Py-ART import error under Anaconda Python 3.6

[Paul Hein]

I just installed anaconda python 3.6 on a CentOS 7.5 machine and I used conda to install the modules.  I get an error when I simply type "import pyart".  It looks like the error is due to geos module which I did not install but I think Basemap did need it.  Pyart has almost all the optional dependencies (trmm_rsl, h5py, Basemap, wradlib, nose, gdal).  Cartopy is also installed. Attached is the list of installed modules. I am not finding any answers.  Here is the error:
mycomputer:~$ python
Python 3.6.4 |Anaconda custom (64-bit)| (default, Jan 16 2018, 18:10:19)
[GCC 7.2.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import pyart

## You are using the Python ARM Radar Toolkit (Py-ART), an open source
## library for working with weather radar data. Py-ART is partly
## supported by the U.S. Department of Energy as part of the Atmospheric
## Radiation Measurement (ARM) Climate Research Facility, an Office of
## Science user facility.
##
## If you use this software to prepare a publication, please cite:
##
##     JJ Helmus and SM Collis, JORS 2016, doi: 10.5334/jors.119

/usr/local64/python-3.6/anaconda3/lib/python3.6/site-packages/pyart/config.py:22: DeprecationWarning: the imp module is deprecated in favour of importlib; see the module's documentation for alternative uses
  import imp
python: geos_ts_c.cpp:3408: int GEOSCoordSeq_setOrdinate_r(GEOSContextHandle_HS*, geos::geom::CoordinateSequence*, unsigned int, unsigned int, double): Assertion `0 != cs' failed.
Abort (core dumped)

Thank you for your help!
Paul

[Kai Mühlbauer]

Hi Paul,

most likely the problem is due to working in the anaconda root/base environment.

Looking into your package list you can see, that packages from default-channel and conda-forge are mixed. This can lead to the shown behaviour.

Please try to create a dedicated conda environment and install pyart and other needed packages into this environment.

HTH
Kai

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[Nick Guy]

Kai is likely correct, but if that doesn't work. In the last 6 months, I've seen instances where the order in which you install gdal is important. This happened during a couple of updates to both gdal and anaconda. At those times, gdal had to be among the first packages installed. It may be sorted by now.

Nick

[Scott Collis]

Oh yeah.. GDAL plays not nice with NetCDF and HDF5 at times..

I know it is a paradigm shift but using conda environments for packages really helps.. 

Take a look at several I have here:

https://github.com/EVS-ATMOS/environments/tree/master/radar

Py-ART full will give you all you need

https://github.com/EVS-ATMOS/environments/blob/master/radar/pyart_full.yml

Note, read the instructions in the file about setting paths for the LP compile..

Some times csuradartools will fail here on MacOS.. if you get that issue make sure you

conda install gfortran_osx-64

IN YOUR base conda (so start with a source deactivate)

Scott Collis

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[Paul Hein]

I have been playing around and trying to get it to work, and I have used your pyart_full.yml and I came up with the exact same geos error.  So I am still striking out.  I am wondering if it is the geos module that is the problem since that is what the error shows and not the gdal module. Removing the gdal module does not solve the problem.  The same error is still there. Unfortunately geos module is used by many packages (basemap and cartopy in particular).  What gets loaded is geos 3.6.2.  Removing geos does allow pyart to be imported but that removes too much.    Again this is with CentOS 7.

(By the way, using yml file is a nice way to install.  This was a first for me.  Thanks!)

[Kai Mühlbauer]

Hi Paul,

Did you install inside a dedicated environment or in the root env? If you've created a new env, can you post the output of 'conda list' from inside the env?

The error you are facing has most likely to do with mixing different channels. To track this down, we need to find which clashes are happening.

Cheers,
Kai

[Paul & Gail Hein]

I figured out the problem.  If I import basemap and then import cartopy python crashes with the error.  If I import cartopy and then import basemap there is no error.  So removing module cartopy allows pyart to load with out an error.  Not an ideal solution but it works.  Thank you, everyone!

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[Paul Hein]

Kai - You are correct.  Cartopy is part of the main distribution and basemap is on the conda-forge channel.  Thanks!  Paul

On Tuesday, June 12, 2018 at 3:30:30 PM UTC-6, Paul Hein wrote:

I figured out the problem.  If I import basemap and then import cartopy python crashes with the error.  If I import cartopy and then import basemap there is no error.  So removing module cartopy allows pyart to load with out an error.  Not an ideal solution but it works.  Thank you, everyone!

On Tue, Jun 12, 2018 at 2:54 PM, Kai Mühlbauer wrote:

Hi Paul,

Did you install inside a dedicated environment or in the root env? If you've created a new env, can you post the output of 'conda list' from inside the env?

The error you are facing has most likely to do with mixing different channels. To track this down, we need to find which clashes are happening.

Cheers,
Kai

[Scott Collis]

Yup.. That’l do it!

Tip: 

Import SOME_PACKAGE

print(SOME_PACKAGE.__file__)

Scott Collis

[Kai Mühlbauer]

Hey Paul,

glad you got it working!

Cheers,
Kai