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

* commit '048ae59d2970dd21810577c999f756c028b6faaf':
  Correct errors with non-"instrumented library" builds (production & parallel, generally speaking).
  Update java error stack tests
  Revert using H5MF_sect_small_can_shrink and H5MF_sect_small_shrink for the file's free space manager (and add a comment about them).
  Add comment for the file flush when the file low / high bounds are changed after a file is open.
  Expanded comments abuot H5CX_t fields.
  Add an assert to verify that we don't write when between MPI_Barrier() calls during a flush.
  Add comments for internal structs.
  Remove redundant 'is_collective' parameter from H5CX_set_loc.
  Correct typo in comment.
  Revert some tangential code cleanups.
  Add API context source files to CMake configuration file.
  Corrections for parallel I/O & tests.
  Update handling of reporting for breaking collective I/O when the default DXPL is used.
  Update encoded DXPLs to reflect changes in properties.
  Correct typo for error checking malloc return value.
  Refactor H5CX code to reduce duplication.
  Cleanup API context function usage.
  Add API context interface and use it throughout the library.

1 files changed, 34 insertions, 30 deletions

diff --git a/src/H5Dlayout.c b/src/H5Dlayout.c
index 980b810..c8afb8e 100644
--- a/src/H5Dlayout.c
+++ b/src/H5Dlayout.c
@@ -25,6 +25,7 @@
 #include "H5Dpkg.h"             /* Datasets                                 */
 #include "H5Eprivate.h"         /* Error handling                           */
 #include "H5HLprivate.h"        /* Local heaps                              */
+#include "H5MMprivate.h"        /* Memory management                        */
 
 
 /****************/
@@ -459,8 +460,7 @@ done:
  *-------------------------------------------------------------------------
  */
 herr_t
-H5D__layout_oh_create(H5F_t *file, hid_t dxpl_id, H5O_t *oh, H5D_t *dset,
-    hid_t dapl_id)
+H5D__layout_oh_create(H5F_t *file, H5O_t *oh, H5D_t *dset, hid_t dapl_id)
 {
     H5O_layout_t        *layout;        /* Dataset's layout information */
     const H5O_fill_t    *fill_prop;     /* Pointer to dataset's fill value information */
@@ -468,7 +468,7 @@ H5D__layout_oh_create(H5F_t *file, hid_t dxpl_id, H5O_t *oh, H5D_t *dset,
     hbool_t             layout_init = FALSE;    /* Flag to indicate that chunk information was initialized */
     herr_t ret_value = SUCCEED;         /* Return value */
 
-    FUNC_ENTER_PACKAGE_TAG(dxpl_id, dset->oloc.addr, FAIL)
+    FUNC_ENTER_PACKAGE_TAG(dset->oloc.addr)
 
     /* Sanity checking */
     HDassert(file);
@@ -484,12 +484,12 @@ H5D__layout_oh_create(H5F_t *file, hid_t dxpl_id, H5O_t *oh, H5D_t *dset,
         H5O_pline_t     *pline;         /* Dataset's I/O pipeline information */
 
         pline = &dset->shared->dcpl_cache.pline;
-        if(pline->nused > 0 && H5O_msg_append_oh(file, dxpl_id, oh, H5O_PLINE_ID, H5O_MSG_FLAG_CONSTANT, 0, pline) < 0)
+        if(pline->nused > 0 && H5O_msg_append_oh(file, oh, H5O_PLINE_ID, H5O_MSG_FLAG_CONSTANT, 0, pline) < 0)
             HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to update filter header message")
     } /* end if */
 
     /* Initialize the layout information for the new dataset */
-    if(dset->shared->layout.ops->init && (dset->shared->layout.ops->init)(file, dxpl_id, dset, dapl_id) < 0)
+    if(dset->shared->layout.ops->init && (dset->shared->layout.ops->init)(file, dset, dapl_id) < 0)
         HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize layout information")
 
     /* Indicate that the layout information was initialized */
@@ -503,12 +503,11 @@ H5D__layout_oh_create(H5F_t *file, hid_t dxpl_id, H5O_t *oh, H5D_t *dset,
         H5D_io_info_t io_info;
 
         io_info.dset = dset;
-        io_info.raw_dxpl_id = H5AC_rawdata_dxpl_id;
-        io_info.md_dxpl_id = dxpl_id;
 
         if(H5D__alloc_storage(&io_info, H5D_ALLOC_CREATE, FALSE, NULL) < 0)
             HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize storage")
-    }
+    } /* end if */
+
     /* Update external storage message, if it's used */
     if(dset->shared->dcpl_cache.efl.nused > 0) {
         H5O_efl_t *efl = &dset->shared->dcpl_cache.efl; /* Dataset's external file list */
@@ -521,15 +520,15 @@ H5D__layout_oh_create(H5F_t *file, hid_t dxpl_id, H5O_t *oh, H5D_t *dset,
             heap_size += H5HL_ALIGN(HDstrlen(efl->slot[u].name) + 1);
 
         /* Create the heap for the EFL file names */
-        if(H5HL_create(file, dxpl_id, heap_size, &efl->heap_addr/*out*/) < 0)
+        if(H5HL_create(file, heap_size, &efl->heap_addr/*out*/) < 0)
             HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to create EFL file name heap")
 
         /* Pin the heap down in memory */
-        if(NULL == (heap = H5HL_protect(file, dxpl_id, efl->heap_addr, H5AC__NO_FLAGS_SET)))
+        if(NULL == (heap = H5HL_protect(file, efl->heap_addr, H5AC__NO_FLAGS_SET)))
             HGOTO_ERROR(H5E_DATASET, H5E_CANTPROTECT, FAIL, "unable to protect EFL file name heap")
 
         /* Insert "empty" name first */
-        if(UFAIL == H5HL_insert(file, dxpl_id, heap, (size_t)1, "")) {
+        if(UFAIL == H5HL_insert(file, heap, (size_t)1, "")) {
             H5HL_unprotect(heap);
             HGOTO_ERROR(H5E_DATASET, H5E_CANTINSERT, FAIL, "unable to insert file name into heap")
         } /* end if */
@@ -538,7 +537,7 @@ H5D__layout_oh_create(H5F_t *file, hid_t dxpl_id, H5O_t *oh, H5D_t *dset,
             size_t offset;      /* Offset of file name in heap */
 
             /* Insert file name into heap */
-            if(UFAIL == (offset = H5HL_insert(file, dxpl_id, heap,
+            if(UFAIL == (offset = H5HL_insert(file, heap,
                         HDstrlen(efl->slot[u].name) + 1, efl->slot[u].name))) {
                 H5HL_unprotect(heap);
                 HGOTO_ERROR(H5E_DATASET, H5E_CANTINSERT, FAIL, "unable to insert file name into heap")
@@ -554,11 +553,10 @@ H5D__layout_oh_create(H5F_t *file, hid_t dxpl_id, H5O_t *oh, H5D_t *dset,
         heap = NULL;
 
         /* Insert EFL message into dataset object header */
-        if(H5O_msg_append_oh(file, dxpl_id, oh, H5O_EFL_ID, H5O_MSG_FLAG_CONSTANT, 0, efl) < 0)
+        if(H5O_msg_append_oh(file, oh, H5O_EFL_ID, H5O_MSG_FLAG_CONSTANT, 0, efl) < 0)
             HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to update external file list message")
     } /* end if */
 
-    /* Create layout message */
     /* (Don't make layout message constant unless allocation time is early and non-filtered, since space may not be allocated) */
     /* (Note: this is relying on H5D__alloc_storage not calling H5O_msg_write during dataset creation) */
     if(fill_prop->alloc_time == H5D_ALLOC_TIME_EARLY && H5D_COMPACT != layout->type
@@ -566,7 +564,14 @@ H5D__layout_oh_create(H5F_t *file, hid_t dxpl_id, H5O_t *oh, H5D_t *dset,
         layout_mesg_flags = H5O_MSG_FLAG_CONSTANT;
     else
         layout_mesg_flags =  0;
-    if(H5O_msg_append_oh(file, dxpl_id, oh, H5O_LAYOUT_ID, layout_mesg_flags, 0, layout) < 0)
+
+    /* Store VDS info in global heap */
+    if(H5D_VIRTUAL == layout->type)
+        if(H5D__virtual_store_layout(file, layout) < 0)
+             HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "unable to store VDS info")
+
+    /* Create layout message */
+    if(H5O_msg_append_oh(file, oh, H5O_LAYOUT_ID, layout_mesg_flags, 0, layout) < 0)
          HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to update layout")
 
 done:
@@ -574,10 +579,10 @@ done:
     if(ret_value < 0)
         if(layout_init)
             /* Destroy any cached layout information for the dataset */
-            if(dset->shared->layout.ops->dest && (dset->shared->layout.ops->dest)(dset, dxpl_id) < 0)
+            if(dset->shared->layout.ops->dest && (dset->shared->layout.ops->dest)(dset) < 0)
                 HDONE_ERROR(H5E_DATASET, H5E_CANTRELEASE, FAIL, "unable to destroy layout info")
 
-    FUNC_LEAVE_NOAPI_TAG(ret_value, FAIL)
+    FUNC_LEAVE_NOAPI_TAG(ret_value)
 } /* end H5D__layout_oh_create() */
 
 
@@ -595,7 +600,7 @@ done:
  *-------------------------------------------------------------------------
  */
 herr_t
-H5D__layout_oh_read(H5D_t *dataset, hid_t dxpl_id, hid_t dapl_id, H5P_genplist_t *plist)
+H5D__layout_oh_read(H5D_t *dataset, hid_t dapl_id, H5P_genplist_t *plist)
 {
     htri_t msg_exists;                  /* Whether a particular type of message exists */
     hbool_t layout_copied = FALSE;      /* Flag to indicate that layout message was copied */
@@ -608,11 +613,11 @@ H5D__layout_oh_read(H5D_t *dataset, hid_t dxpl_id, hid_t dapl_id, H5P_genplist_t
     HDassert(plist);
 
     /* Get the optional filters message */
-    if((msg_exists = H5O_msg_exists(&(dataset->oloc), H5O_PLINE_ID, dxpl_id)) < 0)
+    if((msg_exists = H5O_msg_exists(&(dataset->oloc), H5O_PLINE_ID)) < 0)
         HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't check if message exists")
     if(msg_exists) {
         /* Retrieve the I/O pipeline message */
-        if(NULL == H5O_msg_read(&(dataset->oloc), H5O_PLINE_ID, &dataset->shared->dcpl_cache.pline, dxpl_id))
+        if(NULL == H5O_msg_read(&(dataset->oloc), H5O_PLINE_ID, &dataset->shared->dcpl_cache.pline))
             HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't retrieve message")
 
         /* Set the I/O pipeline info in the property list */
@@ -626,16 +631,16 @@ H5D__layout_oh_read(H5D_t *dataset, hid_t dxpl_id, hid_t dapl_id, H5P_genplist_t
      * values are copied to the dataset create plist so the user can query
      * them.
      */
-    if(NULL == H5O_msg_read(&(dataset->oloc), H5O_LAYOUT_ID, &(dataset->shared->layout), dxpl_id))
+    if(NULL == H5O_msg_read(&(dataset->oloc), H5O_LAYOUT_ID, &(dataset->shared->layout)))
         HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to read data layout message")
     layout_copied = TRUE;
 
     /* Check for external file list message (which might not exist) */
-    if((msg_exists = H5O_msg_exists(&(dataset->oloc), H5O_EFL_ID, dxpl_id)) < 0)
+    if((msg_exists = H5O_msg_exists(&(dataset->oloc), H5O_EFL_ID)) < 0)
         HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't check if message exists")
     if(msg_exists) {
         /* Retrieve the EFL  message */
-        if(NULL == H5O_msg_read(&(dataset->oloc), H5O_EFL_ID, &dataset->shared->dcpl_cache.efl, dxpl_id))
+        if(NULL == H5O_msg_read(&(dataset->oloc), H5O_EFL_ID, &dataset->shared->dcpl_cache.efl))
             HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't retrieve message")
 
         /* Set the EFL info in the property list */
@@ -650,7 +655,7 @@ H5D__layout_oh_read(H5D_t *dataset, hid_t dxpl_id, hid_t dapl_id, H5P_genplist_t
     HDassert(dataset->shared->layout.ops);
 
     /* Initialize the layout information for the dataset */
-    if(dataset->shared->layout.ops->init && (dataset->shared->layout.ops->init)(dataset->oloc.file, dxpl_id, dataset, dapl_id) < 0)
+    if(dataset->shared->layout.ops->init && (dataset->shared->layout.ops->init)(dataset->oloc.file, dataset, dapl_id) < 0)
         HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize layout information")
 
     /* Adjust chunk dimensions to omit datatype size (in last dimension) for creation property */
@@ -662,16 +667,15 @@ H5D__layout_oh_read(H5D_t *dataset, hid_t dxpl_id, hid_t dapl_id, H5P_genplist_t
         HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't set layout")
 
     /* Set chunk sizes */
-    if(H5D_CHUNKED == dataset->shared->layout.type) {
+    if(H5D_CHUNKED == dataset->shared->layout.type)
         if(H5D__chunk_set_sizes(dataset) < 0)
             HGOTO_ERROR(H5E_DATASET, H5E_BADVALUE, FAIL, "unable to set chunk sizes")
-    }
 
 done:
-    if(ret_value < 0 && layout_copied) {
+    if(ret_value < 0 && layout_copied)
         if(H5O_msg_reset(H5O_LAYOUT_ID, &dataset->shared->layout) < 0)
             HDONE_ERROR(H5E_DATASET, H5E_CANTRESET, FAIL, "unable to reset layout info")
-    }
+
     FUNC_LEAVE_NOAPI(ret_value)
 } /* end H5D__layout_oh_read() */
 
@@ -690,7 +694,7 @@ done:
  *-------------------------------------------------------------------------
  */
 herr_t
-H5D__layout_oh_write(H5D_t *dataset, hid_t dxpl_id, H5O_t *oh, unsigned update_flags)
+H5D__layout_oh_write(const H5D_t *dataset, H5O_t *oh, unsigned update_flags)
 {
     htri_t msg_exists;                  /* Whether the layout message exists */
     herr_t ret_value = SUCCEED;         /* Return value */
@@ -706,7 +710,7 @@ H5D__layout_oh_write(H5D_t *dataset, hid_t dxpl_id, H5O_t *oh, unsigned update_f
         HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "unable to check if layout message exists")
     if(msg_exists) {
         /* Write the layout message to the dataset's header */
-        if(H5O_msg_write_oh(dataset->oloc.file, dxpl_id, oh, H5O_LAYOUT_ID, 0, update_flags, &dataset->shared->layout) < 0)
+        if(H5O_msg_write_oh(dataset->oloc.file, oh, H5O_LAYOUT_ID, 0, update_flags, &dataset->shared->layout) < 0)
             HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "unable to update layout message")
     } /* end if */