<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Raj,<div class=""><br class=""></div><div class="">After you have activated the pyn_test environment, run “<font face="Courier New" class="">conda install -c conda-forge netcdf4</font>”.<div class=""><br class=""></div><div class="">If you need any additional packages in this environment, be sure to use “<font face="Courier New" class="">conda install -c conda-forge _____</font>” to install them. Alternatively, you can permanently add conda-forge to your list of searchable channels by running:</div><div class=""><code class=""><font face="Courier New" class="">conda config --add channels conda-forge</font></code></div><div class=""><br class=""></div><div class="">This is necessary to avoid broken dependencies (such as libjpeg from before).</div><div class=""><br class=""></div><div class=""><div>Kevin</div><div><br class=""><blockquote type="cite" class=""><div class="">On Mar 8, 2017, at 2:32 PM, Raju Ankleshwaria <<a href="mailto:raju.ankleshwaria@gmail.com" class="">raju.ankleshwaria@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class=""><div class="">Kevin,</div><div class=""><br class=""></div><div class="">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 class=""><br class=""></div><div class="">(pyn_test) [root@air ~]$ python<br class="">Python 2.7.12 | packaged by conda-forge | (default, Feb 9 2017, 14:36:30) <br class="">[GCC 4.8.2 20140120 (Red Hat 4.8.2-15)] on linux2<br class="">Type "help", "copyright", "credits" or "license" for more information.<br class="">>>> import Nio<br class="">>>> import Ngl<br class="">>>> import netCDF4<br class="">Traceback (most recent call last):<br class=""> File "<stdin>", line 1, in <module><br class="">ImportError: No module named netCDF4<br class="">>>> </div><div class=""><br class=""></div></div><div class="gmail_extra"><br class=""><div class="gmail_quote">On Wed, Mar 8, 2017 at 1:24 PM, Kevin Hallock <span dir="ltr" class=""><<a href="mailto:hallock@ucar.edu" target="_blank" class="">hallock@ucar.edu</a>></span> wrote:<br class=""><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;" class=""><div class="">Raj,</div><span class=""><div class=""><br class=""></div><div class=""><blockquote type="cite" class=""><div dir="ltr" class=""><div class="">[root@air pyn_test]$ echo $SHELL<br class="">/bin/tcsh<br class=""></div></div></blockquote></div><div class=""><br class=""></div></span>Many of the features provided by conda (particularly environments) require bash or zsh to work properly. Would you be willing to try running bash and then “source activate pyn_test”?<div class=""><br class=""></div><div class="">All of the other output seems correct, so I believe the issue is just that conda cannot configure tcsh to work.</div><span class="HOEnZb"><font color="#888888" class=""><div class=""><br class=""></div></font></span><div class=""><span class="HOEnZb"><font color="#888888" class="">Kevin</font></span><div class=""><div class="h5"><div class=""><br class=""><div class=""><blockquote type="cite" class=""><div class="">On Mar 8, 2017, at 2:17 PM, Raju Ankleshwaria <<a href="mailto:raju.ankleshwaria@gmail.com" target="_blank" class="">raju.ankleshwaria@gmail.com</a>> wrote:</div><br class="m_4075683797019200014Apple-interchange-newline"><div class=""><div dir="ltr" class=""><div class="">Here are the outputs:</div><div class=""><br class=""></div><div class="">[root@air pyn_test]$ echo $SHELL<br class="">/bin/tcsh<br class="">[root@air pyn_test]$ which conda<br class="">/data/soft/anaconda2/bin/conda<br class="">[root@air pyn_test]$ which activate<br class="">/data/soft/anaconda2/bin/<wbr class="">activate<br class="">[root@air pyn_test]$ conda list -n pyn_test<br class=""># packages in environment at /data/soft/anaconda2/envs/pyn_<wbr class="">test:<br class="">#<br class="">bzip2 1.0.6 0 conda-forge<br class="">ca-certificates 2017.1.23 0 conda-forge<br class="">cairo 1.14.6 4 conda-forge<br class="">certifi 2017.1.23 py27_0 conda-forge<br class="">curl 7.52.1 0 conda-forge<br class="">esmf 7.0.0 5 conda-forge<br class="">expat 2.1.0 2 conda-forge<br class="">fontconfig 2.12.1 4 conda-forge<br class="">freetype 2.7 1 conda-forge<br class="">freexl 1.0.2 1 conda-forge<br class="">g2clib 1.6.0 2 conda-forge<br class="">gdal 2.1.3 np112py27_1 conda-forge<br class="">geos 3.5.1 1 conda-forge<br class="">gettext 0.19.7 1 conda-forge<br class="">giflib 5.1.4 0 conda-forge<br class="">glib 2.51.4 0 conda-forge<br class="">gsl 2.2.1 1 conda-forge<br class="">hdf4 4.2.12 0 conda-forge<br class="">hdf5 1.8.17 9 conda-forge<br class="">hdfeos2 2.19.1 7 conda-forge<br class="">hdfeos5 5.1.15 6 conda-forge<br class="">icu 58.1 1 conda-forge<br class="">jasper 1.900.1 4 conda-forge<br class="">jpeg 9b 0 conda-forge<br class="">json-c 0.12 0 conda-forge<br class="">kealib 1.4.6 3 conda-forge<br class="">libdap4 3.18.3 2 conda-forge<br class="">libffi 3.2.1 3 conda-forge<br class="">libgcc 5.2.0 0 <br class="">libgfortran 3.0.0 1 <br class="">libiconv 1.14 4 conda-forge<br class="">libnetcdf 4.4.1.1 2 conda-forge<br class="">libpng 1.6.28 0 conda-forge<br class="">libpq 9.5.4 3 conda-forge<br class="">libspatialite 4.3.0a 14 conda-forge<br class="">libtiff 4.0.6 7 conda-forge<br class="">libxml2 2.9.4 4 conda-forge<br class="">mkl 2017.0.1 0 <br class="">ncl 6.4.0 0 conda-forge<br class="">ncurses 5.9 10 conda-forge<br class="">netcdf-fortran 4.4.4 2 conda-forge<br class="">numpy 1.12.0 py27_0 <br class="">openjpeg 2.1.2 2 conda-forge<br class="">openssl 1.0.2h 3 conda-forge<br class="">pcre 8.39 0 conda-forge<br class="">pip 9.0.1 py27_0 conda-forge<br class="">pixman 0.34.0 0 conda-forge<br class="">pkg-config 0.29.1 1 conda-forge<br class="">proj4 4.9.3 2 conda-forge<br class="">pyngl 1.5.0_beta20161122 np112py27_2 conda-forge<br class="">pynio 1.5.0_beta20160623 np112py27_14 conda-forge<br class="">python 2.7.12 2 conda-forge<br class="">readline 6.2 0 conda-forge<br class="">setuptools 33.1.0 py27_0 conda-forge<br class="">sqlite 3.13.0 1 conda-forge<br class="">tk 8.5.19 1 conda-forge<br class="">udunits2 2.2.23 0 conda-forge<br class="">util-linux 2.21 0 <br class="">wheel 0.29.0 py27_0 conda-forge<br class="">xerces-c 3.1.4 3 conda-forge<br class="">xz 5.2.2 0 conda-forge<br class="">zlib 1.2.11 0 conda-forge<br class="">[root@air pyn_test]$ <br class=""></div></div><div class="gmail_extra"><br class=""><div class="gmail_quote">On Wed, Mar 8, 2017 at 1:14 PM, Kevin Hallock <span dir="ltr" class=""><<a href="mailto:hallock@ucar.edu" target="_blank" class="">hallock@ucar.edu</a>></span> wrote:<br class=""><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 class="">Hi Raj,<div class=""><br class=""></div><div class="">Could you please run the following commands:</div><div class=""><font face="Courier New" class="">echo $SHELL</font></div><div class=""><font face="Courier New" class="">which conda</font></div><div class=""><font face="Courier New" class="">which activate</font></div><div class=""><font face="Courier New" class="">conda list -n pyn_test</font></div><div class=""><br class=""></div><div class="">Thanks,</div><div class="">Kevin</div><div class=""><div class="m_4075683797019200014h5"><div class=""><br class=""><div class=""><blockquote type="cite" class=""><div class="">On Mar 8, 2017, at 1:53 PM, Raju Ankleshwaria <<a href="mailto:raju.ankleshwaria@gmail.com" target="_blank" class="">raju.ankleshwaria@gmail.com</a>> wrote:</div><br class="m_4075683797019200014m_2570258976223485099Apple-interchange-newline"><div class=""><div dir="ltr" class=""><div class="">Hi Kevin,</div><div class=""><br class=""></div><div class="">I installed PyNGL (<font face="Courier New" class="">conda install -c conda-forge pyngl=1.5.0_beta20161122)</font> and PyNIO and did ceated conda environment. However, I am getting error when I source it.</div><div class="">Please see below:</div><div class=""><br class=""></div><div class="">Extracting packages ...<br class="">[ COMPLETE ]|############################<wbr class="">##############################<wbr class="">##############################<wbr class="">##############################<wbr class="">###########################| 100%<br class="">Linking packages ...<br class="">[ COMPLETE ]|############################<wbr class="">##############################<wbr class="">##############################<wbr class="">##############################<wbr class="">###########################| 100%<br class="">#<br class=""># To activate this environment, use:<br class=""># > source activate pyn_test<br class="">#<br class=""># To deactivate this environment, use:<br class=""># > source deactivate pyn_test<br class="">#</div><div class="">[root@air ~]$ source activate pyn_test<br class="">activate: No such file or directory.<br class=""></div></div><div class="gmail_extra"><br class=""><div class="gmail_quote">On Wed, Mar 8, 2017 at 11:49 AM, Kevin Hallock <span dir="ltr" class=""><<a href="mailto:hallock@ucar.edu" target="_blank" class="">hallock@ucar.edu</a>></span> wrote:<br class=""><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 class="">Hi Raj,<div class=""><br class=""></div><div class="">It appears as though there is a dependency conflict between that particular version of PyNIO and the rest of Anaconda.</div><div class=""><br class=""></div><div class="">Our recommended instructions for installing PyNIO and PyNGL are as follows:</div><div class=""><blockquote type="cite" class="">To install PyNIO and PyNGL under conda, we recommend creating a conda environment:<br class=""><br class=""><div class=""> conda create --name pyn_test --channel conda-forge pynio pyngl</div><div class=""> source activate pyn_test</div><br class="m_4075683797019200014m_2570258976223485099m_1718728134641760625Apple-interchange-newline"></blockquote><br class=""></div><div class="">We generally recommend creating a conda environment, especially when using Anaconda, due to dependency issues like what you experienced with libjpeg.</div><div class=""><br class=""></div><div class="">Please let me know if this helps.</div><span class="m_4075683797019200014m_2570258976223485099HOEnZb"><font color="#888888" class=""><div class=""><br class=""></div><div class="">Kevin</div></font></span><div class=""><div class="m_4075683797019200014m_2570258976223485099h5"><div class=""><br class=""><div class=""><blockquote type="cite" class=""><div class="">On Mar 8, 2017, at 12:24 PM, Raju Ankleshwaria <<a href="mailto:raju.ankleshwaria@gmail.com" target="_blank" class="">raju.ankleshwaria@gmail.com</a>> wrote:</div><br class="m_4075683797019200014m_2570258976223485099m_1718728134641760625Apple-interchange-newline"><div class=""><div dir="ltr" class=""><div class="">for PyNIO conda install -c ncar pynio=1.4.3</div><div class="">for PyNGL conda is unable to search the package. conda search pyngl</div></div><div class="gmail_extra"><br class=""><div class="gmail_quote">On Wed, Mar 8, 2017 at 11:18 AM, Kevin Hallock <span dir="ltr" class=""><<a href="mailto:hallock@ucar.edu" target="_blank" class="">hallock@ucar.edu</a>></span> wrote:<br class=""><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 class="">Hi Raj,<div class=""><br class=""></div><div class="">What was the full conda command you used to install PyNIO and PyNGL?</div><span class="m_4075683797019200014m_2570258976223485099m_1718728134641760625HOEnZb"><font color="#888888" class=""><div class=""><br class=""></div><div class="">Kevin</div></font></span><div class=""><div class="m_4075683797019200014m_2570258976223485099m_1718728134641760625h5"><div class=""><br class=""><div class=""><blockquote type="cite" class=""><div class="">On Mar 8, 2017, at 11:43 AM, Raju Ankleshwaria <<a href="mailto:raju.ankleshwaria@gmail.com" target="_blank" class="">raju.ankleshwaria@gmail.com</a>> wrote:</div><br class="m_4075683797019200014m_2570258976223485099m_1718728134641760625m_7011304894923456380Apple-interchange-newline"><div class=""><div dir="ltr" class=""><div class="">Hi kevin,</div><div class=""><br class=""></div><div class="">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 class=""><br class=""></div><div class="">Thanks,</div><div class="">raj</div><div class=""><br class=""></div><div class="">[root@air runIndia]$ python <br class="">Python 2.7.13 |Anaconda custom (64-bit)| (default, Dec 20 2016, 23:09:15) <br class="">[GCC 4.4.7 20120313 (Red Hat 4.4.7-1)] on linux2<br class="">Type "help", "copyright", "credits" or "license" for more information.<br class="">Anaconda is brought to you by Continuum Analytics.<br class="">Please check out: <a href="http://continuum.io/thanks" target="_blank" class="">http://continuum.io/thanks</a> and <a href="https://anaconda.org/" target="_blank" class="">https://anaconda.org</a><br class="">>>> import Nio<br class="">Traceback (most recent call last):<br class=""> File "<stdin>", line 1, in <module><br class=""> File "/data/soft/anaconda2/lib/pyth<wbr class="">on2.7/site-packages/PyNIO/Nio.<wbr class="">py", line 63, in <module><br class=""> from nio import *<br class="">ImportError: libjpeg.so.8: cannot open shared object file: No such file or directory<br class="">>>> <br class="">KeyboardInterrupt<br class="">>>> <br class="">[root@air runIndia]$ locate libjpeg<br class="">/data/soft/anaconda2/lib/libjp<wbr class="">eg.a<br class="">/data/soft/anaconda2/lib/<a href="http://libjpeg.la/" target="_blank" class="">libjp<wbr class="">eg.la</a><br class="">/data/soft/anaconda2/lib/libjp<wbr class="">eg.so<br class="">/data/soft/anaconda2/lib/libjp<wbr class="">eg.so.9<br class="">/data/soft/anaconda2/lib/libjp<wbr class="">eg.so.9.2.0<br class="">/data/soft/anaconda2/pkgs/jpeg<wbr class="">-9b-0/lib/libjpeg.a<br class="">/data/soft/anaconda2/pkgs/jpeg<wbr class="">-9b-0/lib/<a href="http://libjpeg.la/" target="_blank" class="">libjpeg.la</a><br class="">/data/soft/anaconda2/pkgs/jpeg<wbr class="">-9b-0/lib/libjpeg.so<br class="">/data/soft/anaconda2/pkgs/jpeg<wbr class="">-9b-0/lib/libjpeg.so.9<br class="">/data/soft/anaconda2/pkgs/jpeg<wbr class="">-9b-0/lib/libjpeg.so.9.2.0<br class="">/usr/lib64/libjpeg.so<br class="">/usr/lib64/libjpeg.so.62<br class="">/usr/lib64/libjpeg.so.62.1.0<br class="">/usr/local/lib/libjpeg.a<br class="">/usr/local/lib/<a href="http://libjpeg.la/" target="_blank" class="">libjpeg.la</a><br class="">/usr/local/lib/libjpeg.so<br class="">/usr/local/lib/libjpeg.so.9<br class="">/usr/local/lib/libjpeg.so.9.2.<wbr class="">0<br class=""><br class=""></div><div class=""><br class=""></div></div><div class="gmail_extra"><br class=""><div class="gmail_quote">On Tue, Mar 7, 2017 at 11:44 AM, Kevin Hallock <span dir="ltr" class=""><<a href="mailto:hallock@ucar.edu" target="_blank" class="">hallock@ucar.edu</a>></span> wrote:<br class=""><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 class="">Hi Raj,<div class=""><br class=""></div><div class="">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" class="">https://www.pyngl.uca<wbr class="">r.edu/Download/</a></div><div class=""><br class=""></div><div class="">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 class=""><br class=""></div><div class="">Kevin</div><div class=""><br class=""><div class=""><blockquote type="cite" class=""><div class=""><div class="m_4075683797019200014m_2570258976223485099m_1718728134641760625m_7011304894923456380h5"><div class="">On Mar 6, 2017, at 2:04 PM, Raju Ankleshwaria <<a href="mailto:raju.ankleshwaria@gmail.com" target="_blank" class="">raju.ankleshwaria@gmail.com</a>> wrote:</div><br class="m_4075683797019200014m_2570258976223485099m_1718728134641760625m_7011304894923456380m_-6332578306778971185Apple-interchange-newline"></div></div><div class=""><div class=""><div class="m_4075683797019200014m_2570258976223485099m_1718728134641760625m_7011304894923456380h5"><div dir="ltr" class=""><div class="">Dear Users,</div><div class=""><br class=""></div><div class="">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 class=""><br class=""></div><div class="">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 class=""><br class=""></div><div class="">I need your help.</div><div class="">Raj</div><div class=""><br class=""></div><div class="">Version of PyNIO: 1.4.1 linux-redhat-x86_64-gcc412-py2<wbr class="">71-numpy160</div><div class="">PyNGL: 1.4.0 linux-redhat-x86_64-gcc412-py2<wbr class="">71-numpy160</div><div class=""><br class=""></div><div class=""><br class=""></div><div class="">[root@air site-packages]# python<br class="">Python 2.7.5 (default, Nov 6 2016, 00:28:07) <br class="">[GCC 4.8.5 20150623 (Red Hat 4.8.5-11)] on linux2<br class="">Type "help", "copyright", "credits" or "license" for more information.<br class="">>>> import Ngl<br class="">Traceback (most recent call last):<br class=""> File "<stdin>", line 1, in <module><br class=""> File "/usr/lib/python2.7/site-packa<wbr class="">ges/PyNGL/Ngl.py", line 39, in <module><br class=""> import fplib<br class="">ImportError: /lib64/libgfortran.so.1: undefined symbol: sqrtq<br class="">>>> <br class="">[root@air site-packages]# python<br class="">Python 2.7.5 (default, Nov 6 2016, 00:28:07) <br class="">[GCC 4.8.5 20150623 (Red Hat 4.8.5-11)] on linux2<br class="">Type "help", "copyright", "credits" or "license" for more information.<br class="">>>> import Nio<br class="">Traceback (most recent call last):<br class=""> File "<stdin>", line 1, in <module><br class=""> File "/usr/lib64/python2.7/site-pac<wbr class="">kages/PyNIO/Nio.py", line 63, in <module><br class=""> from nio import *<br class="">ImportError: /lib64/libgfortran.so.1: undefined symbol: sqrtq<br class="">>>> import Ngl<br class="">Traceback (most recent call last):<br class=""> File "<stdin>", line 1, in <module><br class=""> File "/usr/lib/python2.7/site-packa<wbr class="">ges/PyNGL/Ngl.py", line 39, in <module><br class=""> import fplib<br class="">ImportError: /lib64/libgfortran.so.1: undefined symbol: sqrtq<br class="">>>> <br class="">[root@air site-packages]# locate libgfortran.so.1<br class="">/usr/lib64/libgfortran.so.1<br class="">/usr/lib64/libgfortran.so.1.0.<wbr class="">0<br class="">[root@air site-packages]# </div></div></div></div>
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