[pyngl-talk] PyNIO and PyNGL installation error

Kevin Hallock hallock at ucar.edu
Wed Mar 8 14:24:15 MST 2017


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> 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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