[pyngl-talk] Unable to import Nio in a Linux system
Gerry Creager - NOAA Affiliate
gerry.creager at noaa.gov
Thu Feb 14 14:35:20 MST 2019
Good catch. I'm downgrading to 2.2.4 to see how it handles things.
gerry
On Thu, Feb 14, 2019 at 3:07 PM Herzmann, Daryl E [AGRON] <
akrherz at iastate.edu> wrote:
> 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:
>
> https://github.com/conda-forge/gdal-feedstock/issues/264
>
>
> daryl
>
> /**
> * 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
>
> Daryl
>
> 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.
>
> Gerry
>
> 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:
> 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<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 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><mailto: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<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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>
>
> --
> Gerry Creager
> NSSL/CIMMS
> 405.325.6371
> ++++++++++++++++++++++
> The way to get started is to quit talking and begin doing.
> Walt Disney
>
--
Gerry Creager
NSSL/CIMMS
405.325.6371
++++++++++++++++++++++
*The way to get started is to quit talking and begin doing.*
* Walt Disney*
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