[pyngl-talk] Help with PyNIO installation
Mary Haley
haley at ucar.edu
Mon Dec 12 13:33:55 MST 2016
Hi Kate,
The Python 3.5 timeline is a tough one to answer. We plan to migrate PyNGL
and PyNIO to Python 3.x, but right now we have to focus on getting the next
release of NCL out. NCL is our main package and the one that requires the
most attention from us since it has more users than PyNGL or PyNIO.
The NCL release is scheduled for the end of this month, and then we'll
probably have a bug fix release shortly after in February or so.
I imagine after that we'll turn the focus back on our Python tools. The
hope is that PyNGL won't be as difficult to port, because it uses swig
under the hood, and we should be able to use the Python 3.x swig on the
code.
With PyNIO, however, more changes will likely be required.
I imagine both packages could be a 2-month effort total, so we may be
looking at Spring 2017 for a Python 3.x release.
--Mary
On Mon, Dec 12, 2016 at 11:18 AM, Katherine Hedstrom <kshedstrom at alaska.edu>
wrote:
> Hi Kevin,
>
> I just tried this and got:
>
> Error: Unsatisfiable package specifications.
> Generating hint:
> [ COMPLETE ]|############################
> ###################################################################| 100%
>
>
> Hint: the following packages conflict with each other:
> - pyngl
> - python 3.5*
>
> What's the timeline on getting a python 3 version?
>
> Kate
>
> On Mon, Dec 12, 2016 at 8:43 AM, Kevin Hallock <hallock at ucar.edu> wrote:
>
>> 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.
>>
>> Kevin
>>
>> On Dec 10, 2016, at 7:55 AM, Fan, Xingang <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|1.8.15.1|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!
>>
>> Xingang
>>
>> 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 3.2.3.2 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 1.9.5.1 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 3.4.0.3 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 3.4.0.2 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>
>> Date: Wednesday, December 7, 2016 2:19 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,
>>
>> 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.
>>
>> Kevin
>>
>> On Dec 7, 2016, at 12:41 PM, Fan, Xingang <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!
>>
>> Xingang
>>
>> From: Kevin Hallock <hallock at ucar.edu>
>> Date: Wednesday, December 7, 2016 1:37 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,
>>
>> 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!
>>
>> Thanks,
>> Kevin
>>
>> On Dec 6, 2016, at 12:38 PM, Fan, Xingang <xingang.fan at wku.edu> wrote:
>>
>> Hi,
>>
>> 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 '''
>> 62
>> ---> 63 from nio import *
>> 64 from nio import _C_API
>> 65
>>
>> ImportError: /home/xfan/Canopy/appdata/canopy-1.7.4.3348.rh5-x86_64/lib/libgfortran.so.3:
>> version `GFORTRAN_1.4' not found (required by /home/xfan/Enthought/Canopy_64
>> bit/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
>>
>> Thanks,
>> --
>> Xingang Fan, Ph. D., | Department of Geography and Geology
>> Associate Professor | Western Kentucky University
>> of Meteorology | 1906 College Heights Blvd., #31066
>> 270-745-5980 <(270)%20745-5980> | Bowling Green, KY
>> 42101-1066
>> xingang.fan at wku.edu
>> http://people.wku.edu/xingang.fan
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