[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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