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, 137 insertions, 57 deletions

diff --git a/src/H5Oflush.c b/src/H5Oflush.c
index b1592dd..e8e077e 100644
--- a/src/H5Oflush.c
+++ b/src/H5Oflush.c
@@ -33,17 +33,24 @@
 /***********/
 
 #include "H5private.h"      /* Generic Functions */
+#include "H5CXprivate.h"    /* API Contexts */
 #include "H5Dprivate.h"     /* Datasets */
 #include "H5Eprivate.h"     /* Errors   */
 #include "H5Fprivate.h"     /* Files    */
-#include "H5Gprivate.h"        /* Groups    */
-#include "H5Iprivate.h"        /* IDs    */
+#include "H5Gprivate.h"     /* Groups   */
+#include "H5Iprivate.h"     /* IDs      */
 #include "H5Opkg.h"         /* Objects  */
 
+
 /********************/
 /* Local Prototypes */
 /********************/
-static herr_t H5O_oh_tag(const H5O_loc_t *oloc, hid_t dxpl_id, haddr_t *tag);
+static herr_t H5O__flush(hid_t obj_id);
+static herr_t H5O__oh_tag(const H5O_loc_t *oloc, haddr_t *tag);
+static herr_t H5O__refresh_metadata_close(hid_t oid, H5O_loc_t oloc,
+	H5G_loc_t *obj_loc);
+static herr_t H5O__refresh(hid_t obj_id);
+
 
 /*************/
 /* Functions */
@@ -66,38 +73,24 @@ static herr_t H5O_oh_tag(const H5O_loc_t *oloc, hid_t dxpl_id, haddr_t *tag);
 herr_t
 H5Oflush(hid_t obj_id)
 {
-    H5O_loc_t *oloc;            /* object location */
-    void *obj_ptr;		/* Pointer to object */
-    const H5O_obj_class_t  *obj_class = NULL;       /* Class of object */
-    herr_t ret_value = SUCCEED; /* return value */
+    herr_t ret_value = SUCCEED;         /* Return value */
 
     FUNC_ENTER_API(FAIL)
     H5TRACE1("e", "i", obj_id);
 
-    /* Check args */
-    if(NULL == (oloc = H5O_get_loc(obj_id)))
-        HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not an object")
-
-    /* Get the object pointer */
-    if(NULL == (obj_ptr = H5I_object(obj_id)))
-        HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "invalid object identifier")
+    /* Set up collective metadata if appropriate */
+    if(H5CX_set_loc(obj_id) < 0)
+        HGOTO_ERROR(H5E_DATATYPE, H5E_CANTSET, FAIL, "can't set access property list info")
 
-    /* Get the object class */
-    if(NULL == (obj_class = H5O_obj_class(oloc, H5AC_ind_read_dxpl_id)))
-        HGOTO_ERROR(H5E_OHDR, H5E_CANTINIT, FAIL, "unable to determine object class")
-
-    /* Flush the object of this class */
-    if(obj_class->flush && obj_class->flush(obj_ptr, H5AC_ind_read_dxpl_id) < 0)
+    /* Call internal routine */
+    if(H5O__flush(obj_id) < 0)
         HGOTO_ERROR(H5E_OHDR, H5E_CANTFLUSH, FAIL, "unable to flush object")
 
-    /* Flush the object metadata and invoke flush callback */
-    if(H5O_flush_common(oloc, obj_id, H5AC_ind_read_dxpl_id) < 0)
-        HGOTO_ERROR(H5E_OHDR, H5E_CANTFLUSH, FAIL, "unable to flush object and object flush callback")
-
 done:
     FUNC_LEAVE_API(ret_value)
 } /* end H5Oflush() */
 
+
 /*-------------------------------------------------------------------------
  * Function:    H5O_flush_common
  *
@@ -111,7 +104,7 @@ done:
  *-------------------------------------------------------------------------
  */
 herr_t
-H5O_flush_common(H5O_loc_t *oloc, hid_t obj_id, hid_t dxpl_id)
+H5O_flush_common(H5O_loc_t *oloc, hid_t obj_id)
 {
     haddr_t 	tag = 0;
     herr_t      ret_value = SUCCEED;    /* Return value */
@@ -119,11 +112,11 @@ H5O_flush_common(H5O_loc_t *oloc, hid_t obj_id, hid_t dxpl_id)
     FUNC_ENTER_NOAPI(FAIL)
 
     /* Retrieve tag for object */
-    if(H5O_oh_tag(oloc, dxpl_id, &tag) < 0)
+    if(H5O__oh_tag(oloc, &tag) < 0)
         HGOTO_ERROR(H5E_OHDR, H5E_CANTFLUSH, FAIL, "unable to flush object metadata")
 
     /* Flush metadata based on tag value of the object */
-    if(H5F_flush_tagged_metadata(oloc->file, tag, dxpl_id) < 0)
+    if(H5F_flush_tagged_metadata(oloc->file, tag) < 0)
         HGOTO_ERROR(H5E_FILE, H5E_CANTFLUSH, FAIL, "unable to flush tagged metadata")
 
     /* Check to invoke callback */
@@ -136,7 +129,58 @@ done:
 
 
 /*-------------------------------------------------------------------------
- * Function:    H5O_oh_tag
+ * Function:    H5O__flush
+ *
+ * Purpose:     Internal routine to flush an object
+ *
+ * Note:        This routine is needed so that there's a non-API routine
+ *              that can set up VOL / SWMR info (which need a DXPL).
+ *
+ * Return:	Success:	Non-negative
+ *		Failure:	Negative
+ *
+ * Programmer:	Quincey Koziol
+ *		December 29, 2017
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5O__flush(hid_t obj_id)
+{
+    H5O_loc_t *oloc;            /* Object location */
+    void *obj_ptr;		/* Pointer to object */
+    const H5O_obj_class_t  *obj_class;	/* Class of object */
+    herr_t ret_value = SUCCEED;	/* Return value */
+
+    FUNC_ENTER_STATIC_VOL
+
+    /* Check args */
+    if(NULL == (oloc = H5O_get_loc(obj_id)))
+        HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not an object")
+
+    /* Get the object pointer */
+    if(NULL == (obj_ptr = H5I_object(obj_id)))
+        HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "invalid object identifier")
+
+    /* Get the object class */
+    if(NULL == (obj_class = H5O__obj_class(oloc)))
+        HGOTO_ERROR(H5E_OHDR, H5E_CANTINIT, FAIL, "unable to determine object class")
+
+    /* Flush the object of this class */
+    if(obj_class->flush && obj_class->flush(obj_ptr) < 0)
+        HGOTO_ERROR(H5E_OHDR, H5E_CANTFLUSH, FAIL, "unable to flush object")
+
+    /* Flush the object metadata and invoke flush callback */
+    if(H5O_flush_common(oloc, obj_id) < 0)
+        HGOTO_ERROR(H5E_OHDR, H5E_CANTFLUSH, FAIL, "unable to flush object and object flush callback")
+
+done:
+    FUNC_LEAVE_NOAPI_VOL(ret_value)
+} /* end H5O__flush() */
+
+
+/*-------------------------------------------------------------------------
+ * Function:    H5O__oh_tag
  *
  * Purpose:     Get object header's address--tag value for the object
  *
@@ -149,18 +193,18 @@ done:
  *-------------------------------------------------------------------------
  */
 static herr_t
-H5O_oh_tag(const H5O_loc_t *oloc, hid_t dxpl_id, haddr_t *tag)
+H5O__oh_tag(const H5O_loc_t *oloc, haddr_t *tag)
 {
     H5O_t       *oh = NULL;             /* Object header */
     herr_t      ret_value = SUCCEED;    /* Return value */
 
-    FUNC_ENTER_NOAPI(FAIL)
+    FUNC_ENTER_STATIC
 
     /* Check args */
     HDassert(oloc);
 
     /* Get object header for object */
-    if(NULL == (oh = H5O_protect(oloc, dxpl_id, H5AC__READ_ONLY_FLAG, FALSE)))
+    if(NULL == (oh = H5O_protect(oloc, H5AC__READ_ONLY_FLAG, FALSE)))
         HGOTO_ERROR(H5E_OHDR, H5E_CANTPROTECT, FAIL, "unable to protect object's object header")
 
     /* Get object header's address (i.e. the tag value for this object) */
@@ -169,11 +213,11 @@ H5O_oh_tag(const H5O_loc_t *oloc, hid_t dxpl_id, haddr_t *tag)
 
 done:
     /* Unprotect object header on failure */
-    if(oh && H5O_unprotect(oloc, dxpl_id, oh, H5AC__NO_FLAGS_SET) < 0)
+    if(oh && H5O_unprotect(oloc, oh, H5AC__NO_FLAGS_SET) < 0)
         HDONE_ERROR(H5E_OHDR, H5E_CANTUNPROTECT, FAIL, "unable to release object header")
 
     FUNC_LEAVE_NOAPI(ret_value)
-} /* end H5O_oh_tag() */
+} /* end H5O__oh_tag() */
 
 
 /*-------------------------------------------------------------------------
@@ -191,18 +235,17 @@ done:
 herr_t
 H5Orefresh(hid_t oid)
 {
-    H5O_loc_t *oloc;            /* object location */
-    herr_t ret_value = SUCCEED; /* return value */
+    herr_t ret_value = SUCCEED;		/* Return value */
     
     FUNC_ENTER_API(FAIL)
     H5TRACE1("e", "i", oid);
 
-    /* Check args */
-    if(NULL == (oloc = H5O_get_loc(oid)))
-        HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not an object")
+    /* Set up collective metadata if appropriate */
+    if(H5CX_set_loc(oid) < 0)
+        HGOTO_ERROR(H5E_DATATYPE, H5E_CANTSET, FAIL, "can't set access property list info")
 
-    /* Private function */
-    if(H5O_refresh_metadata(oid, *oloc, H5AC_ind_read_dxpl_id) < 0)
+    /* Call internal routine */
+    if(H5O__refresh(oid) < 0)
         HGOTO_ERROR(H5E_OHDR, H5E_CANTLOAD, FAIL, "unable to refresh object")
 
 done:
@@ -231,7 +274,7 @@ done:
  *-------------------------------------------------------------------------
  */
 herr_t
-H5O_refresh_metadata(hid_t oid, H5O_loc_t oloc, hid_t dxpl_id)
+H5O_refresh_metadata(hid_t oid, H5O_loc_t oloc)
 {
     hbool_t objs_incr = FALSE;          /* Whether the object count in the file was incremented */
     herr_t ret_value = SUCCEED;         /* Return value */
@@ -256,11 +299,11 @@ H5O_refresh_metadata(hid_t oid, H5O_loc_t oloc, hid_t dxpl_id)
         objs_incr = TRUE;
 
         /* Close object & evict its metadata */
-        if((H5O_refresh_metadata_close(oid, oloc, &obj_loc, dxpl_id)) < 0)
+        if((H5O__refresh_metadata_close(oid, oloc, &obj_loc)) < 0)
             HGOTO_ERROR(H5E_OHDR, H5E_CANTLOAD, FAIL, "unable to refresh object")
 
         /* Re-open the object, re-fetching its metadata */
-        if((H5O_refresh_metadata_reopen(oid, &obj_loc, dxpl_id, FALSE)) < 0)
+        if((H5O_refresh_metadata_reopen(oid, &obj_loc, FALSE)) < 0)
             HGOTO_ERROR(H5E_OHDR, H5E_CANTLOAD, FAIL, "unable to refresh object")
     } /* end if */
 
@@ -273,7 +316,7 @@ done:
 
 
 /*-------------------------------------------------------------------------
- * Function:    H5O_refresh_metadata_close
+ * Function:    H5O__refresh_metadata_close
  *
  * Purpose:     This is the first part of the original routine H5O_refresh_metadata().
  *		(1) Save object location information.
@@ -291,14 +334,14 @@ done:
  *
  *-------------------------------------------------------------------------
  */
-herr_t
-H5O_refresh_metadata_close(hid_t oid, H5O_loc_t oloc, H5G_loc_t *obj_loc, hid_t dxpl_id)
+static herr_t
+H5O__refresh_metadata_close(hid_t oid, H5O_loc_t oloc, H5G_loc_t *obj_loc)
 {
     haddr_t tag = 0;            /* Tag for object */
     hbool_t corked = FALSE;     /* Whether object's metadata is corked */
     herr_t ret_value = SUCCEED; /* Return value */
 
-    FUNC_ENTER_NOAPI(FAIL)
+    FUNC_ENTER_STATIC
     
     /* Make deep local copy of object's location information */
     if(obj_loc) {
@@ -310,11 +353,11 @@ H5O_refresh_metadata_close(hid_t oid, H5O_loc_t oloc, H5G_loc_t *obj_loc, hid_t
 
     /* Get object's type */
     if(H5I_get_type(oid) == H5I_DATASET)
-	if(H5D_mult_refresh_close(oid, dxpl_id) < 0)
+	if(H5D_mult_refresh_close(oid) < 0)
 	    HGOTO_ERROR(H5E_DATASET, H5E_CANTOPENOBJ, FAIL, "unable to prepare refresh for dataset")
 
     /* Retrieve tag for object */
-    if(H5O_oh_tag(&oloc, dxpl_id, &tag) < 0)
+    if(H5O__oh_tag(&oloc, &tag) < 0)
         HGOTO_ERROR(H5E_DATASET, H5E_CANTFLUSH, FAIL, "unable to get object header address")
 
     /* Get cork status of the object with tag */
@@ -326,11 +369,11 @@ H5O_refresh_metadata_close(hid_t oid, H5O_loc_t oloc, H5G_loc_t *obj_loc, hid_t
         HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to close object")
 
     /* Flush metadata based on tag value of the object */
-    if(H5F_flush_tagged_metadata(oloc.file, tag, dxpl_id) < 0)
+    if(H5F_flush_tagged_metadata(oloc.file, tag) < 0)
         HGOTO_ERROR(H5E_FILE, H5E_CANTFLUSH, FAIL, "unable to flush tagged metadata")
 
     /* Evict the object's tagged metadata */
-    if(H5F_evict_tagged_metadata(oloc.file, tag, dxpl_id) < 0)
+    if(H5F_evict_tagged_metadata(oloc.file, tag) < 0)
         HGOTO_ERROR(H5E_FILE, H5E_CANTFLUSH, FAIL, "unable to evict metadata")
 
     /* Re-cork object with tag */
@@ -340,7 +383,7 @@ H5O_refresh_metadata_close(hid_t oid, H5O_loc_t oloc, H5G_loc_t *obj_loc, hid_t
 
 done:
     FUNC_LEAVE_NOAPI(ret_value);
-} /* end H5O_refresh_metadata_close() */
+} /* end H5O__refresh_metadata_close() */
 
 
 /*-------------------------------------------------------------------------
@@ -358,7 +401,7 @@ done:
  *-------------------------------------------------------------------------
  */
 herr_t
-H5O_refresh_metadata_reopen(hid_t oid, H5G_loc_t *obj_loc, hid_t dxpl_id, hbool_t start_swmr)
+H5O_refresh_metadata_reopen(hid_t oid, H5G_loc_t *obj_loc, hbool_t start_swmr)
 {
     void *object = NULL;        /* Dataset for this operation */
     H5I_type_t type;            /* Type of object for the ID */
@@ -372,22 +415,22 @@ H5O_refresh_metadata_reopen(hid_t oid, H5G_loc_t *obj_loc, hid_t dxpl_id, hbool_
     switch(type) {
         case H5I_GROUP:
             /* Re-open the group */
-            if(NULL == (object = H5G_open(obj_loc, dxpl_id)))
+            if(NULL == (object = H5G_open(obj_loc)))
                 HGOTO_ERROR(H5E_SYM, H5E_CANTOPENOBJ, FAIL, "unable to open group")
             break;
 
         case H5I_DATATYPE:
             /* Re-open the named datatype */
-            if(NULL == (object = H5T_open(obj_loc, dxpl_id)))
+            if(NULL == (object = H5T_open(obj_loc)))
                 HGOTO_ERROR(H5E_DATATYPE, H5E_CANTOPENOBJ, FAIL, "unable to open named datatype")
             break;
 
         case H5I_DATASET:
             /* Re-open the dataset */
-            if(NULL == (object = H5D_open(obj_loc, H5P_DATASET_ACCESS_DEFAULT, dxpl_id)))
+            if(NULL == (object = H5D_open(obj_loc, H5P_DATASET_ACCESS_DEFAULT)))
                 HGOTO_ERROR(H5E_DATASET, H5E_CANTOPENOBJ, FAIL, "unable to open dataset")
             if(!start_swmr) /* No need to handle multiple opens when H5Fstart_swmr_write() */
-                if(H5D_mult_refresh_reopen((H5D_t *)object, dxpl_id) < 0)
+                if(H5D_mult_refresh_reopen((H5D_t *)object) < 0)
                     HGOTO_ERROR(H5E_DATASET, H5E_CANTOPENOBJ, FAIL, "unable to finish refresh for dataset")
             break;
 
@@ -417,3 +460,40 @@ done:
     FUNC_LEAVE_NOAPI(ret_value);
 } /* end H5O_refresh_metadata_reopen() */
 
+
+/*-------------------------------------------------------------------------
+ * Function:    H5O__refresh
+ *
+ * Purpose:     Internal routine to refresh an object
+ *
+ * Note:        This routine is needed so that there's a non-API routine
+ *              that can set up VOL / SWMR info (which need a DXPL).
+ *
+ * Return:	Success:	Non-negative
+ *		Failure:	Negative
+ *
+ * Programmer:	Quincey Koziol
+ *		December 29, 2017
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5O__refresh(hid_t obj_id)
+{
+    H5O_loc_t *oloc;            /* Object location */
+    herr_t ret_value = SUCCEED;	/* Return value */
+
+    FUNC_ENTER_STATIC_VOL
+
+    /* Check args */
+    if(NULL == (oloc = H5O_get_loc(obj_id)))
+        HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not an object")
+
+    /* Private function */
+    if(H5O_refresh_metadata(obj_id, *oloc) < 0)
+        HGOTO_ERROR(H5E_OHDR, H5E_CANTLOAD, FAIL, "unable to refresh object")
+
+done:
+    FUNC_LEAVE_NOAPI_VOL(ret_value)
+} /* end H5O__refresh() */
+