Collaboration diagram for HDF5ParallelReader:
Public Member Functions | |
| ~HDF5ParallelReader () | |
| HDF5ParallelReader (const char *inputFile, MeshBuilder *builder, MPI_Comm comm) | |
| void | read () |
| void | export_dist (char *file) |
| int | main (int argc, char **argv) |
Private Member Functions | |
| double | seconds () |
| void | print_tet_global_id () |
| void | read_tets () |
| void | read_mats () |
| void | partition () |
| void | sort_buffer (int *sendcnts) |
| void | distribute () |
| void | generate_point_global_id (int *slab_offsets, int *slab_lengths, int slab_count) |
| void | read_points () |
| void | read_boundary () |
| void | open_file () |
| void | close_file () |
Private Attributes | |
| const char * | _inputFile |
| MeshBuilder * | _builder |
| MPI_Comm | _comm |
| MPI_Info | _info |
| int | _mpi_size |
| int | _mpi_rank |
| double * | _point_coords |
| int | _numpoints_global |
| int | _numpoints_local |
| int * | _tetids |
| int | _numtets_global |
| int | _numtets_local |
| int * | _matids |
| int * | _faces |
| int | _numbfaces_global |
| int | _numbfaces_local |
| int * | _tet_partition |
| int * | _tet_global_id |
| int * | _point_global_id |
| hid_t | _file_id |
| hid_t | _plist_id |
Definition at line 23 of file HDF5ParallelReader.h.
| HDF5ParallelReader::~HDF5ParallelReader | ( | ) |
Deconstructor FIXME add some cleanup here?
Definition at line 4 of file HDF5ParallelReader.cpp.
References _matids, _point_coords, _point_global_id, _tet_global_id, _tet_partition, and _tetids.
| HDF5ParallelReader::HDF5ParallelReader | ( | const char * | inputFile, | |
| MeshBuilder * | builder, | |||
| MPI_Comm | comm | |||
| ) |
Contruct new reader.
| inputFile | character array containing path and name of input file | |
| builder | MeshBuilder object recieving data | |
| comm | MPI communicator |
Definition at line 13 of file HDF5ParallelReader.cpp.
References _comm, _info, _mpi_rank, and _mpi_size.
Referenced by main().
| void HDF5ParallelReader::close_file | ( | ) | [private] |
| void HDF5ParallelReader::distribute | ( | ) | [private] |
Redistribute tetrahedra across processors according to partition
Definition at line 280 of file HDF5ParallelReader.cpp.
References _comm, _matids, _mpi_size, _numtets_local, _tet_global_id, _tet_partition, _tetids, and sort_buffer().
Referenced by main(), and read().
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| void HDF5ParallelReader::export_dist | ( | char * | file | ) |
Export tet distribution to vtk file
Definition at line 569 of file HDF5ParallelReader.cpp.
References _comm, _file_id, _mpi_rank, _mpi_size, _numpoints_global, _numtets_global, _numtets_local, _tetids, and REALMEMTYPE.
| void HDF5ParallelReader::generate_point_global_id | ( | int * | slab_offsets, | |
| int * | slab_lengths, | |||
| int | slab_count | |||
| ) | [private] |
Generate global ID of poins (Re)generate the node global ID's from HDF5 hyperslab data
| slab_offsets | starting point of slabs | |
| slab_lengths | lengths of slabs | |
| slab_count | number of slabs |
Definition at line 368 of file HDF5ParallelReader.cpp.
References _numpoints_local, and _point_global_id.
Referenced by read_points().
| int HDF5ParallelReader::main | ( | int | argc, | |
| char ** | argv | |||
| ) |
Test method used in the making of HDF5ParallelReader
Definition at line 709 of file HDF5ParallelReader.cpp.
References _builder, _matids, _mpi_rank, _numpoints_local, _numtets_local, _point_coords, _point_global_id, _tet_partition, _tetids, close_file(), comm, distribute(), export_dist(), MeshBuilder::finalize_coord(), MeshBuilder::finalize_tet(), TetMeshBuilder::get_mesh(), HDF5ParallelReader(), MeshBuilder::init_coord(), MeshBuilder::init_tet(), open_file(), partition(), read_boundary(), read_mats(), read_points(), read_tets(), seconds(), MeshBuilder::set_coord(), and MeshBuilder::set_tet().
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| void HDF5ParallelReader::open_file | ( | ) | [private] |
Open HDF5 file
Definition at line 663 of file HDF5ParallelReader.cpp.
References _comm, _file_id, _info, _inputFile, and _plist_id.
| void HDF5ParallelReader::partition | ( | ) | [private] |
Generate a tetrahedra partition with ParMETIS
Definition at line 165 of file HDF5ParallelReader.cpp.
References _comm, _mpi_size, _numtets_global, _numtets_local, _tet_partition, and _tetids.
| void HDF5ParallelReader::print_tet_global_id | ( | ) | [private] |
Print tetrahedra global ID's
Definition at line 26 of file HDF5ParallelReader.cpp.
References _mpi_rank, _numtets_local, and _tet_global_id.
| void HDF5ParallelReader::read | ( | ) |
Read mesh data from input stream and call corresponding builder methods.
Definition at line 678 of file HDF5ParallelReader.cpp.
References _builder, _matids, _numpoints_local, _numtets_local, _point_coords, _point_global_id, _tetids, close_file(), distribute(), MeshBuilder::finalize_coord(), MeshBuilder::finalize_tet(), MeshBuilder::init_coord(), MeshBuilder::init_tet(), open_file(), partition(), read_boundary(), read_mats(), read_points(), read_tets(), MeshBuilder::set_coord(), and MeshBuilder::set_tet().
Referenced by FemaxxDriver::load_mesh(), and main().
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| void HDF5ParallelReader::read_boundary | ( | ) | [private] |
Read boundary data from HDF5 file
Definition at line 520 of file HDF5ParallelReader.cpp.
References _builder, _file_id, _numbfaces_global, _numbfaces_local, _plist_id, MeshBuilder::finalize_bc(), INTMEMTYPE, MeshBuilder::set_bc(), and x.
Referenced by main(), and read().
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| void HDF5ParallelReader::read_mats | ( | ) | [private] |
Read materials from HDF5 file
Definition at line 102 of file HDF5ParallelReader.cpp.
References _file_id, _matids, _mpi_rank, _mpi_size, _numtets_global, _numtets_local, _plist_id, INTMEMTYPE, and x.
| void HDF5ParallelReader::read_points | ( | ) | [private] |
Read node coordinates from HDF5 file
Definition at line 385 of file HDF5ParallelReader.cpp.
References _file_id, _numpoints_global, _numpoints_local, _numtets_local, _plist_id, _point_coords, _tetids, generate_point_global_id(), REALMEMTYPE, and x.
Referenced by main(), and read().
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| void HDF5ParallelReader::read_tets | ( | ) | [private] |
Read tetrahedra from HDF5 file
Definition at line 36 of file HDF5ParallelReader.cpp.
References _file_id, _mpi_rank, _mpi_size, _numtets_global, _numtets_local, _plist_id, _tet_global_id, _tetids, INTMEMTYPE, rInfoAll, and x.
| double HDF5ParallelReader::seconds | ( | ) | [private] |
| void HDF5ParallelReader::sort_buffer | ( | int * | sendcnts | ) | [private] |
Sort tetrahedra buffer according to ParMETIS partition This sorts the sendbuffer by the target proc. A bin/bucket sort where the sizes of the buckets is known The bucket sizes are the number of tetrahedra to send to proc i.
| sendcnts | pointer to array of bucket sizes |
Definition at line 235 of file HDF5ParallelReader.cpp.
References _matids, _mpi_size, _numtets_local, _tet_global_id, _tet_partition, and _tetids.
Referenced by distribute().
MeshBuilder* HDF5ParallelReader::_builder [private] |
Meshbuilder to which to pass the data read
Definition at line 98 of file HDF5ParallelReader.h.
Referenced by main(), read(), and read_boundary().
MPI_Comm HDF5ParallelReader::_comm [private] |
MPI communicator
Definition at line 101 of file HDF5ParallelReader.h.
Referenced by distribute(), export_dist(), HDF5ParallelReader(), open_file(), and partition().
int* HDF5ParallelReader::_faces [private] |
Array containing node ID's of boundary faces
Definition at line 134 of file HDF5ParallelReader.h.
hid_t HDF5ParallelReader::_file_id [private] |
HDF5 object identifying the inputfile
Definition at line 152 of file HDF5ParallelReader.h.
Referenced by close_file(), export_dist(), open_file(), read_boundary(), read_mats(), read_points(), and read_tets().
MPI_Info HDF5ParallelReader::_info [private] |
MPI internal information needed by HDF5 for parallel file access
Definition at line 104 of file HDF5ParallelReader.h.
Referenced by HDF5ParallelReader(), and open_file().
const char* HDF5ParallelReader::_inputFile [private] |
Name of input HDF5 file
Definition at line 95 of file HDF5ParallelReader.h.
Referenced by open_file().
int* HDF5ParallelReader::_matids [private] |
Array containing material ID's of tetrahedra
Definition at line 131 of file HDF5ParallelReader.h.
Referenced by distribute(), main(), read(), read_mats(), sort_buffer(), and ~HDF5ParallelReader().
int HDF5ParallelReader::_mpi_rank [private] |
ID number of this processor
Definition at line 110 of file HDF5ParallelReader.h.
Referenced by export_dist(), HDF5ParallelReader(), main(), print_tet_global_id(), read_mats(), and read_tets().
int HDF5ParallelReader::_mpi_size [private] |
Number of processors
Definition at line 107 of file HDF5ParallelReader.h.
Referenced by distribute(), export_dist(), HDF5ParallelReader(), partition(), read_mats(), read_tets(), and sort_buffer().
int HDF5ParallelReader::_numbfaces_global [private] |
Number of boundary faces globally
Definition at line 137 of file HDF5ParallelReader.h.
Referenced by read_boundary().
int HDF5ParallelReader::_numbfaces_local [private] |
Number of boundary faces locally
Definition at line 140 of file HDF5ParallelReader.h.
Referenced by read_boundary().
int HDF5ParallelReader::_numpoints_global [private] |
Number of nodes globally
Definition at line 116 of file HDF5ParallelReader.h.
Referenced by export_dist(), and read_points().
int HDF5ParallelReader::_numpoints_local [private] |
Number of nodes locally
Definition at line 119 of file HDF5ParallelReader.h.
Referenced by generate_point_global_id(), main(), read(), and read_points().
int HDF5ParallelReader::_numtets_global [private] |
Number of tetrahedra globally
Definition at line 125 of file HDF5ParallelReader.h.
Referenced by export_dist(), partition(), read_mats(), and read_tets().
int HDF5ParallelReader::_numtets_local [private] |
Number of tetrahedra locally
Definition at line 128 of file HDF5ParallelReader.h.
Referenced by distribute(), export_dist(), main(), partition(), print_tet_global_id(), read(), read_mats(), read_points(), read_tets(), and sort_buffer().
hid_t HDF5ParallelReader::_plist_id [private] |
HDF5 object containing parallel file reading access parameters
Definition at line 155 of file HDF5ParallelReader.h.
Referenced by close_file(), open_file(), read_boundary(), read_mats(), read_points(), and read_tets().
double* HDF5ParallelReader::_point_coords [private] |
Array containing node coordinates
Definition at line 113 of file HDF5ParallelReader.h.
Referenced by main(), read(), read_points(), and ~HDF5ParallelReader().
int* HDF5ParallelReader::_point_global_id [private] |
Array containing the global ID (input file order) of local nodes
Definition at line 149 of file HDF5ParallelReader.h.
Referenced by generate_point_global_id(), main(), read(), and ~HDF5ParallelReader().
int* HDF5ParallelReader::_tet_global_id [private] |
Array containing the global ID (input file order) of local tets
Definition at line 146 of file HDF5ParallelReader.h.
Referenced by distribute(), print_tet_global_id(), read_tets(), sort_buffer(), and ~HDF5ParallelReader().
int* HDF5ParallelReader::_tet_partition [private] |
Array containing ID's of the processors to which to send local tetrahedra
Definition at line 143 of file HDF5ParallelReader.h.
Referenced by distribute(), main(), partition(), sort_buffer(), and ~HDF5ParallelReader().
int* HDF5ParallelReader::_tetids [private] |
Array containing node ID's of tetrahedra
Definition at line 122 of file HDF5ParallelReader.h.
Referenced by distribute(), export_dist(), main(), partition(), read(), read_points(), read_tets(), sort_buffer(), and ~HDF5ParallelReader().
1.4.7