I tried installing pygmt with conda and have a somewhat similar problem with libgmt not loading. I tried doing the conda clean --all and reinstalled pygmt, but I get the same error:
python -c "import pygmt; pygmt.show_versions()"
dyld: Library not loaded: @rpath/libgeos_c.1.dylib
Referenced from: /Users/fielding/anaconda3/envs/pygmt/lib/libgmt.6.2.0.dylib
Reason: Incompatible library version: libgmt.6.dylib requires version 16.0.0 or later, but libgeos_c.1.dylib provides version 1.0.0
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/Users/fielding/anaconda3/envs/pygmt/lib/python3.9/site-packages/pygmt/__init__.py", line 70, in <module>
_begin()
File "/Users/fielding/anaconda3/envs/pygmt/lib/python3.9/site-packages/pygmt/session_management.py", line 16, in begin
with Session() as lib:
File "/Users/fielding/anaconda3/envs/pygmt/lib/python3.9/site-packages/pygmt/clib/session.py", line 183, in __enter__
self.create("pygmt-session")
File "/Users/fielding/anaconda3/envs/pygmt/lib/python3.9/site-packages/pygmt/clib/session.py", line 329, in create
c_create_session = self.get_libgmt_func(
File "/Users/fielding/anaconda3/envs/pygmt/lib/python3.9/site-packages/pygmt/clib/session.py", line 281, in get_libgmt_func
self._libgmt = load_libgmt()
File "/Users/fielding/anaconda3/envs/pygmt/lib/python3.9/site-packages/pygmt/clib/loading.py", line 59, in load_libgmt
raise GMTCLibNotFoundError("\n".join(error_msg))
pygmt.exceptions.GMTCLibNotFoundError: Error loading GMT shared library at 'libgmt.dylib'.
dlopen(libgmt.dylib, 6): Library not loaded: @rpath/libgeos_c.1.dylib
Referenced from: /Users/fielding/anaconda3/envs/pygmt/lib/libgmt.6.2.0.dylib
Reason: Incompatible library version: libgmt.dylib requires version 16.0.0 or later, but libgeos_c.1.dylib provides version 1.0.0
I am on a Mac running macOS 10.15.7 in case that matters.