Errors running PyART

[Paul McCrone - NOAA Federal]

Hello all,

I have been running PyART and suddenly, I am getting errors. Can you help?  I am not sure what to do. Here is the error below.

It indicated to try "import cfgrib" and look at the errors. I did this and the module loaded without error. 

I see an error that talks about 'libc.musl-x86_64.so.1'. I guess it it not installed. What should I tell my system admin? I was running pyart with no problems.

Paul McCrone

[mccrone@lnxappsa nexrad]$ /home/pmccrone/anaconda3/bin/python ./mynexrad_KDDC_zoom7z.py
..Loading Modules 0...

## 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

/home/pmccrone/anaconda3/lib/python3.8/site-packages/ecmwflibs/__init__.py:75: UserWarning: /home/mccrone/anaconda3/bin/../lib/libgobject-2.0.so.0: undefined symbol: g_atomic_rc_box_release_full
  warnings.warn(str(e))
/home/mccrone/.local/lib/python3.8/site-packages/xarray/backends/cfgrib_.py:27: UserWarning: Failed to load cfgrib - most likely there is a problem accessing the ecCodes library. Try `import cfgrib` to get the full error message
  warnings.warn(
Traceback (most recent call last):
  File "./mynexrad_KDDC_zoom7z.py", line 16, in <module>
    import pyart
  File "/home/mccrone/anaconda3/lib/python3.8/site-packages/pyart/__init__.py", line 35, in <module>
    from . import graph
  File "/home/mccrone/anaconda3/lib/python3.8/site-packages/pyart/graph/__init__.py", line 59, in <module>
    from .gridmapdisplay import GridMapDisplay
  File "/home/mccrone/anaconda3/lib/python3.8/site-packages/pyart/graph/gridmapdisplay.py", line 13, in <module>
    import cartopy
  File "/home/mccrone/anaconda3/lib/python3.8/site-packages/cartopy/__init__.py", line 96, in <module>
    import cartopy.crs
  File "/home/mccrone/anaconda3/lib/python3.8/site-packages/cartopy/crs.py", line 32, in <module>
    import shapely.geometry as sgeom
  File "/home/mccrone/anaconda3/lib/python3.8/site-packages/shapely/geometry/__init__.py", line 4, in <module>
    from .base import CAP_STYLE, JOIN_STYLE
  File "/home/mccrone/anaconda3/lib/python3.8/site-packages/shapely/geometry/base.py", line 19, in <module>
    from shapely.coords import CoordinateSequence
  File "/home/mccrone/anaconda3/lib/python3.8/site-packages/shapely/coords.py", line 8, in <module>
    from shapely.geos import lgeos
  File "/home/mccrone/anaconda3/lib/python3.8/site-packages/shapely/geos.py", line 92, in <module>
    free = load_dll('c', fallbacks=c_alt_paths).free
  File "/home/mccrone/anaconda3/lib/python3.8/site-packages/shapely/geos.py", line 60, in load_dll
    raise OSError(
OSError: Could not find lib c or load any of its variants ['libc.musl-x86_64.so.1'].
[mccrone@lnxappsa nexrad]$ /home/pmccrone/anaconda3/bin/python
Python 3.8.8 (default, Apr 13 2021, 19:58:26)
[GCC 7.3.0] :: Anaconda, Inc. on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import cfgrib
>>> quit
Use quit() or Ctrl-D (i.e. EOF) to exit
>>> quit()
[mccrone@lnxappsa nexrad]$
[mccrone@lnxappsa nexrad]$ pwd
/home/mccrone/python/src/nexrad
[mccrone@lnxappsa nexrad]$ cd
[mccrone@lnxappsa ~]$ cd anaconda3/bin
[mccrone@lnxappsa bin]$
[mccrone@lnxappsa bin]$
[mccrone@lnxappsa bin]$
[mccrone@lnxappsa bin]$ ./pip install Cython
Requirement already satisfied: Cython in /home/mccrone/anaconda3/lib/python3.8/site-packages (0.29.23)
[mccrone@lnxappsa bin]$ ./pip install cython
Requirement already satisfied: cython in /home/mccrone/anaconda3/lib/python3.8/site-packages (0.29.23)
[mccrone@lnxappsa bin]$ 

[sherma...@gmail.com]

Hi Paul,

I'm wondering if there was a conflict from a recent install. Have you installed or updated anything recently? I did find that shapely sometimes breaks, and possibly a reinstall of it might help: https://stackoverflow.com/questions/39991765/shapely-oserror-could-not-find-lib-c-or-load-any-of-its-variants

If that doesn't work, are you using a conda environment or base environment? But being lib C wondering if the anaconda compilers might be needed. https://docs.conda.io/projects/conda-build/en/latest/resources/compiler-tools.html

What I would try is possible a fresh environment, if you haven't already with: conda create -n pyart_env -c conda-forge python=3.8 arm_pyart etc etc

Zach S.

[Paul McCrone - NOAA Federal]

Hi Zach, 

Thanks, I will try your ideas.

Paul

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V/R,

Paul McCrone

National Weather Service Radar Operations Center, Field Requirements Branch

120 David L. Boren Blvd., Suite 3700

Norman, OK 73072

Paul.M...@noaa.gov

Telephone:  405-546-1013 (*Google*)

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