Hi Brendan, Could you please try more recent version of zlib? If you see the same problem, please send the example that demonstrates the problem to our Helpdesk.
Thank you! Elena ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Elena Pourmal The HDF Group http://hdfgroup.org 1800 So. Oak St., Suite 203, Champaign IL 61820 217.531.6112 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ On Jan 27, 2015, at 9:57 AM, Brendan Kochunas <[email protected]> wrote: > Hi all (new to the list), > > I am currently experiencing/investigating an issue where our usage of HDF5 > with compression is leading to some defects reported by valgrind (apologies > for not having debug symbols for line numbers). These defects are also > reported when I run valgrind on > > http://www.hdfgroup.org/ftp/HDF5/examples/examples-by-api/hdf5-examples/1_8/FORTRAN/H5D/h5ex_d_gzip.f90 > > The valgrind output I get from the above example is: > ==54559== Conditional jump or move depends on uninitialised value(s) > ==54559== at 0x63664E0: inflateReset2 (in > /lib/x86_64-linux-gnu/libz.so.1.2.3.4) > ==54559== by 0x63665D8: inflateInit2_ (in > /lib/x86_64-linux-gnu/libz.so.1.2.3.4) > ==54559== by 0x5989E13: H5Z_filter_deflate (in > /opt/hdf5/1.8.11/gcc_4.6.3/lib/libhdf5.so.8.0.0) > ==54559== by 0x59891A0: H5Z_pipeline (in > /opt/hdf5/1.8.11/gcc_4.6.3/lib/libhdf5.so.8.0.0) > ==54559== by 0x57C96A1: H5D__chunk_lock (in > /opt/hdf5/1.8.11/gcc_4.6.3/lib/libhdf5.so.8.0.0) > ==54559== by 0x57CA5D0: H5D__chunk_read (in > /opt/hdf5/1.8.11/gcc_4.6.3/lib/libhdf5.so.8.0.0) > ==54559== by 0x57DA482: H5D__read (in > /opt/hdf5/1.8.11/gcc_4.6.3/lib/libhdf5.so.8.0.0) > ==54559== by 0x57DB7B3: H5Dread (in > /opt/hdf5/1.8.11/gcc_4.6.3/lib/libhdf5.so.8.0.0) > ==54559== by 0x4E5B143: h5dread_c_ (in > /opt/hdf5/1.8.11/gcc_4.6.3/lib/libhdf5_fortran.so.8.0.0) > ==54559== by 0x4E69593: __h5d_provisional_MOD_h5dread_integer_2 (in > /opt/hdf5/1.8.11/gcc_4.6.3/lib/libhdf5_fortran.so.8.0.0) > ==54559== by 0x40198E: MAIN__ (h5ex_d_gzip.f90:134) > ==54559== by 0x401B81: main (h5ex_d_gzip.f90:16) > > In my situation, when I am performing parallel reads I get anomalous > behavior, where sometimes the executable works, and sometimes it does not. > When it does not work I get the following diagnostic messages from HDF5. > HDF5-DIAG: Error detected in HDF5 (1.8.13) MPI-process 4223: > #000: H5Dio.c line 173 in H5Dread(): can't read data > major: Dataset > minor: Read failed > #001: H5Dio.c line 545 in H5D__read(): can't read data > major: Dataset > minor: Read failed > #002: H5Dchunk.c line 1861 in H5D__chunk_read(): unable to read raw data > chunk > major: Low-level I/O > minor: Read failed > #003: H5Dchunk.c line 2891 in H5D__chunk_lock(): data pipeline read failed > major: Data filters > minor: Filter operation failed > #004: H5Z.c line 1383 in H5Z_pipeline(): filter returned failure during read > major: Data filters > minor: Read failed > #005: H5Zdeflate.c line 136 in H5Z_filter_deflate(): memory allocation > failed for deflate uncompression > major: Resource unavailable > minor: No space available for allocation > > Which has a similar call stack, and I wonder if it's trying to allocate using > an undefined value. My gut tells me these may be related. > > Is the valgrind issue I am reporting a known issue? Has anyone else run into > this? > > Can anyone provide some advice on how might continue debugging this? > Any thoughts on whether this is an issue with HDF5, zlib or some combination? > > In my use case, it is extremely desirable to use compression as I am dealing > with files that are 2.2GB compressed (4.5GB uncompressed). I can probably > post some code if needed, but since the example has the same issue perhaps it > is better to work from that. > > My hope is that the root cause of this issue is: > A. Something in my usage of the library > B. Something wrong with the configure/build/install of the library (which I > cannot necessarily change) > C. Something wrong with the HDF5 library > > Any feedback is welcome. > > Thanks, > -Brendan > > _______________________________________________ > 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
