Mixing upstream HDF5 bindings and JavaCPP bindings, HDF5 1.14.0 #1320

mkitti · 2023-02-01T00:11:57Z

mkitti
Feb 1, 2023

The upstream HDF5 library comes with Java bindings itself:
https://github.com/HDFGroup/hdf5/tree/develop/java

Is there a way to build both those bindings and the JavaCPP bindings together?

Also HDF5 1.14.0 has been released:
https://www.hdfgroup.org/2022/12/release-of-hdf5-1-14-0-newsletter-189/

saudet · 2023-02-01T00:34:02Z

saudet
Feb 1, 2023
Maintainer

We can bundle those Java bindings with the presets, yes. Contributions are welcome! It's probably just a matter of copying those Java sources files to cppbuild/java as part of the cppbuild.sh script, for example, as per the one for OpenCV here:
https://github.com/bytedeco/javacpp-presets/blob/master/opencv/cppbuild.sh#L453

5 replies

mkitti Feb 1, 2023
Author

Yes, but there is also additional C code to facilitate the JNI bindings there:
https://github.com/HDFGroup/hdf5/tree/develop/java/src/jni
Some of this likely duplicates the JavaCPP generated bindings.

We can activate the generation of their JNI binary via a cmake option HDF5_BUILD_JAVA=ON.

saudet Feb 1, 2023
Maintainer

Right, we need the JNI code as well. Enabling it in the build like that and bundling it should work.

mkitti Feb 19, 2023
Author

I would still like to do this as well though. Let me see if I can work on the pull request.

mkitti Feb 23, 2023
Author

I'm getting myself a bit confused. There are two artifacts of interest here:

libhdf5_java.so
jarhdf5-1.14.0.jar

My main goal here is to capture libhdf5_java.so into the platform specific jars. I'm questioning if we should repackage the contents of jarhdf5-1.14.0.jar. Those classes come with some of their own dependencies (slf4j, hamcrest).

javacpp-presets/hdf5/cppbuild/linux-x86_64/lib$ ls
jarhdf5-1.14.0.jar  libhdf5_cpp.la      libhdf5_cpp.so.310.0.0  libhdf5_hl_cpp.la      libhdf5_hl_cpp.so.310.0.0  libhdf5_hl.so.310      libhdf5_java.so   libhdf5.so
libhdf5.a           libhdf5_cpp.so      libhdf5_hl.a            libhdf5_hl_cpp.so      libhdf5_hl.la              libhdf5_hl.so.310.0.0  libhdf5.la        libhdf5.so.310
libhdf5_cpp.a       libhdf5_cpp.so.310  libhdf5_hl_cpp.a        libhdf5_hl_cpp.so.310  libhdf5_hl.so              libhdf5_java.la        libhdf5.settings  libhdf5.so.310.0.0

javacpp-presets/hdf5/cppbuild/linux-x86_64/lib$ jar tvf jarhdf5-1.14.0.jar 
     0 Thu Feb 23 10:46:00 EST 2023 META-INF/
    77 Thu Feb 23 10:46:00 EST 2023 META-INF/MANIFEST.MF
     0 Thu Feb 23 09:31:50 EST 2023 hdf/hdf5lib/
  3510 Thu Feb 23 09:31:50 EST 2023 hdf/hdf5lib/HDFNativeData.class
  4180 Thu Feb 23 09:31:50 EST 2023 hdf/hdf5lib/ArrayDescriptor.class
 12551 Thu Feb 23 09:31:50 EST 2023 hdf/hdf5lib/HDFArray.class
 46612 Thu Feb 23 09:31:50 EST 2023 hdf/hdf5lib/HDF5Constants.class
     0 Thu Feb 23 09:31:48 EST 2023 hdf/hdf5lib/structs/
  1749 Thu Feb 23 09:31:48 EST 2023 hdf/hdf5lib/structs/H5FD_ros3_fapl_t.class
   804 Thu Feb 23 09:31:48 EST 2023 hdf/hdf5lib/structs/H5L_info_t.class
   714 Thu Feb 23 09:31:48 EST 2023 hdf/hdf5lib/structs/H5O_token_t.class
  1779 Thu Feb 23 09:31:48 EST 2023 hdf/hdf5lib/structs/H5AC_cache_config_t.class
   720 Thu Feb 23 09:31:48 EST 2023 hdf/hdf5lib/structs/H5O_info_t.class
   592 Thu Feb 23 09:31:48 EST 2023 hdf/hdf5lib/structs/H5_ih_info_t.class
   794 Thu Feb 23 09:31:48 EST 2023 hdf/hdf5lib/structs/H5F_info2_t.class
   921 Thu Feb 23 09:31:48 EST 2023 hdf/hdf5lib/structs/H5O_native_info_t.class
  1105 Thu Feb 23 09:31:48 EST 2023 hdf/hdf5lib/structs/H5O_hdr_info_t.class
   664 Thu Feb 23 09:31:48 EST 2023 hdf/hdf5lib/structs/H5E_error2_t.class
   481 Thu Feb 23 09:31:48 EST 2023 hdf/hdf5lib/structs/H5A_info_t.class
   393 Thu Feb 23 09:31:48 EST 2023 hdf/hdf5lib/structs/H5G_info_t.class
  1879 Thu Feb 23 09:31:48 EST 2023 hdf/hdf5lib/structs/H5FD_hdfs_fapl_t.class
 57116 Thu Feb 23 09:31:48 EST 2023 hdf/hdf5lib/H5.class
     0 Thu Feb 23 09:31:48 EST 2023 hdf/hdf5lib/callbacks/
   252 Thu Feb 23 09:31:48 EST 2023 hdf/hdf5lib/callbacks/H5P_cls_copy_func_cb.class
   121 Thu Feb 23 09:31:48 EST 2023 hdf/hdf5lib/callbacks/Callbacks.class
   127 Thu Feb 23 09:31:48 EST 2023 hdf/hdf5lib/callbacks/H5D_append_t.class
   227 Thu Feb 23 09:31:48 EST 2023 hdf/hdf5lib/callbacks/H5P_prp_set_func_cb.class
   129 Thu Feb 23 09:31:48 EST 2023 hdf/hdf5lib/callbacks/H5P_iterate_t.class
   123 Thu Feb 23 09:31:48 EST 2023 hdf/hdf5lib/callbacks/H5E_walk_t.class
   143 Thu Feb 23 09:31:48 EST 2023 hdf/hdf5lib/callbacks/H5P_cls_close_func_t.class
   129 Thu Feb 23 09:31:48 EST 2023 hdf/hdf5lib/callbacks/H5D_iterate_t.class
   232 Thu Feb 23 09:31:48 EST 2023 hdf/hdf5lib/callbacks/H5P_prp_create_func_cb.class
   257 Thu Feb 23 09:31:48 EST 2023 hdf/hdf5lib/callbacks/H5P_cls_create_func_cb.class
   129 Thu Feb 23 09:31:48 EST 2023 hdf/hdf5lib/callbacks/H5A_iterate_t.class
   288 Thu Feb 23 09:31:48 EST 2023 hdf/hdf5lib/callbacks/H5O_iterate_t.class
   230 Thu Feb 23 09:31:48 EST 2023 hdf/hdf5lib/callbacks/H5P_prp_close_func_cb.class
   258 Thu Feb 23 09:31:48 EST 2023 hdf/hdf5lib/callbacks/H5E_walk_cb.class
   288 Thu Feb 23 09:31:48 EST 2023 hdf/hdf5lib/callbacks/H5L_iterate_t.class
   228 Thu Feb 23 09:31:48 EST 2023 hdf/hdf5lib/callbacks/H5P_prp_copy_func_cb.class
   227 Thu Feb 23 09:31:48 EST 2023 hdf/hdf5lib/callbacks/H5P_prp_get_func_cb.class
   143 Thu Feb 23 09:31:48 EST 2023 hdf/hdf5lib/callbacks/H5O_iterate_opdata_t.class
   232 Thu Feb 23 09:31:48 EST 2023 hdf/hdf5lib/callbacks/H5D_append_cb.class
   141 Thu Feb 23 09:31:48 EST 2023 hdf/hdf5lib/callbacks/H5P_cls_copy_func_t.class
   251 Thu Feb 23 09:31:48 EST 2023 hdf/hdf5lib/callbacks/H5P_iterate_cb.class
   254 Thu Feb 23 09:31:48 EST 2023 hdf/hdf5lib/callbacks/H5P_cls_close_func_cb.class
   143 Thu Feb 23 09:31:48 EST 2023 hdf/hdf5lib/callbacks/H5L_iterate_opdata_t.class
   218 Thu Feb 23 09:31:48 EST 2023 hdf/hdf5lib/callbacks/H5P_prp_compare_func_cb.class
   238 Thu Feb 23 09:31:48 EST 2023 hdf/hdf5lib/callbacks/H5D_iterate_cb.class
   233 Thu Feb 23 09:31:48 EST 2023 hdf/hdf5lib/callbacks/H5P_prp_delete_func_cb.class
   283 Thu Feb 23 09:31:48 EST 2023 hdf/hdf5lib/callbacks/H5A_iterate_cb.class
   145 Thu Feb 23 09:31:48 EST 2023 hdf/hdf5lib/callbacks/H5P_cls_create_func_t.class
     0 Thu Feb 23 09:31:48 EST 2023 hdf/hdf5lib/exceptions/
   350 Thu Feb 23 09:31:48 EST 2023 hdf/hdf5lib/exceptions/HDF5DataFiltersException.class
   370 Thu Feb 23 09:31:48 EST 2023 hdf/hdf5lib/exceptions/HDF5PropertyListInterfaceException.class
   354 Thu Feb 23 09:31:48 EST 2023 hdf/hdf5lib/exceptions/HDF5InternalErrorException.class
   346 Thu Feb 23 09:31:48 EST 2023 hdf/hdf5lib/exceptions/HDF5ReferenceException.class
   362 Thu Feb 23 09:31:48 EST 2023 hdf/hdf5lib/exceptions/HDF5DatatypeInterfaceException.class
   364 Thu Feb 23 09:31:48 EST 2023 hdf/hdf5lib/exceptions/HDF5DataspaceInterfaceException.class
   338 Thu Feb 23 09:31:48 EST 2023 hdf/hdf5lib/exceptions/HDF5BtreeException.class
   362 Thu Feb 23 09:31:48 EST 2023 hdf/hdf5lib/exceptions/HDF5FunctionEntryExitException.class
  7490 Thu Feb 23 09:31:48 EST 2023 hdf/hdf5lib/exceptions/HDF5LibraryException.class
   346 Thu Feb 23 09:31:48 EST 2023 hdf/hdf5lib/exceptions/HDF5AttributeException.class
   332 Thu Feb 23 09:31:48 EST 2023 hdf/hdf5lib/exceptions/HDF5IdException.class
   348 Thu Feb 23 09:31:48 EST 2023 hdf/hdf5lib/exceptions/HDF5LowLevelIOException.class
   350 Thu Feb 23 09:31:48 EST 2023 hdf/hdf5lib/exceptions/HDF5SymbolTableException.class
   329 Thu Feb 23 09:31:48 EST 2023 hdf/hdf5lib/exceptions/HDF5JavaException.class
   366 Thu Feb 23 09:31:48 EST 2023 hdf/hdf5lib/exceptions/HDF5ResourceUnavailableException.class
   360 Thu Feb 23 09:31:48 EST 2023 hdf/hdf5lib/exceptions/HDF5DatasetInterfaceException.class
   354 Thu Feb 23 09:31:48 EST 2023 hdf/hdf5lib/exceptions/HDF5FileInterfaceException.class
   360 Thu Feb 23 09:31:48 EST 2023 hdf/hdf5lib/exceptions/HDF5FunctionArgumentException.class
   352 Thu Feb 23 09:31:48 EST 2023 hdf/hdf5lib/exceptions/HDF5ObjectHeaderException.class
   350 Thu Feb 23 09:31:48 EST 2023 hdf/hdf5lib/exceptions/HDF5DataStorageException.class
   447 Thu Feb 23 09:31:48 EST 2023 hdf/hdf5lib/exceptions/HDF5Exception.class
   336 Thu Feb 23 09:31:48 EST 2023 hdf/hdf5lib/exceptions/HDF5HeapException.class
   354 Thu Feb 23 09:31:48 EST 2023 hdf/hdf5lib/exceptions/HDF5MetaDataCacheException.class
   360 Thu Feb 23 09:31:48 EST 2023 hdf/hdf5lib/exceptions/HDF5ExternalFileListException.class

mkitti Feb 23, 2023
Author

I accomplished my initial goals here:
#1327

saudet · 2023-02-19T01:58:41Z

saudet
Feb 19, 2023
Maintainer

I've upgraded the presets for HDF5 1.14.0! Please give it a try with the snapshots: http://bytedeco.org/builds/

1 reply

mkitti Feb 19, 2023
Author

Oh thanks, you got to it before I could.

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Mixing upstream HDF5 bindings and JavaCPP bindings, HDF5 1.14.0 #1320

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Mixing upstream HDF5 bindings and JavaCPP bindings, HDF5 1.14.0 #1320

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