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Collective Calling Requirements in Parallel HDF5 Applications
Introduction
This document addresses two topics of concern in a parallel computing environment:
- HDF5 functions that must be called collectively and when
- Properties that must be used in a coordinated manner The term Macro in the “Additional notes” column indicates that the first item in the “Function” column of the same row is a macro that is selectively mapped to one of the two immediately-following functions. For example, H5Acreate is a macro that can be mapped to either H5Acreate1 or H5Acreate2. This mapping is configurable and is explained in API Compatibility Macros in HDF5. The macro structure was introduced at HDF5 Release 1.8.0.
Always collective
The following functions must always be called collectively.
| API | Function | All processes: same datatype & dataspace |
All processes: same access properties |
All processes: same creation properties |
Available in releases since |
Additional notes |
|---|---|---|---|---|---|---|
| H5A | H5Acreate H5Acreate1 H5Acreate2 |
✓ | ✓ | ✓ | 1.8.x | Macro The function H5Acreate was renamed to H5Acreate1 at Release 1.8.0. |
| H5Acreate_by_name | ✓ | ✓ | ✓ | 1.8.x | ||
| H5Adelete | ||||||
| H5Adelete_by_idx | 1.8.x | |||||
| H5Adelete_by_name | 1.8.x | |||||
| H5Arename | 1.6.x | |||||
| H5Arename_by_name | 1.8.x | |||||
| H5Awrite | Because raw data for an attribute is cached locally, all processes must participate in order to guarantee that future H5Aread calls return correct results on all processes. | |||||
| H5D | H5Dcreate H5Dcreate1 H5Dcreate2 |
✓ | ✓ | ✓ | 1.8.x | Macro The function H5Dcreate was renamed to H5Dcreate1 at Release 1.8.0. |
| H5Dcreate_anon | ✓ | ✓ | ✓ | 1.8.x | ||
| H5Dextend | All processes must participate only if the number of chunks in the dataset actually changes. All processes must use the same dataspace dimensions. |
|||||
| H5Dset_extent | 1.6.x | All processes must participate only if the number of chunks in the dataset actually changes. All processes must use the same dataspace dimensions. |
||||
| H5F | H5Fclose | All processes must participate only if this is the last reference to the file identifier. | ||||
| H5Fcreate | ✓ | ✓ | ||||
| H5Fflush | ||||||
| H5Fmount | ||||||
| H5Fopen | ✓ | |||||
| H5Freopen | ||||||
| H5Funmount | ||||||
| H5G | H5Gcreate H5Gcreate1 H5Gcreate2 |
✓ | ✓ | 1.8.x | Macro The function H5Gcreate was renamed to H5Gcreate1 at Release 1.8.0. |
|
| H5Gcreate_anon | ✓ | ✓ | 1.8.x | |||
| H5Glink | ||||||
| H5Glink2 | 1.6.x | |||||
| H5Gmove | ||||||
| H5Gmove2 | 1.6.x | |||||
| H5Gset_comment | ||||||
| H5Gunlink | ||||||
| H5I | H5Idec_ref | 1.6.x | This function may be called independently if the object identifier does not refer to an object that was collectively opened. | |||
| H5LIinc_ref | 1.6.x | This function may be called independently if the object identifier does not refer to an object that was collectively opened. | ||||
| H5L | H5Lcopy | 1.8.x | ||||
| H5Lcreate_external | ✓ | 1.8.x | ||||
| H5Lcreate_hard | ✓ | 1.8.x | ||||
| H5Lcreate_soft | ✓ | 1.8.x | ||||
| H5Lcreate_ud | ✓ | 1.8.x | ||||
| H5Ldelete | 1.8.x | |||||
| H5Ldelete_by_idx | 1.8.x | |||||
| H5Lmove | 1.8.x | |||||
| H5O | H5Ocopy | 1.8.x | ||||
| H5Odecr_refcount | 1.8.x | |||||
| H5Oincr_refcount | 1.8.x | |||||
| H5Olink | 1.8.x | |||||
| H5Oset_comment | 1.8.x | |||||
| H5Oset_comment_by_name | 1.8.x | |||||
| H5R | H5Rcreate | |||||
| H5T | H5Tcommit H5Tcommit1 H5Tcommit2 |
✓ | ✓ | 1.8.x | Macro The function H5Tcommit was renamed to H5Tcommit1 at Release 1.8.0. |
|
| H5Tcommit_anon | ✓ | ✓ | 1.8.x |
Collective, unless target object will not be modified
The following functions must normally be called collectively. If, however, the target object will not be modified, they may be called independently.
| API | Function | All processes:
same datatype
& dataspace | All processes:
same access
properties | All processes:
same creation
properties | Available
in releases since | Additional notes |
| — | ———– | —————- | —————————————- | —————————————— | —————————— | ———– |
| H5A | H5Aclose | | ✓ | | 1.8.x | All processes must participate only if all file identifiers for a file have been closed and this is the last outstanding object identifier. |
| | H5Aopen | | ✓ | | 1.8.x | |
| | H5Aopen_by_idx | | ✓ | | 1.8.x | |
| | H5Aopen_by_name | | ✓ | | 1.8.x | |
| | H5Aopen_idx | | ✓ | | | |
| | H5Aopen_name | | ✓ | | | |
| H5D | H5Dclose | | | | 1.8.x | All processes must participate only if all file identifiers for a file have been closed and this is the last outstanding object identifier. |
| | H5Dopen
H5Dopen1
H5Dopen2 | | ✓ | | 1.8.x | Macro
The function H5Dopen was renamed to H5Dopen1 at Release 1.8.0. |
| H5G | H5Gclose | | | | | All processes must participate only if all file identifiers for a file have been closed and this is the last outstanding object identifier. |
| | H5Gopen
H5Gopen1
H5Gopen2 | | ✓ | | 1.8.x | Macro
The function H5Gopen was renamed to H5Dopen1 at Release 1.8.0. |
| H5I | H5Iget_file_id | | | | 1.8.x | |
| H5O | H5Oclose | | | | 1.8.x | All processes must participate only if all file identifiers for a file have been closed and this is the last outstanding object identifier. |
| | H5Oopen | | ✓ | | 1.8.x | |
| | H5Oopen_by_addr | | ✓ | | 1.8.x | |
| | H5Oopen_by_idx | | ✓ | | 1.8.x | |
| H5R | H5Rdereference | | | | | |
| H5T | H5Tclose | | | | | All processes must participate only if the datatype is for a committed datatype, all the file identifiers for the file have been closed, and this is the last outstanding object identifier. |
H5Topen
H5Topen1
H5Topen2 ✓ 1.8.x Macro
The function H5Topen was renamed to H5Topen1 at Release 1.8.0.
Properties
The following properties must be set to the same values for an object or link in all cases where the object or link is accessed in a parallel program.
Function Available in
releases since
Dataset creation properties
H5Pmodify_filter 1.8.x
H5Premove_filter 1.8.x
H5Pset_alloc_time
H5Pset_chunk
H5Pset_external
H5Pset_fill_time
H5Pset_fill_value
H5Pset_filter
H5Pset_fletcher32 1.8.x
H5Pset_layout
H5Pset_nbit 1.8.x
H5Pset_shuffle
H5Pset_szip
Dataset transfer properties
H5Pset_btree_ratios
H5Pset_buffer
H5Pset_dxpl_mpio
H5Pset_hyper_cache
H5Pset_preserve
File access properties
H5Pset_alignment
H5Pset_cache
H5Pset_fapl_mpio
H5Pset_fclose_degree
H5Pset_gc_references
H5Pset_latest_format 1.8.x
H5Pset_libver_bounds 1.8.x
H5Pset_mdc_config
H5Pset_meta_block_size
H5Pset_small_data_block_size
H5Pset_sieve_buf_size
Function Available in
releases since
File creation properties
H5Pset_istore_k
H5Pset_shared_mesg_index 1.8.x
H5Pset_shared_mesg_nindexes 1.8.x
H5Pset_shared_mesg_phase_change 1.8.x
H5Pset_sizes
H5Pset_sym_k
H5Pset_userblock
Group creation properties H5Pset_ext_link_info 1.8.x H5Pset_link_creation_order 1.8.x H5Pset_link_phase_change 1.8.x H5Pset_local_heap_size_hint 1.8.x
Link creation properties H5Pset_char_encoding 1.8.x H5Pset_create_intermediate_group 1.8.x
Object creation properties H5Pset_attr_phase_change 1.8.x H5Pset_attr_creation_order 1.8.x H5Pset_obj_track_times 1.8.x
Object copy properties H5Pset_copy_object 1.8.x