Merge remote-tracking branch 'canonical/develop' into threadsafe_stat…

…ic_windows
derobins · Oct 3, 2023 · b0107f4 · b0107f4
2 parents 8fbf9c4 + cb6de06
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diff --git a/CMakeInstallation.cmake b/CMakeInstallation.cmake
@@ -335,7 +335,7 @@ if (NOT HDF5_EXTERNALLY_CONFIGURED AND NOT HDF5_NO_PACKAGES)
       set (CPACK_NSIS_INSTALL_ROOT "$PROGRAMFILES")
       set (CPACK_PACKAGE_INSTALL_REGISTRY_KEY "${CPACK_PACKAGE_NAME}-${CPACK_PACKAGE_VERSION}")
     endif ()
-    # set the install/unistall icon used for the installer itself
+    # set the install/uninstall icon used for the installer itself
     # There is a bug in NSI that does not handle full unix paths properly.
     set (CPACK_NSIS_MUI_ICON "${HDF_RESOURCES_DIR}\\\\hdf.ico")
     set (CPACK_NSIS_MUI_UNIICON "${HDF_RESOURCES_DIR}\\\\hdf.ico")

diff --git a/README.md b/README.md
@@ -14,6 +14,8 @@ HDF5 version 1.15.0 currently under development
 [![1.10 build status](https://img.shields.io/github/actions/workflow/status/HDFGroup/hdf5/main.yml?branch=hdf5_1_10&label=1.10)](https://github.com/HDFGroup/hdf5/actions?query=branch%3Ahdf5_1_10)
 [![BSD](https://img.shields.io/badge/License-BSD-blue.svg)](https://github.com/HDFGroup/hdf5/blob/develop/COPYING)
 
+[HPC configure/build/test results](https://my.cdash.org/index.php?project=HDF5)
+
 *Please refer to the release_docs/INSTALL file for installation instructions.*
 
 This repository contains a high-performance library's source code and a file format

diff --git a/config/cmake/UseJava.cmake b/config/cmake/UseJava.cmake
@@ -1474,7 +1474,7 @@ function (create_javah)
       "CLASSES;CLASSPATH;DEPENDS"
       ${ARGN})
 
-    # ckeck parameters
+    # check parameters
     if (NOT _create_javah_TARGET AND NOT _create_javah_GENERATED_FILES)
       message (FATAL_ERROR "create_javah: TARGET or GENERATED_FILES must be specified.")
     endif()

diff --git a/doc/getting-started-with-hdf5-development.md b/doc/getting-started-with-hdf5-development.md
@@ -496,7 +496,7 @@ files at configure time by the `bin/make_err` script. The original intent was fo
 codes to be strongly associated. i.e., a given minor code would *only* be used
 with its associated major code. Unfortunately, this has not been the case in
 practice, and the emitted text can appear nonsensical in error
-stack dumps. Even worse, the major and minor error codes are used inconsitently
+stack dumps. Even worse, the major and minor error codes are used inconsistently
 throughout the library, making interpreting them almost impossible for
 external users. We hope to address this deficiency in the near future.
 
@@ -556,7 +556,7 @@ configure/CMake options, but it's normally easier to use external tools like
 valgrind or the compiler's memory debugging options.
 
 `H5FL` provides memory pools (*Free Lists*) that create a set of fixed-size allocations
-of a certain type that the library will re-use as needed. They use `H5MM` calls
+of a certain type that the library will reuse as needed. They use `H5MM` calls
 under the hood and can be useful when the library creates and frees a lot of
 objects of that type. It's difficult to give a good guideline as to when to use
 the `H5FL` calls and when to use the `H5MM` calls, but it's probably best to

diff --git a/doxygen/examples/H5.format.1.0.html b/doxygen/examples/H5.format.1.0.html
@@ -2020,7 +2020,7 @@ <h4><a name="DataSpaceMessage">Name: Complex Dataspace (Fiber Bundle?)</a></h4>
 	<dl>
 	  <dt>Mesh Type: (unsigned 32-bit integer)
 	  <dd>This value indicates whether the grid is
-	    polar/spherical/cartesion,
+	    polar/spherical/cartesian,
 	    structured/unstructured and regular/irregular. <br>
 	    The mesh type value is broken up as follows: <br>
 

diff --git a/doxygen/examples/H5.format.1.1.html b/doxygen/examples/H5.format.1.1.html
@@ -2596,7 +2596,7 @@ <h4><a name="DataSpaceMessage">Name: Complex Dataspace (Fiber Bundle?)</a></h4>
 	<dl>
 	  <dt>Mesh Type: (unsigned 32-bit integer)
 	  <dd>This value indicates whether the grid is
-	    polar/spherical/cartesion,
+	    polar/spherical/cartesian,
 	    structured/unstructured and regular/irregular. <br>
 	    The mesh type value is broken up as follows: <br>
 

diff --git a/doxygen/examples/H5.format.2.0.html b/doxygen/examples/H5.format.2.0.html
@@ -8458,7 +8458,7 @@ <h4><a name="DataSpaceMessage">Header Message Name: Complex Dataspace (Fiber Bun
     <dl>
       <dt>Mesh Type: (unsigned 32-bit integer)
       <dd>This value indicates whether the grid is
-        polar/spherical/cartesion,
+        polar/spherical/cartesian,
         structured/unstructured and regular/irregular. <br />
         The mesh type value is broken up as follows: <br />
 

diff --git a/doxygen/examples/H5.format.html b/doxygen/examples/H5.format.html
@@ -9123,7 +9123,7 @@ <h4><a name="DataSpaceMessage">Header Message Name: Complex Dataspace (Fiber Bun
 	  <dl>
 	    <dt>Mesh Type: (unsigned 32-bit integer)
 	      <dd>This value indicates whether the grid is
-	        polar/spherical/cartesion,
+	        polar/spherical/cartesian,
 	        structured/unstructured and regular/irregular. <br />
 	        The mesh type value is broken up as follows: <br />
 

diff --git a/hl/fortran/src/H5IMff.F90 b/hl/fortran/src/H5IMff.F90
@@ -380,7 +380,7 @@ END SUBROUTINE h5imlink_palette_f
 !>
 !! \ingroup FH5IM
 !!
-!! \brief This function dettaches a palette to an existing image dataset.
+!! \brief This function detaches a palette to an existing image dataset.
 !!
 !! \param loc_id     Location identifier. The identifier may be that of a file or group.
 !! \param image_name The name of the image dataset.

diff --git a/hl/src/H5IM.c b/hl/src/H5IM.c
@@ -600,7 +600,7 @@ H5IMlink_palette(hid_t loc_id, const char *image_name, const char *pal_name)
 /*-------------------------------------------------------------------------
  * Function: H5IMunlink_palette
  *
- * Purpose: This function dettaches a palette from an existing image dataset
+ * Purpose: This function detaches a palette from an existing image dataset
  *
  * Return: Success: 0, Failure: -1
  *

diff --git a/hl/src/H5IMpublic.h b/hl/src/H5IMpublic.h
@@ -66,7 +66,7 @@ extern "C" {
  * - \ref H5IMread_image
  *   \n Reads image data from disk.
  * - \ref H5IMunlink_palette
- *   \n Dettaches a palette from an image.
+ *   \n Detaches a palette from an image.
  *
  */
 
@@ -229,15 +229,15 @@ H5_HLDLL herr_t H5IMlink_palette(hid_t loc_id, const char *image_name, const cha
  * --------------------------------------------------------------------------
  * \ingroup H5IM
  *
- * \brief Dettaches a palette from an image.
+ * \brief Detaches a palette from an image.
  *
  * \fg_loc_id
  * \param[in] image_name    The name of the image dataset
  * \param[in] pal_name      The name of the palette
  *
  * \return \herr_t
  *
- * \details H5IMunlink_palette() dettaches a palette from an image
+ * \details H5IMunlink_palette() detaches a palette from an image
  *          specified by \p image_name.
  *
  */

diff --git a/java/src/hdf/hdf5lib/H5.java b/java/src/hdf/hdf5lib/H5.java
@@ -9434,10 +9434,10 @@ public synchronized static native void H5Pset_meta_block_size(long fapl_id, long
     /**
      * @ingroup JH5P
      *
-     * H5Pset_sieve_buf_size Sets the maximum size of the data seive buffer used for file
+     * H5Pset_sieve_buf_size Sets the maximum size of the data sieve buffer used for file
      *      drivers which are capable of using data sieving.  The data sieve
      *      buffer is used when performing I/O on datasets in the file.  Using a
-     *      buffer which is large anough to hold several pieces of the dataset
+     *      buffer which is large enough to hold several pieces of the dataset
      *      being read in for hyperslab selections boosts performance by quite a
      *      bit.
      * <p>
@@ -9448,7 +9448,7 @@ public synchronized static native void H5Pset_meta_block_size(long fapl_id, long
      * @param fapl_id
      *            IN: Identifier of property list to modify.
      * @param size
-     *            IN: maximum size of the data seive buffer.
+     *            IN: maximum size of the data sieve buffer.
      *
      * @exception HDF5LibraryException
      *            Error from the HDF5 Library.

diff --git a/release_docs/HISTORY-1_0-1_8_0.txt b/release_docs/HISTORY-1_0-1_8_0.txt
@@ -1443,7 +1443,7 @@ Known Problems
   filter script.
 
 * H5Ocopy() does not copy reg_ref attributes correctly when shared-message
-  is turn on. The value of the reference in the destination attriubte is
+  is turn on. The value of the reference in the destination attribute is
   wrong. This H5Ocopy problem will affect h5copy tool
 
 %%%%1.6.7%%%%   Release Information for hdf5-1.6.7 (31/January/08)

diff --git a/release_docs/HISTORY-1_10_0-1_12_0.txt b/release_docs/HISTORY-1_10_0-1_12_0.txt
@@ -409,7 +409,7 @@ Bug Fixes since HDF5-1.10.3 release
     - Fixed a bug caused by bad tag value when condensing object header
       messages
 
-      There was an assertion failure when moving meessages from running a
+      There was an assertion failure when moving messages from running a
       user test program with library release hdf5.1.10.4. It was because
       the tag value (object header's address) was not set up when entering
       the library routine H5O__chunk_update_idx(), which will eventually

diff --git a/release_docs/HISTORY-1_12_0-1_14_0.txt b/release_docs/HISTORY-1_12_0-1_14_0.txt
@@ -3163,7 +3163,7 @@ New Features
 
       Some of the tools accepted shortened versions of the long options
       (ex: --datas instead of --dataset). These were implemented inconsistently,
-      are difficult to maintian, and occasionally block useful long option
+      are difficult to maintain, and occasionally block useful long option
       names. These partial long options have been removed from all the tools.
 
       (DER - 2021/08/03)

diff --git a/release_docs/HISTORY-1_8_0-1_10_0.txt b/release_docs/HISTORY-1_8_0-1_10_0.txt
@@ -837,7 +837,7 @@ Bug Fixes since HDF5-1.8.0 release
     - Support for TFLOPS, config/intel-osf1, is removed since the TFLOPS
       machine has long retired. AKC - 2009/10/06.
     - Added $(EXEEXT) extension to H5detect when it's executed in the
-      src/Makfile to generate H5Tinit.c so it works correctly on platforms
+      src/Makefile to generate H5Tinit.c so it works correctly on platforms
       that require the full extension when running executables.
       MAM - 2009/10/01 - BZ #1613
     - Configure will now set FC and CXX to "no" when fortran and c++
@@ -1734,6 +1734,6 @@ Known Problems
   filter script.
 
 * H5Ocopy() does not copy reg_ref attributes correctly when shared-message
-  is turn on. The value of the reference in the destination attriubte is
+  is turn on. The value of the reference in the destination attribute is
   wrong. This H5Ocopy problem will affect h5copy tool
 
diff --git a/src/H5ACmpio.c b/src/H5ACmpio.c
@@ -971,7 +971,7 @@ H5AC__log_inserted_entry(const H5AC_info_t *entry_ptr)
  *		dirty bytes count.
  *
  *		The rank 0 process then removes any references to the
- *		entry under its old address from the cleands and dirtied
+ *		entry under its old address from the clean and dirtied
  *		lists, and inserts an entry in the dirtied list under the
  *		new address.
  *

diff --git a/src/H5ACprivate.h b/src/H5ACprivate.h
@@ -25,7 +25,7 @@
 
 #include "H5ACpublic.h" /*public prototypes            */
 
-/* Pivate headers needed by this header */
+/* Private headers needed by this header */
 #include "H5private.h"   /* Generic Functions            */
 #include "H5Cprivate.h"  /* Cache                */
 #include "H5Fprivate.h"  /* File access                */

diff --git a/src/H5Centry.c b/src/H5Centry.c
@@ -1737,7 +1737,7 @@ H5C__destroy_pf_entry_child_flush_deps(H5C_t *cache_ptr, H5C_cache_entry_t *pf_e
  *              deserialized entry after it is inserted in the cache.
  *
  *              Since deserializing a prefetched entry is semantically
- *              equivalent to a load, issue an entry loaded nofification
+ *              equivalent to a load, issue an entry loaded notification
  *              if the notify callback is defined.
  *
  * Return:      SUCCEED on success, and FAIL on failure.

diff --git a/src/H5Cprivate.h b/src/H5Cprivate.h
@@ -537,7 +537,7 @@ typedef struct H5C_t H5C_t;
  *    ensure that the entry is ready to be flushed -- in particular,
  *    if the entry contains references to other entries that are in
  *    temporary file space, the pre-serialize callback must move those
- *    entries into real file space so that the serialzed entry will
+ *    entries into real file space so that the serialized entry will
  *    contain no invalid data.
  *
  *    One would think that the base address and length of

diff --git a/src/H5Dscatgath.c b/src/H5Dscatgath.c
@@ -1335,7 +1335,7 @@ H5D__scatgath_write_select(H5D_io_info_t *io_info)
         write_mem_spaces = NULL;
     }
 
-    /* Free bakcground buffer parameter arrays */
+    /* Free background buffer parameter arrays */
     H5MM_free(bkg_mem_spaces);
     bkg_mem_spaces = NULL;
     H5MM_free(bkg_file_spaces);

diff --git a/src/H5FDhdfs.c b/src/H5FDhdfs.c
@@ -926,7 +926,7 @@ hdfs__fprint_stats(FILE *stream, const H5FD_hdfs_t *file)
     unsigned long long max_raw      = 0;
     unsigned long long bytes_raw    = 0;
     unsigned long long bytes_meta   = 0;
-    double             re_dub       = 0.0; /* re-usable double variable */
+    double             re_dub       = 0.0; /* reusable double variable */
     unsigned           suffix_i     = 0;
     const char         suffixes[]   = {' ', 'K', 'M', 'G', 'T', 'P'};
 

diff --git a/src/H5FDonion.c b/src/H5FDonion.c
@@ -492,7 +492,7 @@ H5FD__onion_commit_new_revision_record(H5FD_onion_t *file)
     /* Update history info to accommodate new revision */
 
     if (history->n_revisions == 0) {
-        unsigned char *ptr = buf; /* re-use buffer space to compute checksum */
+        unsigned char *ptr = buf; /* reuse buffer space to compute checksum */
 
         assert(history->record_locs == NULL);
         history->n_revisions = 1;
@@ -508,7 +508,7 @@ H5FD__onion_commit_new_revision_record(H5FD_onion_t *file)
         file->header.history_size += H5FD_ONION_ENCODED_SIZE_RECORD_POINTER;
     } /* end if no extant revisions in history */
     else {
-        unsigned char *ptr = buf; /* re-use buffer space to compute checksum */
+        unsigned char *ptr = buf; /* reuse buffer space to compute checksum */
 
         assert(history->record_locs != NULL);
 

diff --git a/src/H5FDpublic.h b/src/H5FDpublic.h
@@ -76,7 +76,7 @@
 /*
  * Defining H5FD_FEAT_DATA_SIEVE for a VFL driver means that
  * the library will attempt to cache raw data as it is read from/written to
- * a file in a "data seive" buffer.  See Rajeev Thakur's papers:
+ * a file in a "data sieve" buffer.  See Rajeev Thakur's papers:
  *  http://www.mcs.anl.gov/~thakur/papers/romio-coll.ps.gz
  *  http://www.mcs.anl.gov/~thakur/papers/mpio-high-perf.ps.gz
  */

diff --git a/src/H5FDros3.c b/src/H5FDros3.c
@@ -960,7 +960,7 @@ H5FD__ros3_open(const char *url, unsigned flags, hid_t fapl_id, haddr_t maxaddr)
     if (fa.authenticate == true) {
         /* compute signing key (part of AWS/S3 REST API)
          * can be re-used by user/key for 7 days after creation.
-         * find way to re-use/share
+         * find way to reuse/share
          */
         now = gmnow();
         assert(now != NULL);
@@ -1084,7 +1084,7 @@ ros3_fprint_stats(FILE *stream, const H5FD_ros3_t *file)
     unsigned long long max_raw      = 0;
     unsigned long long bytes_raw    = 0;
     unsigned long long bytes_meta   = 0;
-    double             re_dub       = 0.0; /* re-usable double variable */
+    double             re_dub       = 0.0; /* reusable double variable */
     unsigned           suffix_i     = 0;
     const char         suffixes[]   = {' ', 'K', 'M', 'G', 'T', 'P'};
 

diff --git a/src/H5FDs3comms.c b/src/H5FDs3comms.c
@@ -571,7 +571,7 @@ H5FD_s3comms_hrb_node_set(hrb_node_t **L, const char *name, const char *value)
  *
  *    Headers list at `first_header` is not touched.
  *
- *    - Programmer should re-use or destroy `first_header` pointer
+ *    - Programmer should reuse or destroy `first_header` pointer
  *      (hrb_node_t *) as suits their purposes.
  *    - Recommend fetching prior to destroy()
  *      e.g., `reuse_node = hrb_to_die->first_header; destroy(hrb_to_die);`
@@ -2531,7 +2531,7 @@ H5FD_s3comms_percent_encode_char(char *repr, const unsigned char c, size_t *repr
  *     Create AWS4 "Signing Key" from secret key, AWS region, and timestamp.
  *
  *     Sequentially runs HMAC_SHA256 on strings in specified order,
- *     generating re-usable checksum (according to documentation, valid for
+ *     generating reusable checksum (according to documentation, valid for
  *     7 days from time given).
  *
  *     `secret` is `access key id` for targeted service/bucket/resource.

diff --git a/src/H5FDs3comms.h b/src/H5FDs3comms.h
@@ -211,7 +211,7 @@
  *
  * `magic` (unsigned long)
  *
- *     "unique" idenfier number for the structure type
+ *     "unique" identifier number for the structure type
  *
  * `name` (char *)
  *
@@ -458,7 +458,7 @@ typedef struct {
  *
  * `signing_key` (unsigned char *)
  *
- *     Pointer to `SHA256_DIGEST_LENGTH`-long string for "re-usable" signing
+ *     Pointer to `SHA256_DIGEST_LENGTH`-long string for "reusable" signing
  *     key, generated via
  *     `HMAC-SHA256(HMAC-SHA256(HMAC-SHA256(HMAC-SHA256("AWS4<secret_key>",
  *         "<yyyyMMDD"), "<aws-region>"), "<aws-service>"), "aws4_request")`

diff --git a/src/H5FDsubfiling/H5FDsubfiling.c b/src/H5FDsubfiling/H5FDsubfiling.c
@@ -2031,7 +2031,7 @@ H5FD__subfiling_write(H5FD_t *_file, H5FD_mem_t type, hid_t H5_ATTR_UNUSED dxpl_
  *                          The contents of supplied buffers are undefined.
  *
  * Notes:       Thus function doesn't actually implement vector read.
- *              Instead, it comverts the vector read call into a series
+ *              Instead, it converts the vector read call into a series
  *              of scalar read calls.  Fix this when time permits.
  *
  *              Also, it didn't support the sizes and types optimization.
@@ -2191,7 +2191,7 @@ H5FD__subfiling_read_vector(H5FD_t *_file, hid_t dxpl_id, uint32_t count, H5FD_m
  *                          subfiling writes have failed for some reason.
  *
  * Notes:       Thus function doesn't actually implement vector write.
- *              Instead, it comverts the vector write call into a series
+ *              Instead, it converts the vector write call into a series
  *              of scalar read calls.  Fix this when time permits.
  *
  *              Also, it didn't support the sizes and types optimization.

diff --git a/src/H5FDsubfiling/H5subfiling_common.c b/src/H5FDsubfiling/H5subfiling_common.c
@@ -618,7 +618,7 @@ H5_open_subfiling_stub_file(const char *name, unsigned flags, MPI_Comm file_comm
  *              new MPI communicators that facilitate messaging between
  *              HDF5 clients and the IOCs.
  *
- * Return:      Success (0) or Faiure (non-zero)
+ * Return:      Success (0) or Failure (non-zero)
  * Errors:      If MPI operations fail for some reason.
  *
  *-------------------------------------------------------------------------
@@ -1951,7 +1951,7 @@ init_subfiling_context(subfiling_context_t *sf_context, const char *base_filenam
  *              discovery.  The number and mapping of IOC to MPI_rank
  *              is part of the sf_context->topology structure.
  *
- * Return:      Success (0) or Faiure (non-zero)
+ * Return:      Success (0) or Failure (non-zero)
  * Errors:      If MPI operations fail for some reason.
  *
  *-------------------------------------------------------------------------
@@ -2686,7 +2686,7 @@ H5_resolve_pathname(const char *filepath, MPI_Comm comm, char **resolved_filepat
  *              which actually manages all subfile closing via commands
  *              to the set of IO Concentrators.
  *
- * Return:      Success (0) or Faiure (non-zero)
+ * Return:      Success (0) or Failure (non-zero)
  * Errors:      If MPI operations fail for some reason.
  *
  *-------------------------------------------------------------------------
@@ -2707,7 +2707,7 @@ H5_resolve_pathname(const char *filepath, MPI_Comm comm, char **resolved_filepat
  *              Once the subfiles are closed, we initiate a teardown of
  *              the IOC and associated thread_pool threads.
  *
- * Return:      Success (0) or Faiure (non-zero)
+ * Return:      Success (0) or Failure (non-zero)
  * Errors:      If MPI operations fail for some reason.
  *
  *-------------------------------------------------------------------------

diff --git a/src/H5FLprivate.h b/src/H5FLprivate.h
@@ -201,7 +201,7 @@ typedef struct H5FL_blk_head_t {
 #define H5FL_BLK_REALLOC(t, blk, new_size)                                                                   \
     (uint8_t *)H5FL_blk_realloc(&(H5FL_BLK_NAME(t)), blk, new_size H5FL_TRACK_INFO)
 
-/* Check if there is a free block available to re-use */
+/* Check if there is a free block available to reuse */
 #define H5FL_BLK_AVAIL(t, size) H5FL_blk_free_block_avail(&(H5FL_BLK_NAME(t)), size)
 
 #else /* H5_NO_BLK_FREE_LISTS */

diff --git a/src/H5Gpublic.h b/src/H5Gpublic.h
@@ -809,7 +809,7 @@ H5_DLL herr_t H5Gmove2(hid_t src_loc_id, const char *src_name, hid_t dst_loc_id,
  *          any object identifier is open for the object, the space will not be
  *          released until after the object identifier is closed.
  *
- *          Note that space identified as freespace is available for re-use only
+ *          Note that space identified as freespace is available for reuse only
  *          as long as the file remains open; once a file has been closed, the
  *          HDF5 library loses track of freespace. See “Freespace Management” in
  *          the \ref UG for further details.