ncarg ncl fails on hdf5 mismatch

[basmac]

The update of ncarg to ncarg @6.3.0_1 (science), refers to libraries libhdf5.9.dylib and libhdf5_hl.9.dylib, which I do not have currently in macports install. I copied them from an old macports install and then ncl runs, but with the following warnings, which can be turned off, but user has to force quit. Also tried linking the libs to version 10, with the same result. With HDF5_DISABLE_VERSION_CHECK set to 1 or 2, ncl runs ok.

ncl stationTS_compare.ncl 

 Copyright (C) 1995-2015 - All Rights Reserved

 University Corporation for Atmospheric Research

 NCAR Command Language Version 6.3.0

 The use of this software is governed by a License Agreement.

 See http://www.ncl.ucar.edu/ for more details.

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 1.8.15, library is 1.8.14

    SUMMARY OF THE HDF5 CONFIGURATION

    =================================


General Information:

-------------------

  HDF5 Version: 1.8.14

  Configured on: Mon Jan  5 09:39:26 PST 2015

  Configured by: macports@tenten-slave.macports.org

Configure mode: production

    Host system: i386-apple-darwin14.0.0

      Uname information: Darwin tenten-slave.macports.org 14.0.0 Darwin Kernel Version 14.0.0: Fri Sep 19 00:26:44 PDT 2014; root:xnu-2782.1.97~2/RELEASE_X86_64 x86_64

      Byte sex: little-endian

      Libraries: static, shared

    Installation point: /opt/local


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:  -L/opt/local/lib

 	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)

         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

Bye...

Abort

[mf2k (Frank Schima)]

In the future, please use WikiFormatting.

[tenomoto (Takeshi Enomoto)]

What do you get with the following command? Do you have hdf5 outside of MacPorts?

$ otool -L /opt/local/bin/ncl | grep hdf5

[basmac]

Currently we have an ncl install in /usr/local. I will try with macports ncl. We do have various versions of libhdf as well as macports

[mac27:~/info] bmcinnes% locate libhdf5
/Applications/HDFView.app/Contents/Resources/lib/libhdf5.a
/Applications/HDFView.app/Contents/Resources/share/cmake/hdf5/libhdf5.settings
/Applications/MATLAB_R2015a.app/bin/maci64/libhdf5.8.dylib
/Applications/MATLAB_R2015a.app/bin/maci64/libhdf5.dylib
/Applications/MATLAB_R2015a.app/bin/maci64/libhdf5_hl.8.dylib
/Applications/MATLAB_R2015a.app/bin/maci64/libhdf5_hl.dylib
/Applications/scilab-5.5.0.app/Contents/MacOS/lib/thirdparty/10.5/libhdf5.0.0.0.dylib
/Applications/scilab-5.5.0.app/Contents/MacOS/lib/thirdparty/10.5/libhdf5.0.0.dylib
/Applications/scilab-5.5.0.app/Contents/MacOS/lib/thirdparty/10.5/libhdf5.0.dylib
/Applications/scilab-5.5.0.app/Contents/MacOS/lib/thirdparty/10.5/libhdf5.6.dylib
/Applications/scilab-5.5.0.app/Contents/MacOS/lib/thirdparty/10.5/libhdf5.dylib
/Applications/scilab-5.5.0.app/Contents/MacOS/lib/thirdparty/libhdf5.0.0.0.dylib
/Applications/scilab-5.5.0.app/Contents/MacOS/lib/thirdparty/libhdf5.0.0.dylib
/Applications/scilab-5.5.0.app/Contents/MacOS/lib/thirdparty/libhdf5.0.dylib
/Applications/scilab-5.5.0.app/Contents/MacOS/lib/thirdparty/libhdf5.6.dylib
/Applications/scilab-5.5.0.app/Contents/MacOS/lib/thirdparty/libhdf5.dylib
/Volumes/Cluster/opt/local/lib/libhdf5.10.dylib
/Volumes/Cluster/opt/local/lib/libhdf5.8.dylib
/Volumes/Cluster/opt/local/lib/libhdf5.9.dylib
/Volumes/Cluster/opt/local/lib/libhdf5.a
/Volumes/Cluster/opt/local/lib/libhdf5.dylib
/Volumes/Cluster/opt/local/lib/libhdf5.settings
/Volumes/Cluster/opt/local/lib/libhdf5_cpp.10.dylib
/Volumes/Cluster/opt/local/lib/libhdf5_cpp.8.dylib
/Volumes/Cluster/opt/local/lib/libhdf5_cpp.a
/Volumes/Cluster/opt/local/lib/libhdf5_cpp.dylib
/Volumes/Cluster/opt/local/lib/libhdf5_hl.10.dylib
/Volumes/Cluster/opt/local/lib/libhdf5_hl.8.dylib
/Volumes/Cluster/opt/local/lib/libhdf5_hl.9.dylib
/Volumes/Cluster/opt/local/lib/libhdf5_hl.a
/Volumes/Cluster/opt/local/lib/libhdf5_hl.dylib
/Volumes/Cluster/opt/local/lib/libhdf5_hl_cpp.10.dylib
/Volumes/Cluster/opt/local/lib/libhdf5_hl_cpp.8.dylib
/Volumes/Cluster/opt/local/lib/libhdf5_hl_cpp.a
/Volumes/Cluster/opt/local/lib/libhdf5_hl_cpp.dylib
/Volumes/Cluster/usr/local/ifort/lib/libhdf5.8.dylib
/Volumes/Cluster/usr/local/ifort/lib/libhdf5.a
/Volumes/Cluster/usr/local/ifort/lib/libhdf5.dylib
/Volumes/Cluster/usr/local/ifort/lib/libhdf5.la
/Volumes/Cluster/usr/local/ifort/lib/libhdf5.settings
/Volumes/Cluster/usr/local/ifort/lib/libhdf5_fortran.a
/Volumes/Cluster/usr/local/ifort/lib/libhdf5_fortran.la
/Volumes/Cluster/usr/local/ifort/lib/libhdf5_hl.8.dylib
/Volumes/Cluster/usr/local/ifort/lib/libhdf5_hl.a
/Volumes/Cluster/usr/local/ifort/lib/libhdf5_hl.dylib
/Volumes/Cluster/usr/local/ifort/lib/libhdf5_hl.la
/Volumes/Cluster/usr/local/ifort/lib/libhdf5hl_fortran.a
/Volumes/Cluster/usr/local/ifort/lib/libhdf5hl_fortran.la
[mac27:~/info]

[basmac]

[mac27:/] root# otool -L /opt/local/bin/ncl | grep hdf5
	/opt/local/lib/libhdf5.10.dylib (compatibility version 11.0.0, current version 11.0.0)
	/opt/local/lib/libhdf5_hl.10.dylib (compatibility version 11.0.0, current version 11.0.0)
[mac27:/] root#

Sorry, I used to have macports and newer versions of nacre in /usr/local. Seems like the macports ncl is fine and refers to hdf 11

The macports ncl install works fine without any hdf5 library errors.

Again, sorry for the wasted time, you can close the ticket.