[pyngl-talk] Unable to import Nio in a Linux system
Herzmann, Daryl E [AGRON]
akrherz at iastate.edu
Tue Feb 12 20:26:14 MST 2019
Greetings,
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.
daryl
/**
* daryl herzmann
* Systems Analyst III -- Iowa Environmental Mesonet
* https://mesonet.agron.iastate.edu
*/
________________________________________
From: lbqnj's QQMail Calendars <lbqnj at qq.com>
Sent: Tuesday, February 12, 2019 6:39:40 PM
To: Herzmann, Daryl E [AGRON]
Cc: pyngl-talk at ucar.edu talk
Subject: Re: [pyngl-talk] Unable to import Nio in a Linux system
Dear daryl,
I have tried your suggestion, but unfortunately it is not working for me.
Attached is my conda list results:
(ncl_to_python) bash-4.1$ conda list
# packages in environment at /data2/anaconda3/envs/ncl_to_python:
#
# Name Version Build Channel
blas 1.1 openblas conda-forge
boost-cpp 1.68.0 h11c811c_1000 conda-forge
bzip2 1.0.6 h14c3975_1002 conda-forge
ca-certificates 2018.11.29 ha4d7672_0 conda-forge
cairo 1.14.12 h80bd089_1005 conda-forge
certifi 2018.11.29 py36_1000 conda-forge
cftime 1.0.3.4 py36h3010b51_1000 conda-forge
curl 7.64.0 h646f8bb_0 conda-forge
esmf 7.1.0r ha678704_2 conda-forge
expat 2.2.5 hf484d3e_1002 conda-forge
fontconfig 2.13.1 h2176d3f_1000 conda-forge
freetype 2.9.1 h94bbf69_1005 conda-forge
freexl 1.0.5 h14c3975_1002 conda-forge
g2clib 1.6.0 hf3f1b0b_9 conda-forge
geos 3.6.2 hfc679d8_4 conda-forge
geotiff 1.4.2 hfe6da40_1005 conda-forge
gettext 0.19.8.1 h9745a5d_1001 conda-forge
giflib 5.1.4 h14c3975_1001 conda-forge
glib 2.56.2 had28632_1001 conda-forge
gsl 2.2.1 blas_openblashddceaf2_6 [blas_openblas] conda-forge
hdf4 4.2.13 h9a582f1_1002 conda-forge
hdf5 1.10.2 hc401514_3 conda-forge
hdfeos2 2.20 h64bfcee_1000 conda-forge
hdfeos5 5.1.16 h647bee3_2 conda-forge
icu 58.2 hf484d3e_1000 conda-forge
jasper 1.900.1 h07fcdf6_1006 conda-forge
jpeg 9c h14c3975_1001 conda-forge
json-c 0.12.1 h470a237_1 conda-forge
kealib 1.4.9 h0bee7d0_2 conda-forge
krb5 1.16.3 hc83ff2d_1000 conda-forge
libcurl 7.64.0 h01ee5af_0 conda-forge
libdap4 3.19.1 hd48c02d_1000 conda-forge
libedit 3.1.20170329 hf8c457e_1001 conda-forge
libffi 3.2.1 hf484d3e_1005 conda-forge
libgcc-ng 7.3.0 hdf63c60_0 conda-forge
libgdal 2.2.4 hbd6f514_9 conda-forge
libgfortran 3.0.0 1 conda-forge
libgfortran-ng 7.2.0 hdf63c60_3 conda-forge
libiconv 1.15 h14c3975_1004 conda-forge
libkml 1.3.0 h328b03d_1009 conda-forge
libnetcdf 4.6.1 h628ed10_200 conda-forge
libpng 1.6.36 h84994c4_1000 conda-forge
libpq 10.6 h13b8bad_1000 conda-forge
libspatialite 4.3.0a h9968ff2_1023 conda-forge
libssh2 1.8.0 h1ad7b7a_1003 conda-forge
libstdcxx-ng 7.3.0 hdf63c60_0 conda-forge
libtiff 4.0.10 h648cc4a_1001 conda-forge
libuuid 2.32.1 h14c3975_1000 conda-forge
libxcb 1.13 h14c3975_1002 conda-forge
libxml2 2.9.8 h143f9aa_1005 conda-forge
lz4 2.1.6 py36ha8eefa0_1000 conda-forge
lz4-c 1.8.1.2 0 conda-forge
mpi 1.0 mpich conda-forge
mpich 3.2.1 h1c2f66e_1008 conda-forge
ncl 6.5.0 blas_openblashd40de8d_1 [blas_openblas] conda-forge
ncurses 6.1 hf484d3e_1002 conda-forge
netcdf-fortran 4.4.4 h4363f12_9 conda-forge
netcdf4 1.4.1 py36ha292673_200 conda-forge
numpy 1.16.1 py36_blas_openblash1522bff_0 [blas_openblas] conda-forge
openblas 0.3.3 h9ac9557_1001 conda-forge
openjpeg 2.3.0 hf38bd82_1003 conda-forge
openssl 1.0.2p h14c3975_1002 conda-forge
pandas 0.24.1 py36hf484d3e_0 conda-forge
pcre 8.41 hf484d3e_1003 conda-forge
pip 19.0.2 py36_0 conda-forge
pixman 0.34.0 h14c3975_1003 conda-forge
poppler 0.67.0 h2fc8fa2_1002 conda-forge
poppler-data 0.4.9 1 conda-forge
postgresql 10.6 h66cca7a_1000 conda-forge
proj4 4.9.3 h470a237_8 conda-forge
pthread-stubs 0.4 h14c3975_1001 conda-forge
pyngl 1.6.1 py36h4217dbb_0 conda-forge
pynio 1.5.4 py36h36f4ed2_0 conda-forge
python 3.6.7 hd21baee_1001 conda-forge
python-dateutil 2.8.0 py_0 conda-forge
pytz 2018.9 py_0 conda-forge
readline 7.0 hf8c457e_1001 conda-forge
scipy 1.2.0 py36_blas_openblash1522bff_1201 [blas_openblas] conda-forge
setuptools 40.8.0 py36_0 conda-forge
six 1.12.0 py36_1000 conda-forge
sqlite 3.26.0 h67949de_1000 conda-forge
tk 8.6.9 h84994c4_1000 conda-forge
tzcode 2018g h14c3975_1001 conda-forge
udunits2 2.2.27.6 h4e0c4b3_1001 conda-forge
wheel 0.33.0 py36_0 conda-forge
xarray 0.11.3 py36_0 conda-forge
xerces-c 3.2.0 h5d6a6da_2 conda-forge
xorg-imake 1.0.7 0 conda-forge
xorg-kbproto 1.0.7 h14c3975_1002 conda-forge
xorg-libice 1.0.9 h14c3975_1004 conda-forge
xorg-libsm 1.2.3 h4937e3b_1000 conda-forge
xorg-libx11 1.6.7 h14c3975_1000 conda-forge
xorg-libxau 1.0.9 h14c3975_0 conda-forge
xorg-libxaw 1.0.13 h14c3975_1002 conda-forge
xorg-libxdmcp 1.1.2 h14c3975_1007 conda-forge
xorg-libxext 1.3.3 h14c3975_1004 conda-forge
xorg-libxmu 1.1.2 h14c3975_1002 conda-forge
xorg-libxpm 3.5.12 h14c3975_1002 conda-forge
xorg-libxrender 0.9.10 h14c3975_1002 conda-forge
xorg-libxt 1.1.5 h14c3975_1002 conda-forge
xorg-makedepend 1.0.5 0 conda-forge
xorg-renderproto 0.11.1 h14c3975_1002 conda-forge
xorg-xextproto 7.3.0 h14c3975_1002 conda-forge
xorg-xproto 7.0.31 h14c3975_1007 conda-forge
xz 5.2.4 h14c3975_1001 conda-forge
zlib 1.2.11 h14c3975_1004 conda-forge
zstd 1.3.8 h7510944_1002 conda-forge
Thanks for your quick response, and any other potential solution?
Regards.
BL
在 2019年2月12日，22:10，Herzmann, Daryl E [AGRON] <akrherz at iastate.edu<mailto:akrherz at iastate.edu>> 写道：
Greetings,
This is likely a conflict between a package provided by `conda-forge` and one that is provided by the `defaults` channel.
https://conda-forge.org/docs/conda-forge_gotchas.html
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.
daryl
/**
* daryl herzmann
* Systems Analyst III -- Iowa Environmental Mesonet
* https://mesonet.agron.iastate.edu
*/
________________________________________
From: pyngl-talk <pyngl-talk-bounces at ucar.edu> on behalf of lbqnj's QQMail Calendars via pyngl-talk <pyngl-talk at ucar.edu>
Sent: Tuesday, February 12, 2019 3:01:39 AM
To: pyngl-talk at ucar.edu
Subject: [pyngl-talk] Unable to import Nio in a Linux system
Dear all,
I’m a user changing from NCL to pynio.
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).
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:
import Nio
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/data2/anaconda3/envs/ncl_to_python/lib/python3.6/site-packages/PyNIO/Nio.py", line 83, in <module>
from _nio import *
ImportError: /data2/anaconda3/envs/ncl_to_python/lib/python3.6/site-packages/PyNIO/../../../libgdal.so.20: undefined symbol: _ZN6libdap3DDSC1EPNS_15BaseTypeFactoryERKSs
Attached is my system information provided by “uname -a”:
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.
Is it a bug in the PyNIO 1.5.4, or any other problems in my Linux system?
Many thanks for your help.
Best wishes.
B. Liu
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