[MacPorts] #52289: hdf5, hdf5-18 header & library runtime error

[MacPorts]

#52289: hdf5, hdf5-18 header & library runtime error
----------------------------+---------------------------------------
 Reporter:  gryphon.csd8@…  |      Owner:  macports-tickets@…
     Type:  defect          |     Status:  new
 Priority:  Normal          |  Milestone:
Component:  ports           |    Version:  2.3.4
 Keywords:                  |       Port:  hdf5 hdf5-18 netcdf ncarg
----------------------------+---------------------------------------
 Hi, we are experiencing runtime errors with netcdf and nacre (ncl
 commands) that have to do with the hdf5 headers used for compilation, and
 the hdf5-18 library used during compilation of netcdf.

 system on which this occurs:
 Mac OS X 10.10.5
 Xcode 7.2.1

 The runtime error can be generated by doing a simple "ncdump" on a netcdf4
 format file, shown here below:
 {{{
 Tue Sep 20 10:45:33 beowulf test> ncdump
 tro3_Amon_reanalysis_ENS_198101-201012.3D.cg.ltm.nc
 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 1.10.0, library is 1.8.16
             SUMMARY OF THE HDF5 CONFIGURATION
             =================================

 General Information:
 -------------------
                    HDF5 Version: 1.8.16
                   Configured on: Wed Aug  3 06:43:51 PDT 2016
                   Configured by: macports at tenten-slave.macports.org
                  Configure mode: production
                     Host system: i386-apple-darwin14.5.0
               Uname information: Darwin tenten-slave.macports.org 14.5.0
 Darwin Kernel Version 14.5.0: Mon Jan 11 18:48:35 PST 2016;
 root:xnu-2782.50.2~1/RELEASE_X86_64 x86_64
                        Byte sex: little-endian
                       Libraries: static, shared
              Installation point: /opt/local/lib/hdf5-18

 Compiling Options:
 ------------------
                Compilation Mode: production
                      C Compiler: /usr/bin/clang
                          CFLAGS: -pipe -Os
                       H5_CFLAGS:
                       AM_CFLAGS:
                        CPPFLAGS: -I/opt/local/include
                     H5_CPPFLAGS:   -DNDEBUG -UH5_DEBUG_API
                     AM_CPPFLAGS:
                Shared C Library: yes
                Static C Library: yes
   Statically Linked Executables: no
                         LDFLAGS: -L/opt/local/lib
 -Wl,-headerpad_max_install_names
                      H5_LDFLAGS:
                      AM_LDFLAGS:
                 Extra libraries: -lz -ldl -lm
                        Archiver: ar
                          Ranlib: ranlib
               Debugged Packages:
                     API Tracing: no

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

                             C++: yes
                    C++ Compiler: /usr/bin/clang++
                       C++ Flags: -pipe -Os  -stdlib=libc++
                    H5 C++ Flags:
                    AM C++ Flags:
              Shared C++ Library: yes
              Static C++ Library: yes

 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...
 Abort trap: 6
 }}}

 It appears that hdf5-18 is necessary for the netcdf and hdfeos5 ports,
 while hdf5 is necessary for a handful of others.  These are the ports we
 are using that are dependent upon a version of hdf5:
 {{{
 Tue Sep 20 12:26:35 beowulf ~> port depend hdf5
 cdo depends on hdf5
 grads depends on hdf5
 grib_api depends on hdf5
 nco depends on hdf5
 ncview depends on hdf5
 wgrib2 depends on hdf5
 Tue Sep 20 12:26:42 beowulf ~> port depend hdf5-18
 hdfeos5 depends on hdf5-18
 netcdf depends on hdf5-18
 }}}

 I've been unable to get all these dependent ports to install, using only
 one of the hdf5 ports, it appears I must use both for the compilations.
 Then we have the runtime headers/library problem.

 ideas?

 thanks,
 Roy

-- 
Ticket URL: <https://trac.macports.org/ticket/52289>
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