[MacPorts] #54210: HDF5 library mismatch at runtime

MacPorts noreply at macports.org
Mon May 22 08:28:51 UTC 2017

#54210: HDF5 library mismatch at runtime
 Reporter:  aaschwanden  |      Owner:
     Type:  defect       |     Status:  new
 Priority:  Normal       |  Milestone:
Component:  ports        |    Version:
 Keywords:               |       Port:  py27-netcdf4

 I'm just re-installed macports from scratch, including ports hdf5 (needed
 by e.g. gdal) and hdf5-18 (needed by netcdf).

 Installing py27-netcdf4 works fine but when running python code that uses
 the netCDF4python module, I always get a seg fault, see below. (The same
 happens when installing netcdf4python by hand ("USE_SETUPCFG=0 CC=mpicc
 CXX=mpicxx HDF5_DIR=/opt/local/lib/hdf5-18
 HDF5_LIBDIR=/opt/local/lib/hdf5-18/lib/ python setup.py install --user").
 Could this be a runtime issue?


 export LD_LIBRARY_PATH=/opt/local/lib/hdf5-18/lib:$LD_LIBRARY_PATH

 did not solve the problem. Any thoughts?

 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
 This can happen when an application was compiled by one version of HDF5
 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 1.8.18, library is 1.10.0

 General Information:
                    HDF5 Version: 1.10.0-patch1
                   Configured on: Sun May 21 09:37:49 CEST 2017
                   Configured by: macports at storstrommen.local
                     Host system: x86_64-apple-darwin16.5.0
               Uname information: Darwin storstrommen.local 16.5.0 Darwin
 Kernel Version 16.5.0: Fri Mar  3 16:52:33 PST 2017;
 root:xnu-3789.51.2~3/RELEASE_X86_64 x86_64
                        Byte sex: little-endian
              Installation point: /opt/local

 Compiling Options:
                      Build Mode: production
               Debugging Symbols: no
                         Asserts: no
                       Profiling: no
              Optimization Level: high

 Linking Options:
                       Libraries: static, shared
   Statically Linked Executables:
                         LDFLAGS: -L/opt/local/lib
                 Extra libraries: -lz -ldl -lm
                        Archiver: ar
                          Ranlib: ranlib

                               C: yes
                      C Compiler: /opt/local/bin/mpicc-mpich-mp
                        CPPFLAGS: -I/opt/local/include
                     H5_CPPFLAGS:   -DNDEBUG -UH5_DEBUG_API
                         C Flags: -pipe -Os
                      H5 C Flags:
                      AM C Flags:
                Shared C Library: yes
                Static C Library: yes

                         Fortran: no

                             C++: yes
                    C++ Compiler: /opt/local/bin/mpicxx-mpich-mp
                       C++ Flags: -pipe -Os
                    H5 C++ Flags:
                    AM C++ Flags:
              Shared C++ Library: yes
              Static C++ Library: yes

                            Java: no

                   Parallel HDF5: yes
              High-level library: yes
                    Threadsafety: no
             Default API mapping: v110
  With deprecated public symbols: yes
          I/O filters (external): deflate(zlib)
                      Direct VFD: no
                         dmalloc: no
  Packages w/ extra debug output: none
                     API tracing: no
            Using memory checker: no
 Memory allocation sanity checks: no
             Metadata trace file: no
          Function stack tracing: no
       Strict file format checks: no
    Optimization instrumentation: no


Ticket URL: <https://trac.macports.org/ticket/54210>
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