Merging in latest from upstream (HDFFV/hdf5:refs/heads/develop)

* commit 'ab3963b28e59419f8e857ec224dd4efa3ea6dd8e': (214 commits)
  Merge SWMR-related testing to existing tests.
  Bring over tweak for missing environment variable.
  Update CMake configuration files with SWMR accumulator changes.
  Add missing accumulator test.
  Merge SWMR-oriented accumulator tests from revise_chunks to develop.
  Bring Java SWMR changes from revise_chunks to develop branch
  Snapshot version 1.9 release 235
  Change dlopen from RTLD_NOW to RTLD_LAZY
  Fix bad implementation of Windows nanosleep equivalent.
  Removed NDEBUG guards from H5AC test functions.
  Bring SWMR-related tools changes from revise_chunks to develop.
  Bring over changes from revise_chunks that cleanup recent SWMR changes from code review feedback.
  Updated the H5FS cache code to grab the correct tag and modified the freespace test to use dxpls that have been tagged with the H5AC__FREESPACE_TAG global tag instead of H5AC_ind_read_dxpl_id. The library code now expects the owner of the free space manager to tag it so the owner-less free space managers in the freespace tag had to be tagged with *something* to avoid cache errors.
  Updated the comment for the valgrind fix.
  Fixed a valgrind problem in file shutdown exposed by the swmr.c test.
  Reduce timeout as normal run time on windows is less then 10 min
  Updated the icc flags (C flags only).
  Another Java oversight (sorry, don't have Java configured on my Mac)
  Correct oversight in Java test and remove direct VFD from SWMR supported drivers.
  Bring SWMR support in to the main development branch.  (Finally!)  More tests and the tool and API wrappers will be coming in over the weekend.
  ...

7 files changed, 211 insertions, 5 deletions

diff --git a/java/test/CMakeLists.txt b/java/test/CMakeLists.txt
index 8cb41f7..b3a996b 100644
--- a/java/test/CMakeLists.txt
+++ b/java/test/CMakeLists.txt
@@ -16,6 +16,7 @@ set (HDF5_JAVA_TEST_SOURCES
     TestH5Fparams.java
     TestH5Fbasic.java
     TestH5F.java
+    TestH5Fswmr.java
     TestH5Gbasic.java
     TestH5G.java
     TestH5Giterate.java
diff --git a/java/test/JUnit-interface.txt b/java/test/JUnit-interface.txt
index cbd93e0..7fd80f8 100644
--- a/java/test/JUnit-interface.txt
+++ b/java/test/JUnit-interface.txt
@@ -93,6 +93,8 @@ JUnit version 4.11
 .testH5Fget_intent_rdonly
 .testH5Fget_create_plist
 .testH5Fget_obj_count
+.testH5Fstart_swmr_write
+.testH5Fswmr_read_attempts
 .testH5Gget_info_by_name_not_exists
 .testH5Gget_info_by_idx_not_exists
 .testH5Gget_info_by_name
@@ -496,6 +498,7 @@ JUnit version 4.11
 .testH5P_fapl_family
 .testH5P_chunk_cache
 .testH5P_meta_block_size
+.testH5Fmdc_logging
 .testH5Pget_elink_fapl
 .testH5Pset_mdc_config
 .testH5P_small_data_block_size
@@ -634,7 +637,7 @@ JUnit version 4.11
 
 Time:  XXXX
 
-OK (632 tests)
+OK (635 tests)
 
 HDF5-DIAG: Error detected in HDF5 (version (number)) thread (IDs):
   #000: (file name) line (number) in H5Fopen(): can't set access and transfer property lists
diff --git a/java/test/Makefile.am b/java/test/Makefile.am
index 9f29f1c..92ac12d 100644
--- a/java/test/Makefile.am
+++ b/java/test/Makefile.am
@@ -43,6 +43,7 @@ noinst_JAVA = \
     TestH5Fparams.java \
     TestH5Fbasic.java \
     TestH5F.java \
+    TestH5Fswmr.java \
     TestH5Gbasic.java \
     TestH5G.java \
     TestH5Giterate.java \
diff --git a/java/test/TestAll.java b/java/test/TestAll.java
index e3abe21..a4b44c3 100644
--- a/java/test/TestAll.java
+++ b/java/test/TestAll.java
@@ -23,7 +23,7 @@ import org.junit.runners.Suite;
         TestH5Eregister.class,
         TestH5Edefault.class,
         TestH5E.class,
-        TestH5Fparams.class, TestH5Fbasic.class, TestH5F.class,
+        TestH5Fparams.class, TestH5Fbasic.class, TestH5F.class, TestH5Fswmr.class,
         TestH5Gbasic.class, TestH5G.class, TestH5Giterate.class,
         TestH5Sbasic.class, TestH5S.class,
         TestH5Tparams.class, TestH5Tbasic.class, TestH5T.class,
diff --git a/java/test/TestH5Fswmr.java b/java/test/TestH5Fswmr.java
new file mode 100644
index 0000000..b65ebf2
--- /dev/null
+++ b/java/test/TestH5Fswmr.java
@@ -0,0 +1,118 @@
+/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
+ * Copyright by The HDF Group.                                               *
+ * Copyright by the Board of Trustees of the University of Illinois.         *
+ * All rights reserved.                                                      *
+ *                                                                           *
+ * This file is part of HDF5.  The full HDF5 copyright notice, including     *
+ * terms governing use, modification, and redistribution, is contained in    *
+ * the files COPYING and Copyright.html.  COPYING can be found at the root   *
+ * of the source code distribution tree; Copyright.html can be found at the  *
+ * root level of an installed copy of the electronic HDF5 document set and   *
+ * is linked from the top-level documents page.  It can also be found at     *
+ * http://hdfgroup.org/HDF5/doc/Copyright.html.  If you do not have          *
+ * access to either file, you may request a copy from help@hdfgroup.org.     *
+ * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
+
+package test;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+
+import java.io.File;
+
+import hdf.hdf5lib.H5;
+import hdf.hdf5lib.HDF5Constants;
+import hdf.hdf5lib.exceptions.HDF5LibraryException;
+
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Rule;
+import org.junit.Test;
+import org.junit.rules.TestName;
+
+public class TestH5Fswmr {
+    @Rule public TestName testname = new TestName();
+    private static final String H5_FILE = "testswmr.h5";
+
+    long H5fid = -1;
+    long H5fapl = -1;
+    long H5fcpl = -1;
+
+    private final void _deleteFile(String filename) {
+        File file = new File(filename);
+
+        if (file.exists()) {
+            try {file.delete();} catch (SecurityException e) {}
+        }
+    }
+
+    @Before
+    public void createH5file()
+            throws HDF5LibraryException, NullPointerException {
+        assertTrue("H5 open ids is 0",H5.getOpenIDCount()==0);
+        System.out.print(testname.getMethodName());
+
+        H5fapl = H5.H5Pcreate(HDF5Constants.H5P_FILE_ACCESS);
+        H5fcpl = H5.H5Pcreate(HDF5Constants.H5P_FILE_CREATE);
+        H5.H5Pset_libver_bounds(H5fapl, HDF5Constants.H5F_LIBVER_LATEST, HDF5Constants.H5F_LIBVER_LATEST);
+
+        H5fid = H5.H5Fcreate(H5_FILE, HDF5Constants.H5F_ACC_TRUNC, H5fcpl, H5fapl);
+        H5.H5Fflush(H5fid, HDF5Constants.H5F_SCOPE_LOCAL);
+    }
+
+    @After
+    public void deleteH5file() throws HDF5LibraryException {
+        if (H5fapl > 0) {
+            try {H5.H5Pclose(H5fapl);} catch (Exception ex) {}
+            H5fapl = -1;
+        }
+        if (H5fcpl > 0) {
+            try {H5.H5Pclose(H5fcpl);} catch (Exception ex) {}
+            H5fcpl = -1;
+        }
+       if (H5fid > 0) {
+            try {H5.H5Fclose(H5fid);} catch (Exception ex) {}
+            H5fid = -1;
+        }
+        _deleteFile(H5_FILE);
+        System.out.println();
+    }
+
+    @Test
+    public void testH5Fstart_swmr_write() {
+        try {
+            H5.H5Fstart_swmr_write(H5fid);
+        }
+        catch (Throwable err) {
+            fail("H5.H5Fstart_swmr_write: " + err);
+        }
+    }
+
+    @Test
+    public void testH5Fswmr_read_attempts() {
+        long read_attempts = 0;
+
+        try {
+            read_attempts = H5.H5Pget_metadata_read_attempts(H5fapl);
+        }
+        catch (Throwable err) {
+            fail("H5.testH5Fswmr_read_attempts: " + err);
+        }
+        assertTrue(read_attempts == 1);
+
+        try {
+            H5.H5Pset_metadata_read_attempts(H5fapl, 20);
+        }
+        catch (Throwable err) {
+            fail("H5.testH5Fswmr_read_attempts: " + err);
+        }
+        try {
+            read_attempts = H5.H5Pget_metadata_read_attempts(H5fapl);
+        }
+        catch (Throwable err) {
+            fail("H5.testH5Fswmr_read_attempts: " + err);
+        }
+        assertTrue(read_attempts == 20);
+    }
+}
diff --git a/java/test/TestH5Pfapl.java b/java/test/TestH5Pfapl.java
index 555afe0..e888e20 100644
--- a/java/test/TestH5Pfapl.java
+++ b/java/test/TestH5Pfapl.java
@@ -16,6 +16,7 @@
 package test;
 
 import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
 import static org.junit.Assert.assertTrue;
 import static org.junit.Assert.fail;
 
@@ -1322,4 +1323,59 @@ public class TestH5Pfapl {
             }
         }
     }
+
+    @Test
+    public void testH5Fmdc_logging() {
+        boolean[] mdc_logging_status = {false, false};
+        boolean[] mdc_log_options = {false, false};
+
+        try {
+            boolean is_enabled = true;
+            boolean start_on_access = false;
+            H5.H5Pset_mdc_log_options(fapl_id, is_enabled, H5_LOG_FILE, start_on_access);
+
+            String location = H5.H5Pget_mdc_log_options(fapl_id, mdc_log_options);
+            assertTrue("H5.H5Pget_mdc_log_options: is_enabled", mdc_log_options[0]);
+            assertFalse("H5.H5Pget_mdc_log_options: start_on_access_out", mdc_log_options[1]);
+
+            H5.H5Pset_libver_bounds(fapl_id, HDF5Constants.H5F_LIBVER_LATEST, HDF5Constants.H5F_LIBVER_LATEST);
+        }
+        catch (Throwable err) {
+            err.printStackTrace();
+            fail("mdc_log_option: " + err);
+        }
+        _createH5File(fapl_id);
+
+        try {
+            H5.H5Fget_mdc_logging_status(H5fid, mdc_logging_status);
+        }
+        catch (Throwable err) {
+            fail("H5.H5Fget_mdc_logging_status: " + err);
+        }
+        assertTrue("initial: is_enabled", mdc_logging_status[0]);
+        assertFalse("initial: is_currently_logging", mdc_logging_status[1]);
+
+        try {
+            H5.H5Fstart_mdc_logging(H5fid);
+            H5.H5Fget_mdc_logging_status(H5fid, mdc_logging_status);
+        }
+        catch (Throwable err) {
+            fail("start H5.H5Fget_mdc_logging_status: " + err);
+        }
+        assertTrue("start: is_enabled", mdc_logging_status[0]);
+        assertTrue("start: is_currently_logging", mdc_logging_status[1]);
+
+        try {
+            H5.H5Fstop_mdc_logging(H5fid);
+            H5.H5Fget_mdc_logging_status(H5fid, mdc_logging_status);
+        }
+        catch (Throwable err) {
+            fail("stop H5.H5Fget_mdc_logging_status: " + err);
+        }
+//        assertFalse("stop: is_enabled", mdc_logging_status[0]);
+        assertFalse("stop: is_currently_logging", mdc_logging_status[1]);
+
+        deleteH5file();
+        _deleteLogFile();
+    }
 }
diff --git a/java/test/junit.sh.in b/java/test/junit.sh.in
index 5001c32..a9a71cb 100644
--- a/java/test/junit.sh.in
+++ b/java/test/junit.sh.in
@@ -39,7 +39,7 @@ myos=`uname -s`
 
 # where the libs exist
 HDFLIB_HOME="$top_srcdir/java/lib"
-BLDLIBDIR="$top_builddir/java/lib"
+BLDLIBDIR="$top_builddir/hdf5/lib"
 BLDDIR="."
 HDFTEST_HOME="$top_srcdir/java/test"
 JARFILE=jar@PACKAGE_TARNAME@-@PACKAGE_VERSION@.jar
@@ -55,12 +55,14 @@ test -d $BLDLIBDIR || mkdir -p $BLDLIBDIR
 #       Comment '#' without space can be used.
 # --------------------------------------------------------------------
 LIST_LIBRARY_FILES="
+$top_builddir/src/.libs/libhdf5.*
+$top_builddir/java/src/jni/.libs/libhdf5_java.*
+"
+LIST_JAR_FILES="
 $HDFLIB_HOME/hamcrest-core.jar
 $HDFLIB_HOME/junit.jar
 $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_DATA_FILES="
@@ -77,6 +79,7 @@ actual_ext="JUnit-interface.ext"
 # copy files from source dirs to test dir
 #
 COPY_LIBFILES="$LIST_LIBRARY_FILES"
+COPY_JARFILES="$LIST_JAR_FILES"
 
 COPY_LIBFILES_TO_BLDLIBDIR()
 {
@@ -104,6 +107,30 @@ COPY_LIBFILES_TO_BLDLIBDIR()
             fi
         fi
     done
+    # copy jar files. Used -f to make sure get a new copy
+    for tstfile in $COPY_JARFILES
+    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()