Yes, sorry I'm on Red Hat Enterprise Linux Server release 6.5. I did not find any zlib/deflate text in the libhdf5.settings file. I will work on adding zlib and rebuilding hdf5.
Features: --------- Parallel HDF5: no High Level library: yes Threadsafety: no Default API Mapping: v18 With Deprecated Public Symbols: yes I/O filters (external): I/O filters (internal): shuffle,fletcher32,nbit,scaleoffset MPE: no Direct VFD: no dmalloc: no Clear file buffers before write: yes Using memory checker: no Function Stack Tracing: no Strict File Format Checks: no Optimization Instrumentation: no Large File Support (LFS): yes In the meantime I will contact the helpdesk. Appreciate the assistance. Thanks, Patrick On Sun, Jan 18, 2015 at 6:11 PM, Elena Pourmal <[email protected]> wrote: > Patrick, > > On Jan 16, 2015, at 3:29 PM, Patrick Weinandy <[email protected]> > wrote: > > Hi All, > > Currently on unix using the hdf5-1.8.14 package (standard installation). > > I have a .gh5 file with many datasets in this format: > DATATYPE H5T_IEEE_F32LE > DATASPACE SIMPLE { ( 133004 ) / ( H5S_UNLIMITED ) > } > STORAGE_LAYOUT { > CHUNKED ( 4096 ) > SIZE 3406 (156.200:1 COMPRESSION) > } > FILTERS { > COMPRESSION DEFLATE { LEVEL 4 } > } > > I'm simply trying to extract a dataset using the command: > "./tools/h5dump/h5dump -d", however I keep getting this error: h5dump > error: unable to print data. > > > This error usually occurs when a compression filter is not available to > HDF5. Deflate filter (zlib compression) is enabled by default and will be > configured in if libz.* libraries are present on the build system in the > /usr/lib directory. (I am assuming you are on UNIX system). > > Could you please check the libhdf5.settings file found under the lib > directory of the HDF5 installation point? This is a text file. Check if the > line as shown below contains “deflate(zlib)”: > I/O filters (external): deflate(zlib),szip(encoder) > > If “deflate" is not there, you will need to rebuild HDF5 to get your > data, but first, please make sure that you have zlib on your system. > > The output file is created nut the data area is empty. > > DATASET "/MEASURED" { > DATATYPE H5T_IEEE_F32LE > DATASPACE SIMPLE { ( 133004 ) / ( H5S_UNLIMITED ) } > DATA { > } > > > I have been able to run other variations and commands without any issues > (h5repack, h5stat, h5dump -a/H/n, etc). > > When checking using "--enable-error-stack" this is the output > > *** glibc detected *** > /training/config/hdf5/hdf5-1.8.14/tools/h5dump/.libs/lt-h5dump: double free > or corruption (!prev): > > Unfortunately, I cannot reproduce this error when I use HDF5 built without > zlib. Could you please contact our Helpdesk ([email protected]) and send > us your file for further investigation? > > Thank you! > > Elena > > > 0x0000000001a9e430 *** > > ======= Backtrace: ========= > > /lib64/libc.so.6[0x34e4275e76] > > /lib64/libc.so.6[0x34e42789b3] > > /training/config/hdf5/hdf5-1.8.14/tools/h5dump/.libs/lt-h5dump[0x407ef1] > > /lib64/libc.so.6(__libc_start_main+0xfd)[0x34e421ed5d] > > /training/config/hdf5/hdf5-1.8.14/tools/h5dump/.libs/lt-h5dump[0x4053f9] > > ======= Memory map: ======== > > ... > > .... > > Aborted (core dumped) > > > > I can create a brand new file with no compression, copy the dataset from > the file I can't extract from to the new file and then use h5dump on the > new file (so I don't think its memory related).. I'm leaning towards > something with the original file's compression? I'm unable to remove > compression/filter on the file, I receive an error for each dataset: file > cannot > be read, deflate filter is not available. > > > Any help/direction/insight is much appreciated. > > > Thank you > > > > _______________________________________________ > Hdf-forum is for HDF software users discussion. > [email protected] > > http://mail.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://mail.lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org > Twitter: https://twitter.com/hdf5 > -- *Patrick Weinandy* 614-736-8522
_______________________________________________ Hdf-forum is for HDF software users discussion. [email protected] http://mail.lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org Twitter: https://twitter.com/hdf5
