HDF5 library version mismatched error (in ARCSI)

[Theo Awo]

I was trying to convert kea to another format using gdal_translate (after atmospheric correction with ARCSI) but kept getting an HDF5 library version mismatched error.

Solution from people with better experience will be greatly appreciated.

Error details below:

Warning! ***HDF5 library version mismatched error***
The HDF5 header files used to compile this application do not match
the version used by the HDF5 library to which this application is linked.
Data corruption or segmentation faults may occur if the application continues.
This can happen when an application was compiled by one version of HDF5 but
linked with a different version of static or shared HDF5 library.
You should recompile the application or check your shared library related
settings such as 'LD_LIBRARY_PATH'.
You can, at your own risk, disable this warning by setting the environment
variable 'HDF5_DISABLE_VERSION_CHECK' to a value of '1'.
Setting it to 2 or higher will suppress the warning messages totally.
Headers are 1.8.14, library is 1.8.15
        SUMMARY OF THE HDF5 CONFIGURATION
        =================================

General Information:
-------------------
           HDF5 Version: 1.8.15-patch1
          Configured on: Fri Jul 17 17:55:45 AEST 2015
          Configured by: s...@centos-6.6-x64
         Configure mode: production
            Host system: x86_64-unknown-linux-gnu
          Uname information: Linux centos-6.6-x64 2.6.32-504.23.4.el6.x86_64 #1 SMP Tue Jun 9 20:57:37 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux
               Byte sex: little-endian
              Libraries: shared
         Installation point: /home/sam/miniconda3/envs/_build

Compiling Options:
------------------
               Compilation Mode: production
                     C Compiler: /usr/bin/gcc ( gcc (GCC) 4.4.7 20120313 )
                         CFLAGS:
                      H5_CFLAGS: -std=c99 -pedantic -Wall -Wextra -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wcast-qual -Wcast-align -Wwrite-strings -Wconversion -Waggregate-return -Wstrict-prototypes -Wmissing-prototypes -Wmissing-declarations -Wredundant-decls -Wnested-externs -Winline -Wno-long-long -Wfloat-equal -Wmissing-format-attribute -Wmissing-noreturn -Wpacked -Wdisabled-optimization -Wformat=2 -Wunreachable-code -Wendif-labels -Wdeclaration-after-statement -Wold-style-definition -Winvalid-pch -Wvariadic-macros -Wnonnull -Winit-self -Wmissing-include-dirs -Wswitch-default -Wswitch-enum -Wunused-macros -Wunsafe-loop-optimizations -Wc++-compat -Wstrict-overflow -Wlogical-op -Wlarger-than=2048 -Wvla -Wsync-nand -Wframe-larger-than=16384 -Wpacked-bitfield-compat -O3 -fomit-frame-pointer -finline-functions
                      AM_CFLAGS:
                       CPPFLAGS:
                    H5_CPPFLAGS: -D_DEFAULT_SOURCE -D_BSD_SOURCE -D_GNU_SOURCE -D_POSIX_C_SOURCE=200112L   -DNDEBUG -UH5_DEBUG_API
                    AM_CPPFLAGS: -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE  -I/home/sam/miniconda3/envs/_build/include
               Shared C Library: yes
               Static C Library: no
  Statically Linked Executables: no
                        LDFLAGS:
                     H5_LDFLAGS:
                     AM_LDFLAGS:  -L/home/sam/miniconda3/envs/_build/lib
          Extra libraries: -lrt -lz -ldl -lm
                Archiver: ar
               Ranlib: ranlib
           Debugged Packages:
            API Tracing: no

Languages:
----------
                        Fortran: no

                            C++: yes
                   C++ Compiler: /usr/bin/g++ ( g++ (GCC) 4.4.7 20120313 )
                      C++ Flags:
                   H5 C++ Flags: 
                   AM C++ Flags:
             Shared C++ Library: yes
             Static C++ Library: no

Features:
---------
                  Parallel HDF5: no
             High Level library: yes
                   Threadsafety: no
            Default API Mapping: v18
 With Deprecated Public Symbols: yes
         I/O filters (external): deflate(zlib)
                            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
Bye...
Aborted (core dumped)

[Daniel Clewley]

Hi Theo,

Is this the version of gdal_translate installed through conda? Is the hdf5 package the one installed thought our osgeo channel?

Can you post the output of:

conda list

As this will have the versions of each package you have installed and the channel they were installed from. 

Thanks,

Dan

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[Daniel Clewley]

Hi Theo,

I’m a little confused, from the conda list output you sent you don’t have ARCSI installed. When you install ARCSI using:

conda install -c osgeo arcsi

It will install a version of GDAL we have built which should export to KEA format without any problems. For some reason ARCSI, GDAL and many of the other packages required by ARCSI have been removed (if you had them installed). Try running the command again to reinstall.

conda install -c osgeo arcsi

For converting from KEA you need to use the version of gdal installed through conda not through the package manager (apt-get). You can check the version which is being used with the command:

which gdal_translate

Which will print the path to the executable (should be /home/chris/anaconda3/bin/gdal_translate)

As for using Canopy, this uses a completely different Python distribution and as far as I am aware only supports Python 2.7 whereas all our builds are for the Python distribution provided through Anaconda and only support 3.5. You could use the two together but you need to be very careful they are kept isolated and don’t conflict.

Please make sure you cc the list when you reply don’t just reply to me.

Thanks,

Dan

On 20 Jun 2016, at 17:58, Theo Awo <philu...@gmail.com> wrote:

Hi Dan,

Thanks so much for your prompt response.

Not sure about where my gdal_translate version is from (perhaps gdal?) but hdf5 is from Conda. As you can see below I have both hdf and hdf5 on my ubuntu, which could be causing the conflict? I'm not that experience in these things, but I tried to get info about my gdal (see outputs after output from conda list below). Not sure if this info will be helpful - I know I used Canopy for most of my installations too.

Thanks so much!

(1) Output from conda list:

(2) info on gdal

# packages in environment at /home/chris/anaconda3:
#
abstract-rendering        0.5.1               np110py35_0    defaults
anaconda-client           1.2.1                    py35_0    defaults
blaze-core                0.8.3                    py35_0    defaults
bokeh                     0.10.0                   py35_0    defaults
click-plugins             1.0.3                     <pip>
conda-build               1.18.2                   py35_0    defaults
conda-env                 2.4.5                    py35_0    defaults
cryptography              1.0.2                    py35_0    defaults
cython                    0.23.4                   py35_0    defaults
datashape                 0.4.7               np110py35_1    defaults
dynd-python               0.7.0                    py35_0    defaults
fastcache                 1.0.2                    py35_0    defaults
h5py                      2.5.0               np110py35_4    defaults
hdf4                      4.2.11                        3    https://conda.binstar.org/osgeo/linux-64/hdf4-4.2.11-3.tar.bz2
hdf5                      1.8.15.1                     14    https://conda.binstar.org/osgeo/linux-64/hdf5-1.8.15.1-14.tar.bz2
homura                    0.1.3                     <pip>
humanize                  0.5.1                     <pip>
ipython                   4.0.1                    py35_0    defaults
ipython-genutils          0.1.0                     <pip>
ipython-notebook          4.0.4                    py35_0    defaults
ipython-qtconsole         4.0.1                    py35_0    defaults
ipython_genutils          0.1.0                    py35_0    defaults
jsonschema                2.4.0                    py35_0    defaults
jupyter-client            4.1.1                     <pip>
jupyter-console           4.0.3                     <pip>
jupyter-core              4.0.6                     <pip>
landsat-util              0.12.1                    <pip>
multipledispatch          0.4.8                    py35_0    defaults
patchelf                  0.6                           0    defaults
path.py                   8.1.2                    py35_1    defaults
pickleshare               0.5                      py35_0    defaults
python                    3.5.1                         0    defaults
python-dateutil           2.5.3                    py35_0    defaults
redis-py                  2.10.3                   py35_0    defaults
requests-futures          0.9.7                     <pip>
rope-py3k                 0.9.4.post1               <pip>
scikit-image              0.11.3              np110py35_0    defaults
scikit-learn              0.17                np110py35_1    defaults
sockjs-tornado            1.0.1                    py35_0    defaults
sphinx                    1.3.1                    py35_0    defaults
sphinx-rtd-theme          0.1.7                     <pip>
sphinx_rtd_theme          0.1.7                    py35_0    defaults
spyder-app                2.3.8                    py35_0    defaults
sqlalchemy                1.0.9                    py35_0    defaults
theano                    0.7.0               np110py35_0    defaults
util-linux                2.21                          0    defaults
wheel                     0.29.0                   py35_0    defaults
xerces-c                  3.1.2                         0    defaults


(2)

cs@cs-Inspiron-5547:~$ apt-cache show libgdal-dev
Package: libgdal-dev
Source: gdal
Priority: optional
Section: libdevel
Installed-Size: 28250
Maintainer: Debian GIS Project <pkg-gra...@lists.alioth.debian.org>
Architecture: amd64
Version: 1.11.2+dfsg-1~exp2~trusty
Replaces: libgdal1-dev (<< 1.9.0-1~)
Suggests: libgdal-doc
Depends: libgdal1h (= 1.11.2+dfsg-1~exp2~trusty), libc6-dev, libnetcdf-dev, libjasper-dev, libpng-dev, libjpeg-dev, libgif-dev, libwebp-dev, libhdf4-alt-dev, libhdf5-dev, libpq-dev, libxerces-c-dev, unixodbc-dev, libsqlite3-dev, libgeos-dev, libmysqlclient-dev, libltdl-dev, libcurl4-gnutls-dev | libcurl-ssl-dev, libspatialite-dev, libdap-dev
Breaks: libgdal1-dev (<< 1.9.0-1~)
Filename: pool/main/g/gdal/libgdal-dev_1.11.2+dfsg-1~exp2~trusty_amd64.deb
Size: 4726800
MD5sum: 9dac77fd740a9a79819f4d8acd313fa5
SHA1: e3759587c6eb9ef1a760ef63f8f00f15939fa97b
SHA256: 49ff014071da0526dd65c17dc9a564b25a446e2598ef2759353e8ad5740416a0
Description-en_CA: Geospatial Data Abstraction Library - Development files
 GDAL is a translator library for raster geospatial data formats. As a
 library, it presents a single abstract data model to the calling
 application for all supported formats. The related OGR library (which
 lives within the GDAL source tree) provides a similar capability for
 simple features vector data.
 .
 GDAL supports many popular data formats, including commonly used ones
 (GeoTIFF, JPEG, PNG and more) as well as the ones used in GIS and remote
 sensing software packages (ERDAS Imagine, ESRI Arc/Info, ENVI, PCI
 Geomatics). Also supported many remote sensing and scientific data
 distribution formats such as HDF, EOS FAST, NOAA L1B, NetCDF, FITS.
 .
 OGR library supports popular vector formats like ESRI Shapefile, TIGER
 data, S57, MapInfo File, DGN, GML and more.
 .
 This package contains the files needed to develop a software that will use
 the GDAL/OGR (headers, static objects, configuration script).
Description-md5: fe1355584b1a93438b3699e1581cff4b

Package: libgdal-dev
Priority: extra
Section: universe/libdevel
Installed-Size: 27074
Maintainer: Ubuntu Developers <ubuntu-dev...@lists.ubuntu.com>
Original-Maintainer: Debian GIS Project <pkg-gra...@lists.alioth.debian.org>
Architecture: amd64
Source: gdal
Version: 1.10.1+dfsg-5ubuntu1
Replaces: libgdal1-dev (<< 1.9.0-1~)
Depends: libgdal1h (= 1.10.1+dfsg-5ubuntu1), libc6-dev, libnetcdf-dev, libjasper-dev, libpng-dev, libjpeg-dev, libgif-dev, libwebp-dev, libhdf4-alt-dev, libhdf5-dev, libpq-dev, libxerces-c-dev, unixodbc-dev, libsqlite3-dev, libgeos-dev, libmysqlclient-dev, libltdl-dev, libcurl4-gnutls-dev | libcurl-ssl-dev, libspatialite-dev, libdap-dev
Suggests: libgdal-doc
Breaks: libgdal1-dev (<< 1.9.0-1~)
Filename: pool/universe/g/gdal/libgdal-dev_1.10.1+dfsg-5ubuntu1_amd64.deb
Size: 4307810
MD5sum: 1f496f44bb44ce01f1b73a39afc55bee
SHA1: 8765d0b874b8f03b52f6c56f461c83b75c0f5cd5
SHA256: 94531bc0b4f672a5b97432f60b6c8eea31875d7f9a1a2913cb69d3a2331f392e
Description-en_CA: Geospatial Data Abstraction Library - Development files
 GDAL is a translator library for raster geospatial data formats. As a
 library, it presents a single abstract data model to the calling
 application for all supported formats. The related OGR library (which
 lives within the GDAL source tree) provides a similar capability for
 simple features vector data.

Origin: Ubuntu