conda recipe fails for windows 11 / WSL2 ubuntu 24.04

[joemcglinchy]

Environment Information

• geospatial version: 0.11.2
• Python version: > 3.9
• Operating System: Windows 11 / WSL2 ubuntu 24.04

Description

I tried following the conda+mamba recipe to install geospatial, but for python > 3.9 gdal fails to install correctly. I was only able to achieve a successful gdal install with:

conda create -n geo python=3.9
conda activate geo
conda install -c conda-forge mamba
mamba install -c conda-forge geospatial

What I Did

>>> from osgeo import gdal
Traceback (most recent call last):
  File "/home/jmcglinchy/miniconda3/envs/geo/lib/python3.11/site-packages/osgeo/__init__.py", line 50, in swig_import_helper
    return importlib.import_module(mname)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/jmcglinchy/miniconda3/envs/geo/lib/python3.11/importlib/__init__.py", line 126, in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "<frozen importlib._bootstrap>", line 1204, in _gcd_import
  File "<frozen importlib._bootstrap>", line 1176, in _find_and_load
  File "<frozen importlib._bootstrap>", line 1147, in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 676, in _load_unlocked
  File "<frozen importlib._bootstrap>", line 573, in module_from_spec
  File "<frozen importlib._bootstrap_external>", line 1233, in create_module
  File "<frozen importlib._bootstrap>", line 241, in _call_with_frames_removed
ImportError: /home/jmcglinchy/miniconda3/envs/geo/lib/python3.11/site-packages/osgeo/../../../libgdal.so.35: undefined symbol: sqlite3_total_changes64

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/jmcglinchy/miniconda3/envs/geo/lib/python3.11/site-packages/osgeo/__init__.py", line 55, in <module>
    _gdal = swig_import_helper()
            ^^^^^^^^^^^^^^^^^^^^
  File "/home/jmcglinchy/miniconda3/envs/geo/lib/python3.11/site-packages/osgeo/__init__.py", line 52, in swig_import_helper
    return importlib.import_module('_gdal')
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/jmcglinchy/miniconda3/envs/geo/lib/python3.11/importlib/__init__.py", line 126, in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
ModuleNotFoundError: No module named '_gdal'

lastly, even with the successful gdal python install, the CLI is broken, as every tool (gdalinfo, gdalwarp, etc.) produce a Segmentation Fault

[giswqs]

Thank you for reporting! Can you try installing gdal without geospatial to see if the problem persists?

[joemcglinchy]

hi, yes I was able to get it to work with something like the following:

conda create -n geo python=3.10 gdal libgdal scikit-image scikit-learn rasterio geopandas rioxarray xarray dask matplotlib seaborn ipyleaflet ipykernel pillow rasterstats shapely

[giswqs]

Can you share the gdal versions that were installed with and without the geospatial package?

[joemcglinchy]

Can you share the gdal versions that were installed with and without the geospatial package?

gdal 3.6.4 with python 3.9, gdal 3.9.3 with python >=3.10 IIRC

[giswqs]

What is the gdal version with Python 3.11 that you initially reported?

[joemcglinchy]

ok i just double checked. with the command i pasted above using python=3.10:

Python 3.10.16
conda list | grep gdal

gdal                      3.6.2           py310h0daa840_9  
libgdal                   3.6.2                he9acc32_9

with python 3.11 using the recipe:

Python 3.11.8
conda list | grep gdal

gdal                      3.9.3           py311h5159542_2    conda-forge
libgdal                   3.9.3               hea5fcb0_14    conda-forge
libgdal-arrow-parquet     3.9.3                h706f8e0_6    conda-forge
libgdal-core              3.9.3                hd5b9bfb_2    conda-forge
libgdal-fits              3.9.3                h2db7d5a_6    conda-forge
libgdal-grib              3.9.3                hba94bef_6    conda-forge
libgdal-hdf4              3.9.3                hbbee16a_6    conda-forge
libgdal-hdf5              3.9.3                hd75530a_6    conda-forge
libgdal-jp2openjpeg       3.9.3                h4d17120_6    conda-forge
libgdal-kea               3.9.3                h5afcd41_6    conda-forge
libgdal-netcdf            3.9.3                h2b12c9b_6    conda-forge
libgdal-pdf               3.9.3                h10c30d1_6    conda-forge
libgdal-pg                3.9.3                h5cc4e75_3    conda-forge
libgdal-postgisraster     3.9.3                h5cc4e75_3    conda-forge
libgdal-tiledb            3.9.3                h24303b0_6    conda-forge
libgdal-xls               3.9.3                h9ae506c_6    conda-forge

[giswqs]

So gdal 3.6.x is working and 3.9.3 is not working?

[joemcglinchy]

it seems a factor of the recipe. If i install gdal directly with the conda environment creation, i'm seeing no issues. If it's not repeatable though, may be a "me" issue :)

[giswqs]

gdal is always a bit tricky to install. Certainly not your issue only. I ran into similar issues myself from time to time. Certain gdal version sometime may not work properly on some operating systems. Sometimes I have to pin a specific gdal version, sometimes I have to install gdal from the offical conda channel instead of the conda-forge channel.