Thanks for sending the CMakeCache.txt file.
As we discussed offline just now, your initial seg fault is now fixed (the problem mentioned in this post above: libgdal.so.29: undefined symbol: opj_encoder_set_extra_options). By compiling pygplates in conda, both pygplates and pygmt use the same version of GDAL (thus avoiding the conflict).
The problem you’re now having (mentioned in this post) is a different issue that’s covered in this post: it’s an issue with pygplates seg faulting on exit when using version 3.9 of Python that I’m currently looking into.
So now you’re compiling pygplates in a Python 3.8 (not 3.9) conda environment as a workaround.