From 3a079e839099e1fbc6cbe5e6510606c25583a96e Mon Sep 17 00:00:00 2001 From: Allen Byrne <50328838+byrnHDF@users.noreply.github.com> Date: Tue, 19 Jul 2022 07:29:36 -0500 Subject: Add doxygen chapter for files, fix autotools images (#1908) --- configure.ac | 2 + doxygen/CMakeLists.txt | 1 + doxygen/Doxyfile.in | 2 +- doxygen/img/Files_fig3.gif | Bin 0 -> 44382 bytes doxygen/img/Files_fig4.gif | Bin 0 -> 38862 bytes doxygen/img/UML_FileAndProps.gif | Bin 0 -> 6161 bytes doxygen/img/VFL_Drivers.gif | Bin 0 -> 17638 bytes src/H5Fmodule.h | 1401 ++++++++++++++++++++++++++++++++++++++ 8 files changed, 1405 insertions(+), 1 deletion(-) create mode 100644 doxygen/img/Files_fig3.gif create mode 100644 doxygen/img/Files_fig4.gif create mode 100644 doxygen/img/UML_FileAndProps.gif create mode 100644 doxygen/img/VFL_Drivers.gif diff --git a/configure.ac b/configure.ac index 976f1c9..dd4f8c8 100644 --- a/configure.ac +++ b/configure.ac @@ -1185,6 +1185,7 @@ if test "X$HDF5_DOXYGEN" = "Xyes"; then AC_SUBST([DOXYGEN_PACKAGE]) AC_SUBST([DOXYGEN_VERSION_STRING]) + AC_SUBST([DOXYGEN_DIR]) AC_SUBST([DOXYGEN_INCLUDE_ALIASES]) AC_SUBST([DOXYGEN_PROJECT_LOGO]) AC_SUBST([DOXYGEN_PROJECT_BRIEF]) @@ -1209,6 +1210,7 @@ if test "X$HDF5_DOXYGEN" = "Xyes"; then # SRCDIR Environment variables used inside doxygen macro for the source location: DOXYGEN_PACKAGE=${PACKAGE_NAME} DOXYGEN_VERSION_STRING=${PACKAGE_VERSION} + DOXYGEN_DIR='$(SRCDIR)/doxygen' DOXYGEN_INCLUDE_ALIASES='$(SRCDIR)/doxygen/aliases' DOXYGEN_PROJECT_LOGO='$(SRCDIR)/doxygen/img/HDFG-logo.png' DOXYGEN_PROJECT_BRIEF='' diff --git a/doxygen/CMakeLists.txt b/doxygen/CMakeLists.txt index 1a3946f..17d8da7 100644 --- a/doxygen/CMakeLists.txt +++ b/doxygen/CMakeLists.txt @@ -7,6 +7,7 @@ project (HDF5_DOXYGEN C) if (DOXYGEN_FOUND) set (DOXYGEN_PACKAGE ${HDF5_PACKAGE_NAME}) set (DOXYGEN_VERSION_STRING ${HDF5_PACKAGE_VERSION_STRING}) + set (DOXYGEN_DIR ${HDF5_DOXYGEN_DIR}) set (DOXYGEN_INCLUDE_ALIASES_PATH ${HDF5_DOXYGEN_DIR}) set (DOXYGEN_INCLUDE_ALIASES aliases) set (DOXYGEN_VERBATIM_VARS DOXYGEN_INCLUDE_ALIASES) diff --git a/doxygen/Doxyfile.in b/doxygen/Doxyfile.in index 1837027..297c7b2 100644 --- a/doxygen/Doxyfile.in +++ b/doxygen/Doxyfile.in @@ -941,7 +941,7 @@ EXAMPLE_RECURSIVE = NO # that contain images that are to be included in the documentation (see the # \image command). -IMAGE_PATH = @HDF5_DOXYGEN_DIR@/img +IMAGE_PATH = @DOXYGEN_DIR@/img # The INPUT_FILTER tag can be used to specify a program that doxygen should # invoke to filter for each input file. Doxygen will invoke the filter program diff --git a/doxygen/img/Files_fig3.gif b/doxygen/img/Files_fig3.gif new file mode 100644 index 0000000..6912f5c Binary files /dev/null and b/doxygen/img/Files_fig3.gif differ diff --git a/doxygen/img/Files_fig4.gif b/doxygen/img/Files_fig4.gif new file mode 100644 index 0000000..b4ff107 Binary files /dev/null and b/doxygen/img/Files_fig4.gif differ diff --git a/doxygen/img/UML_FileAndProps.gif b/doxygen/img/UML_FileAndProps.gif new file mode 100644 index 0000000..1de96c6 Binary files /dev/null and b/doxygen/img/UML_FileAndProps.gif differ diff --git a/doxygen/img/VFL_Drivers.gif b/doxygen/img/VFL_Drivers.gif new file mode 100644 index 0000000..4b626c6 Binary files /dev/null and b/doxygen/img/VFL_Drivers.gif differ diff --git a/src/H5Fmodule.h b/src/H5Fmodule.h index 8904d9c..4da58a4 100644 --- a/src/H5Fmodule.h +++ b/src/H5Fmodule.h @@ -33,38 +33,1439 @@ * * \section sec_file The HDF5 File * \subsection subsec_file_intro Introduction + * The purpose of this chapter is to describe how to work with HDF5 data files. + * + * If HDF5 data is to be written to or read from a file, the file must first be explicitly created or + * opened with the appropriate file driver and access privileges. Once all work with the file is + * complete, the file must be explicitly closed. + * + * This chapter discusses the following: + * \li File access modes + * \li Creating, opening, and closing files + * \li The use of file creation property lists + * \li The use of file access property lists + * \li The use of low-level file drivers + * + * This chapter assumes an understanding of the material presented in the data model chapter. For + * more information, @see @ref sec_data_model. + * * \subsection subsec_file_access_modes File Access Modes + * There are two issues regarding file access: + * + * + * Four access modes address these concerns. Two of these modes can be used with #H5Fcreate, and + * two modes can be used with #H5Fopen. + * \li #H5Fcreate accepts #H5F_ACC_EXCL or #H5F_ACC_TRUNC + * \li #H5Fopen accepts #H5F_ACC_RDONLY or #H5F_ACC_RDWR + * + * The access modes are described in the table below. + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + *
Access flags and modes
Access FlagResulting Access Mode
#H5F_ACC_EXCLIf the file already exists, #H5Fcreate fails. If the file does not exist, + * it is created and opened with read-write access. (Default)
#H5F_ACC_TRUNCIf the file already exists, the file is opened with read-write access, + * and new data will overwrite any existing data. If the file does not exist, + * it is created and opened with read-write access.
#H5F_ACC_RDONLYAn existing file is opened with read-only access. If the file does not + * exist, #H5Fopen fails. (Default)
#H5F_ACC_RDWRAn existing file is opened with read-write access. If the file does not + * exist, #H5Fopen fails.
+ * + * By default, #H5Fopen opens a file for read-only access; passing #H5F_ACC_RDWR allows + * read-write access to the file. + * + * By default, #H5Fcreate fails if the file already exists; only passing #H5F_ACC_TRUNC allows + * the truncating of an existing file. + * * \subsection subsec_file_creation_access File Creation and File Access Properties + * File creation and file access property lists control the more complex aspects of creating and + * accessing files. + * + * File creation property lists control the characteristics of a file such as the size of the userblock, + * a user-definable data block; the size of data address parameters; properties of the B-trees that are + * used to manage the data in the file; and certain HDF5 Library versioning information. + * + * For more information, @see @ref subsubsec_file_property_lists_props. + * + * This section has a more detailed discussion of file creation properties. If you have no special + * requirements for these file characteristics, you can simply specify #H5P_DEFAULT for the default + * file creation property list when a file creation property list is called for. + * + * File access property lists control properties and means of accessing a file such as data alignment + * characteristics, metadata block and cache sizes, data sieve buffer size, garbage collection + * settings, and parallel I/O. Data alignment, metadata block and cache sizes, and data sieve buffer + * size are factors in improving I/O performance. + * + * For more information, @see @ref subsubsec_file_property_lists_access. + * + * This section has a more detailed discussion of file access properties. If you have no special + * requirements for these file access characteristics, you can simply specify #H5P_DEFAULT for the + * default file access property list when a file access property list is called for. + * + * + * + * + * + * + *
Figure 10 - More sample file structures
+ * \image html UML_FileAndProps.gif "UML model for an HDF5 file and its property lists" + *
+ * * \subsection subsec_file_drivers Low-level File Drivers + * The concept of an HDF5 file is actually rather abstract: the address space for what is normally + * thought of as an HDF5 file might correspond to any of the following at the storage level: + * \li Single file on a standard file system + * \li Multiple files on a standard file system + * \li Multiple files on a parallel file system + * \li Block of memory within an application’s memory space + * \li More abstract situations such as virtual files + * + * This HDF5 address space is generally referred to as an HDF5 file regardless of its organization at + * the storage level. + * + * HDF5 accesses a file (the address space) through various types of low-level file drivers. The + * default HDF5 file storage layout is as an unbuffered permanent file which is a single, contiguous + * file on local disk. Alternative layouts are designed to suit the needs of a variety of systems, + * environments, and applications. + * * \subsection subsec_file_program_model Programming Model for Files + * Programming models for creating, opening, and closing HDF5 files are described in the + * sub-sections below. + * * \subsubsection subsubsec_file_program_model_create Creating a New File + * The programming model for creating a new HDF5 file can be summarized as follows: + * \li Define the file creation property list + * \li Define the file access property list + * \li Create the file + * + * First, consider the simple case where we use the default values for the property lists. See the + * example below. + * + * Creating an HDF5 file using property list defaults + * \code + * file_id = H5Fcreate ("SampleFile.h5", H5F_ACC_EXCL, H5P_DEFAULT, H5P_DEFAULT) + * \endcode + * + * Note: The example above specifies that #H5Fcreate should fail if SampleFile.h5 already exists. + * + * A more complex case is shown in the example below. In this example, we define file creation + * and access property lists (though we do not assign any properties), specify that #H5Fcreate + * should fail if SampleFile.h5 already exists, and create a new file named SampleFile.h5. The example + * does not specify a driver, so the default driver, #H5FD_SEC2, will be used. + * + * Creating an HDF5 file using property lists + * \code + * fcplist_id = H5Pcreate (H5P_FILE_CREATE) + * <...set desired file creation properties...> + * faplist_id = H5Pcreate (H5P_FILE_ACCESS) + * <...set desired file access properties...> + * file_id = H5Fcreate ("SampleFile.h5", H5F_ACC_EXCL, fcplist_id, faplist_id) + * \endcode + * Notes: + * 1. A root group is automatically created in a file when the file is first created. + * + * 2. File property lists, once defined, can be reused when another file is created within the same + * application. + * * \subsubsection subsubsec_file_program_model_open Opening an Existing File + * The programming model for opening an existing HDF5 file can be summarized as follows: + * + * + * The code in the example below shows how to open an existing file with read-only access. + * + * Opening an HDF5 file + * \code + * faplist_id = H5Pcreate (H5P_FILE_ACCESS) + * status = H5Pset_fapl_stdio (faplist_id) + * file_id = H5Fopen ("SampleFile.h5", H5F_ACC_RDONLY, faplist_id) + * \endcode + * * \subsubsection subsubsec_file_program_model_close Closing a File + * The programming model for closing an HDF5 file is very simple: + * \li Close file + * + * We close SampleFile.h5 with the code in the example below. + * + * Closing an HDF5 file + * \code + * status = H5Fclose (file_id) + * \endcode + * Note that #H5Fclose flushes all unwritten data to storage and that file_id is the identifier returned + * for SampleFile.h5 by #H5Fopen. + * + * More comprehensive discussions regarding all of these steps are provided below. + * * \subsection subsec_file_h5dump Using h5dump to View a File + * h5dump is a command-line utility that is included in the HDF5 distribution. This program + * provides a straight-forward means of inspecting the contents of an HDF5 file. You can use + * h5dump to verify that a program is generating the intended HDF5 file. h5dump displays ASCII + * output formatted according to the HDF5 DDL grammar. + * + * The following h5dump command will display the contents of SampleFile.h5: + * \code + * h5dump SampleFile.h5 + * \endcode + * + * If no datasets or groups have been created in and no data has been written to the file, the output + * will look something like the following: + * \code + * HDF5 "SampleFile.h5" { + * GROUP "/" { + * } + * } + * \endcode + * + * Note that the root group, indicated above by /, was automatically created when the file was created. + * + * h5dump is described on the + * Tools + * page under + * + * Libraries and Tools Reference. + * The HDF5 DDL grammar is described in the document \ref DDLBNF110. + * * \subsection subsec_file_summary File Function Summaries + * General library (\ref H5 functions and macros), (\ref H5F functions), file related + * (\ref H5P functions), and file driver (\ref H5P functions) are listed below. + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + *
General library functions and macros
FunctionPurpose
#H5check_versionVerifies that HDF5 library versions are consistent.
#H5closeFlushes all data to disk, closes all open identifiers, and cleans up memory.
#H5dont_atexitInstructs the library not to install the atexit cleanup routine.
#H5garbage_collectGarbage collects on all free-lists of all types.
#H5get_libversionReturns the HDF library release number.
#H5openInitializes the HDF5 library.
#H5set_free_list_limitsSets free-list size limits.
#H5_VERSION_GEDetermines whether the version of the library being used is greater than or equal + * to the specified version.
#H5_VERSION_LEDetermines whether the version of the library being used is less than or equal + * to the specified version.
+ * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + *
File functions
FunctionPurpose
#H5Fclear_elink_file_cacheClears the external link open file cache for a file.
#H5FcloseCloses HDF5 file.
#H5FcreateCreates new HDF5 file.
#H5FflushFlushes data to HDF5 file on storage medium.
#H5Fget_access_plistReturns a file access property list identifier.
#H5Fget_create_plistReturns a file creation property list identifier.
#H5Fget_file_imageRetrieves a copy of the image of an existing, open file.
#H5Fget_filesizeReturns the size of an HDF5 file.
#H5Fget_freespaceReturns the amount of free space in a file.
#H5Fget_infoReturns global information for a file.
#H5Fget_intentDetermines the read/write or read-only status of a file.
#H5Fget_mdc_configObtain current metadata cache configuration for target file.
#H5Fget_mdc_hit_rateObtain target file’s metadata cache hit rate.
#H5Fget_mdc_sizeObtain current metadata cache size data for specified file.
#H5Fget_mpi_atomicityRetrieves the atomicity mode in use.
#H5Fget_nameRetrieves the name of the file to which the object belongs.
#H5Fget_obj_countReturns the number of open object identifiers for an open file.
#H5Fget_obj_idsReturns a list of open object identifiers.
#H5Fget_vfd_handleReturns pointer to the file handle from the virtual file driver.
#H5Fis_hdf5Determines whether a file is in the HDF5 format.
#H5FmountMounts a file.
#H5FopenOpens an existing HDF5 file.
#H5FreopenReturns a new identifier for a previously-opened HDF5 file.
#H5Freset_mdc_hit_rate_statsReset hit rate statistics counters for the target file.
#H5Fset_mdc_configUse to configure metadata cache of target file.
#H5Fset_mpi_atomicityUse to set the MPI atomicity mode.
#H5FunmountUnmounts a file.
+ * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + *
File creation property list functions
FunctionPurpose
#H5Pset_userblock/#H5Pget_userblockSets/retrieves size of userblock.
#H5Pset_sizes/#H5Pget_sizesSets/retrieves byte size of offsets and lengths used to address objects in HDF5 file.
#H5Pset_sym_k/#H5Pget_sym_kSets/retrieves size of parameters used to control symbol table nodes.
#H5Pset_istore_k/#H5Pget_istore_kSets/retrieves size of parameter used to control B-trees for indexing chunked datasets.
#H5Pset_file_imageSets an initial file image in a memory buffer.
#H5Pget_file_imageRetrieves a copy of the file image designated as the initial content and structure of a file.
#H5Pset_shared_mesg_nindexes/#H5Pget_shared_mesg_nindexesSets or retrieves number of shared object header message indexes in file + * creation property list.
#H5Pset_shared_mesg_indexConfigures the specified shared object header message index.
#H5Pget_shared_mesg_indexRetrieves the configuration settings for a shared message index.
#H5Pset_shared_mesg_phase_change/#H5Pget_shared_mesg_phase_changeSets or retrieves shared object header message storage phase change thresholds.
#H5Pget_version
+ * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + *
File access property list functions
FunctionPurpose
#H5Pset_alignment/#H5Pget_alignmentSets/retrieves alignment properties.
#H5Pset_cache/#H5Pget_cacheSets/retrieves metadata cache and raw data chunk cache parameters.
#H5Pset_elink_file_cache_size/#H5Pget_elink_file_cache_sizeSets/retrieves the size of the external link open file cache from the specified + * file access property list.
#H5Pset_gc_references/#H5Pget_gc_referencesSets/retrieves garbage collecting references flag.
#H5Pset_family_offsetSets offset property for low-level access to a file in a family of files.
#H5Pget_family_offsetRetrieves a data offset from the file access property list.
#H5Pset_meta_block_size/#H5Pget_meta_block_sizeSets the minimum metadata blocksize or retrieves the current metadata block size setting.
#H5Pset_mdc_configSet the initial metadata cache configuration in the indicated File Access Property List + * to the supplied value.
#H5Pget_mdc_configGet the current initial metadata cache config-uration from the indicated File Access + * Property List.
#H5Pset_sieve_buf_size/#H5Pget_sieve_buf_sizeSets/retrieves maximum size of data sieve buffer.
#H5Pset_libver_boundsSets bounds on library versions, and indirectly format versions, to be used + * when creating objects.
#H5Pget_libver_boundsRetrieves library version bounds settings that indirectly control the format + * versions used when creating objects.
#H5Pset_small_data_block_sizeSets the size of a contiguous block reserved for small data.
#H5Pget_small_data_block_sizeRetrieves the current small data block size setting.
+ * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + *
File driver functions
FunctionPurpose
#H5Pset_driverSets a file driver.
#H5Pget_driverReturns the identifier for the driver used to create a file.
#H5Pget_driver_infoReturns a pointer to file driver information.
#H5Pset_fapl_core/#H5Pget_fapl_coreSets the driver for buffered memory files (in RAM) or retrieves information regarding + * the driver.
#H5Pset_fapl_direct/#H5Pget_fapl_directSets up use of the direct I/O driver or retrieves the direct I/O driver settings.
#H5Pset_fapl_family/#H5Pget_fapl_familySets driver for file families, designed for systems that do not support files + * larger than 2 gigabytes, or retrieves information regarding driver.
#H5Pset_fapl_logSets logging driver.
#H5Pset_fapl_mpio/#H5Pget_fapl_mpioSets driver for files on parallel file systems (MPI I/O) or retrieves information + * regarding the driver.
H5Pset_fapl_mpiposix/H5Pget_fapl_mpiposixNo longer available.
#H5Pset_fapl_multi/#H5Pget_fapl_multiSets driver for multiple files, separating categories of metadata and raw data, + * or retrieves information regarding driver.
#H5Pset_fapl_sec2Sets driver for unbuffered permanent files or retrieves information regarding driver.
#H5Pset_fapl_splitSets driver for split files, a limited case of multiple files with one metadata file + * and one raw data file.
#H5Pset_fapl_stdioSets driver for buffered permanent files.
#H5Pset_fapl_windowsSets the Windows I/O driver.
#H5Pset_multi_typeSpecifies type of data to be accessed via the MULTI driver enabling more direct access.
#H5Pget_multi_typeRetrieves type of data property for MULTI driver.
+ * * \subsection subsec_file_create Creating or Opening an HDF5 File + * This section describes in more detail how to create and how to open files. + * + * New HDF5 files are created and opened with #H5Fcreate; existing files are opened with + * #H5Fopen. Both functions return an object identifier which must eventually be released by calling + * #H5Fclose. + * + * To create a new file, call #H5Fcreate: + * \code + * hid_t H5Fcreate (const char *name, unsigned flags, hid_t fcpl_id, hid_t fapl_id) + * \endcode + * + * #H5Fcreate creates a new file named name in the current directory. The file is opened with read + * and write access; if the #H5F_ACC_TRUNC flag is set, any pre-existing file of the same name in + * the same directory is truncated. If #H5F_ACC_TRUNC is not set or #H5F_ACC_EXCL is set and + * if a file of the same name exists, #H5Fcreate will fail. + * + * The new file is created with the properties specified in the property lists fcpl_id and fapl_id. + * fcpl is short for file creation property list. fapl is short for file access property list. Specifying + * #H5P_DEFAULT for either the creation or access property list will use the library’s default + * creation or access properties. + * + * If #H5Fcreate successfully creates the file, it returns a file identifier for the new file. This + * identifier will be used by the application any time an object identifier, an OID, for the file is + * required. Once the application has finished working with a file, the identifier should be released + * and the file closed with #H5Fclose. + * + * To open an existing file, call #H5Fopen: + * \code + * hid_t H5Fopen (const char *name, unsigned flags, hid_t fapl_id) + * \endcode + * + * #H5Fopen opens an existing file with read-write access if #H5F_ACC_RDWR is set and read-only + * access if #H5F_ACC_RDONLY is set. + * + * fapl_id is the file access property list identifier. Alternatively, #H5P_DEFAULT indicates that the + * application relies on the default I/O access parameters. Creating and changing access property + * lists is documented further below. + * + * A file can be opened more than once via multiple #H5Fopen calls. Each such call returns a unique + * file identifier and the file can be accessed through any of these file identifiers as long as they + * remain valid. Each of these file identifiers must be released by calling #H5Fclose when it is no + * longer needed. + * + * For more information, @see @ref subsubsec_file_property_lists_access. + * For more information, @see @ref subsec_file_property_lists. + * * \subsection subsec_file_closes Closing an HDF5 File + * #H5Fclose both closes a file and releases the file identifier returned by #H5Fopen or #H5Fcreate. + * #H5Fclose must be called when an application is done working with a file; while the HDF5 + * Library makes every effort to maintain file integrity, failure to call #H5Fclose may result in the + * file being abandoned in an incomplete or corrupted state. + * + * To close a file, call #H5Fclose: + * \code + * herr_t H5Fclose (hid_t file_id) + * \endcode + * This function releases resources associated with an open file. After closing a file, the file + * identifier, file_id, cannot be used again as it will be undefined. + * + * #H5Fclose fulfills three purposes: to ensure that the file is left in an uncorrupted state, to ensure + * that all data has been written to the file, and to release resources. Use #H5Fflush if you wish to + * ensure that all data has been written to the file but it is premature to close it. + * + * Note regarding serial mode behavior: When #H5Fclose is called in serial mode, it closes the file + * and terminates new access to it, but it does not terminate access to objects that remain + * individually open within the file. That is, if #H5Fclose is called for a file but one or more objects + * within the file remain open, those objects will remain accessible until they are individually + * closed. To illustrate, assume that a file, fileA, contains a dataset, data_setA, and that both are + * open when #H5Fclose is called for fileA. data_setA will remain open and accessible, including + * writable, until it is explicitly closed. The file will be automatically and finally closed once all + * objects within it have been closed. + * + * Note regarding parallel mode behavior: Once #H5Fclose has been called in parallel mode, access + * is no longer available to any object within the file. + * * \subsection subsec_file_property_lists File Property Lists + * Additional information regarding file structure and access are passed to #H5Fcreate and + * #H5Fopen through property list objects. Property lists provide a portable and extensible method of + * modifying file properties via simple API functions. There are two kinds of file-related property + * lists: + * \li File creation property lists + * \li File access property lists + * + * In the following sub-sections, we discuss only one file creation property, userblock size, in detail + * as a model for the user. Other file creation and file access properties are mentioned and defined + * briefly, but the model is not expanded for each; complete syntax, parameter, and usage + * information for every property list function is provided in the \ref H5P + * section of the HDF5 Reference Manual. + * + * For more information, @see @ref sec_plist. + * * \subsubsection subsubsec_file_property_lists_create Creating a Property List + * If you do not wish to rely on the default file creation and access properties, you must first create + * a property list with #H5Pcreate. + * \code + * hid_t H5Pcreate (hid_t cls_id) + * \endcode + * cls_id is the type of property list being created. In this case, the appropriate values are + * #H5P_FILE_CREATE for a file creation property list and #H5P_FILE_ACCESS for a file access + * property list. + * + * Thus, the following calls create a file creation property list and a file access property list with + * identifiers fcpl_id and fapl_id, respectively: + * \code + * fcpl_id = H5Pcreate (H5P_FILE_CREATE) + * fapl_id = H5Pcreate (H5P_FILE_ACCESS) + * \endcode + * + * Once the property lists have been created, the properties themselves can be modified via the + * functions described in the following sub-sections. + * * \subsubsection subsubsec_file_property_lists_props File Creation Properties + * File creation property lists control the file metadata, which is maintained in the superblock of the + * file. These properties are used only when a file is first created. + * + *

Userblock Size

+ * \code + * herr_t H5Pset_userblock (hid_t plist, hsize_t size) + * herr_t H5Pget_userblock (hid_t plist, hsize_t *size) + * \endcode + * + * The userblock is a fixed-length block of data located at the beginning of the file and is ignored + * by the HDF5 library. This block is specifically set aside for any data or information that + * developers determine to be useful to their applications but that will not be used by the HDF5 + * library. The size of the userblock is defined in bytes and may be set to any power of two with a + * minimum size of 512 bytes. In other words, userblocks might be 512, 1024, or 2048 bytes in + * size. + * + * This property is set with #H5Pset_userblock and queried via #H5Pget_userblock. For example, if + * an application needed a 4K userblock, then the following function call could be used: + * \code + * status = H5Pset_userblock(fcpl_id, 4096) + * \endcode + * + * The property list could later be queried with: + * \code + * status = H5Pget_userblock(fcpl_id, size) + * \endcode + * and the value 4096 would be returned in the parameter size. + * + * Other properties, described below, are set and queried in exactly the same manner. Syntax and + * usage are detailed in the @ref H5P section of the HDF5 Reference Manual. + * + *

Offset and Length Sizes

+ * This property specifies the number of bytes used to store the offset and length of objects in the + * HDF5 file. Values of 2, 4, and 8 bytes are currently supported to accommodate 16-bit, 32-bit, + * and 64-bit file address spaces. + * + * These properties are set and queried via #H5Pset_sizes and #H5Pget_sizes. + * + *

Symbol Table Parameters

+ * The size of symbol table B-trees can be controlled by setting the 1/2-rank and 1/2-node size + * parameters of the B-tree. + * + * These properties are set and queried via #H5Pset_sym_k and #H5Pget_sym_k + * + *

Indexed Storage Parameters

+ * The size of indexed storage B-trees can be controlled by setting the 1/2-rank and 1/2-node size + * parameters of the B-tree. + * + * These properties are set and queried via #H5Pset_istore_k and #H5Pget_istore_k. + * + *

Version Information

+ * Various objects in an HDF5 file may over time appear in different versions. The HDF5 Library + * keeps track of the version of each object in the file. + * + * Version information is retrieved via #H5Pget_version. + * * \subsubsection subsubsec_file_property_lists_access File Access Properties + * This section discusses file access properties that are not related to the low-level file drivers. File + * drivers are discussed separately later in this chapter. + * For more information, @see @ref subsec_file_alternate_drivers. + * + * File access property lists control various aspects of file I/O and structure. + * + *

Data Alignment

+ * Sometimes file access is faster if certain data elements are aligned in a specific manner. This can + * be controlled by setting alignment properties via the #H5Pset_alignment function. There are two + * values involved: + * \li A threshold value + * \li An alignment interval + * + * Any allocation request at least as large as the threshold will be aligned on an address that is a + * multiple of the alignment interval. + * + *

Metadata Block Allocation Size

+ * Metadata typically exists as very small chunks of data; storing metadata elements in a file + * without blocking them can result in hundreds or thousands of very small data elements in the + * file. This can result in a highly fragmented file and seriously impede I/O. By blocking metadata + * elements, these small elements can be grouped in larger sets, thus alleviating both problems. + * + * #H5Pset_meta_block_size sets the minimum size in bytes of metadata block allocations. + * #H5Pget_meta_block_size retrieves the current minimum metadata block allocation size. + * + *

Metadata Cache

+ * Metadata and raw data I/O speed are often governed by the size and frequency of disk reads and + * writes. In many cases, the speed can be substantially improved by the use of an appropriate + * cache. + * + * #H5Pset_cache sets the minimum cache size for both metadata and raw data and a preemption + * value for raw data chunks. #H5Pget_cache retrieves the current values. + * + *

Data Sieve Buffer Size

+ * Data sieve buffering is used by certain file drivers to speed data I/O and is most commonly when + * working with dataset hyperslabs. For example, using a buffer large enough to hold several pieces + * of a dataset as it is read in for hyperslab selections will boost performance noticeably. + * + * #H5Pset_sieve_buf_size sets the maximum size in bytes of the data sieve buffer. + * #H5Pget_sieve_buf_size retrieves the current maximum size of the data sieve buffer. + * + *

Garbage Collection References

+ * Dataset region references and other reference types use space in an HDF5 file’s global heap. If + * garbage collection is on (1) and the user passes in an uninitialized value in a reference structure, + * the heap might become corrupted. When garbage collection is off (0), however, and the user reuses + * a reference, the previous heap block will be orphaned and not returned to the free heap + * space. When garbage collection is on, the user must initialize the reference structures to 0 or risk + * heap corruption. + * + * #H5Pset_gc_references sets the garbage collecting references flag. + * * \subsection subsec_file_alternate_drivers Alternate File Storage Layouts and Low-level File Drivers + * The concept of an HDF5 file is actually rather abstract: the address space for what is normally + * thought of as an HDF5 file might correspond to any of the following: + * \li Single file on standard file system + * \li Multiple files on standard file system + * \li Multiple files on parallel file system + * \li Block of memory within application’s memory space + * \li More abstract situations such as virtual files + * + * This HDF5 address space is generally referred to as an HDF5 file regardless of its organization at + * the storage level. + * + * HDF5 employs an extremely flexible mechanism called the virtual file layer, or VFL, for file + * I/O. A full understanding of the VFL is only necessary if you plan to write your own drivers + * @see \ref VFL in the HDF5 Technical Notes. + * + * For our + * purposes here, it is sufficient to know that the low-level drivers used for file I/O reside in the + * VFL, as illustrated in the following figure. Note that H5FD_STREAM is not available with 1.8.x + * and later versions of the library. + * + * + * + * + * + *
+ * \image html VFL_Drivers.gif "I/O path from application to VFL and low-level drivers to storage" + *
+ * + * As mentioned above, HDF5 applications access HDF5 files through various low-level file + * drivers. The default driver for that layout is the POSIX driver (also known as the SEC2 driver), + * #H5FD_SEC2. Alternative layouts and drivers are designed to suit the needs of a variety of + * systems, environments, and applications. The drivers are listed in the table below. + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + *
Supported file drivers
Driver NameDriver IdentifierDescriptionRelated API
POSIX#H5FD_SEC2This driver uses POSIX file-system functions like read and write to perform I/O to a single, + * permanent file on local disk with no system buffering. This driver is POSIX-compliant and is + * the default file driver for all systems.#H5Pset_fapl_sec2
Direct#H5FD_DIRECTThis is the #H5FD_SEC2 driver except data is written to or read from the file + * synchronously without being cached by the system.#H5Pset_fapl_direct
Log#H5FD_LOGThis is the #H5FD_SEC2 driver with logging capabilities.#H5Pset_fapl_log
Windows#H5FD_WINDOWSThis driver was modified in HDF5-1.8.8 to be a wrapper of the POSIX driver, + * #H5FD_SEC2. This change should not affect user applications.#H5Pset_fapl_windows
STDIO#H5FD_STDIOThis driver uses functions from the standard C stdio.h to perform I/O + * to a single, permanent file on local disk with additional system buffering.#H5Pset_fapl_stdio
Memory#H5FD_COREWith this driver, an application can work with a file in memory for faster reads and + * writes. File contents are kept in memory until the file is closed. At closing, the memory + * version of the file can be written back to disk or abandoned.#H5Pset_fapl_core
Family#H5FD_FAMILYWith this driver, the HDF5 file’s address space is partitioned into pieces and sent to + * separate storage files using an underlying driver of the user’s choice. This driver is for + * systems that do not support files larger than 2 gigabytes.#H5Pset_fapl_family
Multi#H5FD_MULTIWith this driver, data can be stored in multiple files according to the type of the data. + * I/O might work better if data is stored in separate files based on the type of data. The Split + * driver is a special case of this driver.#H5Pset_fapl_multi
SplitH5FD_SPLITThis file driver splits a file into two parts. One part stores metadata, and the other part + * stores raw data. This splitting a file into two parts is a limited case of the Multi driver.#H5Pset_fapl_split
Parallel#H5FD_MPIOThis is the standard HDF5 file driver for parallel file systems. This driver uses the MPI + * standard for both communication and file I/O.#H5Pset_fapl_mpio
Parallel POSIXH5FD_MPIPOSIXThis driver is no longer available
StreamH5FD_STREAMThis driver is no longer available.
+ * + * For more information, see the HDF5 Reference Manual entries for the function calls shown in + * the column on the right in the table above. + * + * Note that the low-level file drivers manage alternative file storage layouts. Dataset storage + * layouts (chunking, compression, and external dataset storage) are managed independently of file + * storage layouts. + * + * If an application requires a special-purpose low-level driver, the VFL provides a public API for + * creating one. For more information on how to create a driver, + * @see @ref VFL in the HDF5 Technical Notes. + * * \subsubsection subsubsec_file_alternate_drivers_id Identifying the Previously‐used File Driver + * When creating a new HDF5 file, no history exists, so the file driver must be specified if it is to be + * other than the default. + * + * When opening existing files, however, the application may need to determine which low-level + * driver was used to create the file. The function #H5Pget_driver is used for this purpose. See the + * example below. + * + * Identifying a driver + * \code + * hid_t H5Pget_driver (hid_t fapl_id) + * \endcode + * + * #H5Pget_driver returns a constant identifying the low-level driver for the access property list + * fapl_id. For example, if the file was created with the POSIX (aka SEC2) driver, + * #H5Pget_driver returns #H5FD_SEC2. + * + * If the application opens an HDF5 file without both determining the driver used to create the file + * and setting up the use of that driver, the HDF5 Library will examine the superblock and the + * driver definition block to identify the driver. + * See the HDF5 File Format Specification + * for detailed descriptions of the superblock and the driver definition block. + * * \subsubsection subsubsec_file_alternate_drivers_sec2 The POSIX (aka SEC2) Driver + * The POSIX driver, #H5FD_SEC2, uses functions from section 2 of the POSIX manual to access + * unbuffered files stored on a local file system. This driver is also known as the SEC2 driver. The + * HDF5 Library buffers metadata regardless of the low-level driver, but using this driver prevents + * data from being buffered again by the lowest layers of the library. + * + * The function #H5Pset_fapl_sec2 sets the file access properties to use the POSIX driver. See the + * example below. + * + * Using the POSIX, aka SEC2, driver + * \code + * herr_t H5Pset_fapl_sec2 (hid_t fapl_id) + * \endcode + * + * Any previously-defined driver properties are erased from the property list. + * + * Additional parameters may be added to this function in the future. Since there are no additional + * variable settings associated with the POSIX driver, there is no H5Pget_fapl_sec2 function. + * * \subsubsection subsubsec_file_alternate_drivers_direct The Direct Driver + * The Direct driver, #H5FD_DIRECT, functions like the POSIX driver except that data is written to + * or read from the file synchronously without being cached by the system. + * + * The functions #H5Pset_fapl_direct and #H5Pget_fapl_direct are used to manage file access properties. + * See the example below. + * + * Using the Direct driver + * \code + * herr_t H5Pset_fapl_direct(hid_t fapl_id, size_t alignment, size_t block_size, size_t cbuf_size) + * herr_t H5Pget_fapl_direct(hid_t fapl_id, size_t *alignment, size_t *block_size, size_t *cbuf_size) + * \endcode + * + * #H5Pset_fapl_direct sets the file access properties to use the Direct driver; any previously defined + * driver properties are erased from the property list. #H5Pget_fapl_direct retrieves the file access + * properties used with the Direct driver. fapl_id is the file access property list identifier. + * alignment is the memory alignment boundary. block_size is the file system block size. + * cbuf_size is the copy buffer size. + * + * Additional parameters may be added to this function in the future. + * * \subsubsection subsubsec_file_alternate_drivers_log The Log Driver + * The Log driver, #H5FD_LOG, is designed for situations where it is necessary to log file access + * activity. + * + * The function #H5Pset_fapl_log is used to manage logging properties. See the example below. + * + * Logging file access + * \code + * herr_t H5Pset_fapl_log (hid_t fapl_id, const char *logfile, unsigned int flags, size_t buf_size) + * \endcode + * + * #H5Pset_fapl_log sets the file access property list to use the Log driver. File access characteristics + * are identical to access via the POSIX driver. Any previously defined driver properties are erased + * from the property list. + * + * Log records are written to the file logfile. + * + * The logging levels set with the verbosity parameter are shown in the table below. + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + *
Logging levels
LevelComments
0Performs no logging.
1Records where writes and reads occur in the file.
2Records where writes and reads occur in the file and what kind of data is written + * at each location. This includes raw data or any of several types of metadata + * (object headers, superblock, B-tree data, local headers, or global headers).
+ * + * There is no H5Pget_fapl_log function. + * + * Additional parameters may be added to this function in the future. + * * \subsubsection subsubsec_file_alternate_drivers_win The Windows Driver + * The Windows driver, #H5FD_WINDOWS, was modified in HDF5-1.8.8 to be a wrapper of the + * POSIX driver, #H5FD_SEC2. In other words, if the Windows drivers is used, any file I/O will + * instead use the functionality of the POSIX driver. This change should be transparent to all user + * applications. The Windows driver used to be the default driver for Windows systems. The + * POSIX driver is now the default. + * + * The function #H5Pset_fapl_windows sets the file access properties to use the Windows driver. + * See the example below. + * + * Using the Windows driver + * \code + * herr_t H5Pset_fapl_windows (hid_t fapl_id) + * \endcode + * + * Any previously-defined driver properties are erased from the property list. + * + * Additional parameters may be added to this function in the future. Since there are no additional + * variable settings associated with the POSIX driver, there is no H5Pget_fapl_windows function. + * * \subsubsection subsubsec_file_alternate_drivers_stdio The STDIO Driver + * The STDIO driver, #H5FD_STDIO, accesses permanent files in a local file system like the + * POSIX driver does. The STDIO driver also has an additional layer of buffering beneath the + * HDF5 Library. + * + * The function #H5Pset_fapl_stdio sets the file access properties to use the STDIO driver. See the + * example below. + * + * Using the STDIO driver + * \code + * herr_t H5Pset_fapl_stdio (hid_t fapl_id) + * \endcode + * + * Any previously defined driver properties are erased from the property list. + * + * Additional parameters may be added to this function in the future. Since there are no additional + * variable settings associated with the STDIO driver, there is no H5Pget_fapl_stdio function. + * * \subsubsection subsubsec_file_alternate_drivers_mem The Memory (aka Core) Driver + * There are several situations in which it is reasonable, sometimes even required, to maintain a file + * entirely in system memory. You might want to do so if, for example, either of the following + * conditions apply: + * + * + * The Memory driver, #H5FD_CORE, provides a mechanism for creating and managing such in memory files. + * The functions #H5Pset_fapl_core and #H5Pget_fapl_core manage file access + * properties. See the example below. + * + * Managing file access for in-memory files + * \code + * herr_t H5Pset_fapl_core (hid_t access_properties, size_t block_size, hbool_t backing_store) + * herr_t H5Pget_fapl_core (hid_t access_properties, size_t *block_size), hbool_t *backing_store) + * \endcode + * + * #H5Pset_fapl_core sets the file access property list to use the Memory driver; any previously + * defined driver properties are erased from the property list. + * + * Memory for the file will always be allocated in units of the specified block_size. + * + * The backing_store Boolean flag is set when the in-memory file is created. + * backing_store indicates whether to write the file contents to disk when the file is closed. If + * backing_store is set to 1 (TRUE), the file contents are flushed to a file with the same name as the + * in-memory file when the file is closed or access to the file is terminated in memory. If + * backing_store is set to 0 (FALSE), the file is not saved. + * + * The application is allowed to open an existing file with the #H5FD_CORE driver. While using + * #H5Fopen to open an existing file, if backing_store is set to 1 and the flag for #H5Fopen is set to + * #H5F_ACC_RDWR, changes to the file contents will be saved to the file when the file is closed. + * If backing_store is set to 0 and the flag for #H5Fopen is set to #H5F_ACC_RDWR, changes to the + * file contents will be lost when the file is closed. If the flag for #H5Fopen is set to + * #H5F_ACC_RDONLY, no change to the file will be allowed either in memory or on file. + * + * If the file access property list is set to use the Memory driver, #H5Pget_fapl_core will return + * block_size and backing_store with the relevant file access property settings. + * + * Note the following important points regarding in-memory files: + * + * + * Additional parameters may be added to these functions in the future. + * + * @see + * HDF5 File Image Operations + * section for information on more advanced usage of the Memory file driver, and + * @see + * Modified Region Writes + * section for information on how to set write operations so that only modified regions are written + * to storage. + * * \subsubsection subsubsec_file_alternate_drivers_family The Family Driver + * HDF5 files can become quite large, and this can create problems on systems that do not support + * files larger than 2 gigabytes. The HDF5 file family mechanism is designed to solve the problems + * this creates by splitting the HDF5 file address space across several smaller files. This structure + * does not affect how metadata and raw data are stored: they are mixed in the address space just as + * they would be in a single, contiguous file. + * + * HDF5 applications access a family of files via the Family driver, #H5FD_FAMILY. The + * functions #H5Pset_fapl_family and #H5Pget_fapl_family are used to manage file family + * properties. See the example below. + * + * Managing file family properties + * \code + * herr_t H5Pset_fapl_family (hid_t fapl_id, + * hsize_t memb_size, hid_t member_properties) + * herr_t H5Pget_fapl_family (hid_t fapl_id, + * hsize_t *memb_size, hid_t *member_properties) + * \endcode + * + * Each member of the family is the same logical size though the size and disk storage reported by + * file system listing tools may be substantially smaller. Examples of file system listing tools are + * \code + * ls -l + * \endcode + * on a Unix system or the detailed folder listing on an Apple or Microsoft Windows + * system. The name passed to #H5Fcreate or #H5Fopen should include a printf(3c)-style integer + * format specifier which will be replaced with the family member number. The first family + * member is numbered zero (0). + * + * #H5Pset_fapl_family sets the access properties to use the Family driver; any previously defined + * driver properties are erased from the property list. member_properties will serve as the file + * access property list for each member of the file family. memb_size specifies the logical size, in + * bytes, of each family member. memb_size is used only when creating a new file or truncating an + * existing file; otherwise the member size is determined by the size of the first member of the + * family being opened. Note: If the size of the off_t type is four bytes, the maximum family + * member size is usually 2^31-1 because the byte at offset 2,147,483,647 is generally inaccessible. + * + * #H5Pget_fapl_family is used to retrieve file family properties. If the file access property list is set + * to use the Family driver, member_properties will be returned with a pointer to a copy of the + * appropriate member access property list. If memb_size is non-null, it will contain the logical + * size, in bytes, of family members. + * + * Additional parameters may be added to these functions in the future. + * + *

Unix Tools and an HDF5 Utility

+ * It occasionally becomes necessary to repartition a file family. A command-line utility for this + * purpose, h5repart, is distributed with the HDF5 library. + * + * \code + * h5repart [-v] [-b block_size[suffix]] [-m member_size[suffix]] source destination + * \endcode + * + * h5repart repartitions an HDF5 file by copying the source file or file family to the destination file + * or file family, preserving holes in the underlying UNIX files. Families are used for the source + * and/or destination if the name includes a printf-style integer format such as %d. The -v switch + * prints input and output file names on the standard error stream for progress monitoring, -b sets + * the I/O block size (the default is 1KB), and -m sets the output member size if the destination is a + * family name (the default is 1GB). block_size and member_size may be suffixed with the letters + * g, m, or k for GB, MB, or KB respectively. + * + * The h5repart utility is described on the Tools page of the HDF5 Reference Manual. + * + * An existing HDF5 file can be split into a family of files by running the file through split(1) on a + * UNIX system and numbering the output files. However, the HDF5 Library is lazy about + * extending the size of family members, so a valid file cannot generally be created by + * concatenation of the family members. + * + * Splitting the file and rejoining the segments by concatenation (split(1) and cat(1) on UNIX + * systems) does not generate files with holes; holes are preserved only through the use of h5repart. + * * \subsubsection subsubsec_file_alternate_drivers_multi The Multi Driver + * In some circumstances, it is useful to separate metadata from raw data and some types of + * metadata from other types of metadata. Situations that would benefit from use of the Multi driver + * include the following: + * + * + * In either case, access to the metadata is substantially easier with the smaller, and possibly more + * localized, metadata files. This often results in improved application performance. + * + * The Multi driver, #H5FD_MULTI, provides a mechanism for segregating raw data and different + * types of metadata into multiple files. The functions #H5Pset_fapl_multi and + * #H5Pget_fapl_multi are used to manage access properties for these multiple files. See the example + * below. + * + * Managing access properties for multiple files + * \code + * herr_t H5Pset_fapl_multi (hid_t fapl_id, const H5FD_mem_t *memb_map, const hid_t *memb_fapl, + * const char * const *memb_name, const haddr_t *memb_addr, + * hbool_t relax) + * herr_t H5Pget_fapl_multi (hid_t fapl_id, const H5FD_mem_t *memb_map, const hid_t *memb_fapl, + * const char **memb_name, const haddr_t *memb_addr, hbool_t *relax) + * \endcode + * + * #H5Pset_fapl_multi sets the file access properties to use the Multi driver; any previously defined + * driver properties are erased from the property list. With the Multi driver invoked, the application + * will provide a base name to #H5Fopen or #H5Fcreate. The files will be named by that base name as + * modified by the rule indicated in memb_name. File access will be governed by the file access + * property list memb_properties. + * + * See #H5Pset_fapl_multi and #H5Pget_fapl_multi in the HDF5 Reference Manual for descriptions + * of these functions and their usage. + * + * Additional parameters may be added to these functions in the future. + * * \subsubsection subsubsec_file_alternate_drivers_split The Split Driver + * The Split driver, H5FD_SPLIT, is a limited case of the Multi driver where only two files are + * created. One file holds metadata, and the other file holds raw data. + * The function #H5Pset_fapl_split is used to manage Split file access properties. See the example + * below. + * + * Managing access properties for split files + * \code + * herr_t H5Pset_fapl_split (hid_t access_properties, const char *meta_extension, + * hid_t meta_properties,const char *raw_extension, hid_t raw_properties) + * \endcode + * + * #H5Pset_fapl_split sets the file access properties to use the Split driver; any previously defined + * driver properties are erased from the property list. + * + * With the Split driver invoked, the application will provide a base file name such as file_name to + * #H5Fcreate or #H5Fopen. The metadata and raw data files in storage will then be named + * file_name.meta_extension and file_name.raw_extension, respectively. For example, if + * meta_extension is defined as .meta and raw_extension is defined as .raw, the final filenames will + * be file_name.meta and file_name.raw. + * + * Each file can have its own file access property list. This allows the creative use of other lowlevel + * file drivers. For instance, the metadata file can be held in RAM and accessed via the + * Memory driver while the raw data file is stored on disk and accessed via the POSIX driver. + * Metadata file access will be governed by the file access property list in meta_properties. Raw + * data file access will be governed by the file access property list in raw_properties. + * + * Additional parameters may be added to these functions in the future. Since there are no + * additional variable settings associated with the Split driver, there is no H5Pget_fapl_split + * function. + * * \subsubsection subsubsec_file_alternate_drivers_par The Parallel Driver + * Parallel environments require a parallel low-level driver. HDF5’s default driver for parallel + * systems is called the Parallel driver, #H5FD_MPIO. This driver uses the MPI standard for both + * communication and file I/O. + * + * The functions #H5Pset_fapl_mpio and #H5Pget_fapl_mpio are used to manage file access + * properties for the #H5FD_MPIO driver. See the example below. + * + * Managing parallel file access properties + * \code + * herr_t H5Pset_fapl_mpio (hid_t fapl_id, MPI_Comm comm, MPI_info info) + * herr_t H5Pget_fapl_mpio (hid_t fapl_id, MPI_Comm *comm, MPI_info *info) + * \endcode + * + * The file access properties managed by #H5Pset_fapl_mpio and retrieved by + * #H5Pget_fapl_mpio are the MPI communicator, comm, and the MPI info object, info. comm and + * info are used for file open. info is an information object much like an HDF5 property list. Both + * are defined in MPI_FILE_OPEN of MPI-2. + * + * The communicator and the info object are saved in the file access property list fapl_id. + * fapl_id can then be passed to MPI_FILE_OPEN to create and/or open the file. + * + * #H5Pset_fapl_mpio and #H5Pget_fapl_mpio are available only in the parallel HDF5 Library and + * are not collective functions. The Parallel driver is available only in the parallel HDF5 Library. + * + * Additional parameters may be added to these functions in the future. + * * \subsection subsec_file_examples Code Examples for Opening and Closing Files * \subsubsection subsubsec_file_examples_trunc Example Using the H5F_ACC_TRUNC Flag + * The following example uses the #H5F_ACC_TRUNC flag when it creates a new file. The default + * file creation and file access properties are also used. Using #H5F_ACC_TRUNC means the + * function will look for an existing file with the name specified by the function. In this case, that + * name is FILE. If the function does not find an existing file, it will create one. If it does find an + * existing file, it will empty the file in preparation for a new set of data. The identifier for the + * "new" file will be passed back to the application program. + * For more information, @see @ref subsec_file_access_modes. + * + * Creating a file with default creation and access properties + * \code + * hid_t file; // identifier + * + * // Create a new file using H5F_ACC_TRUNC access, default + * // file creation properties, and default file access + * // properties. + * file = H5Fcreate(FILE, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT); + * + * // Close the file. + * status = H5Fclose(file); + * \endcode + * * \subsubsection subsubsec_file_examples_props Example with the File Creation Property List + * The example below shows how to create a file with 64-bit object offsets and lengths. + * + * Creating a file with 64-bit offsets + * \code + * hid_t create_plist; + * hid_t file_id; + * + * create_plist = H5Pcreate(H5P_FILE_CREATE); + * H5Pset_sizes(create_plist, 8, 8); + * file_id = H5Fcreate(“test.h5”, H5F_ACC_TRUNC, create_plist, H5P_DEFAULT); + * . + * . + * . + * + * H5Fclose(file_id); + * \endcode + * * \subsubsection subsubsec_file_examples_access Example with the File Access Property List + * This example shows how to open an existing file for independent datasets access by MPI parallel + * I/O: + * + * Opening an existing file for parallel I/O + * \code + * hid_t access_plist; + * hid_t file_id; + * + * access_plist = H5Pcreate(H5P_FILE_ACCESS); + * H5Pset_fapl_mpi(access_plist, MPI_COMM_WORLD, MPI_INFO_NULL); + * + * // H5Fopen must be called collectively + * file_id = H5Fopen(“test.h5”, H5F_ACC_RDWR, access_plist); + * . + * . + * . + * + * // H5Fclose must be called collectively + * H5Fclose(file_id); + * \endcode + * * \subsection subsec_file_multiple Working with Multiple HDF5 Files + * Multiple HDF5 files can be associated so that the files can be worked with as though all the + * information is in a single HDF5 file. A temporary association can be set up by means of the + * #H5Fmount function. A permanent association can be set up by means of the external link + * function #H5Lcreate_external. + * + * The purpose of this section is to describe what happens when the #H5Fmount function is used to + * mount one file on another. + * + * When a file is mounted on another, the mounted file is mounted at a group, and the root group of + * the mounted file takes the place of that group until the mounted file is unmounted or until the + * files are closed. + * + * The figure below shows two files before one is mounted on the other. File1 has two groups and + * three datasets. The group that is the target of the A link has links, Z and Y, to two of the datasets. + * The group that is the target of the B link has a link, W, to the other dataset. File2 has three + * groups and three datasets. The groups in File2 are the targets of the AA, BB, and CC links. The + * datasets in File2 are the targets of the ZZ, YY, and WW links. + * + * + * + * + * + *
+ * \image html Files_fig3.gif "Two separate files" + *
+ * + * The figure below shows the two files after File2 has been mounted File1 at the group that is the + * target of the B link. + * + * + * + * + * + *
+ * \image html Files_fig4.gif "File2 mounted on File1" + *
+ * + * Note: In the figure above, the dataset that is the target of the W link is not shown. That dataset is + * masked by the mounted file. + * + * If a file is mounted on a group that has members, those members are hidden until the mounted + * file is unmounted. There are two ways around this if you need to work with a group member. + * One is to mount the file on an empty group. Another is to open the group member before you + * mount the file. Opening the group member will return an identifier that you can use to locate the + * group member. + * + * The example below shows how #H5Fmount might be used to mount File2 onto File1. + * + * Using H5Fmount + * \code + * status = H5Fmount(loc_id, "/B", child_id, plist_id) + * \endcode + * + * Note: In the code example above, loc_id is the file identifier for File1, /B is the link path to the + * group where File2 is mounted, child_id is the file identifier for File2, and plist_id is a property + * list identifier. + * For more information, @see @ref sec_group. + * + * See the entries for #H5Fmount, #H5Funmount, and #H5Lcreate_external in the HDF5 Reference Manual. + * + * Previous Chapter \ref sec_program - Next Chapter \ref sec_group * */ -- cgit v0.12