Kernel died restarting, segmentation fault: 11, PyGMT-Anaconda-JupyterLab, Mac

Q&A PyGMT Q&A
1

Dear PyGMT team,

First, thanks so much for all the effort to make the GMT tools available via Python. I have been gradually shifting to it. A few days ago, my Jupyter-Lab/Anaconda started NOT working at all with a script that was running fine until a day before. It gives the following error message.

Screen Shot 2021-11-19 at 8.23.41 AM
Screen Shot 2021-11-19 at 8.23.41 AM1690×738 41.6 KB

If I run in Terminal:
(pygmt) computer-MBP-3:~ mtominaga$ python
Python 3.9.7 | packaged by conda-forge | (default, Sep 29 2021, 20:33:18)
[Clang 11.1.0 ] on darwin
Type “help”, “copyright”, “credits” or “license” for more information.

import pygmt
pygmt.show_versions()
Segmentation fault: 11

So I have tried from scratch again -
*completely uninstalled Anaconda (rm -rf)
*uninstalled pygmt, jupyter,
then installed Anaconda again followed by:
**conda config --prepend channels conda-forge
**conda create --name pygmt python=3.9 numpy pandas xarray netcdf4 packaging gmt
**conda activate pygmt
**conda install pygmt
**[if you are paranoic] conda update pygmt

The results were the same - kernel died (; segmentation fault:11.

Also tried:
(pygmt) Computer-MBP-3:~ mtominaga$ python -m ipykernel install --user --name pygmt
Installed kernelspec pygmt in /Users/mtominaga/Library/Jupyter/kernels/pygmt

with the following check:

Screen Shot 2021-11-19 at 8.31.10 AM
Screen Shot 2021-11-19 at 8.31.10 AM944×1196 180 KB

Could you please share with me what can I do to run the PyGMT again with jupyterlab…I depleted options from both my knowledge and search.

Thanks so much for your help!

2

An update:
I tried and installed PyGMT via Anaconda (clean install) on another mac machine (followed the PyGMT installation page) - which yielded the exact same kernel error message.

3

Could you try installing jupyter lab inside the conda environment? These steps work for me on macOS 12.0.1 to use PyGMT with jupyter lab:

conda config --prepend channels conda-forge
conda create --name pygmt python=3.9 numpy pandas xarray netcdf4 packaging gmt
conda activate pygmt
conda install pygmt
conda install jupyterlab
jupyter-lab