[pyngl-talk] Help with PyNIO installation
Kevin Hallock
hallock at ucar.edu
Mon Dec 12 10:43:32 MST 2016
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 <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.
>
> Kevin
>
>> 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!
>>
>> Xingang
>>
>> 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
>>
>> 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/ <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 <mailto: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_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
>>>
>>> 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 | Bowling Green, KY 42101-1066
>>> xingang.fan at wku.edu <mailto:xingang.fan at wku.edu>
>>> http://people.wku.edu/xingang.fan <http://people.wku.edu/xingang.fan>_______________________________________________
>>> pyngl-talk mailing list
>>> List instructions, subscriber options, unsubscribe:
>>> http://mailman.ucar.edu/mailman/listinfo/pyngl-talk <http://mailman.ucar.edu/mailman/listinfo/pyngl-talk>
>>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mailman.ucar.edu/pipermail/pyngl-talk/attachments/20161212/288df19b/attachment-0001.html
More information about the pyngl-talk
mailing list