[pyngl-talk] PyNIO and PyNGL installation error
Raju Ankleshwaria
raju.ankleshwaria at gmail.com
Wed Mar 8 14:17:09 MST 2017
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> wrote:
> Hi Raj,
>
> Could you please run the following commands:
> echo $SHELL
> which conda
> which activate
> conda list -n pyn_test
>
> Thanks,
> Kevin
>
> On Mar 8, 2017, at 1:53 PM, Raju Ankleshwaria <raju.ankleshwaria at gmail.com>
> wrote:
>
> Hi Kevin,
>
> I installed PyNGL (conda install -c conda-forge pyngl=1.5.0_beta20161122) and
> PyNIO and did ceated conda environment. However, I am getting error when I
> source it.
> Please see below:
>
> Extracting packages ...
> [ COMPLETE ]|############################
> ############################################################
> #########################################################| 100%
> Linking packages ...
> [ COMPLETE ]|############################
> ############################################################
> #########################################################| 100%
> #
> # To activate this environment, use:
> # > source activate pyn_test
> #
> # To deactivate this environment, use:
> # > source deactivate pyn_test
> #
> [root at air ~]$ 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> 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> 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> 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> 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 and 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
>>> /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
>>> /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
>>> /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> 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/
>>>>
>>>> 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> 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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