Merge3 839 hdf5 1 12 (#907)

* Reorganization of C and POSIX headers in H5public.h & H5private.h (#793)

* Reorganization of C and POSIX headers in H5public.h & H5private.h

Consolidated and removed duplicates

* It turns out Windows has sys/types.h

Co-authored-by: Larry Knox <lrknox@hdfgroup.org>

* Brings the tools getopt(3) replacement into the main library (#803)

* Moves get_option from the tools library to the C library

* Adds H5 prefix to get_option call and variables

* Renames the H5_get_option long options struct and enum

* Remove version-check for relnum in H5check. (#812)

* Remove version-check for relnum in H5check.

* Add in release exception code check

* Fix typos

* Fix more typos

* Rework comments

* format change

* format whitespace

* Library version must be less than or equal to headers

* Need the NOT version of the compare

* Enable release+1 check for PASS

* Add release note

* Update note

* Remove checks for winsock2.h (#813)

This is only needed on Windows and always available, so there's no need
to check for it.

* Removes develop header cruft (#828)

* OESS-168:Remove implicit conversion warnings. (#829)

* OESS-168:Remove implicit conversion increases floating-point precision warnings.

* OESS-168:Remove clang warnings.

* Add support for parallel filters to h5repack (#832)

* Perform option arg variables (#834)

* Correct option name

* Undo accidental commit

* Note LLVM 10 to 11 format default changes

* Update format plugin

* Undo clang-format version 11 changes

* One more correction

* Update supported platforms

* Revert whitespace changes

* Correct whitespace

* Changes from PR#3

* HDFFV-11213 added option to control gcc10 warnings diagnostics

* HDFFV-11212 Use the new references correctly in JNI utility and tests

* format source

* Fix typo

* Add new test file

* HDFFV-11212 - update test and remove unused arg

* Minor non-space formatting changes

* Use H5I_INVALID_ID instead of "-1"

* source formatting

* add missing testfile, update jni function

* Undo commit of debug code

* remove mislocated file

* Fix h5repack test for handling of fapls and id close

* Update h5diff test files usage text

* HDFFV-11212 add new ref tests for JNI export dataset

* src format update

* Remove blank line typo

* src format typo

* long double requires %Lg

* Another long double foramt specifer S.B. %Lg

* issue with t128bit test

* Windows issue with h5dump and type.

* Fix review issues

* refactor function nesting and fix error checks

* format fixes

* Remove untested functions and javadoc quiet comments

* Restore TRY block.

* Change string append errors to memory exception

* revert to H5_JNI_FATAL_ERROR - support functions need work

* Add assertion error for h5util functions

* remove duplicate function

* format fix

* Revert HD function error handling

* Update copyright comments

* GH #386 java folder copyright corrections

* Whitespace

* GH #359 implement and fix tools 1.6 API usage

* remove excessive comments

* Flip inits to correct ifdef section

* rework ifdef to be simpler

* format issue

* Reformat ifdef inits

* remove static attribute

* format compliance

* Update names

* Revert because logic relies on float not being int

* Changes noticed from creating merge of #412

* Double underscore change

* Correct compiler version variable used

* Remove header guard underscores

* Whitespace cleanup

* Split format source and commit changes on repo push

* remove pre-split setting

* Change windows TS to use older VS.

* correct window os name

* HDFFV-11212 JNI export util and Javadoc

* Suggested review changes

* Another change found

* Committing clang-format changes

* HDFFV-11113 long double in tools

* HDFFV-11113 add note

* Disable long double tests for now

* HDFFV-11228 remove arbitrary CMake warning groups.

* Make each flag a string

* Some Javadoc warning fixes

* Updated javadoc fixes

* # WARNING: head commit changed in the meantime

HDFFV-11229 Fix long double usage in tools and java

Changed h5dump and h5ls to just print 128-bit for long double type.
Added test and file for dataset and attributes with all three float
types.

* Committing clang-format changes

* HDFFV-11229 Add release note

* HDFFV-11229 windows testfile needed

* fix typo

* Remove non supported message text

* HDFFV-11229 - change ldouble test to check both native and general

* HDFFV-11229 add second file compare

* HDFFV-11229 fix reference file

* HDFFV-11229 autotools check two refs

* HDFFV-11229 revert back to removal of NATIVE_LDOUBLE in tools output

* Committing clang-format changes

* Update release note

* Update attribute type of ref file

* Change source of ninja for macs

* try port instead of brew

* Recommended is to use brew.

* Undo non long double changes

* remove unneeded file

* Fix perl and doxygen CMake code

* Add "option" command for clang options

* Rework CMake add_custom to use the BYPRODUCTS argument

* Add stamp files to BYPRODUCTS

* Only one copy of file exists

* Fix custom cmmand depends targets

* Fix fortran custom command DEPENDS

* Add LD_LIBRARY_PATH to tests

* Add custom target for DEPENDS

* Add h5detect conditionaly to generated target DEPENDS

* Correct DEPENDS targets

* Parallel builds need the mpi compiler for pkgconfig scripts.

* install only if MPI build

* Fortran target depends

* Remove incorrect source attribute

* doxygen adjustments

* doxygen build updates

* Correct version

* Correct function version - function has been merged to 1.12

* Correct version string for map functions

* Cleanup warnings for tools debug builds

* TRILAB-227 - fix indexing for h5diff selections

* Correct location of pos to index function call

* TRILAB-227 Enable test

* Quote subset args

* Use MATCHES because of AppleClang

* if blocks needed for build modes

* Update list of DT platforms

* VS2019 correctly displays float values

* revert VS2019 change

* Issue #669 remove version from pkgcfg filename

* remove version from h5cc script

* Java reference functions updated

enabled fortran in cmake gcc action yaml file
java reference test changed to correctly test refs
jni reference functions that create ids changed to use jni id logging

* Correct BYPRODUCTS argument

* Correct more genereated files BYPRODUCTS

* BYPRODUCTS must have unique locations

* Fix typo

* Fix fortran configure checks

* Rework H5_PAC_C_MAX_REAL_PRECISION setting logic

* Add note about fortran configure change

* Adds a quick for for some egregious chunk_info badness (#722)

* Fixes issue with ccmake that prevents building Fortran (#723)

ccmake runs iteratively, and the check_fortran_source_runs
macros were clobbering a single output file that did not
get updated on further configure iterations

* Fix conflicts with merge

* Move MAX_PRECISION back to HDF5UseFortran.cmake

* Use STREQUAL to test macro argument

* Move C language test to ConfigureChecks from HDF5UseFortran

* MAX_PRECISION defines must be defined

* Organize flags and align autotools and cmake

* Fix comment in no-error-general warnings files.

* Flag cleanup and fix typos

* Add comment

* Correct VAR used to find configure time file

* Set the path correctly

* Update missing release note info.

* Update code owners

* Correct JIRA note

* add known problem.

* Use only core library for testing dynamic plugins.

* Fix static perform tools compile for arg options

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>

* OESS-168:Remove clang warnings. (#835)

* OESS-168:Remove implicit conversion increases floating-point precision warnings.

* OESS-168:Remove clang warnings.

* OESS-168:Remove clang warnings.

* Committing clang-format changes

* OESS-168:Remove clang warnings.

* Committing clang-format changes

* OESS-168:Remove clang warning.

* OESS-168:Remove clang warnings.

* OESS-168:Address @byrnHDF review.

* Remove line added to generated hl/src/H5LTanalyze.c file.
Issue #854 created for creating a fix.

* Remove extra whitespace from H5LTanalyze.c.

* Remove extra blank line.

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Larry Knox <lrknox@hdfgroup.org>

* Removes unused commented-out code from h5jamgentest.c (#851)

* Updates a comment in H5mpi.c (#863)

MPI_Type_struct() is an MPI-1 call we no longer use.

* Unsigned comparison to 0 warning avoidance (#869)

* Added int variable for comparison with H5_VERS_RELEASE in H5.c to avoid
warning that unsigned comparison < 0 is always false, which is known,
        but for later versions the comparison can possibly be true.

* Better solution for avoiding warning that unsigned comparison < 0.

* Updates the RELEASE.txt file with a note about the variable-length fill (#871)

value issue. A fix is in progress, but it might be a while before
we have time to finish it up.

* Add parallel version of h5pfc script (#881)

Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
Co-authored-by: Allen Byrne <50328838+byrnHDF@users.noreply.github.com>
Co-authored-by: H. Joe Lee <hyoklee@hdfgroup.org>
Co-authored-by: jhendersonHDF <jhenderson@hdfgroup.org>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

5 files changed, 383 insertions, 105 deletions

diff --git a/src/H5.c b/src/H5.c
index 5a07b28..1b7407c 100644
--- a/src/H5.c
+++ b/src/H5.c
@@ -63,6 +63,10 @@ hbool_t H5_PKG_INIT_VAR = FALSE;
 /* Library Private Variables */
 /*****************************/
 
+/* Library incompatible release versions */
+const unsigned VERS_RELEASE_EXCEPTIONS[]    = {0};
+const unsigned VERS_RELEASE_EXCEPTIONS_SIZE = 0;
+
 /* statically initialize block for pthread_once call used in initializing */
 /* the first global mutex                                                 */
 #ifdef H5_HAVE_THREADSAFE
@@ -264,13 +268,13 @@ done:
 } /* end H5_init_library() */
 
 /*-------------------------------------------------------------------------
- * Function:	H5_term_library
+ * Function:    H5_term_library
  *
- * Purpose:	Terminate interfaces in a well-defined order due to
- *		dependencies among the interfaces, then terminate
- *		library-specific data.
+ * Purpose:    Terminate interfaces in a well-defined order due to
+ *        dependencies among the interfaces, then terminate
+ *        library-specific data.
  *
- * Return:	void
+ * Return:    void
  *
  *-------------------------------------------------------------------------
  */
@@ -456,22 +460,22 @@ done:
 } /* end H5_term_library() */
 
 /*-------------------------------------------------------------------------
- * Function:	H5dont_atexit
+ * Function:    H5dont_atexit
  *
- * Purpose:	Indicates that the library is not to clean up after itself
- *		when the application exits by calling exit() or returning
- *		from main().  This function must be called before any other
- *		HDF5 function or constant is used or it will have no effect.
+ * Purpose:    Indicates that the library is not to clean up after itself
+ *        when the application exits by calling exit() or returning
+ *        from main().  This function must be called before any other
+ *        HDF5 function or constant is used or it will have no effect.
  *
- *		If this function is used then certain memory buffers will not
- *		be de-allocated nor will open files be flushed automatically.
- *		The application may still call H5close() explicitly to
- *		accomplish these things.
+ *        If this function is used then certain memory buffers will not
+ *        be de-allocated nor will open files be flushed automatically.
+ *        The application may still call H5close() explicitly to
+ *        accomplish these things.
  *
- * Return:	Success:	non-negative
+ * Return:    Success:    non-negative
  *
- *		Failure:	negative if this function is called more than
- *				once or if it is called too late.
+ *        Failure:    negative if this function is called more than
+ *                once or if it is called too late.
  *
  *-------------------------------------------------------------------------
  */
@@ -492,19 +496,19 @@ H5dont_atexit(void)
 } /* end H5dont_atexit() */
 
 /*-------------------------------------------------------------------------
- * Function:	H5garbage_collect
+ * Function:    H5garbage_collect
  *
- * Purpose:	Walks through all the garbage collection routines for the
- *		library, which are supposed to free any unused memory they have
- *		allocated.
+ * Purpose:    Walks through all the garbage collection routines for the
+ *        library, which are supposed to free any unused memory they have
+ *        allocated.
  *
  *      These should probably be registered dynamically in a linked list of
  *          functions to call, but there aren't that many right now, so we
  *          hard-wire them...
  *
- * Return:	Success:	non-negative
+ * Return:    Success:    non-negative
  *
- *		Failure:	negative
+ *        Failure:    negative
  *
  *-------------------------------------------------------------------------
  */
@@ -525,9 +529,9 @@ done:
 } /* end H5garbage_collect() */
 
 /*-------------------------------------------------------------------------
- * Function:	H5set_free_list_limits
+ * Function:    H5set_free_list_limits
  *
- * Purpose:	Sets limits on the different kinds of free lists.  Setting a value
+ * Purpose:    Sets limits on the different kinds of free lists.  Setting a value
  *      of -1 for a limit means no limit of that type.  These limits are global
  *      for the entire library.  Each "global" limit only applies to free lists
  *      of that type, so if an application sets a limit of 1 MB on each of the
@@ -545,9 +549,9 @@ done:
  *  int blk_global_lim;  IN: The limit on all "block" free list memory used
  *  int blk_list_lim;    IN: The limit on memory used in each "block" free list
  *
- * Return:	Success:	non-negative
+ * Return:    Success:    non-negative
  *
- *		Failure:	negative
+ *        Failure:    negative
  *
  *-------------------------------------------------------------------------
  */
@@ -571,11 +575,11 @@ done:
 } /* end H5set_free_list_limits() */
 
 /*-------------------------------------------------------------------------
- * Function:	H5get_free_list_sizes
+ * Function:    H5get_free_list_sizes
  *
- * Purpose:	Gets the current size of the different kinds of free lists that
- *	the library uses to manage memory.  The free list sizes can be set with
- *	H5set_free_list_limits and garbage collected with H5garbage_collect.
+ * Purpose:    Gets the current size of the different kinds of free lists that
+ *    the library uses to manage memory.  The free list sizes can be set with
+ *    H5set_free_list_limits and garbage collected with H5garbage_collect.
  *      These lists are global for the entire library.
  *
  * Parameters:
@@ -584,8 +588,8 @@ done:
  *  size_t *blk_size;    OUT: The current size of all "block" free list memory used
  *  size_t *fac_size;    OUT: The current size of all "factory" free list memory used
  *
- * Return:	Success:	non-negative
- *		Failure:	negative
+ * Return:    Success:    non-negative
+ *        Failure:    negative
  *
  * Programmer:  Quincey Koziol
  *              Friday, March 6, 2020
@@ -609,23 +613,23 @@ done:
 } /* end H5get_free_list_sizes() */
 
 /*-------------------------------------------------------------------------
- * Function:	H5get_alloc_stats
+ * Function:    H5get_alloc_stats
  *
- * Purpose:	Gets the memory allocation statistics for the library, if the
- *	--enable-memory-alloc-sanity-check option was given when building the
+ * Purpose:    Gets the memory allocation statistics for the library, if the
+ *    --enable-memory-alloc-sanity-check option was given when building the
  *      library.  Applications can check whether this option was enabled by
- *	detecting if the 'H5_MEMORY_ALLOC_SANITY_CHECK' macro is defined.  This
- *	option is enabled by default for debug builds of the library and
- *	disabled by default for non-debug builds.  If the option is not enabled,
- *	all the values returned with be 0.  These statistics are global for the
- *	entire library, but don't include allocations from chunked dataset I/O
- *	filters or non-native VOL connectors.
+ *    detecting if the 'H5_MEMORY_ALLOC_SANITY_CHECK' macro is defined.  This
+ *    option is enabled by default for debug builds of the library and
+ *    disabled by default for non-debug builds.  If the option is not enabled,
+ *    all the values returned with be 0.  These statistics are global for the
+ *    entire library, but don't include allocations from chunked dataset I/O
+ *    filters or non-native VOL connectors.
  *
  * Parameters:
  *  H5_alloc_stats_t *stats;            OUT: Memory allocation statistics
  *
- * Return:	Success:	non-negative
- *		Failure:	negative
+ * Return:    Success:    non-negative
+ *        Failure:    negative
  *
  * Programmer:  Quincey Koziol
  *              Saturday, March 7, 2020
@@ -758,12 +762,12 @@ H5__debug_mask(const char *s)
 #ifdef H5_HAVE_PARALLEL
 
 /*-------------------------------------------------------------------------
- * Function:	H5__mpi_delete_cb
+ * Function:    H5__mpi_delete_cb
  *
- * Purpose:	Callback attribute on MPI_COMM_SELF to terminate the HDF5
+ * Purpose:    Callback attribute on MPI_COMM_SELF to terminate the HDF5
  *              library when the communicator is destroyed, i.e. on MPI_Finalize.
  *
- * Return:	MPI_SUCCESS
+ * Return:    MPI_SUCCESS
  *
  *-------------------------------------------------------------------------
  */
@@ -777,18 +781,18 @@ H5__mpi_delete_cb(MPI_Comm H5_ATTR_UNUSED comm, int H5_ATTR_UNUSED keyval, void
 #endif /*H5_HAVE_PARALLEL*/
 
 /*-------------------------------------------------------------------------
- * Function:	H5get_libversion
+ * Function:    H5get_libversion
  *
- * Purpose:	Returns the library version numbers through arguments. MAJNUM
- *		will be the major revision number of the library, MINNUM the
- *		minor revision number, and RELNUM the release revision number.
+ * Purpose:    Returns the library version numbers through arguments. MAJNUM
+ *        will be the major revision number of the library, MINNUM the
+ *        minor revision number, and RELNUM the release revision number.
  *
- * Note:	When printing an HDF5 version number it should be printed as
+ * Note:    When printing an HDF5 version number it should be printed as
  *
- * 		printf("%u.%u.%u", maj, min, rel)		or
- *		printf("version %u.%u release %u", maj, min, rel)
+ *         printf("%u.%u.%u", maj, min, rel)        or
+ *        printf("version %u.%u release %u", maj, min, rel)
  *
- * Return:	Non-negative on success/Negative on failure
+ * Return:    Non-negative on success/Negative on failure
  *
  *-------------------------------------------------------------------------
  */
@@ -813,17 +817,20 @@ done:
 } /* end H5get_libversion() */
 
 /*-------------------------------------------------------------------------
- * Function:	H5check_version
+ * Function:    H5check_version
  *
- * Purpose:	Verifies that the arguments match the version numbers
- *		compiled into the library.  This function is intended to be
- *		called from user to verify that the versions of header files
- *		compiled into the application match the version of the hdf5
- *		library.
+ * Purpose:    Verifies that the arguments match the version numbers
+ *        compiled into the library.  This function is intended to be
+ *        called from user to verify that the versions of header files
+ *        compiled into the application match the version of the hdf5
+ *        library.
+ *        Within major.minor.release version, the expectation
+ *        is that all release versions are compatible, exceptions to
+ *        this rule must be added to the VERS_RELEASE_EXCEPTIONS list.
  *
- * Return:	Success:	SUCCEED
+ * Return:    Success:    SUCCEED
  *
- *		Failure:	abort()
+ *        Failure:    abort()
  *
  *-------------------------------------------------------------------------
  */
@@ -836,6 +843,15 @@ done:
     "linked with a different version of static or shared HDF5 library.\n"                                    \
     "You should recompile the application or check your shared library related\n"                            \
     "settings such as 'LD_LIBRARY_PATH'.\n"
+#define RELEASE_MISMATCH_WARNING                                                                             \
+    "Warning! ***HDF5 library release mismatched error***\n"                                                 \
+    "The HDF5 header files used to compile this application are not compatible with\n"                       \
+    "the version used by the HDF5 library to which this application is linked.\n"                            \
+    "Data corruption or segmentation faults may occur if the application continues.\n"                       \
+    "This can happen when an application was compiled by one version of HDF5 but\n"                          \
+    "linked with an incompatible version of static or shared HDF5 library.\n"                                \
+    "You should recompile the application or check your shared library related\n"                            \
+    "settings such as 'LD_LIBRARY_PATH'.\n"
 
 herr_t
 H5check_version(unsigned majnum, unsigned minnum, unsigned relnum)
@@ -864,7 +880,11 @@ H5check_version(unsigned majnum, unsigned minnum, unsigned relnum)
             disable_version_check = (unsigned int)HDstrtol(s, NULL, 0);
     }
 
-    if (H5_VERS_MAJOR != majnum || H5_VERS_MINOR != minnum || H5_VERS_RELEASE != relnum) {
+    /* H5_VERS_MAJOR and H5_VERS_MINOR must match */
+    /* Cast relnum to int to avoid warning for unsigned < 0 comparison
+     * in first release versions */
+    if (H5_VERS_MAJOR != majnum || H5_VERS_MINOR != minnum || H5_VERS_RELEASE > (int)relnum) {
+
         switch (disable_version_check) {
             case 0:
                 HDfprintf(stderr, "%s%s", version_mismatch_warning,
@@ -899,7 +919,51 @@ H5check_version(unsigned majnum, unsigned minnum, unsigned relnum)
                 break;
         } /* end switch */
 
-    } /* end if */
+    } /* end if (H5_VERS_MAJOR != majnum || H5_VERS_MINOR != minnum || H5_VERS_RELEASE > relnum) */
+
+    /* H5_VERS_RELEASE should be compatible, we will only add checks for exceptions */
+    if (H5_VERS_RELEASE != relnum) {
+        for (unsigned i = 0; i < VERS_RELEASE_EXCEPTIONS_SIZE; i++) {
+            /* Check for incompatible headers or incompatible library */
+            if (VERS_RELEASE_EXCEPTIONS[i] == relnum || VERS_RELEASE_EXCEPTIONS[i] == H5_VERS_RELEASE) {
+                switch (disable_version_check) {
+                    case 0:
+                        HDfprintf(
+                            stderr, "%s%s", version_mismatch_warning,
+                            "You can, at your own risk, disable this warning by setting the environment\n"
+                            "variable 'HDF5_DISABLE_VERSION_CHECK' to a value of '1'.\n"
+                            "Setting it to 2 or higher will suppress the warning messages totally.\n");
+                        /* Mention the versions we are referring to */
+                        HDfprintf(stderr, "Headers are %u.%u.%u, library is %u.%u.%u\n", majnum, minnum,
+                                  relnum, (unsigned)H5_VERS_MAJOR, (unsigned)H5_VERS_MINOR,
+                                  (unsigned)H5_VERS_RELEASE);
+
+                        /* Bail out now. */
+                        HDfputs("Bye...\n", stderr);
+                        HDabort();
+                    case 1:
+                        /* continue with a warning */
+                        /* Note that the warning message is embedded in the format string.*/
+                        HDfprintf(stderr,
+                                  "%s'HDF5_DISABLE_VERSION_CHECK' "
+                                  "environment variable is set to %d, application will\n"
+                                  "continue at your own risk.\n",
+                                  version_mismatch_warning, disable_version_check);
+                        /* Mention the versions we are referring to */
+                        HDfprintf(stderr, "Headers are %u.%u.%u, library is %u.%u.%u\n", majnum, minnum,
+                                  relnum, (unsigned)H5_VERS_MAJOR, (unsigned)H5_VERS_MINOR,
+                                  (unsigned)H5_VERS_RELEASE);
+                        break;
+                    default:
+                        /* 2 or higher: continue silently */
+                        break;
+                } /* end switch */
+
+            } /* end if */
+
+        } /* end for */
+
+    } /* end if (H5_VERS_RELEASE != relnum) */
 
     /* Indicate that the version check has been performed */
     checked = 1;
@@ -944,7 +1008,7 @@ done:
  *              is failing inexplicably, then try calling this function
  *              first.
  *
- * Return:	Non-negative on success/Negative on failure
+ * Return:    Non-negative on success/Negative on failure
  *
  *-------------------------------------------------------------------------
  */
@@ -965,9 +1029,9 @@ done:
 /*-------------------------------------------------------------------------
  * Function:	H5close
  *
- * Purpose:	Terminate the library and release all resources.
+ * Purpose:    Terminate the library and release all resources.
  *
- * Return:	Non-negative on success/Negative on failure
+ * Return:    Non-negative on success/Negative on failure
  *
  *-------------------------------------------------------------------------
  */
@@ -988,9 +1052,9 @@ H5close(void)
 } /* end H5close() */
 
 /*-------------------------------------------------------------------------
- * Function:	H5allocate_memory
+ * Function:    H5allocate_memory
  *
- * Purpose:	    Allocate a memory buffer with the semantics of malloc().
+ * Purpose:        Allocate a memory buffer with the semantics of malloc().
  *
  *              NOTE: This function is intended for use with filter
  *              plugins so that all allocation and free operations
@@ -1028,9 +1092,9 @@ H5allocate_memory(size_t size, hbool_t clear)
 } /* end H5allocate_memory() */
 
 /*-------------------------------------------------------------------------
- * Function:	H5resize_memory
+ * Function:    H5resize_memory
  *
- * Purpose:	    Resize a memory buffer with the semantics of realloc().
+ * Purpose:        Resize a memory buffer with the semantics of realloc().
  *
  *              NOTE: This function is intended for use with filter
  *              plugins so that all allocation and free operations
@@ -1065,14 +1129,14 @@ H5resize_memory(void *mem, size_t size)
 } /* end H5resize_memory() */
 
 /*-------------------------------------------------------------------------
- * Function:	H5free_memory
+ * Function:    H5free_memory
  *
- * Purpose:	    Frees memory allocated by the library that it is the user's
+ * Purpose:        Frees memory allocated by the library that it is the user's
  *              responsibility to free.  Ensures that the same library
  *              that was used to allocate the memory frees it.  Passing
  *              NULL pointers is allowed.
  *
- * Return:	    SUCCEED/FAIL
+ * Return:        SUCCEED/FAIL
  *
  *-------------------------------------------------------------------------
  */
@@ -1089,12 +1153,12 @@ H5free_memory(void *mem)
 } /* end H5free_memory() */
 
 /*-------------------------------------------------------------------------
- * Function:	H5is_library_threadsafe
+ * Function:    H5is_library_threadsafe
  *
- * Purpose:	    Checks to see if the library was built with thread-safety
+ * Purpose:        Checks to see if the library was built with thread-safety
  *              enabled.
  *
- * Return:	    SUCCEED/FAIL
+ * Return:        SUCCEED/FAIL
  *
  *-------------------------------------------------------------------------
  */
diff --git a/src/H5mpi.c b/src/H5mpi.c
index 9749721..4a8aa44 100644
--- a/src/H5mpi.c
+++ b/src/H5mpi.c
@@ -523,7 +523,7 @@ H5_mpio_create_large_type(hsize_t num_elements, MPI_Aint stride_bytes, MPI_Datat
             MPI_Type_get_extent(old_type, &unused_lb_arg, &old_extent);
         }
 
-        /* Set up the arguments for MPI_Type_struct constructor */
+        /* Set up the arguments for MPI_Type_create_struct() */
         type[0]      = outer_type;
         type[1]      = leftover_type;
         block_len[0] = 1;
diff --git a/src/H5private.h b/src/H5private.h
index 808c2ce..1fd95dc 100644
--- a/src/H5private.h
+++ b/src/H5private.h
@@ -31,19 +31,19 @@
 #include <errno.h>
 #include <fcntl.h>
 #include <float.h>
-#include <limits.h>
 #include <math.h>
 #include <signal.h>
-#include <stdint.h>
 #include <stdio.h>
 #include <stdlib.h>
 #include <string.h>
 
 /* POSIX headers */
+#ifdef H5_HAVE_SYS_TIME_H
+#include <sys/time.h>
+#endif
 #ifdef H5_HAVE_UNISTD_H
 #include <pwd.h>
 #include <unistd.h>
-#include <sys/types.h>
 #include <sys/wait.h>
 #endif
 
@@ -130,22 +130,21 @@
 #define H5_DEFAULT_VOL H5VL_NATIVE
 
 #ifdef H5_HAVE_WIN32_API
+
 /* The following two defines must be before any windows headers are included */
 #define WIN32_LEAN_AND_MEAN /* Exclude rarely-used stuff from Windows headers */
 #define NOGDI               /* Exclude Graphic Display Interface macros */
 
-#ifdef H5_HAVE_WINSOCK2_H
-#include <winsock2.h>
-#endif
+#include <windows.h>
+
+#include <direct.h>   /* For _getcwd() */
+#include <io.h>       /* POSIX I/O */
+#include <winsock2.h> /* For GetUserName() */
 
 #ifdef H5_HAVE_THREADSAFE
 #include <process.h> /* For _beginthread() */
 #endif
 
-#include <windows.h>
-#include <direct.h> /* For _getcwd() */
-#include <io.h>     /* POSIX I/O */
-
 #endif /*H5_HAVE_WIN32_API*/
 
 #ifndef F_OK
@@ -2524,6 +2523,57 @@ H5_DLL double H5_get_time(void);
 H5_DLL herr_t H5_build_extpath(const char *name, char **extpath /*out*/);
 H5_DLL herr_t H5_combine_path(const char *path1, const char *path2, char **full_name /*out*/);
 
+/* getopt(3) equivalent that papers over the lack of long options on BSD
+ * and lack of Windows support.
+ */
+H5_DLLVAR int         H5_opterr; /* get_option prints errors if this is on */
+H5_DLLVAR int         H5_optind; /* token pointer */
+H5_DLLVAR const char *H5_optarg; /* flag argument (or value) */
+
+enum h5_arg_level {
+    no_arg = 0,  /* doesn't take an argument     */
+    require_arg, /* requires an argument          */
+    optional_arg /* argument is optional         */
+};
+
+/*
+ * get_option determines which options are specified on the command line and
+ * returns a pointer to any arguments possibly associated with the option in
+ * the ``H5_optarg'' variable. get_option returns the shortname equivalent of
+ * the option. The long options are specified in the following way:
+ *
+ * struct h5_long_options foo[] = {
+ *   { "filename", require_arg, 'f' },
+ *   { "append", no_arg, 'a' },
+ *   { "width", require_arg, 'w' },
+ *   { NULL, 0, 0 }
+ * };
+ *
+ * Long named options can have arguments specified as either:
+ *
+ *   ``--param=arg'' or ``--param arg''
+ *
+ * Short named options can have arguments specified as either:
+ *
+ *   ``-w80'' or ``-w 80''
+ *
+ * and can have more than one short named option specified at one time:
+ *
+ *   -aw80
+ *
+ * in which case those options which expect an argument need to come at the
+ * end.
+ */
+struct h5_long_options {
+    const char *      name;     /* Name of the long option */
+    enum h5_arg_level has_arg;  /* Whether we should look for an arg */
+    char              shortval; /* The shortname equivalent of long arg
+                                 * this gets returned from get_option
+                                 */
+};
+
+H5_DLL int H5_get_option(int argc, const char **argv, const char *opt, const struct h5_long_options *l_opt);
+
 #ifdef H5_HAVE_PARALLEL
 /* Generic MPI functions */
 H5_DLL hsize_t H5_mpi_set_bigio_count(hsize_t new_count);
diff --git a/src/H5public.h b/src/H5public.h
index 30d297e..495af6f 100644
--- a/src/H5public.h
+++ b/src/H5public.h
@@ -35,22 +35,23 @@
 #include <features.h> /* For setting POSIX, BSD, etc. compatibility */
 #endif
 
-#ifdef H5_HAVE_SYS_TYPES_H
-#include <sys/types.h>
-#endif
-
-#include <limits.h> /* For H5T_NATIVE_CHAR defn in H5Tpublic.h  */
-#include <stdarg.h> /* For variadic functions in H5VLpublic.h   */
-
-#include <stdint.h> /* For C9x types */
-
+/* C library header files for things that appear in HDF5 public headers */
 #ifdef __cplusplus
 #define __STDC_FORMAT_MACROS
 #endif
-#include <inttypes.h> /* C99/POSIX.1 header for uint64_t, PRIu64 */
-
-#ifdef H5_HAVE_STDDEF_H
+#include <inttypes.h>
+#include <limits.h>
+#include <stdarg.h>
+#include <stdbool.h>
 #include <stddef.h>
+#include <stdint.h>
+
+/* Unlike most sys/ headers, which are POSIX-only, sys/types.h is avaible
+ * on Windows, though it doesn't necessarily contain all the POSIX types
+ * we need for HDF5 (e.g. ssize_t).
+ */
+#ifdef H5_HAVE_SYS_TYPES_H
+#include <sys/types.h>
 #endif
 
 #ifdef H5_HAVE_PARALLEL
@@ -214,7 +215,6 @@ typedef int herr_t;
  * }
  * \endcode
  */
-#include <stdbool.h>
 typedef bool hbool_t;
 typedef int  htri_t;
 
diff --git a/src/H5system.c b/src/H5system.c
index 4aae743..56110ea 100644
--- a/src/H5system.c
+++ b/src/H5system.c
@@ -487,7 +487,7 @@ Wsetenv(const char *name, const char *value, int overwrite)
     return (int)_putenv_s(name, value);
 } /* end Wsetenv() */
 
-#ifdef H5_HAVE_WINSOCK2_H
+#ifdef H5_HAVE_WIN32_API
 #pragma comment(lib, "advapi32.lib")
 #endif
 
@@ -572,12 +572,12 @@ char *
 Wgetlogin(void)
 {
 
-#ifdef H5_HAVE_WINSOCK2_H
+#ifdef H5_HAVE_WIN32_API
     DWORD bufferCount = WloginBuffer_count;
     if (GetUserName(Wlogin_buffer, &bufferCount) != 0)
         return (Wlogin_buffer);
     else
-#endif /* H5_HAVE_WINSOCK2_H */
+#endif
         return NULL;
 }
 
@@ -1058,3 +1058,167 @@ done:
     FUNC_LEAVE_NOAPI(ret_value)
 } /* end H5_expand_windows_env_vars() */
 #endif /* H5_HAVE_WIN32_API */
+
+/* Global variables */
+int         H5_opterr = 1; /* Get_option prints errors if this is on */
+int         H5_optind = 1; /* Token pointer                          */
+const char *H5_optarg;     /* Flag argument (or value)               */
+
+/*-------------------------------------------------------------------------
+ * Function: H5_get_option
+ *
+ * Purpose:  Determine the command-line options a user specified. We can
+ *           accept both short and long type command-lines.
+ *
+ * Return:  Success:    The short valued "name" of the command line
+ *                      parameter or EOF if there are no more
+ *                      parameters to process.
+ *
+ *          Failure:    A question mark.
+ *-------------------------------------------------------------------------
+ */
+int
+H5_get_option(int argc, const char **argv, const char *opts, const struct h5_long_options *l_opts)
+{
+    static int sp     = 1;   /* character index in current token */
+    int        optopt = '?'; /* option character passed back to user */
+
+    if (sp == 1) {
+        /* check for more flag-like tokens */
+        if (H5_optind >= argc || argv[H5_optind][0] != '-' || argv[H5_optind][1] == '\0') {
+            return EOF;
+        }
+        else if (HDstrcmp(argv[H5_optind], "--") == 0) {
+            H5_optind++;
+            return EOF;
+        }
+    }
+
+    if (sp == 1 && argv[H5_optind][0] == '-' && argv[H5_optind][1] == '-') {
+        /* long command line option */
+        int        i;
+        const char ch      = '=';
+        char *     arg     = HDstrdup(&argv[H5_optind][2]);
+        size_t     arg_len = 0;
+
+        H5_optarg = strchr(&argv[H5_optind][2], ch);
+        arg_len   = HDstrlen(&argv[H5_optind][2]);
+        if (H5_optarg) {
+            arg_len -= HDstrlen(H5_optarg);
+            H5_optarg++; /* skip the equal sign */
+        }
+        arg[arg_len] = 0;
+
+        for (i = 0; l_opts && l_opts[i].name; i++) {
+            if (HDstrcmp(arg, l_opts[i].name) == 0) {
+                /* we've found a matching long command line flag */
+                optopt = l_opts[i].shortval;
+
+                if (l_opts[i].has_arg != no_arg) {
+                    if (H5_optarg == NULL) {
+                        if (l_opts[i].has_arg != optional_arg) {
+                            if (H5_optind < (argc - 1))
+                                if (argv[H5_optind + 1][0] != '-')
+                                    H5_optarg = argv[++H5_optind];
+                        }
+                        else if (l_opts[i].has_arg == require_arg) {
+                            if (H5_opterr)
+                                HDfprintf(stderr, "%s: option required for \"--%s\" flag\n", argv[0], arg);
+
+                            optopt = '?';
+                        }
+                    }
+                }
+                else {
+                    if (H5_optarg) {
+                        if (H5_opterr)
+                            HDfprintf(stderr, "%s: no option required for \"%s\" flag\n", argv[0], arg);
+
+                        optopt = '?';
+                    }
+                }
+                break;
+            }
+        }
+
+        if (l_opts[i].name == NULL) {
+            /* exhausted all of the l_opts we have and still didn't match */
+            if (H5_opterr)
+                HDfprintf(stderr, "%s: unknown option \"%s\"\n", argv[0], arg);
+
+            optopt = '?';
+        }
+
+        H5_optind++;
+        sp = 1;
+
+        HDfree(arg);
+    }
+    else {
+        register char *cp; /* pointer into current token */
+
+        /* short command line option */
+        optopt = argv[H5_optind][sp];
+
+        if (optopt == ':' || (cp = HDstrchr(opts, optopt)) == 0) {
+            if (H5_opterr)
+                HDfprintf(stderr, "%s: unknown option \"%c\"\n", argv[0], optopt);
+
+            /* if no chars left in this token, move to next token */
+            if (argv[H5_optind][++sp] == '\0') {
+                H5_optind++;
+                sp = 1;
+            }
+            return '?';
+        }
+
+        if (*++cp == ':') {
+            /* if a value is expected, get it */
+            if (argv[H5_optind][sp + 1] != '\0') {
+                /* flag value is rest of current token */
+                H5_optarg = &argv[H5_optind++][sp + 1];
+            }
+            else if (++H5_optind >= argc) {
+                if (H5_opterr)
+                    HDfprintf(stderr, "%s: value expected for option \"%c\"\n", argv[0], optopt);
+
+                optopt = '?';
+            }
+            else {
+                /* flag value is next token */
+                H5_optarg = argv[H5_optind++];
+            }
+
+            sp = 1;
+        }
+        /* wildcard argument */
+        else if (*cp == '*') {
+            /* check the next argument */
+            H5_optind++;
+            /* we do have an extra argument, check if not last */
+            if ((H5_optind + 1) < argc) {
+                if (argv[H5_optind][0] != '-') {
+                    H5_optarg = argv[H5_optind++];
+                }
+                else {
+                    H5_optarg = NULL;
+                }
+            }
+            else {
+                H5_optarg = NULL;
+            }
+        }
+        else {
+            /* set up to look at next char in token, next time */
+            if (argv[H5_optind][++sp] == '\0') {
+                /* no more in current token, so setup next token */
+                H5_optind++;
+                sp = 1;
+            }
+            H5_optarg = NULL;
+        }
+    }
+
+    /* return the current flag character found */
+    return optopt;
+}