Merge issue 839 develop PRs to hdf5 1 10 - round 2

bin/trace

@@ -298,10 +298,33 @@ sub rewrite_func ($$$$$) {
     # Compose the trace macro
     $trace = "H5TRACE" . scalar(@arg_str) . "(\"$rettype\", \"";
     $trace .= join("", @arg_str) . "\"";
-    my $len = 4 + length $trace;        # Add 4, for indenting the line
-    for (@arg_name) {
-      # Wrap lines that will be longer than the limit, after ');' is added
-      if ($len + length >= ($max_trace_macro_line_len - 2)) {
+    $argtrace .= join("", @arg_str) . "\"";
+
+    # Add 4 for indenting the line
+    my $len = 4 + length($trace);
+
+    for my $i (0 .. $#arg_name) {
+      # Handle wrapping
+
+      # Be VERY careful here! clang-format and this script MUST agree
+      # on which lines get wrapped or there will be churn as each tries
+      # to undo the other's output.
+      #
+      # TWO cases must be handled:
+      # 1) The argument is that last one and ');' will be appended
+      # 2) The argument is NOT the last one and ',' will be appended
+      #
+      # NB: clang-format does NOT consider terminal newlines when
+      #     counting columns for the ColumnLimit
+      #
+      # The extra '2' added after $len includes the ', ' that would be
+      # added BEFORE the argument.
+      #
+      my $adjust = ($i + 1 == scalar(@arg_str)) ? 2 : 1;
+      my $len_if_added = $len + 2 + length($arg_name[$i]) + $adjust;
+
+      # Wrap lines that will be longer than the limit
+      if ($len_if_added > $max_trace_macro_line_len) {
         # Wrap line, with indention
         $trace .= ",\n             ";
         $len = 13;              # Set to 13, for indention
@@ -317,8 +340,11 @@ sub rewrite_func ($$$$$) {
       }
 
       # Append argument
-      $trace .= "$_";
-      $len += length;     # Add length of appended argument name
+      $trace .= "$arg_name[$i]";
+      $argtrace .= ", $arg_name[$i]";
+
+      # Add length of appended argument name
+      $len += length($arg_name[$i]);
     }
 
     # Append final ');' for macro

config/cmake/H5pubconf.h.in

@@ -198,15 +198,9 @@
    optimization operation */
 #cmakedefine H5_HAVE_INSTRUMENTED_LIBRARY @H5_HAVE_INSTRUMENTED_LIBRARY@
 
-/* Define to 1 if you have the <inttypes.h> header file. */
-#cmakedefine H5_HAVE_INTTYPES_H @H5_HAVE_INTTYPES_H@
-
 /* Define to 1 if you have the `ioctl' function. */
 #cmakedefine H5_HAVE_IOCTL @H5_HAVE_IOCTL@
 
-/* Define to 1 if you have the <io.h> header file. */
-#cmakedefine H5_HAVE_IO_H @H5_HAVE_IO_H@
-
 /* Define to 1 if you have the `crypto' library (-lcrypto). */
 #cmakedefine H5_HAVE_LIBCRYPTO @H5_HAVE_LIBCRYPTO@
 
@@ -358,18 +352,9 @@
 /* Define if `struct stat' has the `st_blocks' field */
 #cmakedefine H5_HAVE_STAT_ST_BLOCKS @H5_HAVE_STAT_ST_BLOCKS@
 
-/* Define to 1 if you have the <stdbool.h> header file. */
-#cmakedefine H5_HAVE_STDBOOL_H @H5_HAVE_STDBOOL_H@
-
 /* Define to 1 if you have the <stddef.h> header file. */
 #cmakedefine H5_HAVE_STDDEF_H @H5_HAVE_STDDEF_H@
 
-/* Define to 1 if you have the <stdint.h> header file. */
-#cmakedefine H5_HAVE_STDINT_H @H5_HAVE_STDINT_H@
-
-/* Define to 1 if you have the <stdint.h> header file for Cplusplus. */
-#cmakedefine H5_HAVE_STDINT_H_CXX @H5_HAVE_STDINT_H_CXX@
-
 /* Define to 1 if you have the <stdlib.h> header file. */
 #cmakedefine H5_HAVE_STDLIB_H @H5_HAVE_STDLIB_H@
 
@@ -713,9 +698,6 @@
 /* The size of `__int64', as computed by sizeof. */
 #define H5_SIZEOF___INT64 @H5_SIZEOF___INT64@
 
-/* Define to 1 if you have the ANSI C header files. */
-#cmakedefine H5_STDC_HEADERS @H5_STDC_HEADERS@
-
 /* Define if strict file format checks are enabled */
 #cmakedefine H5_STRICT_FORMAT_CHECKS @H5_STRICT_FORMAT_CHECKS@
 

config/cmake_ext_mod/ConfigureChecks.cmake

@@ -120,23 +120,13 @@ CHECK_INCLUDE_FILE_CONCAT ("features.h"      ${HDF_PREFIX}_HAVE_FEATURES_H)
 CHECK_INCLUDE_FILE_CONCAT ("dirent.h"        ${HDF_PREFIX}_HAVE_DIRENT_H)
 CHECK_INCLUDE_FILE_CONCAT ("setjmp.h"        ${HDF_PREFIX}_HAVE_SETJMP_H)
 CHECK_INCLUDE_FILE_CONCAT ("stddef.h"        ${HDF_PREFIX}_HAVE_STDDEF_H)
-CHECK_INCLUDE_FILE_CONCAT ("stdint.h"        ${HDF_PREFIX}_HAVE_STDINT_H)
 CHECK_INCLUDE_FILE_CONCAT ("unistd.h"        ${HDF_PREFIX}_HAVE_UNISTD_H)
 
 # Windows
-CHECK_INCLUDE_FILE_CONCAT ("io.h"            ${HDF_PREFIX}_HAVE_IO_H)
 if (NOT CYGWIN)
   CHECK_INCLUDE_FILE_CONCAT ("winsock2.h"      ${HDF_PREFIX}_HAVE_WINSOCK2_H)
 endif ()
 
-if (CMAKE_SYSTEM_NAME MATCHES "OSF")
-  CHECK_INCLUDE_FILE_CONCAT ("sys/sysinfo.h" ${HDF_PREFIX}_HAVE_SYS_SYSINFO_H)
-  CHECK_INCLUDE_FILE_CONCAT ("sys/proc.h"    ${HDF_PREFIX}_HAVE_SYS_PROC_H)
-else ()
-  set (${HDF_PREFIX}_HAVE_SYS_SYSINFO_H "" CACHE INTERNAL "" FORCE)
-  set (${HDF_PREFIX}_HAVE_SYS_PROC_H    "" CACHE INTERNAL "" FORCE)
-endif ()
-
 CHECK_INCLUDE_FILE_CONCAT ("globus/common.h" ${HDF_PREFIX}_HAVE_GLOBUS_COMMON_H)
 CHECK_INCLUDE_FILE_CONCAT ("pdb.h"           ${HDF_PREFIX}_HAVE_PDB_H)
 CHECK_INCLUDE_FILE_CONCAT ("pthread.h"       ${HDF_PREFIX}_HAVE_PTHREAD_H)
@@ -146,12 +136,9 @@ CHECK_INCLUDE_FILE_CONCAT ("strings.h"       ${HDF_PREFIX}_HAVE_STRINGS_H)
 CHECK_INCLUDE_FILE_CONCAT ("stdlib.h"        ${HDF_PREFIX}_HAVE_STDLIB_H)
 CHECK_INCLUDE_FILE_CONCAT ("memory.h"        ${HDF_PREFIX}_HAVE_MEMORY_H)
 CHECK_INCLUDE_FILE_CONCAT ("dlfcn.h"         ${HDF_PREFIX}_HAVE_DLFCN_H)
-CHECK_INCLUDE_FILE_CONCAT ("inttypes.h"      ${HDF_PREFIX}_HAVE_INTTYPES_H)
 CHECK_INCLUDE_FILE_CONCAT ("netinet/in.h"    ${HDF_PREFIX}_HAVE_NETINET_IN_H)
 CHECK_INCLUDE_FILE_CONCAT ("netdb.h"         ${HDF_PREFIX}_HAVE_NETDB_H)
 CHECK_INCLUDE_FILE_CONCAT ("arpa/inet.h"     ${HDF_PREFIX}_HAVE_ARPA_INET_H)
-# _Bool type support
-CHECK_INCLUDE_FILE_CONCAT (stdbool.h    ${HDF_PREFIX}_HAVE_STDBOOL_H)
 
 ## Check for non-standard extenstion quadmath.h
 
@@ -237,11 +224,6 @@ macro (HDF_FUNCTION_TEST OTHER_TEST)
   endif ()
 endmacro ()
 
-#-----------------------------------------------------------------------------
-# Check for these functions before the time headers are checked
-#-----------------------------------------------------------------------------
-HDF_FUNCTION_TEST (STDC_HEADERS)
-
 #-----------------------------------------------------------------------------
 #  Check for large file support
 #-----------------------------------------------------------------------------
@@ -416,13 +398,9 @@ HDF_CHECK_TYPE_SIZE (time_t          ${HDF_PREFIX}_SIZEOF_TIME_T)
 # Extra C99 types
 #-----------------------------------------------------------------------------
 
-# _Bool type support
-if (HAVE_STDBOOL_H)
-  set (CMAKE_EXTRA_INCLUDE_FILES stdbool.h)
-  HDF_CHECK_TYPE_SIZE (bool         ${HDF_PREFIX}_SIZEOF_BOOL)
-else ()
-  HDF_CHECK_TYPE_SIZE (_Bool        ${HDF_PREFIX}_SIZEOF_BOOL)
-endif ()
+# Size of bool
+set (CMAKE_EXTRA_INCLUDE_FILES stdbool.h)
+HDF_CHECK_TYPE_SIZE (_Bool        ${HDF_PREFIX}_SIZEOF_BOOL)
 
 if (MINGW OR NOT WINDOWS)
   #-----------------------------------------------------------------------------
@@ -560,7 +538,6 @@ if (MINGW OR NOT WINDOWS)
   foreach (other_test
       HAVE_ATTRIBUTE
       HAVE_C99_FUNC
-#      STDC_HEADERS
       HAVE_FUNCTION
       HAVE_C99_DESIGNATED_INITIALIZER
       SYSTEM_SCOPE_THREADS

config/cmake_ext_mod/HDFTests.c

@@ -88,14 +88,6 @@ int main(void)
 }
 #endif
 
-#ifdef STDC_HEADERS
-#include <stdlib.h>
-#include <stdarg.h>
-#include <string.h>
-#include <float.h>
-int main() { return 0; }
-#endif /* STDC_HEADERS */
-
 
 #ifdef HAVE_ATTRIBUTE
 

config/cmake_ext_mod/HDFUseCXX.cmake

@@ -32,17 +32,6 @@ endif ()
 include (CheckIncludeFileCXX)
 include (TestForSTDNamespace)
 
-# IF the c compiler found stdint, check the C++ as well. On some systems this
-# file will be found by C but not C++, only do this test IF the C++ compiler
-# has been initialized (e.g. the project also includes some c++)
-if (${HDF_PREFIX}_HAVE_STDINT_H AND CMAKE_CXX_COMPILER_LOADED)
-  CHECK_INCLUDE_FILE_CXX ("stdint.h" ${HDF_PREFIX}_HAVE_STDINT_H_CXX)
-  if (NOT ${HDF_PREFIX}_HAVE_STDINT_H_CXX)
-    set (${HDF_PREFIX}_HAVE_STDINT_H "" CACHE INTERNAL "Have includes HAVE_STDINT_H")
-    set (USE_INCLUDES ${USE_INCLUDES} "stdint.h")
-  endif ()
-endif ()
-
 # For other CXX specific tests, use this MACRO.
 macro (HDF_CXX_FUNCTION_TEST OTHER_TEST)
   if (NOT DEFINED ${OTHER_TEST})

configure.ac

@@ -1224,8 +1224,6 @@ AC_CHECK_HEADERS([sys/resource.h sys/time.h unistd.h sys/ioctl.h sys/stat.h])
 AC_CHECK_HEADERS([sys/socket.h sys/types.h sys/file.h])
 AC_CHECK_HEADERS([stddef.h setjmp.h features.h])
 AC_CHECK_HEADERS([dirent.h])
-AC_CHECK_HEADERS([stdint.h], [C9x=yes])
-AC_CHECK_HEADERS([stdbool.h])
 AC_CHECK_HEADERS([netdb.h netinet/in.h arpa/inet.h])
 
 ## Darwin
@@ -1241,15 +1239,15 @@ esac
 ## Windows
 case "`uname`" in
   CYGWIN*)
-    AC_CHECK_HEADERS([io.h sys/timeb.h])
+    AC_CHECK_HEADERS([sys/timeb.h])
     UNAME_CYGWIN="yes"
     ;;
   MINGW*)
-    AC_CHECK_HEADERS([io.h winsock2.h sys/timeb.h])
+    AC_CHECK_HEADERS([winsock2.h sys/timeb.h])
     AC_HAVE_LIBRARY([ws2_32])
     ;;
   *)
-    AC_CHECK_HEADERS([io.h winsock2.h sys/timeb.h])
+    AC_CHECK_HEADERS([winsock2.h sys/timeb.h])
     ;;
 esac
 
@@ -1340,16 +1338,15 @@ CFLAGS="$H5_CFLAGS $AM_CFLAGS $CFLAGS"
 ## Checkpoint the cache
 AC_CACHE_SAVE
 
-## Posix.1g types (C9x)
+## Write the confdefs.h header for checking sizes
 cat >>confdefs.h <<\EOF
-#include <sys/types.h>
-EOF
-
-if test "X$C9x" = "Xyes"; then
-  cat >>confdefs.h <<\EOF
+#include <stdbool.h>
 #include <stdint.h>
+#ifdef HAVE_UNISTD_H
+#include <sys/types.h>
+#endif
+#include <time.h>
 EOF
-fi
 
 AC_CHECK_SIZEOF(        [int8_t])
 AC_CHECK_SIZEOF(       [uint8_t])
@@ -1379,34 +1376,12 @@ AC_CHECK_SIZEOF([uint_least64_t])
 AC_CHECK_SIZEOF(  [int_fast64_t])
 AC_CHECK_SIZEOF( [uint_fast64_t])
 
+AC_CHECK_SIZEOF([bool])
+AC_CHECK_SIZEOF([off_t])
+AC_CHECK_SIZEOF([ptrdiff_t])
 AC_CHECK_SIZEOF([size_t])
 AC_CHECK_SIZEOF([ssize_t])
-AC_CHECK_SIZEOF([ptrdiff_t])
-
-cat >>confdefs.h <<\EOF
-#include <sys/types.h> /*for off_t definition*/
-EOF
-AC_CHECK_SIZEOF([off_t])
-
-if test "X$C9x" = "Xyes"; then
-  cat >>confdefs.h <<\EOF
-#ifdef HAVE_STDBOOL_H
-#include <stdbool.h> /* for bool definition */
-#else
-#define bool _Bool
-#endif
-EOF
-AC_CHECK_SIZEOF([bool])
-fi
-
-AC_CHECK_SIZEOF(time_t, [], [
-#ifdef HAVE_SYS_TYPES_H
-#include <sys/types.h>
-#endif
-#ifdef HAVE_TIME_H
-#include <time.h>
-#endif
-])
+AC_CHECK_SIZEOF([time_t])
 
 ## Checkpoint the cache
 AC_CACHE_SAVE
@@ -1911,10 +1886,8 @@ if test "X$THREADSAFE" = "Xyes"; then
     AC_CACHE_VAL([hdf5_cv_system_scope_threads],
       [AC_RUN_IFELSE(
         [AC_LANG_PROGRAM([
-            #if STDC_HEADERS
             #include <stdlib.h>
             #include <pthread.h>
-            #endif
         ],[
               pthread_attr_t attribute;
               int ret;

release_docs/RELEASE.txt

@@ -262,6 +262,49 @@ New Features
 
     Library:
     --------
+    - H5Gcreate1() now rejects size_hint parameters larger than UINT32_MAX
+
+      The size_hint value is ultimately stored in a uint32_t struct field,
+      so specifying a value larger than this on a 64-bit machine can cause
+      undefined behavior including crashing the system.
+
+      The documentation for this API call was also incorrect, stating that
+      passing a negative value would cause the library to use a default
+      value. Instead, passing a "negative" value actually passes a very large
+      value, which is probably not what the user intends and can cause
+      crashes on 64-bit systems.
+
+      The Doxygen documentation has been updated and passing values larger
+      than UINT32_MAX for size_hint will now produce a normal HDF5 error.
+
+        (DER - 2021/04/29, HDFFV-11241)
+
+
+    - H5Pset_fapl_log() no longer crashes when passed an invalid fapl ID
+
+      When passed an invalid fapl ID, H5Pset_fapl_log() would usually
+      segfault when attempting to free an uninitialized pointer in the error
+      handling code. This behavior is more common in release builds or
+      when the memory sanitization checks were not selected as a build
+      option.
+
+      The pointer is now correctly initialized and the API call now
+      produces a normal HDF5 error when fed an invalid fapl ID.
+
+        (DER - 2021/04/28, HDFFV-11240)
+
+    - Fixes a segfault when H5Pset_mdc_log_options() is called multiple times
+
+      The call incorrectly attempts to free an internal copy of the previous
+      log location string, which causes a segfault. This only happens
+      when the call is invoked multiple times on the same property list.
+      On the first call to a given fapl, the log location is set to NULL so
+      the segfault does not occur.
+
+      The string is now handled properly and the segfault no longer occurs.
+
+        (DER - 2021/04/27, HDFFV-11239)
+
     - HSYS_GOTO_ERROR now emits the results of GetLastError() on Windows
 
       HSYS_GOTO_ERROR is an internal macro that is used to produce error

src/H5Dpublic.h

@@ -28,8 +28,8 @@
 /*****************/
 
 /* Macros used to "unset" chunk cache configuration parameters */
-#define H5D_CHUNK_CACHE_NSLOTS_DEFAULT SIZE_MAX
-#define H5D_CHUNK_CACHE_NBYTES_DEFAULT SIZE_MAX
+#define H5D_CHUNK_CACHE_NSLOTS_DEFAULT ((size_t)-1)
+#define H5D_CHUNK_CACHE_NBYTES_DEFAULT ((size_t)-1)
 #define H5D_CHUNK_CACHE_W0_DEFAULT     (-1.0)
 
 /* Bit flags for the H5Pset_chunk_opts() and H5Pget_chunk_opts() */

src/H5FDlog.c

@@ -326,12 +326,15 @@ H5Pset_fapl_log(hid_t fapl_id, const char *logfile, unsigned long long flags, si
     FUNC_ENTER_API(FAIL)
     H5TRACE4("e", "i*sULz", fapl_id, logfile, flags, buf_size);
 
+    /* Do this first, so that we don't try to free a wild pointer if
+     * H5P_object_verify() fails.
+     */
+    HDmemset(&fa, 0, sizeof(H5FD_log_fapl_t));
+
     /* Check arguments */
     if (NULL == (plist = H5P_object_verify(fapl_id, H5P_FILE_ACCESS)))
         HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a file access property list")
 
-    HDmemset(&fa, 0, sizeof(H5FD_log_fapl_t));
-
     /* Duplicate the log file string
      * A little wasteful, since this string will just be copied later, but
      * passing it in as a pointer sets off a chain of impossible-to-resolve