Yes, the HDF5 installation needs to include LZO compression in order to read your file. The link you mentioned is the correct location to
obtain the source code for LZO: https://support.hdfgroup.org/services/contributions.html
As of HDF5-1.8.11, we provide support for dynamically loaded filters, to make third-party filters available at runtime.
See this page for details on that:
It should be fine to set optimization to –O3. You can set that in CFLAGS before you build the software.
···
From: Hei Chan [mailto:structurechart@yahoo.com]
Sent: Monday, October 23, 2017 9:11 PM
To: HDF Users Discussion List; Barbara Jones
Subject: Re: [Hdf-forum] h5dump error: unable to print data
Hi Barbara,
Thanks for your reply.
The information is very helpful.
I just yum-installed hdf5 1.8.5 from epel repo so I didn't get to configure the build parameters.
I think the setting file explains why I couldn't h5dump my file:
Extra libraries: -lz -lm
I/O filters (external): deflate(zlib)
h5dump -pH my.h5:
FILTERS {
UNKNOWN_FILTER {
FILTER_ID 305
COMMENT lzo
PARAMS { 1 }
}
According to https://support.hdfgroup.org/services/contributions.html, 305 is for lzo. I guess I have to compile myself with lzo.
Before I compile to try again, I noticed libhdf5.sttings contains a mix of -O0, -O2, and -O3. Is it possible and safe to build with just -O3?
Compiling Options:
------------------
Compilation Mode: production
C Compiler: /usr/bin/gcc ( gcc (GCC) 4.4.7 20120313 )
CFLAGS: -O0 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic
Thanks in advance.
On Monday, October 23, 2017, 10:57:11 PM GMT+8, Barbara Jones <bljones@hdfgroup.org<mailto:bljones@hdfgroup.org>> wrote:
Hello!
Do you get the same errors without the additional options? For example: h5dump my.h5
A possibility is that your datasets are compressed with a filter that is not included in your HDF5 library.
You can use the “h5dump -pH” option to see the properties of a dataset. For example:
$ h5dump -pH cmprss.h5
HDF5 "cmprss.h5" {
GROUP "/" {
DATASET "Compressed_Data" {
DATATYPE H5T_STD_I32BE
DATASPACE SIMPLE { ( 100, 20 ) / ( 100, 20 ) }
STORAGE_LAYOUT {
CHUNKED ( 20, 20 )
SIZE 520 (15.385:1 COMPRESSION)
}
FILTERS {
COMPRESSION DEFLATE { LEVEL 6 }
}
FILLVALUE {
FILL_TIME H5D_FILL_TIME_IFSET
VALUE H5D_FILL_VALUE_DEFAULT
}
ALLOCATION_TIME {
H5D_ALLOC_TIME_INCR
}
}
}
}
The libhdf5.settings file that is placed in the location of the HDF5 libraries when it is built has information on the
external filters that were used to build the HDF5 library. For example:
$ ls
libhdf5.a libhdf5_fortran.a libhdf5_hl_cpp.a libhdf5.settings libz.a
libhdf5_cpp.a libhdf5_hl.a libhdf5hl_fortran.a libsz.a
$ more libhdf5.settings
SUMMARY OF THE HDF5 CONFIGURATION
=================================
General Information:
-------------------
HDF5 Version: 1.10.1
Configured on: Thu Apr 27 10:15:49 CDT 2017
--- >8 cut ---
Features:
---------
Parallel HDF5: no
High-level library: yes
Threadsafety: no
Default API mapping: v110
With deprecated public symbols: yes
I/O filters (external): deflate(zlib),szip(encoder)
--- >8 cut ---
If you cannot resolve the issue, you can send the file to the helpdesk, and we will take a look.
Thanks!
-Barbara
HDF Helpdesk: help@hdfgroup.org<mailto:help@hdfgroup.org>
From: Hdf-forum [mailto:hdf-forum-bounces@lists.hdfgroup.org] On Behalf Of Hei Chan
Sent: Sunday, October 22, 2017 2:58 AM
To: hdf-forum@lists.hdfgroup.org<mailto:hdf-forum@lists.hdfgroup.org>
Subject: [Hdf-forum] h5dump error: unable to print data
Hi,
I ran the following command:
$ h5dump -d /A/B/960 -d /A/C/D88 -d /A/E/D88 -b LE -o tmp.o my.h5 --enable-error-stack
And I got:
HDF5 "my.h5" {
DATASET "/A/B/960" {
DATATYPE H5T_COMPOUND {
H5T_STD_U32LE "a";
H5T_STD_I8LE "b";
H5T_STD_I64LE "c";
}
DATASPACE SIMPLE { ( 15265747 ) / ( H5S_UNLIMITED ) }
DATA {
h5dump error: unable to print data
}
}
DATASET "/A/C/D88" {
DATATYPE H5T_COMPOUND {
H5T_STD_I32LE "d";
H5T_STD_U32LE "e";
H5T_STD_U32LE "f";
H5T_STD_U32LE "g";
H5T_STD_I32LE "h";
H5T_STD_I32LE "i";
H5T_STD_I8LE "j";
H5T_STD_I16LE "k";
H5T_IEEE_F64LE "l";
H5T_STD_U32LE "m";
H5T_STD_I8LE "n";
H5T_STD_I64LE "o";
H5T_STD_U32LE "p";
}
DATASPACE SIMPLE { ( 2114658 ) / ( H5S_UNLIMITED ) }
DATA {
h5dump error: unable to print data
}
}
DATASET "/A/E/D88" {
DATATYPE H5T_COMPOUND {
H5T_STD_I32LE "q";
H5T_STD_U32LE "r";
H5T_STD_U32LE "s";
H5T_STD_I32LE "t";
H5T_STD_I32LE "u";
H5T_STD_I8LE "v";
H5T_IEEE_F64LE "x";
H5T_STD_I8LE "y";
H5T_STD_I64LE "z";
}
DATASPACE SIMPLE { ( 121815 ) / ( H5S_UNLIMITED ) }
DATA {
h5dump error: unable to print data
}
}
}
Any idea what goes wrong?
Thanks in advance!
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