Re: [Hdf-forum] Reading an HDF5 file in Java
You have to use the HDF5 JNI libray, which was built with Java JNI and the HDF5 C library. You can find the instructions for installing and using HDF-Java at http://www.hdfgroup.org/hdf-java-html/install_use_hdf_java_products.pdf Thanks --pc On 5/17/2013 1:44 AM, marko.kurm wrote: Ok, didn't realize that. Thanks! Now I downloaded the actual HDF5 library and installed it. I added the following to the VM arguments: -Djava.library.path=C:\Program Files\HDF_Group\HDF5\1.8.11\bin ( this is where the DLLs are). And at least this code runs through without exceptions: System.loadLibrary(hdf5); System.loadLibrary(hdf5_hl); System.loadLibrary(jhdf5); So it seems that the libraries are loaded at least. But when I run the following, I still get the same exception (java.lang.UnsatisfiedLinkError: ncsa.hdf.hdf5lib.H5.H5Gget_obj_info_all(ILjava/lang/String;[Ljava/lang/String;[I[JI)I): H5File h5file = new H5File(C:\\dev\\workspaces\\hdf5\\hdf5\\src\\main\\java\\com\\vaisala\\hdf5\\hdf5_test.h5, HDF5Constants.H5F_ACC_RDONLY); h5file.open(); h5file.close(); Is there something I could still try? -- View this message in context: http://hdf-forum.184993.n3.nabble.com/Reading-an-HDF5-file-in-Java-tp4026180p4026196.html Sent from the hdf-forum mailing list archive at Nabble.com. ___ Hdf-forum is for HDF software users discussion. Hdf-forum@hdfgroup.org http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org ___ Hdf-forum is for HDF software users discussion. Hdf-forum@hdfgroup.org http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
Re: [Hdf-forum] Reading an HDF5 file in Java
Ok, didn't realize that. Thanks! Now I downloaded the actual HDF5 library and installed it. I added the following to the VM arguments: -Djava.library.path=C:\Program Files\HDF_Group\HDF5\1.8.11\bin ( this is where the DLLs are). And at least this code runs through without exceptions: System.loadLibrary(hdf5); System.loadLibrary(hdf5_hl); System.loadLibrary(jhdf5); So it seems that the libraries are loaded at least. But when I run the following, I still get the same exception (java.lang.UnsatisfiedLinkError: ncsa.hdf.hdf5lib.H5.H5Gget_obj_info_all(ILjava/lang/String;[Ljava/lang/String;[I[JI)I): H5File h5file = new H5File(C:\\dev\\workspaces\\hdf5\\hdf5\\src\\main\\java\\com\\vaisala\\hdf5\\hdf5_test.h5, HDF5Constants.H5F_ACC_RDONLY); h5file.open(); h5file.close(); Is there something I could still try? -- View this message in context: http://hdf-forum.184993.n3.nabble.com/Reading-an-HDF5-file-in-Java-tp4026180p4026196.html Sent from the hdf-forum mailing list archive at Nabble.com. ___ Hdf-forum is for HDF software users discussion. Hdf-forum@hdfgroup.org http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
Re: [Hdf-forum] Reading an HDF5 file in Java
Thanks for the help guys!I have the DLL files in the system path + I added the following arguments to the run configuration:-Djava.library.path=C:/dev/hdf5/hdf-java/lib/win-Dncsa.hdf.hdf5lib.H5.hdf5lib=C:/dev/hdf5/hdf-java/lib/win/jhdf5.dlland inside C:/dev/hdf5/hdf-java/lib/win folder, I have two files: jhdf5.dll jhdf.dll. At first I had the problem that the DLL-s where not on the path, but in that case, it throws a java.lang.UnsatisfiedLinkError: no jhdf5 in java.library.path exception so this is not the case.Anyway, I still get the same error message: Exception in thread main java.lang.UnsatisfiedLinkError: ncsa.hdf.hdf5lib.H5.H5Gget_obj_info_all(ILjava/lang/String;[Ljava/lang/String;[I[JI)II took a look inside the DLL-s (with DLL Export Viewer http://www.nirsoft.net/utils/dll_export_viewer.html ) to see what functions they export and I didn't see the H5Gget_obj_info_all function there. Maybe I'm missing some DLL? I only have the two that came with downloading this file http://www.hdfgroup.org/ftp/HDF5/hdf-java/bin/win64/hdf-java-2.9-bin.tar What kind of HDF DLL-s do you have on your paths? -- View this message in context: http://hdf-forum.184993.n3.nabble.com/Reading-an-HDF5-file-in-Java-tp4026180p4026189.html Sent from the hdf-forum mailing list archive at Nabble.com.___ Hdf-forum is for HDF software users discussion. Hdf-forum@hdfgroup.org http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
Re: [Hdf-forum] Reading an HDF5 file in Java
Sorry, the formatting didn't work. Here it is again: I have the DLL files in the system path + I added the following arguments to the run configuration: -Djava.library.path=C:/dev/hdf5/hdf-java/lib/win -Dncsa.hdf.hdf5lib.H5.hdf5lib=C:/dev/hdf5/hdf-java/lib/win/jhdf5.dll and inside C:/dev/hdf5/hdf-java/lib/win folder, I have two files: jhdf5.dll jhdf.dll. At first I had the problem that the DLL-s where not on the path, but in that case, it throws a java.lang.UnsatisfiedLinkError: no jhdf5 in java.library.path exception so this is not the case. Anyway, I still get the same error message: Exception in thread main java.lang.UnsatisfiedLinkError: ncsa.hdf.hdf5lib.H5.H5Gget_obj_info_all(ILjava/lang/ String;[Ljava/lang/String;[I[JI)I I took a look inside the DLL-s (with DLL Export Viewerhttp://www.nirsoft.net/utils/dll_export_viewer.html) to see what functions they export and I didn't see the H5Gget_obj_info_all function there. Maybe I'm missing some DLL? I only have the two that came with downloading this filehttp://www.hdfgroup.org/ftp/HDF5/hdf-java/bin/win64/hdf-java-2.9-bin.tar What kind of HDF DLL-s do you have on your paths? 2013/5/16 marko.kurm marko.k...@gmail.com Thanks for the help guys! I have the DLL files in the system path + I added the following arguments to the run configuration: -Djava.library.path=C:/dev/hdf5/hdf-java/lib/win -Dncsa.hdf.hdf5lib.H5.hdf5lib=C:/dev/hdf5/hdf-java/lib/win/jhdf5.dll and inside C:/dev/hdf5/hdf-java/lib/win folder, I have two files: jhdf5.dll jhdf.dll. At first I had the problem that the DLL-s where not on the path, but in that case, it throws a java.lang.UnsatisfiedLinkError: no jhdf5 in java.library.path exception so this is not the case. Anyway, I still get the same error message: Exception in thread main java.lang.UnsatisfiedLinkError: ncsa.hdf.hdf5lib.H5.H5Gget_obj_info_all(ILjava/lang/String;[Ljava/lang/String;[I[JI)I I took a look inside the DLL-s (with DLL Export Viewerhttp://www.nirsoft.net/utils/dll_export_viewer.html) to see what functions they export and I didn't see the H5Gget_obj_info_all function there. Maybe I'm missing some DLL? I only have the two that came with downloading this filehttp://www.hdfgroup.org/ftp/HDF5/hdf-java/bin/win64/hdf-java-2.9-bin.tarWhat kind of HDF DLL-s do you have on your paths? -- View this message in context: Re: Reading an HDF5 file in Javahttp://hdf-forum.184993.n3.nabble.com/Reading-an-HDF5-file-in-Java-tp4026180p4026189.html Sent from the hdf-forum mailing list archivehttp://hdf-forum.184993.n3.nabble.com/at Nabble.com. ___ Hdf-forum is for HDF software users discussion. Hdf-forum@hdfgroup.org http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org ___ Hdf-forum is for HDF software users discussion. Hdf-forum@hdfgroup.org http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
Re: [Hdf-forum] Reading an HDF5 file in Java
Peter is referring to the HDF5 libs; not just the java native interface ones (e.g. jhdf5) The ones of HDF5 itself as in hdf5.dll and hdf5_hl.dll etc. jhdf5.dll jhdf.dll are only the native glue System.load(full path to libs/ jhdf.dll); will show what is needed clearly On 05/16/2013 03:10 AM, Marko Kurm wrote: Sorry, the formatting didn't work. Here it is again: I have the DLL files in the system path + I added the following arguments to the run configuration: -Djava.library.path=C:/dev/hdf5/hdf-java/lib/win -Dncsa.hdf.hdf5lib.H5.hdf5lib=C:/dev/hdf5/hdf-java/lib/win/jhdf5.dll and inside C:/dev/hdf5/hdf-java/lib/win folder, I have two files: jhdf5.dll jhdf.dll. At first I had the problem that the DLL-s where not on the path, but in that case, it throws a java.lang.UnsatisfiedLinkError: no jhdf5 in java.library.path exception so this is not the case. Anyway, I still get the same error message: Exception in thread main java.lang.UnsatisfiedLinkError: ncsa.hdf.hdf5lib.H5.H5Gget_obj_info_all(ILjava/lang/String;[Ljava/lang/String;[I[JI)I I took a look inside the DLL-s (with DLL Export Viewer http://www.nirsoft.net/utils/dll_export_viewer.html) to see what functions they export and I didn't see the H5Gget_obj_info_all function there. Maybe I'm missing some DLL? I only have the two that came with downloading this file http://www.hdfgroup.org/ftp/HDF5/hdf-java/bin/win64/hdf-java-2.9-bin.tar What kind of HDF DLL-s do you have on your paths? 2013/5/16 marko.kurm marko.k...@gmail.com mailto:marko.k...@gmail.com Thanks for the help guys! I have the DLL files in the system path + I added the following arguments to the run configuration: -Djava.library.path=C:/dev/hdf5/hdf-java/lib/win -Dncsa.hdf.hdf5lib.H5.hdf5lib=C:/dev/hdf5/hdf-java/lib/win/jhdf5.dll and inside C:/dev/hdf5/hdf-java/lib/win folder, I have two files: jhdf5.dll jhdf.dll. At first I had the problem that the DLL-s where not on the path, but in that case, it throws a java.lang.UnsatisfiedLinkError: no jhdf5 in java.library.path exception so this is not the case. Anyway, I still get the same error message: Exception in thread main java.lang.UnsatisfiedLinkError: ncsa.hdf.hdf5lib.H5.H5Gget_obj_info_all(ILjava/lang/String;[Ljava/lang/String;[I[JI)I I took a look inside the DLL-s (with DLL Export Viewer http://www.nirsoft.net/utils/dll_export_viewer.html) to see what functions they export and I didn't see the H5Gget_obj_info_all function there. Maybe I'm missing some DLL? I only have the two that came with downloading this file http://www.hdfgroup.org/ftp/HDF5/hdf-java/bin/win64/hdf-java-2.9-bin.tar What kind of HDF DLL-s do you have on your paths? View this message in context: Re: Reading an HDF5 file in Java http://hdf-forum.184993.n3.nabble.com/Reading-an-HDF5-file-in-Java-tp4026180p4026189.html Sent from the hdf-forum mailing list archive http://hdf-forum.184993.n3.nabble.com/ at Nabble.com. ___ Hdf-forum is for HDF software users discussion. Hdf-forum@hdfgroup.org mailto:Hdf-forum@hdfgroup.org http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org ___ Hdf-forum is for HDF software users discussion. Hdf-forum@hdfgroup.org http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org ___ Hdf-forum is for HDF software users discussion. Hdf-forum@hdfgroup.org http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
Re: [Hdf-forum] Reading an HDF5 file in Java
Maybe need to be in a static scope to get it to happen earlier than the
H5 one
example from a linux case I was debugging
..
static
{
try {
//System.loadLibrary(jqb);
//System.load(System.getProperty(QB_HOME)+/lib/libjqb.so);
//System.load(/home/roger/NetBeansProjects/jhdf5hl/dist/libjhdf5hl.so);
//System.load(/home/roger/Software/hdf5-1.8.5/dist/lib/libhdf5_hl.so);
//System.load(/home/roger/Software/hdf5-1.8.5/dist/lib/libhdf5.so);
//System.load(/home/roger/Software/openmpi-1.4.3/dist/lib/libmpi.so);
//System.load(/home/roger/Software/openmpi-1.4.3/dist/lib/libmpi_cxx.so);
//System.loadLibrary(mpi);
System.loadLibrary(open-rte);
System.loadLibrary(open-pal);
System.loadLibrary(mpi);
System.loadLibrary(hdf5);
System.loadLibrary(hdf5_hl);
System.loadLibrary(jhdf5);
//System.loadLibrary(mpi_cxx);
H5.H5open();
//H5.
} catch (UnsatisfiedLinkError e) {
System.err.println(Native code library failed to load.
Unsatisfied Link Error\n + e);
} catch (Exception e) {
System.err.println(Native code library failed to load.
\n + e);
}
int plist = HDF5Constants.H5P_DEFAULT;
int[] version_info = new int[4];
try {
H5.H5Pget_version(plist,version_info);
} catch (Exception ex) {
}
}
..
where I open the commented System.load's to test
On 05/14/2013 09:52 AM, Marko Kurm wrote:
I'm trying to open/read an existing HDF5 file using the Java library.
I have the jhdf.dll and jhdf5.dll files on the system path. The
code I have in my main method is taken from the HDF samples, and looks
like this:
H5File h5file = new
H5File(C:\\dev\\workspaces\\hdf5\\hdf5\\src\\main\\java\\com\\vaisala\\hdf5\\hdf5_test.h5,
HDF5Constants.H5F_ACC_RDONLY);
try
{
// open file and retrieve the file structure
h5file.open();
}
catch (Exception ex)
{
System.out.println(ex);
}
When I run it, it throws the following exception:
Exception in thread main java.lang.UnsatisfiedLinkError:
ncsa.hdf.hdf5lib.H5.H5Gget_obj_info_all(ILjava/lang/String;[Ljava/lang/String;[I[JI)I
at ncsa.hdf.hdf5lib.H5.H5Gget_obj_info_all(Native Method)
at ncsa.hdf.hdf5lib.H5.H5Gget_obj_info_all(H5.java:4588)
at ncsa.hdf.object.h5.H5File.depth_first(H5File.java:1617)
at ncsa.hdf.object.h5.H5File.loadTree(H5File.java:1554)
at ncsa.hdf.object.h5.H5File.open(H5File.java:1520)
at ncsa.hdf.object.h5.H5File.open(H5File.java:1464)
at ncsa.hdf.object.h5.H5File.open(H5File.java:825)
at com.vaisala.hdf5.TestH5File.main(TestH5File.java:24)
Any ideas what could be wrong?
Marko Kurm
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Re: [Hdf-forum] Reading an HDF5 file in Java
you need to set the HDF library path.
If you are running your application from your script, add the library to
the command line, e.g.
java -Djava.library.path=%PATH_TO_THE_DLLS% ...
If you are running with eclipse, set VM argument,
-Djava.library.path=%PATH_TO_THE_DLLS%
under run-Run Configurations-Arguments
On 5/14/2013 8:52 AM, Marko Kurm wrote:
I'm trying to open/read an existing HDF5 file using the Java library.
I have the jhdf.dll and jhdf5.dll files on the system path. The
code I have in my main method is taken from the HDF samples, and looks
like this:
H5File h5file = new
H5File(C:\\dev\\workspaces\\hdf5\\hdf5\\src\\main\\java\\com\\vaisala\\hdf5\\hdf5_test.h5,
HDF5Constants.H5F_ACC_RDONLY);
try
{
// open file and retrieve the file structure
h5file.open();
}
catch (Exception ex)
{
System.out.println(ex);
}
When I run it, it throws the following exception:
Exception in thread main java.lang.UnsatisfiedLinkError:
ncsa.hdf.hdf5lib.H5.H5Gget_obj_info_all(ILjava/lang/String;[Ljava/lang/String;[I[JI)I
at ncsa.hdf.hdf5lib.H5.H5Gget_obj_info_all(Native Method)
at ncsa.hdf.hdf5lib.H5.H5Gget_obj_info_all(H5.java:4588)
at ncsa.hdf.object.h5.H5File.depth_first(H5File.java:1617)
at ncsa.hdf.object.h5.H5File.loadTree(H5File.java:1554)
at ncsa.hdf.object.h5.H5File.open(H5File.java:1520)
at ncsa.hdf.object.h5.H5File.open(H5File.java:1464)
at ncsa.hdf.object.h5.H5File.open(H5File.java:825)
at com.vaisala.hdf5.TestH5File.main(TestH5File.java:24)
Any ideas what could be wrong?
Marko Kurm
___
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___
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
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[Hdf-forum] Reading an HDF5 file in Java
I'm trying to open/read an existing HDF5 file using the Java library. I
have the jhdf.dll and jhdf5.dll files on the system path. The code I
have in my main method is taken from the HDF samples, and looks like this:
H5File h5file = new
H5File(C:\\dev\\workspaces\\hdf5\\hdf5\\src\\main\\java\\com\\vaisala\\hdf5\\hdf5_test.h5,
HDF5Constants.H5F_ACC_RDONLY);
try
{
// open file and retrieve the file structure
h5file.open();
}
catch (Exception ex)
{
System.out.println(ex);
}
When I run it, it throws the following exception:
Exception in thread main java.lang.UnsatisfiedLinkError:
ncsa.hdf.hdf5lib.H5.H5Gget_obj_info_all(ILjava/lang/String;[Ljava/lang/String;[I[JI)I
at ncsa.hdf.hdf5lib.H5.H5Gget_obj_info_all(Native Method)
at ncsa.hdf.hdf5lib.H5.H5Gget_obj_info_all(H5.java:4588)
at ncsa.hdf.object.h5.H5File.depth_first(H5File.java:1617)
at ncsa.hdf.object.h5.H5File.loadTree(H5File.java:1554)
at ncsa.hdf.object.h5.H5File.open(H5File.java:1520)
at ncsa.hdf.object.h5.H5File.open(H5File.java:1464)
at ncsa.hdf.object.h5.H5File.open(H5File.java:825)
at com.vaisala.hdf5.TestH5File.main(TestH5File.java:24)
Any ideas what could be wrong?
Marko Kurm
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