Merge pull request #826 in HDFFV/hdf5 from ~BYRN/hdf5_adb:develop to develop

* commit 'e94ed99c5bf7c4ae5df56f75606ef1b486e16bb2':
  Add HD prefix
  HDFFV-9724 Remove VDS file cache functionality
  Removed incorrect MPI text
  Par example needs to link with mpi libs
  Because of MPI requirements in library ALWAYS add include path
  Cleanup comments and if() in TRY blocks
  Skip test if 1.6 API
  HDFFV-9724 Add ENV VAR to vds test
  HDFFV-9724 Copy efc_open search from Lextern_traverse
  Add prefix dir to the clear command
  HDFFV-9724 Add H5LS prefix test with ${ORIGIN}
  Add h5dump VDS prefix tests
  HDFFV-9724 combine efc and vds into one function
  Correct var name
  Fix VDS file cache var names
  Remove return from void functions
  Added java wrappers and tests
  HDFFV-9724 Initial changes and test
  Changed reference from dl to CMake variable
  H5detect and H5make_libsettings need include folder

1 files changed, 54 insertions, 24 deletions

diff --git a/src/H5Dint.c b/src/H5Dint.c
index b6c0341..8b663b8 100644
--- a/src/H5Dint.c
+++ b/src/H5Dint.c
@@ -61,8 +61,8 @@ static herr_t H5D__cache_dataspace_info(const H5D_t *dset);
 static herr_t H5D__init_space(H5F_t *file, const H5D_t *dset, const H5S_t *space);
 static herr_t H5D__update_oh_info(H5F_t *file, hid_t dxpl_id, H5D_t *dset,
         hid_t dapl_id);
-static herr_t H5D_build_extfile_prefix(const H5D_t *dset, hid_t dapl_id,
-        char **extfile_prefix);
+static herr_t H5D_build_file_prefix(const H5D_t *dset, hid_t dapl_id, const char * prefix_type,
+        char **vds_prefix);
 static herr_t H5D__open_oid(H5D_t *dataset, hid_t dapl_id, hid_t dxpl_id);
 static herr_t H5D__init_storage(const H5D_io_info_t *io_info, hbool_t full_overwrite,
         hsize_t old_dim[]);
@@ -963,24 +963,25 @@ done:
 } /* end H5D__update_oh_info() */
 
 
+
 /*--------------------------------------------------------------------------
- * Function:    H5D_build_extfile_prefix
+ * Function:    H5D_build_file_prefix
  *
- * Purpose:     Determine the external file prefix to be used and store
- *              it in extfile_prefix. Stores an empty string if no prefix
+ * Purpose:     Determine the file prefix to be used and store
+ *              it in file_prefix. Stores an empty string if no prefix
  *              should be used.
  *
  * Return:      SUCCEED/FAIL
  *--------------------------------------------------------------------------
  */
 static herr_t
-H5D_build_extfile_prefix(const H5D_t *dset, hid_t dapl_id, char **extfile_prefix /*out*/)
+H5D_build_file_prefix(const H5D_t *dset, hid_t dapl_id, const char *prefix_type, char **file_prefix /*out*/)
 {
     char            *prefix = NULL;       /* prefix used to look for the file               */
-    char            *extpath = NULL;      /* absolute path of directory the HDF5 file is in */
-    size_t          extpath_len;          /* length of extpath                              */
+    char            *filepath = NULL;     /* absolute path of directory the HDF5 file is in */
+    size_t          filepath_len;         /* length of file path                            */
     size_t          prefix_len;           /* length of prefix                               */
-    size_t          extfile_prefix_len;   /* length of expanded prefix                      */
+    size_t          file_prefix_len;      /* length of expanded prefix                      */
     H5P_genplist_t  *plist = NULL;        /* Property list pointer                          */
     herr_t          ret_value = SUCCEED;  /* Return value                                   */
 
@@ -990,20 +991,25 @@ H5D_build_extfile_prefix(const H5D_t *dset, hid_t dapl_id, char **extfile_prefix
     HDassert(dset);
     HDassert(dset->oloc.file);
 
-    extpath = H5F_EXTPATH(dset->oloc.file);
-    HDassert(extpath);
+    filepath = H5F_EXTPATH(dset->oloc.file);
+    HDassert(filepath);
 
     /* XXX: Future thread-safety note - getenv is not required
      *      to be reentrant.
      */
-    prefix = HDgetenv("HDF5_EXTFILE_PREFIX");
+    if (HDstrcmp(prefix_type, H5D_ACS_VDS_PREFIX_NAME) == 0)
+        prefix = HDgetenv("HDF5_VDS_PREFIX");
+    else if (HDstrcmp(prefix_type, H5D_ACS_EFILE_PREFIX_NAME) == 0)
+        prefix = HDgetenv("HDF5_EXTFILE_PREFIX");
+    else
+        HGOTO_ERROR(H5E_PLIST, H5E_BADTYPE, FAIL, "prefix name is not sensible")
 
     if(prefix == NULL || *prefix == '\0') {
-        /* Set prefix to value of H5D_ACS_EFILE_PREFIX_NAME property */
+        /* Set prefix to value of prefix_type property */
         if(NULL == (plist = H5P_object_verify(dapl_id, H5P_DATASET_ACCESS)))
             HGOTO_ERROR(H5E_ATOM, H5E_BADATOM, FAIL, "can't find object for ID")
-        if(H5P_peek(plist, H5D_ACS_EFILE_PREFIX_NAME, &prefix) < 0)
-            HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't get external file prefix")
+        if(H5P_peek(plist, prefix_type, &prefix) < 0)
+            HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't get file prefix")
     } /* end if */
 
     /* Prefix has to be checked for NULL / empty string again because the
@@ -1013,29 +1019,29 @@ H5D_build_extfile_prefix(const H5D_t *dset, hid_t dapl_id, char **extfile_prefix
         /* filename is interpreted as relative to the current directory,
          * does not need to be expanded
          */
-        if(NULL == (*extfile_prefix = (char *)H5MM_strdup("")))
+        if(NULL == (*file_prefix = (char *)H5MM_strdup("")))
             HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed")
     } /* end if */
     else {
         if (HDstrncmp(prefix, "${ORIGIN}", HDstrlen("${ORIGIN}")) == 0) {
             /* Replace ${ORIGIN} at beginning of prefix by directory of HDF5 file */
-            extpath_len = HDstrlen(extpath);
+            filepath_len = HDstrlen(filepath);
             prefix_len = HDstrlen(prefix);
-            extfile_prefix_len = extpath_len + prefix_len - HDstrlen("${ORIGIN}") + 1;
+            file_prefix_len = filepath_len + prefix_len - HDstrlen("${ORIGIN}") + 1;
 
-            if(NULL == (*extfile_prefix = (char *)H5MM_malloc(extfile_prefix_len)))
+            if(NULL == (*file_prefix = (char *)H5MM_malloc(file_prefix_len)))
                 HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "unable to allocate buffer")
-            HDsnprintf(*extfile_prefix, extfile_prefix_len, "%s%s", extpath, prefix + HDstrlen("${ORIGIN}"));
+            HDsnprintf(*file_prefix, file_prefix_len, "%s%s", filepath, prefix + HDstrlen("${ORIGIN}"));
         } /* end if */
         else {
-            if(NULL == (*extfile_prefix = (char *)H5MM_strdup(prefix)))
+            if(NULL == (*file_prefix = (char *)H5MM_strdup(prefix)))
                 HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed")
         } /* end else */
     } /* end else */
 
 done:
     FUNC_LEAVE_NOAPI(ret_value)
-} /* H5D_build_extfile_prefix() */
+} /* H5D_build_file_prefix() */
 
 
 /*-------------------------------------------------------------------------
@@ -1217,9 +1223,13 @@ H5D__create(H5F_t *file, hid_t type_id, const H5S_t *space, hid_t dcpl_id,
     HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to set up flush append property")
 
     /* Set the external file prefix */
-    if(H5D_build_extfile_prefix(new_dset, dapl_id, &new_dset->shared->extfile_prefix) < 0)
+    if(H5D_build_file_prefix(new_dset, dapl_id, H5D_ACS_EFILE_PREFIX_NAME, &new_dset->shared->extfile_prefix) < 0)
         HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to initialize external file prefix")
 
+    /* Set the vds file prefix */
+    if(H5D_build_file_prefix(new_dset, dapl_id, H5D_ACS_VDS_PREFIX_NAME, &new_dset->shared->vds_prefix) < 0)
+        HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to initialize vds  prefix")
+
     /* Add the dataset to the list of opened objects in the file */
     if(H5FO_top_incr(new_dset->oloc.file, new_dset->oloc.addr) < 0)
         HGOTO_ERROR(H5E_DATASET, H5E_CANTINC, NULL, "can't incr object ref. count")
@@ -1265,6 +1275,7 @@ done:
             if(new_dset->shared->dcpl_id != 0 && H5I_dec_ref(new_dset->shared->dcpl_id) < 0)
                 HDONE_ERROR(H5E_DATASET, H5E_CANTDEC, NULL, "unable to decrement ref count on property list")
             new_dset->shared->extfile_prefix = (char *)H5MM_xfree(new_dset->shared->extfile_prefix);
+            new_dset->shared->vds_prefix = (char *)H5MM_xfree(new_dset->shared->vds_prefix);
             new_dset->shared = H5FL_FREE(H5D_shared_t, new_dset->shared);
         } /* end if */
         new_dset->oloc.file = NULL;
@@ -1351,6 +1362,7 @@ H5D_open(const H5G_loc_t *loc, hid_t dapl_id, hid_t dxpl_id)
     H5D_shared_t    *shared_fo = NULL;
     H5D_t           *dataset = NULL;
     char            *extfile_prefix = NULL;  /* Expanded external file prefix */
+    char            *vds_prefix = NULL;      /* Expanded vds prefix */
     H5D_t           *ret_value = NULL;       /* Return value */
 
     FUNC_ENTER_NOAPI(NULL)
@@ -1371,9 +1383,13 @@ H5D_open(const H5G_loc_t *loc, hid_t dapl_id, hid_t dxpl_id)
         HGOTO_ERROR(H5E_DATASET, H5E_CANTCOPY, NULL, "can't copy path")
 
     /* Get the external file prefix */
-    if(H5D_build_extfile_prefix(dataset, dapl_id, &extfile_prefix) < 0)
+    if(H5D_build_file_prefix(dataset, dapl_id, H5D_ACS_EFILE_PREFIX_NAME, &extfile_prefix) < 0)
         HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to initialize external file prefix")
 
+    /* Get the vds prefix */
+    if(H5D_build_file_prefix(dataset, dapl_id, H5D_ACS_VDS_PREFIX_NAME, &vds_prefix) < 0)
+        HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to initialize vds prefix")
+
     /* Check if dataset was already open */
     if(NULL == (shared_fo = (H5D_shared_t *)H5FO_opened(dataset->oloc.file, dataset->oloc.addr))) {
         /* Clear any errors from H5FO_opened() */
@@ -1399,6 +1415,11 @@ H5D_open(const H5G_loc_t *loc, hid_t dapl_id, hid_t dxpl_id)
         /* Prevent string from being freed during done: */
         extfile_prefix = NULL;
 
+        /* Set the vds file prefix */
+        dataset->shared->vds_prefix = vds_prefix;
+        /* Prevent string from being freed during done: */
+        vds_prefix = NULL;
+
     } /* end if */
     else {
         /* Point to shared info */
@@ -1430,12 +1451,14 @@ H5D_open(const H5G_loc_t *loc, hid_t dapl_id, hid_t dxpl_id)
 
 done:
     extfile_prefix = (char *)H5MM_xfree(extfile_prefix);
+    vds_prefix = (char *)H5MM_xfree(vds_prefix);
 
     if(ret_value == NULL) {
         /* Free the location--casting away const*/
         if(dataset) {
             if(shared_fo == NULL && dataset->shared) {   /* Need to free shared fo */
                 dataset->shared->extfile_prefix = (char *)H5MM_xfree(dataset->shared->extfile_prefix);
+                dataset->shared->vds_prefix = (char *)H5MM_xfree(dataset->shared->vds_prefix);
                 dataset->shared = H5FL_FREE(H5D_shared_t, dataset->shared);
             }
 
@@ -1818,6 +1841,9 @@ H5D_close(H5D_t *dataset)
         /* Free the external file prefix */
         dataset->shared->extfile_prefix = (char *)H5MM_xfree(dataset->shared->extfile_prefix);
 
+        /* Free the vds file prefix */
+        dataset->shared->vds_prefix = (char *)H5MM_xfree(dataset->shared->vds_prefix);
+
         /* Release layout, fill-value, efl & pipeline messages */
         if(dataset->shared->dcpl_id != H5P_DATASET_CREATE_DEFAULT)
             free_failed |= (H5O_msg_reset(H5O_PLINE_ID, &dataset->shared->dcpl_cache.pline) < 0) ||
@@ -3360,6 +3386,10 @@ H5D_get_access_plist(H5D_t *dset)
     if(H5P_set(new_plist, H5D_ACS_VDS_PRINTF_GAP_NAME, &(dset->shared->layout.storage.u.virt.printf_gap)) < 0)
         HGOTO_ERROR(H5E_PLIST, H5E_CANTSET, FAIL, "can't set VDS printf gap")
 
+    /* Set the vds prefix option */
+    if(H5P_set(new_plist, H5D_ACS_VDS_PREFIX_NAME, &(dset->shared->vds_prefix)) < 0)
+        HGOTO_ERROR(H5E_PLIST, H5E_CANTSET, FAIL, "can't set vds prefix")
+
     /* Set the external file prefix option */
     if(H5P_set(new_plist, H5D_ACS_EFILE_PREFIX_NAME, &(dset->shared->extfile_prefix)) < 0)
         HGOTO_ERROR(H5E_PLIST, H5E_CANTSET, FAIL, "can't set external file prefix")