GDAL issue?

[yfialko]

Description of the problem

I did a clean conda install in a new environment,
conda install pygmt
(Red Hat linux)
The install finished with no errors, however GMT is non-functional, producing an error message about GDAL library and "undefined symbol" sqlite3_total_changes64 (see the error message).
Is there a workaround?
Thanks,
Yuri

Minimal Complete Verifiable Example

Full error message

gmt: symbol lookup error: /nobackupp17/yfialko/anaconda3/envs/pygmt/bin/../lib/./libgdal.so.36: undefined symbol: sqlite3_total_changes64

System information

python -c "import pygmt; pygmt.show_versions()"
/nobackupp17/yfialko/anaconda3/envs/pygmt/bin/gmt: symbol lookup error: /nobackupp17/yfialko/anaconda3/envs/pygmt/bin/../lib/./libgdal.so.36: undefined symbol: sqlite3_total_changes64                                                             
Traceback (most recent call last):                                                                    
  File "<string>", line 1, in <module>                                                                
  File "/nobackupp17/yfialko/anaconda3/envs/pygmt/lib/python3.12/site-packages/pygmt/__init__.py", line 24, in <module>
    from pygmt import datasets                                                                        
  File "/nobackupp17/yfialko/anaconda3/envs/pygmt/lib/python3.12/site-packages/pygmt/datasets/__init__.py", line 7, in <module>
    from pygmt.datasets.earth_age import load_earth_age                                               
  File "/nobackupp17/yfialko/anaconda3/envs/pygmt/lib/python3.12/site-packages/pygmt/datasets/earth_age.py", line 12, in <module>
    from pygmt.datasets.load_remote_dataset import _load_remote_dataset                               
  File "/nobackupp17/yfialko/anaconda3/envs/pygmt/lib/python3.12/site-packages/pygmt/datasets/load_remote_dataset.py", line 9, in <module>
    from pygmt.clib import Session                                                                    
  File "/nobackupp17/yfialko/anaconda3/envs/pygmt/lib/python3.12/site-packages/pygmt/clib/__init__.py", line 9, in <module>
    from pygmt.clib.session import Session, __gmt_version__
  File "/nobackupp17/yfialko/anaconda3/envs/pygmt/lib/python3.12/site-packages/pygmt/clib/session.py", line 111, in <module>
    _libgmt = load_libgmt()
              ^^^^^^^^^^^^^
  File "/nobackupp17/yfialko/anaconda3/envs/pygmt/lib/python3.12/site-packages/pygmt/clib/loading.py", line 62, in load_libgmt
    raise GMTCLibNotFoundError("\n".join(error_msg))
pygmt.exceptions.GMTCLibNotFoundError: Error loading GMT shared library at 'libgmt.so'.
/nobackupp17/yfialko/anaconda3/envs/pygmt/lib/python3.12/lib-dynload/../.././libgdal.so.36: undefined symbol: sqlite3_total_changes64

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[seisman]

Please show your output of conda list.

Since you're using Anaconda, it's most likely because you're installing packages from both the main and conda-forge channels, which usually cause conflicts.

The easiest solution is to use miniforge, not anaconda.

[seisman]

Or you can try to reinstall gdal from the conda-forge channel, e.g.,

conda install gdal --force-reinstall -c conda-forge

but the installation may be still broken since other packages may also come from the main channel.

[yfialko]

Yes, removing the main channel, leaving only the conda-forge channel, and re-installing miniforge solved the problem.
Thanks!