Can't import pygmt after installing GMT from Mac package

Q&A PyGMT Q&A
1

Hello,

I’ve installed GMT using the most recent Mac package (gmt-6.2.0-darwin-x86_64.dmg) and tested that it works. I then installed pygmt via pip. However, “import pygmt” from the Python command line produces the following:

import pygmt
Traceback (most recent call last):
File “”, line 1, in
File “/opt/anaconda3/lib/python3.8/site-packages/pygmt/init.py”, line 57, in
_begin()
File “/opt/anaconda3/lib/python3.8/site-packages/pygmt/session_management.py”, line 16, in begin
with Session() as lib:
File “/opt/anaconda3/lib/python3.8/site-packages/pygmt/clib/session.py”, line 185, in enter
self.create(“pygmt-session”)
File “/opt/anaconda3/lib/python3.8/site-packages/pygmt/clib/session.py”, line 332, in create
c_create_session = self.get_libgmt_func(
File “/opt/anaconda3/lib/python3.8/site-packages/pygmt/clib/session.py”, line 284, in get_libgmt_func
self._libgmt = load_libgmt()
File “/opt/anaconda3/lib/python3.8/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 ‘/Applications/GMT-6.2.0.app/Contents/Resources/lib/libgmt.dylib’.
dlopen(/Applications/GMT-6.2.0.app/Contents/Resources/lib/libgmt.dylib, 6): Library not loaded: @executable_path/…/lib/libcurl.4.dylib
Referenced from: /Applications/GMT-6.2.0.app/Contents/Resources/lib/libgmt.6.2.0.dylib
Reason: Incompatible library version: libgmt.dylib requires version 12.0.0 or later, but libcurl.4.dylib provides version 11.0.0
Error loading GMT shared library at ‘libgmt.dylib’.
dlopen(libgmt.dylib, 6): image not found

This is made even more confusing when I check on libcurl.4.dylib:

otool -L libcurl.4.dylib
libcurl.4.dylib:
@executable_path/…/lib/libcurl.4.dylib (compatibility version 12.0.0, current version 12.0.0)

In case it matters, I’m on Big Sur 11.6.

Any suggestion would be awesome.

Thanks,
Ryan

2

I’m just new at GMT, but I have both GMT and PyGMT running on MacOS 11.6. I installed the GMT dmg. But I also just independently installed the PyGMT and GMT python modules from conda-forge as per: https://www.pygmt.org/latest/install.html#installing-gmt-and-other-dependencies

3

Yes, it’s a known issue that the macOS bundle doesn’t work for GMT wrappers like PyGMT, GMT.jl or GMT/Matlab.

macOS bundle doesn’t work for pygmt · Issue #1930 · GenericMappingTools/gmt (github.com)

4

Thanks, this is what I did on my Mac and a remote Linux machine, and it was successful.

5

I still have to run this script in macOS bundle doesn't work for pygmt · Issue #1930 · GenericMappingTools/gmt · GitHub
even on GMT 6.5.0.

The issue is closed, but this is standing in the way of convincing my colleagues on Mac to adopt pygmt over matplotlib :-). Since we don’t work with conda environments, we install GMT from the binary package and would like for pygmt to just be able to access the library. Is it not possible to fix this in the Mac GMT binary package?

6

That problem is common to all wrappers not only PyGMT and we have no solution for it. It’s due to mysterious rules in creating dynamic libraries on Mac. One solution is to build GMT yourself locally with Brew for example.