Logo


Got HDF5?

Visualization of an HDF5 file
Curious to see what’s inside? Try this
(This free tool will show you the contents of an HDF5 file in your browser, without any data leaving your computer! For more info, check out H5Web.)

Collective Calling Requirements in Parallel HDF5 Applications

Introduction

This document addresses two topics of concern in a parallel computing environment:

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