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

* commit '4c558700ab33934e7358483c5d20fea4823baf9e':
  Update RELEASE.txt for reference changes
  Fix reference type comparison in h5dump
  Make wrappers, tests and tools use H5Treclaim() instead of H5Dvlen_reclaim()
  Add new H5R API that abstracts object, region and attribute reference types
  Remove ability to loc by ref from H5VL layer
  Add support for retrieving object name by token
  Add H5VL_OBJECT_GET_TYPE to get object type
  Add H5VL_MAX_TOKEN_SIZE and H5VL_token_t
  Adapt Jerome's "file info" H5VL 'get' query to retrieve container token info.
  Fix H5VL_blob_get to return size of blob
  Add 'blob' callbacks to VOL, along with a native implementation to store them in the global heap, and changed the VL datatype conversion code to use blobs.
  Remove debugging logic from the new t_bigio test
  Expanded t_bigio.c to include Jordan's test from HDFFV-10539
  Another cleanup pass as suggested by the reviewers.
  Fix some typos and remove an unused prototype from H5Sprivate.h
  At the suggestion of the PR reviewers, moved the mpio_create_large_type to H5mpi.c and renamed the function appropriately.  Also moved some support functions to set and get the vvalue where we transistion to using derived datatypes.
  Made code review edit suggested by Jerome, plus various code updates to files that I touched to eliminate compile warnings (on my Linux box).
  No functional changes, just removed some tab characters
  Make the initial bug fixes to allow >2GB writes with Independent IO

1 files changed, 0 insertions, 198 deletions

diff --git a/src/H5Ocopy.c b/src/H5Ocopy.c
index 9578f95..6e0db25 100644
--- a/src/H5Ocopy.c
+++ b/src/H5Ocopy.c
@@ -85,8 +85,6 @@ static herr_t H5O__copy_header(const H5O_loc_t *oloc_src, H5O_loc_t *oloc_dst /*
     hid_t ocpypl_id, hid_t lcpl_id);
 static herr_t H5O__copy_obj(H5G_loc_t *src_loc, H5G_loc_t *dst_loc,
     const char *dst_name, hid_t ocpypl_id, hid_t lcpl_id);
-static herr_t H5O__copy_obj_by_ref(H5O_loc_t *src_oloc, H5O_loc_t *dst_oloc,
-    H5G_loc_t *dst_root_loc, H5O_copy_t *cpy_info);
 static herr_t H5O__copy_free_comm_dt_cb(void *item, void *key, void *op_data);
 static int H5O__copy_comm_dt_cmp(const void *dt1, const void *dt2);
 static herr_t H5O__copy_search_comm_dt_cb(hid_t group, const char *name,
@@ -110,7 +108,6 @@ H5FL_DEFINE(H5O_copy_search_comm_dt_key_t);
 /* Declare a free list to manage haddr_t variables */
 H5FL_DEFINE(haddr_t);
 
-
 /*****************************/
 /* Library Private Variables */
 /*****************************/
@@ -1235,201 +1232,6 @@ done:
 
 
 /*-------------------------------------------------------------------------
- * Function:    H5O__copy_obj_by_ref
- *
- * Purpose:     Copy the object pointed by _src_ref.
- *
- * Return:      Non-negative on success/Negative on failure
- *
- * Programmer:  Peter Cao
- *              Aug 7 2006
- *
- *-------------------------------------------------------------------------
- */
-static herr_t
-H5O__copy_obj_by_ref(H5O_loc_t *src_oloc, H5O_loc_t *dst_oloc,
-    H5G_loc_t *dst_root_loc, H5O_copy_t *cpy_info)
-{
-    herr_t  ret_value = SUCCEED;
-
-    FUNC_ENTER_STATIC
-
-    HDassert(src_oloc);
-    HDassert(dst_oloc);
-
-    /* Perform the copy, or look up existing copy */
-    if((ret_value = H5O_copy_header_map(src_oloc, dst_oloc, cpy_info, FALSE, NULL, NULL)) < 0)
-        HGOTO_ERROR(H5E_OHDR, H5E_CANTCOPY, FAIL, "unable to copy object")
-
-    /* Check if a new valid object is copied to the destination */
-    if(H5F_addr_defined(dst_oloc->addr) && (ret_value > SUCCEED)) {
-        char    tmp_obj_name[80];
-        H5G_name_t      new_path;
-        H5O_loc_t       new_oloc;
-        H5G_loc_t       new_loc;
-
-        /* Set up group location for new object */
-        new_loc.oloc = &new_oloc;
-        new_loc.path = &new_path;
-        H5G_loc_reset(&new_loc);
-        new_oloc.file = dst_oloc->file;
-        new_oloc.addr = dst_oloc->addr;
-
-        /* Pick a default name for the new object */
-        HDsnprintf(tmp_obj_name, sizeof(tmp_obj_name), "~obj_pointed_by_%llu", (unsigned long long)dst_oloc->addr);
-
-        /* Create a link to the newly copied object */
-        /* Note: since H5O_copy_header_map actually copied the target object, it
-         * must exist either in cache or on disk, therefore it is is safe to not
-         * pass the obj_type and udata fields returned by H5O_copy_header_map.
-         * This could be changed in the future to slightly improve performance
-         * --NAF */
-        if(H5L_link(dst_root_loc, tmp_obj_name, &new_loc, cpy_info->lcpl_id) < 0)
-            HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "unable to insert link")
-
-        H5G_loc_free(&new_loc);
-    } /* if (H5F_addr_defined(dst_oloc.addr)) */
-
-done:
-    FUNC_LEAVE_NOAPI(ret_value)
-} /* end H5O__copy_obj_by_ref() */
-
-
-/*-------------------------------------------------------------------------
- * Function:	H5O_copy_expand_ref
- *
- * Purpose:	Copy the object pointed by _src_ref.
- *
- * Return:	Non-negative on success/Negative on failure
- *
- * Programmer:  Peter Cao
- *		Aug 7 2006
- *
- *-------------------------------------------------------------------------
- */
-herr_t
-H5O_copy_expand_ref(H5F_t *file_src, void *_src_ref, H5F_t *file_dst,
-    void *_dst_ref, size_t ref_count, H5R_type_t ref_type, H5O_copy_t *cpy_info)
-{
-    H5O_loc_t 	dst_oloc;         	/* Copied object object location */
-    H5O_loc_t	src_oloc;          	/* Temporary object location for source object */
-    H5G_loc_t   dst_root_loc;           /* The location of root group of the destination file */
-    const uint8_t *q;                   /* Pointer to source OID to store */
-    uint8_t     *p;                     /* Pointer to destination OID to store */
-    size_t      i;                      /* Local index variable */
-    herr_t	ret_value = SUCCEED;
-
-    FUNC_ENTER_NOAPI(FAIL)
-
-    /* Sanity checks */
-    HDassert(file_src);
-    HDassert(_src_ref);
-    HDassert(file_dst);
-    HDassert(_dst_ref);
-    HDassert(ref_count);
-    HDassert(cpy_info);
-
-    /* Initialize object locations */
-    H5O_loc_reset(&src_oloc);
-    H5O_loc_reset(&dst_oloc);
-    src_oloc.file = file_src;
-    dst_oloc.file = file_dst;
-
-    /* Set up the root group in the destination file */
-    if(NULL == (dst_root_loc.oloc = H5G_oloc(H5G_rootof(file_dst))))
-        HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "unable to get object location for root group")
-    if(NULL == (dst_root_loc.path = H5G_nameof(H5G_rootof(file_dst))))
-        HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "unable to get path for root group")
-
-    /* Copy object references */
-    if(H5R_OBJECT == ref_type) {
-        hobj_ref_t *src_ref = (hobj_ref_t *)_src_ref;
-        hobj_ref_t *dst_ref = (hobj_ref_t *)_dst_ref;
-
-        /* Making equivalent references in the destination file */
-        for(i = 0; i < ref_count; i++) {
-            /* Set up for the object copy for the reference */
-            q = (uint8_t *)(&src_ref[i]);
-            H5F_addr_decode(src_oloc.file, (const uint8_t **)&q, &(src_oloc.addr));
-            dst_oloc.addr = HADDR_UNDEF;
-
-            /* Attempt to copy object from source to destination file */
-            if(src_oloc.addr != (haddr_t)0) {
-                if(H5O__copy_obj_by_ref(&src_oloc, &dst_oloc, &dst_root_loc, cpy_info) < 0)
-                    HGOTO_ERROR(H5E_OHDR, H5E_CANTCOPY, FAIL, "unable to copy object")
-            } /* end if */
-            else
-                /* Set parameters so the reference is written as all 0's */
-                HDmemset(&dst_oloc.addr, 0, sizeof(dst_oloc.addr));
-
-            /* Set the object reference info for the destination file */
-            p = (uint8_t *)(&dst_ref[i]);
-            H5F_addr_encode(dst_oloc.file, &p, dst_oloc.addr);
-	} /* end for */
-    }  /* end if */
-    /* Copy region references */
-    else if(H5R_DATASET_REGION == ref_type) {
-        hdset_reg_ref_t *src_ref = (hdset_reg_ref_t *)_src_ref;
-        hdset_reg_ref_t *dst_ref = (hdset_reg_ref_t *)_dst_ref;
-        uint8_t *buf = NULL;    /* Buffer to store serialized selection in */
-        H5HG_t hobjid;          /* Heap object ID */
-        size_t buf_size;        /* Length of object in heap */
-
-        /* Making equivalent references in the destination file */
-        for(i = 0; i < ref_count; i++) {
-            /* Get the heap ID for the dataset region */
-            q = (const uint8_t *)(&src_ref[i]);
-            H5F_addr_decode(src_oloc.file, (const uint8_t **)&q, &(hobjid.addr));
-            UINT32DECODE(q, hobjid.idx);
-
-            if(hobjid.addr != (haddr_t)0) {
-                /* Get the dataset region from the heap (allocate inside routine) */
-                if((buf = (uint8_t *)H5HG_read(src_oloc.file, &hobjid, NULL, &buf_size)) == NULL)
-                    HGOTO_ERROR(H5E_REFERENCE, H5E_READERROR, FAIL, "Unable to read dataset region information")
-
-                /* Get the object oid for the dataset */
-                q = (const uint8_t *)buf;
-                H5F_addr_decode(src_oloc.file, (const uint8_t **)&q, &(src_oloc.addr));
-                dst_oloc.addr = HADDR_UNDEF;
-
-                /* copy the object pointed by the ref to the destination */
-                if(H5O__copy_obj_by_ref(&src_oloc, &dst_oloc, &dst_root_loc, cpy_info) < 0) {
-                    H5MM_xfree(buf);
-                    HGOTO_ERROR(H5E_OHDR, H5E_CANTCOPY, FAIL, "unable to copy object")
-                } /* end if */
-
-                /* Serialize object ID */
-                p = (uint8_t *)buf;
-                H5F_addr_encode(dst_oloc.file, &p, dst_oloc.addr);
-
-                /* Save the serialized buffer to the destination */
-                if(H5HG_insert(dst_oloc.file, buf_size, buf, &hobjid) < 0) {
-                    H5MM_xfree(buf);
-                    HGOTO_ERROR(H5E_OHDR, H5E_CANTCOPY, FAIL, "Unable to write dataset region information")
-                } /* end if */
-            } /* end if */
-            else
-                /* Set parameters so the reference is written as all 0's */
-                HDmemset(&hobjid, 0, sizeof(hobjid));
-
-            /* Set the dataset region reference info for the destination file */
-            p = (uint8_t *)(&dst_ref[i]);
-            H5F_addr_encode(dst_oloc.file, &p, hobjid.addr);
-            UINT32ENCODE(p, hobjid.idx);
-
-            /* Free the buffer allocated in H5HG_read() */
-            H5MM_xfree(buf);
-        } /* end for */
-    } /* end if */
-    else
-        HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "invalid reference type")
-
-done:
-    FUNC_LEAVE_NOAPI(ret_value)
-} /* end H5O_copy_expand_ref() */
-
-
-/*-------------------------------------------------------------------------
  * Function:    H5O__copy_free_comm_dt_cb
  *
  * Purpose:     Frees the merge committed dt skip list key and object.