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| -rw-r--r-- | MANIFEST | 1 | ||||
| -rw-r--r-- | doxygen/Doxyfile.in | 1 | ||||
| -rw-r--r-- | doxygen/dox/H5AC_cache_config_t.dox | 415 | ||||
| -rw-r--r-- | doxygen/dox/mainpage.dox | 70 | ||||
| -rw-r--r-- | src/H5Fpublic.h | 868 |
5 files changed, 1311 insertions, 44 deletions
@@ -197,6 +197,7 @@ ./doxygen/aliases ./doxygen/Doxyfile.in ./doxygen/dox/api-compat-macros.dox +./doxygen/dox/H5AC_cache_config_t.dox ./doxygen/dox/H5Acreate.dox ./doxygen/dox/H5Aiterate.dox ./doxygen/dox/H5Fget_info.dox diff --git a/doxygen/Doxyfile.in b/doxygen/Doxyfile.in index 711fa7a..24fc4ba 100644 --- a/doxygen/Doxyfile.in +++ b/doxygen/Doxyfile.in @@ -854,6 +854,7 @@ INPUT_ENCODING = UTF-8 FILE_PATTERNS = H5*public.h \ H5*module.h \ + H5FDmpio.h \ H5VLconnector.h \ H5VLconnector_passthru.h \ H5VLnative.h \ diff --git a/doxygen/dox/H5AC_cache_config_t.dox b/doxygen/dox/H5AC_cache_config_t.dox new file mode 100644 index 0000000..9b9862b --- /dev/null +++ b/doxygen/dox/H5AC_cache_config_t.dox @@ -0,0 +1,415 @@ +/** + * \page H5AC-cache-config-t Metadata Cache Configuration + * \tableofcontents + * + * \section gcf General configuration fields + * + * \par version + * Integer field containing the version number of this version + * of the H5AC_cache_config_t structure. Any instance of + * H5AC_cache_config_t passed to the cache must have a known + * version number, or an error will be flagged. + * + * \par rpt_fcn_enabled + * \parblock + * Boolean field used to enable and disable the default + * reporting function. This function is invoked every time the + * automatic cache resize code is run, and reports on its activities. + * + * This is a debugging function, and should normally be turned off. + * \endparblock + * + * \par open_trace_file + * \parblock + * Boolean field indicating whether the trace_file_name + * field should be used to open a trace file for the cache. + * + * \Emph{*** DEPRECATED ***} Use \Code{H5Fstart/stop} logging functions instead + * + * The trace file is a debuging feature that allow the capture of + * top level metadata cache requests for purposes of debugging and/or + * optimization. This field should normally be set to \c FALSE, as + * trace file collection imposes considerable overhead. + * + * This field should only be set to \c TRUE when the trace_file_name + * contains the full path of the desired trace file, and either + * there is no open trace file on the cache, or the \c close_trace_file + * field is also \c TRUE. + * \endparblock + * + * \par close_trace_file + * \parblock + * Boolean field indicating whether the current trace + * file (if any) should be closed. + * + * \Emph{*** DEPRECATED ***} Use \Code{H5Fstart/stop} logging functions instead + * + * See the above comments on the open_trace_file field. This field + * should be set to \c FALSE unless there is an open trace file on the + * cache that you wish to close. + * \endparblock + * + * \par trace_file_name + * \parblock + * Full path of the trace file to be opened if the + * open_trace_file field is \c TRUE. + * + * \Emph{*** DEPRECATED ***} Use \Code{H5Fstart/stop} logging functions instead + * + * In the parallel case, an ascii representation of the mpi rank of + * the process will be appended to the file name to yield a unique + * trace file name for each process. + * + * The length of the path must not exceed #H5AC__MAX_TRACE_FILE_NAME_LEN + * characters. + * \endparblock + * + * \par evictions_enabled + * \parblock + * Boolean field used to either report the current + * evictions enabled status of the cache, or to set the cache's + * evictions enabled status. + * + * In general, the metadata cache should always be allowed to + * evict entries. However, in some cases it is advantageous to + * disable evictions briefly, and thereby postpone metadata + * writes. However, this must be done with care, as the cache + * can grow quickly. If you do this, re-enable evictions as + * soon as possible and monitor cache size. + * + * At present, evictions can only be disabled if automatic + * cache resizing is also disabled (that is, \Code{(incr_mode == + * H5C_incr__off ) && ( decr_mode == H5C_decr__off )}). There + * is no logical reason why this should be so, but it simplifies + * implementation and testing, and I can't think of any reason + * why it would be desireable. If you can think of one, I'll + * revisit the issue. (JM) + * \endparblock + * + * \par set_initial_size + * Boolean flag indicating whether the size of the + * initial size of the cache is to be set to the value given in + * the initial_size field. If set_initial_size is \c FALSE, the + * initial_size field is ignored. + * + * \par initial_size + * If enabled, this field contain the size the cache is + * to be set to upon receipt of this structure. Needless to say, + * initial_size must lie in the closed interval \Code{[min_size, max_size]}. + * + * \par min_clean_fraction + * \c double in the range 0 to 1 indicating the fraction + * of the cache that is to be kept clean. This field is only used + * in parallel mode. Typical values are 0.1 to 0.5. + * + * \par max_size + * Maximum size to which the cache can be adjusted. The + * supplied value must fall in the closed interval + * \Code{[MIN_MAX_CACHE_SIZE, MAX_MAX_CACHE_SIZE]}. Also, \c max_size must + * be greater than or equal to \c min_size. + * + * \par min_size + * Minimum size to which the cache can be adjusted. The + * supplied value must fall in the closed interval + * \Code{[H5C__MIN_MAX_CACHE_SIZE, H5C__MAX_MAX_CACHE_SIZE]}. Also, \c min_size + * must be less than or equal to \c max_size. + * + * \par epoch_length + * \parblock + * Number of accesses on the cache over which to collect + * hit rate stats before running the automatic cache resize code, + * if it is enabled. + * + * At the end of an epoch, we discard prior hit rate data and start + * collecting afresh. The epoch_length must lie in the closed + * interval \Code{[H5C__MIN_AR_EPOCH_LENGTH, H5C__MAX_AR_EPOCH_LENGTH]}. + * \endparblock + * + * + * \section csicf Cache size increase control fields + * + * \par incr_mode + * Instance of the \c H5C_cache_incr_mode enumerated type whose + * value indicates how we determine whether the cache size should be + * increased. At present there are two possible values: + * \li \c H5C_incr__off: Don't attempt to increase the size of the cache + * automatically.\n + * When this increment mode is selected, the remaining fields + * in the cache size increase section ar ignored. + * \li \c H5C_incr__threshold: Attempt to increase the size of the cache + * whenever the average hit rate over the last epoch drops + * below the value supplied in the \c lower_hr_threshold + * field.\n + * Note that this attempt will fail if the cache is already + * at its maximum size, or if the cache is not already using + * all available space. + * + * Note that you must set \c decr_mode to \c H5C_incr__off if you + * disable metadata cache entry evictions. + * + * \par lower_hr_threshold + * \parblock + * Lower hit rate threshold. If the increment mode + * (\c incr_mode) is \c H5C_incr__threshold and the hit rate drops below the + * value supplied in this field in an epoch, increment the cache size by + * \c size_increment. Note that cache size may not be incremented above + * \c max_size, and that the increment may be further restricted by the + * \c max_increment field if it is enabled. + * + * When enabled, this field must contain a value in the range [0.0, 1.0]. + * Depending on the \c incr_mode selected, it may also have to be less than + * \c upper_hr_threshold. + * \endparblock + * + * \par increment + * \parblock + * Double containing the multiplier used to derive the new + * cache size from the old if a cache size increment is triggered. + * The increment must be greater than 1.0, and should not exceed 2.0. + * + * The new cache size is obtained my multiplying the current max cache + * size by the increment, and then clamping to \c max_size and to stay + * within the \c max_increment as necessary. + * \endparblock + * + * \par apply_max_increment + * Boolean flag indicating whether the \c max_increment + * field should be used to limit the maximum cache size increment. + * + * \par max_increment + * If enabled by the \c apply_max_increment field described + * above, this field contains the maximum number of bytes by which the + * cache size can be increased in a single re-size. + * + * \par flash_incr_mode + * \parblock + * Instance of the \c H5C_cache_flash_incr_mode enumerated + * type whose value indicates whether and by which algorithm we should + * make flash increases in the size of the cache to accommodate insertion + * of large entries and large increases in the size of a single entry. + * + * The addition of the flash increment mode was occasioned by performance + * problems that appear when a local heap is increased to a size in excess + * of the current cache size. While the existing re-size code dealt with + * this eventually, performance was very bad for the remainder of the + * epoch. + * + * At present, there are two possible values for the \c flash_incr_mode: + * + * \li \c H5C_flash_incr__off: Don't perform flash increases in the size of the cache. + * + * \li \c H5C_flash_incr__add_space: Let \c x be either the size of a newly + * newly inserted entry, or the number of bytes by which the + * size of an existing entry has been increased.\n + * If \Code{x > flash_threshold * current max cache size}, + * increase the current maximum cache size by \Code{x * flash_multiple} + * less any free space in the cache, and star a new epoch. For + * now at least, pay no attention to the maximum increment. + * + * In both of the above cases, the flash increment pays no attention to + * the maximum increment (at least in this first incarnation), but DOES + * stay within max_size. + * + * With a little thought, it should be obvious that the above flash + * cache size increase algorithm is not sufficient for all circumstances + * -- for example, suppose the user round robins through + * \Code{(1/flash_threshold) +1} groups, adding one data set to each on each + * pass. Then all will increase in size at about the same time, requiring + * the max cache size to at least double to maintain acceptable + * performance, however the above flash increment algorithm will not be + * triggered. + * + * Hopefully, the add space algorithms detailed above will be sufficient + * for the performance problems encountered to date. However, we should + * expect to revisit the issue. + * \endparblock + * + * \par flash_multiple + * Double containing the multiple described above in the + * \c H5C_flash_incr__add_space section of the discussion of the + * \c flash_incr_mode section. This field is ignored unless \c flash_incr_mode + * is \c H5C_flash_incr__add_space. + * + * \par flash_threshold + * Double containing the factor by which current max cache + * size is multiplied to obtain the size threshold for the add_space flash + * increment algorithm. The field is ignored unless \c flash_incr_mode is + * \c H5C_flash_incr__add_space. + * + * + * \section csdcf Cache size decrease control fields + * + * \par decr_mode + * \parblock + * Instance of the \c H5C_cache_decr_mode enumerated type whose + * value indicates how we determine whether the cache size should be + * decreased. At present there are four possibilities. + * + * \li \c H5C_decr__off: Don't attempt to decrease the size of the cache + * automatically.\n + * When this increment mode is selected, the remaining fields + * in the cache size decrease section are ignored. + * \li \c H5C_decr__threshold: Attempt to decrease the size of the cache + * whenever the average hit rate over the last epoch rises + * above the value supplied in the \c upper_hr_threshold + * field. + * \li \c H5C_decr__age_out: At the end of each epoch, search the cache for + * entries that have not been accessed for at least the number + * of epochs specified in the epochs_before_eviction field, and + * evict these entries. Conceptually, the maximum cache size + * is then decreased to match the new actual cache size. However, + * this reduction may be modified by the \c min_size, the + * \c max_decrement, and/or the \c empty_reserve. + * \li \c H5C_decr__age_out_with_threshold: Same as age_out, but we only + * attempt to reduce the cache size when the hit rate observed + * over the last epoch exceeds the value provided in the + * \c upper_hr_threshold field. + * + * Note that you must set \c decr_mode to \c H5C_decr__off if you + * disable metadata cache entry evictions. + * \endparblock + * + * \par upper_hr_threshold + * \parblock + * Upper hit rate threshold. The use of this field + * varies according to the current \c decr_mode : + * + * \c H5C_decr__off or \c H5C_decr__age_out: The value of this field is + * ignored. + * + * \li \c H5C_decr__threshold: If the hit rate exceeds this threshold in any + * epoch, attempt to decrement the cache size by size_decrement.\n + * Note that cache size may not be decremented below \c min_size.\n + * Note also that if the \c upper_threshold is 1.0, the cache size\n + * will never be reduced. + * + * \li \c H5C_decr__age_out_with_threshold: If the hit rate exceeds this + * threshold in any epoch, attempt to reduce the cache size + * by evicting entries that have not been accessed for more + * than the specified number of epochs. + * \endparblock + * + * \par decrement + * \parblock + * This field is only used when the decr_mode is + * \c H5C_decr__threshold. + * + * The field is a double containing the multiplier used to derive the + * new cache size from the old if a cache size decrement is triggered. + * The decrement must be in the range 0.0 (in which case the cache will + * try to contract to its minimum size) to 1.0 (in which case the + * cache will never shrink). + * \endparblock + * + * \par apply_max_decrement + * Boolean flag used to determine whether decrements + * in cache size are to be limited by the \c max_decrement field. + * + * \par max_decrement + * Maximum number of bytes by which the cache size can be + * decreased in a single re-size. Note that decrements may also be + * restricted by the \c min_size of the cache, and (in age out modes) by + * the \c empty_reserve field. + * + * \par epochs_before_eviction + * \parblock + * Integer field used in \c H5C_decr__age_out and + * \c H5C_decr__age_out_with_threshold decrement modes. + * + * This field contains the number of epochs an entry must remain + * unaccessed before it is evicted in an attempt to reduce the + * cache size. If applicable, this field must lie in the range + * \Code{[1, H5C__MAX_EPOCH_MARKERS]}. + * \endparblock + * + * \par apply_empty_reserve + * Boolean field controlling whether the empty_reserve + * field is to be used in computing the new cache size when the + * decr_mode is H5C_decr__age_out or H5C_decr__age_out_with_threshold. + * + * \par empty_reserve + * \parblock + * To avoid a constant racheting down of cache size by small + * amounts in the \c H5C_decr__age_out and \c H5C_decr__age_out_with_threshold + * modes, this field allows one to require that any cache size + * reductions leave the specified fraction of unused space in the cache. + * + * The value of this field must be in the range [0.0, 1.0]. I would + * expect typical values to be in the range of 0.01 to 0.1. + * \endparblock + * + * + * \section pcf Parallel Configuration Fields + * + * In PHDF5, all operations that modify metadata must be executed collectively. + * + * We used to think that this was enough to ensure consistency across the + * metadata caches, but since we allow processes to read metadata individually, + * the order of dirty entries in the LRU list can vary across processes, + * which can result in inconsistencies between the caches. + * + * PHDF5 uses several strategies to prevent such inconsistencies in metadata, + * all of which use the fact that the same stream of dirty metadata is seen + * by all processes for purposes of synchronization. This is done by + * having each process count the number of bytes of dirty metadata generated, + * and then running a "sync point" whenever this count exceeds a user + * specified threshold (see \c dirty_bytes_threshold below). + * + * The current metadata write strategy is indicated by the + * \c metadata_write_strategy field. The possible values of this field, along + * with the associated metadata write strategies are discussed below. + * + * \par dirty_bytes_threshold + * \parblock + * Threshold of dirty byte creation used to + * synchronize updates between caches. (See above for outline and + * motivation.) + * + * This value MUST be consistent across all processes accessing the + * file. This field is ignored unless HDF5 has been compiled for + * parallel. + * \endparblock + * + * \par metadata_write_strategy + * Integer field containing a code indicating the + * desired metadata write strategy. The valid values of this field + * are enumerated and discussed below: + * + * \li #H5AC_METADATA_WRITE_STRATEGY__PROCESS_0_ONLY\n + * When metadata_write_strategy is set to this value, only process + * zero is allowed to write dirty metadata to disk. All other + * processes must retain dirty metadata until they are informed at + * a sync point that the dirty metadata in question has been written + * to disk.\n + * When the sync point is reached (or when there is a user generated + * flush), process zero flushes sufficient entries to bring it into + * complience with its min clean size (or flushes all dirty entries in + * the case of a user generated flush), broad casts the list of + * entries just cleaned to all the other processes, and then exits + * the sync point.\n + * Upon receipt of the broadcast, the other processes mark the indicated + * entries as clean, and leave the sync point as well. + * + * \li #H5AC_METADATA_WRITE_STRATEGY__DISTRIBUTED\n + * In the distributed metadata write strategy, process zero still makes + * the decisions as to what entries should be flushed, but the actual + * flushes are distributed across the processes in the computation to + * the extent possible.\n + * In this strategy, when a sync point is triggered (either by dirty + * metadata creation or manual flush), all processes enter a barrier.\n + * On the other side of the barrier, process 0 constructs an ordered + * list of the entries to be flushed, and then broadcasts this list + * to the caches in all the processes.\n + * All processes then scan the list of entries to be flushed, flushing + * some, and marking the rest as clean. The algorithm for this purpose + * ensures that each entry in the list is flushed exactly once, and + * all are marked clean in each cache.\n + * Note that in the case of a flush of the cache, no message passing + * is necessary, as all processes have the same list of dirty entries, + * and all of these entries must be flushed. Thus in this case it is + * sufficient for each process to sort its list of dirty entries after + * leaving the initial barrier, and use this list as if it had been + * received from process zero.\n + * To avoid possible messages from the past/future, all caches must + * wait until all caches are done before leaving the sync point. + */
\ No newline at end of file diff --git a/doxygen/dox/mainpage.dox b/doxygen/dox/mainpage.dox index 83fc323..eda967b 100644 --- a/doxygen/dox/mainpage.dox +++ b/doxygen/dox/mainpage.dox @@ -1,36 +1,44 @@ -/*! \mainpage API Documentation for HDF5 Version 1.13 (Draft) +/*! \mainpage HDF5 C-API Reference + * + * The HDF5 C-API provides applications with fine-grained control over all + * aspects HDF5 functionality. This functionality is grouped into the following + * \Emph{modules}: + * \li \ref H5A "Attributes" — Management of HDF5 attributes (\ref H5A) + * \li \ref H5D "Datasets" — Management of HDF5 datasets (\ref H5D) + * \li \ref H5S "Dataspaces" — Management of HDF5 dataspaces which describe the shape of datasets and attributes (\ref H5S) + * \li \ref H5T "Datatypes" — Management of datatypes which describe elements of datasets and attributes (\ref H5T) + * \li \ref H5E "Error Handling" — Functions for handling errors that occur within HDF5 (\ref H5E) + * \li \ref H5F "Files" — Management of HDF5 files (\ref H5F) + * \li \ref H5Z "Filters" — Configuration of filters that process data during I/O operation (\ref H5Z) + * \li \ref H5G "Groups" — Management of groups in HDF5 files (\ref H5G) + * \li \ref H5I "Identifiers" — Management of object identifiers and object names (\ref H5I) + * \li \ref H5 "Library" — General purpose library functions (\ref H5) + * \li \ref H5L "Links" — Management of links in HDF5 groups (\ref H5L) + * \li \ref H5O "Objects" — Management of objects in HDF5 files (\ref H5O) + * \li \ref H5PL "Plugins" — Programmatic control over dynamically loaded plugins (\ref H5PL) + * \li \ref H5P "Property Lists" — Management of property lists to control HDF5 library behavior (\ref H5P) + * \li \ref H5R "References" — Management of references to specific objects and data regions in an HDF5 file (\ref H5R) + * \li \ref H5VL "Virtual Object Layer" — Management of the Virtual Object Layer (\ref H5VL) + * + * Here are a few simple rules to follow: + * + * \li \Bold{Handle discipline:} If you acquire a handle (by creation or coopy), \Emph{you own it!} (..., i.e., you have to close it.) + * \li \Bold{Dynamic memory allocation:} ... + * \li \Bold{Use of locations:} Identifier + name combo + * + * \attention \Bold{C++ Developers using HDF5 C-API functions beware:}\n + * If a C routine that takes a function pointer as an argument is called from + * within C++ code, the C routine should be returned from normally. + * Examples of this kind of routine include callbacks such as H5Pset_elink_cb() + * and H5Pset_type_conv_cb() and functions such as H5Tconvert() and H5Ewalk2().\n + * Exiting the routine in its normal fashion allows the HDF5 C library to clean + * up its work properly. In other words, if the C++ application jumps out of + * the routine back to the C++ \c catch statement, the library is not given the + * opportunity to close any temporary data structures that were set up when the + * routine was called. The C++ application should save some state as the + * routine is started so that any problem that occurs might be diagnosed. * * \todo Fix the search form for server deployments. * \todo Make it mobile-friendly * - * \section intro_sec Introduction - * - * \todo Write an introduction. - * - * \section quick_links Quick Links - * - * <ul> - * <li>\ref PDT "Predefined Datatypes"</li> - * <li>\ref api-compat-macros "API Compatibility Macros"</li> - * <li><a href="https://hdf5.wiki/">HDF5 Wiki</a></li> - * </ul> - * - * \section using_locations The Use of Locations (Identifier + Name) in the HDF5 API - * - * \todo Make this crystal clear! - * - * \section cpp_note Programming Note for C++ Developers Using C Functions - * - * If a C routine that takes a function pointer as an argument is called from - * within C++ code, the C routine should be returned from normally. - * - * Examples of this kind of routine include callbacks such as H5Pset_elink_cb() - * and H5Pset_type_conv_cb() and functions such as H5Tconvert() and H5Ewalk2(). - * - * Exiting the routine in its normal fashion allows the HDF5 C library to clean - * up its work properly. In other words, if the C++ application jumps out of - * the routine back to the C++ \c catch statement, the library is not given the - * opportunity to close any temporary data structures that were set up when the - * routine was called. The C++ application should save some state as the - * routine is started so that any problem that occurs might be diagnosed. */
\ No newline at end of file diff --git a/src/H5Fpublic.h b/src/H5Fpublic.h index be8eced..82895a8 100644 --- a/src/H5Fpublic.h +++ b/src/H5Fpublic.h @@ -226,6 +226,7 @@ typedef enum H5F_file_space_type_t { H5F_FILE_SPACE_NTYPES /**< Sentinel */ } H5F_file_space_type_t; +//! [H5F_retry_info_t_snip] #define H5F_NUM_METADATA_READ_RETRY_TYPES 21 /** @@ -236,6 +237,7 @@ typedef struct H5F_retry_info_t { unsigned nbins; uint32_t *retries[H5F_NUM_METADATA_READ_RETRY_TYPES]; } H5F_retry_info_t; +//! [H5F_retry_info_t_snip] /** * Callback for H5Pset_object_flush_cb() in a file access property list @@ -953,32 +955,542 @@ H5_DLL ssize_t H5Fget_file_image(hid_t file_id, void *buf_ptr, size_t buf_len); /** * \ingroup MDC * - * \todo Finish this! + * \brief Obtains current metadata cache configuration for target file + * + * \file_id + * \param[in,out] config_ptr Pointer to the H5AC_cache_config_t instance in which + * the current metadata cache configuration is to be + * reported. The fields of this structure are discussed + * \ref H5AC-cache-config-t "here". + * \return \herr_t + * + * \details H5Fget_mdc_config() loads the current metadata cache configuration + * into the instance of H5AC_cache_config_t pointed to by the \p config_ptr + * parameter. + * + * Note that the \c version field of \p config_ptr must be initialized + * --this allows the library to support old versions of the H5AC_cache_config_t + * structure. + * + * \par General configuration section + * <table> + * <tr> + * <td><em>int</em> <code>version</code> </td> + * <td>IN: Integer field indicating the the version of the H5AC_cache_config_t in use. This field should + * be set to #H5AC__CURR_CACHE_CONFIG_VERSION (defined in H5ACpublic.h).</td> + * </tr> + * <tr> + * <td><em>hbool_t</em> <code>rpt_fcn_enabled</code> </td> + * <td><p>OUT: Boolean flag indicating whether the adaptive cache resize report function is enabled. This + * field should almost always be set to disabled (<code>0</code>). Since resize algorithm activity is + * reported via stdout, it MUST be set to disabled (<code>0</code>) on Windows machines.</p><p>The + * report function is not supported code, and can be expected to change between versions of the + * library. Use it at your own risk.</p></td> + * </tr> + * <tr> + * <td><em>hbool_t</em> <code>open_trace_file</code> </td> + * <td>OUT: Boolean field indicating whether the <code>trace_file_name</code> field should be used to open + * a trace file for the cache. This field will always be set to <code>0</code> in this context.</td> + * </tr> + * <tr> + * <td><em>hbool_t</em> <code>close_trace_file</code> </td> + * <td>OUT: Boolean field indicating whether the current trace file (if any) should be closed. This field + * will always be set to <code>0</code> in this context.</td></tr> + * <tr> + * <td><em>char*</em><code>trace_file_name</code> </td> + * <td>OUT: Full path name of the trace file to be opened if the <code>open_trace_file</code> field is set + * to <code>1</code>. This field will always be set to the empty string in this context.</td></tr> + * <tr> + * <td><em>hbool_t</em> <code>evictions_enabled</code> </td> + * <td>OUT: Boolean flag indicating whether metadata cache entry evictions are + * enabled.</td> + * </tr> + * <tr> + * <td><em>hbool_t</em> <code>set_initial_size</code> </td> + * <td>OUT: Boolean flag indicating whether the cache should be created with a user specified initial + * maximum size.<p>If the configuration is loaded from the cache, this flag will always be set + * to <code>0</code>.</p></td> + * </tr> + * <tr> + * <td><em>size_t</em> <code>initial_size</code> </td> + * <td>OUT: Initial maximum size of the cache in bytes, if applicable.<p>If the configuration is loaded + * from the cache, this field will contain the cache maximum size as of the time of the + * call.</p></td> + * </tr> + * <tr> + * <td><em>double</em> <code>min_clean_fraction</code> </td> + * <td>OUT: Float value specifying the minimum fraction of the cache that must be kept either clean or + * empty when possible.</td> + * </tr> + * <tr> + * <td><em>size_t</em> <code>max_size</code> </td> + * <td>OUT: Upper bound (in bytes) on the range of values that the adaptive cache resize code can select + * as the maximum cache size.</td> + * </tr> + * <tr> + * <td><em>size_t</em> <code>min_size</code> </td> + * <td>OUT: Lower bound (in bytes) on the range of values that the adaptive cache resize code can select + * as the maximum cache size.</td> + * </tr> + * <tr> + * <td><em>long int</em> <code>epoch_length</code> </td> + * <td>OUT: Number of cache accesses between runs of the adaptive cache resize + * code.</td> + * </tr> + * </table> + * + * \par Increment configuration section + * <table> + * <tr> + * <td><em>enum H5C_cache_incr_mode</em> <code>incr_mode</code> </td> + * <td>OUT: Enumerated value indicating the operational mode of the automatic cache size increase code. At + * present, only the following values are legal:<p>\c H5C_incr__off: Automatic cache size increase is + * disabled.</p><p>\c H5C_incr__threshold: Automatic cache size increase is enabled using the hit rate + * threshold algorithm.</p></td> + * </tr> + * <tr> + * <td><em>double</em> <code>lower_hr_threshold</code> </td> + * <td>OUT: Hit rate threshold used in the hit rate threshold cache size increase algorithm.</td> + * </tr> + * <tr> + * <td><em>double</em> <code>increment</code> </td> + * <td>OUT: The factor by which the current maximum cache size is multiplied to obtain an initial new + * maximum cache size if a size increase is triggered in the hit rate threshold cache size increase + * algorithm.</td> + * </tr> + * <tr> + * <td><em>hbool_t</em> <code>apply_max_increment</code> </td> + * <td>OUT: Boolean flag indicating whether an upper limit will be applied to the size of cache size + * increases.</td> + * </tr> + * <tr> + * <td><em>size_t</em> <code>max_increment</code> </td> + * <td>OUT: The maximum number of bytes by which the maximum cache size can be increased in a single step + * -- if applicable.</td> + * </tr> + * <tr> + * <td><em>enum H5C_cache_flash_incr_mode</em> <code>flash_incr_mode</code> </td> + * <td>OUT: Enumerated value indicating the operational mode of the flash cache size increase code. At + * present, only the following values are legal:<p>\c H5C_flash_incr__off: Flash cache size increase is + * disabled.</p><p>\c H5C_flash_incr__add_space: Flash cache size increase is enabled using the add space + * algorithm.</p></td> + * </tr> + * <tr> + * <td><em>double</em> <code>flash_threshold</code> </td> + * <td>OUT: The factor by which the current maximum cache size is multiplied to obtain the minimum size + * entry / entry size increase which may trigger a flash cache size + * increase.</td> + * </tr> + * <tr> + * <td><em>double</em> <code>flash_multiple</code> </td> + * <td>OUT: The factor by which the size of the triggering entry / entry size increase is multiplied to + * obtain the initial cache size increment. This increment may be reduced to reflect existing free space + * in the cache and the <code>max_size</code> field above.</td> + * </tr> + * </table> + * + * \par Decrement configuration section + * <table> + * <tr><td colspan="2"><strong>Decrement configuration + * section:</strong></td> + * </tr> + * <tr> + * <td><em>enum H5C_cache_decr_mode</em> <code>decr_mode</code> </td> + * <td>OUT: Enumerated value indicating the operational mode of the automatic cache size decrease code. At + * present, the following values are legal:<p>H5C_decr__off: Automatic cache size decrease is disabled, + * and the remaining decrement fields are ignored.</p><p>H5C_decr__threshold: Automatic cache size + * decrease is enabled using the hit rate threshold algorithm.</p><p>H5C_decr__age_out: Automatic cache + * size decrease is enabled using the ageout algorithm.</p><p>H5C_decr__age_out_with_threshold: + * Automatic cache size decrease is enabled using the ageout with hit rate threshold + * algorithm</p></td> + * </tr> + * <tr><td><em>double</em> <code>upper_hr_threshold</code> </td> + * <td>OUT: Upper hit rate threshold. This value is only used if the decr_mode is either + * H5C_decr__threshold or H5C_decr__age_out_with_threshold.</td> + * </tr> + * <tr> + * <td><em>double</em> <code>decrement</code> </td> + * <td>OUT: Factor by which the current max cache size is multiplied to obtain an initial value for the + * new cache size when cache size reduction is triggered in the hit rate threshold cache size reduction + * algorithm.</td> + * </tr> + * <tr> + * <td><em>hbool_t</em> <code>apply_max_decrement</code> </td> + * <td>OUT: Boolean flag indicating whether an upper limit should be applied to the size of cache size + * decreases.</td> + * </tr> + * <tr> + * <td><em>size_t</em> <code>max_decrement</code> </td> + * <td>OUT: The maximum number of bytes by which cache size can be decreased if any single step, if + * applicable.</td> + * </tr> + * <tr> + * <td><em>int</em> <code>epochs_before_eviction</code> </td> + * <td>OUT: The minimum number of epochs that an entry must reside unaccessed in cache before being + * evicted under either of the ageout cache size reduction algorithms.</td> + * </tr> + * <tr> + * <td><em>hbool_t</em> <code>apply_empty_reserve</code> </td> + * <td>OUT: Boolean flag indicating whether an empty reserve should be maintained under either of the + * ageout cache size reduction algorithms.</td> + * </tr> + * <tr> + * <td><em>double</em> <code>empty_reserve</code> </td> + * <td>OUT: Empty reserve for use with the ageout cache size reduction algorithms, if applicable.</td> + * </tr> + * </table> + * + * \par Parallel configuration section + * <table> + * <tr><td><em>int</em> <code>dirty_bytes_threshold</code> </td> + * <td>OUT: Threshold number of bytes of dirty metadata generation for triggering synchronizations of the + * metadata caches serving the target file in the parallel case.<p>Synchronization occurs whenever the + * number of bytes of dirty metadata created since the last synchronization exceeds this limit.</p></td> + * </tr> + * </table> + * + * \since 1.8.0 + * + * \todo Fix the reference! + * */ H5_DLL herr_t H5Fget_mdc_config(hid_t file_id, H5AC_cache_config_t *config_ptr); /** * \ingroup MDC * - * \todo Finish this! + * \brief Attempts to configure metadata cache of target file + * + * \file_id + * \param[in,out] config_ptr Pointer to the H5AC_cache_config_t instance + * containing the desired configuration. + * The fields of this structure are discussed + * \ref H5AC-cache-config-t "here". + * \return \herr_t + * + * \details H5Fset_mdc_config() attempts to configure the file's metadata cache + * according configuration supplied in \p config_ptr. + * + * \par General configuration fields + * <table> + * <tr> + * <td><em>int</em> <code>version</code></td> + * <td>IN: Integer field indicating the the version of the H5AC_cache_config_t in use. This + * field should be set to #H5AC__CURR_CACHE_CONFIG_VERSION (defined + * in H5ACpublic.h).</td> + * </tr> + * <tr> + * <td><em>hbool_t</em> <code>rpt_fcn_enabled</code></td> + * <td>IN: Boolean flag indicating whether the adaptive cache resize report function is enabled. This + * field should almost always be set to disabled (<code>0</code>). Since resize algorithm activity is reported + * via stdout, it MUST be set to disabled (<code>0</code>) on Windows machines.<p>The report function is not + * supported code, and can be expected to change between versions of the library. Use it at your own + * risk.</p></td> + * </tr> + * <tr> + * <td><em>hbool_t</em> <code>open_trace_File</code></td> + * <td>IN: Boolean field indicating whether the <code>trace_file_name</code> field should be used to open + * a trace file for the cache.<p>The trace file is a debuging feature that allows the capture of top level + * metadata cache requests for purposes of debugging and/or optimization. This field should normally be set + * to <code>0</code>, as trace file collection imposes considerable overhead.</p><p>This field should only be + * set to <code>1</code> when the <code>trace_file_name</code> contains the full path of the desired trace + * file, and either there is no open trace file on the cache, or the <code>close_trace_file</code> field is + * also <code>1</code>.</p><p>The trace file feature is unsupported unless used at the direction of The HDF + * Group. It is intended to allow The HDF Group to collect a trace of cache activity in cases of occult + * failures and/or poor performance seen in the field, so as to aid in reproduction in the lab. If you use it + * absent the direction of The HDF Group, you are on your + * own.</p></td> + * </tr> + * <tr><td><em>hbool_t</em> <code>close_trace_file</code></td> + * <td>IN: Boolean field indicating whether the current trace file (if any) should be closed.<p>See the + * above comments on the <code>open_trace_file</code> field. This field should be set to <code>0</code> unless + * there is an open trace file on the cache that you wish to close.</p><p>The trace file feature is + * unsupported unless used at the direction of The HDF Group. It is intended to allow The HDF Group to collect + * a trace of cache activity in cases of occult failures and/or poor performance seen in the field, so as to + * aid in reproduction in the lab. If you use it absent the direction of The HDF Group, you are on your + * own.</p></td> + * </tr> + * <tr> + * <td><em>char</em> <code>trace_file_name[]</code></td> + * <td>IN: Full path of the trace file to be opened if the <code>open_trace_file</code> field is set + * to <code>1</code>.<p>In the parallel case, an ascii representation of the mpi rank of the process will be + * appended to the file name to yield a unique trace file name for each process.</p><p>The length of the path + * must not exceed #H5AC__MAX_TRACE_FILE_NAME_LEN characters.</p><p>The trace file feature is + * unsupported unless used at the direction of The HDF Group. It is intended to allow The HDF Group to collect + * a trace of cache activity in cases of occult failures and/or poor performance seen in the field, so as to + * aid in reproduction in the lab. If you use it absent the direction of The HDF Group, you are on your + * own.</p></td> + * </tr> + * <tr> + * <td><em>hbool_t</em> <code>evictions_enabled</code></td> + * <td>IN: A boolean flag indicating whether evictions from the metadata cache are enabled. This flag is + * initially set to enabled (<code>1</code>).<p>In rare circumstances, the raw data throughput requirements + * may be so high that the user wishes to postpone metadata writes so as to reserve I/O throughput for raw + * data. The <code>evictions_enabled</code> field exists to allow this. However, this is an extreme step, and + * you have no business doing it unless you have read the User Guide section on metadata caching, and have + * considered all other options carefully.</p><p>The <code>evictions_enabled</code> field may not be set to + * disabled (<code>0</code>) unless all adaptive cache resizing code is disabled via + * the <code>incr_mode</code>, <code>flash_incr_mode</code>, and <code>decr_mode</code> fields.</p><p>When + * this flag is set to disabled (<code>0</code>), the metadata cache will not attempt to evict entries to make + * space for new entries, and thus will grow without bound.</p><p>Evictions will be re-enabled when this field + * is set back to <code>1</code>. This should be done as soon as + * possible.</p></td> + * </tr> + * <tr> + * <td><em>hbool_t</em> <code>set_initial_size</code></td> + * <td>IN: Boolean flag indicating whether the cache should be forced to the user specified initial + * size.</td> + * </tr> + * <tr> + * <td><em>size_t</em> <code>initial_size</code></td> + * <td>IN: If <code>set_initial_size</code> is set to <code>1</code>, then <code>initial_size</code> must + * contain the desired initial size in bytes. This value must lie in the closed interval <code>[min_size, + * max_size]</code>. (see below)</td> + * </tr> + * <tr><td><em>double</em> <code>min_clean_fraction</code></td> + * <td>IN: This field specifies the minimum fraction of the cache that must be kept either clean or + * empty.<p>The value must lie in the interval [0.0, 1.0]. 0.01 is a good place to start in the serial case. + * In the parallel case, a larger value is needed -- + * see <a href="/display/HDF5/Metadata+Caching+in+HDF5">Metadata Caching in HDF5</a> in the collection + * "Advanced Topics in HDF5."</p></td> + * </tr> + * <tr><td><em>size_t</em> <code>max_size</code></td> + * <td>IN: Upper bound (in bytes) on the range of values that the adaptive cache resize code can select as + * the maximum cache size.</td> + * </tr> + * <tr> + * <td><em>size_t</em> <code>min_size</code></td> + * <td>IN: Lower bound (in bytes) on the range of values that the adaptive cache resize code can select as + * the maximum cache size.</td> + * </tr> + * <tr><td><em>long int</em> <code>epoch_length</code></td> + * <td>IN: Number of cache accesses between runs of the adaptive cache resize code. 50,000 is a good + * starting number.</td> + * </tr> + * </table> + * + * \par Increment configuration fields + * <table> + * <tr> + * <td><em>enum H5C_cache_incr_mode</em> <code>incr_mode</code></td> + * <td>IN: Enumerated value indicating the operational mode of the automatic cache size increase code. At + * present, only two values are legal:<p>\c H5C_incr__off: Automatic cache size increase is disabled, and the + * remaining increment fields are ignored.</p><p>\c H5C_incr__threshold: Automatic cache size increase is enabled + * using the hit rate threshold + * algorithm.</p></td> + * </tr> + * <tr> + * <td><em>double</em> <code>lower_hr_threshold</code></td> + * <td>IN: Hit rate threshold used by the hit rate threshold cache size increment algorithm.<p>When the + * hit rate over an epoch is below this threshold and the cache is full, the maximum size of the cache is + * multiplied by increment (below), and then clipped as necessary to stay within max_size, and possibly + * max_increment.</p><p>This field must lie in the interval [0.0, 1.0]. 0.8 or 0.9 is a good starting + * point.</p></td> + * </tr> + * <tr> + * <td><em>double</em> <code>increment</code></td> + * <td>IN: Factor by which the hit rate threshold cache size increment algorithm multiplies the current + * maximum cache size to obtain a tentative new cache size.<p>The actual cache size increase will be clipped + * to satisfy the max_size specified in the general configuration, and possibly max_increment below.</p><p>The + * parameter must be greater than or equal to 1.0 -- 2.0 is a reasonable value.</p><p>If you set it to 1.0, + * you will effectively disable cache size + * increases.</p></td> + * </tr> + * <tr> + * <td><em>hbool_t</em> <code>apply_max_increment</code></td> + * <td>IN: Boolean flag indicating whether an upper limit should be applied to the size of cache size + * increases.</td> + * </tr> + * <tr> + * <td><em>size_t</em> <code>max_increment</code></td> + * <td>IN: Maximum number of bytes by which cache size can be increased in a single step -- if + * applicable.</td> + * </tr> + * <tr> + * <td><em>enum H5C_cache_flash_incr_mode</em> <code>flash_incr_mode</code></td> + * <td>IN: Enumerated value indicating the operational mode of the flash cache size increase code. At + * present, only the following values are legal:<p>\c H5C_flash_incr__off: Flash cache size increase is + * disabled.</p><p>\c H5C_flash_incr__add_space: Flash cache size increase is enabled using the add space + * algorithm.</p></td> + * </tr> + * <tr> + * <td><em>double</em> <code>flash_threshold</code></td> + * <td>IN: The factor by which the current maximum cache size is multiplied to obtain the minimum size + * entry / entry size increase which may trigger a flash cache size increase.<p>At present, this value must + * lie in the range [0.1, 1.0].</p></td> + * </tr> + * <tr> + * <td><em>double</em> <code>flash_multiple</code></td> + * <td>IN: The factor by which the size of the triggering entry / entry size increase is multiplied to + * obtain the initial cache size increment. This increment may be reduced to reflect existing free space in + * the cache and the <code>max_size</code> field above.<p>At present, this field must lie in the range [0.1, + * 10.0].</p></td> + * </tr> + * </table> + * + * \par Decrement configuration fields + * <table> + * <tr> + * <td><em>enum H5C_cache_decr_mode</em> <code>decr_mode</code></td> + * <td>IN: Enumerated value indicating the operational mode of the automatic cache size decrease code. At + * present, the following values are legal:<p>\c H5C_decr__off: Automatic cache size decrease is + * disabled.</p><p>\c H5C_decr__threshold: Automatic cache size decrease is enabled using the hit rate threshold + * algorithm.</p><p>\c H5C_decr__age_out: Automatic cache size decrease is enabled using the ageout + * algorithm.</p><p>\c H5C_decr__age_out_with_threshold: Automatic cache size decrease is enabled using the + * ageout with hit rate threshold + * algorithm</p></td> + * </tr> + * <tr> + * <td><em>double</em> <code>upper_hr_threshold</code></td> + * <td>IN: Hit rate threshold for the hit rate threshold and ageout with hit rate threshold cache size + * decrement algorithms.<p>When \c decr_mode is \c H5C_decr__threshold, and the hit rate over a given epoch exceeds + * the supplied threshold, the current maximum cache size is multiplied by decrement to obtain a tentative new + * (and smaller) maximum cache size.</p><p>When \c decr_mode is \c H5C_decr__age_out_with_threshold, there is no + * attempt to find and evict aged out entries unless the hit rate in the previous epoch exceeded the supplied + * threshold.</p><p>This field must lie in the interval [0.0, 1.0].</p><p>For \c H5C_incr__threshold, .9995 or + * .99995 is a good place to start.</p><p>For \c H5C_decr__age_out_with_threshold, .999 might be more + * useful.</p></td> + * </tr> + * <tr> + * <td><em>double</em> <code>decrement</code></td> + * <td>IN: In the hit rate threshold cache size decrease algorithm, this parameter contains the factor by + * which the current max cache size is multiplied to produce a tentative new cache size.<p>The actual cache + * size decrease will be clipped to satisfy the min_size specified in the general configuration, and possibly + * max_decrement below.</p><p>The parameter must be be in the interval [0.0, 1.0].</p><p>If you set it to 1.0, + * you will effectively disable cache size decreases. 0.9 is a reasonable starting + * point.</p></td> + * </tr> + * <tr> + * <td><em>hbool_t</em> <code>apply_max_decrement</code></td> + * <td>IN: Boolean flag indicating whether an upper limit should be applied to the size of cache size + * decreases.</td> + * </tr> + * <tr> + * <td><em>size_t</em> <code>max_decrement</code></td> + * <td>IN: Maximum number of bytes by which the maximum cache size can be decreased in any single step -- + * if applicable.</td> + * </tr> + * <tr> + * <td><em>int</em> <code>epochs_before_eviction</code></td> + * <td>IN: In the ageout based cache size reduction algorithms, this field contains the minimum number of + * epochs an entry must remain unaccessed in cache before the cache size reduction algorithm tries to evict + * it. 3 is a reasonable value.</td> + * </tr> + * <tr> + * <td><em>hbool_t</em> <code>apply_empty_reserve</code></td> + * <td>IN: Boolean flag indicating whether the ageout based decrement algorithms will maintain a empty + * reserve when decreasing cache size.</td> + * </tr> + * <tr> + * <td><em>double</em> <code>empty_reserve</code></td> + * <td>IN: Empty reserve as a fraction of maximum cache size if applicable.<p>When so directed, the ageout + * based algorithms will not decrease the maximum cache size unless the empty reserve can be met.</p><p>The + * parameter must lie in the interval [0.0, 1.0]. 0.1 or 0.05 is a good place to + * start.</p></td> + * </tr> + * </table> + * + * \par Parallel configuration fields + * <table> + * <tr> + * <td><em>int</em> <code>dirty_bytes_threshold</code></td> + * <td>IN: Threshold number of bytes of dirty metadata generation for triggering synchronizations of the + * metadata caches serving the target file in the parallel case.<p>Synchronization occurs whenever the number + * of bytes of dirty metadata created since the last synchronization exceeds this limit.</p><p>This field only + * applies to the parallel case. While it is ignored elsewhere, it can still draw a value out of bounds + * error.</p><p>It must be consistant across all caches on any given file.</p><p>By default, this field is set + * to 256 KB. It shouldn't be more than half the current maximum cache size times the minimum clean + * fraction.</p></td> + * </tr> + * </table> + * + * \since 1.8.0 + * + * \todo Fix the MDC document reference! */ H5_DLL herr_t H5Fset_mdc_config(hid_t file_id, H5AC_cache_config_t *config_ptr); /** * \ingroup MDC * - * \todo Finish this! + * \brief Obtains target file's metadata cache hit rate + * + * \file_id + * \param[out] hit_rate_ptr Pointer to the double in which the hit rate is returned. Note that + * \p hit_rate_ptr is undefined if the API call fails + * \return \herr_t + * + * \details H5Fget_mdc_hit_rate() queries the metadata cache of the target file to obtain its hit rate + * \Code{(cache hits / (cache hits + cache misses))} since the last time hit rate statistics + * were reset. If the cache has not been accessed since the last time the hit rate stats were + * reset, the hit rate is defined to be 0.0. + * + * The hit rate stats can be reset either manually (via H5Freset_mdc_hit_rate_stats()), or + * automatically. If the cache's adaptive resize code is enabled, the hit rate stats will be + * reset once per epoch. If they are reset manually as well, the cache may behave oddly. + * + * See the overview of the metadata cache in the special topics section of the user manual for + * details on the metadata cache and its adaptive resize algorithms. + * */ H5_DLL herr_t H5Fget_mdc_hit_rate(hid_t file_id, double *hit_rate_ptr); /** * \ingroup MDC * - * \todo Finish this! + * \brief Obtains current metadata cache size data for specified file + * + * \file_id + * \param[out] max_size_ptr Pointer to the location in which the current cache maximum size is to be + * returned, or NULL if this datum is not desired + * \param[out] min_clean_size_ptr Pointer to the location in which the current cache minimum clean + * size is to be returned, or NULL if that datum is not desired + * \param[out] cur_size_ptr Pointer to the location in which the current cache size is to be returned, + * or NULL if that datum is not desired + * \param[out] cur_num_entries_ptr Pointer to the location in which the current number of entries in + * the cache is to be returned, or NULL if that datum is not desired + * \returns \herr_t + * + * \details H5Fget_mdc_size() queries the metadata cache of the target file for the desired size + * information, and returns this information in the locations indicated by the pointer + * parameters. If any pointer parameter is NULL, the associated data is not returned. + * + * If the API call fails, the values returned via the pointer parameters are undefined. + * + * If adaptive cache resizing is enabled, the cache maximum size and minimum clean size + * may change at the end of each epoch. Current size and current number of entries can + * change on each cache access. + * + * Current size can exceed maximum size under certain conditions. See the overview of the + * metadata cache in the special topics section of the user manual for a discussion of this. + * */ H5_DLL herr_t H5Fget_mdc_size(hid_t file_id, size_t *max_size_ptr, size_t *min_clean_size_ptr, size_t *cur_size_ptr, int *cur_num_entries_ptr); /** * \ingroup MDC * - * \todo Finish this! + * \brief Resets hit rate statistics counters for the target file + * + * \file_id + * \returns \herr_t + * + * \details + * \parblock + * H5Freset_mdc_hit_rate_stats() resets the hit rate statistics counters in the metadata cache + * associated with the specified file. + * + * If the adaptive cache resizing code is enabled, the hit rate statistics are reset at the beginning + * of each epoch. This API call allows you to do the same thing from your program. + * + * The adaptive cache resizing code may behave oddly if you use this call when adaptive cache resizing + * is enabled. However, the call should be useful if you choose to control metadata cache size from your + * program. + * + * See "Metadata Caching in HDF5" for details about the metadata cache and the adaptive cache resizing + * algorithms. If you have not read, understood, and thought about the material covered in that + * documentation, + * you should not be using this API call. + * \endparblock + * + * \todo Fix the MDC document reference! */ H5_DLL herr_t H5Freset_mdc_hit_rate_stats(hid_t file_id); /** @@ -1068,13 +1580,118 @@ H5_DLL herr_t H5Fget_info2(hid_t obj_id, H5F_info2_t *file_info); /** * \ingroup SWMR * - * \todo Finish this! + * \brief Retrieves the collection of read retries for metadata entries with checksum + * + * \file_id + * \param[out] info Struct containing the collection of read retries for metadata + * entries with checksum + * \return \herr_t\n + * + * \details \Bold{Failure Modes:} + * \li When the input identifier is not a file identifier. + * \li When the pointer to the output structure is NULL. + * \li When the memory allocation for \p retries failed. + * + * \details H5Fget_metadata_read_retry_info() retrieves information regarding the number + * of read retries for metadata entries with checksum for the file \p file_id. + * This information is reported in the H5F_retry_info_t struct defined in + * H5Fpublic.h as follows: + * \snippet this H5F_retry_info_t_snip + * \c nbins is the number of bins for each \c retries[i] of metadata entry \c i. + * It is calculated based on the current number of read attempts used in the + * library and logarithmic base 10. + * + * If read retries are incurred for a metadata entry \c i, the library will + * allocate memory for \Code{retries[i] (nbins * sizeof(uint32_t)} and store + * the collection of retries there. If there are no retries for a metadata entry + * \c i, \Code{retries[i]} will be NULL. After a call to this routine, users should + * free each \Code{retries[i]} that is non-NULL, otherwise resource leak will occur. + * + * For the library default read attempts of 100 for SWMR access, nbins will be 2 + * as depicted below: + * \li \Code{retries[i][0]} is the number of 1 to 9 read retries. + * \li \Code{retries[i][1]} is the number of 10 to 99 read retries. + * For the library default read attempts of 1 for non-SWMR access, \c nbins will + * be 0 and each \Code{retries[i]} will be NULL. + * + * The following table lists the 21 metadata entries of \Code{retries[]}: + * <table> + * <tr> + * <th>Index for \Code{retries[]}</th> + * <th>Metadata entries<sup>*</sup></th> + * </tr> + * <tr><td>0</td><td>Object header (version 2)</td></tr> + * <tr><td>1</td><td>Object header chunk (version 2)</td></tr> + * <tr><td>2</td><td>B-tree header (version 2)</td></tr> + * <tr><td>3</td><td>B-tree internal node (version 2)</td></tr> + * <tr><td>4</td><td>B-tree leaf node (version 2)</td></tr> + * <tr><td>5</td><td>Fractal heap header</td></tr> + * <tr><td>6</td><td>Fractal heap direct block (optional checksum)</td></tr> + * <tr><td>7</td><td>Fractal heap indirect block</td></tr> + * <tr><td>8</td><td>Free-space header</td></tr> + * <tr><td>9</td><td>Free-space sections</td></tr> + * <tr><td>10</td><td>Shared object header message table</td></tr> + * <tr><td>11</td><td>Shared message record list</td></tr> + * <tr><td>12</td><td>Extensive array header</td></tr> + * <tr><td>13</td><td>Extensive array index block</td></tr> + * <tr><td>14</td><td>Extensive array super block</td></tr> + * <tr><td>15</td><td>Extensive array data block</td></tr> + * <tr><td>16</td><td>Extensive array data block page</td></tr> + * <tr><td>17</td><td>Fixed array super block</td></tr> + * <tr><td>18</td><td>Fixed array data block</td></tr> + * <tr><td>19</td><td>Fixed array data block page</td></tr> + * <tr><td>20</td><td>File's superblock (version 2)</td></tr> + * <tr><td colspan=2><sup>*</sup> All entries are of version 0 (zero) unless indicated otherwise.</td></tr> + * </table> + * + * \note On a system that is not atomic, the library might possibly read inconsistent + * metadata with checksum when performing single-writer/multiple-reader (SWMR) + * operations for an HDF5 file. Upon encountering such situations, the library + * will try reading the metadata again for a set number of times to attempt to + * obtain consistent data. The maximum number of read attempts used by the library + * will be either the value set via H5Pset_metadata_read_attempts() or the library + * default value when a value is not set.\n + * When the current number of metadata read attempts used in the library is unable + * to remedy the reading of inconsistent metadata on a system, the user can assess + * the information obtained via this routine to derive a different maximum value. + * The information can also be helpful for debugging purposes to identify potential + * issues with metadata flush dependencies and SWMR implementation in general. + * + * \since 1.10.0 + * */ H5_DLL herr_t H5Fget_metadata_read_retry_info(hid_t file_id, H5F_retry_info_t *info); /** * \ingroup SWMR * - * \todo Finish this! + * \brief Retrieves free-space section information for a file + * + * \file_id + * + * \return \herr_t + * + * \details H5Fstart_swmr_write() will activate SWMR writing mode for a file + * associated with \p file_id. This routine will prepare and ensure + * the file is safe for SWMR writing as follows: + * \li Check that the file is opened with write access (#H5F_ACC_RDWR). + * \li Check that the file is opened with the latest library format to + * ensure data structures with check-summed metadata are used. + * \li Check that the file is not already marked in SWMR writing mode. + * \li Enable reading retries for check-summed metadata to remedy + * possible checksum failures from reading inconsistent metadata + * on a system that is not atomic. + * \li Turn off usage of the library's accumulator to avoid possible + * ordering problem on a system that is not atomic. + * \li Perform a flush of the file’s data buffers and metadata to set + * a consistent state for starting SWMR write operations. + * + * Library objects are groups, datasets, and committed datatypes. For + * the current implementation, groups and datasets can remain open when + * activating SWMR writing mode, but not committed datatypes. Attributes + * attached to objects cannot remain open either. + * + * \since 1.10.0 + * */ H5_DLL herr_t H5Fstart_swmr_write(hid_t file_id); /** @@ -1175,19 +1792,141 @@ H5_DLL herr_t H5Fset_libver_bounds(hid_t file_id, H5F_libver_t low, H5F_libver /** * \ingroup MDC * - * \todo Finish this! + * \brief Starts logging metadata cache events if logging was previously enabled + * + * \file_id + * + * \return \herr_t + * + * \details The metadata cache is a central part of the HDF5 library through + * which all \Emph{file metadata} reads and writes take place. File + * metadata is normally invisible to the user and is used by the + * library for purposes such as locating and indexing data. File + * metadata should not be confused with user metadata, which consists + * of attributes created by users and attached to HDF5 objects such + * as datasets via H5A API calls. + * + * Due to the complexity of the cache, a trace/logging feature has been + * created that can be used by HDF5 developers for debugging and performance + * analysis. The functions that control this functionality will normally be + * of use to a very limited number of developers outside of The HDF Group. + * The functions have been documented to help users create logs that can + * be sent with bug reports. + * + * Control of the log functionality is straightforward. Logging is enabled + * via the H5Pset_mdc_log_options() function, which will modify the file + * access property list used to open or create a file. This function has + * a flag that determines whether logging begins at file open or starts + * in a paused state. Log messages can then be controlled via the + * H5Fstart_mdc_logging() and H5Fstop_mdc_logging() functions. + * H5Pget_mdc_log_options() can be used to examine a file access property + * list, and H5Fget_mdc_logging_status() will return the current state of + * the logging flags. + * + * The log format is described in the \Emph{Metadata Cache Logging} document. + * + * \note Logging can only be started or stopped if metadata cache logging was enabled + * via H5Pset_mdc_log_options().\n + * When enabled and currently logging, the overhead of the logging feature will + * almost certainly be significant.\n + * The log file is opened when the HDF5 file is opened or created and not when + * this function is called for the first time.\n + * This function opens the log file and starts logging metadata cache operations + * for a particular file. Calling this function when logging has already been + * enabled will be considered an error. + * + * \since 1.10.0 + * + * \todo Fix the document reference! + * */ H5_DLL herr_t H5Fstart_mdc_logging(hid_t file_id); /** * \ingroup MDC * - * \todo Finish this! + * \brief Stops logging metadata cache events if logging was previously enabled and is currently ongoing + * + * \file_id + * + * \return \herr_t + * + * \details The metadata cache is a central part of the HDF5 library through + * which all \Emph{file metadata} reads and writes take place. File + * metadata is normally invisible to the user and is used by the + * library for purposes such as locating and indexing data. File + * metadata should not be confused with user metadata, which consists + * of attributes created by users and attached to HDF5 objects such + * as datasets via H5A API calls. + * + * Due to the complexity of the cache, a trace/logging feature has been + * created that can be used by HDF5 developers for debugging and performance + * analysis. The functions that control this functionality will normally be + * of use to a very limited number of developers outside of The HDF Group. + * The functions have been documented to help users create logs that can + * be sent with bug reports. + * + * Control of the log functionality is straightforward. Logging is enabled + * via the H5Pset_mdc_log_options() function, which will modify the file + * access property list used to open or create a file. This function has + * a flag that determines whether logging begins at file open or starts + * in a paused state. Log messages can then be controlled via the + * H5Fstart_mdc_logging() and H5Fstop_mdc_logging() functions. + * H5Pget_mdc_log_options() can be used to examine a file access property + * list, and H5Fget_mdc_logging_status() will return the current state of + * the logging flags. + * + * The log format is described in the \Emph{Metadata Cache Logging} document. + * + * \note Logging can only be started or stopped if metadata cache logging was enabled + * via H5Pset_mdc_log_options().\n + * This function only suspends the logging operations. The log file will remain + * open and will not be closed until the HDF5 file is closed. + * + * \since 1.10.0 + * */ H5_DLL herr_t H5Fstop_mdc_logging(hid_t file_id); /** * \ingroup MDC * - * \todo Finish this! + * \brief Gets the current metadata cache logging status + * + * \file_id + * \param[out] is_enabled Whether logging is enabled + * \param[out] is_currently_logging Whether events are currently being logged + * \return \herr_t + * + * \details The metadata cache is a central part of the HDF5 library through + * which all \Emph{file metadata} reads and writes take place. File + * metadata is normally invisible to the user and is used by the + * library for purposes such as locating and indexing data. File + * metadata should not be confused with user metadata, which consists + * of attributes created by users and attached to HDF5 objects such + * as datasets via H5A API calls. + * + * Due to the complexity of the cache, a trace/logging feature has been + * created that can be used by HDF5 developers for debugging and performance + * analysis. The functions that control this functionality will normally be + * of use to a very limited number of developers outside of The HDF Group. + * The functions have been documented to help users create logs that can + * be sent with bug reports. + * + * Control of the log functionality is straightforward. Logging is enabled + * via the H5Pset_mdc_log_options() function, which will modify the file + * access property list used to open or create a file. This function has + * a flag that determines whether logging begins at file open or starts + * in a paused state. Log messages can then be controlled via the + * H5Fstart_mdc_logging() and H5Fstop_mdc_logging() functions. + * H5Pget_mdc_log_options() can be used to examine a file access property + * list, and H5Fget_mdc_logging_status() will return the current state of + * the logging flags. + * + * The log format is described in the \Emph{Metadata Cache Logging} document. + * + * \note Unlike H5Fstart_mdc_logging() and H5Fstop_mdc_logging(), this function can + * be called on any open file identifier. + * + * \since 1.10.0 */ H5_DLL herr_t H5Fget_mdc_logging_status(hid_t file_id, /*OUT*/ hbool_t *is_enabled, @@ -1246,7 +1985,32 @@ H5_DLL herr_t H5Fget_page_buffering_stats(hid_t file_id, unsigned accesses[2], /** * \ingroup MDC * - * \todo Finish this! + * \brief Obtains information about a cache image if it exists + * + * \file_id + * \param[out] image_addr Offset of the cache image if it exists, or #HADDR_UNDEF if it does not + * \param[out] image_size Length of the cache image if it exists, or 0 if it does not + * \returns \herr_t + * + * \details + * \parblock + * H5Fget_mdc_image_info() returns information about a cache image if it exists. + * + * When an HDF5 file is opened in Read/Write mode, any metadata cache image will + * be read and deleted from the file on the first metadata cache access (or, if + * persistent free space managers are enabled, on the first file space + * allocation / deallocation, or read of free space manager status, whichever + * comes first). + * + * Thus, if the file is opened Read/Write, H5Fget_mdc_image_info() should be called + * immediately after file open and before any other operation. If H5Fget_mdc_image_info() + * is called after the cache image is loaded, it will correctly report that no cache image + * exists, as the image will have already been read and deleted from the file. In the Read Only + * case, the function may be called at any time, as any cache image will not be deleted + * from the file. + * \endparblock + * + * \since 1.10.1 */ H5_DLL herr_t H5Fget_mdc_image_info(hid_t file_id, haddr_t *image_addr, hsize_t *image_size); /** @@ -1308,13 +2072,91 @@ H5_DLL herr_t H5Fset_dset_no_attrs_hint(hid_t file_id, hbool_t minimize); /** * \ingroup PH5F * - * \todo Finish this! + * \brief Sets the MPI atomicity mode + * + * \file_id + * \param[in] flag Logical flag for atomicity setting. Valid values are: + * \li \c 1 -- Sets MPI file access to atomic mode. + * \li \c 0 -- Sets MPI file access to nonatomic mode. + * \returns \herr_t + * + * \par Motivation + * H5Fset_mpi_atomicity() is applicable only in parallel environments using MPI I/O. + * The function is one of the tools used to ensure sequential consistency. This means + * that a set of operations will behave as though they were performed in a serial + * order consistent with the program order. + * + * \details + * \parblock + * H5Fset_mpi_atomicity() sets MPI consistency semantics for data access to the file, + * \p file_id. + * + * If \p flag is set to \c 1, all file access operations will appear atomic, guaranteeing + * sequential consistency. If \p flag is set to \c 0, enforcement of atomic file access + * will be turned off. + * + * H5Fset_mpi_atomicity() is a collective function and all participating processes must + * pass the same values for \p file_id and \p flag. + * + * This function is available only when the HDF5 library is configured with parallel support + * (\Code{--enable-parallel}). It is useful only when used with the #H5FD_MPIO driver + * (see H5Pset_fapl_mpio()). + * \endparblock + * + * \attention + * \parblock + * H5Fset_mpi_atomicity() calls \Code{MPI_File_set_atomicity} underneath and is not supported + * if the execution platform does not support \Code{MPI_File_set_atomicity}. When it is + * supported and used, the performance of data access operations may drop significantly. + * + * In certain scenarios, even when \Code{MPI_File_set_atomicity} is supported, setting + * atomicity with H5Fset_mpi_atomicity() and \p flag set to 1 does not always yield + * strictly atomic updates. For example, some H5Dwrite() calls translate to multiple + * \Code{MPI_File_write_at} calls. This happens in all cases where the high-level file + * access routine translates to multiple lower level file access routines. + * The following scenarios will raise this issue: + * \li Non-contiguous file access using independent I/O + * \li Partial collective I/O using chunked access + * \li Collective I/O using filters or when data conversion is required + * + * This issue arises because MPI atomicity is a matter of MPI file access operations rather + * than HDF5 access operations. But the user is normally seeking atomicity at the HDF5 level. + * To accomplish this, the application must set a barrier after a write, H5Dwrite(), but before + * the next read, H5Dread(), in addition to calling H5Fset_mpi_atomicity().The barrier will + * guarantee that all underlying write operations execute atomically before the read + * operations starts. This ensures additional ordering semantics and will normally produce + * the desired behavior. + * \endparblock + * + * \see Enabling a Strict Consistency Semantics Model in Parallel HDF5 + * + * \since 1.8.9 + * + * \todo Fix the reference! */ H5_DLL herr_t H5Fset_mpi_atomicity(hid_t file_id, hbool_t flag); /** * \ingroup PH5F * - * \todo Finish this! + * \brief Retrieves the atomicity mode in use + * + * \file_id + * \param[out] flag Logical flag for atomicity setting. Valid values are: + * \li 1 -- MPI file access is set to atomic mode. + * \li 0 -- MPI file access is set to nonatomic mode. + * \returns \herr_t + * + * \details H5Fget_mpi_atomicity() retrieves the current consistency semantics mode for + * data access for the file \p file_id. + * + * Upon successful return, \p flag will be set to \c 1 if file access is set + * to atomic mode and \c 0 if file access is set to nonatomic mode. + * + * \see Enabling a Strict Consistency Semantics Model in Parallel HDF5 + * + * \since 1.8.9 + * + * \todo Fix the reference! */ H5_DLL herr_t H5Fget_mpi_atomicity(hid_t file_id, hbool_t *flag); #endif /* H5_HAVE_PARALLEL */ |