<div dir="ltr"><div>Kevin,</div><div><br></div><div>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:</div><div><br></div><div>(pyn_test) [root@air ~]$ python<br>Python 2.7.12 | packaged by conda-forge | (default, Feb 9 2017, 14:36:30) <br>[GCC 4.8.2 20140120 (Red Hat 4.8.2-15)] on linux2<br>Type "help", "copyright", "credits" or "license" for more information.<br>>>> import Nio<br>>>> import Ngl<br>>>> import netCDF4<br>Traceback (most recent call last):<br> File "<stdin>", line 1, in <module><br>ImportError: No module named netCDF4<br>>>> </div><div><br></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Wed, Mar 8, 2017 at 1:24 PM, Kevin Hallock <span dir="ltr"><<a href="mailto:hallock@ucar.edu" target="_blank">hallock@ucar.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="-ms-word-wrap: break-word;"><div>Raj,</div><span><div><br></div><div><blockquote type="cite"><div dir="ltr"><div>[root@air pyn_test]$ echo $SHELL<br>/bin/tcsh<br></div></div></blockquote></div><div><br></div></span>Many of the features provided by conda (particularly environments) require bash or zsh to work properly. Would you be willing to try running bash and then “source activate pyn_test”?<div><br></div><div>All of the other output seems correct, so I believe the issue is just that conda cannot configure tcsh to work.</div><span class="HOEnZb"><font color="#888888"><div><br></div></font></span><div><span class="HOEnZb"><font color="#888888">Kevin</font></span><div><div class="h5"><div><br><div><blockquote type="cite"><div>On Mar 8, 2017, at 2:17 PM, Raju Ankleshwaria <<a href="mailto:raju.ankleshwaria@gmail.com" target="_blank">raju.ankleshwaria@gmail.com</a>> wrote:</div><br class="m_4075683797019200014Apple-interchange-newline"><div><div dir="ltr"><div>Here are the outputs:</div><div><br></div><div>[root@air pyn_test]$ echo $SHELL<br>/bin/tcsh<br>[root@air pyn_test]$ which conda<br>/data/soft/anaconda2/bin/conda<br>[root@air pyn_test]$ which activate<br>/data/soft/anaconda2/bin/<wbr>activate<br>[root@air pyn_test]$ conda list -n pyn_test<br># packages in environment at /data/soft/anaconda2/envs/pyn_<wbr>test:<br>#<br>bzip2 1.0.6 0 conda-forge<br>ca-certificates 2017.1.23 0 conda-forge<br>cairo 1.14.6 4 conda-forge<br>certifi 2017.1.23 py27_0 conda-forge<br>curl 7.52.1 0 conda-forge<br>esmf 7.0.0 5 conda-forge<br>expat 2.1.0 2 conda-forge<br>fontconfig 2.12.1 4 conda-forge<br>freetype 2.7 1 conda-forge<br>freexl 1.0.2 1 conda-forge<br>g2clib 1.6.0 2 conda-forge<br>gdal 2.1.3 np112py27_1 conda-forge<br>geos 3.5.1 1 conda-forge<br>gettext 0.19.7 1 conda-forge<br>giflib 5.1.4 0 conda-forge<br>glib 2.51.4 0 conda-forge<br>gsl 2.2.1 1 conda-forge<br>hdf4 4.2.12 0 conda-forge<br>hdf5 1.8.17 9 conda-forge<br>hdfeos2 2.19.1 7 conda-forge<br>hdfeos5 5.1.15 6 conda-forge<br>icu 58.1 1 conda-forge<br>jasper 1.900.1 4 conda-forge<br>jpeg 9b 0 conda-forge<br>json-c 0.12 0 conda-forge<br>kealib 1.4.6 3 conda-forge<br>libdap4 3.18.3 2 conda-forge<br>libffi 3.2.1 3 conda-forge<br>libgcc 5.2.0 0 <br>libgfortran 3.0.0 1 <br>libiconv 1.14 4 conda-forge<br>libnetcdf 4.4.1.1 2 conda-forge<br>libpng 1.6.28 0 conda-forge<br>libpq 9.5.4 3 conda-forge<br>libspatialite 4.3.0a 14 conda-forge<br>libtiff 4.0.6 7 conda-forge<br>libxml2 2.9.4 4 conda-forge<br>mkl 2017.0.1 0 <br>ncl 6.4.0 0 conda-forge<br>ncurses 5.9 10 conda-forge<br>netcdf-fortran 4.4.4 2 conda-forge<br>numpy 1.12.0 py27_0 <br>openjpeg 2.1.2 2 conda-forge<br>openssl 1.0.2h 3 conda-forge<br>pcre 8.39 0 conda-forge<br>pip 9.0.1 py27_0 conda-forge<br>pixman 0.34.0 0 conda-forge<br>pkg-config 0.29.1 1 conda-forge<br>proj4 4.9.3 2 conda-forge<br>pyngl 1.5.0_beta20161122 np112py27_2 conda-forge<br>pynio 1.5.0_beta20160623 np112py27_14 conda-forge<br>python 2.7.12 2 conda-forge<br>readline 6.2 0 conda-forge<br>setuptools 33.1.0 py27_0 conda-forge<br>sqlite 3.13.0 1 conda-forge<br>tk 8.5.19 1 conda-forge<br>udunits2 2.2.23 0 conda-forge<br>util-linux 2.21 0 <br>wheel 0.29.0 py27_0 conda-forge<br>xerces-c 3.1.4 3 conda-forge<br>xz 5.2.2 0 conda-forge<br>zlib 1.2.11 0 conda-forge<br>[root@air pyn_test]$ <br></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Wed, Mar 8, 2017 at 1:14 PM, Kevin Hallock <span dir="ltr"><<a href="mailto:hallock@ucar.edu" target="_blank">hallock@ucar.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;padding-left:1ex;border-left-color:rgb(204,204,204);border-left-width:1px;border-left-style:solid"><div>Hi Raj,<div><br></div><div>Could you please run the following commands:</div><div><font face="Courier New">echo $SHELL</font></div><div><font face="Courier New">which conda</font></div><div><font face="Courier New">which activate</font></div><div><font face="Courier New">conda list -n pyn_test</font></div><div><br></div><div>Thanks,</div><div>Kevin</div><div><div class="m_4075683797019200014h5"><div><br><div><blockquote type="cite"><div>On Mar 8, 2017, at 1:53 PM, Raju Ankleshwaria <<a href="mailto:raju.ankleshwaria@gmail.com" target="_blank">raju.ankleshwaria@gmail.com</a>> wrote:</div><br class="m_4075683797019200014m_2570258976223485099Apple-interchange-newline"><div><div dir="ltr"><div>Hi Kevin,</div><div><br></div><div>I installed PyNGL (<font face="Courier New">conda install -c conda-forge pyngl=1.5.0_beta20161122)</font> and PyNIO and did ceated conda environment. However, I am getting error when I source it.</div><div>Please see below:</div><div><br></div><div>Extracting packages ...<br>[ COMPLETE ]|############################<wbr>##############################<wbr>##############################<wbr>##############################<wbr>###########################| 100%<br>Linking packages ...<br>[ COMPLETE ]|############################<wbr>##############################<wbr>##############################<wbr>##############################<wbr>###########################| 100%<br>#<br># To activate this environment, use:<br># > source activate pyn_test<br>#<br># To deactivate this environment, use:<br># > source deactivate pyn_test<br>#</div><div>[root@air ~]$ source activate pyn_test<br>activate: No such file or directory.<br></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Wed, Mar 8, 2017 at 11:49 AM, Kevin Hallock <span dir="ltr"><<a href="mailto:hallock@ucar.edu" target="_blank">hallock@ucar.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;padding-left:1ex;border-left-color:rgb(204,204,204);border-left-width:1px;border-left-style:solid"><div>Hi Raj,<div><br></div><div>It appears as though there is a dependency conflict between that particular version of PyNIO and the rest of Anaconda.</div><div><br></div><div>Our recommended instructions for installing PyNIO and PyNGL are as follows:</div><div><blockquote type="cite">To install PyNIO and PyNGL under conda, we recommend creating a conda environment:<br><br><div> conda create --name pyn_test --channel conda-forge pynio pyngl</div><div> source activate pyn_test</div><br class="m_4075683797019200014m_2570258976223485099m_1718728134641760625Apple-interchange-newline"></blockquote><br></div><div>We generally recommend creating a conda environment, especially when using Anaconda, due to dependency issues like what you experienced with libjpeg.</div><div><br></div><div>Please let me know if this helps.</div><span class="m_4075683797019200014m_2570258976223485099HOEnZb"><font color="#888888"><div><br></div><div>Kevin</div></font></span><div><div class="m_4075683797019200014m_2570258976223485099h5"><div><br><div><blockquote type="cite"><div>On Mar 8, 2017, at 12:24 PM, Raju Ankleshwaria <<a href="mailto:raju.ankleshwaria@gmail.com" target="_blank">raju.ankleshwaria@gmail.com</a>> wrote:</div><br class="m_4075683797019200014m_2570258976223485099m_1718728134641760625Apple-interchange-newline"><div><div dir="ltr"><div>for PyNIO conda install -c ncar pynio=1.4.3</div><div>for PyNGL conda is unable to search the package. conda search pyngl</div></div><div class="gmail_extra"><br><div class="gmail_quote">On Wed, Mar 8, 2017 at 11:18 AM, Kevin Hallock <span dir="ltr"><<a href="mailto:hallock@ucar.edu" target="_blank">hallock@ucar.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;padding-left:1ex;border-left-color:rgb(204,204,204);border-left-width:1px;border-left-style:solid"><div>Hi Raj,<div><br></div><div>What was the full conda command you used to install PyNIO and PyNGL?</div><span class="m_4075683797019200014m_2570258976223485099m_1718728134641760625HOEnZb"><font color="#888888"><div><br></div><div>Kevin</div></font></span><div><div class="m_4075683797019200014m_2570258976223485099m_1718728134641760625h5"><div><br><div><blockquote type="cite"><div>On Mar 8, 2017, at 11:43 AM, Raju Ankleshwaria <<a href="mailto:raju.ankleshwaria@gmail.com" target="_blank">raju.ankleshwaria@gmail.com</a>> wrote:</div><br class="m_4075683797019200014m_2570258976223485099m_1718728134641760625m_7011304894923456380Apple-interchange-newline"><div><div dir="ltr"><div>Hi kevin,</div><div><br></div><div>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.</div><div><br></div><div>Thanks,</div><div>raj</div><div><br></div><div>[root@air runIndia]$ python <br>Python 2.7.13 |Anaconda custom (64-bit)| (default, Dec 20 2016, 23:09:15) <br>[GCC 4.4.7 20120313 (Red Hat 4.4.7-1)] on linux2<br>Type "help", "copyright", "credits" or "license" for more information.<br>Anaconda is brought to you by Continuum Analytics.<br>Please check out: <a href="http://continuum.io/thanks" target="_blank">http://continuum.io/thanks</a> and <a href="https://anaconda.org/" target="_blank">https://anaconda.org</a><br>>>> import Nio<br>Traceback (most recent call last):<br> File "<stdin>", line 1, in <module><br> File "/data/soft/anaconda2/lib/pyth<wbr>on2.7/site-packages/PyNIO/Nio.<wbr>py", line 63, in <module><br> from nio import *<br>ImportError: libjpeg.so.8: cannot open shared object file: No such file or directory<br>>>> <br>KeyboardInterrupt<br>>>> <br>[root@air runIndia]$ locate libjpeg<br>/data/soft/anaconda2/lib/libjp<wbr>eg.a<br>/data/soft/anaconda2/lib/<a href="http://libjpeg.la/" target="_blank">libjp<wbr>eg.la</a><br>/data/soft/anaconda2/lib/libjp<wbr>eg.so<br>/data/soft/anaconda2/lib/libjp<wbr>eg.so.9<br>/data/soft/anaconda2/lib/libjp<wbr>eg.so.9.2.0<br>/data/soft/anaconda2/pkgs/jpeg<wbr>-9b-0/lib/libjpeg.a<br>/data/soft/anaconda2/pkgs/jpeg<wbr>-9b-0/lib/<a href="http://libjpeg.la/" target="_blank">libjpeg.la</a><br>/data/soft/anaconda2/pkgs/jpeg<wbr>-9b-0/lib/libjpeg.so<br>/data/soft/anaconda2/pkgs/jpeg<wbr>-9b-0/lib/libjpeg.so.9<br>/data/soft/anaconda2/pkgs/jpeg<wbr>-9b-0/lib/libjpeg.so.9.2.0<br>/usr/lib64/libjpeg.so<br>/usr/lib64/libjpeg.so.62<br>/usr/lib64/libjpeg.so.62.1.0<br>/usr/local/lib/libjpeg.a<br>/usr/local/lib/<a href="http://libjpeg.la/" target="_blank">libjpeg.la</a><br>/usr/local/lib/libjpeg.so<br>/usr/local/lib/libjpeg.so.9<br>/usr/local/lib/libjpeg.so.9.2.<wbr>0<br><br></div><div><br></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Tue, Mar 7, 2017 at 11:44 AM, Kevin Hallock <span dir="ltr"><<a href="mailto:hallock@ucar.edu" target="_blank">hallock@ucar.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;padding-left:1ex;border-left-color:rgb(204,204,204);border-left-width:1px;border-left-style:solid"><div>Hi Raj,<div><br></div><div>If the pre-compiled versions of PyNIO and PyNGL are causing problems on your system, you may want to consider using conda instead: <a href="https://www.pyngl.ucar.edu/Download/" target="_blank">https://www.pyngl.uca<wbr>r.edu/Download/</a></div><div><br></div><div>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.</div><div><br></div><div>Kevin</div><div><br><div><blockquote type="cite"><div><div class="m_4075683797019200014m_2570258976223485099m_1718728134641760625m_7011304894923456380h5"><div>On Mar 6, 2017, at 2:04 PM, Raju Ankleshwaria <<a href="mailto:raju.ankleshwaria@gmail.com" target="_blank">raju.ankleshwaria@gmail.com</a>> wrote:</div><br class="m_4075683797019200014m_2570258976223485099m_1718728134641760625m_7011304894923456380m_-6332578306778971185Apple-interchange-newline"></div></div><div><div><div class="m_4075683797019200014m_2570258976223485099m_1718728134641760625m_7011304894923456380h5"><div dir="ltr"><div>Dear Users,</div><div><br></div><div>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.</div><div><br></div><div>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.</div><div><br></div><div>I need your help.</div><div>Raj</div><div><br></div><div>Version of PyNIO: 1.4.1 linux-redhat-x86_64-gcc412-py2<wbr>71-numpy160</div><div>PyNGL: 1.4.0 linux-redhat-x86_64-gcc412-py2<wbr>71-numpy160</div><div><br></div><div><br></div><div>[root@air site-packages]# python<br>Python 2.7.5 (default, Nov 6 2016, 00:28:07) <br>[GCC 4.8.5 20150623 (Red Hat 4.8.5-11)] on linux2<br>Type "help", "copyright", "credits" or "license" for more information.<br>>>> import Ngl<br>Traceback (most recent call last):<br> File "<stdin>", line 1, in <module><br> File "/usr/lib/python2.7/site-packa<wbr>ges/PyNGL/Ngl.py", line 39, in <module><br> import fplib<br>ImportError: /lib64/libgfortran.so.1: undefined symbol: sqrtq<br>>>> <br>[root@air site-packages]# python<br>Python 2.7.5 (default, Nov 6 2016, 00:28:07) <br>[GCC 4.8.5 20150623 (Red Hat 4.8.5-11)] on linux2<br>Type "help", "copyright", "credits" or "license" for more information.<br>>>> import Nio<br>Traceback (most recent call last):<br> File "<stdin>", line 1, in <module><br> File "/usr/lib64/python2.7/site-pac<wbr>kages/PyNIO/Nio.py", line 63, in <module><br> from nio import *<br>ImportError: /lib64/libgfortran.so.1: undefined symbol: sqrtq<br>>>> import Ngl<br>Traceback (most recent call last):<br> File "<stdin>", line 1, in <module><br> File "/usr/lib/python2.7/site-packa<wbr>ges/PyNGL/Ngl.py", line 39, in <module><br> import fplib<br>ImportError: /lib64/libgfortran.so.1: undefined symbol: sqrtq<br>>>> <br>[root@air site-packages]# locate libgfortran.so.1<br>/usr/lib64/libgfortran.so.1<br>/usr/lib64/libgfortran.so.1.0.<wbr>0<br>[root@air site-packages]# </div></div></div></div>
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