Please help me with installation! Thank you very much!

[Lei Wang]

Dear Iris experts, 

Greetings! I am very interested in using Iris and I have literally spend days on trying to install the Iris on my Macbook Pro running Mac OS Mavericks. Although I believe that I have installed all the dependencies (there is really a lot ...), but I still receive the error message like this:

AttributeError: dlsym(RTLD_DEFAULT, cv_convert_float): symbol not found 

Could anyone tell me what I should do in order to overcome this error? Thank you a lot for your time! 

Sincerely,

Lei Wang

Grad Student

For your information, here I attached all the screen outputs: 

 leiwang$ python setup.py install

running install

running bdist_egg

running egg_info

writing lib/Iris.egg-info/PKG-INFO

writing top-level names to lib/Iris.egg-info/top_level.txt

writing dependency_links to lib/Iris.egg-info/dependency_links.txt

reading manifest file 'lib/Iris.egg-info/SOURCES.txt'

reading manifest template 'MANIFEST.in'

warning: no previously-included files matching '*' found under directory 'docs/iris/build'

warning: no files found matching '*.cc' under directory 'src'

warning: no files found matching '*.cpp' under directory 'src'

warning: no files found matching '*.h' under directory 'src'

writing manifest file 'lib/Iris.egg-info/SOURCES.txt'

installing library code to build/bdist.macosx-10.9-x86_64/egg

running install_lib

running build_py

/usr/local/opt/python/bin/python2.7 tools/generate_std_names.py etc/cf-standard-name-table.xml build/lib/iris/std_names.py

Traceback (most recent call last):

  File "setup.py", line 279, in <module>

    'clean_source': CleanSource},

  File "/usr/local/Cellar/python/2.7.8/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/core.py", line 151, in setup

    dist.run_commands()

  File "/usr/local/Cellar/python/2.7.8/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/dist.py", line 953, in run_commands

    self.run_command(cmd)

  File "/usr/local/Cellar/python/2.7.8/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/dist.py", line 972, in run_command

    cmd_obj.run()

  File "build/bdist.macosx-10.9-x86_64/egg/setuptools/command/install.py", line 67, in run

  File "build/bdist.macosx-10.9-x86_64/egg/setuptools/command/install.py", line 109, in do_egg_install

  File "/usr/local/Cellar/python/2.7.8/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/cmd.py", line 326, in run_command

    self.distribution.run_command(command)

  File "/usr/local/Cellar/python/2.7.8/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/dist.py", line 972, in run_command

    cmd_obj.run()

  File "build/bdist.macosx-10.9-x86_64/egg/setuptools/command/bdist_egg.py", line 161, in run

  File "build/bdist.macosx-10.9-x86_64/egg/setuptools/command/bdist_egg.py", line 147, in call_command

  File "/usr/local/Cellar/python/2.7.8/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/cmd.py", line 326, in run_command

    self.distribution.run_command(command)

  File "/usr/local/Cellar/python/2.7.8/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/dist.py", line 972, in run_command

    cmd_obj.run()

  File "build/bdist.macosx-10.9-x86_64/egg/setuptools/command/install_lib.py", line 9, in run

  File "/usr/local/Cellar/python/2.7.8/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/command/install_lib.py", line 109, in build

    self.run_command('build_py')

  File "/usr/local/Cellar/python/2.7.8/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/cmd.py", line 326, in run_command

    self.distribution.run_command(command)

  File "/usr/local/Cellar/python/2.7.8/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/dist.py", line 972, in run_command

    cmd_obj.run()

  File "setup.py", line 243, in run

    MakePykeRules._pyke_rule_compile()

  File "setup.py", line 196, in _pyke_rule_compile

    import iris.fileformats._pyke_rules

  File "build/lib/iris/__init__.py", line 104, in <module>

    import iris.cube

  File "build/lib/iris/cube.py", line 36, in <module>

    import iris.analysis

  File "build/lib/iris/analysis/__init__.py", line 57, in <module>

    from iris.analysis._interpolator import (_LINEAR_EXTRAPOLATION_MODES,

  File "build/lib/iris/analysis/_interpolator.py", line 25, in <module>

    from iris.analysis.cartography import wrap_lons as wrap_circular_points

  File "build/lib/iris/analysis/cartography.py", line 32, in <module>

    import iris.coords

  File "build/lib/iris/coords.py", line 34, in <module>

    import iris.aux_factory

  File "build/lib/iris/aux_factory.py", line 28, in <module>

    from iris._cube_coord_common import CFVariableMixin

  File "build/lib/iris/_cube_coord_common.py", line 24, in <module>

    import iris.unit

  File "build/lib/iris/unit.py", line 195, in <module>

    _cv_convert_float = _lib_ud.cv_convert_float

  File "/usr/local/Cellar/python/2.7.8/Frameworks/Python.framework/Versions/2.7/lib/python2.7/ctypes/__init__.py", line 378, in __getattr__

    func = self.__getitem__(name)

  File "/usr/local/Cellar/python/2.7.8/Frameworks/Python.framework/Versions/2.7/lib/python2.7/ctypes/__init__.py", line 383, in __getitem__

    func = self._FuncPtr((name_or_ordinal, self))

AttributeError: dlsym(RTLD_DEFAULT, cv_convert_float): symbol not found 

[Olivier Marti]

Hi every body,

I have exactly the same problem as Lei with python installed by uv-cdat 2.0.0. With the homebrew python it works well. As Lei seems to have the problem with homebrewed python, this is rather puzzling. 

Any clue someone ?

Olivier

[Гузий Саша]

Hi I am not an Iris expert, but did get the error that you describe today. And I believe

$ brew install udunits 

Resolved the problem. Also I recommend reading the INSTALL file distributed with iris and installing all the requirements mentioned there.

Cheers

[Phil Elson]

If you are able to, installing via conda is by far the easiest option at this point:

conda install -c scitools iris

If it isn't an option, and you end up building the dependencies by hand / pulling them in from another package manger, it is worth taking a look at how we build iris for the conda channel: https://github.com/SciTools/conda-recipes-scitools.

Specifically, we configure Iris to look for udunits in a specific location: https://github.com/SciTools/conda-recipes-scitools/blob/master/iris/build.sh#L14 . It may simply be that you need to add a site.cfg which points to the udunits so/dylib/dll.

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[Oleksandr Huziy]

Thanks Phil:

conda has some issues with qt libraries on Kubuntu, presumably a conflicting library with the one provided by the system. This was actually encountered by my friend to whom I advised conda earlier ))

It is OK for me to use setup.py or pip (As long as I can compile/apt-get or brew underlying C/C++/F dependencies). I have accidentally discovered another library with the same name (Iris) on pip (probably this is the reason why you did not upload it). So had to take it from github.

Cheers and thanks for your work with all the iris/cartopy/... libraries.

 

--

Sasha

[Phil Elson]

There is no problem using the setup.py - that is what we have to do to create the conda distribution in the first place. (https://github.com/SciTools/conda-recipes-scitools/blob/master/iris/build.sh#L16)

Thanks,

Phil

[Andrew Dawson]

conda has some issues with qt libraries on Kubuntu, presumably a conflicting library with the one provided by the system. This was actually encountered by my friend to whom I advised conda earlier ))

There is a work-around for this. First set the environment variable QT_PLUGIN_PATH to empty, for example in Bash:

export QT_PLUGIN_PATH=""

Secondly place a file named qt.conf in the bin/ directory of your python from your conda environment (same location as given by `which python`) with the following contents:

[Paths]
Plugins = "."

This seems to fix the Qt issues and allow you to use matplotlib with conda on Ubuntu 14.04. This is not ideal but it may be useful to some.