Merge branch 'develop' into openmpi_tweaks

1 files changed, 106 insertions, 52 deletions

diff --git a/java/src/hdf/hdf5lib/H5.java b/java/src/hdf/hdf5lib/H5.java
index bce0034..e354207 100644
--- a/java/src/hdf/hdf5lib/H5.java
+++ b/java/src/hdf/hdf5lib/H5.java
@@ -499,9 +499,9 @@ public class H5 implements java.io.Serializable {
     private synchronized static native boolean H5is_library_threadsafe();
 
     // /////// unimplemented ////////
-    // H5_DLL herr_t H5free_memory(void *mem);
-    // H5_DLL void *H5allocate_memory(size_t size, hbool_t clear);
-    // H5_DLL void *H5resize_memory(void *mem, size_t size);
+    //  herr_t H5free_memory(void *mem);
+    //  void *H5allocate_memory(size_t size, hbool_t clear);
+    //  void *H5resize_memory(void *mem, size_t size);
 
     // ////////////////////////////////////////////////////////////
     // //
@@ -2402,10 +2402,10 @@ public class H5 implements java.io.Serializable {
     public synchronized static native void H5Drefresh(long dset_id) throws HDF5LibraryException;
 
     // /////// unimplemented ////////
-    // H5_DLL herr_t H5Ddebug(hid_t dset_id);
-    // H5_DLL herr_t H5Dget_chunk_storage_size(hid_t dset_id, const hsize_t *offset, hsize_t *chunk_bytes);
-    // H5_DLL herr_t H5Dformat_convert(hid_t dset_id);
-    // H5_DLL herr_t H5Dget_chunk_index_type(hid_t did, H5D_chunk_index_t *idx_type);
+    //  herr_t H5Ddebug(hid_t dset_id);
+    //  herr_t H5Dget_chunk_storage_size(hid_t dset_id, const hsize_t *offset, hsize_t *chunk_bytes);
+    //  herr_t H5Dformat_convert(hid_t dset_id);
+    //  herr_t H5Dget_chunk_index_type(hid_t did, H5D_chunk_index_t *idx_type);
 
     // herr_t H5Dgather(hid_t src_space_id, const void *src_buf, hid_t type_id,
     //                  size_t dst_buf_size, void *dst_buf, H5D_gather_func_t op, void *op_data);
@@ -3230,20 +3230,20 @@ public class H5 implements java.io.Serializable {
             throws HDF5LibraryException, NullPointerException;
 
     // /////// unimplemented ////////
-    // H5_DLL herr_t H5Fget_eoa(hid_t file_id, haddr_t *eoa);
-    // H5_DLL herr_t H5Fincrement_filesize(hid_t file_id, hsize_t increment);
+    //  herr_t H5Fget_eoa(hid_t file_id, haddr_t *eoa);
+    //  herr_t H5Fincrement_filesize(hid_t file_id, hsize_t increment);
     // 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*/);
-    // H5_DLL herr_t H5Fset_libver_bounds(hid_t file_id, H5F_libver_t low, H5F_libver_t high);
-    // H5_DLL herr_t H5Fformat_convert(hid_t fid);
-    // H5_DLL herr_t H5Freset_page_buffering_stats(hid_t file_id);
-    // H5_DLL herr_t H5Fget_page_buffering_stats(hid_t file_id, unsigned accesses[2],
+    //  herr_t H5Fset_libver_bounds(hid_t file_id, H5F_libver_t low, H5F_libver_t high);
+    //  herr_t H5Fformat_convert(hid_t fid);
+    //  herr_t H5Freset_page_buffering_stats(hid_t file_id);
+    //  herr_t H5Fget_page_buffering_stats(hid_t file_id, unsigned accesses[2],
     //     unsigned hits[2], unsigned misses[2], unsigned evictions[2], unsigned bypasses[2]);
-    // H5_DLL herr_t H5Fget_mdc_image_info(hid_t file_id, haddr_t *image_addr, hsize_t *image_size);
+    //  herr_t H5Fget_mdc_image_info(hid_t file_id, haddr_t *image_addr, hsize_t *image_size);
     // #ifdef H5_HAVE_PARALLEL
-    //   H5_DLL herr_t H5Fset_mpi_atomicity(hid_t file_id, hbool_t flag);
-    //   H5_DLL herr_t H5Fget_mpi_atomicity(hid_t file_id, hbool_t *flag);
+    //    herr_t H5Fset_mpi_atomicity(hid_t file_id, hbool_t flag);
+    //    herr_t H5Fget_mpi_atomicity(hid_t file_id, hbool_t *flag);
     // #endif /* H5_HAVE_PARALLEL */
 
     // /**
@@ -3303,25 +3303,25 @@ public class H5 implements java.io.Serializable {
     // ////////////////////////////////////////////////////////////
 
     // /////// unimplemented ////////
-    // H5_DLL hid_t H5FDregister(const H5FD_class_t *cls);
-    // H5_DLL herr_t H5FDunregister(hid_t driver_id);
-    // H5_DLL H5FD_t *H5FDopen(const char *name, unsigned flags, hid_t fapl_id, haddr_t maxaddr);
-    // H5_DLL herr_t H5FDclose(H5FD_t *file);
-    // H5_DLL int H5FDcmp(const H5FD_t *f1, const H5FD_t *f2);
-    // H5_DLL int H5FDquery(const H5FD_t *f, unsigned long *flags);
-    // H5_DLL haddr_t H5FDalloc(H5FD_t *file, H5FD_mem_t type, hid_t dxpl_id, hsize_t size);
-    // H5_DLL herr_t H5FDfree(H5FD_t *file, H5FD_mem_t type, hid_t dxpl_id, haddr_t addr, hsize_t size);
-    // H5_DLL haddr_t H5FDget_eoa(H5FD_t *file, H5FD_mem_t type);
-    // H5_DLL herr_t H5FDset_eoa(H5FD_t *file, H5FD_mem_t type, haddr_t eoa);
-    // H5_DLL haddr_t H5FDget_eof(H5FD_t *file, H5FD_mem_t type);
-    // H5_DLL herr_t H5FDget_vfd_handle(H5FD_t *file, hid_t fapl, void**file_handle);
-    // H5_DLL herr_t H5FDread(H5FD_t *file, H5FD_mem_t type, hid_t dxpl_id, haddr_t addr, size_t size, void *buf/*out*/);
-    // H5_DLL herr_t H5FDwrite(H5FD_t *file, H5FD_mem_t type, hid_t dxpl_id, haddr_t addr, size_t size, const void *buf);
-    // H5_DLL herr_t H5FDflush(H5FD_t *file, hid_t dxpl_id, hbool_t closing);
-    // H5_DLL herr_t H5FDtruncate(H5FD_t *file, hid_t dxpl_id, hbool_t closing);
-    // H5_DLL herr_t H5FDlock(H5FD_t *file, hbool_t rw);
-    // H5_DLL herr_t H5FDunlock(H5FD_t *file);
-    // H5_DLL herr_t H5FDdriver_query(hid_t driver_id, unsigned long *flags/*out*/);
+    //  hid_t H5FDregister(const H5FD_class_t *cls);
+    //  herr_t H5FDunregister(hid_t driver_id);
+    //  H5FD_t *H5FDopen(const char *name, unsigned flags, hid_t fapl_id, haddr_t maxaddr);
+    //  herr_t H5FDclose(H5FD_t *file);
+    //  int H5FDcmp(const H5FD_t *f1, const H5FD_t *f2);
+    //  int H5FDquery(const H5FD_t *f, unsigned long *flags);
+    //  haddr_t H5FDalloc(H5FD_t *file, H5FD_mem_t type, hid_t dxpl_id, hsize_t size);
+    //  herr_t H5FDfree(H5FD_t *file, H5FD_mem_t type, hid_t dxpl_id, haddr_t addr, hsize_t size);
+    //  haddr_t H5FDget_eoa(H5FD_t *file, H5FD_mem_t type);
+    //  herr_t H5FDset_eoa(H5FD_t *file, H5FD_mem_t type, haddr_t eoa);
+    //  haddr_t H5FDget_eof(H5FD_t *file, H5FD_mem_t type);
+    //  herr_t H5FDget_vfd_handle(H5FD_t *file, hid_t fapl, void**file_handle);
+    //  herr_t H5FDread(H5FD_t *file, H5FD_mem_t type, hid_t dxpl_id, haddr_t addr, size_t size, void *buf/*out*/);
+    //  herr_t H5FDwrite(H5FD_t *file, H5FD_mem_t type, hid_t dxpl_id, haddr_t addr, size_t size, const void *buf);
+    //  herr_t H5FDflush(H5FD_t *file, hid_t dxpl_id, hbool_t closing);
+    //  herr_t H5FDtruncate(H5FD_t *file, hid_t dxpl_id, hbool_t closing);
+    //  herr_t H5FDlock(H5FD_t *file, hbool_t rw);
+    //  herr_t H5FDunlock(H5FD_t *file);
+    //  herr_t H5FDdriver_query(hid_t driver_id, unsigned long *flags/*out*/);
 
     // ////////////////////////////////////////////////////////////
     // //
@@ -3794,7 +3794,7 @@ public class H5 implements java.io.Serializable {
 
     // ////////////////////////////////////////////////////////////
     // //
-    // H5I: HDF5 1.8 Identifier Interface API Functions //
+    // H5I: HDF5 Identifier Interface API Functions //
     // //
     // ////////////////////////////////////////////////////////////
 
@@ -3950,12 +3950,20 @@ public class H5 implements java.io.Serializable {
 
     // hid_t H5Iregister(H5I_type_t type, const void *object);
 
+    // typedef herr_t (*H5I_free_t)(void *);
     // H5I_type_t H5Iregister_type(size_t hash_size, unsigned reserved, H5I_free_t free_func);
 
     // void *H5Iremove_verify(hid_t id, H5I_type_t id_type);
 
+    // Type of the function to compare objects & keys
+    // typedef int (*H5I_search_func_t)(void *obj, hid_t id, void *key);
     // void *H5Isearch(H5I_type_t type, H5I_search_func_t func, void *key);
 
+    // Type of the H5Iiterate callback function
+    // typedef herr_t (*H5I_iterate_func_t)(hid_t id, void *udata);
+    // herr_t H5Iiterate(H5I_type_t type, H5I_iterate_func_t op, void *op_data);
+
+
     // //////////////////////////////////////////////////////////////////
     // H5L: Link Interface Functions //
     // //////////////////////////////////////////////////////////////////
@@ -4983,9 +4991,9 @@ public class H5 implements java.io.Serializable {
     public synchronized static native void H5Orefresh(long object_id) throws HDF5LibraryException;
 
     // /////// unimplemented ////////
-    // H5_DLL herr_t H5Odisable_mdc_flushes(hid_t object_id);
-    // H5_DLL herr_t H5Oenable_mdc_flushes(hid_t object_id);
-    // H5_DLL herr_t H5Oare_mdc_flushes_disabled(hid_t object_id, hbool_t *are_disabled);
+    //  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);
 
     // ////////////////////////////////////////////////////////////
     // //
@@ -5270,6 +5278,27 @@ public class H5 implements java.io.Serializable {
 
     private synchronized static native long _H5Pcopy(long plist) throws HDF5LibraryException;
 
+    // Define property list class callback function pointer types
+    // typedef herr_t (*H5P_cls_create_func_t)(hid_t prop_id, void *create_data);
+    // typedef herr_t (*H5P_cls_copy_func_t)(hid_t new_prop_id, hid_t old_prop_id, void *copy_data);
+    // typedef herr_t (*H5P_cls_close_func_t)(hid_t prop_id, void *close_data);
+
+    // Define property list callback function pointer types
+    // typedef herr_t (*H5P_prp_cb1_t)(const char *name, size_t size, void *value);
+    // typedef herr_t (*H5P_prp_cb2_t)(hid_t prop_id, const char *name, size_t size, void *value);
+    // typedef H5P_prp_cb1_t H5P_prp_create_func_t;
+    // typedef H5P_prp_cb2_t H5P_prp_set_func_t;
+    // typedef H5P_prp_cb2_t H5P_prp_get_func_t;
+    // typedef herr_t (*H5P_prp_encode_func_t)(const void *value, void **buf, size_t *size);
+    // typedef herr_t (*H5P_prp_decode_func_t)(const void **buf, void *value);
+    // typedef H5P_prp_cb2_t H5P_prp_delete_func_t;
+    // typedef H5P_prp_cb1_t H5P_prp_copy_func_t;
+    // typedef int (*H5P_prp_compare_func_t)(const void *value1, const void *value2, size_t size);
+    // typedef H5P_prp_cb1_t H5P_prp_close_func_t;
+
+    // Define property list iteration function type
+    // typedef herr_t (*H5P_iterate_t)(hid_t id, const char *name, void *iter_data);
+
     public static long H5Pcreate_class_nocb(long parent_class, String name) throws HDF5LibraryException {
         long id = _H5Pcreate_class_nocb(parent_class, name);
           if (id > 0) {
@@ -6433,6 +6462,11 @@ public class H5 implements java.io.Serializable {
     public synchronized static native void H5Pset_evict_on_close(long fapl_id, boolean evict_on_close)
             throws HDF5LibraryException;
 
+    //  /////  unimplemented /////
+    // herr_t H5Pset_vol(hid_t plist_id, hid_t new_vol_id, const void *new_vol_info);
+    // herr_t H5Pget_vol_id(hid_t plist_id, hid_t *vol_id);
+    // herr_t H5Pget_vol_info(hid_t plist_id, void **vol_info);
+
     // Dataset creation property list (DCPL) routines //
 
     /**
@@ -7811,13 +7845,13 @@ public class H5 implements java.io.Serializable {
     // herr_t H5Pget_core_write_tracking(hid_t fapl_id, hbool_t *is_enabled, size_t *page_size);
     // #ifdef H5_HAVE_PARALLEL
     // herr_t H5Pset_all_coll_metadata_ops(hid_t accpl_id, hbool_t is_collective);
-    // H5_DLL herr_t H5Pget_all_coll_metadata_ops(hid_t plist_id, hbool_t *is_collective);
+    //  herr_t H5Pget_all_coll_metadata_ops(hid_t plist_id, hbool_t *is_collective);
     // herr_t H5Pset_coll_metadata_write(hid_t fapl_id, hbool_t is_collective);
     // herr_t H5Pget_coll_metadata_write(hid_t fapl_id, hbool_t *is_collective);
     // #endif /* H5_HAVE_PARALLEL */
-    // H5_DLL herr_t H5Pset_mdc_image_config(hid_t plist_id, H5AC_cache_image_config_t *config_ptr);
-    // H5_DLL herr_t H5Pget_mdc_image_config(hid_t plist_id, H5AC_cache_image_config_t *config_ptr /*out*/);
-    // H5_DLL herr_t H5Pset_page_buffer_size(hid_t plist_id, size_t buf_size, unsigned min_meta_per, unsigned min_raw_per);
+    //  herr_t H5Pset_mdc_image_config(hid_t plist_id, H5AC_cache_image_config_t *config_ptr);
+    //  herr_t H5Pget_mdc_image_config(hid_t plist_id, H5AC_cache_image_config_t *config_ptr /*out*/);
+    //  herr_t H5Pset_page_buffer_size(hid_t plist_id, size_t buf_size, unsigned min_meta_per, unsigned min_raw_per);
     // herr_t H5Pget_page_buffer_size(hid_t fapl_id, size_t *buf_size, unsigned *min_meta_perc, unsigned *min_raw_perc);
     // herr_t H5Pset_object_flush_cb (hid_t fapl_id, H5F_flush_cb_t func, void *user_data);
     // herr_t H5Pget_object_flush_cb (hid_t fapl_id, H5F_flush_cb_t *func, void **user_data);
@@ -7840,9 +7874,9 @@ public class H5 implements java.io.Serializable {
     // herr_t H5Pget_type_conv_cb(hid_t plist, H5T_conv_except_func_t *func, void **op_data)
     // herr_t H5Pset_type_conv_cb( hid_t plist, H5T_conv_except_func_t func, void *op_data)
     // #ifdef H5_HAVE_PARALLEL
-    // H5_DLL herr_t H5Pget_mpio_actual_chunk_opt_mode(hid_t plist_id, H5D_mpio_actual_chunk_opt_mode_t *actual_chunk_opt_mode);
-    // H5_DLL herr_t H5Pget_mpio_actual_io_mode(hid_t plist_id, H5D_mpio_actual_io_mode_t *actual_io_mode);
-    // H5_DLL herr_t H5Pget_mpio_no_collective_cause(hid_t plist_id, uint32_t *local_no_collective_cause, uint32_t *global_no_collective_cause);
+    //  herr_t H5Pget_mpio_actual_chunk_opt_mode(hid_t plist_id, H5D_mpio_actual_chunk_opt_mode_t *actual_chunk_opt_mode);
+    //  herr_t H5Pget_mpio_actual_io_mode(hid_t plist_id, H5D_mpio_actual_io_mode_t *actual_io_mode);
+    //  herr_t H5Pget_mpio_no_collective_cause(hid_t plist_id, uint32_t *local_no_collective_cause, uint32_t *global_no_collective_cause);
     // #endif /* H5_HAVE_PARALLEL */
 
     // Link creation property list (LCPL) routines //
@@ -8785,16 +8819,17 @@ public class H5 implements java.io.Serializable {
 
     // /////// unimplemented ////////
     // #ifdef NEW_HYPERSLAB_API
-    // H5_DLL hid_t H5Scombine_hyperslab(hid_t space_id, H5S_seloper_t op,
+    //  hid_t H5Scombine_hyperslab(hid_t space_id, H5S_seloper_t op,
     //                                  const hsize_t start[],
     //                                  const hsize_t _stride[],
     //                                  const hsize_t count[],
     //                                  const hsize_t _block[]);
-    // H5_DLL herr_t H5Sselect_select(hid_t space1_id, H5S_seloper_t op,
+    // herr_t H5Sselect_select(hid_t space1_id, H5S_seloper_t op,
     //                                  hid_t space2_id);
-    // H5_DLL hid_t H5Scombine_select(hid_t space1_id, H5S_seloper_t op,
+    // hid_t H5Scombine_select(hid_t space1_id, H5S_seloper_t op,
     //                                  hid_t space2_id);
     // #endif /* NEW_HYPERSLAB_API */
+    // herr_t H5Sselect_copy(hid_t dst_id, hid_t src_id);
 
 
 
@@ -10273,6 +10308,25 @@ public class H5 implements java.io.Serializable {
 
     // ////////////////////////////////////////////////////////////
     // //
+    // H5VL: VOL Interface Functions //
+    // //
+    // ////////////////////////////////////////////////////////////
+
+    /// VOL Connector Functionality
+    public synchronized static native long H5VLregister_connector_by_name(String connector_name, long vipl_id);
+    public synchronized static native long H5VLregister_connector_by_value(int connector_value, long vipl_id);
+    public synchronized static native boolean H5VLis_connector_registered(String name);
+    public synchronized static native long H5VLget_connector_id(String name);
+    public synchronized static native String H5VLget_connector_name(long object_id);
+    public synchronized static native void H5VLclose(long connector_id);
+    public synchronized static native void H5VLunregister_connector(long connector_id);
+
+    // /////// unimplemented ////////
+    // hid_t H5VLregister_connector(const H5VL_class_t *cls, hid_t vipl_id);
+
+
+    // ////////////////////////////////////////////////////////////
+    // //
     // H5Z: Filter Interface Functions //
     // //
     // ////////////////////////////////////////////////////////////
@@ -10283,9 +10337,9 @@ public class H5 implements java.io.Serializable {
 
     public synchronized static native int H5Zunregister(int filter) throws HDF5LibraryException, NullPointerException;
 
-}
+    // /////// unimplemented ////////
 
-// /////// unimplemented ////////
+    // herr_t H5Zregister(const void *cls);
 
-// herr_t H5Zregister(const void *cls);
+}