HYGEOS support forum

Hello everyone
i try to process sentinel use polymer_cli.py
the error is:
./polymer_cli.py /home/a/Sentinel-2/L1/S2A_MSIL1C_20201017T022711_N0209_R046_T52TCP_20201017T043702.SAFE/GRANULE/L1C_T52TCP_A027785_20201017T023425/ /home/a/Sentinel-2/17.nc
Starting processing at 2021-10-09 03:19:30.218156
Traceback (most recent call last):
File "./polymer_cli.py", line 35, in <module>
Level2(filename=args.output_file, fmt=args.fmt))
File "/home/a/polymer-v4.13/polymer/main.py", line 496, in run_atm_corr
with level2 as l2, level1 as l1:
File "/home/a/polymer-v4.13/polymer/level1.py", line 100, in __enter__
from polymer.level1_msi import Level1_MSI
File "/home/a/polymer-v4.13/polymer/level1_msi.py", line 7, in <module>
from glymur import Jp2k
File "/home/a/anaconda3/lib/python3.6/site-packages/glymur/__init__.py", line 8, in <module>
from .jp2k import Jp2k
File "/home/a/anaconda3/lib/python3.6/site-packages/glymur/jp2k.py", line 26, in <module>
from .jp2box import (
File "/home/a/anaconda3/lib/python3.6/site-packages/glymur/jp2box.py", line 26, in <module>
from osgeo import gdal
File "/home/a/anaconda3/lib/python3.6/site-packages/osgeo/__init__.py", line 21, in <module>
_gdal = swig_import_helper()
File "/home/a/anaconda3/lib/python3.6/site-packages/osgeo/__init__.py", line 17, in swig_import_helper
_mod = imp.load_module('_gdal', fp, pathname, description)
File "/home/a/anaconda3/lib/python3.6/imp.py", line 243, in load_module
return load_dynamic(name, filename, file)
File "/home/a/anaconda3/lib/python3.6/imp.py", line 343, in load_dynamic
return _load(spec)
ImportError: libcharset.so.1: cannot open shared object file: No such file or directory
How to fix this problem? Thank you in advance!

Kind regards,
Tian.

Hello,

Sorry for the late reply. This problem seems to be due to the installation of the python environment, because the failure happend at "from osgeo import gdal".
I recommend to have a look at the latest Polymer release v4.14, which should provide a better installation procedure using anaconda environments.
I hope this helps,
Cheers,
François

I was having the same problem as the gdal version installed was <2.0. Despite the channels specified in environment.yml this was version 1.9 from bioconda. Forcing install of gdal >2 from -c conda-forge solved the problem.

conda install gdal>2.0 -c conda-forge

Franc,ois, I suggest that the environment.yml file is corrected to express this incompabitlity with older gdal version:

- gdal>2.0

Another recent imcompatiliblity with with cython 3.0 so I suggest to add:
- cython<3.0
until polymer is is made compatible with Cython default compilation directives.

Tiago

Thanks Tiago, I will check and update the dependencies in next release.