Merge issue 839 changes to hdf5 1 10

MANIFEST

@@ -1114,6 +1114,7 @@
 ./test/cache_tagging.c
 ./test/chunk_info.c
 ./test/cmpd_dset.c
+./test/cmpd_dtransform.c
 ./test/cork.c
 ./test/corrupt_stab_msg.h5
 ./test/cross_read.c

config/cmake/ConfigureChecks.cmake

@@ -86,14 +86,6 @@ else ()
   set (HDF5_FILE_LOCKING_SETTING "no")
 endif ()
 
-#-----------------------------------------------------------------------------
-#  Are we going to use HSIZE_T
-#-----------------------------------------------------------------------------
-option (HDF5_ENABLE_HSIZET "Enable datasets larger than memory" ON)
-if (HDF5_ENABLE_HSIZET)
-  set (${HDF_PREFIX}_HAVE_LARGE_HSIZET 1)
-endif ()
-
 # so far we have no check for this
 set (${HDF_PREFIX}_HAVE_TMPFILE 1)
 

hl/src/H5LTanalyze.c

@@ -916,7 +916,7 @@ char *yytext;
 #include "H5LTparse.h"
 
 static char *trim_quotes(const char *);
-int my_yyinput(char *, int);
+static int my_yyinput(char *, int);
 #undef YY_INPUT
 #define YY_INPUT(b, r, ms) (r=my_yyinput(b, ms))
 #define token(x)        (int)x
@@ -2554,7 +2554,7 @@ trim_quotes(const char *quoted)
     return trimmed;
 }
 
-int my_yyinput(char *buf, int max_size)
+static int my_yyinput(char *buf, int max_size)
 {
    int ret;
 

hl/src/H5LTanalyze.l

@@ -27,7 +27,7 @@
 #include "H5LTparse.h"
 
 static char *trim_quotes(const char *);
-int my_yyinput(char *, int);
+static int my_yyinput(char *, int);
 #undef YY_INPUT
 #define YY_INPUT(b, r, ms) (r=my_yyinput(b, ms))
 #define token(x)        (int)x
@@ -144,7 +144,7 @@ trim_quotes(const char *quoted)
     return trimmed;
 }
 
-int my_yyinput(char *buf, int max_size)
+static int my_yyinput(char *buf, int max_size)
 {
    int ret;
 

release_docs/INSTALL_CMake.txt

@@ -753,7 +753,6 @@ HDF5_ENABLE_DEBUG_APIS         "Turn on extra debug output in all packages"
 HDF5_ENABLE_DEPRECATED_SYMBOLS "Enable deprecated public API symbols"                         ON
 HDF5_ENABLE_DIRECT_VFD         "Build the Direct I/O Virtual File Driver"                     OFF
 HDF5_ENABLE_EMBEDDED_LIBINFO   "embed library info into executables"                          ON
-HDF5_ENABLE_HSIZET             "Enable datasets larger than memory"                           ON
 HDF5_ENABLE_PARALLEL           "Enable parallel build (requires MPI)"                         OFF
 HDF5_ENABLE_PREADWRITE         "Use pread/pwrite in sec2/log/core VFDs in place of read/write (when available)" ON
 HDF5_ENABLE_TRACE              "Enable API tracing capability"                                OFF
@@ -795,8 +794,7 @@ HDF5_BUILD_DOC                 "Build documentation"
 HDF5_ENABLE_ANALYZER_TOOLS     "enable the use of Clang tools"                    OFF
 HDF5_ENABLE_SANITIZERS         "execute the Clang sanitizer"                      OFF
 HDF5_ENABLE_FORMATTERS         "format source files"                              OFF
-HDF5_USE_FILE_LOCKING          "Use file locking by default (mainly for SWMR)"    ON
-HDF5_IGNORE_DISABLED_FILE_LOCKS "Ignore file locks when disabled on file system"  ON
+TEST_SHELL_SCRIPTS             "Enable shell script tests"                        ON
 
 ---------------- External Library Options ---------------------
 HDF5_ALLOW_EXTERNAL_SUPPORT "Allow External Library Building (NO GIT TGZ)"        "NO"

release_docs/RELEASE.txt

@@ -73,6 +73,22 @@ New Features
 
       (DER - 2021/06/02)
 
+    - CMake will now run the shell script tests in test/ by default
+
+      The test directory includes several shell script tests that previously
+      were not run by CMake. These are now run by default. TEST_SHELL_SCRIPTS
+      has been set to ON and SH_PROGRAM has been set to bash (some test
+      scripts use bash-isms). Platforms without bash (e.g., Windows) will
+      ignore the script tests.
+
+      (DER - 2021/05/23)
+
+    - Removed unused HDF5_ENABLE_HSIZET option from CMake
+
+      This has been unused for some time and has no effect.
+
+      (DER - 2021/05/23)
+
     - CMake no longer builds the C++ library by default
 
       HDF5_BUILD_CPP_LIB now defaults to OFF, which is in line with the

src/H5.c

@@ -63,10 +63,6 @@ hbool_t H5_PKG_INIT_VAR = FALSE;
 /* Library Private Variables */
 /*****************************/
 
-/* HDF5 API Entered variable */
-/* (move to H5.c when new FUNC_ENTER macros in actual use -QAK) */
-hbool_t H5_api_entered_g = FALSE;
-
 /* statically initialize block for pthread_once call used in initializing */
 /* the first global mutex                                                 */
 #ifdef H5_HAVE_THREADSAFE

src/H5Clog_json.c

@@ -118,32 +118,32 @@ static herr_t H5C__json_write_remove_entry_log_msg(void *udata, const H5C_cache_
 /* Note that there's no cache set up call since that's the
  * place where this struct is wired into the cache.
  */
-static H5C_log_class_t H5C_json_log_class_g = {"json",
-                                               H5C__json_tear_down_logging,
-                                               NULL, /* start logging */
-                                               NULL, /* stop logging */
-                                               H5C__json_write_start_log_msg,
-                                               H5C__json_write_stop_log_msg,
-                                               H5C__json_write_create_cache_log_msg,
-                                               H5C__json_write_destroy_cache_log_msg,
-                                               H5C__json_write_evict_cache_log_msg,
-                                               H5C__json_write_expunge_entry_log_msg,
-                                               H5C__json_write_flush_cache_log_msg,
-                                               H5C__json_write_insert_entry_log_msg,
-                                               H5C__json_write_mark_entry_dirty_log_msg,
-                                               H5C__json_write_mark_entry_clean_log_msg,
-                                               H5C__json_write_mark_unserialized_entry_log_msg,
-                                               H5C__json_write_mark_serialized_entry_log_msg,
-                                               H5C__json_write_move_entry_log_msg,
-                                               H5C__json_write_pin_entry_log_msg,
-                                               H5C__json_write_create_fd_log_msg,
-                                               H5C__json_write_protect_entry_log_msg,
-                                               H5C__json_write_resize_entry_log_msg,
-                                               H5C__json_write_unpin_entry_log_msg,
-                                               H5C__json_write_destroy_fd_log_msg,
-                                               H5C__json_write_unprotect_entry_log_msg,
-                                               H5C__json_write_set_cache_config_log_msg,
-                                               H5C__json_write_remove_entry_log_msg};
+static const H5C_log_class_t H5C_json_log_class_g = {"json",
+                                                     H5C__json_tear_down_logging,
+                                                     NULL, /* start logging */
+                                                     NULL, /* stop logging */
+                                                     H5C__json_write_start_log_msg,
+                                                     H5C__json_write_stop_log_msg,
+                                                     H5C__json_write_create_cache_log_msg,
+                                                     H5C__json_write_destroy_cache_log_msg,
+                                                     H5C__json_write_evict_cache_log_msg,
+                                                     H5C__json_write_expunge_entry_log_msg,
+                                                     H5C__json_write_flush_cache_log_msg,
+                                                     H5C__json_write_insert_entry_log_msg,
+                                                     H5C__json_write_mark_entry_dirty_log_msg,
+                                                     H5C__json_write_mark_entry_clean_log_msg,
+                                                     H5C__json_write_mark_unserialized_entry_log_msg,
+                                                     H5C__json_write_mark_serialized_entry_log_msg,
+                                                     H5C__json_write_move_entry_log_msg,
+                                                     H5C__json_write_pin_entry_log_msg,
+                                                     H5C__json_write_create_fd_log_msg,
+                                                     H5C__json_write_protect_entry_log_msg,
+                                                     H5C__json_write_resize_entry_log_msg,
+                                                     H5C__json_write_unpin_entry_log_msg,
+                                                     H5C__json_write_destroy_fd_log_msg,
+                                                     H5C__json_write_unprotect_entry_log_msg,
+                                                     H5C__json_write_set_cache_config_log_msg,
+                                                     H5C__json_write_remove_entry_log_msg};
 
 /*-------------------------------------------------------------------------
  * Function:    H5C__json_write_log_message

src/H5Clog_trace.c

@@ -113,32 +113,32 @@ static herr_t H5C__trace_write_remove_entry_log_msg(void *udata, const H5C_cache
 /* Note that there's no cache set up call since that's the
  * place where this struct is wired into the cache.
  */
-static H5C_log_class_t H5C_trace_log_class_g = {"trace",
-                                                H5C__trace_tear_down_logging,
-                                                NULL, /* start logging */
-                                                NULL, /* stop logging */
-                                                NULL, /* write start message */
-                                                NULL, /* write stop message */
-                                                NULL, /* write create cache message */
-                                                NULL, /* write destroy cache message */
-                                                NULL, /* write evict cache message */
-                                                H5C__trace_write_expunge_entry_log_msg,
-                                                H5C__trace_write_flush_cache_log_msg,
-                                                H5C__trace_write_insert_entry_log_msg,
-                                                H5C__trace_write_mark_entry_dirty_log_msg,
-                                                H5C__trace_write_mark_entry_clean_log_msg,
-                                                H5C__trace_write_mark_unserialized_entry_log_msg,
-                                                H5C__trace_write_mark_serialized_entry_log_msg,
-                                                H5C__trace_write_move_entry_log_msg,
-                                                H5C__trace_write_pin_entry_log_msg,
-                                                H5C__trace_write_create_fd_log_msg,
-                                                H5C__trace_write_protect_entry_log_msg,
-                                                H5C__trace_write_resize_entry_log_msg,
-                                                H5C__trace_write_unpin_entry_log_msg,
-                                                H5C__trace_write_destroy_fd_log_msg,
-                                                H5C__trace_write_unprotect_entry_log_msg,
-                                                H5C__trace_write_set_cache_config_log_msg,
-                                                H5C__trace_write_remove_entry_log_msg};
+static const H5C_log_class_t H5C_trace_log_class_g = {"trace",
+                                                      H5C__trace_tear_down_logging,
+                                                      NULL, /* start logging */
+                                                      NULL, /* stop logging */
+                                                      NULL, /* write start message */
+                                                      NULL, /* write stop message */
+                                                      NULL, /* write create cache message */
+                                                      NULL, /* write destroy cache message */
+                                                      NULL, /* write evict cache message */
+                                                      H5C__trace_write_expunge_entry_log_msg,
+                                                      H5C__trace_write_flush_cache_log_msg,
+                                                      H5C__trace_write_insert_entry_log_msg,
+                                                      H5C__trace_write_mark_entry_dirty_log_msg,
+                                                      H5C__trace_write_mark_entry_clean_log_msg,
+                                                      H5C__trace_write_mark_unserialized_entry_log_msg,
+                                                      H5C__trace_write_mark_serialized_entry_log_msg,
+                                                      H5C__trace_write_move_entry_log_msg,
+                                                      H5C__trace_write_pin_entry_log_msg,
+                                                      H5C__trace_write_create_fd_log_msg,
+                                                      H5C__trace_write_protect_entry_log_msg,
+                                                      H5C__trace_write_resize_entry_log_msg,
+                                                      H5C__trace_write_unpin_entry_log_msg,
+                                                      H5C__trace_write_destroy_fd_log_msg,
+                                                      H5C__trace_write_unprotect_entry_log_msg,
+                                                      H5C__trace_write_set_cache_config_log_msg,
+                                                      H5C__trace_write_remove_entry_log_msg};
 
 /*-------------------------------------------------------------------------
  * Function:    H5C__trace_write_log_message

src/H5Dpublic.h

@@ -28,9 +28,9 @@
 /*****************/
 
 /* Macros used to "unset" chunk cache configuration parameters */
-#define H5D_CHUNK_CACHE_NSLOTS_DEFAULT ((size_t)-1)
-#define H5D_CHUNK_CACHE_NBYTES_DEFAULT ((size_t)-1)
-#define H5D_CHUNK_CACHE_W0_DEFAULT     (-1.0f)
+#define H5D_CHUNK_CACHE_NSLOTS_DEFAULT SIZE_MAX
+#define H5D_CHUNK_CACHE_NBYTES_DEFAULT SIZE_MAX
+#define H5D_CHUNK_CACHE_W0_DEFAULT     (-1.0)
 
 /* Bit flags for the H5Pset_chunk_opts() and H5Pget_chunk_opts() */
 #define H5D_CHUNK_DONT_FILTER_PARTIAL_CHUNKS (0x0002u)
@@ -46,11 +46,11 @@
 typedef enum H5D_layout_t {
     H5D_LAYOUT_ERROR = -1,
 
-    H5D_COMPACT    = 0, /**< raw data is very small             */
-    H5D_CONTIGUOUS = 1, /**< the default                     */
-    H5D_CHUNKED    = 2, /**< slow and fancy                 */
-    H5D_VIRTUAL    = 3, /**< actual data is stored in other datasets     */
-    H5D_NLAYOUTS   = 4  /**< this one must be last!             */
+    H5D_COMPACT    = 0, /**< raw data is very small */
+    H5D_CONTIGUOUS = 1, /**< the default */
+    H5D_CHUNKED    = 2, /**< slow and fancy */
+    H5D_VIRTUAL    = 3, /**< actual data is stored in other datasets */
+    H5D_NLAYOUTS   = 4  /**< this one must be last! */
 } H5D_layout_t;
 //! <!-- [H5D_layout_t_snip] -->
 

src/H5E.c

@@ -85,6 +85,7 @@ static H5E_t *    H5E__get_current_stack(void);
 static herr_t     H5E__set_current_stack(H5E_t *estack);
 static herr_t     H5E__close_stack(H5E_t *err_stack);
 static ssize_t    H5E__get_num(const H5E_t *err_stack);
+static herr_t     H5E__print2(hid_t err_stack, FILE *stream);
 
 /*********************/
 /* Package Variables */
@@ -311,10 +312,10 @@ H5E__set_default_auto(H5E_t *stk)
 #endif /* H5_USE_16_API_DEFAULT */
 
     stk->auto_op.func1 = stk->auto_op.func1_default = (H5E_auto1_t)H5Eprint1;
-    stk->auto_op.func2 = stk->auto_op.func2_default = (H5E_auto2_t)H5Eprint2;
+    stk->auto_op.func2 = stk->auto_op.func2_default = (H5E_auto2_t)H5E__print2;
     stk->auto_op.is_default                         = TRUE;
 #else  /* H5_NO_DEPRECATED_SYMBOLS */
-    stk->auto_op.func2 = (H5E_auto2_t)H5Eprint2;
+    stk->auto_op.func2 = (H5E_auto2_t)H5E__print2;
 #endif /* H5_NO_DEPRECATED_SYMBOLS */
 
     stk->auto_data = NULL;
@@ -1462,13 +1463,37 @@ H5Eclear2(hid_t err_stack)
 herr_t
 H5Eprint2(hid_t err_stack, FILE *stream)
 {
-    H5E_t *estack;              /* Error stack to operate on */
     herr_t ret_value = SUCCEED; /* Return value */
 
     /* Don't clear the error stack! :-) */
     FUNC_ENTER_API_NOCLEAR(FAIL)
     /*NO TRACE*/
 
+    /* Print error stack */
+    if ((ret_value = H5E__print2(err_stack, stream)) < 0)
+        HGOTO_ERROR(H5E_ERROR, H5E_CANTLIST, FAIL, "can't display error stack")
+
+done:
+    FUNC_LEAVE_API(ret_value)
+} /* end H5Eprint2() */
+
+/*-------------------------------------------------------------------------
+ * Function:    H5E__print2
+ *
+ * Purpose:     Internal helper routine for H5Eprint2.
+ *
+ * Return:      Non-negative on success/Negative on failure
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5E__print2(hid_t err_stack, FILE *stream)
+{
+    H5E_t *estack;              /* Error stack to operate on */
+    herr_t ret_value = SUCCEED; /* Return value */
+
+    FUNC_ENTER_STATIC
+
     /* Need to check for errors */
     if (err_stack == H5E_DEFAULT) {
         if (NULL == (estack = H5E__get_my_stack())) /*lint !e506 !e774 Make lint 'constant value Boolean' in
@@ -1488,8 +1513,8 @@ H5Eprint2(hid_t err_stack, FILE *stream)
         HGOTO_ERROR(H5E_ERROR, H5E_CANTLIST, FAIL, "can't display error stack")
 
 done:
-    FUNC_LEAVE_API(ret_value)
-} /* end H5Eprint2() */
+    FUNC_LEAVE_NOAPI(ret_value)
+} /* end H5E__print2() */
 
 /*-------------------------------------------------------------------------
  * Function:    H5Ewalk2