Merge pull request #1629 in HDFFV/hdf5 from ~DEROBINS/hdf5_der:feature/json_vol to feature/json_vol

* commit '799a732650735b8ad05a0398781d2a26ec47b288': (185 commits)
  Updated the VOL struct. The json_vol test fails, though, because the plugin can't be found. Will diagnose later.
  Correct examples for packaging
  HDFFV-10738 Wrong INTENT for H5LTread_dataset_double_f
  Changes that show the right way to iterate over enums.
  Changes that show the right way to iterate over enums.
  Test improvement Description     Moved the new tests to a more appropriate test function. Platforms tested:     Linux/64 (jelly)
  Used the H5_INC_ENUM macro to squash enum value increment warnings.
  Fixed HDFFV-10210 and HDFFV-10587 Description:     - Added parameter validation (HDFFV-10210)     - Added detection of division by zero (HDFFV-10587 - CVE-2018-17438)     - Fixed typos in various tests Platforms tested:     Linux/64 (jelly)     Linux/64 (platypus)     Darwin (osx1011test)
  Fix CMake error in name
  Commented out memcpy overlap check while we investigate parallel filters issues.
  Yanked check for memcpy n > 0
  - Added H5MMprivate.h #includes where needed - Added casts to quiet H5MM_memcpy warnings - Removed char * casts from HDmemcpy
  Added an H5MM_memcpy call that checks for buffer overlap.
  Added the HDopen work-around on windows to pio_engine.c
  Adds _wopen support on Windows so that files with UTF-8 names can be opened.
  CMake: fix pthread linking to only be private
  Add API routines to retrieve, restore, reset, and free library state.
  Added a note of bug fix for HDFFV-10705.
  Fixed the MANIFEST
  Fix issue with direct chunk write not updating the "last chunk" index cache.  Fix issues involving datasets being "no allocated" when they contain cached raw data.
  ...

1 files changed, 12 insertions, 11 deletions

diff --git a/src/H5PB.c b/src/H5PB.c
index a325ad1..25c5f43 100644
--- a/src/H5PB.c
+++ b/src/H5PB.c
@@ -36,6 +36,7 @@
 #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				*/
 
@@ -252,7 +253,7 @@ H5PB_print_stats(const H5PB_t *page_buf)
 
     HDassert(page_buf);
 
-    printf("PAGE BUFFER STATISTICS:\n");
+    HDprintf("PAGE BUFFER STATISTICS:\n");
 
     HDprintf("******* METADATA\n");
     HDprintf("\t Total Accesses: %u\n", page_buf->accesses[0]);
@@ -609,7 +610,7 @@ H5PB_update_entry(H5PB_t *page_buf, haddr_t addr, size_t size, const void *buf)
 
         HDassert(addr + size <= page_addr + page_buf->page_size);
         offset = addr - page_addr;
-        HDmemcpy((uint8_t *)page_entry->page_buf_ptr + offset, buf, size);
+        H5MM_memcpy((uint8_t *)page_entry->page_buf_ptr + offset, buf, size);
 
         /* move to top of LRU list */
         H5PB__MOVE_TO_TOP_LRU(page_buf, page_entry)
@@ -818,7 +819,7 @@ H5PB_read(H5F_t *f, H5FD_mem_t type, haddr_t addr, size_t size, void *buf/*out*/
                         offset = addr - first_page_addr;
                         HDassert(page_buf->page_size > offset);
 
-                        HDmemcpy(buf, (uint8_t *)page_entry->page_buf_ptr + offset, 
+                        H5MM_memcpy(buf, (uint8_t *)page_entry->page_buf_ptr + offset, 
                                  page_buf->page_size - (size_t)offset);
 
                         /* move to top of LRU list */
@@ -829,7 +830,7 @@ H5PB_read(H5F_t *f, H5FD_mem_t type, haddr_t addr, size_t size, void *buf/*out*/
                         offset = (num_touched_pages-2)*page_buf->page_size + 
                             (page_buf->page_size - (addr - first_page_addr));
 
-                        HDmemcpy((uint8_t *)buf + offset, page_entry->page_buf_ptr,
+                        H5MM_memcpy((uint8_t *)buf + offset, page_entry->page_buf_ptr,
                                  (size_t)((addr + size) - last_page_addr));
 
                         /* move to top of LRU list */
@@ -839,7 +840,7 @@ H5PB_read(H5F_t *f, H5FD_mem_t type, haddr_t addr, size_t size, void *buf/*out*/
                     else {
                         offset = i*page_buf->page_size;
 
-                        HDmemcpy((uint8_t *)buf+(i*page_buf->page_size) , page_entry->page_buf_ptr, 
+                        H5MM_memcpy((uint8_t *)buf+(i*page_buf->page_size) , page_entry->page_buf_ptr, 
                              page_buf->page_size);
                     } /* end else */
                 } /* end if */
@@ -872,7 +873,7 @@ H5PB_read(H5F_t *f, H5FD_mem_t type, haddr_t addr, size_t size, void *buf/*out*/
                 buf_offset = (0 == i ? 0 : size - access_size);
 
                 /* copy the requested data from the page into the input buffer */
-                HDmemcpy((uint8_t *)buf + buf_offset, (uint8_t *)page_entry->page_buf_ptr + offset, access_size);
+                H5MM_memcpy((uint8_t *)buf + buf_offset, (uint8_t *)page_entry->page_buf_ptr + offset, access_size);
 
                 /* Update LRU */
                 H5PB__MOVE_TO_TOP_LRU(page_buf, page_entry)
@@ -937,7 +938,7 @@ H5PB_read(H5F_t *f, H5FD_mem_t type, haddr_t addr, size_t size, void *buf/*out*/
                 /* Copy the requested data from the page into the input buffer */
                 offset = (0 == i ? addr - search_addr : 0);
                 buf_offset = (0 == i ? 0 : size - access_size);
-                HDmemcpy((uint8_t *)buf + buf_offset, (uint8_t *)new_page_buf + offset, access_size);
+                H5MM_memcpy((uint8_t *)buf + buf_offset, (uint8_t *)new_page_buf + offset, access_size);
 
                 /* Create the new PB entry */
                 if(NULL == (page_entry = H5FL_CALLOC(H5PB_entry_t)))
@@ -1102,7 +1103,7 @@ H5PB_write(H5F_t *f, H5FD_mem_t type, haddr_t addr,
                     HDassert(page_buf->page_size > offset);
 
                     /* Update page's data */
-                    HDmemcpy((uint8_t *)page_entry->page_buf_ptr + offset, buf, page_buf->page_size - (size_t)offset);
+                    H5MM_memcpy((uint8_t *)page_entry->page_buf_ptr + offset, buf, page_buf->page_size - (size_t)offset);
 
                     /* Mark page dirty and push to top of LRU */
                     page_entry->is_dirty = TRUE;
@@ -1121,7 +1122,7 @@ H5PB_write(H5F_t *f, H5FD_mem_t type, haddr_t addr,
                         (page_buf->page_size - (addr - first_page_addr));
 
                     /* Update page's data */
-                    HDmemcpy(page_entry->page_buf_ptr, (const uint8_t *)buf + offset, 
+                    H5MM_memcpy(page_entry->page_buf_ptr, (const uint8_t *)buf + offset, 
                              (size_t)((addr + size) - last_page_addr));
 
                     /* Mark page dirty and push to top of LRU */
@@ -1173,7 +1174,7 @@ H5PB_write(H5F_t *f, H5FD_mem_t type, haddr_t addr,
                 buf_offset = (0 == i ? 0 : size - access_size);
 
                 /* Copy the requested data from the input buffer into the page */
-                HDmemcpy((uint8_t *)page_entry->page_buf_ptr + offset, (const uint8_t *)buf + buf_offset, access_size);
+                H5MM_memcpy((uint8_t *)page_entry->page_buf_ptr + offset, (const uint8_t *)buf + buf_offset, access_size);
 
                 /* Mark page dirty and push to top of LRU */
                 page_entry->is_dirty = TRUE;
@@ -1289,7 +1290,7 @@ H5PB_write(H5F_t *f, H5FD_mem_t type, haddr_t addr,
                 } /* end else */
 
                 /* Copy the requested data from the page into the input buffer */
-                HDmemcpy((uint8_t *)new_page_buf + offset, (const uint8_t *)buf+buf_offset, access_size);
+                H5MM_memcpy((uint8_t *)new_page_buf + offset, (const uint8_t *)buf+buf_offset, access_size);
 
                 /* Page is dirty now */
                 page_entry->is_dirty = TRUE;