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Collective Calling Requirements in Parallel HDF5 Applications

Navigate back: Main / Getting Started with HDF5 / A Brief Introduction to Parallel HDF5

# 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 Compatibility Macro Mapping Options 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. 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 | X | X | X | 1.8.x | Compatibility Macro Mapping Options The function H5Acreate was renamed to H5Acreate1 at Release 1.8.0.
| H5Acreate_by_name | X | X | X | 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 | X | X | X | 1.8.x | Compatibility Macro Mapping Options The function H5Dcreate was renamed to H5Dcreate1 at Release 1.8.0.
| H5Dcreate_anon | X | X | X | 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 |  | X | X |  |
| H5Fflush |  |  |  |  |
| H5Fmount |  |  |  |  |
| H5Fopen |  | X |  |  |
| H5Freopen |  |  |  |  |
| H5Funmount |  |  |  |  |
H5G | H5Gcreate H5Gcreate1 H5Gcreate2 |  | X | X | 1.8.x | Compatibility Macro Mapping Options The function H5Gcreate was renamed to H5Gcreate1 at Release 1.8.0.
| H5Gcreate_anon |  | X | X | 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.
| H5Iinc_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 |  |  | X | 1.8.x |
| H5Lcreate_hard |  |  | X | 1.8.x |
| H5Lcreate_soft |  |  | X | 1.8.x |
| H5Lcreate_ud |  |  | X | 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 |  | X | X | 1.8.x | Compatibility Macro Mapping Options The function H5Tcommit was renamed to H5Tcommit1 at Release 1.8.0.
| H5Tcommit_anon |  | X | X | 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 |  |  |  |  | All processes must participate only if all file identifiers for a file have been closed and this is the last outstanding object identifier.
| H5Aopen |  | X |  | 1.8.x |
| H5Aopen_by_idx |  | X |  | 1.8.x |
| H5Aopen_by_name |  | X |  | 1.8.x |
| H5Aopen_idx |  | X |  |  |
| H5Aopen_name |  | X |  |  |
H5D | H5Dclose |  |  |  |  | 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 |  | X |  | 1.8.x | Compatibility Macro Mapping Options 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 |  | X |  | 1.8.x | Compatibility Macro Mapping Options The function H5Gopen was renamed to H5Gopen1 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 |  | X |  | 1.8.x |
| H5Oopen_by_addr |  | X |  | 1.8.x |
| H5Oopen_by_idx |  | X |  | 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 |  | X |  | 1.8.x | Compatibility Macro Mapping Options 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_preserve |
File access properties
H5Pset_alignment |
H5Pset_cache |
H5Pset_fapl_mpio |
H5Pset_fclose_degree |
H5Pset_gc_references |
H5Fset_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_est_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

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