[pyngl-talk] PyNIO and PyNGL installation error
Kevin Hallock
hallock at ucar.edu
Wed Mar 8 14:41:25 MST 2017
Raj,
After you have activated the pyn_test environment, run “conda install -c conda-forge netcdf4”.
If you need any additional packages in this environment, be sure to use “conda install -c conda-forge _____” to install them. Alternatively, you can permanently add conda-forge to your list of searchable channels by running:
conda config --add channels conda-forge
This is necessary to avoid broken dependencies (such as libjpeg from before).
Kevin
> On Mar 8, 2017, at 2:32 PM, Raju Ankleshwaria <raju.ankleshwaria at gmail.com> wrote:
>
> Kevin,
>
> I changed to bash and activated pyn_test. Nio and Ngl are able to import. However, in this settgin I am unable to import netCDF4. Please see it below:
>
> (pyn_test) [root at air ~]$ python
> Python 2.7.12 | packaged by conda-forge | (default, Feb 9 2017, 14:36:30)
> [GCC 4.8.2 20140120 (Red Hat 4.8.2-15)] on linux2
> Type "help", "copyright", "credits" or "license" for more information.
> >>> import Nio
> >>> import Ngl
> >>> import netCDF4
> Traceback (most recent call last):
> File "<stdin>", line 1, in <module>
> ImportError: No module named netCDF4
> >>>
>
>
> On Wed, Mar 8, 2017 at 1:24 PM, Kevin Hallock <hallock at ucar.edu <mailto:hallock at ucar.edu>> wrote:
> Raj,
>
>> [root at air pyn_test]$ echo $SHELL
>> /bin/tcsh
>
>
> Many of the features provided by conda (particularly environments) require bash or zsh to work properly. Would you be willing to try running bash and then “source activate pyn_test”?
>
> All of the other output seems correct, so I believe the issue is just that conda cannot configure tcsh to work.
>
> Kevin
>
>> On Mar 8, 2017, at 2:17 PM, Raju Ankleshwaria <raju.ankleshwaria at gmail.com <mailto:raju.ankleshwaria at gmail.com>> wrote:
>>
>> Here are the outputs:
>>
>> [root at air pyn_test]$ echo $SHELL
>> /bin/tcsh
>> [root at air pyn_test]$ which conda
>> /data/soft/anaconda2/bin/conda
>> [root at air pyn_test]$ which activate
>> /data/soft/anaconda2/bin/activate
>> [root at air pyn_test]$ conda list -n pyn_test
>> # packages in environment at /data/soft/anaconda2/envs/pyn_test:
>> #
>> bzip2 1.0.6 0 conda-forge
>> ca-certificates 2017.1.23 0 conda-forge
>> cairo 1.14.6 4 conda-forge
>> certifi 2017.1.23 py27_0 conda-forge
>> curl 7.52.1 0 conda-forge
>> esmf 7.0.0 5 conda-forge
>> expat 2.1.0 2 conda-forge
>> fontconfig 2.12.1 4 conda-forge
>> freetype 2.7 1 conda-forge
>> freexl 1.0.2 1 conda-forge
>> g2clib 1.6.0 2 conda-forge
>> gdal 2.1.3 np112py27_1 conda-forge
>> geos 3.5.1 1 conda-forge
>> gettext 0.19.7 1 conda-forge
>> giflib 5.1.4 0 conda-forge
>> glib 2.51.4 0 conda-forge
>> gsl 2.2.1 1 conda-forge
>> hdf4 4.2.12 0 conda-forge
>> hdf5 1.8.17 9 conda-forge
>> hdfeos2 2.19.1 7 conda-forge
>> hdfeos5 5.1.15 6 conda-forge
>> icu 58.1 1 conda-forge
>> jasper 1.900.1 4 conda-forge
>> jpeg 9b 0 conda-forge
>> json-c 0.12 0 conda-forge
>> kealib 1.4.6 3 conda-forge
>> libdap4 3.18.3 2 conda-forge
>> libffi 3.2.1 3 conda-forge
>> libgcc 5.2.0 0
>> libgfortran 3.0.0 1
>> libiconv 1.14 4 conda-forge
>> libnetcdf 4.4.1.1 2 conda-forge
>> libpng 1.6.28 0 conda-forge
>> libpq 9.5.4 3 conda-forge
>> libspatialite 4.3.0a 14 conda-forge
>> libtiff 4.0.6 7 conda-forge
>> libxml2 2.9.4 4 conda-forge
>> mkl 2017.0.1 0
>> ncl 6.4.0 0 conda-forge
>> ncurses 5.9 10 conda-forge
>> netcdf-fortran 4.4.4 2 conda-forge
>> numpy 1.12.0 py27_0
>> openjpeg 2.1.2 2 conda-forge
>> openssl 1.0.2h 3 conda-forge
>> pcre 8.39 0 conda-forge
>> pip 9.0.1 py27_0 conda-forge
>> pixman 0.34.0 0 conda-forge
>> pkg-config 0.29.1 1 conda-forge
>> proj4 4.9.3 2 conda-forge
>> pyngl 1.5.0_beta20161122 np112py27_2 conda-forge
>> pynio 1.5.0_beta20160623 np112py27_14 conda-forge
>> python 2.7.12 2 conda-forge
>> readline 6.2 0 conda-forge
>> setuptools 33.1.0 py27_0 conda-forge
>> sqlite 3.13.0 1 conda-forge
>> tk 8.5.19 1 conda-forge
>> udunits2 2.2.23 0 conda-forge
>> util-linux 2.21 0
>> wheel 0.29.0 py27_0 conda-forge
>> xerces-c 3.1.4 3 conda-forge
>> xz 5.2.2 0 conda-forge
>> zlib 1.2.11 0 conda-forge
>> [root at air pyn_test]$
>>
>> On Wed, Mar 8, 2017 at 1:14 PM, Kevin Hallock <hallock at ucar.edu <mailto:hallock at ucar.edu>> wrote:
>> Hi Raj,
>>
>> Could you please run the following commands:
>> echo $SHELL
>> which conda
>> which activate
>> conda list -n pyn_test
>>
>> Thanks,
>> Kevin
>>
>>> On Mar 8, 2017, at 1:53 PM, Raju Ankleshwaria <raju.ankleshwaria at gmail.com <mailto:raju.ankleshwaria at gmail.com>> wrote:
>>>
>>> Hi Kevin,
>>>
>>> I installed PyNGL (conda install -c conda-forge pyngl=1.5.0_beta20161122) and PyNIO and did ceated conda environment. However, I am getting error when I source it.
>>> Please see below:
>>>
>>> Extracting packages ...
>>> [ COMPLETE ]|#################################################################################################################################################| 100%
>>> Linking packages ...
>>> [ COMPLETE ]|#################################################################################################################################################| 100%
>>> #
>>> # To activate this environment, use:
>>> # > source activate pyn_test
>>> #
>>> # To deactivate this environment, use:
>>> # > source deactivate pyn_test
>>> #
>>> [root at air ~]$ source activate pyn_test
>>> activate: No such file or directory.
>>>
>>> On Wed, Mar 8, 2017 at 11:49 AM, Kevin Hallock <hallock at ucar.edu <mailto:hallock at ucar.edu>> wrote:
>>> Hi Raj,
>>>
>>> It appears as though there is a dependency conflict between that particular version of PyNIO and the rest of Anaconda.
>>>
>>> Our recommended instructions for installing PyNIO and PyNGL are as follows:
>>>> To install PyNIO and PyNGL under conda, we recommend creating a conda environment:
>>>>
>>>> conda create --name pyn_test --channel conda-forge pynio pyngl
>>>> source activate pyn_test
>>>>
>>>
>>> We generally recommend creating a conda environment, especially when using Anaconda, due to dependency issues like what you experienced with libjpeg.
>>>
>>> Please let me know if this helps.
>>>
>>> Kevin
>>>
>>>> On Mar 8, 2017, at 12:24 PM, Raju Ankleshwaria <raju.ankleshwaria at gmail.com <mailto:raju.ankleshwaria at gmail.com>> wrote:
>>>>
>>>> for PyNIO conda install -c ncar pynio=1.4.3
>>>> for PyNGL conda is unable to search the package. conda search pyngl
>>>>
>>>> On Wed, Mar 8, 2017 at 11:18 AM, Kevin Hallock <hallock at ucar.edu <mailto:hallock at ucar.edu>> wrote:
>>>> Hi Raj,
>>>>
>>>> What was the full conda command you used to install PyNIO and PyNGL?
>>>>
>>>> Kevin
>>>>
>>>>> On Mar 8, 2017, at 11:43 AM, Raju Ankleshwaria <raju.ankleshwaria at gmail.com <mailto:raju.ankleshwaria at gmail.com>> wrote:
>>>>>
>>>>> Hi kevin,
>>>>>
>>>>> I installed Anaconda in my Linux3 x64 and NIO. However, I am getting the below error of libjpecg.so.8. I do not have this file but version 9. see below information for your review.
>>>>>
>>>>> Thanks,
>>>>> raj
>>>>>
>>>>> [root at air runIndia]$ python
>>>>> Python 2.7.13 |Anaconda custom (64-bit)| (default, Dec 20 2016, 23:09:15)
>>>>> [GCC 4.4.7 20120313 (Red Hat 4.4.7-1)] on linux2
>>>>> Type "help", "copyright", "credits" or "license" for more information.
>>>>> Anaconda is brought to you by Continuum Analytics.
>>>>> Please check out: http://continuum.io/thanks <http://continuum.io/thanks> and https://anaconda.org <https://anaconda.org/>
>>>>> >>> import Nio
>>>>> Traceback (most recent call last):
>>>>> File "<stdin>", line 1, in <module>
>>>>> File "/data/soft/anaconda2/lib/python2.7/site-packages/PyNIO/Nio.py", line 63, in <module>
>>>>> from nio import *
>>>>> ImportError: libjpeg.so.8: cannot open shared object file: No such file or directory
>>>>> >>>
>>>>> KeyboardInterrupt
>>>>> >>>
>>>>> [root at air runIndia]$ locate libjpeg
>>>>> /data/soft/anaconda2/lib/libjpeg.a
>>>>> /data/soft/anaconda2/lib/libjpeg.la <http://libjpeg.la/>
>>>>> /data/soft/anaconda2/lib/libjpeg.so
>>>>> /data/soft/anaconda2/lib/libjpeg.so.9
>>>>> /data/soft/anaconda2/lib/libjpeg.so.9.2.0
>>>>> /data/soft/anaconda2/pkgs/jpeg-9b-0/lib/libjpeg.a
>>>>> /data/soft/anaconda2/pkgs/jpeg-9b-0/lib/libjpeg.la <http://libjpeg.la/>
>>>>> /data/soft/anaconda2/pkgs/jpeg-9b-0/lib/libjpeg.so
>>>>> /data/soft/anaconda2/pkgs/jpeg-9b-0/lib/libjpeg.so.9
>>>>> /data/soft/anaconda2/pkgs/jpeg-9b-0/lib/libjpeg.so.9.2.0
>>>>> /usr/lib64/libjpeg.so
>>>>> /usr/lib64/libjpeg.so.62
>>>>> /usr/lib64/libjpeg.so.62.1.0
>>>>> /usr/local/lib/libjpeg.a
>>>>> /usr/local/lib/libjpeg.la <http://libjpeg.la/>
>>>>> /usr/local/lib/libjpeg.so
>>>>> /usr/local/lib/libjpeg.so.9
>>>>> /usr/local/lib/libjpeg.so.9.2.0
>>>>>
>>>>>
>>>>>
>>>>> On Tue, Mar 7, 2017 at 11:44 AM, Kevin Hallock <hallock at ucar.edu <mailto:hallock at ucar.edu>> wrote:
>>>>> Hi Raj,
>>>>>
>>>>> If the pre-compiled versions of PyNIO and PyNGL are causing problems on your system, you may want to consider using conda instead: https://www.pyngl.ucar.edu/Download/ <https://www.pyngl.ucar.edu/Download/>
>>>>>
>>>>> The conda package manager handles all dependencies (including gfortran) for you so that situations like this shouldn’t happen. Please let me know if you have any questions.
>>>>>
>>>>> Kevin
>>>>>
>>>>>> On Mar 6, 2017, at 2:04 PM, Raju Ankleshwaria <raju.ankleshwaria at gmail.com <mailto:raju.ankleshwaria at gmail.com>> wrote:
>>>>>>
>>>>>> Dear Users,
>>>>>>
>>>>>> I am installing PyNIO and PyNGL for the first time and getting errors. My system is CenOS 7 64-bit. I downloaded pre compiled files for my system with non-opendap.
>>>>>>
>>>>>> I am getting error while import in Nio and Ngl. Please see the error below. I check the libgfortran and that file is there. Please see below.
>>>>>>
>>>>>> I need your help.
>>>>>> Raj
>>>>>>
>>>>>> Version of PyNIO: 1.4.1 linux-redhat-x86_64-gcc412-py271-numpy160
>>>>>> PyNGL: 1.4.0 linux-redhat-x86_64-gcc412-py271-numpy160
>>>>>>
>>>>>>
>>>>>> [root at air site-packages]# python
>>>>>> Python 2.7.5 (default, Nov 6 2016, 00:28:07)
>>>>>> [GCC 4.8.5 20150623 (Red Hat 4.8.5-11)] on linux2
>>>>>> Type "help", "copyright", "credits" or "license" for more information.
>>>>>> >>> import Ngl
>>>>>> Traceback (most recent call last):
>>>>>> File "<stdin>", line 1, in <module>
>>>>>> File "/usr/lib/python2.7/site-packages/PyNGL/Ngl.py", line 39, in <module>
>>>>>> import fplib
>>>>>> ImportError: /lib64/libgfortran.so.1: undefined symbol: sqrtq
>>>>>> >>>
>>>>>> [root at air site-packages]# python
>>>>>> Python 2.7.5 (default, Nov 6 2016, 00:28:07)
>>>>>> [GCC 4.8.5 20150623 (Red Hat 4.8.5-11)] on linux2
>>>>>> Type "help", "copyright", "credits" or "license" for more information.
>>>>>> >>> import Nio
>>>>>> Traceback (most recent call last):
>>>>>> File "<stdin>", line 1, in <module>
>>>>>> File "/usr/lib64/python2.7/site-packages/PyNIO/Nio.py", line 63, in <module>
>>>>>> from nio import *
>>>>>> ImportError: /lib64/libgfortran.so.1: undefined symbol: sqrtq
>>>>>> >>> import Ngl
>>>>>> Traceback (most recent call last):
>>>>>> File "<stdin>", line 1, in <module>
>>>>>> File "/usr/lib/python2.7/site-packages/PyNGL/Ngl.py", line 39, in <module>
>>>>>> import fplib
>>>>>> ImportError: /lib64/libgfortran.so.1: undefined symbol: sqrtq
>>>>>> >>>
>>>>>> [root at air site-packages]# locate libgfortran.so.1
>>>>>> /usr/lib64/libgfortran.so.1
>>>>>> /usr/lib64/libgfortran.so.1.0.0
>>>>>> [root at air site-packages]#
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>>>>>
>>>>>
>>>>
>>>>
>>>
>>>
>>
>>
>
>
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