Merge remote-tracking branch 'origin/develop' into monotonic_timer

7 files changed, 146 insertions, 139 deletions

diff --git a/java/examples/groups/CMakeLists.txt b/java/examples/groups/CMakeLists.txt
index bb5f80f..c2c7d0f 100644
--- a/java/examples/groups/CMakeLists.txt
+++ b/java/examples/groups/CMakeLists.txt
@@ -1,13 +1,8 @@
-cmake_minimum_required (VERSION 3.2.2)
-PROJECT (HDFJAVA_EXAMPLES_GROUPS Java)
+cmake_minimum_required (VERSION 3.12)
+project (HDFJAVA_EXAMPLES_GROUPS Java)
 
 set (CMAKE_VERBOSE_MAKEFILE 1)
 
-INCLUDE_DIRECTORIES (
-    ${HDF5_JAVA_JNI_BINARY_DIR}
-    ${HDF5_JAVA_HDF5_LIB_DIR}
-)
-
 set (HDF_JAVA_EXAMPLES
     H5Ex_G_Create
     H5Ex_G_Iterate
@@ -18,7 +13,7 @@ set (HDF_JAVA_EXAMPLES
     H5Ex_G_Visit
 )
 
-if (WIN32)
+if (WIN32 OR MINGW)
   set (CMAKE_JAVA_INCLUDE_FLAG_SEP ";")
 else ()
   set (CMAKE_JAVA_INCLUDE_FLAG_SEP ":")
@@ -60,69 +55,55 @@ foreach (h5_file ${HDF_JAVA_TEST_FILES})
 endforeach ()
 add_custom_target(H5Ex_G_Visit_files ALL COMMENT "Copying files needed by H5Ex_G_Visit tests" DEPENDS ${H5Ex_G_Visit_files_list})
 
-MACRO (ADD_H5_TEST resultfile resultcode)
-  if (CMAKE_BUILD_TYPE MATCHES Debug)
-    if (WIN32)
-      set (CMD_ARGS "-Dhdf.hdf5lib.H5.loadLibraryName=hdf5_java_D;")
-    else ()
-      set (CMD_ARGS "-Dhdf.hdf5lib.H5.loadLibraryName=hdf5_java_debug;")
-    endif ()
-  endif ()
-  add_test (
-      NAME JAVA_groups-${resultfile}
-      COMMAND "${CMAKE_COMMAND}"
-          -D "TEST_TESTER=${CMAKE_Java_RUNTIME};${CMAKE_Java_RUNTIME_FLAGS}"
-          -D "TEST_PROGRAM=examples.groups.${resultfile}"
-          -D "TEST_ARGS:STRING=${CMD_ARGS}${ARGN}"
-          -D "TEST_CLASSPATH:STRING=${CMAKE_JAVA_CLASSPATH}${CMAKE_JAVA_INCLUDE_FLAG_SEP}${${resultfile}_JAR_FILE}"
-          -D "TEST_LIBRARY_DIRECTORY=${CMAKE_TEST_OUTPUT_DIRECTORY}"
-          -D "TEST_FOLDER=${HDFJAVA_EXAMPLES_BINARY_DIR}"
-          -D "TEST_OUTPUT=groups/${resultfile}.out"
-          -D "TEST_EXPECT=${resultcode}"
-          -D "TEST_REFERENCE=groups/${resultfile}.txt"
-          -P "${HDF_RESOURCES_DIR}/jrunTest.cmake"
-  )
-  if (NOT "${last_test}" STREQUAL "")
-    set_tests_properties (JAVA_groups-${resultfile} PROPERTIES DEPENDS ${last_test})
-  endif ()
-  set (last_test "JAVA_groups-${resultfile}")
-ENDMACRO ()
+if (BUILD_TESTING AND HDF5_TEST_EXAMPLES AND HDF5_TEST_SERIAL)
+  get_property (target_name TARGET ${HDF5_JAVA_JNI_LIB_TARGET} PROPERTY OUTPUT_NAME)
+  set (CMD_ARGS "-Dhdf.hdf5lib.H5.loadLibraryName=${target_name}$<$<CONFIG:Debug>:${CMAKE_DEBUG_POSTFIX}>;")
 
-if (BUILD_TESTING)
   foreach (example ${HDF_JAVA_EXAMPLES})
-    if (NOT ${example} STREQUAL "H5Ex_G_Iterate" AND NOT ${example} STREQUAL "H5Ex_G_Visit")
-      if (${example} STREQUAL "H5Ex_G_Compact")
+    if (NOT example STREQUAL "H5Ex_G_Iterate" AND NOT example STREQUAL "H5Ex_G_Visit")
+      if (example STREQUAL "H5Ex_G_Compact")
         add_test (
-            NAME JAVA_groups-${example}-clear-h5s
-            COMMAND    ${CMAKE_COMMAND}
-                -E remove
+            NAME JAVA_groups-${example}-clear-objects
+            COMMAND ${CMAKE_COMMAND} -E remove
                 ${HDFJAVA_EXAMPLES_BINARY_DIR}/${example}1.h5
                 ${HDFJAVA_EXAMPLES_BINARY_DIR}/${example}2.h5
         )
       else ()
         add_test (
-            NAME JAVA_groups-${example}-clear-h5s
-            COMMAND    ${CMAKE_COMMAND}
-                -E remove
-                ${HDFJAVA_EXAMPLES_BINARY_DIR}/${example}.h5
+            NAME JAVA_groups-${example}-clear-objects
+            COMMAND ${CMAKE_COMMAND} -E remove ${HDFJAVA_EXAMPLES_BINARY_DIR}/${example}.h5
         )
       endif ()
-      if (NOT "${last_test}" STREQUAL "")
-        set_tests_properties (JAVA_groups-${example}-clear-h5s PROPERTIES DEPENDS ${last_test})
-      endif ()
-      set (last_test "JAVA_groups-${example}-clear-h5s")
+    else ()
+      add_test (
+          NAME JAVA_groups-${example}-clear-objects
+          COMMAND ${CMAKE_COMMAND} -E echo "${HDFJAVA_EXAMPLES_BINARY_DIR}/${example}.h5 exists"
+      )
     endif ()
+
     add_test (
         NAME JAVA_groups-${example}-copy-objects
-        COMMAND    ${CMAKE_COMMAND}
-            -E copy_if_different
+        COMMAND ${CMAKE_COMMAND} -E copy_if_different
             ${HDFJAVA_EXAMPLES_SOURCE_DIR}/testfiles/examples.groups.${example}.txt
             ${HDFJAVA_EXAMPLES_GROUPS_BINARY_DIR}/${example}.txt
     )
-    if (NOT "${last_test}" STREQUAL "")
-      set_tests_properties (JAVA_groups-${example}-copy-objects PROPERTIES DEPENDS ${last_test})
-    endif ()
-    set (last_test "JAVA_groups-${example}-copy-objects")
-    ADD_H5_TEST (${example} 0)
+    set_tests_properties (JAVA_groups-${example}-copy-objects PROPERTIES DEPENDS JAVA_groups-${example}-clear-objects)
+    add_test (
+        NAME JAVA_groups-${example}
+        COMMAND "${CMAKE_COMMAND}"
+            -D "TEST_TESTER=${CMAKE_Java_RUNTIME};${CMAKE_Java_RUNTIME_FLAGS}"
+            -D "TEST_PROGRAM=examples.groups.${example}"
+            -D "TEST_ARGS:STRING=${CMD_ARGS}"
+            -D "TEST_CLASSPATH:STRING=${CMAKE_JAVA_CLASSPATH}${CMAKE_JAVA_INCLUDE_FLAG_SEP}${${example}_JAR_FILE}"
+            -D "TEST_LIBRARY_DIRECTORY=${CMAKE_TEST_OUTPUT_DIRECTORY}"
+            -D "TEST_FOLDER=${HDFJAVA_EXAMPLES_BINARY_DIR}"
+            -D "TEST_OUTPUT=groups/${example}.out"
+            -D "TEST_EXPECT=0"
+            -D "TEST_REFERENCE=groups/${example}.txt"
+            -P "${HDF_RESOURCES_DIR}/jrunTest.cmake"
+    )
+    set_tests_properties (JAVA_groups-${example} PROPERTIES
+        DEPENDS JAVA_groups-${example}-copy-objects
+    )
   endforeach ()
 endif ()
diff --git a/java/examples/groups/H5Ex_G_Intermediate.java b/java/examples/groups/H5Ex_G_Intermediate.java
index f7d5a50..e97e5f8 100644
--- a/java/examples/groups/H5Ex_G_Intermediate.java
+++ b/java/examples/groups/H5Ex_G_Intermediate.java
@@ -19,8 +19,8 @@ package examples.groups;
 
 import hdf.hdf5lib.H5;
 import hdf.hdf5lib.HDF5Constants;
-import hdf.hdf5lib.callbacks.H5O_iterate_cb;
 import hdf.hdf5lib.callbacks.H5O_iterate_t;
+import hdf.hdf5lib.callbacks.H5O_iterate_opdata_t;
 import hdf.hdf5lib.structs.H5O_info_t;
 
 import java.util.ArrayList;
@@ -53,9 +53,9 @@ public class H5Ex_G_Intermediate {
             // Print all the objects in the file_ids to show that intermediate group_ids have been created.
             System.out.println("Objects in the file_id:");
 
-            // H5O_iterate_t iter_data = null;
-            H5O_iterate_t iter_data = new H5O_iter_data();
-            H5O_iterate_cb iter_cb = new H5O_iter_callback();
+            // H5O_iterate_opdata_t iter_data = null;
+            H5O_iterate_opdata_t iter_data = new H5O_iter_data();
+            H5O_iterate_t iter_cb = new H5O_iter_callback();
 
             H5.H5Ovisit(file_id, HDF5Constants.H5_INDEX_NAME, HDF5Constants.H5_ITER_NATIVE, iter_cb, iter_data);
         }
@@ -92,12 +92,12 @@ public class H5Ex_G_Intermediate {
         }
     }
 
-    private class H5O_iter_data implements H5O_iterate_t {
+    private class H5O_iter_data implements H5O_iterate_opdata_t {
         public ArrayList<idata> iterdata = new ArrayList<idata>();
     }
 
-    private class H5O_iter_callback implements H5O_iterate_cb {
-        public int callback(long group, String name, H5O_info_t info, H5O_iterate_t op_data) {
+    private class H5O_iter_callback implements H5O_iterate_t {
+        public int callback(long group, String name, H5O_info_t info, H5O_iterate_opdata_t op_data) {
             idata id = new idata(name, info.type);
             ((H5O_iter_data) op_data).iterdata.add(id);
 
diff --git a/java/examples/groups/H5Ex_G_Iterate.java b/java/examples/groups/H5Ex_G_Iterate.java
index 3c9ca82..5acbf65 100644
--- a/java/examples/groups/H5Ex_G_Iterate.java
+++ b/java/examples/groups/H5Ex_G_Iterate.java
@@ -19,6 +19,7 @@ package examples.groups;
 
 import hdf.hdf5lib.H5;
 import hdf.hdf5lib.HDF5Constants;
+import hdf.hdf5lib.structs.H5O_token_t;
 
 import java.util.EnumSet;
 import java.util.HashMap;
@@ -75,8 +76,8 @@ public class H5Ex_G_Iterate {
                 String[] oname = new String[count];
                 int[] otype = new int[count];
                 int[] ltype = new int[count];
-                long[] orefs = new long[count];
-                H5.H5Gget_obj_info_all(file_id, DATASETNAME, oname, otype, ltype, orefs, HDF5Constants.H5_INDEX_NAME);
+                H5O_token_t[] otokens = new H5O_token_t[count];
+                H5.H5Gget_obj_info_all(file_id, DATASETNAME, oname, otype, ltype, otokens, HDF5Constants.H5_INDEX_NAME);
 
                 // Get type of the object and display its name and type.
                 for (int indx = 0; indx < otype.length; indx++) {
diff --git a/java/examples/groups/H5Ex_G_Traverse.java b/java/examples/groups/H5Ex_G_Traverse.java
index 2a2cba3..6225a9e 100644
--- a/java/examples/groups/H5Ex_G_Traverse.java
+++ b/java/examples/groups/H5Ex_G_Traverse.java
@@ -25,22 +25,22 @@ package examples.groups;
 
 import hdf.hdf5lib.H5;
 import hdf.hdf5lib.HDF5Constants;
-import hdf.hdf5lib.callbacks.H5L_iterate_cb;
 import hdf.hdf5lib.callbacks.H5L_iterate_t;
+import hdf.hdf5lib.callbacks.H5L_iterate_opdata_t;
 import hdf.hdf5lib.structs.H5L_info_t;
 import hdf.hdf5lib.structs.H5O_info_t;
 import examples.groups.H5Ex_G_Iterate.H5O_type;
 
-class opdata implements H5L_iterate_t {
+class opdata implements H5L_iterate_opdata_t {
     int recurs;
     opdata prev;
-    long addr;
+    H5O_token_t obj_token;
 }
 
 public class H5Ex_G_Traverse {
 
     private static String FILE = "h5ex_g_traverse.h5";
-    public static H5L_iterate_cb iter_cb = new H5L_iter_callbackT();
+    public static H5L_iterate_t iter_cb = new H5L_iter_callbackT();
 
     private static void OpenGroup() {
         long file_id = -1;
@@ -54,7 +54,7 @@ public class H5Ex_G_Traverse {
                 infobuf = H5.H5Oget_info(file_id);
                 od.recurs = 0;
                 od.prev = null;
-                od.addr = infobuf.addr;
+                od.obj_token = infobuf.token;
             }
         }
         catch (Exception e) {
@@ -64,7 +64,7 @@ public class H5Ex_G_Traverse {
         // Print the root group and formatting, begin iteration.
         try {
             System.out.println("/ {");
-            // H5L_iterate_cb iter_cb = new H5L_iter_callbackT();
+            // H5L_iterate_t iter_cb = new H5L_iter_callbackT();
             H5.H5Literate(file_id, HDF5Constants.H5_INDEX_NAME, HDF5Constants.H5_ITER_NATIVE, 0L, iter_cb, od);
             System.out.println("}");
         }
@@ -87,8 +87,8 @@ public class H5Ex_G_Traverse {
     }
 }
 
-class H5L_iter_callbackT implements H5L_iterate_cb {
-    public int callback(long group, String name, H5L_info_t info, H5L_iterate_t op_data) {
+class H5L_iter_callbackT implements H5L_iterate_t {
+    public int callback(long group, String name, H5L_info_t info, H5L_iterate_opdata_t op_data) {
 
         H5O_info_t infobuf;
         int return_val = 0;
@@ -105,7 +105,7 @@ class H5L_iter_callbackT implements H5L_iterate_cb {
             switch (H5O_type.get(infobuf.type)) {
             case H5O_TYPE_GROUP:
                 System.out.println("Group: " + name + " { ");
-                // Check group address against linked list of operator
+                // Check group object token against linked list of operator
                 // data structures. We will always run the check, as the
                 // reference count cannot be relied upon if there are
                 // symbolic links, and H5Oget_info_by_name always follows
@@ -114,7 +114,7 @@ class H5L_iter_callbackT implements H5L_iterate_cb {
                 // links, however it could still fail if an object's
                 // reference count was manually manipulated with
                 // H5Odecr_refcount.
-                if (group_check(od, infobuf.addr)) {
+                if (group_check(od, infobuf.token)) {
                     for (int i = 0; i < spaces; i++)
                         System.out.print(" ");
                     System.out.println("  Warning: Loop detected!");
@@ -127,8 +127,8 @@ class H5L_iter_callbackT implements H5L_iterate_cb {
                     opdata nextod = new opdata();
                     nextod.recurs = od.recurs + 1;
                     nextod.prev = od;
-                    nextod.addr = infobuf.addr;
-                    H5L_iterate_cb iter_cb2 = new H5L_iter_callbackT();
+                    nextod.obj_token = infobuf.token;
+                    H5L_iterate_t iter_cb2 = new H5L_iter_callbackT();
                     return_val = H5.H5Literate_by_name(group, name, HDF5Constants.H5_INDEX_NAME,
                             HDF5Constants.H5_ITER_NATIVE, 0L, iter_cb2, nextod, HDF5Constants.H5P_DEFAULT);
                 }
@@ -153,13 +153,13 @@ class H5L_iter_callbackT implements H5L_iterate_cb {
         return return_val;
     }
 
-    public boolean group_check(opdata od, long target_addr) {
-        if (od.addr == target_addr)
-            return true; // Addresses match
+    public boolean group_check(opdata od, H5O_token_t target_token) {
+        if (od.obj_token.equals(target_token))
+            return true; // Object tokens match
         else if (od.recurs == 0)
             return false; // Root group reached with no matches
         else
-            return group_check(od.prev, target_addr); // Recursively examine the next node
+            return group_check(od.prev, target_token); // Recursively examine the next node
     }
 
 }
diff --git a/java/examples/groups/H5Ex_G_Visit.java b/java/examples/groups/H5Ex_G_Visit.java
index f91c707..4255316 100644
--- a/java/examples/groups/H5Ex_G_Visit.java
+++ b/java/examples/groups/H5Ex_G_Visit.java
@@ -23,10 +23,10 @@ package examples.groups;
 
 import hdf.hdf5lib.H5;
 import hdf.hdf5lib.HDF5Constants;
-import hdf.hdf5lib.callbacks.H5L_iterate_cb;
 import hdf.hdf5lib.callbacks.H5L_iterate_t;
-import hdf.hdf5lib.callbacks.H5O_iterate_cb;
+import hdf.hdf5lib.callbacks.H5L_iterate_opdata_t;
 import hdf.hdf5lib.callbacks.H5O_iterate_t;
+import hdf.hdf5lib.callbacks.H5O_iterate_opdata_t;
 import hdf.hdf5lib.structs.H5L_info_t;
 import hdf.hdf5lib.structs.H5O_info_t;
 
@@ -55,13 +55,13 @@ public class H5Ex_G_Visit {
 
             // Begin iteration using H5Ovisit
             System.out.println("Objects in the file:");
-            H5O_iterate_t iter_data = new H5O_iter_data();
-            H5O_iterate_cb iter_cb = new H5O_iter_callback();
+            H5O_iterate_opdata_t iter_data = new H5O_iter_data();
+            H5O_iterate_t iter_cb = new H5O_iter_callback();
             H5.H5Ovisit(file_id, HDF5Constants.H5_INDEX_NAME, HDF5Constants.H5_ITER_NATIVE, iter_cb, iter_data);
             System.out.println();
             // Repeat the same process using H5Lvisit
-            H5L_iterate_t iter_data2 = new H5L_iter_data();
-            H5L_iterate_cb iter_cb2 = new H5L_iter_callback();
+            H5L_iterate_opdata_t iter_data2 = new H5L_iter_data();
+            H5L_iterate_t iter_cb2 = new H5L_iter_callback();
             System.out.println("Links in the file:");
             H5.H5Lvisit(file_id, HDF5Constants.H5_INDEX_NAME, HDF5Constants.H5_ITER_NATIVE, iter_cb2, iter_data2);
 
@@ -91,12 +91,12 @@ public class H5Ex_G_Visit {
         }
     }
 
-    private class H5L_iter_data implements H5L_iterate_t {
+    private class H5L_iter_data implements H5L_iterate_opdata_t {
         public ArrayList<idata> iterdata = new ArrayList<idata>();
     }
 
-    private class H5L_iter_callback implements H5L_iterate_cb {
-        public int callback(long group, String name, H5L_info_t info, H5L_iterate_t op_data) {
+    private class H5L_iter_callback implements H5L_iterate_t {
+        public int callback(long group, String name, H5L_info_t info, H5L_iterate_opdata_t op_data) {
 
             idata id = new idata(name, info.type);
             ((H5L_iter_data) op_data).iterdata.add(id);
@@ -107,8 +107,8 @@ public class H5Ex_G_Visit {
                 // Get type of the object and display its name and type. The name of the object is passed to this
                 // function by the Library.
                 infobuf = H5.H5Oget_info_by_name(group, name, HDF5Constants.H5P_DEFAULT);
-                H5O_iterate_cb iter_cbO = new H5O_iter_callback();
-                H5O_iterate_t iter_dataO = new H5O_iter_data();
+                H5O_iterate_t iter_cbO = new H5O_iter_callback();
+                H5O_iterate_opdata_t iter_dataO = new H5O_iter_data();
                 ret = iter_cbO.callback(group, name, infobuf, iter_dataO);
             }
             catch (Exception e) {
@@ -119,12 +119,12 @@ public class H5Ex_G_Visit {
         }
     }
 
-    private class H5O_iter_data implements H5O_iterate_t {
+    private class H5O_iter_data implements H5O_iterate_opdata_t {
         public ArrayList<idata> iterdata = new ArrayList<idata>();
     }
 
-    private class H5O_iter_callback implements H5O_iterate_cb {
-        public int callback(long group, String name, H5O_info_t info, H5O_iterate_t op_data) {
+    private class H5O_iter_callback implements H5O_iterate_t {
+        public int callback(long group, String name, H5O_info_t info, H5O_iterate_opdata_t op_data) {
             idata id = new idata(name, info.type);
             ((H5O_iter_data) op_data).iterdata.add(id);
 
diff --git a/java/examples/groups/runExample.sh.in b/java/examples/groups/JavaGroupExample.sh.in
index 3732e7f..acc606f 100644
--- a/java/examples/groups/runExample.sh.in
+++ b/java/examples/groups/JavaGroupExample.sh.in
@@ -34,13 +34,13 @@ nerrors=0
 # where the libs exist
 HDFLIB_HOME="$top_srcdir/java/lib"
 BLDLIBDIR="$top_builddir/hdf5/lib"
-BLDREFDIR="./groups"
+BLDITERDIR="./groups"
 BLDDIR="."
 HDFTEST_HOME="$top_srcdir/java/examples/groups"
 JARFILE=jar@PACKAGE_TARNAME@-@PACKAGE_VERSION@.jar
 TESTJARFILE=jar@PACKAGE_TARNAME@groups.jar
 test -d $BLDLIBDIR || mkdir -p $BLDLIBDIR
-test -d $BLDREFDIR || mkdir -p $BLDREFDIR
+test -d $BLDITERDIR || mkdir -p $BLDITERDIR
 
 ######################################################################
 # library files
@@ -51,13 +51,15 @@ test -d $BLDREFDIR || mkdir -p $BLDREFDIR
 #       Comment '#' without space can be used.
 # --------------------------------------------------------------------
 LIST_LIBRARY_FILES="
-$HDFLIB_HOME/slf4j-api-1.7.5.jar
-$HDFLIB_HOME/ext/slf4j-simple-1.7.5.jar
 $top_builddir/src/.libs/libhdf5.*
 $top_builddir/java/src/jni/.libs/libhdf5_java.*
 $top_builddir/java/src/$JARFILE
 "
-LIST_REF_FILES="
+LIST_JAR_TESTFILES="
+$HDFLIB_HOME/slf4j-api-1.7.25.jar
+$HDFLIB_HOME/ext/slf4j-simple-1.7.25.jar
+"
+LIST_ITER_FILES="
 $HDFTEST_HOME/h5ex_g_iterate.h5
 $HDFTEST_HOME/h5ex_g_visit.h5
 "
@@ -75,6 +77,7 @@ $HDFTEST_HOME/../testfiles/examples.groups.H5Ex_G_Visit.txt
 # copy files from source dirs to test dir
 #
 COPY_LIBFILES="$LIST_LIBRARY_FILES"
+COPY_JARTESTFILES="$LIST_JAR_TESTFILES"
 
 COPY_LIBFILES_TO_BLDLIBDIR()
 {
@@ -102,6 +105,30 @@ COPY_LIBFILES_TO_BLDLIBDIR()
             fi
         fi
     done
+    # copy jar files. Used -f to make sure get a new copy
+    for tstfile in $COPY_JARTESTFILES
+    do
+        # ignore '#' comment
+        echo $tstfile | tr -d ' ' | grep '^#' > /dev/null
+        RET=$?
+        if [ $RET -eq 1 ]; then
+            # skip cp if srcdir is same as destdir
+            # this occurs when build/test performed in source dir and
+            # make cp fail
+            SDIR=`$DIRNAME $tstfile`
+            INODE_SDIR=`$LS -i -d $SDIR | $AWK -F' ' '{print $1}'`
+            INODE_DDIR=`$LS -i -d $BLDLIBDIR | $AWK -F' ' '{print $1}'`
+            if [ "$INODE_SDIR" != "$INODE_DDIR" ]; then
+                $CP -f $tstfile $BLDLIBDIR
+                if [ $? -ne 0 ]; then
+                    echo "Error: FAILED to copy $tstfile ."
+
+                    # Comment out this to CREATE expected file
+                    exit $EXIT_FAILURE
+                fi
+            fi
+        fi
+    done
 }
 
 CLEAN_LIBFILES_AND_BLDLIBDIR()
@@ -109,11 +136,14 @@ CLEAN_LIBFILES_AND_BLDLIBDIR()
     # skip rm if srcdir is same as destdir
     # this occurs when build/test performed in source dir and
     # make cp fail
-    SDIR=`$DIRNAME $HDFLIB_HOME/slf4j-api-1.7.5.jar`
+    SDIR=$HDFLIB_HOME
     INODE_SDIR=`$LS -i -d $SDIR | $AWK -F' ' '{print $1}'`
     INODE_DDIR=`$LS -i -d $BLDLIBDIR | $AWK -F' ' '{print $1}'`
     if [ "$INODE_SDIR" != "$INODE_DDIR" ]; then
-        $RM $BLDLIBDIR
+        for tstfile in $COPY_JARTESTFILES
+        do
+            $RM $BLDLIBDIR/tstfile
+        done
     fi
 }
 
@@ -149,24 +179,17 @@ COPY_DATAFILES_TO_BLDDIR()
 
 CLEAN_DATAFILES_AND_BLDDIR()
 {
-        $RM $BLDDIR/examples.groups.H5Ex_G_*.txt
-        $RM $BLDDIR/H5Ex_G_*.out
-        $RM $BLDDIR/H5Ex_G_*.h5
-        SDIR=`$DIRNAME $tstfile`
-        INODE_SDIR=`$LS -i -d $SDIR | $AWK -F' ' '{print $1}'`
-        INODE_DDIR=`$LS -i -d $BLDDIR | $AWK -F' ' '{print $1}'`
-        if [ "$INODE_SDIR" != "$INODE_DDIR" ]; then            SDIR=`$DIRNAME $tstfile`
-            $RM $BLDDIR/h5ex_g_iterate.h5
-            $RM $BLDDIR/h5ex_g_visit.h5
-        fi  
+    $RM $BLDDIR/examples.groups.H5Ex_G_*.txt
+    $RM $BLDDIR/H5Ex_G_*.out
+    $RM $BLDDIR/H5Ex_G_*.h5
 }
 
-COPY_REFFILES="$LIST_REF_FILES"
+COPY_ITERFILES="$LIST_ITER_FILES"
 
-COPY_REFFILES_TO_BLDREFDIR()
+COPY_ITERFILES_TO_BLDITERDIR()
 {
     # copy test files. Used -f to make sure get a new copy
-    for tstfile in $COPY_REFFILES
+    for tstfile in $COPY_ITERFILES
     do
         # ignore '#' comment
         echo $tstfile | tr -d ' ' | grep '^#' > /dev/null
@@ -177,9 +200,9 @@ COPY_REFFILES_TO_BLDREFDIR()
             # make cp fail
             SDIR=`$DIRNAME $tstfile`
             INODE_SDIR=`$LS -i -d $SDIR | $AWK -F' ' '{print $1}'`
-            INODE_DDIR=`$LS -i -d $BLDREFDIR | $AWK -F' ' '{print $1}'`
+            INODE_DDIR=`$LS -i -d $BLDITERDIR | $AWK -F' ' '{print $1}'`
             if [ "$INODE_SDIR" != "$INODE_DDIR" ]; then
-                $CP -f $tstfile $BLDREFDIR
+                $CP -f $tstfile $BLDITERDIR
                 if [ $? -ne 0 ]; then
                     echo "Error: FAILED to copy $tstfile ."
 
@@ -191,16 +214,16 @@ COPY_REFFILES_TO_BLDREFDIR()
     done
 }
 
-CLEAN_REFFILES_AND_BLDREFDIR()
+CLEAN_ITERFILES_AND_BLDITERDIR()
 {
     # skip rm if srcdir is same as destdir
     # this occurs when build/test performed in source dir and
     # make cp fail
     SDIR=`$DIRNAME $HDFTEST_HOME/h5ex_g_iterate.h5`
     INODE_SDIR=`$LS -i -d $SDIR | $AWK -F' ' '{print $1}'`
-    INODE_DDIR=`$LS -i -d $BLDREFDIR | $AWK -F' ' '{print $1}'`
+    INODE_DDIR=`$LS -i -d $BLDITERDIR | $AWK -F' ' '{print $1}'`
     if [ "$INODE_SDIR" != "$INODE_DDIR" ]; then
-        $RM $BLDREFDIR
+        $RM $BLDITERDIR
     fi
 }
 
@@ -223,9 +246,9 @@ JAVAEXEFLAGS=@H5_JAVAFLAGS@
 # prepare for test
 COPY_LIBFILES_TO_BLDLIBDIR
 COPY_DATAFILES_TO_BLDDIR
-COPY_REFFILES_TO_BLDREFDIR
+COPY_ITERFILES_TO_BLDITERDIR
 
-CPATH=".:"$BLDLIBDIR"/"$JARFILE":"$BLDLIBDIR"/slf4j-api-1.7.5.jar:"$BLDLIBDIR"/slf4j-simple-1.7.5.jar:"$TESTJARFILE""
+CPATH=".:"$BLDLIBDIR"/"$JARFILE":"$BLDLIBDIR"/slf4j-api-1.7.25.jar:"$BLDLIBDIR"/slf4j-simple-1.7.25.jar:"$TESTJARFILE""
 
 TEST=/usr/bin/test
 if [ ! -x /usr/bin/test ]
@@ -257,11 +280,6 @@ if $TEST -z "$LD_LIBRARY_PATH" ; then
 fi
 
 case  $os_name in
-    Darwin)
-    DYLD_LIBRARY_PATH=$BLDLIBDIR:$DYLD_LIBRARY_PATH
-    export DYLD_LIBRARY_PATH
-    LD_LIBRARY_PATH=$DYLD_LIBRARY_PATH
-    ;;
     *)
     LD_LIBRARY_PATH=$BLDLIBDIR:$LD_LIBRARY_PATH
     ;;
@@ -270,7 +288,8 @@ esac
 export LD_LIBRARY_PATH
 
 echo "$JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.groups.H5Ex_G_Create"
-($JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.groups.H5Ex_G_Create > H5Ex_G_Create.out)
+TESTING examples.groups.H5Ex_G_Create
+($RUNSERIAL $JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.groups.H5Ex_G_Create > H5Ex_G_Create.out)
 if diff H5Ex_G_Create.out examples.groups.H5Ex_G_Create.txt > /dev/null; then
     echo "  PASSED      groups.H5Ex_G_Create"
 else
@@ -279,7 +298,8 @@ else
 fi
 
 echo "$JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.groups.H5Ex_G_Iterate"
-($JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.groups.H5Ex_G_Iterate > H5Ex_G_Iterate.out)
+TESTING examples.groups.H5Ex_G_Iterate
+($RUNSERIAL $JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.groups.H5Ex_G_Iterate > H5Ex_G_Iterate.out)
 if diff H5Ex_G_Iterate.out examples.groups.H5Ex_G_Iterate.txt > /dev/null; then
     echo "  PASSED      groups.H5Ex_G_Iterate"
 else
@@ -288,7 +308,8 @@ else
 fi
 
 echo "$JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.groups.H5Ex_G_Compact"
-($JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.groups.H5Ex_G_Compact > H5Ex_G_Compact.out)
+TESTING examples.groups.H5Ex_G_Compact
+($RUNSERIAL $JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.groups.H5Ex_G_Compact > H5Ex_G_Compact.out)
 if diff H5Ex_G_Compact.out examples.groups.H5Ex_G_Compact.txt > /dev/null; then
     echo "  PASSED      groups.H5Ex_G_Compact"
 else
@@ -297,7 +318,8 @@ else
 fi
 
 echo "$JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.groups.H5Ex_G_Corder"
-($JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.groups.H5Ex_G_Corder > H5Ex_G_Corder.out)
+TESTING examples.groups.H5Ex_G_Corder
+($RUNSERIAL $JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.groups.H5Ex_G_Corder > H5Ex_G_Corder.out)
 if diff H5Ex_G_Corder.out examples.groups.H5Ex_G_Corder.txt > /dev/null; then
     echo "  PASSED      groups.H5Ex_G_Corder"
 else
@@ -306,7 +328,8 @@ else
 fi
 
 echo "$JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.groups.H5Ex_G_Intermediate"
-($JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.groups.H5Ex_G_Intermediate > H5Ex_G_Intermediate.out)
+TESTING examples.groups.H5Ex_G_Intermediate
+($RUNSERIAL $JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.groups.H5Ex_G_Intermediate > H5Ex_G_Intermediate.out)
 if diff H5Ex_G_Intermediate.out examples.groups.H5Ex_G_Intermediate.txt > /dev/null; then
     echo "  PASSED      groups.H5Ex_G_Intermediate"
 else
@@ -315,7 +338,8 @@ else
 fi
 
 echo "$JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.groups.H5Ex_G_Phase"
-($JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.groups.H5Ex_G_Phase > H5Ex_G_Phase.out)
+TESTING examples.groups.H5Ex_G_Phase
+($RUNSERIAL $JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.groups.H5Ex_G_Phase > H5Ex_G_Phase.out)
 if diff H5Ex_G_Phase.out examples.groups.H5Ex_G_Phase.txt > /dev/null; then
     echo "  PASSED      groups.H5Ex_G_Phase"
 else
@@ -324,7 +348,8 @@ else
 fi
 
 echo "$JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.groups.H5Ex_G_Visit"
-($JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.groups.H5Ex_G_Visit > H5Ex_G_Visit.out)
+TESTING examples.groups.H5Ex_G_Visit
+($RUNSERIAL $JAVAEXE $JAVAEXEFLAGS -Xmx1024M -Dorg.slf4j.simpleLogger.defaultLog=trace -Djava.library.path=$BLDLIBDIR -cp $CLASSPATH examples.groups.H5Ex_G_Visit > H5Ex_G_Visit.out)
 if diff H5Ex_G_Visit.out examples.groups.H5Ex_G_Visit.txt > /dev/null; then
     echo "  PASSED      groups.H5Ex_G_Visit"
 else
@@ -333,9 +358,9 @@ else
 fi
 
 # Clean up temporary files/directories
+CLEAN_ITERFILES_AND_BLDITERDIR
 CLEAN_LIBFILES_AND_BLDLIBDIR
 CLEAN_DATAFILES_AND_BLDDIR
-CLEAN_REFFILES_AND_BLDREFDIR
 
 # Report test results and exit
 if test $nerrors -eq 0 ; then
diff --git a/java/examples/groups/Makefile.am b/java/examples/groups/Makefile.am
index 08721e0..d5824e8 100644
--- a/java/examples/groups/Makefile.am
+++ b/java/examples/groups/Makefile.am
@@ -28,13 +28,13 @@ classes:
 
 pkgpath = examples/groups
 hdfjarfile = jar$(PACKAGE_TARNAME)-$(PACKAGE_VERSION).jar
-CLASSPATH_ENV=CLASSPATH=.:$(JAVAROOT):$(top_builddir)/java/src/$(hdfjarfile):$(top_srcdir)/java/lib/slf4j-api-1.7.5.jar:$(top_srcdir)/java/lib/ext/slf4j-simple-1.7.5.jar:$$CLASSPATH
+CLASSPATH_ENV=CLASSPATH=.:$(JAVAROOT):$(top_builddir)/java/src/$(hdfjarfile):$(top_srcdir)/java/lib/slf4j-api-1.7.25.jar:$(top_srcdir)/java/lib/ext/slf4j-simple-1.7.25.jar:$$CLASSPATH
 
 jarfile = jar$(PACKAGE_TARNAME)groups.jar
 
 AM_JAVACFLAGS = $(H5_JAVACFLAGS) -deprecation
 
-TESTPACKAGE = 
+TESTPACKAGE =
 
 noinst_JAVA = \
     H5Ex_G_Create.java \
@@ -53,10 +53,10 @@ noinst_DATA = $(jarfile)
 
 .PHONY: classes
 
-check_SCRIPTS = runExample.sh
+check_SCRIPTS = JavaGroupExample.sh
 TEST_SCRIPT = $(check_SCRIPTS)
 
-CLEANFILES = classnoinst.stamp $(jarfile) $(JAVAROOT)/$(pkgpath)/*.class runExample.sh
+CLEANFILES = classnoinst.stamp $(jarfile) $(JAVAROOT)/$(pkgpath)/*.class JavaGroupExample.sh
 
 clean:
 	rm -rf $(JAVAROOT)/*