[pyngl-talk] Unable to import Nio in a Linux system

Herzmann, Daryl E [AGRON] akrherz at iastate.edu
Thu Feb 14 14:07:06 MST 2019

Hi Gerry,

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:



 * daryl herzmann
 * Systems Analyst III -- Iowa Environmental Mesonet
 * https://mesonet.agron.iastate.edu

From: Gerry Creager - NOAA Affiliate <gerry.creager at noaa.gov>
Sent: Thursday, February 14, 2019 3:02:40 PM
To: Herzmann, Daryl E [AGRON]
Cc: lbqnj's QQMail Calendars; pyngl-talk at ucar.edu talk
Subject: Re: [pyngl-talk] Unable to import Nio in a Linux system


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.

(ncl_to_python) [gerry.creager at godzilla 2019]$ python -c "import Nio; print(Nio.__version__)"
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/home/gerry.creager/.conda/envs/ncl_to_python/lib/python3.6/site-packages/PyNIO/Nio.py", line 83, in <module>
    from _nio import *
ImportError: /home/gerry.creager/.conda/envs/ncl_to_python/lib/python3.6/site-packages/PyNIO/../../../libgdal.so.20: undefined symbol: _ZN6libdap3DDSC1EPNS_15BaseTypeFactoryERKSs

I agree that it looks a lot like a gdal issue from close range.


On Tue, Feb 12, 2019 at 9:26 PM Herzmann, Daryl E [AGRON] via pyngl-talk <pyngl-talk at ucar.edu<mailto:pyngl-talk at ucar.edu>> wrote:

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 herzmann
 * Systems Analyst III -- Iowa Environmental Mesonet
 * https://mesonet.agron.iastate.edu

From: lbqnj's QQMail Calendars <lbqnj at qq.com<mailto:lbqnj at qq.com>>
Sent: Tuesday, February 12, 2019 6:39:40 PM
To: Herzmann, Daryl E [AGRON]
Cc: pyngl-talk at ucar.edu<mailto: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                   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                   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                                  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                  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?

在 2019年2月12日,22:10,Herzmann, Daryl E [AGRON] <akrherz at iastate.edu<mailto:akrherz at iastate.edu><mailto:akrherz at iastate.edu<mailto:akrherz at iastate.edu>>> 写道:


This is likely a conflict between a package provided by `conda-forge` and one that is provided by the `defaults` channel.


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 herzmann
* Systems Analyst III -- Iowa Environmental Mesonet
* https://mesonet.agron.iastate.edu

From: pyngl-talk <pyngl-talk-bounces at ucar.edu<mailto:pyngl-talk-bounces at ucar.edu>> on behalf of lbqnj's QQMail Calendars via pyngl-talk <pyngl-talk at ucar.edu<mailto:pyngl-talk at ucar.edu>>
Sent: Tuesday, February 12, 2019 3:01:39 AM
To: pyngl-talk at ucar.edu<mailto: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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