Merging in latest from upstream (HDFFV/hdf5:refs/heads/develop)

* commit '30776671fb0a27a98b0640aa968f850241a862ce': (31 commits)
  * Fix intermittent error with Splitter VFD.     Mismatch in time of test file creation was creating false negatives.
  Added note for HDFFV-10591.
  Fix HDFFV-10591
  Reduce overhead for H5open, which is involved in the public symbols like H5T_NATIVE_INT, etc.
  Remove unnecessary version conditions for Clang compilers.
  Fix for HDFFV-10961: Couple changes to the tests' usage output files for h5clear.
  Fix for HDFFV-10961: add description to usage for --increment option.
  Add c++ to --enable-sanitize-checks option.
  Remove duplicate entries in MANIFEST.
  Make changes to CMake CompilerFlags.cmake files so extra flags are loaded for non-GNU compilers.
  Fix MANIFEST
  Add tests for all version to H5_NO_DEPRECATED_SYMBOLS section and to section for current version, with and without default API version flags.
  HDFFV-11000:  update-testh5cc.sh.in to test sample versioned functions in HDF5 1.10, 1.12 and develop.
  Remember the info for the last ID looked up for a given ID type.
  Eliminate allocating file & memory offset & length arrays when performing I/O on a single element.
  Update new clang files to not pick up clang as vendor for pgCC. Add new files to MANIFEST Temporary demotion of 2 -Werror warning flags that fail on macos 10.12 Remove Production flag unknown to Apple clang.
  Remove redundant metadata cache tagging from some low-level internal chunk functions.  The metadata cache tagging has already been done by routines further up the call stack.
  Clean up code to get clang version in config/linux-gnulibc1
  Minor normalizations with HDF5 1.10.
  Add flags from config/clang-warnings/*general files to H5 C and CXX flags for all versions of Clang and Clang++ compilers. Switched from cut to awk in testcheck_version.sh.in to avoid dependence on tab vs. " " in version definitions in H5public.h.
  ...

1 files changed, 84 insertions, 82 deletions

diff --git a/src/H5PB.c b/src/H5PB.c
index 45f24e3..907fe82 100644
--- a/src/H5PB.c
+++ b/src/H5PB.c
@@ -24,21 +24,21 @@
 /* Module Setup */
 /****************/
 
-#define H5F_FRIEND		/*suppress error about including H5Fpkg	  */
+#define H5F_FRIEND              /* Suppress error about including H5Fpkg            */
 #include "H5PBmodule.h"         /* This source code file is part of the H5PB module */
 
 
 /***********/
 /* Headers */
 /***********/
-#include "H5private.h"		/* Generic Functions			*/
-#include "H5Eprivate.h"		/* Error handling		  	*/
-#include "H5Fpkg.h"		/* Files				*/
-#include "H5FDprivate.h"	/* File drivers				*/
-#include "H5Iprivate.h"		/* IDs			  		*/
-#include "H5MMprivate.h"	/* Memory management			*/
-#include "H5PBpkg.h"            /* File access				*/
-#include "H5SLprivate.h"	/* Skip List				*/
+#include "H5private.h"          /* Generic Functions                */
+#include "H5Eprivate.h"         /* Error handling                   */
+#include "H5Fpkg.h"             /* Files                            */
+#include "H5FDprivate.h"        /* File drivers                     */
+#include "H5Iprivate.h"         /* IDs                              */
+#include "H5MMprivate.h"        /* Memory management                */
+#include "H5PBpkg.h"            /* File access                      */
+#include "H5SLprivate.h"        /* Skip List                        */
 
 
 /****************/
@@ -153,7 +153,7 @@ H5FL_DEFINE_STATIC(H5PB_entry_t);
 
 
 /*-------------------------------------------------------------------------
- * Function:	H5PB_reset_stats
+ * Function:    H5PB_reset_stats
  *
  * Purpose:     This function was created without documentation.
  *              What follows is my best understanding of Mohamad's intent.
@@ -162,7 +162,7 @@ H5FL_DEFINE_STATIC(H5PB_entry_t);
  *
  * Return:      Non-negative on success/Negative on failure
  *
- * Programmer:	Mohamad Chaarawi
+ * Programmer:  Mohamad Chaarawi
  *
  *-------------------------------------------------------------------------
  */
@@ -190,7 +190,7 @@ H5PB_reset_stats(H5PB_t *page_buf)
 
 
 /*-------------------------------------------------------------------------
- * Function:	H5PB_get_stats
+ * Function:    H5PB_get_stats
  *
  * Purpose:     This function was created without documentation.
  *              What follows is my best understanding of Mohamad's intent.
@@ -202,9 +202,9 @@ H5PB_reset_stats(H5PB_t *page_buf)
  *              --evictions: the number of metadata and raw data evictions from the page buffer layer
  *              --bypasses: the number of metadata and raw data accesses that bypass the page buffer layer
  *
- * Return:	    Non-negative on success/Negative on failure
+ * Return:      Non-negative on success/Negative on failure
  *
- * Programmer:	Mohamad Chaarawi
+ * Programmer:  Mohamad Chaarawi
  *
  *-------------------------------------------------------------------------
  */
@@ -233,16 +233,16 @@ H5PB_get_stats(const H5PB_t *page_buf, unsigned accesses[2], unsigned hits[2],
 
 
 /*-------------------------------------------------------------------------
- * Function:	H5PB_print_stats()
+ * Function:    H5PB_print_stats()
  *
  * Purpose:     This function was created without documentation.
  *              What follows is my best understanding of Mohamad's intent.
  *
  *              Print out statistics collected for the page buffer layer.
  *
- * Return:	    Non-negative on success/Negative on failure
+ * Return:      Non-negative on success/Negative on failure
  *
- * Programmer:	Mohamad Chaarawi
+ * Programmer:  Mohamad Chaarawi
  *
  *-------------------------------------------------------------------------
  */
@@ -278,13 +278,13 @@ H5PB_print_stats(const H5PB_t *page_buf)
 
 
 /*-------------------------------------------------------------------------
- * Function:	H5PB_create
+ * Function:    H5PB_create
  *
- * Purpose:	Create and setup the PB on the file.
+ * Purpose:     Create and setup the PB on the file.
  *
- * Return:	Non-negative on success/Negative on failure
+ * Return:      Non-negative on success/Negative on failure
  *
- * Programmer:	Mohamad Chaarawi
+ * Programmer:  Mohamad Chaarawi
  *
  *-------------------------------------------------------------------------
  */
@@ -314,7 +314,7 @@ H5PB_create(H5F_shared_t *f_sh, size_t size, unsigned page_buf_min_meta_perc, un
 
     /* Allocate the new page buffering structure */
     if(NULL == (page_buf = H5FL_CALLOC(H5PB_t)))
-	HGOTO_ERROR(H5E_PAGEBUF, H5E_NOSPACE, FAIL, "memory allocation failed")
+        HGOTO_ERROR(H5E_PAGEBUF, H5E_NOSPACE, FAIL, "memory allocation failed")
 
     page_buf->max_size = size;
     H5_CHECKED_ASSIGN(page_buf->page_size, size_t, f_sh->fs_page_size, hsize_t);
@@ -355,13 +355,13 @@ done:
 
 
 /*-------------------------------------------------------------------------
- * Function:	H5PB__flush_cb
+ * Function:    H5PB__flush_cb
  *
- * Purpose:	Callback to flush PB skiplist entries.
+ * Purpose:     Callback to flush PB skiplist entries.
  *
- * Return:	Non-negative on success/Negative on failure
+ * Return:      Non-negative on success/Negative on failure
  *
- * Programmer:	Mohamad Chaarawi
+ * Programmer:  Mohamad Chaarawi
  *
  *-------------------------------------------------------------------------
  */
@@ -389,13 +389,13 @@ done:
 
 
 /*-------------------------------------------------------------------------
- * Function:	H5PB_flush
+ * Function:    H5PB_flush
  *
- * Purpose:	Flush/Free all the PB entries to the file.
+ * Purpose:     Flush/Free all the PB entries to the file.
  *
- * Return:	Non-negative on success/Negative on failure
+ * Return:      Non-negative on success/Negative on failure
  *
- * Programmer:	Mohamad Chaarawi
+ * Programmer:  Mohamad Chaarawi
  *
  *-------------------------------------------------------------------------
  */
@@ -424,13 +424,13 @@ done:
 
 
 /*-------------------------------------------------------------------------
- * Function:	H5PB__dest_cb
+ * Function:    H5PB__dest_cb
  *
- * Purpose:	Callback to free PB skiplist entries.
+ * Purpose:     Callback to free PB skiplist entries.
  *
- * Return:	Non-negative on success/Negative on failure
+ * Return:      Non-negative on success/Negative on failure
  *
- * Programmer:	Mohamad Chaarawi
+ * Programmer:  Mohamad Chaarawi
  *
  *-------------------------------------------------------------------------
  */
@@ -461,13 +461,13 @@ H5PB__dest_cb(void *item, void H5_ATTR_UNUSED *key, void *_op_data)
 
 
 /*-------------------------------------------------------------------------
- * Function:	H5PB_dest
+ * Function:    H5PB_dest
  *
- * Purpose:	Flush and destroy the PB on the file if it exists.
+ * Purpose:     Flush and destroy the PB on the file if it exists.
  *
- * Return:	Non-negative on success/Negative on failure
+ * Return:      Non-negative on success/Negative on failure
  *
- * Programmer:	Mohamad Chaarawi
+ * Programmer:  Mohamad Chaarawi
  *
  *-------------------------------------------------------------------------
  */
@@ -515,16 +515,16 @@ done:
 
 
 /*-------------------------------------------------------------------------
- * Function:	H5PB_add_new_page
+ * Function:    H5PB_add_new_page
  *
- * Purpose:	Add a new page to the new page skip list. This is called
+ * Purpose:     Add a new page to the new page skip list. This is called
  *              from the MF layer when a new page is allocated to
  *              indicate to the page buffer layer that a read of the page
  *              from the file is not necessary since it's an empty page.
  *
- * Return:	Non-negative on success/Negative on failure
+ * Return:      Non-negative on success/Negative on failure
  *
- * Programmer:	Mohamad Chaarawi
+ * Programmer:  Mohamad Chaarawi
  *
  *-------------------------------------------------------------------------
  */
@@ -575,16 +575,16 @@ done:
 
 
 /*-------------------------------------------------------------------------
- * Function:	H5PB_update_entry
+ * Function:    H5PB_update_entry
  *
- * Purpose:	In PHDF5, entries that are written by other processes and just
+ * Purpose:     In PHDF5, entries that are written by other processes and just
  *              marked clean by this process have to have their corresponding
  *              pages updated if they exist in the page buffer.
  *              This routine checks and update the pages.
  *
- * Return:	Non-negative on success/Negative on failure
+ * Return:      Non-negative on success/Negative on failure
  *
- * Programmer:	Mohamad Chaarawi
+ * Programmer:  Mohamad Chaarawi
  *
  *-------------------------------------------------------------------------
  */
@@ -675,14 +675,14 @@ done:
 
 
 /*-------------------------------------------------------------------------
- * Function:	H5PB_read
+ * Function:    H5PB_read
  *
- * Purpose:	Reads in the data from the page containing it if it exists
+ * Purpose:     Reads in the data from the page containing it if it exists
  *              in the PB cache; otherwise reads in the page through the VFD.
  *
- * Return:	Non-negative on success/Negative on failure
+ * Return:      Non-negative on success/Negative on failure
  *
- * Programmer:	Mohamad Chaarawi
+ * Programmer:  Mohamad Chaarawi
  *
  *-------------------------------------------------------------------------
  */
@@ -971,15 +971,15 @@ done:
 
 
 /*-------------------------------------------------------------------------
- * Function:	H5PB_write
+ * Function:    H5PB_write
  *
- * Purpose: Write data into the Page Buffer. If the page exists in the
- *          cache, update it; otherwise read it from disk, update it, and
- *          insert into cache.
+ * Purpose:     Write data into the Page Buffer. If the page exists in the
+ *              cache, update it; otherwise read it from disk, update it, and
+ *              insert into cache.
  *
- * Return:	Non-negative on success/Negative on failure
+ * Return:      Non-negative on success/Negative on failure
  *
- * Programmer:	Mohamad Chaarawi
+ * Programmer:  Mohamad Chaarawi
  *
  *-------------------------------------------------------------------------
  */
@@ -1311,26 +1311,24 @@ done:
 
 
 /*-------------------------------------------------------------------------
- * Function:	H5PB__insert_entry()
- *
- * Purpose: ???
+ * Function:    H5PB__insert_entry()
  *
- *          This function was created without documentation.
- *          What follows is my best understanding of Mohamad's intent.
+ * Purpose:     This function was created without documentation.
+ *              What follows is my best understanding of Mohamad's intent.
  *
- *	    Insert the supplied page into the page buffer, both the
- *          skip list and the LRU.
+ *              Insert the supplied page into the page buffer, both the
+ *              skip list and the LRU.
  *
- *          As best I can tell, this function imposes no limit on the
- *          number of entries in the page buffer beyond an assertion
- *          failure it the page count exceeds the limit.
+ *              As best I can tell, this function imposes no limit on the
+ *              number of entries in the page buffer beyond an assertion
+ *              failure it the page count exceeds the limit.
  *
  *                                               JRM -- 12/22/16
  *
  *
- * Return:	Non-negative on success/Negative on failure
+ * Return:      Non-negative on success/Negative on failure
  *
- * Programmer:	Mohamad Chaarawi
+ * Programmer:  Mohamad Chaarawi
  *
  *-------------------------------------------------------------------------
  */
@@ -1361,16 +1359,21 @@ done:
 
 
 /*-------------------------------------------------------------------------
- * Function:	H5PB__make_space()
+ * Function:    H5PB__make_space()
  *
- * Purpose: If necessary and if possible, evict a page from the page
- *          buffer to make space for the supplied page.  Depending on
- *	    the page buffer configuration and contents, and the page
- *          supplied this may or may not be possible.
+ * Purpose:     This function was created without documentation.
+ *              What follows is my best understanding of Mohamad's intent.
  *
- * Return:	Non-negative on success/Negative on failure
+ *              If necessary and if possible, evict a page from the page
+ *              buffer to make space for the supplied page.  Depending on
+ *              the page buffer configuration and contents, and the page
+ *              supplied this may or may not be possible.
  *
- * Programmer:	Mohamad Chaarawi
+ *                                             JRM -- 12/22/16
+ *
+ * Return:      Non-negative on success/Negative on failure
+ *
+ * Programmer:  Mohamad Chaarawi
  *
  *-------------------------------------------------------------------------
  */
@@ -1459,17 +1462,16 @@ done:
 
 
 /*-------------------------------------------------------------------------
- * Function:	H5PB__write_entry()
- *
- * Purpose: ???
+ * Function:    H5PB__write_entry()
  *
- *          This function was created without documentation.
- *          What follows is my best understanding of Mohamad's intent.
+ * Purpose:     ???
  *
+ *              This function was created without documentation.
+ *              What follows is my best understanding of Mohamad's intent.
  *
- * Return:	Non-negative on success/Negative on failure
+ * Return:      Non-negative on success/Negative on failure
  *
- * Programmer:	Mohamad Chaarawi
+ * Programmer:  Mohamad Chaarawi
  *
  *-------------------------------------------------------------------------
  */