Hello,
What kind of error are you getting? I was able to get the filter to work on
Linux (CentOS 7) with h5dump from 1.8.16 distribution I built. Please notice
that one has to specify HDF5 include files when building liblzf_filter.so.
Details:
Here is the output of the nm command and h5dump when include files are not
specified:
[epourmal@platypus lzf]$ gcc -O2 -fPIC -shared lzf/*.c lzf_filter.c -o
liblzf_filter.so
epourmal@platypus lzf]$ nm liblzf_filter.so
U H5E_CALLBACK_g
U H5E_CANTREGISTER_g
U H5E_PLINE_g
U H5Epush1
U H5Pget_chunk
U H5Pget_filter_by_id2
U H5Pmodify_filter
U H5Tget_size
U H5Zregister
U H5open
[epourmal@platypus lzf]$ hdf5/hdf5/bin/h5dump test_lzf.hdf5
HDF5 "test_lzf.hdf5" {
GROUP "/" {
DATASET "dset" {
DATATYPE H5T_IEEE_F32LE
DATASPACE SIMPLE { ( 100, 100, 100 ) / ( 100, 100, 100 ) }
DATA {h5dump error: unable to print data
}
}
}
}
[epourmal@platypus lzf]$ hdf5/hdf5/bin/h5dump -pH test_lzf.hdf5
HDF5 "test_lzf.hdf5" {
GROUP "/" {
DATASET "dset" {
DATATYPE H5T_IEEE_F32LE
DATASPACE SIMPLE { ( 100, 100, 100 ) / ( 100, 100, 100 ) }
STORAGE_LAYOUT {
CHUNKED ( 1, 100, 100 )
SIZE 174288 (22.951:1 COMPRESSION)
}
FILTERS {
PREPROCESSING SHUFFLE
USER_DEFINED_FILTER {
FILTER_ID 32000
COMMENT lzf
PARAMS { 4 261 40000 }
}
...
Now if I specify HDF5 include files, I will get (notice two symbols
H5PLget_plugin_info/type in the nm output!)
[epourmal@platypus lzf]$ gcc -I//scr/epourmal/h5py-master/lzf/hdf5/hdf5/include
-O2 -fPIC -shared lzf/*.c lzf_filter.c -o liblzf_filter.so
[epourmal@platypus lzf]$ nm liblzf_filter.so
U H5E_CALLBACK_g
U H5E_CANTREGISTER_g
U H5E_PLINE_g
U H5Epush1
0000000000001080 T H5PLget_plugin_info
0000000000001070 T H5PLget_plugin_type
U H5Pget_chunk
U H5Pget_filter_by_id2
U H5Pmodify_filter
U H5Tget_size
U H5Zregister
U H5open
And here we are:
[epourmal@platypus lzf]$ hdf5/hdf5/bin/h5dump test_lzf.hdf5 |more
HDF5 "test_lzf.hdf5" {
GROUP "/" {
DATASET "dset" {
DATATYPE H5T_IEEE_F32LE
DATASPACE SIMPLE { ( 100, 100, 100 ) / ( 100, 100, 100 ) }
DATA {
(0,0,0): 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17,
(0,0,18): 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32,
(0,0,33): 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47,
(0,0,48): 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62,
(0,0,63): 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77,
(0,0,78): 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92,
(0,0,93): 93, 94, 95, 96, 97, 98, 99,
…….
Hope it will help!
Elena
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Elena Pourmal The HDF Group http://hdfgroup.org
1800 So. Oak St., Suite 203, Champaign IL 61820
217.531.6112
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
On Nov 23, 2015, at 8:50 AM, Daniel Tetlow
<[email protected]<mailto:[email protected]>> wrote:
Hi,
I had a similar problem on Windows. I needed to link the LZF plugin against the
hdf5 library (as expected) to get it to compile, and it worked fine with C++,
but it wouldn’t work with the Java H5 libraries. Attempting to link it against
the jhdf5 2.11 library instead failed. I couldn’t figure out what I was doing
wrong, so in the end I rebuilt jhdf5 with the plugin sources built in.
Cheers,
Dan
From: Hdf-forum [mailto:[email protected]] On Behalf Of Ümit
Seren
Sent: 23 November 2015 14:10
To: [email protected]<mailto:[email protected]>
Subject: [Hdf-forum] Problem with a filter as shared library in Java-HDF5 and
HDF5View
I have been trying to compile the lzf compressor as a shared library (not
linked against hdf5) to be used as a filter plugin for HDF5.
Basically I was following this: https://github.com/h5py/h5py/tree/master/lzf
I compiled lzf as a shared library using this compile command:
gcc -O2 -fPIC -shared lzf/*.c lzf_filter.c -o liblzf_filter.so
This will create a lzf filter plugin that I copied into the
/usr/local/hdf5/lib/plugin folder.
The normal command line tools (h5ls, h5dump) work fine with lzf compressed
dataset, so the plugin seems to work.
However when I try to read the same lzf compressed dataset using Java HDF5 or
HDFView (2.11), I get the error that the lzf filter plugin can not be found.
The only workaround is to link it against the hdf5 library:
gcc -O2 -fPIC -shared lzf/*.c lzf_filter.c -lhdf5 -o liblzf_filter.so
Is this a known issue ?
This was on Ubuntu 14.04 and HDF5 1.8.15patch1
thanks in advance
cheers
Ümit
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