Adding the zlib-package solved the problem! Thanks for your help. ##Checked in lib directory for libz.* /usr/lib64 (no libz.*)
##installed zlib (zlib-devel-1.2.3-29.el6.x86_64) sudo yum install zlib-devely ##reconfigured hdf5 ./configure --with-zlib=/usr/lib64 (checked, config.log now see: I/O filters (external): deflate(zlib)) sudo make sudo make check sudo make install sudo make check-install ##executing ./tools/h5dump/h5dump -d no longer returns error "unable to print data" and outputs data into file able to successfully dump data out of gh5 data On Mon, Jan 19, 2015 at 8:18 AM, Patrick Weinandy <[email protected]> wrote: > 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 > -- *Patrick Weinandy* 614-736-8522
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