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.
  ...

1 files changed, 129 insertions, 1 deletions

diff --git a/java/src/hdf/hdf5lib/H5.java b/java/src/hdf/hdf5lib/H5.java
index 7614292..6b2af4b 100644
--- a/java/src/hdf/hdf5lib/H5.java
+++ b/java/src/hdf/hdf5lib/H5.java
@@ -2852,8 +2852,63 @@ public class H5 implements java.io.Serializable {
      **/
     public synchronized static native void H5Fclear_elink_file_cache(long file_id) throws HDF5LibraryException;
 
+    /**
+     * H5Fstart_swmr_write will activate SWMR writing mode for a file associated with file_id. This routine will
+     * prepare and ensure the file is safe for SWMR writing.
+     *
+     * @param file_id
+     *            IN: Identifier of the target file.
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     **/
+    public synchronized static native void H5Fstart_swmr_write(long file_id) throws HDF5LibraryException;
+
+    /**
+     * H5Fstart_mdc_logging starts logging metadata cache events if logging was previously enabled.
+     *
+     * @param file_id
+     *            IN: Identifier of the target file.
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     **/
+    public synchronized static native void H5Fstart_mdc_logging(long file_id) throws HDF5LibraryException;
+
+    /**
+     * H5Fstop_mdc_logging stops logging metadata cache events if logging was previously enabled and is currently ongoing.
+     *
+     * @param file_id
+     *            IN: Identifier of the target file.
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     **/
+    public synchronized static native void H5Fstop_mdc_logging(long file_id) throws HDF5LibraryException;
+
+    /**
+     * H5Fget_mdc_logging_status gets the current metadata cache logging status.
+     *
+     * @param file_id
+     *            IN: Identifier of the target file.
+     *
+     * @param mdc_logging_status, the status
+     *             mdc_logging_status[0] = is_enabled, whether logging is enabled
+     *             mdc_logging_status[1] = is_currently_logging, whether events are currently being logged
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     * @exception NullPointerException
+     *                - mdc_logging_status is null.
+     **/
+    public synchronized static native void H5Fget_mdc_logging_status(long file_id, boolean[] mdc_logging_status)
+            throws HDF5LibraryException, NullPointerException;
+
+
+
     // /////// unimplemented ////////
     // ssize_t H5Fget_file_image(hid_t file_id, void * buf_ptr, size_t buf_len);
+    // herr_t H5Fget_metadata_read_retry_info(hid_t file_id, H5F_retry_info_t *info);
     // ssize_t H5Fget_free_sections(hid_t file_id, H5F_mem_t type, size_t nsects, H5F_sect_info_t *sect_info/*out*/);
 
     // /**
@@ -5672,6 +5727,79 @@ public class H5 implements java.io.Serializable {
     public synchronized static native void H5Pset_elink_file_cache_size(long fapl_id, int efc_size)
             throws HDF5LibraryException;
 
+    /**
+     * H5Pset_mdc_log_options sets metadata cache logging options.
+     *
+     * @param fapl_id
+     *            IN: File access property list identifier
+     * @param is_enabled
+     *            IN: Whether logging is enabled.
+     * @param location
+     *            IN: Location of log in UTF-8/ASCII (file path/name) (On Windows, this must be ASCII).
+     * @param start_on_access
+     *            IN: Whether the logging begins as soon as the file is opened or created.
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     * @exception NullPointerException
+     *                - location is null.
+     *
+     **/
+    public synchronized static native void H5Pset_mdc_log_options(long fapl_id, boolean is_enabled, String location, boolean start_on_access)
+            throws HDF5LibraryException, NullPointerException;
+
+    /**
+     * H5Pget_mdc_log_options gets metadata cache logging options.
+     *
+     * @param fapl_id
+     *            IN: File access property list identifier
+     * @param mdc_log_options, the options
+     *             mdc_logging_options[0] = is_enabled, whether logging is enabled
+     *             mdc_logging_options[1] = start_on_access, whether the logging begins as soon as the file is opened or created
+     *
+     * @return the location of log in UTF-8/ASCII (file path/name) (On Windows, this must be ASCII).
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     *
+     **/
+    public synchronized static native String H5Pget_mdc_log_options(long fapl_id, boolean[] mdc_log_options)
+            throws HDF5LibraryException;
+
+    /**
+     * H5Pget_metadata_read_attempts retrieves the number of read attempts that is set in the file access property list plist_id.
+     *
+     * @param plist_id
+     *            IN: File access property list identifier
+     *
+     * @return The number of read attempts.
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     *
+     **/
+    public synchronized static native long H5Pget_metadata_read_attempts(long plist_id) throws HDF5LibraryException;
+
+    /**
+     * H5Pset_metadata_read_attempts sets the number of reads that the library will try when reading checksummed
+     * metadata in an HDF5 file opened with SWMR access. When reading such metadata, the library will compare the
+     * checksum computed for the metadata just read with the checksum stored within the piece of checksum. When
+     * performing SWMR operations on a file, the checksum check might fail when the library reads data on a system
+     * that is not atomic. To remedy such situations, the library will repeatedly read the piece of metadata until
+     * the check passes or finally fails the read when the allowed number of attempts is reached.
+     *
+     * @param plist_id
+     *            IN: File access property list identifier
+     * @param attempts
+     *            IN: The number of read attempts which is a value greater than 0.
+     *
+     * @exception HDF5LibraryException
+     *                - Error from the HDF-5 Library.
+     *
+     **/
+    public synchronized static native void H5Pset_metadata_read_attempts(long plist_id, long attempts)
+            throws HDF5LibraryException;
+
     // Dataset creation property list (DCPL) routines //
 
     /**
@@ -6915,7 +7043,7 @@ public class H5 implements java.io.Serializable {
 
     // File access property list (FAPL) routines //
     // herr_t H5Pset_driver( hid_t plist_id, hid_t new_driver_id, const void *new_driver_info )
-    // void *H5Pget_driver_info( hid_t plist_id )
+    // const void *H5Pget_driver_info( hid_t plist_id )
     // herr_t H5Pget_multi_type ( hid_t fapl_id, H5FD_mem_t *type )
     // herr_t H5Pset_multi_type ( hid_t fapl_id, H5FD_mem_t type )
     // herr_t H5Pget_file_image(hid_t fapl_id, void **buf_ptr_ptr, size_t *buf_len_ptr);