Merge branch 'develop' of https://bitbucket.hdfgroup.org/scm/hdffv/hdf5…

… into stackable_vol

config/cmake/ConversionTests.c

@@ -9,7 +9,7 @@
  * If you do not have access to either file, you may request a copy from *
  * help@hdfgroup.org. *
  * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
-+
+
 #if defined(__has_attribute)
 #if __has_attribute(no_sanitize)
 #define HDF_NO_UBSAN __attribute__((no_sanitize("undefined")))

config/cmake_ext_mod/HDFLibMacros.cmake

@@ -75,14 +75,14 @@ macro (EXTERNAL_JPEG_LIBRARY compress_type jpeg_pic)
 # Create imported target jpeg-static
  add_library(jpeg-static STATIC IMPORTED)
  HDF_IMPORT_SET_LIB_OPTIONS (jpeg-static "jpeg" STATIC "")
- add_dependencies (JPEG jpeg-static)
+ add_dependencies (jpeg-static JPEG)
  set (JPEG_STATIC_LIBRARY "jpeg-static")
  set (JPEG_LIBRARIES ${JPEG_STATIC_LIBRARY})
  if (BUILD_SHARED_LIBS)
  # Create imported target jpeg-shared
  add_library(jpeg-shared SHARED IMPORTED)
  HDF_IMPORT_SET_LIB_OPTIONS (jpeg-shared "jpeg" SHARED "")
- add_dependencies (JPEG jpeg-shared)
+ add_dependencies (jpeg-shared JPEG)
  set (JPEG_SHARED_LIBRARY "jpeg-shared")
  set (JPEG_LIBRARIES ${JPEG_LIBRARIES} ${JPEG_SHARED_LIBRARY})
  endif ()
@@ -171,14 +171,14 @@ macro (EXTERNAL_SZIP_LIBRARY compress_type encoding)
 # Create imported target szip-static
  add_library(szip-static STATIC IMPORTED)
  HDF_IMPORT_SET_LIB_OPTIONS (szip-static "szip" STATIC "")
- add_dependencies (SZIP szip-static)
+ add_dependencies (szip-static SZIP)
  set (SZIP_STATIC_LIBRARY "szip-static")
  set (SZIP_LIBRARIES ${SZIP_STATIC_LIBRARY})
  if (BUILD_SHARED_LIBS)
  # Create imported target szip-shared
  add_library(szip-shared SHARED IMPORTED)
  HDF_IMPORT_SET_LIB_OPTIONS (szip-shared "szip" SHARED "")
- add_dependencies (SZIP szip-shared)
+ add_dependencies (szip-shared SZIP)
  set (SZIP_SHARED_LIBRARY "szip-shared")
  set (SZIP_LIBRARIES ${SZIP_LIBRARIES} ${SZIP_SHARED_LIBRARY})
  endif ()
@@ -269,14 +269,14 @@ macro (EXTERNAL_ZLIB_LIBRARY compress_type)
 # Create imported target zlib-static
  add_library(zlib-static STATIC IMPORTED)
  HDF_IMPORT_SET_LIB_OPTIONS (zlib-static ${ZLIB_LIB_NAME} STATIC "")
- add_dependencies (ZLIB zlib-static)
+ add_dependencies (zlib-static ZLIB)
  set (ZLIB_STATIC_LIBRARY "zlib-static")
  set (ZLIB_LIBRARIES ${ZLIB_STATIC_LIBRARY})
  if (BUILD_SHARED_LIBS)
  # Create imported target zlib-shared
  add_library(zlib-shared SHARED IMPORTED)
  HDF_IMPORT_SET_LIB_OPTIONS (zlib-shared ${ZLIB_LIB_NAME} SHARED "")
- add_dependencies (ZLIB zlib-shared)
+ add_dependencies (zlib-shared ZLIB)
  set (ZLIB_SHARED_LIBRARY "zlib-shared")
  set (ZLIB_LIBRARIES ${ZLIB_LIBRARIES} ${ZLIB_SHARED_LIBRARY})
  endif ()

hl/tools/gif2h5/decompress.c

@@ -261,7 +261,7 @@ Decompress(GIFIMAGEDESC *GifImageDesc, GIFHEAD *GifHead)
  * chain puts its associated output code on the output queue.
  */
  while (CurCode > DataMask) {
- if (OutCount > 1024) {
+ if (OutCount >= 1024) {
  /*return error message*/
  }
 

java/src/hdf/hdf5lib/H5.java

@@ -214,7 +214,7 @@
  * exception handlers to print out the HDF-5 error stack.
  * <hr>
  *
- * @version HDF5 1.11.3 <BR>
+ * @version HDF5 1.11.4 <BR>
  * <b>See also: <a href ="./hdf.hdf5lib.HDFArray.html"> hdf.hdf5lib.HDFArray</a> </b><BR>
  * <a href ="./hdf.hdf5lib.HDF5Constants.html"> hdf.hdf5lib.HDF5Constants</a><BR>
  * <a href ="./hdf.hdf5lib.HDF5CDataTypes.html"> hdf.hdf5lib.HDF5CDataTypes</a><BR>
@@ -237,7 +237,7 @@ public class H5 implements java.io.Serializable {
  *
  * Make sure to update the versions number when a different library is used.
  */
- public final static int LIB_VERSION[] = { 1, 11, 3 };
+ public final static int LIB_VERSION[] = { 1, 11, 4 };
 
  public final static String H5PATH_PROPERTY_KEY = "hdf.hdf5lib.H5.hdf5lib";
 

java/test/TestH5.java

@@ -162,7 +162,7 @@ public void testH5set_free_list_limits() {
  */
  @Test
  public void testH5get_libversion() {
- int libversion[] = { 1, 11, 3 };
+ int libversion[] = { 1, 11, 4 };
 
  try {
  H5.H5get_libversion(libversion);
@@ -184,7 +184,7 @@ public void testH5get_libversion() {
  */
  @Test
  public void testH5check_version() {
- int majnum = 1, minnum = 11, relnum = 3;
+ int majnum = 1, minnum = 11, relnum = 4;
 
  try {
  H5.H5check_version(majnum, minnum, relnum);

release_docs/RELEASE.txt

@@ -639,10 +639,9 @@ Supported Platforms
 
  Windows 7 Visual Studio 2015 w/ Intel Fortran 16 (cmake)
 
- Windows 7 x64 Visual Studio 2012 w/ Intel Fortran 15 (cmake)
- Visual Studio 2013 w/ Intel Fortran 15 (cmake)
+ Windows 7 x64 Visual Studio 2013
  Visual Studio 2015 w/ Intel Fortran 16 (cmake)
- Visual Studio 2015 w/ Intel C, Fortran 2017 (cmake)
+ Visual Studio 2015 w/ Intel C, Fortran 2018 (cmake)
  Visual Studio 2015 w/ MSMPI 8 (cmake)
 
  Windows 10 Visual Studio 2015 w/ Intel Fortran 18 (cmake)

src/CMakeLists.txt

@@ -1035,6 +1035,7 @@ option (HDF5_ENABLE_DEBUG_APIS "Turn on extra debug output in all packages" OFF)
 #-----------------------------------------------------------------------------
 set (gen_SRCS ${HDF5_GENERATED_SOURCE_DIR}/H5Tinit.c ${HDF5_BINARY_DIR}/H5lib_settings.c)
 
+add_custom_target (gen_${HDF5_LIB_TARGET} ALL DEPENDS ${gen_SRCS})
 add_library (${HDF5_LIB_TARGET} STATIC ${common_SRCS} ${gen_SRCS} ${H5_PUBLIC_HEADERS} ${H5_PRIVATE_HEADERS} ${H5_GENERATED_HEADERS})
 target_include_directories(${HDF5_LIB_TARGET}
  PRIVATE "${HDF5_SRC_DIR};${HDF5_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>"
@@ -1057,12 +1058,14 @@ target_link_libraries (${HDF5_LIB_TARGET}
 set_global_variable (HDF5_LIBRARIES_TO_EXPORT ${HDF5_LIB_TARGET})
 H5_SET_LIB_OPTIONS (${HDF5_LIB_TARGET} ${HDF5_LIB_NAME} STATIC 0)
 set_target_properties (${HDF5_LIB_TARGET} PROPERTIES FOLDER libraries)
+add_dependencies (${HDF5_LIB_TARGET} gen_${HDF5_LIB_TARGET})
 
 set (install_targets ${HDF5_LIB_TARGET})
 
 if (BUILD_SHARED_LIBS)
  set (shared_gen_SRCS ${HDF5_GENERATED_SOURCE_DIR}/shared/H5Tinit.c ${HDF5_BINARY_DIR}/shared/H5lib_settings.c)
 
+ add_custom_target (gen_${HDF5_LIBSH_TARGET} ALL DEPENDS ${shared_gen_SRCS})
  add_library (${HDF5_LIBSH_TARGET} SHARED ${common_SRCS} ${shared_gen_SRCS} ${H5_PUBLIC_HEADERS} ${H5_PRIVATE_HEADERS} ${H5_GENERATED_HEADERS})
  target_include_directories(${HDF5_LIBSH_TARGET}
  PRIVATE "${HDF5_SRC_DIR};${HDF5_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>"
@@ -1087,6 +1090,7 @@ if (BUILD_SHARED_LIBS)
  set_global_variable (HDF5_LIBRARIES_TO_EXPORT "${HDF5_LIBRARIES_TO_EXPORT};${HDF5_LIBSH_TARGET}")
  H5_SET_LIB_OPTIONS (${HDF5_LIBSH_TARGET} ${HDF5_LIB_NAME} SHARED "LIB")
  set_target_properties (${HDF5_LIBSH_TARGET} PROPERTIES FOLDER libraries)
+ add_dependencies (${HDF5_LIBSH_TARGET} gen_${HDF5_LIBSH_TARGET})
 
  set (install_targets ${install_targets} ${HDF5_LIBSH_TARGET})
 endif ()

test/CMakeLists.txt

@@ -62,6 +62,7 @@ endif ()
 #################################################################################
 # If filter plugin tests can be tested
 #################################################################################
+if (BUILD_SHARED_LIBS)
  # make plugins dir
  file (MAKE_DIRECTORY "${CMAKE_BINARY_DIR}/filter_plugin_dir1")
  file (MAKE_DIRECTORY "${CMAKE_BINARY_DIR}/filter_plugin_dir2")
@@ -159,6 +160,7 @@ endif ()
  "${CMAKE_BINARY_DIR}/vol/$<TARGET_FILE_NAME:${HDF5_VOL_PLUGIN_LIB_TARGET}>"
  )
  endforeach ()
+endif ()
 
 #################################################################################
 # Test program sources

test/CMakeTests.cmake

@@ -1030,29 +1030,31 @@ endif ()
 ##############################################################################
 ### F I L T E R P L U G I N T E S T S
 ##############################################################################
-if (WIN32)
- set (CMAKE_SEP "\;")
- set (BIN_REL_PATH "../../")
-else ()
- set (CMAKE_SEP ":")
- set (BIN_REL_PATH "../")
-endif ()
+if (BUILD_SHARED_LIBS)
+ if (WIN32)
+ set (CMAKE_SEP "\;")
+ set (BIN_REL_PATH "../../")
+ else ()
+ set (CMAKE_SEP ":")
+ set (BIN_REL_PATH "../")
+ endif ()
 
-add_test (NAME H5PLUGIN-filter_plugin COMMAND $<TARGET_FILE:filter_plugin>)
-set_tests_properties (H5PLUGIN-filter_plugin PROPERTIES
- ENVIRONMENT "HDF5_PLUGIN_PATH=${CMAKE_BINARY_DIR}/filter_plugin_dir1${CMAKE_SEP}${CMAKE_BINARY_DIR}/filter_plugin_dir2;srcdir=${HDF5_TEST_BINARY_DIR}"
- WORKING_DIRECTORY ${HDF5_TEST_BINARY_DIR}
-)
+ add_test (NAME H5PLUGIN-filter_plugin COMMAND $<TARGET_FILE:filter_plugin>)
+ set_tests_properties (H5PLUGIN-filter_plugin PROPERTIES
+  ENVIRONMENT "HDF5_PLUGIN_PATH=${CMAKE_BINARY_DIR}/filter_plugin_dir1${CMAKE_SEP}${CMAKE_BINARY_DIR}/filter_plugin_dir2;srcdir=${HDF5_TEST_BINARY_DIR}"
+  WORKING_DIRECTORY ${HDF5_TEST_BINARY_DIR}
+ )
 
 ##############################################################################
 # HDFFV-9655 relative plugin test disabled
 #
-#add_test (NAME H5PLUGIN-pluginRelative COMMAND $<TARGET_FILE:plugin>)
-#set_tests_properties (H5PLUGIN-pluginRelative PROPERTIES
-# ENVIRONMENT "HDF5_PLUGIN_PATH=@/${BIN_REL_PATH}testdir1${CMAKE_SEP}@/${BIN_REL_PATH}testdir2;srcdir=${HDF5_TEST_BINARY_DIR}"
-# WORKING_DIRECTORY ${HDF5_TEST_BINARY_DIR}
-#)
+# add_test (NAME H5PLUGIN-pluginRelative COMMAND $<TARGET_FILE:plugin>)
+# set_tests_properties (H5PLUGIN-pluginRelative PROPERTIES
+#  ENVIRONMENT "HDF5_PLUGIN_PATH=@/${BIN_REL_PATH}testdir1${CMAKE_SEP}@/${BIN_REL_PATH}testdir2;srcdir=${HDF5_TEST_BINARY_DIR}"
+#  WORKING_DIRECTORY ${HDF5_TEST_BINARY_DIR}
+# )
 ##############################################################################
+endif ()
 
 if (TEST_SHELL_SCRIPTS)
  include (ShellTests.cmake)

tools/lib/h5diff.c

@@ -274,12 +274,15 @@ build_match_list (const char *objname1, trav_info_t *info1, const char *objname2
  int cmp;
  trav_table_t *table = NULL;
  size_t idx;
+ int ret_value = 0;
 
  h5difftrace("build_match_list start\n");
  /* init */
  trav_table_init(&table);
- if (table == NULL)
- H5TOOLS_INFO(H5E_tools_min_id_g, "Cannot create tarverse table");
+ if (table == NULL) {
+ H5TOOLS_INFO(H5E_tools_min_id_g, "Cannot create traverse table");
+ HGOTO_DONE(-1);
+ }
  /*
  * This is necessary for the case that given objects are group and
  * have different names (ex: obj1 is /grp1 and obj2 is /grp5).
@@ -367,6 +370,7 @@ build_match_list (const char *objname1, trav_info_t *info1, const char *objname2
 
  free_exclude_path_list (opts);
 
+done:
  *table_out = table;
  h5difftrace("build_match_list finish\n");
 }

tools/lib/h5tools.c

@@ -1241,10 +1241,10 @@ render_bin_output(FILE *stream, hid_t container, hid_t tid, void *_mem, hsize_t
  H5T_class_t type_class;
 
  if((size = H5Tget_size(tid)) == 0)
- H5E_THROW(FAIL, H5E_tools_min_id_g, "H5Tget_size failed");
+ H5E_THROW(FAIL, H5E_tools_min_id_g, "H5Tget_size failed")
 
  if((type_class = H5Tget_class(tid)) < 0)
- H5E_THROW(FAIL, H5E_tools_min_id_g, "H5Tget_class failed");
+ H5E_THROW(FAIL, H5E_tools_min_id_g, "H5Tget_class failed")
 
  switch (type_class) {
  case H5T_INTEGER:
@@ -1264,7 +1264,7 @@ render_bin_output(FILE *stream, hid_t container, hid_t tid, void *_mem, hsize_t
  bytes_wrote = HDfwrite(mem, 1, bytes_in, stream);
 
  if(bytes_wrote != bytes_in || (0 == bytes_wrote && HDferror(stream)))
- H5E_THROW(FAIL, H5E_tools_min_id_g, "fwrite failed");
+ H5E_THROW(FAIL, H5E_tools_min_id_g, "fwrite failed")
 
  block_index -= (hsize_t)bytes_wrote;
  mem = mem + bytes_wrote;
@@ -1287,15 +1287,15 @@ render_bin_output(FILE *stream, hid_t container, hid_t tid, void *_mem, hsize_t
  if (s != NULL)
  size = HDstrlen(s);
  else
- H5E_THROW(FAIL, H5E_tools_min_id_g, "NULL string");
+ H5E_THROW(FAIL, H5E_tools_min_id_g, "NULL string")
  }
  else {
  s = (char *) mem;
  }
  for (i = 0; i < size && (s[i] || pad != H5T_STR_NULLTERM); i++) {
  HDmemcpy(&tempuchar, &s[i], sizeof(unsigned char));
  if (1 != HDfwrite(&tempuchar, sizeof(unsigned char), 1, stream))
- H5E_THROW(FAIL, H5E_tools_min_id_g, "fwrite failed");
+ H5E_THROW(FAIL, H5E_tools_min_id_g, "fwrite failed")
  } /* i */
  } /* for (block_index = 0; block_index < block_nelmts; block_index++) */
  }
@@ -1306,7 +1306,7 @@ render_bin_output(FILE *stream, hid_t container, hid_t tid, void *_mem, hsize_t
  unsigned nmembs;
 
  if((snmembs = H5Tget_nmembers(tid)) < 0)
- H5E_THROW(FAIL, H5E_tools_min_id_g, "H5Tget_nmembers of compound failed");
+ H5E_THROW(FAIL, H5E_tools_min_id_g, "H5Tget_nmembers of compound failed")
  nmembs = (unsigned)snmembs;
 
  for (block_index = 0; block_index < block_nelmts; block_index++) {
@@ -1322,7 +1322,7 @@ render_bin_output(FILE *stream, hid_t container, hid_t tid, void *_mem, hsize_t
 
  if (render_bin_output(stream, container, memb, mem + offset, 1) < 0) {
  H5Tclose(memb);
- H5E_THROW(FAIL, H5E_tools_min_id_g, "render_bin_output of compound member failed");
+ H5E_THROW(FAIL, H5E_tools_min_id_g, "render_bin_output of compound member failed")
  }
 
  H5Tclose(memb);
@@ -1350,15 +1350,15 @@ render_bin_output(FILE *stream, hid_t container, hid_t tid, void *_mem, hsize_t
  }
  else {
  H5Tclose(memb);
- H5E_THROW(FAIL, H5E_tools_min_id_g, "calculate the number of array elements failed");
+ H5E_THROW(FAIL, H5E_tools_min_id_g, "calculate the number of array elements failed")
  }
 
  for (block_index = 0; block_index < block_nelmts; block_index++) {
  mem = ((unsigned char*)_mem) + block_index * size;
  /* dump the array element */
  if (render_bin_output(stream, container, memb, mem, nelmts) < 0) {
  H5Tclose(memb);
- H5E_THROW(FAIL, H5E_tools_min_id_g, "render_bin_output failed");
+ H5E_THROW(FAIL, H5E_tools_min_id_g, "render_bin_output failed")
  }
  }
  H5Tclose(memb);
@@ -1380,7 +1380,7 @@ render_bin_output(FILE *stream, hid_t container, hid_t tid, void *_mem, hsize_t
  /* dump the array element */
  if (render_bin_output(stream, container, memb, ((char *) (((hvl_t *) mem)->p)), nelmts) < 0) {
  H5Tclose(memb);
- H5E_THROW(FAIL, H5E_tools_min_id_g, "render_bin_output failed");
+ H5E_THROW(FAIL, H5E_tools_min_id_g, "render_bin_output failed")
  }
  }
  H5Tclose(memb);
@@ -1426,15 +1426,15 @@ render_bin_output(FILE *stream, hid_t container, hid_t tid, void *_mem, hsize_t
  for (block_index = 0; block_index < block_nelmts; block_index++) {
  mem = ((unsigned char*)_mem) + block_index * size;
  if (size != HDfwrite(mem, sizeof(char), size, stream))
- H5E_THROW(FAIL, H5E_tools_min_id_g, "fwrite failed");
+ H5E_THROW(FAIL, H5E_tools_min_id_g, "fwrite failed")
  } /* end for */
  break;
 
  case H5T_NO_CLASS:
  case H5T_NCLASSES:
  default:
  /* Badness */
- H5E_THROW(FAIL, H5E_tools_min_id_g, "bad type class");
+ H5E_THROW(FAIL, H5E_tools_min_id_g, "bad type class")
  break;
  } /* end switch */
 
@@ -1562,12 +1562,12 @@ render_bin_output_region_blocks(hid_t region_space, hid_t region_id,
  hid_t type_id = -1;
 
  if((snblocks = H5Sget_select_hyper_nblocks(region_space)) <= 0)
- H5E_THROW(FALSE, H5E_tools_min_id_g, "H5Sget_select_hyper_nblocks failed");
+ H5E_THROW(FALSE, H5E_tools_min_id_g, "H5Sget_select_hyper_nblocks failed")
  nblocks = (hsize_t)snblocks;
 
  /* Print block information */
  if((sndims = H5Sget_simple_extent_ndims(region_space)) < 0)
- H5E_THROW(FALSE, H5E_tools_min_id_g, "H5Sget_simple_extent_ndims failed");
+ H5E_THROW(FALSE, H5E_tools_min_id_g, "H5Sget_simple_extent_ndims failed")
  ndims = (unsigned)sndims;
 
  alloc_size = nblocks * ndims * 2 * sizeof(ptdata[0]);
@@ -1683,12 +1683,12 @@ render_bin_output_region_points(hid_t region_space, hid_t region_id,
  hid_t type_id = -1;
 
  if((snpoints = H5Sget_select_elem_npoints(region_space)) <= 0)
- H5E_THROW(FALSE, H5E_tools_min_id_g, "H5Sget_select_elem_npoints failed");
+ H5E_THROW(FALSE, H5E_tools_min_id_g, "H5Sget_select_elem_npoints failed")
  npoints = (hsize_t)snpoints;
 
  /* Allocate space for the dimension array */
  if((sndims = H5Sget_simple_extent_ndims(region_space)) < 0)
- H5E_THROW(FALSE, H5E_tools_min_id_g, "H5Sget_simple_extent_ndims failed");
+ H5E_THROW(FALSE, H5E_tools_min_id_g, "H5Sget_simple_extent_ndims failed")
  ndims = (unsigned)sndims;
 
  if((dtype = H5Dget_type(region_id)) < 0)