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-rw-r--r--java/src/hdf/CMakeLists.txt2
-rw-r--r--java/src/hdf/hdf5lib/CMakeLists.txt9
-rw-r--r--java/src/hdf/hdf5lib/H5.java158
3 files changed, 144 insertions, 25 deletions
diff --git a/java/src/hdf/CMakeLists.txt b/java/src/hdf/CMakeLists.txt
index ecff984..161ddf1 100644
--- a/java/src/hdf/CMakeLists.txt
+++ b/java/src/hdf/CMakeLists.txt
@@ -1,4 +1,4 @@
cmake_minimum_required (VERSION 3.10)
-PROJECT (HDF5_JAVA_HDF)
+project (HDF5_JAVA_HDF C)
add_subdirectory (hdf5lib)
diff --git a/java/src/hdf/hdf5lib/CMakeLists.txt b/java/src/hdf/hdf5lib/CMakeLists.txt
index 9506fc1..c171ea8 100644
--- a/java/src/hdf/hdf5lib/CMakeLists.txt
+++ b/java/src/hdf/hdf5lib/CMakeLists.txt
@@ -1,14 +1,9 @@
cmake_minimum_required (VERSION 3.10)
-PROJECT (HDF5_JAVA_HDF_HDF5 Java)
+project (HDF5_JAVA_HDF_HDF5 Java)
set (CMAKE_VERBOSE_MAKEFILE 1)
-INCLUDE_DIRECTORIES (
- ${HDF5_JAVA_HDF_HDF5_SOURCE_DIR}
- ${HDF5_JAVA_HDF_HDF5_BINARY_DIR}
- ${HDF5_JAVA_LIB_DIR}
- ${CMAKE_CURRENT_BINARY_DIR}/CMakeFiles/${HDF5_JAVA_HDF5_LIB_CORENAME}.dir/hdf/hdf5lib
-)
+set_directory_properties(PROPERTIES INCLUDE_DIRECTORIES "${HDF5_JAVA_HDF_HDF5_SOURCE_DIR};${HDF5_JAVA_HDF_HDF5_BINARY_DIR};${HDF5_JAVA_LIB_DIR};${CMAKE_CURRENT_BINARY_DIR}/CMakeFiles/${HDF5_JAVA_HDF5_LIB_CORENAME}.dir/hdf/hdf5lib")
SET_GLOBAL_VARIABLE (HDF5_JAVA_SOURCE_PACKAGES
"${HDF5_JAVA_SOURCE_PACKAGES};hdf.hdf5lib.callbacks;hdf.hdf5lib.exceptions;hdf.hdf5lib.structs;hdf.hdf5lib"
diff --git a/java/src/hdf/hdf5lib/H5.java b/java/src/hdf/hdf5lib/H5.java
index 5c4fc40..a37ddf8 100644
--- a/java/src/hdf/hdf5lib/H5.java
+++ b/java/src/hdf/hdf5lib/H5.java
@@ -1276,6 +1276,38 @@ public class H5 implements java.io.Serializable {
// ////////////////////////////////////////////////////////////
// //
+ // H5AC: Cache Interface Functions //
+ // //
+ // ////////////////////////////////////////////////////////////
+
+ // No public Functions
+
+ // ////////////////////////////////////////////////////////////
+ // //
+ // H5B: B-link-tree Interface Functions //
+ // //
+ // ////////////////////////////////////////////////////////////
+
+ // No public Functions
+
+ // ////////////////////////////////////////////////////////////
+ // //
+ // H5B2: v2 B-tree Interface Functions //
+ // //
+ // ////////////////////////////////////////////////////////////
+
+ // No public Functions
+
+ // ////////////////////////////////////////////////////////////
+ // //
+ // H5C: Cache Interface Functions //
+ // //
+ // ////////////////////////////////////////////////////////////
+
+ // No public Functions
+
+ // ////////////////////////////////////////////////////////////
+ // //
// H5D: Datasets Interface Functions //
// //
// ////////////////////////////////////////////////////////////
@@ -2109,6 +2141,10 @@ public class H5 implements java.io.Serializable {
// /////// 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 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);
// herr_t H5Dscatter(H5D_scatter_func_t op, void *op_data, hid_t type_id, hid_t dst_space_id, void *dst_buf);
@@ -2912,12 +2948,22 @@ public class H5 implements java.io.Serializable {
public synchronized static native void H5Fget_mdc_logging_status(long file_id, boolean[] mdc_logging_status)
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);
// 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],
+ // 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);
+ // #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);
+ // #endif /* H5_HAVE_PARALLEL */
// /**
// * H5Fget_vfd_handle returns a pointer to the file handle from the
@@ -2971,6 +3017,41 @@ public class H5 implements java.io.Serializable {
// ////////////////////////////////////////////////////////////
// //
+ // H5FD: File Driver Interface Functions //
+ // //
+ // ////////////////////////////////////////////////////////////
+
+ // /////// 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*/);
+
+ // ////////////////////////////////////////////////////////////
+ // //
+ // H5FS: File Free Space Interface Functions //
+ // //
+ // ////////////////////////////////////////////////////////////
+
+ // No public Functions
+
+ // ////////////////////////////////////////////////////////////
+ // //
// H5G: Group Interface Functions //
// //
// ////////////////////////////////////////////////////////////
@@ -3408,6 +3489,30 @@ public class H5 implements java.io.Serializable {
// ////////////////////////////////////////////////////////////
// //
+ // H5HF: Fractal Heap Interface Functions //
+ // //
+ // ////////////////////////////////////////////////////////////
+
+ // No public Functions
+
+ // ////////////////////////////////////////////////////////////
+ // //
+ // H5HG: Global Heap Interface Functions //
+ // //
+ // ////////////////////////////////////////////////////////////
+
+ // No public Functions
+
+ // ////////////////////////////////////////////////////////////
+ // //
+ // H5HL: Local Heap Interface Functions //
+ // //
+ // ////////////////////////////////////////////////////////////
+
+ // No public Functions
+
+ // ////////////////////////////////////////////////////////////
+ // //
// H5I: HDF5 1.8 Identifier Interface API Functions //
// //
// ////////////////////////////////////////////////////////////
@@ -4033,6 +4138,15 @@ public class H5 implements java.io.Serializable {
// H5_index_t idx_type, H5_iter_order_t order, hsize_t n,
// void *buf/*out*/, size_t size, hid_t lapl_id);
+ // ////////////////////////////////////////////////////////////
+ // //
+ // H5MM: Memory Management Interface API Functions //
+ // //
+ // ////////////////////////////////////////////////////////////
+
+ // /////// unimplemented ////////
+ // typedef void *(*H5MM_allocate_t)(size_t size, void *alloc_info);
+ // typedef void (*H5MM_free_t)(void *mem, void *free_info);
// ////////////////////////////////////////////////////////////
// //
@@ -4450,6 +4564,9 @@ 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);
// ////////////////////////////////////////////////////////////
// //
@@ -7273,9 +7390,15 @@ public class H5 implements java.io.Serializable {
// herr_t H5Pset_file_image_callbacks(hid_t fapl_id, H5FD_file_image_callbacks_t *callbacks_ptr);
// herr_t H5Pset_core_write_tracking(hid_t fapl_id, hbool_t is_enabled, size_t page_size);
// 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 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 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);
@@ -7297,6 +7420,11 @@ public class H5 implements java.io.Serializable {
// *free_info )
// 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);
+ // #endif /* H5_HAVE_PARALLEL */
// Link creation property list (LCPL) routines //
@@ -7314,21 +7442,6 @@ public class H5 implements java.io.Serializable {
// herr_t H5Pget_mcdt_search_cb(hid_t plist_id, H5O_mcdt_search_cb_t *func, void **op_data);
// herr_t H5Pset_mcdt_search_cb(hid_t plist_id, H5O_mcdt_search_cb_t func, void *op_data);
-
- // Other/Older property list routines //
- // herr_t H5Pget_fapl_mpio( int fapl_id, MPI_Comm *comm, MPI_Info *info )
- // herr_t H5Pset_fapl_mpio( int fapl_id, MPI_Comm comm, MPI_Info info )
-
- // herr_t H5Pget_fapl_mpiposix( int fapl_id, MPI_Comm *comm, hbool_t *use_gpfs_hints )
- // herr_t H5Pset_fapl_mpiposix( int fapl_id, MPI_Comm comm, hbool_t use_gpfs_hints )
-
- // herr_t H5Pget_dxpl_mpio( hid_t dxpl_id, H5FD_mpio_xfer_t *xfer_mode )
- // herr_t H5Pset_dxpl_mpio( hid_t dxpl_id, H5FD_mpio_xfer_t xfer_mode )
- // herr_t H5Pset_dxpl_mpio_chunk_opt (hid_t dxpl_id, H5FD_mpio_chunk_opt_t opt_mode)
- // herr_t H5Pset_dxpl_mpio_chunk_opt_num (hid_t dxpl_id, unsigned num_chunk_per_proc)
- // herr_t H5Pset_dxpl_mpio_chunk_opt_ratio (hid_t dxpl_id, unsigned percent_proc_per_chunk)
- // herr_t H5Pset_dxpl_mpio_collective_opt (hid_t dxpl_id, H5FD_mpio_collective_opt_t opt_mode)
-
// ////////////////////////////////////////////////////////////
// //
// H5PL: HDF5 1.8 Plugin API Functions //
@@ -8252,6 +8365,17 @@ public class H5 implements java.io.Serializable {
public synchronized static native boolean H5Sis_regular_hyperslab(long space_id) throws HDF5LibraryException;
// /////// unimplemented ////////
+ // #ifdef NEW_HYPERSLAB_API
+ // H5_DLL 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,
+ // hid_t space2_id);
+ // H5_DLL hid_t H5Scombine_select(hid_t space1_id, H5S_seloper_t op,
+ // hid_t space2_id);
+ // #endif /* NEW_HYPERSLAB_API */