[pyngl-talk] Help with PyNIO installation

Fan, Xingang xingang.fan at wku.edu
Tue Dec 13 14:18:46 MST 2016

Hi, Kevin:

Thank you so much! That played the trick. Finally I got all three of them working along with basemap on an Ubuntu virtual machine without any warning messages. The order of installing different packages and the updating of packages seem important though.

Now, I am trying to get it to work on my Mac. All of them worked fine with my Mac installation of Anaconda. However, when I tried to use the same way to update NGL and NIO, the entire anaconda seemed messed up. I tried reinstall, still have the following messages when importing Nio, I don't know what to do:

(root) FXG-MacBook:site-packages xng02546$ python
Python 2.7.12 |Anaconda custom (x86_64)| (default, Jul  2 2016, 17:43:17)
[GCC 4.2.1 (Based on Apple Inc. build 5658) (LLVM build 2336.11.00)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
Anaconda is brought to you by Continuum Analytics.
Please check out: http://continuum.io/thanks and https://anaconda.org
>>> import Nio
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "//anaconda/lib/python2.7/site-packages/PyNIO/Nio.py", line 83, in <module>
    from nio import *
ImportError: dlopen(//anaconda/lib/python2.7/site-packages/PyNIO/nio.so, 2): Library not loaded: @rpath/libicui18n.56.dylib
  Referenced from: //anaconda/lib/libgdal.20.dylib
  Reason: no suitable image found.  Did find:
/usr/local/lib/libicui18n.56.dylib: stat() failed with errno=13


From: Kevin Hallock <hallock at ucar.edu<mailto:hallock at ucar.edu>>
Date: Monday, December 12, 2016 11:43 AM
To: Xingang Fan <xingang.fan at wku.edu<mailto:xingang.fan at wku.edu>>
Cc: "pyngl-talk at ucar.edu<mailto:pyngl-talk at ucar.edu>" <pyngl-talk at ucar.edu<mailto:pyngl-talk at ucar.edu>>
Subject: Re: [pyngl-talk] Help with PyNIO installation

Hi Xingang,

Could you please try running “conda install -c conda-forge pyngl pynio” instead of “conda install -c ncar -c khallock pyngl pynio”?

Previously, using the channels “ncar” and “khallock” (with the flags “-c ncar” and “-c khallock”) was the only way to install PyNIO and PyNGL using conda, but we have since uploaded PyNIO, PyNGL, and NCL to the conda-forge channel. Conda-forge provides excellent compatibility between packages in order to avoid the dependency issues you experienced, so I would strongly recommend using “-c conda-forge” in your case.


On Dec 10, 2016, at 7:55 AM, Fan, Xingang <xingang.fan at wku.edu<mailto:xingang.fan at wku.edu>> wrote:

Hi, Kevin:

I am installing the packages in virtual machine that runs Ubuntu. I got it worked one time, but when I later found that I needed basemap. So, I reinstalled everything and nw got a question I don't understand. The following was what I did:

Install anaconda
Conda update --all
Created a new environment where:
     netcdf4 and basemap were installed
Cloned the above environment for adding NGL packages, where:
     pygrib was installed (conda install –c conda-forge pygrib
     Then, when I try to install: conda install –c ncar –c khallock pyngl pynio
           The following messages were given:

UnsatisfiableError: The following specifications were found to be in conflict:
  - h5py -> hdf5 1.8.13|1.8.14||1.8.16|1.8.9
  - h5py -> numpy 1.11*|1.5*|1.6*|1.7*|1.8*
  - h5py -> python 2.6*|3.3*|3.4*|3.5*
  - pynio
Use "conda info <package>" to see the dependencies for each package.

First, I don't understand who and who are in conflict. Second, how to get around?

I remember the time I got pygrib, Nio, Ngl imported without problem was when I didn't have basemap in the same new environment (just create a new environment for my use, not cloned one). But I hope I can have them all in the same place.

Your help is much appreciated!


P.s. A full list of packages in my new environment is attached below:

(metlab) xfan at xfan-VirtualBox:~$ conda list
# packages in environment at /home/xfan/anaconda2/envs/metlab:
_license                  1.1                      py27_1
_nb_ext_conf              0.3.0                    py27_0
alabaster                 0.7.9                    py27_0
anaconda                  custom                   py27_0
anaconda-clean            1.0.2                    py27_0
anaconda-client           1.6.0                    py27_0
anaconda-navigator        1.3.2                    py27_0
argcomplete               1.0.0                    py27_1
astroid                   1.4.7                    py27_0
astropy                   1.2.1               np111py27_0
babel                     2.3.4                    py27_0
backports                 1.0                      py27_0
backports_abc             0.5                      py27_0
basemap                   1.0.7               np111py27_0
beautifulsoup4            4.5.1                    py27_0
bitarray                  0.8.1                    py27_0
blaze                     0.10.1                   py27_0
bokeh                     0.12.3                   py27_0
boto                      2.43.0                   py27_0
bottleneck                1.1.0               np111py27_0
cairo                     1.12.18                       6
cdecimal                  2.3                      py27_2
cffi                      1.9.1                    py27_0
chest                     0.2.3                    py27_0
click                     6.6                      py27_0
cloudpickle               0.2.1                    py27_0
clyent                    1.2.2                    py27_0
colorama                  0.3.7                    py27_0
configobj                 5.0.6                    py27_0
configparser              3.5.0                    py27_0
contextlib2               0.5.4                    py27_0
cryptography              1.6                      py27_0
curl                      7.49.0                        1
cycler                    0.10.0                   py27_0
cython                    0.25.2                   py27_0
cytoolz                   0.8.1                    py27_0
dask                      0.12.0                   py27_0
datashape                 0.5.2                    py27_0
dbus                      1.10.10                       0
decorator                 4.0.10                   py27_1
dill                      0.2.5                    py27_0
docutils                  0.12                     py27_2
dynd-python               0.7.2                    py27_0
ecmwf_grib                1.16.0                        1    conda-forge
entrypoints               0.2.2                    py27_0
enum34                    1.1.6                    py27_0
et_xmlfile                1.0.1                    py27_0
expat                     2.1.0                         0
fastcache                 1.0.2                    py27_1
filelock                  2.0.7                    py27_0
flask                     0.11.1                   py27_0
flask-cors                2.1.2                    py27_0
fontconfig                2.11.1                        6
freetype                  2.5.5                         1
funcsigs                  1.0.2                    py27_0
functools32                       py27_0
futures                   3.0.5                    py27_0
geos                      3.4.2                         0
get_terminal_size         1.0.0                    py27_0
gevent                    1.1.2                    py27_0
glib                      2.43.0                        1
greenlet                  0.4.10                   py27_0
grin                      1.2.1                    py27_3
gst-plugins-base          1.8.0                         0
gstreamer                 1.8.0                         0
h5py                      2.6.0               np111py27_2
harfbuzz                  0.9.39                        1
hdf4                      4.2.12                        0
hdf5                      1.8.17                        1
heapdict                  1.0.0                    py27_1
icu                       54.1                          0
idna                      2.1                      py27_0
imagesize                 0.7.1                    py27_0
ipaddress                 1.0.17                   py27_0
ipykernel                 4.5.2                    py27_0
ipython                   5.1.0                    py27_0
ipython_genutils          0.1.0                    py27_0
ipywidgets                5.2.2                    py27_0
itsdangerous              0.24                     py27_0
jasper                    1.900.1                       1    conda-forge
jbig                      2.1                           0
jdcal                     1.3                      py27_0
jedi                      0.9.0                    py27_1
jinja2                    2.8                      py27_1
jpeg                      8d                            2
jsonschema                2.5.1                    py27_0
jupyter                   1.0.0                    py27_3
jupyter_client            4.4.0                    py27_0
jupyter_console           5.0.0                    py27_0
jupyter_core              4.2.1                    py27_0
lazy-object-proxy         1.2.1                    py27_0
libdynd                   0.7.2                         0
libffi                    3.2.1                         0
libgcc                    5.2.0                         0
libgfortran               3.0.0                         1
libiconv                  1.14                          0
libnetcdf                 4.4.1                         0
libpng                    1.6.26                        0    conda-forge
libsodium                 1.0.10                        0
libtiff                   4.0.6                         2
libxcb                    1.12                          1
libxml2                   2.9.4                         0
libxslt                   1.1.28                        0
llvmlite                  0.14.0                   py27_0
locket                    0.2.0                    py27_1
lxml                      3.6.4                    py27_0
markupsafe                0.23                     py27_2
matplotlib                1.5.3               np111py27_1
mistune                   0.7.3                    py27_0
mkl                       11.3.3                        0
mkl-service               1.1.2                    py27_2
mpmath                    0.19                     py27_1
multipledispatch          0.4.9                    py27_0
nb_anacondacloud          1.2.0                    py27_0
nb_conda                  2.0.0                    py27_0
nb_conda_kernels          2.0.0                    py27_0
nbconvert                 4.2.0                    py27_0
nbformat                  4.2.0                    py27_0
nbpresent                 3.0.2                    py27_0
netcdf4                   1.2.4               np111py27_0
networkx                  1.11                     py27_0
nltk                      3.2.1                    py27_0
nose                      1.3.7                    py27_1
notebook                  4.2.3                    py27_0
numba                     0.29.0              np111py27_0
numexpr                   2.6.1               np111py27_1
numpy                     1.11.2                   py27_0
odo                       0.5.0                    py27_1
openpyxl                  2.4.0                    py27_0
openssl                   1.0.2j                        0
pandas                    0.19.1              np111py27_0
partd                     0.3.6                    py27_0
patchelf                  0.9                           0
path.py                   8.2.1                    py27_0
pathlib2                  2.1.0                    py27_0
patsy                     0.4.1                    py27_0
pep8                      1.7.0                    py27_0
pexpect                   4.0.1                    py27_0
pickleshare               0.7.4                    py27_0
pillow                    3.4.2                    py27_0
pip                       9.0.1                    py27_1
pixman                    0.32.6                        0
pkginfo                   1.4.1                    py27_0
ply                       3.9                      py27_0
prompt_toolkit            1.0.9                    py27_0
psutil                    5.0.0                    py27_0
ptyprocess                0.5.1                    py27_0
py                        1.4.31                   py27_0
pyasn1                    0.1.9                    py27_0
pycairo                   1.10.0                   py27_0
pycosat                   0.6.1                    py27_1
pycparser                 2.17                     py27_0
pycrypto                  2.6.1                    py27_4
pycurl                    7.43.0                   py27_0
pyflakes                  1.3.0                    py27_0
pygments                  2.1.3                    py27_0
pygrib                    2.0.2                    py27_0    conda-forge
pylint                    1.5.4                    py27_1
pyopenssl                 16.2.0                   py27_0
pyparsing                 2.1.4                    py27_0
pyproj                            py27_0    conda-forge
pyqt                      5.6.0                    py27_0
pytables                  3.3.0               np111py27_0
pytest                    3.0.5                    py27_0
python                    2.7.12                        1
python-dateutil           2.6.0                    py27_0
pytz                      2016.10                  py27_0
pyyaml                    3.12                     py27_0
pyzmq                     16.0.2                   py27_0
qt                        5.6.0                         1
qtawesome                 0.3.3                    py27_0
qtconsole                 4.2.1                    py27_1
qtpy                      1.1.2                    py27_0
readline                  6.2                           2
redis                     3.2.0                         0
redis-py                  2.10.5                   py27_0
requests                  2.12.3                   py27_0
rope                      0.9.4                    py27_1
scikit-image              0.12.3              np111py27_1
scikit-learn              0.18.1              np111py27_0
scipy                     0.18.1              np111py27_0
setuptools                27.2.0                   py27_0
simplegeneric             0.8.1                    py27_1
singledispatch                    py27_0
sip                       4.18                     py27_0
six                       1.10.0                   py27_0
snowballstemmer           1.2.1                    py27_0
sockjs-tornado            1.0.3                    py27_0
sphinx                    1.5                      py27_0
spyder                    3.0.2                    py27_0
sqlalchemy                1.1.4                    py27_0
sqlite                    3.13.0                        0
ssl_match_hostname                  py27_1
statsmodels               0.6.1               np111py27_1
sympy                     1.0                      py27_0
terminado                 0.6                      py27_0
tk                        8.5.18                        0
toolz                     0.8.1                    py27_0
tornado                   4.4.2                    py27_0
traitlets                 4.3.1                    py27_0
unicodecsv                0.14.1                   py27_0
wcwidth                   0.1.7                    py27_0
werkzeug                  0.11.11                  py27_1
wheel                     0.29.0                   py27_0
widgetsnbextension        1.2.6                    py27_0
wrapt                     1.10.8                   py27_0
xlrd                      1.0.0                    py27_0
xlsxwriter                0.9.4                    py27_0
xlwt                      1.1.2                    py27_0
xz                        5.2.2                         0
yaml                      0.1.6                         0
zeromq                    4.1.5                         0
zlib                      1.2.8                         3

From: Kevin Hallock <hallock at ucar.edu<mailto:hallock at ucar.edu>>
Date: Wednesday, December 7, 2016 2:19 PM
To: Xingang Fan <xingang.fan at wku.edu<mailto:xingang.fan at wku.edu>>
Cc: "pyngl-talk at ucar.edu<mailto:pyngl-talk at ucar.edu>" <pyngl-talk at ucar.edu<mailto:pyngl-talk at ucar.edu>>
Subject: Re: [pyngl-talk] Help with PyNIO installation

Hi Xingang,

You’re welcome!

While Anaconda can be installed on Windows, we only have Mac OS X and Linux 64-bit versions of PyNGL or PyNIO available on Anaconda. In your case, I think Linux virtual machines would probably be the best/simplest option.


On Dec 7, 2016, at 12:41 PM, Fan, Xingang <xingang.fan at wku.edu<mailto:xingang.fan at wku.edu>> wrote:

Hi, Kevin:

Thank you so much for getting back with me!

I am trying anaconda on my MacBook Pro.

One question: Can anaconda be installed on Windows system with the PyNGL and PyNIO, pygrib to work? Or it has to be on a virtual machine. Our lab have all windows machines. Thanks!


From: Kevin Hallock <hallock at ucar.edu<mailto:hallock at ucar.edu>>
Date: Wednesday, December 7, 2016 1:37 PM
To: Xingang Fan <xingang.fan at wku.edu<mailto:xingang.fan at wku.edu>>
Cc: "pyngl-talk at ucar.edu<mailto:pyngl-talk at ucar.edu>" <pyngl-talk at ucar.edu<mailto:pyngl-talk at ucar.edu>>
Subject: Re: [pyngl-talk] Help with PyNIO installation


Is there any chance you could possibly use Anaconda/Miniconda on these virtual machines instead of Enthought Canopy? As far as I am aware, there is no easy way for us to create and distribute a version of our software that is built against Enthought Canopy’s libraries.

However, we do have up-to-date versions PyNGL and PyNIO (and NCL) available on the "conda-forge” Anaconda channel, which also hosts many other commonly used scientific packages (including pygrib!). Unfortunately, Anaconda and Enthought Canopy may not be compatible; in order for Anaconda to work properly, its provided python needs to be the “default” python.

We have information regarding the installation of Anaconda/Miniconda on the PyNGL/PyNIO download page: https://www.pyngl.ucar.edu/Download/

In order to use the recommended "conda-forge" versions (different from the example on the linked page), create a conda environment using a command such as:
conda create --name <env_name> --channel conda-forge pynio pyngl

and then activate the environment:
source activate <env_name>

Note that “<env_name>” can be whatever you would like your conda environment to be named; for example, the linked documentation above uses “pyn_test”.

If using Anaconda/Miniconda is not possible, then we will have to further troubleshoot building PyNIO from source code.

Please let us know if this information helps!


On Dec 6, 2016, at 12:38 PM, Fan, Xingang <xingang.fan at wku.edu<mailto:xingang.fan at wku.edu>> wrote:


I am using Enthought Canopy as my default python. I would like to get PyNIO and PyNGL installed.

I have tried to download the prebuilt binaries, none of them work for my Ubuntu environment (I have to use the VirtualBox and have a Virtual Machine of Ubuntu system on my windows machines for our classroom use, because I wanted to have pygrib, PyNIO, and PyNGL). Although the prebuilt packages worked for my MacBook Pro, where the Canopy was also installed.

Then I had to try to install from the source code of PyNIO. I have followed the instructions online at https://www.pyngl.ucar.edu/Download/build_pynio_from_src.shtml<https://www.pyngl.ucar.edu/Download/build_pynio_from_src.shtml#HDF4>.
And all non-optional packages have been installed without problem. However, when I get down to install PyNIO, it seemed installed, but the import Nio showed the following error messages:

import Nio
ImportError                               Traceback (most recent call last)
<ipython-input-1-d77b80fd2dfc> in <module>()
----> 1 import Nio

/home/xfan/Enthought/Canopy_64bit/User/lib/python2.7/site-packages/PyNIO/Nio.py in <module>()
     61 '''
---> 63 from nio import *
     64 from nio import _C_API

ImportError: /home/xfan/Canopy/appdata/canopy- version `GFORTRAN_1.4' not found (required by /home/xfan/Enthought/Canopy_64bit/User/lib/python2.7/site-packages/PyNIO/nio.so)

PLEASE help see what's the problem. While installing, I have the following environment variables set:
export HAS_NETCDF4=1
export HAS_HDF5=1
export NETCDF_PREFIX=/usr/local
export F2CLIBS=gfortran
export F2CLIBS_PREFIX=/usr/lib/x86_64-linux-gnu

Xingang Fan, Ph. D.,        |      Department of Geography and Geology
Associate Professor         |      Western Kentucky University
of Meteorology                |      1906 College Heights Blvd., #31066
270-745-5980                 |      Bowling Green, KY 42101-1066
xingang.fan at wku.edu<mailto:xingang.fan at wku.edu>
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