Stamminger, Johannes wrote:
Hi!
On Mo, 2010-04-12 at 15:39 -0500, Peter Cao wrote:
wrapping the native shared libraries. And it is *not* hdf-java as this
does not support the H5PT but using JNA for that purpose.
Still interested?
...
It will be very helpful to see the difference of JNA and JNI. The
current hdf-java JNI was carefully
designed so that the memory allocated in Java is directly used in the
JNI C. The overhead between
Java and C is very small, i.e. the I/O from JNI calls is close to C.
A good way to test is to read and write a simple 1-D array, e.g.
float[10*1024*1024] in JNA and
in C (directly use the HDF5 library) and see the results.
JNA with using there "direct mapping" (as I do) intends to be nearly as
fast as JNI (in the background it seems to do just the same. But it has
to do some initial additional shared library analysis).
Indeed, a JNI comparison would be interesting. Maybe I go for this
later, currently this is not my main target ...
You don't have to compare with JNI. Just compare to a simple C program.
If JNA is close to C in terms of memory usage and io speed, JNA is a way
to go.
FYI find attached my JNA java sources. Put the jna.jar to the classpath,
set the system property jna.library.path to a directory containing the
hdf libs in the same architecture as your java vm (32/64 bit) and write
some java code to access hdf files - that's it.
You have then exactly the same api as when writing plain C stuff with -
as far as i understand the jna - sharing the mem between the native and
the java part, too, as you told for hdf-java.
One of my major problems with this JNA approach remain the hdf constants
as they are not available in the hdf native libs as symbols, only as
#define's. My current workaround is to use - only for this purpose - the
hdf-java's HDF5Constants (implicating to additionally put the hdf native
libs to the java.library.path and the hdf-java jar's to the classpath).
But I will contact the helpdesk to simply add the constants additionally
as symbols to the native libs. And in the meanwhile I will do this
myself with patching and compiling the sources.
Btw the hdf-java suffers the same and has written some JNI code for this
purpose.
Some ( or most) of the HDF5 constant values are defined at runtime.
There is no way to get such
C constants in Java directly. This is why we use private function calls
in JNI to get the values.
Best regards,
Johannes Stamminger
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_______________________________________________
Hdf-forum is for HDF software users discussion.
[email protected]
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
