Merge pull request #3 in ~VCHOI/my_third_fork from develop to bugfix/…

…HDFFV-10579-h5arename-function-fails-when

* commit '52276f3713eec584044bc72d4724507848cfeba0':
  Modifications based on PR feedback: (1) Add H5Sdeprec.c to src/CMakeLists.txt (2) Add test for H5Sencode1.
  Modification for num_elem based on PR feedback.
  HDFFV-10365: Changes as described in the RFC: H5Sencode/H5Sdecode Format Change. This also addresses HDFFV-10255: H5Sencode/decode performance issue.

MANIFEST

@@ -847,6 +847,7 @@
 ./src/H5S.c
 ./src/H5Sall.c
 ./src/H5Sdbg.c
+./src/H5Sdeprec.c
 ./src/H5Shyper.c
 ./src/H5Smodule.h
 ./src/H5Smpio.c

fortran/src/H5Sf.c

@@ -1149,7 +1149,7 @@ h5sdecode_c ( _fcd buf, hid_t_f *obj_id )
 */
 
 int_f
-h5sencode_c (_fcd buf, hid_t_f *obj_id, size_t_f *nalloc )
+h5sencode_c (_fcd buf, hid_t_f *obj_id, size_t_f *nalloc, hid_t_f *fapl_id )
 /******/
 {
   int ret_value = -1;
@@ -1162,7 +1162,7 @@ h5sencode_c (_fcd buf, hid_t_f *obj_id, size_t_f *nalloc )
 
   if (*nalloc == 0) {
 
-    if(H5Sencode((hid_t)*obj_id, c_buf, &c_size) < 0)
+    if(H5Sencode2((hid_t)*obj_id, c_buf, &c_size, (hid_t)*fapl_id) < 0)
       return ret_value;
 
     *nalloc = (size_t_f)c_size;
@@ -1180,7 +1180,7 @@ h5sencode_c (_fcd buf, hid_t_f *obj_id, size_t_f *nalloc )
   /*
    * Call H5Sencode function.
    */
-  if(H5Sencode((hid_t)*obj_id, c_buf, &c_size) < 0){
+  if(H5Sencode2((hid_t)*obj_id, c_buf, &c_size, (hid_t)*fapl_id) < 0){
     return ret_value;
   }
 

fortran/src/H5Sff.F90

@@ -1379,25 +1379,32 @@ END SUBROUTINE h5sdecode_f
 !  M. Scot Breitenfeld
 !  March 26, 2008
 ! SOURCE
-  SUBROUTINE h5sencode_f(obj_id, buf, nalloc, hdferr)
+  SUBROUTINE h5sencode_f(obj_id, buf, nalloc, hdferr, fapl_id)
     IMPLICIT NONE
     INTEGER(HID_T), INTENT(IN) :: obj_id
     CHARACTER(LEN=*), INTENT(OUT) :: buf
     INTEGER(SIZE_T), INTENT(INOUT) :: nalloc
     INTEGER, INTENT(OUT) :: hdferr
+    INTEGER(HID_T), OPTIONAL, INTENT(IN) :: fapl_id ! File access property list
 !*****
+    INTEGER(HID_T) :: fapl_id_default
 
     INTERFACE
-       INTEGER FUNCTION h5sencode_c(buf, obj_id, nalloc) BIND(C,NAME='h5sencode_c')
+       INTEGER FUNCTION h5sencode_c(buf, obj_id, nalloc, fapl_id_default) BIND(C,NAME='h5sencode_c')
          IMPORT :: C_CHAR
          IMPORT :: HID_T, SIZE_T
          INTEGER(HID_T), INTENT(IN) :: obj_id
          CHARACTER(KIND=C_CHAR), DIMENSION(*), INTENT(OUT) :: buf
          INTEGER(SIZE_T), INTENT(INOUT) :: nalloc
+         INTEGER(HID_T) :: fapl_id_default
        END FUNCTION h5sencode_c
     END INTERFACE
 
-    hdferr = h5sencode_c(buf, obj_id, nalloc)
+    fapl_id_default = H5P_DEFAULT_F
+
+    IF(PRESENT(fapl_id)) fapl_id_default = fapl_id
+
+    hdferr = h5sencode_c(buf, obj_id, nalloc, fapl_id_default)
 
   END SUBROUTINE h5sencode_f
 

fortran/src/H5f90proto.h

@@ -121,7 +121,7 @@ H5_FCDLL int_f h5sselect_hyperslab_c( hid_t_f *space_id , int_f *op, hsize_t_f *
 H5_FCDLL int_f h5sget_select_type_c( hid_t_f *space_id , int_f *op);
 H5_FCDLL int_f h5sselect_elements_c( hid_t_f *space_id , int_f *op, size_t_f *nelements, hsize_t_f *coord);
 H5_FCDLL int_f h5sdecode_c( _fcd buf, hid_t_f *obj_id );
-H5_FCDLL int_f h5sencode_c(_fcd buf, hid_t_f *obj_id, size_t_f *nalloc );
+H5_FCDLL int_f h5sencode_c(_fcd buf, hid_t_f *obj_id, size_t_f *nalloc, hid_t_f *fapl_id );
 H5_FCDLL int_f h5sextent_equal_c( hid_t_f * space1_id, hid_t_f *space2_id, hid_t_f *c_equal);
 
 /*

fortran/test/tH5MISC_1_8.F90

@@ -189,8 +189,9 @@ SUBROUTINE test_h5s_encode(total_error)
 
   INTEGER(hid_t) :: sid1, sid3!	 Dataspace ID		
   INTEGER(hid_t) :: decoded_sid1, decoded_sid3
+  INTEGER(hid_t) :: fapl    ! File access property
   INTEGER :: rank    ! LOGICAL rank of dataspace	
-  INTEGER(size_t) :: sbuf_size=0, scalar_size=0
+  INTEGER(size_t) :: new_size = 0, old_size = 0, orig_size=0, scalar_size=0
 
 ! Make sure the size is large
   CHARACTER(LEN=288) :: sbuf
@@ -228,18 +229,36 @@ SUBROUTINE test_h5s_encode(total_error)
 
   ! Encode simple data space in a buffer 
 
-  !         First find the buffer size
-  CALL H5Sencode_f(sid1, sbuf, sbuf_size, error)
-  CALL check("H5Sencode", error, total_error)
+  ! Find the buffer size without fapl
+  CALL H5Sencode_f(sid1, sbuf, orig_size, error)
+  CALL check("H5Sencode_f", error, total_error)
+  CALL verify("H5Sencode_f", INT(orig_size), 279, total_error)
+
+  ! Create file access property list
+  CALL h5pcreate_f(H5P_FILE_ACCESS_F, fapl, error)
+  CALL check("h5pcreate_f", error, total_error)
+
+  ! Find the buffer size with fapl (default old format)
+  CALL H5Sencode_f(sid1, sbuf, old_size, error, fapl)
+  CALL check("H5Sencode_f", error, total_error)
+  CALL verify("H5Sencode_f", INT(old_size), 279, total_error)
 
+  ! Set fapl to latest file format
+  CALL H5Pset_libver_bounds_f(fapl, H5F_LIBVER_LATEST_F, H5F_LIBVER_LATEST_F, error)
+  CALL check("H5Pset_libver_bounds_f",error, total_error)
 
-  !  Try decoding bogus buffer 
+  ! Find the buffer size with fapl set to latest format
+  CALL H5Sencode_f(sid1, sbuf, new_size, error, fapl)
+  CALL check("H5Sencode_f", error, total_error)
+  CALL verify("H5Sencode_f", INT(new_size), 101, total_error)
 
+  !  Try decoding bogus buffer 
   CALL H5Sdecode_f(sbuf, decoded_sid1, error)
   CALL verify("H5Sdecode", error, -1, total_error)
 
-  CALL H5Sencode_f(sid1, sbuf, sbuf_size, error)
-  CALL check("H5Sencode", error, total_error)
+  !  Encode according to the latest file format
+  CALL H5Sencode_f(sid1, sbuf, new_size, error, fapl)
+  CALL check("H5Sencode_f", error, total_error)
 
   !  Decode from the dataspace buffer and return an object handle 
   CALL H5Sdecode_f(sbuf, decoded_sid1, error)

java/src/jni/h5sImp.c

@@ -1141,7 +1141,7 @@ Java_hdf_hdf5lib_H5_H5Sencode
     if (obj_id < 0)
         H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Sencode: invalid object ID");
 
-    if ((status = H5Sencode(obj_id, NULL, &buf_size)) < 0)
+    if ((status = H5Sencode2(obj_id, NULL, &buf_size, H5P_DEFAULT)) < 0)
         H5_LIBRARY_ERROR(ENVONLY);
 
     if (buf_size == 0)
@@ -1150,7 +1150,7 @@ Java_hdf_hdf5lib_H5_H5Sencode
     if (NULL == (bufPtr = (unsigned char *) HDcalloc((size_t) 1, buf_size)))
         H5_JNI_FATAL_ERROR(ENVONLY, "H5Sencode: failed to allocate encoding buffer");
 
-    if ((status = H5Sencode((hid_t) obj_id, bufPtr, &buf_size)) < 0)
+    if ((status = H5Sencode2((hid_t) obj_id, bufPtr, &buf_size, H5P_DEFAULT)) < 0)
         H5_LIBRARY_ERROR(ENVONLY);
 
     if (NULL == (returnedArray = ENVPTR->NewByteArray(ENVONLY, (jsize) buf_size)))

src/CMakeLists.txt

@@ -533,6 +533,7 @@ set (H5S_SOURCES
     ${HDF5_SRC_DIR}/H5S.c
     ${HDF5_SRC_DIR}/H5Sall.c
     ${HDF5_SRC_DIR}/H5Sdbg.c
+    ${HDF5_SRC_DIR}/H5Sdeprec.c
     ${HDF5_SRC_DIR}/H5Shyper.c
     ${HDF5_SRC_DIR}/H5Smpio.c
     ${HDF5_SRC_DIR}/H5Snone.c

src/H5Dmpio.c

@@ -2742,6 +2742,9 @@ H5D__chunk_redistribute_shared_chunks(const H5D_io_info_t *io_info, const H5D_ty
     if ((mpi_size = H5F_mpi_get_size(io_info->dset->oloc.file)) < 0)
         HGOTO_ERROR(H5E_IO, H5E_MPI, FAIL, "unable to obtain mpi size")
 
+    /* Set to latest format for encoding dataspace */
+    H5CX_set_libver_bounds(NULL);
+
     if (*local_chunk_array_num_entries)
         if (NULL == (send_requests = (MPI_Request *) H5MM_malloc(*local_chunk_array_num_entries * sizeof(MPI_Request))))
             HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "couldn't allocate send requests buffer")

src/H5Dvirtual.c

@@ -430,6 +430,10 @@ H5D__virtual_store_layout(H5F_t *f, H5O_layout_t *layout)
 
     /* Create block if # of used entries > 0 */
     if(layout->storage.u.virt.list_nused > 0) {
+
+        /* Set the low/high bounds according to 'f' for the API context */
+        H5CX_set_libver_bounds(f);
+
         /* Allocate array for caching results of strlen */
         if(NULL == (str_size = (size_t *)H5MM_malloc(2 * layout->storage.u.virt.list_nused * sizeof(size_t))))
             HGOTO_ERROR(H5E_OHDR, H5E_RESOURCE, FAIL, "unable to allocate string length array")

src/H5P.c

@@ -817,14 +817,17 @@ H5Pget_size(hid_t id, const char *name, size_t *size)
 
 /*--------------------------------------------------------------------------
  NAME
-    H5Pencode
+    H5Pencode2
  PURPOSE
-    Routine to convert the property values in a property list into a binary buffer
+    Routine to convert the property values in a property list into a binary buffer.
+    The encoding of property values will be done according to the file format 
+    setting in fapl_id.
  USAGE
-    herr_t H5Pencode(plist_id, buf, nalloc)
+    herr_t H5Pencode(plist_id, buf, nalloc, fapl_id)
         hid_t plist_id;         IN: Identifier to property list to encode
         void *buf:              OUT: buffer to gold the encoded plist
         size_t *nalloc;         IN/OUT: size of buffer needed to encode plist
+        hid_t fapl_id;          IN: File access property list ID
  RETURNS
     Returns non-negative on success, negative on failure.
  DESCRIPTION
@@ -837,25 +840,29 @@ H5Pget_size(hid_t id, const char *name, size_t *size)
  REVISION LOG
 --------------------------------------------------------------------------*/
 herr_t
-H5Pencode(hid_t plist_id, void *buf, size_t *nalloc)
+H5Pencode2(hid_t plist_id, void *buf, size_t *nalloc, hid_t fapl_id)
 {
     H5P_genplist_t	*plist;         /* Property list to query */
     herr_t ret_value = SUCCEED;          /* return value */
 
     FUNC_ENTER_API(FAIL)
-    H5TRACE3("e", "i*x*z", plist_id, buf, nalloc);
+    H5TRACE4("e", "i*x*zi", plist_id, buf, nalloc, fapl_id);
 
     /* Check arguments. */
     if(NULL == (plist = (H5P_genplist_t *)H5I_object_verify(plist_id, H5I_GENPROP_LST)))
         HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a property list");
 
+    /* Verify access property list and set up collective metadata if appropriate */
+    if(H5CX_set_apl(&fapl_id, H5P_CLS_FACC, H5I_INVALID_HID, TRUE) < 0)
+        HGOTO_ERROR(H5E_FILE, H5E_CANTSET, H5I_INVALID_HID, "can't set access property list info")
+
     /* Call the internal encode routine */
     if((ret_value = H5P__encode(plist, TRUE, buf, nalloc)) < 0)
         HGOTO_ERROR(H5E_PLIST, H5E_CANTENCODE, FAIL, "unable to encode property list");
 
 done:
     FUNC_LEAVE_API(ret_value)
-}   /* H5Pencode() */
+}   /* H5Pencode2() */
 
 
 /*--------------------------------------------------------------------------

src/H5Pdeprec.c

@@ -486,6 +486,54 @@ H5Pget_version(hid_t plist_id, unsigned *super/*out*/, unsigned *freelist/*out*/
     FUNC_LEAVE_API(ret_value)
 } /* end H5Pget_version() */
 
+
+/*--------------------------------------------------------------------------
+ NAME
+    H5Pencode1
+ PURPOSE
+    Routine to convert the property values in a property list into a binary buffer
+ USAGE
+    herr_t H5Pencode1(plist_id, buf, nalloc)
+        hid_t plist_id;         IN: Identifier to property list to encode
+        void *buf:              OUT: buffer to gold the encoded plist
+        size_t *nalloc;         IN/OUT: size of buffer needed to encode plist
+ RETURNS
+    Returns non-negative on success, negative on failure.
+ DESCRIPTION
+    Encodes a property list into a binary buffer. If the buffer is NULL, then
+    the call will set the size needed to encode the plist in nalloc. Otherwise
+    the routine will encode the plist in buf.
+ GLOBAL VARIABLES
+ COMMENTS, BUGS, ASSUMPTIONS
+ EXAMPLES
+ REVISION LOG
+--------------------------------------------------------------------------*/
+herr_t
+H5Pencode1(hid_t plist_id, void *buf, size_t *nalloc)
+{
+    H5P_genplist_t  *plist;         /* Property list to query */
+    hid_t temp_fapl_id = H5P_DEFAULT;
+    herr_t ret_value = SUCCEED;          /* return value */
+
+    FUNC_ENTER_API(FAIL)
+    H5TRACE3("e", "i*x*z", plist_id, buf, nalloc);
+
+    /* Check arguments. */
+    if(NULL == (plist = (H5P_genplist_t *)H5I_object_verify(plist_id, H5I_GENPROP_LST)))
+        HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a property list");
+
+    /* Verify access property list and set up collective metadata if appropriate */
+    if(H5CX_set_apl(&temp_fapl_id, H5P_CLS_FACC, H5I_INVALID_HID, TRUE) < 0)
+        HGOTO_ERROR(H5E_FILE, H5E_CANTSET, H5I_INVALID_HID, "can't set access property list info")
+
+    /* Call the internal encode routine */
+    if((ret_value = H5P__encode(plist, TRUE, buf, nalloc)) < 0)
+        HGOTO_ERROR(H5E_PLIST, H5E_CANTENCODE, FAIL, "unable to encode property list");
+
+done:
+    FUNC_LEAVE_API(ret_value)
+}   /* H5Pencode1() */
+
 /*-------------------------------------------------------------------------
  * Function:	H5Pset_file_space
  *

src/H5Ppublic.h

@@ -236,7 +236,7 @@ H5_DLL herr_t H5Pinsert2(hid_t plist_id, const char *name, size_t size,
     H5P_prp_compare_func_t prp_cmp, H5P_prp_close_func_t prp_close);
 H5_DLL herr_t H5Pset(hid_t plist_id, const char *name, const void *value);
 H5_DLL htri_t H5Pexist(hid_t plist_id, const char *name);
-H5_DLL herr_t H5Pencode(hid_t plist_id, void *buf, size_t *nalloc);
+H5_DLL herr_t H5Pencode2(hid_t plist_id, void *buf, size_t *nalloc, hid_t fapl_id);
 H5_DLL hid_t  H5Pdecode(const void *buf);
 H5_DLL herr_t H5Pget_size(hid_t id, const char *name, size_t *size);
 H5_DLL herr_t H5Pget_nprops(hid_t id, size_t *nprops);
@@ -536,6 +536,7 @@ H5_DLL herr_t H5Pinsert1(hid_t plist_id, const char *name, size_t size,
     void *value, H5P_prp_set_func_t prp_set, H5P_prp_get_func_t prp_get,
     H5P_prp_delete_func_t prp_delete, H5P_prp_copy_func_t prp_copy,
     H5P_prp_close_func_t prp_close);
+H5_DLL herr_t H5Pencode1(hid_t plist_id, void *buf, size_t *nalloc);
 H5_DLL H5Z_filter_t H5Pget_filter1(hid_t plist_id, unsigned filter,
     unsigned int *flags/*out*/, size_t *cd_nelmts/*out*/,
     unsigned cd_values[]/*out*/, size_t namelen, char name[]);

src/H5Rint.c

@@ -215,6 +215,9 @@ H5R__create(void *_ref, H5G_loc_t *loc, const char *name, H5R_type_t ref_type, H
     obj_loc.path = &path;
     H5G_loc_reset(&obj_loc);
 
+    /* Set the FAPL for the API context */
+    H5CX_set_libver_bounds(loc->oloc->file);
+
     /* Find the object */
     if(H5G_loc_find(loc, name, &obj_loc) < 0)
         HGOTO_ERROR(H5E_REFERENCE, H5E_NOTFOUND, FAIL, "object not found")

src/H5S.c

@@ -23,6 +23,7 @@
 /***********/
 #include "H5private.h"		/* Generic Functions			*/
 #include "H5Eprivate.h"		/* Error handling		  	*/
+#include "H5CXprivate.h"    /* API Contexts         */
 #include "H5Fprivate.h"		/* Files				*/
 #include "H5FLprivate.h"	/* Free lists                           */
 #include "H5Iprivate.h"		/* IDs			  		*/
@@ -1487,13 +1488,15 @@ H5S_create_simple(unsigned rank, const hsize_t dims[/*rank*/],
 
 
 /*-------------------------------------------------------------------------
- * Function:	H5Sencode
+ * Function:	H5Sencode2
  *
  * Purpose:	Given a dataspace ID, converts the object description
  *              (including selection) into binary in a buffer.
+ *          The selection will be encoded according to the file 
+ *          format setting in fapl.
  *
  * Return:	Success:	non-negative
- *		Failure:	negative
+ *          Failure: negative
  *
  * Programmer:	Raymond Lu
  *              [email protected]
@@ -1502,24 +1505,29 @@ H5S_create_simple(unsigned rank, const hsize_t dims[/*rank*/],
  *-------------------------------------------------------------------------
  */
 herr_t
-H5Sencode(hid_t obj_id, void *buf, size_t *nalloc)
+H5Sencode2(hid_t obj_id, void *buf, size_t *nalloc, hid_t fapl_id)
 {
     H5S_t       *dspace;
     herr_t      ret_value=SUCCEED;
 
     FUNC_ENTER_API(FAIL)
-    H5TRACE3("e", "i*x*z", obj_id, buf, nalloc);
+    H5TRACE4("e", "i*x*zi", obj_id, buf, nalloc, fapl_id);
 
     /* Check argument and retrieve object */
     if(NULL == (dspace = (H5S_t *)H5I_object_verify(obj_id, H5I_DATASPACE)))
-	HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataspace")
+         HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataspace")
+
+     /* Verify access property list and set up collective metadata if appropriate */
+    if(H5CX_set_apl(&fapl_id, H5P_CLS_FACC, H5I_INVALID_HID, TRUE) < 0)
+        HGOTO_ERROR(H5E_FILE, H5E_CANTSET, H5I_INVALID_HID, "can't set access property list info")
+
 
     if(H5S_encode(dspace, (unsigned char **)&buf, nalloc) < 0)
-	HGOTO_ERROR(H5E_DATASPACE, H5E_CANTENCODE, FAIL, "can't encode dataspace")
+        HGOTO_ERROR(H5E_DATASPACE, H5E_CANTENCODE, FAIL, "can't encode dataspace")
 
 done:
     FUNC_LEAVE_API(ret_value)
-} /* end H5Sencode() */
+} /* H5Sencode2() */
 
 
 /*-------------------------------------------------------------------------

src/H5Sall.c

@@ -629,7 +629,7 @@ H5S__all_serialize(const H5S_t *space, uint8_t **p)
 
     /* Store the preamble information */
     UINT32ENCODE(pp, (uint32_t)H5S_GET_SELECT_TYPE(space));  /* Store the type of selection */
-    UINT32ENCODE(pp, (uint32_t)1);  /* Store the version number */
+    UINT32ENCODE(pp, (uint32_t)H5S_ALL_VERSION_1);  /* Store the version number */
     UINT32ENCODE(pp, (uint32_t)0);  /* Store the un-used padding */
     UINT32ENCODE(pp, (uint32_t)0);  /* Store the additional information length */