Hi Hei, 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
You can get the HDF5-1.8 source code (version HDF5-1.8.19) from here: https://support.hdfgroup.org/HDF5/release/obtainsrc518.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: https://support.hdfgroup.org/HDF5/doc/Advanced/DynamicallyLoadedFilters/ It should be fine to set optimization to –O3. You can set that in CFLAGS before you build the software. -Barbara [email protected] From: Hei Chan [mailto:[email protected]] 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 <[email protected]<mailto:[email protected]>> 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: [email protected]<mailto:[email protected]> From: Hdf-forum [mailto:[email protected]] On Behalf Of Hei Chan Sent: Sunday, October 22, 2017 2:58 AM To: [email protected]<mailto:[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]<mailto:[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
