[pyngl-talk] Help with PyNIO installation
Bill Ladwig
ladwig at ucar.edu
Fri Dec 16 09:42:29 MST 2016
Hi Xinygang,
The error message is indicating that you are missing __sincos_stret, which
is probably something that is assumed to be on your Mac already, since it
is associated with the compiler math libraries. Can you try installing (or
reinstalling) XCode and the command line tools to see if that fixes your
problem. I know Apple just released an XCode update, and sometimes
libraries need to get reinstalled manually after the update, usually via
installing the command line tools. (Run "xcode-select --install" and see
if it prompts you to install the tools).
If not, what version of OSX are your running? Can you run this command:
otool -L /Users/xng02546/anaconda2/envs/pyncar/lib/
python2.7/site-packages/PyNIO/nio.so
Can you reply with the result of this command? I think that missing
library is supposed to be in libSystem.B.dylib, but we'll have to see what
otool says to try to figure out the problem.
Thanks,
Bill
On Thu, Dec 15, 2016 at 10:49 PM, Fan, Xingang <xingang.fan at wku.edu> wrote:
> I tried a simpler installation, and still has problems as below. Do you
> know if any hidden cache might be left in my Mac home account that might
> cause problems? Since I installed Enthought Canopy in my home directory too
> (before my old working anaconda), when I was cleaning up anaconda
> installations, I was afraid I might delete something belongs to Canopy. But
> I did remove the anaconda entire folder.
>
> conda create -n pyncar -c conda-forge pynio pyngl
> Source activate pyncar
>
> (pyncar) FXG-MacBook:~ xng02546$ python
> Python 2.7.12 | packaged by conda-forge | (default, Sep 8 2016, 14:41:48)
> [GCC 4.2.1 Compatible Apple LLVM 6.0 (clang-600.0.54)] on darwin
> Type "help", "copyright", "credits" or "license" for more information.
> >>>
> >>> import Nio
> Traceback (most recent call last):
> File "<stdin>", line 1, in <module>
> File "/Users/xng02546/anaconda2/envs/pyncar/lib/python2.7/site-packages/PyNIO/Nio.py",
> line 83, in <module>
> from nio import *
> ImportError: dlopen(/Users/xng02546/anaconda2/envs/pyncar/lib/
> python2.7/site-packages/PyNIO/nio.so, 2): Symbol not found:
> ___sincos_stret
> Referenced from: /Users/xng02546/anaconda2/envs/pyncar/lib/libgdal.20.
> dylib
> Expected in: /usr/lib/libSystem.B.dylib
> in /Users/xng02546/anaconda2/envs/pyncar/lib/libgdal.20.dylib
> >>> import Ngl
> >>> print Ngl.__version__
> 1.5.0_beta20161122
> >>> print Nio.__version__
> Traceback (most recent call last):
> File "<stdin>", line 1, in <module>
> NameError: name 'Nio' is not defined
> >>>
>
> From: Xingang Fan <xingang.fan at wku.edu>
> Date: Thursday, December 15, 2016 11:18 PM
> To: Kevin Hallock <hallock at ucar.edu>
> Cc: "pyngl-talk at ucar.edu" <pyngl-talk at ucar.edu>, Bill Ladwig <
> ladwig at ucar.edu>
>
> Subject: Re: [pyngl-talk] Help with PyNIO installation
>
> Dear Kevin and Bill:
>
> I really appreciate your patience with me and help. I am kind of new to
> the python packages and just don't know how to interpret the error messages.
> The following was what I did, considering your suggestions:
>
> FIRST:
> Deleted the anaconda2 directory along with .conda .condrc
> Reinstalled anaconda2: bash Downloads/Anaconda2-4.2.0-MacOSX-x86_64.sh
> condo update condo
> conda update -- all
>
> With these, python and spyder (newest version) starts well.
>
> THEN:
> conda config --add channels conda-forge # This makes the
> installation to search packages first from conda-forge #
> conda create -n test -c conda-forge pynio pyngl netcdf4 basemap spyder
> source activate test
> python Downloads/Basemaps_US_01.py
>
> TESTING RESULTS:
> spyder (2.3.9) starts well, but running one of my code (tested okay in
> earlier installations) had problems with either matplotlib or basemap. So,
> I also run it from command line.
> The problems are shown below. Right following it, is the attempt to import
> Nio directly from running python at command line:
>
> (test) FXG-MacBook:~ xng02546$ python Downloads/Basemaps_US_01.py
> Traceback (most recent call last):
> File "Downloads/Basemaps_US_01.py", line 1, in <module>
> from mpl_toolkits.basemap import Basemap
> File "/Users/xng02546/anaconda2/envs/test/lib/python2.7/site-
> packages/mpl_toolkits/basemap/__init__.py", line 28, in <module>
> from matplotlib.collections import LineCollection, PolyCollection
> File "/Users/xng02546/anaconda2/envs/test/lib/python2.7/site-
> packages/matplotlib/collections.py", line 24, in <module>
> import matplotlib.transforms as transforms
> File "/Users/xng02546/anaconda2/envs/test/lib/python2.7/site-
> packages/matplotlib/transforms.py", line 39, in <module>
> from matplotlib._path import (affine_transform,
> count_bboxes_overlapping_bbox,
> ImportError: dlopen(/Users/xng02546/anaconda2/envs/test/lib/
> python2.7/site-packages/matplotlib/_path.so, 2): Symbol not found:
> ___sincos_stret
> Referenced from: /Users/xng02546/anaconda2/envs/test/lib/python2.7/site-
> packages/matplotlib/_path.so
> Expected in: /usr/lib/libSystem.B.dylib
> in /Users/xng02546/anaconda2/envs/test/lib/python2.7/site-
> packages/matplotlib/_path.so
>
> (test) FXG-MacBook:~ xng02546$ which python
> /Users/xng02546/anaconda2/envs/test/bin/python
>
> (test) FXG-MacBook:~ xng02546$ python
> Python 2.7.12 | packaged by conda-forge | (default, Sep 8 2016, 14:41:48)
> [GCC 4.2.1 Compatible Apple LLVM 6.0 (clang-600.0.54)] on darwin
> Type "help", "copyright", "credits" or "license" for more information.
> >>> import Nio
> Traceback (most recent call last):
> File "<stdin>", line 1, in <module>
> File "/Users/xng02546/anaconda2/envs/test/lib/python2.7/site-packages/PyNIO/Nio.py",
> line 83, in <module>
> from nio import *
> ImportError: dlopen(/Users/xng02546/anaconda2/envs/test/lib/
> python2.7/site-packages/PyNIO/nio.so, 2): Symbol not found:
> ___sincos_stret
> Referenced from: /Users/xng02546/anaconda2/
> envs/test/lib/libgdal.20.dylib
> Expected in: /usr/lib/libSystem.B.dylib
> in /Users/xng02546/anaconda2/envs/test/lib/libgdal.20.dylib
> >>> import Ngl
> >>>
>
> Thanks,
> Xingang
>
> P.s. I had a successful installation before on this computer. It was
> messed up when I tried to update the pyngl and pynio from condo-forge.
> However, I forgot how I installed them the first time. I might have
> installed from downloading the .zip files from Github and then use pip. The
> only thing I didn't have was pygrib. This was the reason why I attempted to
> update my previous working system (all under root env), because on a Ubuntu
> virtual machine system, all three of pyngl pynio and pygrib were
> successfully installed and can be imported without problem. While keep
> trying an easy install, I will see if I can repeat my old installation.
>
> I really need an easy procedure, so that the students would be able to
> follow on their own Mac system. For Windows machine, the virtual machine I
> created can be imported into their VirtualBox.
>
> Thanks again for your help!
>
>
>
> From: Kevin Hallock <hallock at ucar.edu>
> Date: Thursday, December 15, 2016 1:14 PM
> To: Xingang Fan <xingang.fan at wku.edu>
> Cc: "pyngl-talk at ucar.edu" <pyngl-talk at ucar.edu>
> Subject: Re: [pyngl-talk] Help with PyNIO installation
>
> Hi Xingang,
>
> (I) At Conda root, I ran:
> conda create -n metuse -c conda-forge pynio pyngl
> source activate met use
>
> (II) From root, I created a new environment condaX by:
> Conda create –n condaX python=2.7 anaconda
> Source activate condaX
> Conda install netcdf4
> Conda install basemap
> Conda update --all
>
> (III) Based on the working condoX environment, I tried to clone it, then
> wanted to install pyNGL etc.,
> The cloned environment has same results from conda list,
> Running python, it imports matplotlib and basemap okay,
>
> But, somehow, spyder won't start, it shows the following message:
>
>
> Instead of creating these two separate environments and then trying to
> combine them, could you please try creating a single environment using the
> following command:
> conda create -n pyn_testing -c conda-forge python=2.7 pynio pyngl netcdf4
> basemap spyder
> source activate pyn_testing
>
> Even though both of the environments work before combining them, I would
> expect them to fail due to incompatible versions of packages. For example,
> in your “metuse” environment you should have libnetcdf 4.4.1.1 from
> conda-forge installed as a dependency of pynio; in your “condaX”
> environment, you’ll have libnetcdf 4.4.1 from the default channel installed
> as a dependency of netcdf4. This is just one example of the
> incompatibilities that can happen when installing from multiple channels.
> Again, it is important to use “-c conda-forge” on any “conda create
> …”/“conda install …”/“conda update …” commands you may run for the
> environment you’re trying to create.
>
> Also, I noticed that you chose to install the anaconda package when
> creating the condaX environment (in step II above). Installing the
> “anaconda” package is almost guaranteed to make your environment
> incompatible with most packages from the conda-forge channel (including
> pynio and pyngl), as described in the previous paragraph. Is there a
> particular package included in “anaconda” that you need? I would try to
> list specific packages instead of “anaconda”, and I would try to install
> them from the conda-forge channel (“-c conda-forge”) if possible.
>
> I hope this helps!
>
> Kevin
>
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