Merge pull request #21 in ~VCHOI/my_third_fork from develop to bugfix/HDFFV-10585-investigate-slowness-of-regular

* commit '0ea77179d507bd2c29f3b9b357a0c35d4077b29c': (39 commits)
  Fix the errors when updating the versions in the new 1.13 develop branch.
  add missing version to list
  Add new versioned filename to list
  Update N_FSINFO_VERSION_BOUNDS to H5F_LIBVER_NBOUND.
  Remove file script
  Update versioning to next major version
  Update develop branch version to 1.13.0 after creation of hdf5_1_12 branch.
  Merge Binh-Minh's changes for code improvement to chunk_info.c (PR #1942) to develop branch.
  Update to current external file population.
  Revert else-if to single line.
  Fix missing option and incorrect close
  Revert "Moved NDEBUG guards to H5EA_DEBUG in H5EA package."
  Revert "Fix for H5EA debug package when built in release mode."
  Change print calls to HD-wrapped. Minor formatting tweaks (inc. regressions and in-file style-matching).
  Refactor h5repackgentest to have more modular internals, for easier addition of new tests. Update manifest and test script for new hdf5 external-storage .h5 files.
  Remove obsolete symbol
  small syntax changes
  Renamed get/set_time() calls in the tools library to avoid name clash when building static parallel HDF5 w/ static linking to OpenMPI.
  Change unused variable to generic form
  Whitespace cleanup
  ...

3 files changed, 21 insertions, 4 deletions

diff --git a/java/src/hdf/hdf5lib/H5.java b/java/src/hdf/hdf5lib/H5.java
index 4b563fd..adb50f1 100644
--- a/java/src/hdf/hdf5lib/H5.java
+++ b/java/src/hdf/hdf5lib/H5.java
@@ -214,7 +214,7 @@ import hdf.hdf5lib.structs.H5O_info_t;
  * exception handlers to print out the HDF-5 error stack.
  * <hr>
  *
- * @version HDF5 1.11.6 <BR>
+ * @version HDF5 1.13.0 <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, 6 };
+    public final static int LIB_VERSION[] = { 1, 13, 0 };
 
     public final static String H5PATH_PROPERTY_KEY = "hdf.hdf5lib.H5.hdf5lib";
 
diff --git a/java/src/hdf/hdf5lib/HDF5Constants.java b/java/src/hdf/hdf5lib/HDF5Constants.java
index 2e80f2e..f5be38d 100644
--- a/java/src/hdf/hdf5lib/HDF5Constants.java
+++ b/java/src/hdf/hdf5lib/HDF5Constants.java
@@ -218,6 +218,7 @@ public class HDF5Constants {
     public static final int H5F_LIBVER_V18 = H5F_LIBVER_V18();
     public static final int H5F_LIBVER_V110 = H5F_LIBVER_V110();
     public static final int H5F_LIBVER_V112 = H5F_LIBVER_V112();
+    public static final int H5F_LIBVER_V114 = H5F_LIBVER_V114();
     public static final int H5F_LIBVER_NBOUNDS = H5F_LIBVER_NBOUNDS();
     public static final int H5F_LIBVER_LATEST = H5F_LIBVER_LATEST();
     public static final int H5F_OBJ_ALL = H5F_OBJ_ALL();
@@ -1059,6 +1060,8 @@ public class HDF5Constants {
 
     private static native final int H5F_LIBVER_V112();
 
+    private static native final int H5F_LIBVER_V114();
+
     private static native final int H5F_LIBVER_NBOUNDS();
 
     private static native final int H5F_LIBVER_LATEST();
diff --git a/java/src/jni/h5Constants.c b/java/src/jni/h5Constants.c
index ac55a13..69adebd 100644
--- a/java/src/jni/h5Constants.c
+++ b/java/src/jni/h5Constants.c
@@ -405,6 +405,8 @@ Java_hdf_hdf5lib_HDF5Constants_H5F_1LIBVER_1V110(JNIEnv *env, jclass cls){return
 JNIEXPORT jint JNICALL
 Java_hdf_hdf5lib_HDF5Constants_H5F_1LIBVER_1V112(JNIEnv *env, jclass cls){return H5F_LIBVER_V112;}
 JNIEXPORT jint JNICALL
+Java_hdf_hdf5lib_HDF5Constants_H5F_1LIBVER_1V114(JNIEnv *env, jclass cls){return H5F_LIBVER_V114;}
+JNIEXPORT jint JNICALL
 Java_hdf_hdf5lib_HDF5Constants_H5F_1LIBVER_1NBOUNDS(JNIEnv *env, jclass cls){return H5F_LIBVER_NBOUNDS;}
 JNIEXPORT jint JNICALL
 Java_hdf_hdf5lib_HDF5Constants_H5F_1LIBVER_1LATEST(JNIEnv *env, jclass cls){return H5F_LIBVER_LATEST;}
@@ -453,7 +455,13 @@ 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
@@ -463,7 +471,13 @@ 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