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authorGerd Heber <gheber@hdfgroup.org>2021-04-26 19:07:29 (GMT)
committerGitHub <noreply@github.com>2021-04-26 19:07:29 (GMT)
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Merge doxygen2 into develop (#553)
* Fixed warnings and started H5Epublic.h. * Include H5FD* headers to correctly resolve references. * Doxygen2 (#330) * H5Eauto_is_v2. * Added a few more calls. * Added a few more H5E calls. * First cut of H5E v2. * Added the deprecated v1 calls. * Updated spacing. * Once more. * Taking some inspiration from Eigen3. * Add doxygen for the assigned functions: H5Pregister1,H5Pinsert1,H5Pen… (#352) * Add doxygen for the assigned functions: H5Pregister1,H5Pinsert1,H5Pencode1, H5Pget_filter_by_id1,H5Pget_version, H5Pset_file_space,H5Pget_file_space. Someone already adds H5Pget_filter1. Also fixs an extra parameter 'close' call back function for HPregister2. * doxygen work. fixs format by using clang-format. * doxgen work for H5Pregister1 etc. Addressed Barbara and Gerd's comments. For Quincey's comments, since we are not supposed to change the source code. I leave this to future improvements. * added documentation for H5P APIs (#350) * add documenation for H5Pget_buffer,H5Pget_data_transform,H5Pget_edc_check,H5Pget_hyper_vector_size,H5Pget_preserve,H5Pget_type_conv_cb,H5Pget_vlen_mem_manager,H5Pset_btree_ratios * format corrections * fixed grammer * fixed herr_t * Better name. * A fresh look. * add doxygen to H5Ppublic.h * use attention instead of warning * Add doxygen comments in H5Ppublic.h (#375) * Add doxygen comments in H5Ppublic.h * H5Pset_meta_block_size * H5Pset_metadata_read_attempts * H5Pset_multi_type * H5Pset_object_flush_cb * H5Pset_sieve_buf_size * H5Pset_small_data_block_size * H5Pset_all_coll_metadata_ops * H5Pget_all_coll_metadata_ops * Add DOXYGEN_EXAMPLES_DIR to src/CMakeLists.txt * Fix clang-format errors * Fix filenames in doxygen/examples * add doxygen to H5Ppublic.h (#378) * add doxygen to H5Ppublic.h * use attention instead of warning Co-authored-by: Kimmy Mu <kmu@hdfgroup.org> * Revert "add doxygen to H5Ppublic.h (#378)" This reverts commit 2ee1821b138a5c00b15ea57ce9e950367480f5f2. * Updated Doxygen variables. * I forgot to copy two images. * Enable desktop search by default. * Add my assigned Doxygen documentation. * Remove whitespace at EOL. Appease clang-format. * Addressed Chris' comments. * Added an alias for asynchronous functions. * One space is enough for all of us. * Slightly restructured RM page. * address some issues * reformatting * Style external links. * reformatting * reformatting * Added "Metadata Caching in HDF5" as a technical note example. * Revise this soon! * Added specification examples. * Fixed references. * Added H5AC cache image stuff and file format study. * Added older FMT versions. Where did 1.0 go? * Updated C/C++ note and replaced ambiguous labels. * Reformat source with clang v10.0.1. * Added the VFL technical note. * Added what I believe might be called version 1.0 of the format. * Added the remaining specs. * Added H5Z callback documentation and fixed a few mistakes. * Added dox for deprecated H5G calls and fixed a few snippet blockIDs. * clang-format happy? * Ok? * Bonus track: Deprecated H5D functions. * Carry over the more detailed group description. * Added documentation for the missing and deprecated H5R calls. * Life is easier and less repetitive w/ snippets. Use them! * Eliminate the snippet block ID artifacts in the HTML rendering. * Fixed snippet HTML artifacts and added a few missing calls. * Under 20 H5Ps to go! * Almost complete! * "This is a form of pedantry up with which I will not put." (Churchill) * Let's not waste as much space on bulleted lists! * First complete (?) draft of the Doxygen-based RM. * Completeness check and minor fixes along the way. * Pedantry. * Adding missing H5FD calls checkpoint. * Pedantry. * More pedantry. * Added H5Pset_fapl_log. * First draft of H5ES. * Fixed warnings. * Prep. for map module. * First cut of the map module. * Pedantry. * Possible H5F introduction. * Fix the indentation. * Pedantry. * Ditto. * Thanks to the reviewers for their comments. * Added missing images. * Line numbers are a distraction here. * More examples, references, and clean-up. Don't repeat yourself! * Clang pedantry. * Ditto. * More reviewer comments... * Templatized references and cleaned up \todos. * Committing clang-format changes * Fixed MANIFEST. * Addressed Quincey's comments. (OCPLs) * Fixed a few more \todo items. * Fixed more \todo items. * Added attribute life cycle. * Forgot the examples file. * Committing clang-format changes * Pedantry. * Live and learn! * Added a sample H5D life cycle. * Committing clang-format changes * Pedantry. Co-authored-by: kyang2014 <kyang2014@users.noreply.github.com> Co-authored-by: Scot Breitenfeld <brtnfld@hdfgroup.org> Co-authored-by: Kimmy Mu <kmu@hdfgroup.org> Co-authored-by: Christopher Hogan <ChristopherHogan@users.noreply.github.com> Co-authored-by: jya-kmu <53388330+jya-kmu@users.noreply.github.com> Co-authored-by: David Young <dyoung@hdfgroup.org> Co-authored-by: Larry Knox <lrknox@hdfgroup.org> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Diffstat (limited to 'src/H5ACpublic.h')
-rw-r--r--src/H5ACpublic.h343
1 files changed, 283 insertions, 60 deletions
diff --git a/src/H5ACpublic.h b/src/H5ACpublic.h
index e6cebff..f8f4f28 100644
--- a/src/H5ACpublic.h
+++ b/src/H5ACpublic.h
@@ -442,124 +442,347 @@ extern "C" {
#define H5AC_METADATA_WRITE_STRATEGY__PROCESS_0_ONLY 0
#define H5AC_METADATA_WRITE_STRATEGY__DISTRIBUTED 1
+/**
+ * H5AC_cache_config_t is a public structure intended for use in public APIs.
+ * At least in its initial incarnation, it is basically a copy of \c struct
+ * \c H5C_auto_size_ctl_t, minus the \c report_fcn field, and plus the
+ * \c dirty_bytes_threshold field.
+ *
+ * The \c report_fcn field is omitted, as including it would require us to make
+ * \c H5C_t structure public.
+ *
+ * The \c dirty_bytes_threshold field does not appear in \c H5C_auto_size_ctl_t,
+ * as synchronization between caches on different processes is handled at the \c
+ * H5AC level, not at the level of \c H5C. Note however that there is
+ * considerable interaction between this value and the other fields in this
+ * structure.
+ *
+ * Similarly, the \c open_trace_file, \c close_trace_file, and \c
+ * trace_file_name fields do not appear in \c H5C_auto_size_ctl_t, as most trace
+ * file issues are handled at the \c H5AC level. The one exception is storage
+ * of the pointer to the trace file, which is handled by \c H5C.
+ *
+ * The structure is in H5ACpublic.h as we may wish to allow different
+ * configuration options for metadata and raw data caches.
+ */
+
+//! <!-- [H5AC_cache_config_t_snip] -->
typedef struct H5AC_cache_config_t {
/* general configuration fields: */
+ //! <!-- [H5AC_cache_config_t_general_snip] -->
int version;
+ /**< 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). */
hbool_t rpt_fcn_enabled;
+ /**< Boolean flag indicating whether the adaptive cache resize report
+ * function is enabled. This field should almost always be set to disabled
+ * (0). Since resize algorithm activity is reported via stdout, it MUST be
+ * set to disabled (0) on Windows machines.\n
+ * The report function is not supported code, and can be expected to change
+ * between versions of the library. Use it at your own risk. */
hbool_t open_trace_file;
+ /**< Boolean field indicating whether the
+ * \ref H5AC_cache_config_t.trace_file_name "trace_file_name"
+ * field should be used to open a trace file for the cache.\n
+ * The trace file is a debugging 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 0, as
+ * trace file collection imposes considerable overhead.\n
+ * This field should only be set to 1 when the
+ * \ref H5AC_cache_config_t.trace_file_name "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
+ * \ref H5AC_cache_config_t.close_trace_file "close_trace_file"
+ * field is also 1.\n
+ * 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. */
+
hbool_t close_trace_file;
- char trace_file_name[H5AC__MAX_TRACE_FILE_NAME_LEN + 1];
+ /**< Boolean field indicating whether the current trace file
+ *(if any) should be closed.\n
+ * See the above comments on the \ref H5AC_cache_config_t.open_trace_file
+ * "open_trace_file" field. This field should be set to 0 unless there is
+ * an open trace file on the cache that you wish to close.\n
+ * 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. */
+
+ char trace_file_name[H5AC__MAX_TRACE_FILE_NAME_LEN + 1];
+ /**< Full path of the trace file to be opened if the
+ * \ref H5AC_cache_config_t.open_trace_file "open_trace_file" field is set
+ * to 1.\n
+ * 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.\n
+ * The length of the path must not exceed #H5AC__MAX_TRACE_FILE_NAME_LEN
+ * characters.\n
+ * 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. */
hbool_t evictions_enabled;
+ /**< A boolean flag indicating whether evictions from the metadata cache
+ * are enabled. This flag is initially set to enabled (1).\n
+ * In rare circumstances, the raw data throughput quirements may be so high
+ * that the user wishes to postpone metadata writes so as to reserve I/O
+ * throughput for raw data. The \p evictions_enabled 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.\n
+ * The \p evictions_enabled field may not be set to disabled (0)
+ * unless all adaptive cache resizing code is disabled via the
+ * \ref H5AC_cache_config_t.incr_mode "incr_mode",
+ * \ref H5AC_cache_config_t.flash_incr_mode "flash_incr_mode",
+ * \ref H5AC_cache_config_t.decr_mode "decr_mode" fields.\n
+ * When this flag is set to disabled (\c 0), the metadata cache will not
+ * attempt to evict entries to make space for new entries, and thus will
+ * grow without bound.\n
+ * Evictions will be re-enabled when this field is set back to \c 1.
+ * This should be done as soon as possible. */
hbool_t set_initial_size;
- size_t initial_size;
+ /**< Boolean flag indicating whether the cache should be created
+ * with a user specified initial size. */
+
+ size_t initial_size;
+ /**< If \ref H5AC_cache_config_t.set_initial_size "set_initial_size"
+ * is set to 1, \p initial_size must contain he desired initial size in
+ * bytes. This value must lie in the closed interval
+ * [ \p min_size, \p max_size ]. (see below) */
double min_clean_fraction;
+ /**< This field specifies the minimum fraction of the cache
+ * that must be kept either clean or empty.\n
+ * 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 the overview of the metadata cache in the
+ * “Metadata Caching in HDF5” section of the -- <em>HDF5 User’s Guide</em>
+ * for details. */
size_t max_size;
+ /**< Upper bound (in bytes) on the range of values that the
+ * adaptive cache resize code can select as the maximum cache size. */
+
size_t min_size;
+ /**< Lower bound (in bytes) on the range of values that the
+ * adaptive cache resize code can select as the mininum cache * size. */
long int epoch_length;
+ /**< Number of cache accesses between runs of the adaptive cache resize
+ * code. 50,000 is a good starting number. */
+ //! <!-- [H5AC_cache_config_t_general_snip] -->
/* size increase control fields: */
+ //! <!-- [H5AC_cache_config_t_incr_snip] -->
enum H5C_cache_incr_mode incr_mode;
+ /**< Enumerated value indicating the operational mode of the automatic
+ * cache size increase code. At present, only two values listed in
+ * #H5C_cache_incr_mode are legal. */
double lower_hr_threshold;
+ /**< Hit rate threshold used by the hit rate threshold cache size
+ * increment algorithm.\n
+ * 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 \p max_size, and
+ * possibly \p max_increment.\n
+ * This field must lie in the interval [0.0, 1.0]. 0.8 or 0.9 is a good
+ * place to start. */
double increment;
+ /**< Factor by which the hit rate threshold cache size increment
+ * algorithm multiplies the current cache max size to obtain a tentative
+ * new cache size.\n
+ * The actual cache size increase will be clipped to satisfy the \p max_size
+ * specified in the general configuration, and possibly max_increment
+ * below.\n
+ * The parameter must be greater than or equal to 1.0 -- 2.0 is a reasonable
+ * value.\n
+ * If you set it to 1.0, you will effectively disable cache size increases.
+ */
hbool_t apply_max_increment;
- size_t max_increment;
+ /**< Boolean flag indicating whether an upper limit should be applied to
+ * the size of cache size increases. */
+
+ size_t max_increment;
+ /**< Maximum number of bytes by which cache size can be increased in a
+ * single step -- if applicable. */
enum H5C_cache_flash_incr_mode flash_incr_mode;
- double flash_multiple;
- double flash_threshold;
+ /**< Enumerated value indicating the operational mode of the flash cache
+ * size increase code. At present, only two listed values in
+ * #H5C_cache_flash_incr_mode are legal.*/
+
+ double flash_multiple;
+ /**< 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 \p max_size field above.\n
+ * The parameter must lie in the interval [0.0, 1.0]. 0.1 or 0.05 is a good
+ * place to start.\n
+ * At present, this field must lie in the range [0.1, 10.0]. */
+
+ double flash_threshold;
+ /**< 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. \n
+ * At present, this value must lie in the range [0.1, 1.0]. */
+ //! <!-- [H5AC_cache_config_t_incr_snip] -->
/* size decrease control fields: */
+ //! <!-- [H5AC_cache_config_t_decr_snip] -->
enum H5C_cache_decr_mode decr_mode;
+ /**< Enumerated value indicating the operational mode of the tomatic
+ * cache size decrease code. At present, the values listed in
+ * #H5C_cache_decr_mode are legal.*/
double upper_hr_threshold;
+ /**< Hit rate threshold for the hit rate threshold and ageout with hit
+ * rate threshold cache size decrement algorithms.\n
+ * When \p decr_mode is #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.\n
+ * When \p decr_mode is #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.\n
+ * This field must lie in the interval [0.0, 1.0].\n
+ * For #H5C_incr__threshold, .9995 or .99995 is a good place to start.\n
+ * For #H5C_decr__age_out_with_threshold, .999 might be more useful.*/
double decrement;
+ /**< 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.\n
+ * The actual cache size decrease will be clipped to satisfy the
+ * \ref H5AC_cache_config_t.min_size "min_size" specified in the general
+ * configuration, and possibly \ref H5AC_cache_config_t.max_decrement
+ * "max_decrement".\n
+ * The parameter must be be in the interval [0.0, 1.0].\n
+ * If you set it to 1.0, you will effectively
+ * disable cache size decreases. 0.9 is a reasonable starting point. */
hbool_t apply_max_decrement;
- size_t max_decrement;
+ /**< Boolean flag indicating ether an upper limit should be applied to
+ * the size of cache size decreases. */
+
+ size_t max_decrement;
+ /**< Maximum number of bytes by which the maximum cache size can be
+ * decreased in any single step -- if applicable.*/
int epochs_before_eviction;
+ /**< 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. */
hbool_t apply_empty_reserve;
- double empty_reserve;
+ /**< Boolean flag indicating whether the ageout based decrement
+ * algorithms will maintain a empty reserve when decreasing cache size. */
+
+ double empty_reserve;
+ /**< Empty reserve as a fraction maximum cache size if applicable.\n When
+ * so directed, the ageout based algorithms will not decrease the maximum
+ * cache size unless the empty reserve can be met.\n The parameter must lie
+ * in the interval [0.0, 1.0]. 0.1 or 0.05 is a good place to start. */
+ //! <!-- [H5AC_cache_config_t_decr_snip] -->
/* parallel configuration fields: */
+ //! <!-- [H5AC_cache_config_t_parallel_snip] -->
size_t dirty_bytes_threshold;
- int metadata_write_strategy;
-
+ /**< Threshold number of bytes of dirty metadata generation for
+ * triggering synchronizations of the metadata caches serving the target
+ * file in the parallel case.\n Synchronization occurs whenever the number
+ * of bytes of dirty metadata created since the last synchronization exceeds
+ * this limit.\n This field only applies to the parallel case. While it is
+ * ignored elsewhere, it can still draw a value out of bounds error.\n It
+ * must be consistant across all caches on any given file.\n By default,
+ * this field is set to 256 KB. It shouldn't be more than half the current
+ * max cache size times the min clean fraction. */
+
+ int metadata_write_strategy;
+ /**< Desired metadata write strategy. The valid values for this field
+ * are:\n #H5AC_METADATA_WRITE_STRATEGY__PROCESS_0_ONLY: Specifies tha only
+ * process zero is allowed to write dirty metadata to disk.\n
+ * #H5AC_METADATA_WRITE_STRATEGY__DISTRIBUTED: Specifies that 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 The src/H5ACpublic.h include file in the HDF5
+ * library has detailed information on each strategy. */
+ //! <!-- [H5AC_cache_config_t_parallel_snip] -->
} H5AC_cache_config_t;
-
-/****************************************************************************
- *
- * structure H5AC_cache_image_config_t
- *
- * H5AC_cache_image_ctl_t is a public structure intended for use in public
- * APIs. At least in its initial incarnation, it is a copy of struct
- * H5C_cache_image_ctl_t.
- *
- * The fields of the structure are discussed individually below:
- *
- * version: Integer field containing the version number of this version
- * of the H5C_image_ctl_t structure. Any instance of
- * H5C_image_ctl_t passed to the cache must have a known
- * version number, or an error will be flagged.
- *
- * generate_image: Boolean flag indicating whether a cache image should
- * be created on file close.
- *
- * save_resize_status: Boolean flag indicating whether the cache image
- * should include the adaptive cache resize configuration and status.
- * Note that this field is ignored at present.
- *
- * entry_ageout: Integer field indicating the maximum number of
- * times a prefetched entry can appear in subsequent cache images.
- * This field exists to allow the user to avoid the buildup of
- * infrequently used entries in long sequences of cache images.
- *
- * The value of this field must lie in the range
- * H5AC__CACHE_IMAGE__ENTRY_AGEOUT__NONE (-1) to
- * H5AC__CACHE_IMAGE__ENTRY_AGEOUT__MAX (100).
- *
- * H5AC__CACHE_IMAGE__ENTRY_AGEOUT__NONE means that no limit
- * is imposed on number of times a prefeteched entry can appear
- * in subsequent cache images.
- *
- * A value of 0 prevents prefetched entries from being included
- * in cache images.
- *
- * Positive integers restrict prefetched entries to the specified
- * number of appearances.
- *
- * Note that the number of subsequent cache images that a prefetched
- * entry has appeared in is tracked in an 8 bit field. Thus, while
- * H5AC__CACHE_IMAGE__ENTRY_AGEOUT__MAX can be increased from its
- * current value, any value in excess of 255 will be the functional
- * equivalent of H5AC__CACHE_IMAGE__ENTRY_AGEOUT__NONE.
- *
- ****************************************************************************/
+//! <!-- [H5AC_cache_config_t_snip] -->
#define H5AC__CURR_CACHE_IMAGE_CONFIG_VERSION 1
#define H5AC__CACHE_IMAGE__ENTRY_AGEOUT__NONE -1
#define H5AC__CACHE_IMAGE__ENTRY_AGEOUT__MAX 100
+//! <!-- [H5AC_cache_image_config_t_snip] -->
+/**
+ * H5AC_cache_image_config_t is a public structure intended for use in public
+ * APIs. At least in its initial incarnation, it is a copy of \c struct \c
+ * H5C_cache_image_ctl_t.
+ */
+
typedef struct H5AC_cache_image_config_t {
- int version;
+ int version;
+ /**< Integer field containing the version number of this version of the \c
+ * H5C_image_ctl_t structure. Any instance of \c H5C_image_ctl_t passed
+ * to the cache must have a known version number, or an error will be
+ * flagged.
+ */
hbool_t generate_image;
+ /**< Boolean flag indicating whether a cache image should be created on file
+ * close.
+ */
hbool_t save_resize_status;
- int entry_ageout;
+ /**< Boolean flag indicating whether the cache image should include the
+ * adaptive cache resize configuration and status. Note that this field
+ * is ignored at present.
+ */
+ int entry_ageout;
+ /**< Integer field indicating the maximum number of times a
+ * prefetched entry can appear in subsequent cache images. This field
+ * exists to allow the user to avoid the buildup of infrequently used
+ * entries in long sequences of cache images.
+ *
+ * The value of this field must lie in the range \ref
+ * H5AC__CACHE_IMAGE__ENTRY_AGEOUT__NONE (-1) to \ref
+ * H5AC__CACHE_IMAGE__ENTRY_AGEOUT__MAX (100).
+ *
+ * \ref H5AC__CACHE_IMAGE__ENTRY_AGEOUT__NONE means that no limit is
+ * imposed on number of times a prefeteched entry can appear in subsequent
+ * cache images.
+ *
+ * A value of 0 prevents prefetched entries from being included in cache
+ * images.
+ *
+ * Positive integers restrict prefetched entries to the specified number
+ * of appearances.
+ *
+ * Note that the number of subsequent cache images that a prefetched entry
+ * has appeared in is tracked in an 8 bit field. Thus, while \ref
+ * H5AC__CACHE_IMAGE__ENTRY_AGEOUT__MAX can be increased from its current
+ * value, any value in excess of 255 will be the functional equivalent of
+ * \ref H5AC__CACHE_IMAGE__ENTRY_AGEOUT__NONE.
+ */
} H5AC_cache_image_config_t;
+//! <!-- [H5AC_cache_image_config_t_snip] -->
+
#ifdef __cplusplus
}
#endif