HDFFV-10903 merge updated changes

9 files changed, 182 insertions, 20 deletions

diff --git a/config/cmake/FindHDFS.cmake b/config/cmake/FindHDFS.cmake
new file mode 100644
index 0000000..e401a94
--- /dev/null
+++ b/config/cmake/FindHDFS.cmake
@@ -0,0 +1,70 @@
+
+# DerivedFrom: https://github.com/cloudera/Impala/blob/cdh5-trunk/cmake_modules/FindHDFS.cmake
+# - Find HDFS (hdfs.h and libhdfs.so)
+# This module defines
+#  Hadoop_VERSION, version string of ant if found
+#  HDFS_INCLUDE_DIR, directory containing hdfs.h
+#  HDFS_LIBRARIES, location of libhdfs.so
+#  HDFS_FOUND, whether HDFS is found.
+
+exec_program($ENV{HADOOP_HOME}/bin/hadoop ARGS version OUTPUT_VARIABLE Hadoop_VERSION
+             RETURN_VALUE Hadoop_RETURN)
+
+# currently only looking in HADOOP_HOME
+find_path(HDFS_INCLUDE_DIR hdfs.h PATHS
+  $ENV{HADOOP_HOME}/include/
+  # make sure we don't accidentally pick up a different version
+  NO_DEFAULT_PATH
+)
+
+if ("${CMAKE_SIZEOF_VOID_P}" STREQUAL "8")
+  set(arch_hint "x64")
+elseif ("$ENV{LIB}" MATCHES "(amd64|ia64)")
+  set(arch_hint "x64")
+else ()
+  set(arch_hint "x86")
+endif()
+
+message(STATUS "Architecture: ${arch_hint}")
+
+if ("${arch_hint}" STREQUAL "x64")
+  set(HDFS_LIB_PATHS $ENV{HADOOP_HOME}/lib/native)
+else ()
+  set(HDFS_LIB_PATHS $ENV{HADOOP_HOME}/lib/native)
+endif ()
+
+message(STATUS "HDFS_LIB_PATHS: ${HDFS_LIB_PATHS}")
+
+find_library(HDFS_LIB NAMES hdfs PATHS
+  ${HDFS_LIB_PATHS}
+  # make sure we don't accidentally pick up a different version
+  NO_DEFAULT_PATH
+)
+
+if (HDFS_LIB)
+  set(HDFS_FOUND TRUE)
+  set(HDFS_LIBRARIES ${HDFS_LIB})
+  set(HDFS_STATIC_LIB ${HDFS_LIB_PATHS}/${CMAKE_STATIC_LIBRARY_PREFIX}hdfs${CMAKE_STATIC_LIBRARY_SUFFIX})
+
+  add_library(hdfs_static STATIC IMPORTED)
+  set_target_properties(hdfs_static PROPERTIES IMPORTED_LOCATION ${HDFS_STATIC_LIB})
+else ()
+  set(HDFS_FOUND FALSE)
+endif ()
+
+if (HDFS_FOUND)
+  if (NOT HDFS_FIND_QUIETLY)
+    message(STATUS "${Hadoop_VERSION}")
+    message(STATUS "HDFS_INCLUDE_DIR: ${HDFS_INCLUDE_DIR}")
+    message(STATUS "HDFS_LIBRARIES: ${HDFS_LIBRARIES}")
+    message(STATUS "hdfs_static: ${HDFS_STATIC_LIB}")
+  endif ()
+else ()
+  message(FATAL_ERROR "HDFS includes and libraries NOT found."
+    "(${HDFS_INCLUDE_DIR}, ${HDFS_LIB})")
+endif ()
+
+mark_as_advanced(
+  HDFS_LIBRARIES
+  HDFS_INCLUDE_DIR
+)
diff --git a/config/cmake/HDFCompilerFlags.cmake b/config/cmake/HDFCompilerFlags.cmake
index aea417a..37ddcbb 100644
--- a/config/cmake/HDFCompilerFlags.cmake
+++ b/config/cmake/HDFCompilerFlags.cmake
@@ -212,7 +212,8 @@ if (NOT MSVC AND CMAKE_COMPILER_IS_GNUCC)
     if (CMAKE_C_COMPILER_ID STREQUAL "GNU" AND NOT CMAKE_C_COMPILER_VERSION VERSION_LESS 9.0)
       set (H5_CFLAGS4 "${H5_CFLAGS4} -Wattribute-alias=2 -Wmissing-profile")
     endif ()
-
+elseif (CMAKE_C_COMPILER_ID STREQUAL "PGI")
+  set (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -Minform=inform")
 endif ()
 
 #-----------------------------------------------------------------------------
@@ -339,3 +340,76 @@ endif ()
 if (CMAKE_COMPILER_IS_GNUCXX AND CMAKE_CXX_COMPILER_LOADED)
   set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fmessage-length=0")
 endif ()
+
+#-----------------------------------------------------------------------------
+# Option for --enable-asserts
+# By default, CMake adds NDEBUG to CMAKE_${lang}_FLAGS for Release build types
+# This option will force/override the default setting for all configurations
+#-----------------------------------------------------------------------------
+option (HDF5_ENABLE_ASSERTS "Determines whether NDEBUG is defined to control assertions." OFF)
+if (HDF5_ENABLE_ASSERTS)
+  add_compile_options ("-UNDEBUG")
+else ()
+  add_compile_options ("-DNDEBUG")
+endif ()
+MARK_AS_ADVANCED (HDF5_ENABLE_ASSERTS)
+
+#-----------------------------------------------------------------------------
+# Option for --enable-symbols
+# This option will force/override the default setting for all configurations
+#-----------------------------------------------------------------------------
+option (HDF5_ENABLE_SYMBOLS "Add debug symbols to the library independent of the build mode and optimization level." OFF)
+if (HDF5_ENABLE_SYMBOLS)
+  if (CMAKE_C_COMPILER_ID STREQUAL "Intel")
+    set (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -g")
+  elseif (CMAKE_C_COMPILER_ID STREQUAL "GNU")
+    set (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -g -fno-omit-frame-pointer")
+  endif ()
+  if(CMAKE_CXX_COMPILER_LOADED)
+    if (CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
+      set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -g")
+    elseif (CMAKE_CXX_COMPILER_ID STREQUAL "GNU")
+      set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -g")
+    endif ()
+  endif ()
+else ()
+  if (CMAKE_C_COMPILER_ID STREQUAL "Intel")
+    set (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -Wl,-s")
+  elseif (CMAKE_C_COMPILER_ID STREQUAL "GNU")
+    set (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -s")
+  endif ()
+  if(CMAKE_CXX_COMPILER_LOADED)
+    if (CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
+      set (CMAKE_CXX_FLAGS "${CMAKE_C_FLAGS} -Wl,-s")
+    elseif (CMAKE_CXX_COMPILER_ID STREQUAL "GNU")
+      set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -s")
+    endif ()
+  endif ()
+endif ()
+MARK_AS_ADVANCED (HDF5_ENABLE_SYMBOLS)
+
+#-----------------------------------------------------------------------------
+# Option for --enable-profiling
+# This option will force/override the default setting for all configurations
+#-----------------------------------------------------------------------------
+option (HDF5_ENABLE_PROFILING "Enable profiling flags independently from the build mode." OFF)
+if (HDF5_ENABLE_PROFILING)
+  set (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${PROFILE_CFLAGS}")
+  if(CMAKE_CXX_COMPILER_LOADED)
+    set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${PROFILE_CXXFLAGS}")
+  endif ()
+endif ()
+MARK_AS_ADVANCED (HDF5_ENABLE_PROFILING)
+
+#-----------------------------------------------------------------------------
+# Option for --enable-optimization
+# This option will force/override the default setting for all configurations
+#-----------------------------------------------------------------------------
+option (HDF5_ENABLE_OPTIMIZATION "Enable optimization flags/settings independently from the build mode" OFF)
+if (HDF5_ENABLE_OPTIMIZATION)
+  set (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${OPTIMIZE_CFLAGS}")
+  if(CMAKE_CXX_COMPILER_LOADED)
+    set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OPTIMIZE_CXXFLAGS}")
+  endif ()
+endif ()
+MARK_AS_ADVANCED (HDF5_ENABLE_OPTIMIZATION)
diff --git a/config/cmake/libhdf5.settings.cmake.in b/config/cmake/libhdf5.settings.cmake.in
index 3451545..8397d68 100644
--- a/config/cmake/libhdf5.settings.cmake.in
+++ b/config/cmake/libhdf5.settings.cmake.in
@@ -14,10 +14,10 @@ General Information:
 Compiling Options:
 ------------------
                      Build Mode: @CMAKE_BUILD_TYPE@
-              Debugging Symbols: @SYMBOLS@
-                        Asserts: @ASSERTS@
-                      Profiling: @PROFILING@
-             Optimization Level: @OPTIMIZATION@
+              Debugging Symbols: @HDF5_ENABLE_SYMBOLS@
+                        Asserts: @HDF5_ENABLE_ASSERTS@
+                      Profiling: @HDF5_ENABLE_PROFILING@
+             Optimization Level: @HDF5_ENABLE_OPTIMIZATION@
 
 Linking Options:
 ----------------
diff --git a/java/src/jni/h5Constants.c b/java/src/jni/h5Constants.c
index f1bd951..f9b0cfd 100644
--- a/java/src/jni/h5Constants.c
+++ b/java/src/jni/h5Constants.c
@@ -438,7 +438,13 @@ Java_hdf_hdf5lib_HDF5Constants_H5FD_1DIRECT(JNIEnv *env, jclass cls) {
 JNIEXPORT jlong JNICALL
 Java_hdf_hdf5lib_HDF5Constants_H5FD_1FAMILY(JNIEnv *env, jclass cls) { return H5FD_FAMILY; }
 JNIEXPORT jlong JNICALL
-Java_hdf_hdf5lib_HDF5Constants_H5FD_1HDFS(JNIEnv *env, jclass cls) { return H5FD_HDFS; }
+Java_hdf_hdf5lib_HDF5Constants_H5FD_1HDFS(JNIEnv *env, jclass cls) {
+#ifdef H5_HAVE_LIBHDFS
+    return H5FD_HDFS;
+#else
+    return -1;
+#endif
+}
 JNIEXPORT jlong JNICALL
 Java_hdf_hdf5lib_HDF5Constants_H5FD_1LOG(JNIEnv *env, jclass cls) { return H5FD_LOG; }
 JNIEXPORT jlong JNICALL
@@ -448,7 +454,13 @@ Java_hdf_hdf5lib_HDF5Constants_H5FD_1MULTI(JNIEnv *env, jclass cls) { return H5F
 JNIEXPORT jlong JNICALL
 Java_hdf_hdf5lib_HDF5Constants_H5FD_1SEC2(JNIEnv *env, jclass cls) { return H5FD_SEC2; }
 JNIEXPORT jlong JNICALL
-Java_hdf_hdf5lib_HDF5Constants_H5FD_1ROS3(JNIEnv *env, jclass cls) { return H5FD_ROS3; }
+Java_hdf_hdf5lib_HDF5Constants_H5FD_1ROS3(JNIEnv *env, jclass cls) {
+#ifdef H5_HAVE_ROS3_VFD
+    return H5FD_ROS3;
+#else
+    return -1;
+#endif
+}
 JNIEXPORT jlong JNICALL
 Java_hdf_hdf5lib_HDF5Constants_H5FD_1STDIO(JNIEnv *env, jclass cls) { return H5FD_STDIO; }
 JNIEXPORT jlong JNICALL
diff --git a/java/src/jni/h5fImp.c b/java/src/jni/h5fImp.c
index 2924d8f..115e8f4 100644
--- a/java/src/jni/h5fImp.c
+++ b/java/src/jni/h5fImp.c
@@ -161,10 +161,6 @@ Java_hdf_hdf5lib_H5_H5Fis_1hdf5
 
     UNUSED(clss);
 
-#ifdef H5_NO_DEPRECATED_SYMBOLS
-    H5_UNIMPLEMENTED(ENVONLY, "H5Fis_hdf5: not implemented");
-#endif
-
     if (NULL == name)
         H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Fis_hdf5: file name is NULL");
 
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index a3f98ed..fe93d54 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -1079,7 +1079,6 @@ if (NOT ONLY_SHARED_LIBS)
       PUBLIC
           ${HDF_EXTRA_C_FLAGS}
           ${HDF_EXTRA_FLAGS}
-          $<IF:$<CONFIG:Debug>,DEBUG,NDEBUG>
       PRIVATE
           $<$<BOOL:${HDF5_ENABLE_TRACE}>:H5_DEBUG_API>  # Enable tracing of the API
           $<$<BOOL:${HDF5_ENABLE_DEBUG_APIS}>:H5Z_DEBUG;H5T_DEBUG;H5ST_DEBUG;H5S_DEBUG;H5O_DEBUG;H5I_DEBUG;H5HL_DEBUG;H5F_DEBUG;H5D_DEBUG;H5B2_DEBUG;H5AC_DEBUG>
@@ -1117,7 +1116,6 @@ if (BUILD_SHARED_LIBS)
           "H5_BUILT_AS_DYNAMIC_LIB"
           ${HDF_EXTRA_C_FLAGS}
           ${HDF_EXTRA_FLAGS}
-          $<IF:$<CONFIG:Debug>,DEBUG,NDEBUG>
       PRIVATE
           $<$<BOOL:${HDF5_ENABLE_THREADSAFE}>:H5_HAVE_THREADSAFE>
           $<$<BOOL:${HDF5_ENABLE_TRACE}>:H5_DEBUG_API>  # Enable tracing of the API
diff --git a/tools/lib/h5tools_dump.c b/tools/lib/h5tools_dump.c
index 8b36280..beb397c 100644
--- a/tools/lib/h5tools_dump.c
+++ b/tools/lib/h5tools_dump.c
@@ -2289,6 +2289,14 @@ h5tools_print_datatype(FILE *stream, h5tools_str_t *buffer, const h5tool_format_
             h5tools_render_element(stream, info, ctx, buffer, &curr_pos, (size_t)ncols, (hsize_t)0, (hsize_t)0);
 
             H5free_memory(ttag);
+
+            if((size = H5Tget_size(type)) <= 0) {
+                ctx->need_prefix = TRUE;
+
+                h5tools_str_reset(buffer);
+                h5tools_str_append(buffer, "OPAQUE_SIZE \"%s\";", size);
+                h5tools_render_element(stream, info, ctx, buffer, &curr_pos, (size_t)ncols, (hsize_t)0, (hsize_t)0);
+            }
         }
         ctx->indent_level--;
 
diff --git a/tools/test/h5copy/testh5copy.sh.in b/tools/test/h5copy/testh5copy.sh.in
index 50758b5..2440ca4 100644
--- a/tools/test/h5copy/testh5copy.sh.in
+++ b/tools/test/h5copy/testh5copy.sh.in
@@ -504,22 +504,21 @@ fi
     TOOLTEST -i $TESTFILE -o $TESTDIR/dsrename.out.h5 -v -s compound   -d rename
 
     echo "Test copying empty, 'full' & 'nested' groups"
-if test $USE_FILTER_DEFLATE = "yes" ; then
     TOOLTEST -i $TESTFILE -o $TESTDIR/grp_empty.out.h5 -v -s grp_empty  -d grp_empty
-fi
+if test $USE_FILTER_DEFLATE = "yes" ; then
     TOOLTEST -i $TESTFILE -o $TESTDIR/grp_dsets.out.h5 -v -s grp_dsets  -d grp_dsets
     TOOLTEST -i $TESTFILE -o $TESTDIR/grp_nested.out.h5 -v -s grp_nested -d grp_nested
+fi
     TOOLTEST -i $TESTFILE -o $TESTDIR/grp_attr.out.h5 -v -s grp_attr -d grp_attr
 
-if test $USE_FILTER_DEFLATE = "yes" ; then
     echo "Test copying dataset within group in source file to group in destination"
     TOOLTEST_PREFILL -i $TESTFILE -o $TESTDIR/simple_group.out.h5 grp_dsets grp_dsets /grp_dsets/simple /grp_dsets/simple_group
+if test $USE_FILTER_DEFLATE = "yes" ; then
     echo "Test copying & renaming group"
     TOOLTEST -i $TESTFILE -o $TESTDIR/grp_rename.out.h5 -v -s grp_dsets  -d grp_rename
-fi
-
     echo "Test copying 'full' group hierarchy into group in destination file"
     TOOLTEST_PREFILL -i $TESTFILE -o $TESTDIR/grp_dsets_rename.out.h5 grp_dsets grp_rename grp_dsets /grp_rename/grp_dsets
+fi
 
     echo "Test copying objects into group hier. that doesn't exist yet in destination file"
     TOOLTEST -i $TESTFILE -o $TESTDIR/A_B1_simple.out.h5 -vp -s simple    -d /A/B1/simple
diff --git a/tools/test/h5repack/h5repack.sh.in b/tools/test/h5repack/h5repack.sh.in
index a36eb08..1586485 100644
--- a/tools/test/h5repack/h5repack.sh.in
+++ b/tools/test/h5repack/h5repack.sh.in
@@ -1387,7 +1387,12 @@ TOOLTEST add_alignment $arg
 TOOLTEST upgrade_layout h5repack_layouto.h5
 
 # test for datum size > H5TOOLS_MALLOCSIZE
-TOOLTEST gt_mallocsize h5repack_objs.h5 -f GZIP=1
+arg="h5repack_objs.h5 -f GZIP=1"
+if test $USE_FILTER_DEFLATE != "yes" ; then
+ SKIP $arg
+else
+ TOOLTEST gt_mallocsize $arg
+fi
 
 # Check repacking file with committed datatypes in odd configurations
 TOOLTEST committed_dt h5repack_named_dtypes.h5
@@ -1458,7 +1463,7 @@ VERIFY_SUPERBLOCK 1 2 2 h5repack_layout.h5 -j 1 -k 2 h5repack_layout.h5
 # -j 2 -k 2, superblock will be 3
 VERIFY_SUPERBLOCK 2 2 3 h5repack_layout.h5 -j 2 -k 2 h5repack_layout.h5
 # -j 0 -k 1, file cannot be opened
-VERIFY_INVALIDBOUNDS 0 1 bounds_latest_latest.h5 
+VERIFY_INVALIDBOUNDS 0 1 bounds_latest_latest.h5
 
 # Clean up temporary files/directories
 CLEAN_TESTFILES_AND_TESTDIR