conda MacOSX issues and Github actions

[apcraig]

Recently, we ran into some problems with conda on Mac OSX. This is probably related to a change in the conda compiler distribution. In the end, we needed to add -lgcc_eh to get CICE to compile with OpenMP but without MPI (i.e. -p 1x2).

A Forum topic was added to provide some guidance to the community, https://bb.cgd.ucar.edu/cesm/threads/conda-port-issues.5795/

Should we do anything about this in our documentation or implementation.

As an aside, @phil-blain used Github Actions to test the setup and verified the same issue as seen on an actual Mac OSX system. Should we be leveraging Github Actions or a similar cloud/container tool to test additional platforms and/or versions of systems/compilers/etc?

https://github.com/phil-blain/CICE-conda/runs/1573686932

[phil-blain]

Just want to add for @JFLemieux73 who might me reading that I'm working on that in my own time (not for work). CICE is open-source after all :)

[phil-blain]

I just opened an issue in the conda-forge repo where the conda-forge gfortran is built:
conda-forge/gfortran_impl_osx-64-feedstock#36

I managed to isolate the problem to the "threadprivate" directive used in the 1D EVP implementation.

[phil-blain]

This has been fixed in conda-forge. Recreating the "cice" env should install the new build of gfortran from conda-forge and this should not require -lgcc_eh at link time. See for example this successful run: https://github.com/phil-blain/conda-forge-macos-gfortran-openmp-bug/runs/1591889588?check_suite_focus=true

[apcraig]

I can confirm that conda works for me again. Big thanks @phil-blain for leading the effort to resolve the problem!

Do we want to discuss using github actions (or similar) to supplement testing? Or should this be closed for now.

[phil-blain]

I think it could be a good idea, eventually.

[eclare108213]

I started from the instructions here and didn't get very far:

bash-3.2$ which conda
bash-3.2$ curl -l https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86-64.sh -o ~/Downloads/miniconda.sh
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 379 100 379 0 0 796 0 --:--:-- --:--:-- --:--:-- 794
bash-3.2$ bash ~/Downloads/miniconda.sh
/Users/eclare/Downloads/miniconda.sh: line 1: syntax error near unexpected token `newline'

macOS Catalina version 10.15.7

Edit with more info: the contents of the miniconda.sh file is an html "not found" page (click on the url above to go there). Ah, there's a typo... I'll keep working on this.

Edit later: Still having problems

bash-3.2$ bash ~/Downloads/miniconda.sh
[...follow instructions...]
Preparing transaction: done
Executing transaction: done
Traceback (most recent call last):
File "/Users/eclare/miniconda3/pkgs/.cio-config.py", line 83, in
main()
File "/Users/eclare/miniconda3/pkgs/.cio-config.py", line 76, in main
for fn in os.listdir(dir_path):
PermissionError: [Errno 1] Operation not permitted: '/Users/eclare/Downloads'
bash-3.2$ which conda
bash-3.2$
bash-3.2$ ls -l
drwx------@ 120 eclare staff 3840 Dec 29 12:16 Downloads

Continuing edit: The problem is with the permissions of the Downloads folder. An easy workaround is to do the installation in ~/. instead of ~/Downloads. That worked for me and might be worth noting in the doc. On to the next step...

[phil-blain]

Yeah, should be x86_64 and not x86-64 (underscore instead of dash). The doc is OK.

Regarding the permission problem, that looks like a new security feature in Catalina: https://support.apple.com/en-ie/guide/mac-help/mchld5a35146/10.15/mac/10.15. In that light I agree we should change the command so that the installer is downloaded directly to $HOME to work around that problem.

- # Download the Miniconda installer to ~/Downloads/miniconda.sh
- curl -L https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh -o ~/Downloads/miniconda.sh
+ # Download the Miniconda installer to ~/miniconda.sh
+ curl -L https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh -o ~/miniconda.sh
# Install Miniconda
- bash ~/Downloads/miniconda.sh
+ bash ~/miniconda.sh