Hdf5 1 12 doxygen merge (#615)

* OESS-98 fix tools test for plugins

* sync fork

* Merge of changes from dev

* Move problem option to bottom of the list until fixed

* HDFFV-11106 - fix parsing optional args

* HDFFV-11106 add note

* grammer fix

* Whitespace after clang formatting

* Undo format version 11 changes

* Update check to working version

* Merge workflow and minor changes from develop

* Update supported platforms

* PR#3 merge from develop

* Merge gcc 10 diagnostics option from develop

* Merge #318 OSX changes from develop

* Merge serval small changes from dev

* fix typo

* Minor non-space formatting changes

* GH #386 copyright corrections for java folder

* revert because logic requires false return

* Merges from develop

#358 patches from vtk
#361 fix header guard spelling

* Remove case statement for H5I_EVENTSET

* Correct call with versioning

* Remove tabs

* Double underscore change

* Merges from develop

#340 clang -Wformat-security warnings
#360 Fixed uninitialized warnings
Remove more underscores from header guards

* Merge #380 from develop

* Correct date entry

* Split format source and commit changes on repo push

* remove pre-split setting

* Change windows TS to use older VS.

* HDFFV-11212 JNI export util and Javadoc

* Suggested review changes

* Another change found

* Committing clang-format changes

* Some Javadoc warning fixes

* Committing clang-format changes

* Updated javadoc fixes

* HDFFV-11228/9 merges from develop

* remove obsolete debug comment

* Fix conflict

* HDFFV-11229 merge changes from develop

* HDFFV-11229 merge second compare from develop

* HDFFV-11229 fix reference file

* HDFFV-11229 update autotools test script for two ref files

* HDFFV-11229 merge dev changes for long double display in tools

* Committing clang-format changes

* Update with changes from develop

* Add "option" command for clang options

* Rework CMake add_custom to use the BYPRODUCTS argument

Update pkgconfig scripts for parallel builds.
Fix install COPYING file reference.
Remove unused round defines.
Change CMake default setting of BUILD_CPP to off.

* Whitespace changes

* Rework CMake add_custom to use the BYPRODUCTS argument

* Revert CMake configure checks for round defines

* With VS 2015 minimum strdup is supported

* Doxygen comments merged from develop

* doxygen build updates

* Correct version string for map functions

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

1 files changed, 224 insertions, 1 deletions

diff --git a/src/H5FDmpio.h b/src/H5FDmpio.h
index 79b52c7..8caf11c 100644
--- a/src/H5FDmpio.h
+++ b/src/H5FDmpio.h
@@ -44,14 +44,237 @@ H5_DLLVAR hbool_t H5FD_mpi_opt_types_g;
 #ifdef __cplusplus
 extern "C" {
 #endif
-H5_DLL hid_t  H5FD_mpio_init(void);
+H5_DLL hid_t H5FD_mpio_init(void);
+
+/**
+ * \ingroup FAPL
+ *
+ * \brief Stores MPI IO communicator information to the file access property list
+ *
+ * \fapl_id
+ * \param[in] comm MPI-2 communicator
+ * \param[in] info MPI-2 info object
+ * \returns \herr_t
+ *
+ * \details H5Pset_fapl_mpio() stores the user-supplied MPI IO parameters \p
+ *          comm, for communicator, and \p info, for information, in the file
+ *          access property list \p fapl_id. That property list can then be used
+ *          to create and/or open a file.
+ *
+ *          H5Pset_fapl_mpio() is available only in the parallel HDF5 library
+ *          and is not a collective function.
+ *
+ *          \p comm is the MPI communicator to be used for file open, as defined
+ *          in \c MPI_File_open of MPI-2. This function makes a duplicate of the
+ *          communicator, so modifications to \p comm after this function call
+ *          returns have no effect on the file access property list.
+ *
+ *          \p info is the MPI Info object to be used for file open, as defined
+ *          in MPI_File_open() of MPI-2. This function makes a duplicate copy of
+ *          the Info object, so modifications to the Info object after this
+ *          function call returns will have no effect on the file access
+ *          property list.
+ *
+ *          If the file access property list already contains previously-set
+ *          communicator and Info values, those values will be replaced and the
+ *          old communicator and Info object will be freed.
+ *
+ * \note Raw dataset chunk caching is not currently supported when using this
+ *       file driver in read/write mode. All calls to H5Dread() and H5Dwrite()
+ *       will access the disk directly, and H5Pset_cache() and
+ *       H5Pset_chunk_cache() will have no effect on performance.\n
+ *       Raw dataset chunk caching is supported when this driver is used in
+ *       read-only mode.
+ *
+ * \version 1.4.5 Handling of the MPI Communicator and Info object changed at
+ *          this release. A duplicate of each of these is now stored in the property
+ *          list instead of pointers to each.
+ * \since 1.4.0
+ *
+ */
 H5_DLL herr_t H5Pset_fapl_mpio(hid_t fapl_id, MPI_Comm comm, MPI_Info info);
+
+/**
+ * \ingroup FAPL
+ *
+ * \brief Returns MPI IO communicator information
+ *
+ * \fapl_id
+ * \param[out] comm MPI-2 communicator
+ * \param[out] info MPI-2 info object
+ * \returns \herr_t
+ *
+ * \details If the file access property list is set to the #H5FD_MPIO driver,
+ *          H5Pget_fapl_mpio() returns duplicates of the stored MPI communicator
+ *          and Info object through the \p comm and \p info pointers, if those
+ *          values are non-null.
+ *
+ *          Since the MPI communicator and Info object are duplicates of the
+ *          stored information, future modifications to the access property list
+ *          will not affect them. It is the responsibility of the application to
+ *          free these objects.
+ *
+ * \version 1.4.5 Handling of the MPI Communicator and Info object changed at
+ *          this release. A duplicate of each of these is now stored in the
+ *          property list instead of pointers to each.
+ * \since 1.4.0
+ *
+ */
 H5_DLL herr_t H5Pget_fapl_mpio(hid_t fapl_id, MPI_Comm *comm /*out*/, MPI_Info *info /*out*/);
+
+/**
+ * \ingroup DXPL
+ *
+ * \brief Sets data transfer mode
+ *
+ * \dxpl_id
+ * \param[in] xfer_mode Transfer mode
+ * \returns \herr_t
+ *
+ * \details H5Pset_dxpl_mpio() sets the data transfer property list \p dxpl_id
+ *          to use transfer mode \p xfer_mode. The property list can then be
+ *          used to control the I/O transfer mode during data I/O operations.
+ *
+ *          Valid transfer modes are #H5FD_MPIO_INDEPENDENT (default) and
+ *          #H5FD_MPIO_COLLECTIVE.
+ *
+ * \since 1.4.0
+ *
+ */
 H5_DLL herr_t H5Pset_dxpl_mpio(hid_t dxpl_id, H5FD_mpio_xfer_t xfer_mode);
+
+/**
+ * \ingroup DXPL
+ *
+ * \brief Returns the data transfer mode
+ *
+ * \dxpl_id
+ * \param[out] xfer_mode Transfer mode
+ * \returns \herr_t
+ *
+ * \details H5Pget_dxpl_mpio() queries the data transfer mode currently set in
+ *          the data transfer property list \p dxpl_id.
+ *
+ *          Upon return, \p xfer_mode contains the data transfer mode, if it is
+ *          non-null.
+ *
+ *          H5Pget_dxpl_mpio() is not a collective function.
+ *
+ * \since 1.4.0
+ *
+ */
 H5_DLL herr_t H5Pget_dxpl_mpio(hid_t dxpl_id, H5FD_mpio_xfer_t *xfer_mode /*out*/);
+
+/**
+ * \ingroup DXPL
+ *
+ * \brief Sets data transfer mode
+ *
+ * \dxpl_id
+ * \param[in] opt_mode Transfer mode
+ * \returns \herr_t
+ *
+ * \details H5Pset_dxpl_mpio() sets the data transfer property list \p dxpl_id
+ *          to use transfer mode xfer_mode. The property list can then be used
+ *          to control the I/O transfer mode during data I/O operations.
+ *
+ *          Valid transfer modes are #H5FD_MPIO_INDEPENDENT (default) and
+ *          #H5FD_MPIO_COLLECTIVE.
+ *
+ * \since 1.4.0
+ *
+ */
 H5_DLL herr_t H5Pset_dxpl_mpio_collective_opt(hid_t dxpl_id, H5FD_mpio_collective_opt_t opt_mode);
+
+/**
+ * \ingroup DXPL
+ *
+ * \brief Sets a flag specifying linked-chunk I/O or multi-chunk I/O
+ *
+ * \dxpl_id
+ * \param[in] opt_mode Transfer mode
+ * \returns \herr_t
+ *
+ * \details H5Pset_dxpl_mpio_chunk_opt() specifies whether I/O is to be
+ *          performed as linked-chunk I/O or as multi-chunk I/O. This function
+ *          overrides the HDF5 library's internal algorithm for determining
+ *          which mechanism to use.
+ *
+ *          When an application uses collective I/O with chunked storage, the
+ *          HDF5 library normally uses an internal algorithm to determine
+ *          whether that I/O activity should be conducted as one linked-chunk
+ *          I/O or as multi-chunk I/O. H5Pset_dxpl_mpio_chunk_opt() is provided
+ *          so that an application can override the library's algorithm in
+ *          circumstances where the library might lack the information needed to
+ *          make an optimal decision.
+ *
+ *          H5Pset_dxpl_mpio_chunk_opt() works by setting one of the following
+ *          flags in the parameter \p opt_mode:
+ *          - #H5FD_MPIO_CHUNK_ONE_IO -	Do one-link chunked I/O
+ *          - #H5FD_MPIO_CHUNK_MULTI_IO - Do multi-chunked I/O
+ *
+ *          This function works by setting a corresponding property in the
+ *          dataset transfer property list \p dxpl_id.
+ *
+ *          The library performs I/O in the specified manner unless it
+ *          determines that the low-level MPI IO package does not support the
+ *          requested behavior; in such cases, the HDF5 library will internally
+ *          use independent I/O.
+ *
+ *          Use of this function is optional.
+ *
+ * \todo Add missing version information
+ *
+ */
 H5_DLL herr_t H5Pset_dxpl_mpio_chunk_opt(hid_t dxpl_id, H5FD_mpio_chunk_opt_t opt_mode);
+
+/**
+ * \ingroup DXPL
+ *
+ * \brief Sets a numeric threshold for linked-chunk I/O
+ *
+ * \dxpl_id
+ * \param[in] num_chunk_per_proc
+ * \returns \herr_t
+ *
+ * \details H5Pset_dxpl_mpio_chunk_opt_num() sets a numeric threshold for the
+ *          use of linked-chunk I/O.
+ *
+ *          The library will calculate the average number of chunks selected by
+ *          each process when doing collective access with chunked storage. If
+ *          the number is greater than the threshold set in \p
+ *          num_chunk_per_proc, the library will use linked-chunk I/O;
+ *          otherwise, a separate I/O process will be invoked for each chunk
+ *          (multi-chunk I/O).
+ *
+ * \todo Add missing version information
+ *
+ */
 H5_DLL herr_t H5Pset_dxpl_mpio_chunk_opt_num(hid_t dxpl_id, unsigned num_chunk_per_proc);
+
+/**
+ * \ingroup DXPL
+ *
+ * \brief Sets a ratio threshold for collective I/O
+ *
+ * \dxpl_id
+ * \param[in] percent_num_proc_per_chunk
+ * \returns \herr_t
+ *
+ * \details H5Pset_dxpl_mpio_chunk_opt_ratio() sets a threshold for the use of
+ *          collective I/O based on the ratio of processes with collective
+ *          access to a dataset with chunked storage. The decision whether to
+ *          use collective I/O is made on a per-chunk basis.
+ *
+ *          The library will calculate the percentage of the total number of
+ *          processes, the ratio, that hold selections in each chunk. If that
+ *          percentage is greater than the threshold set in \p
+ *          percent_proc_per_chunk, the library will do collective I/O for this
+ *          chunk; otherwise, independent I/O will be done for the chunk.
+ *
+ * \todo Add missing version information
+ *
+ */
 H5_DLL herr_t H5Pset_dxpl_mpio_chunk_opt_ratio(hid_t dxpl_id, unsigned percent_num_proc_per_chunk);
 #ifdef __cplusplus
 }