Merge pull request #19 in ~VCHOI/my_third_fork from develop to bugfix/HDFFV-10585-investigate-slowness-of-regular

* commit '2456a36f46a15ca44840cb64c7aac213f0ca8bf8': (53 commits)
  Fixed some exit calls.
  Reworked the previously refactorred code.
  Improvement of test code
  Fix CMake build of test needing compression libs
  Fixed error code and error messages Tested on Jelly (very minor)
  Changed H5VL_NATIVE_DATASET_GET_CHUNK_INFO_BY_COOR to H5VL_NATIVE_DATASET_GET_CHUNK_INFO_BY_COORD per a review comment.
  Add comment to add tests later to verify conflicting values for MPI-specific properties on multiple opens.
  Updated comments
  Updated based on reviews and refactored test code
  Move ext_path field in H5F_t to H5F_shared_t. Remove unused routine H5F_set_coll_md_read().
  Move coll_md_read and coll_md_write fields in H5F_t to H5F_shared_t.
  Fix namespace usage
  Fix EXISTS test syntax
  Update settings
  Add 32-bit cross-compile toolchain
  Code cleanup and refactor
  Re-ordered items w.r.t. date.
  Whitespace and HD prefix changes
  Fixed typo
  Added notes about HDFFV-10677 and HDFFV-10661
  ...

9 files changed, 168 insertions, 10 deletions

diff --git a/java/src/hdf/hdf5lib/H5.java b/java/src/hdf/hdf5lib/H5.java
index 481ca8c..4b563fd 100644
--- a/java/src/hdf/hdf5lib/H5.java
+++ b/java/src/hdf/hdf5lib/H5.java
@@ -5048,10 +5048,9 @@ public class H5 implements java.io.Serializable {
      **/
     public synchronized static native void H5Orefresh(long object_id) throws HDF5LibraryException;
 
-    // /////// unimplemented ////////
-    //  herr_t H5Odisable_mdc_flushes(hid_t object_id);
-    //  herr_t H5Oenable_mdc_flushes(hid_t object_id);
-    //  herr_t H5Oare_mdc_flushes_disabled(hid_t object_id, hbool_t *are_disabled);
+    public synchronized static native void  H5Odisable_mdc_flushes(long object_id);
+    public synchronized static native void  H5Oenable_mdc_flushes(long object_id);
+    public synchronized static native boolean  H5Oare_mdc_flushes_disabled(long object_id);
 
     // ////////////////////////////////////////////////////////////
     // //
diff --git a/java/src/hdf/hdf5lib/structs/H5FD_hdfs_fapl_t.java b/java/src/hdf/hdf5lib/structs/H5FD_hdfs_fapl_t.java
index f56a038..c13473c 100644
--- a/java/src/hdf/hdf5lib/structs/H5FD_hdfs_fapl_t.java
+++ b/java/src/hdf/hdf5lib/structs/H5FD_hdfs_fapl_t.java
@@ -17,7 +17,7 @@ package hdf.hdf5lib.structs;
 import java.io.Serializable;
 
 /*
- * Java representation of the HDFS VFD file access property list (fapl) 
+ * Java representation of the HDFS VFD file access property list (fapl)
  * structure.
  *
  * Used for the access of files hosted on the Hadoop Distributed File System.
@@ -33,7 +33,7 @@ public class H5FD_hdfs_fapl_t implements Serializable {
     private int    namenode_port;
     private int    stream_buffer_size;
 
-    /**
+    /*
      * Create a fapl_t structure with the specified components.
      */
     public H5FD_hdfs_fapl_t(
@@ -91,7 +91,7 @@ public class H5FD_hdfs_fapl_t implements Serializable {
     public String toString() {
     return "H5FD_hdfs_fapl_t (Version: " + this.version + ") {" +
            "\n    namenode_name: '" + this.namenode_name +
-           "'\n    namenode_port: " + this.namenode_port + 
+           "'\n    namenode_port: " + this.namenode_port +
            "\n    user_name: '" + this.user_name +
            "'\n    kerberos_ticket_cache: '" + this.kerberos_ticket_cache +
            "'\n    stream_buffer_size: " + this.stream_buffer_size +
diff --git a/java/src/hdf/hdf5lib/structs/H5FD_ros3_fapl_t.java b/java/src/hdf/hdf5lib/structs/H5FD_ros3_fapl_t.java
index 6b086c3..881aad3 100644
--- a/java/src/hdf/hdf5lib/structs/H5FD_ros3_fapl_t.java
+++ b/java/src/hdf/hdf5lib/structs/H5FD_ros3_fapl_t.java
@@ -71,7 +71,7 @@ public class H5FD_ros3_fapl_t implements Serializable {
      * @param key "secret key" or "access key" for authenticating request
      */
     public H5FD_ros3_fapl_t (String region, String id, String key) {
-        this.version    = 1; /* must equal H5FD__CURR_ROS3_FAPL_T_VERSION */
+        this.version    = 1; /* must equal H5FD_CURR_ROS3_FAPL_T_VERSION */
                              /* as found in H5FDros3.h                    */
         this.aws_region = region;
         this.secret_id  = id;
diff --git a/java/src/jni/h5oImp.c b/java/src/jni/h5oImp.c
index cc88b81..b49a3e9 100644
--- a/java/src/jni/h5oImp.c
+++ b/java/src/jni/h5oImp.c
@@ -856,6 +856,66 @@ done:
     return;
 } /* end Java_hdf_hdf5lib_H5_H5Orefresh */
 
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Odisable_mdc_flushes
+ * Signature: (J)V
+ */
+JNIEXPORT void JNICALL
+Java_hdf_hdf5lib_H5_H5Odisable_1mdc_1flushes
+    (JNIEnv *env, jclass clss, jlong loc_id)
+{
+    UNUSED(clss);
+
+    if (H5Odisable_mdc_flushes((hid_t)loc_id) < 0)
+        H5_LIBRARY_ERROR(ENVONLY);
+
+done:
+    return;
+} /* end Java_hdf_hdf5lib_H5_H5Odisable_1mdc_1flushes */
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Oenable_mdc_flushes
+ * Signature: (J)V
+ */
+JNIEXPORT void JNICALL
+Java_hdf_hdf5lib_H5_H5Oenable_1mdc_1flushes
+    (JNIEnv *env, jclass clss, jlong loc_id)
+{
+    UNUSED(clss);
+
+    if (H5Oenable_mdc_flushes((hid_t)loc_id) < 0)
+        H5_LIBRARY_ERROR(ENVONLY);
+
+done:
+    return;
+} /* end Java_hdf_hdf5lib_H5_H5Oenable_1mdc_1flushes */
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Oare_mdc_flushes_disabled
+ * Signature: (J)Z
+ */
+JNIEXPORT jboolean JNICALL
+Java_hdf_hdf5lib_H5_H5Oare_1mdc_1flushes_1disabled
+    (JNIEnv *env, jclass clss, jlong loc_id)
+{
+    jboolean bval = JNI_FALSE;
+    hbool_t    is_disabled = FALSE;
+
+    UNUSED(clss);
+
+    if (H5Oare_mdc_flushes_disabled((hid_t)loc_id, &is_disabled) < 0)
+        H5_LIBRARY_ERROR(ENVONLY);
+
+    if (is_disabled == TRUE)
+        bval =  JNI_TRUE;
+
+done:
+    return bval;
+} /* end Java_hdf_hdf5lib_H5_H5Oare_1mdc_1flushes_1disabled */
+
 
 
 #ifdef __cplusplus
diff --git a/java/src/jni/h5oImp.h b/java/src/jni/h5oImp.h
index cb8c776..5241aba 100644
--- a/java/src/jni/h5oImp.h
+++ b/java/src/jni/h5oImp.h
@@ -202,6 +202,33 @@ JNIEXPORT void JNICALL
 Java_hdf_hdf5lib_H5_H5Orefresh
   (JNIEnv*, jclass, jlong);
 
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Odisable_mdc_flushes
+ * Signature: (J)V
+ */
+JNIEXPORT void JNICALL
+Java_hdf_hdf5lib_H5_H5Odisable_1mdc_1flushes
+  (JNIEnv*, jclass, jlong);
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Oenable_mdc_flushes
+ * Signature: (J)V
+ */
+JNIEXPORT void JNICALL
+Java_hdf_hdf5lib_H5_H5Oenable_1mdc_1flushes
+  (JNIEnv*, jclass, jlong);
+
+/*
+ * Class:     hdf_hdf5lib_H5
+ * Method:    H5Oare_mdc_flushes_disabled
+ * Signature: (J)Z
+ */
+JNIEXPORT jboolean JNICALL
+Java_hdf_hdf5lib_H5_H5Oare_1mdc_1flushes_1disabled
+  (JNIEnv*, jclass, jlong);
+
 #ifdef __cplusplus
 } /* end extern "C" */
 #endif /* __cplusplus */
diff --git a/java/test/TestH5Ocreate.java b/java/test/TestH5Ocreate.java
index c3e36b4..de17d8b 100644
--- a/java/test/TestH5Ocreate.java
+++ b/java/test/TestH5Ocreate.java
@@ -557,4 +557,57 @@ public class TestH5Ocreate {
         }
     }
 
+    @Test
+    public void testH5Ocork() {
+        boolean corked = false;
+
+        // Check cork status of the group: not corked
+        try {
+            corked = H5.H5Oare_mdc_flushes_disabled(H5gid);
+        }
+        catch (Throwable err) {
+            err.printStackTrace();
+            fail("testH5Ocork: H5.H5Oare_mdc_flushes_disabled: " + err);
+        }
+        assertFalse("H5Oare_mdc_flushes_disabled: ", corked);
+
+        // Cork the group: an object
+        try {
+            H5.H5Odisable_mdc_flushes(H5gid);
+        }
+        catch (Throwable err) {
+            err.printStackTrace();
+            fail("testH5Ocork: H5.H5Odisable_mdc_flushes: " + err);
+        }
+
+        // Check cork status of the group: corked
+        try {
+            corked = H5.H5Oare_mdc_flushes_disabled(H5gid);
+        }
+        catch (Throwable err) {
+            err.printStackTrace();
+            fail("testH5Ocork: H5.H5Oare_mdc_flushes_disabled: " + err);
+        }
+        assertTrue("H5Oare_mdc_flushes_disabled: ", corked);
+
+        // Unork the group: an object
+        try {
+            H5.H5Oenable_mdc_flushes(H5gid);
+        }
+        catch (Throwable err) {
+            err.printStackTrace();
+            fail("testH5Ocork: H5.H5Oenable_mdc_flushes: " + err);
+        }
+
+        // Check cork status of the group: corked
+        try {
+            corked = H5.H5Oare_mdc_flushes_disabled(H5gid);
+        }
+        catch (Throwable err) {
+            err.printStackTrace();
+            fail("testH5Ocork: H5.H5Oare_mdc_flushes_disabled: " + err);
+        }
+        assertFalse("H5Oare_mdc_flushes_disabled: ", corked);
+    }
+
 }
diff --git a/java/test/TestH5Oparams.java b/java/test/TestH5Oparams.java
index d340ee7..cac3dcd 100644
--- a/java/test/TestH5Oparams.java
+++ b/java/test/TestH5Oparams.java
@@ -159,4 +159,19 @@ public class TestH5Oparams {
         H5.H5Orefresh(-1);
     }
 
+    @Test(expected = HDF5LibraryException.class)
+    public void testH5Odisable_mdc_flushes() throws Throwable {
+        H5.H5Odisable_mdc_flushes(-1);
+    }
+
+    @Test(expected = HDF5LibraryException.class)
+    public void testH5Oenable_mdc_flushes() throws Throwable {
+        H5.H5Oenable_mdc_flushes(-1);
+    }
+
+    @Test(expected = HDF5LibraryException.class)
+    public void testH5Oare_mdc_flushes_disabled() throws Throwable {
+        H5.H5Oare_mdc_flushes_disabled(-1);
+    }
+
 }
diff --git a/java/test/testfiles/JUnit-TestH5Ocreate.txt b/java/test/testfiles/JUnit-TestH5Ocreate.txt
index c2365e5..5bc9e07 100644
--- a/java/test/testfiles/JUnit-TestH5Ocreate.txt
+++ b/java/test/testfiles/JUnit-TestH5Ocreate.txt
@@ -4,6 +4,7 @@ JUnit version 4.11
 .testH5Oget_info_softlink
 .testH5Oget_info_externallink
 .testH5Ocopy
+.testH5Ocork
 .testH5Olink
 .testH5Ocomment_by_name
 .testH5Oget_info_by_idx_n1_create
@@ -17,5 +18,5 @@ JUnit version 4.11
 
 Time:  XXXX
 
-OK (15 tests)
+OK (16 tests)
 
diff --git a/java/test/testfiles/JUnit-TestH5Oparams.txt b/java/test/testfiles/JUnit-TestH5Oparams.txt
index 94220b9..bc23695 100644
--- a/java/test/testfiles/JUnit-TestH5Oparams.txt
+++ b/java/test/testfiles/JUnit-TestH5Oparams.txt
@@ -3,8 +3,10 @@ JUnit version 4.11
 .testH5Ovisit_by_name_nullname
 .testH5Oget_info_invalid
 .testH5Ovisit_by_name_null
+.testH5Odisable_mdc_flushes
 .testH5Oget_comment_invalid
 .testH5Oset_comment_by_name_invalid
+.testH5Oare_mdc_flushes_disabled
 .testH5Oopen_null
 .testH5Oclose_invalid
 .testH5Oflush_invalid
@@ -22,9 +24,10 @@ JUnit version 4.11
 .testH5Ocopy_null_current
 .testH5Oset_comment_invalid
 .testH5Oopen_invalid
+.testH5Oenable_mdc_flushes
 .testH5Ovisit_null
 
 Time:  XXXX
 
-OK (24 tests)
+OK (27 tests)