<div dir="ltr"><div>Good catch. I'm downgrading to 2.2.4 to see how it handles things.</div><div><br></div><div>gerry<br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Thu, Feb 14, 2019 at 3:07 PM Herzmann, Daryl E [AGRON] <<a href="mailto:akrherz@iastate.edu">akrherz@iastate.edu</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Hi Gerry,<br>
<br>
The issue is that conda-forge updated to a new compiler and there's conflicts if you can't run the current release / most recent build of GDAL. For example:<br>
<br>
<a href="https://github.com/conda-forge/gdal-feedstock/issues/264" rel="noreferrer" target="_blank">https://github.com/conda-forge/gdal-feedstock/issues/264</a><br>
<br>
<br>
daryl<br>
<br>
/**<br>
* daryl herzmann<br>
* Systems Analyst III -- Iowa Environmental Mesonet<br>
* <a href="https://mesonet.agron.iastate.edu" rel="noreferrer" target="_blank">https://mesonet.agron.iastate.edu</a><br>
*/<br>
<br>
________________________________________<br>
From: Gerry Creager - NOAA Affiliate <<a href="mailto:gerry.creager@noaa.gov" target="_blank">gerry.creager@noaa.gov</a>><br>
Sent: Thursday, February 14, 2019 3:02:40 PM<br>
To: Herzmann, Daryl E [AGRON]<br>
Cc: lbqnj's QQMail Calendars; <a href="mailto:pyngl-talk@ucar.edu" target="_blank">pyngl-talk@ucar.edu</a> talk<br>
Subject: Re: [pyngl-talk] Unable to import Nio in a Linux system<br>
<br>
Daryl<br>
<br>
I was following along here, and used Liu's recipe to create the environment. Got the same error. I then made sure I had the conda-forge version of gdal installed. Same failure. Then followed with a 'conda update -c conda-forge --all' and... same error.<br>
<br>
(ncl_to_python) [gerry.creager@godzilla 2019]$ python -c "import Nio; print(Nio.__version__)"<br>
Traceback (most recent call last):<br>
File "<string>", line 1, in <module><br>
File "/home/gerry.creager/.conda/envs/ncl_to_python/lib/python3.6/site-packages/PyNIO/Nio.py", line 83, in <module><br>
from _nio import *<br>
ImportError: /home/gerry.creager/.conda/envs/ncl_to_python/lib/python3.6/site-packages/PyNIO/../../../libgdal.so.20: undefined symbol: _ZN6libdap3DDSC1EPNS_15BaseTypeFactoryERKSs<br>
<br>
I agree that it looks a lot like a gdal issue from close range.<br>
<br>
Gerry<br>
<br>
On Tue, Feb 12, 2019 at 9:26 PM Herzmann, Daryl E [AGRON] via pyngl-talk <<a href="mailto:pyngl-talk@ucar.edu" target="_blank">pyngl-talk@ucar.edu</a><mailto:<a href="mailto:pyngl-talk@ucar.edu" target="_blank">pyngl-talk@ucar.edu</a>>> wrote:<br>
Greetings,<br>
<br>
Something is amiss here as your `conda list` does not show GDAL as installed?!?! I was just having issues like yours late last week with GDAL and a `conda update --all` helped resolve it.<br>
<br>
daryl<br>
<br>
/**<br>
* daryl herzmann<br>
* Systems Analyst III -- Iowa Environmental Mesonet<br>
* <a href="https://mesonet.agron.iastate.edu" rel="noreferrer" target="_blank">https://mesonet.agron.iastate.edu</a><br>
*/<br>
<br>
________________________________________<br>
From: lbqnj's QQMail Calendars <<a href="mailto:lbqnj@qq.com" target="_blank">lbqnj@qq.com</a><mailto:<a href="mailto:lbqnj@qq.com" target="_blank">lbqnj@qq.com</a>>><br>
Sent: Tuesday, February 12, 2019 6:39:40 PM<br>
To: Herzmann, Daryl E [AGRON]<br>
Cc: <a href="mailto:pyngl-talk@ucar.edu" target="_blank">pyngl-talk@ucar.edu</a><mailto:<a href="mailto:pyngl-talk@ucar.edu" target="_blank">pyngl-talk@ucar.edu</a>> talk<br>
Subject: Re: [pyngl-talk] Unable to import Nio in a Linux system<br>
<br>
Dear daryl,<br>
I have tried your suggestion, but unfortunately it is not working for me.<br>
Attached is my conda list results:<br>
(ncl_to_python) bash-4.1$ conda list<br>
# packages in environment at /data2/anaconda3/envs/ncl_to_python:<br>
#<br>
# Name Version Build Channel<br>
blas 1.1 openblas conda-forge<br>
boost-cpp 1.68.0 h11c811c_1000 conda-forge<br>
bzip2 1.0.6 h14c3975_1002 conda-forge<br>
ca-certificates 2018.11.29 ha4d7672_0 conda-forge<br>
cairo 1.14.12 h80bd089_1005 conda-forge<br>
certifi 2018.11.29 py36_1000 conda-forge<br>
cftime 1.0.3.4 py36h3010b51_1000 conda-forge<br>
curl 7.64.0 h646f8bb_0 conda-forge<br>
esmf 7.1.0r ha678704_2 conda-forge<br>
expat 2.2.5 hf484d3e_1002 conda-forge<br>
fontconfig 2.13.1 h2176d3f_1000 conda-forge<br>
freetype 2.9.1 h94bbf69_1005 conda-forge<br>
freexl 1.0.5 h14c3975_1002 conda-forge<br>
g2clib 1.6.0 hf3f1b0b_9 conda-forge<br>
geos 3.6.2 hfc679d8_4 conda-forge<br>
geotiff 1.4.2 hfe6da40_1005 conda-forge<br>
gettext 0.19.8.1 h9745a5d_1001 conda-forge<br>
giflib 5.1.4 h14c3975_1001 conda-forge<br>
glib 2.56.2 had28632_1001 conda-forge<br>
gsl 2.2.1 blas_openblashddceaf2_6 [blas_openblas] conda-forge<br>
hdf4 4.2.13 h9a582f1_1002 conda-forge<br>
hdf5 1.10.2 hc401514_3 conda-forge<br>
hdfeos2 2.20 h64bfcee_1000 conda-forge<br>
hdfeos5 5.1.16 h647bee3_2 conda-forge<br>
icu 58.2 hf484d3e_1000 conda-forge<br>
jasper 1.900.1 h07fcdf6_1006 conda-forge<br>
jpeg 9c h14c3975_1001 conda-forge<br>
json-c 0.12.1 h470a237_1 conda-forge<br>
kealib 1.4.9 h0bee7d0_2 conda-forge<br>
krb5 1.16.3 hc83ff2d_1000 conda-forge<br>
libcurl 7.64.0 h01ee5af_0 conda-forge<br>
libdap4 3.19.1 hd48c02d_1000 conda-forge<br>
libedit 3.1.20170329 hf8c457e_1001 conda-forge<br>
libffi 3.2.1 hf484d3e_1005 conda-forge<br>
libgcc-ng 7.3.0 hdf63c60_0 conda-forge<br>
libgdal 2.2.4 hbd6f514_9 conda-forge<br>
libgfortran 3.0.0 1 conda-forge<br>
libgfortran-ng 7.2.0 hdf63c60_3 conda-forge<br>
libiconv 1.15 h14c3975_1004 conda-forge<br>
libkml 1.3.0 h328b03d_1009 conda-forge<br>
libnetcdf 4.6.1 h628ed10_200 conda-forge<br>
libpng 1.6.36 h84994c4_1000 conda-forge<br>
libpq 10.6 h13b8bad_1000 conda-forge<br>
libspatialite 4.3.0a h9968ff2_1023 conda-forge<br>
libssh2 1.8.0 h1ad7b7a_1003 conda-forge<br>
libstdcxx-ng 7.3.0 hdf63c60_0 conda-forge<br>
libtiff 4.0.10 h648cc4a_1001 conda-forge<br>
libuuid 2.32.1 h14c3975_1000 conda-forge<br>
libxcb 1.13 h14c3975_1002 conda-forge<br>
libxml2 2.9.8 h143f9aa_1005 conda-forge<br>
lz4 2.1.6 py36ha8eefa0_1000 conda-forge<br>
lz4-c 1.8.1.2 0 conda-forge<br>
mpi 1.0 mpich conda-forge<br>
mpich 3.2.1 h1c2f66e_1008 conda-forge<br>
ncl 6.5.0 blas_openblashd40de8d_1 [blas_openblas] conda-forge<br>
ncurses 6.1 hf484d3e_1002 conda-forge<br>
netcdf-fortran 4.4.4 h4363f12_9 conda-forge<br>
netcdf4 1.4.1 py36ha292673_200 conda-forge<br>
numpy 1.16.1 py36_blas_openblash1522bff_0 [blas_openblas] conda-forge<br>
openblas 0.3.3 h9ac9557_1001 conda-forge<br>
openjpeg 2.3.0 hf38bd82_1003 conda-forge<br>
openssl 1.0.2p h14c3975_1002 conda-forge<br>
pandas 0.24.1 py36hf484d3e_0 conda-forge<br>
pcre 8.41 hf484d3e_1003 conda-forge<br>
pip 19.0.2 py36_0 conda-forge<br>
pixman 0.34.0 h14c3975_1003 conda-forge<br>
poppler 0.67.0 h2fc8fa2_1002 conda-forge<br>
poppler-data 0.4.9 1 conda-forge<br>
postgresql 10.6 h66cca7a_1000 conda-forge<br>
proj4 4.9.3 h470a237_8 conda-forge<br>
pthread-stubs 0.4 h14c3975_1001 conda-forge<br>
pyngl 1.6.1 py36h4217dbb_0 conda-forge<br>
pynio 1.5.4 py36h36f4ed2_0 conda-forge<br>
python 3.6.7 hd21baee_1001 conda-forge<br>
python-dateutil 2.8.0 py_0 conda-forge<br>
pytz 2018.9 py_0 conda-forge<br>
readline 7.0 hf8c457e_1001 conda-forge<br>
scipy 1.2.0 py36_blas_openblash1522bff_1201 [blas_openblas] conda-forge<br>
setuptools 40.8.0 py36_0 conda-forge<br>
six 1.12.0 py36_1000 conda-forge<br>
sqlite 3.26.0 h67949de_1000 conda-forge<br>
tk 8.6.9 h84994c4_1000 conda-forge<br>
tzcode 2018g h14c3975_1001 conda-forge<br>
udunits2 2.2.27.6 h4e0c4b3_1001 conda-forge<br>
wheel 0.33.0 py36_0 conda-forge<br>
xarray 0.11.3 py36_0 conda-forge<br>
xerces-c 3.2.0 h5d6a6da_2 conda-forge<br>
xorg-imake 1.0.7 0 conda-forge<br>
xorg-kbproto 1.0.7 h14c3975_1002 conda-forge<br>
xorg-libice 1.0.9 h14c3975_1004 conda-forge<br>
xorg-libsm 1.2.3 h4937e3b_1000 conda-forge<br>
xorg-libx11 1.6.7 h14c3975_1000 conda-forge<br>
xorg-libxau 1.0.9 h14c3975_0 conda-forge<br>
xorg-libxaw 1.0.13 h14c3975_1002 conda-forge<br>
xorg-libxdmcp 1.1.2 h14c3975_1007 conda-forge<br>
xorg-libxext 1.3.3 h14c3975_1004 conda-forge<br>
xorg-libxmu 1.1.2 h14c3975_1002 conda-forge<br>
xorg-libxpm 3.5.12 h14c3975_1002 conda-forge<br>
xorg-libxrender 0.9.10 h14c3975_1002 conda-forge<br>
xorg-libxt 1.1.5 h14c3975_1002 conda-forge<br>
xorg-makedepend 1.0.5 0 conda-forge<br>
xorg-renderproto 0.11.1 h14c3975_1002 conda-forge<br>
xorg-xextproto 7.3.0 h14c3975_1002 conda-forge<br>
xorg-xproto 7.0.31 h14c3975_1007 conda-forge<br>
xz 5.2.4 h14c3975_1001 conda-forge<br>
zlib 1.2.11 h14c3975_1004 conda-forge<br>
zstd 1.3.8 h7510944_1002 conda-forge<br>
<br>
Thanks for your quick response, and any other potential solution?<br>
Regards.<br>
BL<br>
<br>
在 2019年2月12日，22:10，Herzmann, Daryl E [AGRON] <<a href="mailto:akrherz@iastate.edu" target="_blank">akrherz@iastate.edu</a><mailto:<a href="mailto:akrherz@iastate.edu" target="_blank">akrherz@iastate.edu</a>><mailto:<a href="mailto:akrherz@iastate.edu" target="_blank">akrherz@iastate.edu</a><mailto:<a href="mailto:akrherz@iastate.edu" target="_blank">akrherz@iastate.edu</a>>>> 写道：<br>
<br>
Greetings,<br>
<br>
This is likely a conflict between a package provided by `conda-forge` and one that is provided by the `defaults` channel.<br>
<br>
<a href="https://conda-forge.org/docs/conda-forge_gotchas.html" rel="noreferrer" target="_blank">https://conda-forge.org/docs/conda-forge_gotchas.html</a><br>
<br>
I am finding the currently best success by removing the `defaults` channel completely and just using a pure conda-forge environment. When you then run `conda list`, you should not see any `defaults` channel packages listed as installed.<br>
<br>
daryl<br>
<br>
/**<br>
* daryl herzmann<br>
* Systems Analyst III -- Iowa Environmental Mesonet<br>
* <a href="https://mesonet.agron.iastate.edu" rel="noreferrer" target="_blank">https://mesonet.agron.iastate.edu</a><br>
*/<br>
<br>
________________________________________<br>
From: pyngl-talk <<a href="mailto:pyngl-talk-bounces@ucar.edu" target="_blank">pyngl-talk-bounces@ucar.edu</a><mailto:<a href="mailto:pyngl-talk-bounces@ucar.edu" target="_blank">pyngl-talk-bounces@ucar.edu</a>>> on behalf of lbqnj's QQMail Calendars via pyngl-talk <<a href="mailto:pyngl-talk@ucar.edu" target="_blank">pyngl-talk@ucar.edu</a><mailto:<a href="mailto:pyngl-talk@ucar.edu" target="_blank">pyngl-talk@ucar.edu</a>>><br>
Sent: Tuesday, February 12, 2019 3:01:39 AM<br>
To: <a href="mailto:pyngl-talk@ucar.edu" target="_blank">pyngl-talk@ucar.edu</a><mailto:<a href="mailto:pyngl-talk@ucar.edu" target="_blank">pyngl-talk@ucar.edu</a>><br>
Subject: [pyngl-talk] Unable to import Nio in a Linux system<br>
<br>
Dear all,<br>
I’m a user changing from NCL to pynio.<br>
Recently I have install the pynio using the recommended conda way (conda create -n ncl_to_python -c conda-forge xarray netcdf4 scipy pyngl pynio ncl).<br>
When I activate the ncl_to_python environment, I cannot import Nio correctly, although the Ngl is running well. The error message is as following:<br>
import Nio<br>
Traceback (most recent call last):<br>
File "<stdin>", line 1, in <module><br>
File "/data2/anaconda3/envs/ncl_to_python/lib/python3.6/site-packages/PyNIO/Nio.py", line 83, in <module><br>
from _nio import *<br>
ImportError: /data2/anaconda3/envs/ncl_to_python/lib/python3.6/site-packages/PyNIO/../../../libgdal.so.20: undefined symbol: _ZN6libdap3DDSC1EPNS_15BaseTypeFactoryERKSs<br>
<br>
Attached is my system information provided by “uname -a”:<br>
Linux R910 2.6.32-431.el6.x86_64 #1 SMP Sun Nov 10 22:19:54 EST 2013 x86_64 x86_64 x86_64 GNU/Linux.<br>
<br>
Is it a bug in the PyNIO 1.5.4, or any other problems in my Linux system?<br>
Many thanks for your help.<br>
Best wishes.<br>
<br>
B. Liu<br>
<br>
<br>
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<br>
<br>
--<br>
Gerry Creager<br>
NSSL/CIMMS<br>
405.325.6371<br>
++++++++++++++++++++++<br>
The way to get started is to quit talking and begin doing.<br>
Walt Disney<br>
</blockquote></div><br clear="all"><br>-- <br><div dir="ltr" class="gmail_signature"><div dir="ltr"><div><div dir="ltr">Gerry Creager<div>NSSL/CIMMS</div><div>405.325.6371</div><div>++++++++++++++++++++++</div><div><div><i>The way to get started is to quit talking and begin doing.</i></div><i> Walt Disney</i></div></div></div></div></div>