Error loading GMT shared library at 'libgmt.dylib'

[jlmaurer]

Description of the problem

Problem with one of the GMT libraries on a fresh install of pygmt in a new conda env.

conda create --name pygmt_test
conda activate pygmt_test
mamba install --channel conda-forge pygmt
python
import pygmt

Full error message

>>> import pygmt
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/Users/jeremym/miniconda3/envs/pygmt_test/lib/python3.10/site-packages/pygmt/__init__.py", line 71, in <module>
    _begin()
  File "/Users/jeremym/miniconda3/envs/pygmt_test/lib/python3.10/site-packages/pygmt/session_management.py", line 16, in begin
    with Session() as lib:
  File "/Users/jeremym/miniconda3/envs/pygmt_test/lib/python3.10/site-packages/pygmt/clib/session.py", line 183, in __enter__
    self.create("pygmt-session")
  File "/Users/jeremym/miniconda3/envs/pygmt_test/lib/python3.10/site-packages/pygmt/clib/session.py", line 330, in create
    c_create_session = self.get_libgmt_func(
  File "/Users/jeremym/miniconda3/envs/pygmt_test/lib/python3.10/site-packages/pygmt/clib/session.py", line 282, in get_libgmt_func
    self._libgmt = load_libgmt()
  File "/Users/jeremym/miniconda3/envs/pygmt_test/lib/python3.10/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 '/Users/jeremym/miniconda3/envs/pygmt_test/lib/libgmt.dylib'.
dlopen(/Users/jeremym/miniconda3/envs/pygmt_test/lib/libgmt.dylib, 0x0006): Symbol not found: _ZSTD_compressBound
  Referenced from: /Users/jeremym/miniconda3/envs/pygmt_test/lib/libgdal.30.dylib
  Expected in: /Users/jeremym/miniconda3/envs/pygmt_test/lib/libblosc.1.21.1.dylib
Error loading GMT shared library at 'libgmt.dylib'.
dlopen(libgmt.dylib, 0x0006): Symbol not found: _ZSTD_compressBound
  Referenced from: /Users/jeremym/miniconda3/envs/pygmt_test/lib/libgdal.30.dylib
  Expected in: /Users/jeremym/miniconda3/envs/pygmt_test/lib/libblosc.1.21.1.dylib

System information
This command: python -c "import pygmt; pygmt.show_versions()" doesn't work due to the above error. sys.version_info gives the following:

sys.version_info(major=3, minor=10, micro=4, releaselevel='final', serial=0)

and platform.platform() gives:

'macOS-12.3.1-x86_64-i386-64bit'

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[weiji14]

Hi @jlmaurer, thanks for the bug report. We're aware of the issue, and it seems to be a problem on conda-forge due to blosc (which gdal depends on) no longer packaging ZSTD, see conda-forge/blosc-feedstock#53 (comment). Hopefully this will get sorted out in the next day or so.

[weiji14]

As a workaround, could you try mamba install --channel conda-forge pygmt blosc=1.21.0 and see if it works? Sorry that I can't test this, don't have a mac with me.

[jlmaurer]

@weiji14 that did the trick! Thanks

[seisman]

The macOS CI works again. I think the upstream issue has been fixed.