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
<[email protected]> wrote:
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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: [email protected]
From: Hdf-forum [mailto:[email protected]]On Behalf Of Hei
Chan
Sent: Sunday, October 22, 2017 2:58 AM
To: [email protected]
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!
_______________________________________________
Hdf-forum is for HDF software users discussion.
[email protected]
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
Twitter: https://twitter.com/hdf5_______________________________________________
Hdf-forum is for HDF software users discussion.
[email protected]
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
Twitter: https://twitter.com/hdf5
