[pyngl-talk] Help with PyNIO installation

Fan, Xingang xingang.fan at wku.edu
Sat Dec 10 07:55:00 MST 2016

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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