WIP: [ci] use XCode 14.1 on macOS-latest gcc jobs (fixes #5589)

[jameslamb]

Fixes #5589.

How this helps with #5587

Installs https://www.html-tidy.org/ in the (debian, r-devel, clang) CI job, to resolve an R CMD check note. I think this also makes that job more closely match the environment CRAN will use for that check, so I've proposed a similar change upstream: r-hub/rhub-linux-builders#64.

If that r-hub PR is merged at some point, we can revert this one. But for now, this PR unblock's LightGBM's CI.

UPDATE: after this PR was opened, the R-devel debian issue was fixed by an upstream change: #5587 (comment)

How this helps with #5589

Manually switches from XCode 14.0 (the default) to XCode 14.1 on macOS-latest GitHub Actions jobs using gcc, as suggested in https:/orgs/Homebrew/discussions/3659#discussioncomment-3936743.

That can be reverted in the future whenever XCode 14.1+ becomes the default on macOS-latest GitHub Actions jobs.

[jameslamb]

Ok I think this is ready for review and will unblock LightGBM's CI.

[jameslamb]

A few of the Linux jobs on Azure DevOps (Ubuntu 14.04) are failing with segfaults.

(build link)

../tests/c_api_test/test_.py ..                                          [  0%]
../tests/python_package_test/test_basic.py ............................. [  4%]
.............................................                            [ 10%]
../tests/python_package_test/test_callback.py ............               [ 11%]
../tests/python_package_test/test_consistency.py ......                  [ 12%]
../tests/python_package_test/test_dask.py Fatal Python error: Bus error

...

/__w/1/s/.ci/test.sh: line 177:  1664 Bus error               (core dumped) pytest $BUILD_DIRECTORY/tests

full logs (click me)

../tests/c_api_test/test_.py ..                                          [  0%]
../tests/python_package_test/test_basic.py ............................. [  4%]
.............................................                            [ 10%]
../tests/python_package_test/test_callback.py ............               [ 11%]
../tests/python_package_test/test_consistency.py ......                  [ 12%]
../tests/python_package_test/test_dask.py Fatal Python error: Bus error

Thread 0x00007f4a52ffd700 (most recent call first):
  File "/opt/miniforge/envs/test-env/lib/python3.8/multiprocessing/popen_fork.py", line 27 in poll
  File "/opt/miniforge/envs/test-env/lib/python3.8/multiprocessing/popen_fork.py", line 47 in wait
  File "/opt/miniforge/envs/test-env/lib/python3.8/multiprocessing/process.py", line 149 in join
  File "/opt/miniforge/envs/test-env/lib/python3.8/site-packages/distributed/process.py", line 234 in _watch_process
  File "/opt/miniforge/envs/test-env/lib/python3.8/threading.py", line 870 in run
  File "/opt/miniforge/envs/test-env/lib/python3.8/threading.py", line 932 in _bootstrap_inner
  File "/opt/miniforge/envs/test-env/lib/python3.8/threading.py", line 890 in _bootstrap

Thread 0x00007f4a537fe700 (most recent call first):
  File "/opt/miniforge/envs/test-env/lib/python3.8/threading.py", line 302 in wait
  File "/opt/miniforge/envs/test-env/lib/python3.8/queue.py", line 170 in get
  File "/opt/miniforge/envs/test-env/lib/python3.8/site-packages/distributed/process.py", line 214 in _watch_message_queue
  File "/opt/miniforge/envs/test-env/lib/python3.8/threading.py", line 870 in run
  File "/opt/miniforge/envs/test-env/lib/python3.8/threading.py", line 932 in _bootstrap_inner
  File "/opt/miniforge/envs/test-env/lib/python3.8/threading.py", line 890 in _bootstrap

Thread 0x00007f4a53fff700 (most recent call first):
  File "/opt/miniforge/envs/test-env/lib/python3.8/multiprocessing/popen_fork.py", line 27 in poll
  File "/opt/miniforge/envs/test-env/lib/python3.8/multiprocessing/popen_fork.py", line 47 in wait
  File "/opt/miniforge/envs/test-env/lib/python3.8/multiprocessing/process.py", line 149 in join
  File "/opt/miniforge/envs/test-env/lib/python3.8/site-packages/distributed/process.py", line 234 in _watch_process
  File "/opt/miniforge/envs/test-env/lib/python3.8/threading.py", line 870 in run

  File "/opt/miniforge/envs/test-env/lib/python3.8/inspect.py", line 997 in getsource
  File "/opt/miniforge/envs/test-env/lib/python3.8/site-packages/distributed/client.py", line 2830 in _get_computation_code
  File "/opt/miniforge/envs/test-env/lib/python3.8/site-packages/distributed/client.py", line 2902 in _graph_to_futures
  File "/opt/miniforge/envs/test-env/lib/python3.8/site-packages/distributed/client.py", line 3193 in compute
  File "/home/AzDevOps_azpcontainer/.local/lib/python3.8/site-packages/lightgbm/dask.py", line 667 in _train
  File "/home/AzDevOps_azpcontainer/.local/lib/python3.8/site-packages/lightgbm/dask.py", line 1051 in _lgb_dask_fit
  File "/home/AzDevOps_azpcontainer/.local/lib/python3.8/site-packages/lightgbm/dask.py", line 1171 in fit
  File "/__w/1/s/tests/python_package_test/test_dask.py", line 278 in test_classifier
  File "/opt/miniforge/envs/test-env/lib/python3.8/site-packages/_pytest/python.py", line 195 in pytest_pyfunc_call
  File "/opt/miniforge/envs/test-env/lib/python3.8/site-packages/pluggy/_callers.py", line 39 in _multicall
  File "/opt/miniforge/envs/test-env/lib/python3.8/site-packages/pluggy/_manager.py", line 80 in _hookexec
  File "/opt/miniforge/envs/test-env/lib/python3.8/site-packages/pluggy/_hooks.py", line 265 in __call__
  File "/opt/miniforge/envs/test-env/lib/python3.8/site-packages/_pytest/python.py", line 1789 in runtest
  File "/opt/miniforge/envs/test-env/lib/python3.8/site-packages/_pytest/runner.py", line 167 in pytest_runtest_call
  File "/opt/miniforge/envs/test-env/lib/python3.8/site-packages/pluggy/_callers.py", line 39 in _multicall
  File "/opt/miniforge/envs/test-env/lib/python3.8/site-packages/pluggy/_manager.py", line 80 in _hookexec
  File "/opt/miniforge/envs/test-env/lib/python3.8/site-packages/pluggy/_hooks.py", line 265 in __call__
  File "/opt/miniforge/envs/test-env/lib/python3.8/site-packages/_pytest/runner.py", line 260 in <lambda>
  File "/opt/miniforge/envs/test-env/lib/python3.8/site-packages/_pytest/runner.py", line 339 in from_call
  File "/opt/miniforge/envs/test-env/lib/python3.8/site-packages/_pytest/runner.py", line 259 in call_runtest_hook
  File "/opt/miniforge/envs/test-env/lib/python3.8/site-packages/_pytest/runner.py", line 220 in call_and_report
  File "/opt/miniforge/envs/test-env/lib/python3.8/site-packages/_pytest/runner.py", line 131 in runtestprotocol
  File "/opt/miniforge/envs/test-env/lib/python3.8/site-packages/_pytest/runner.py", line 112 in pytest_runtest_protocol
  File "/opt/miniforge/envs/test-env/lib/python3.8/site-packages/pluggy/_callers.py", line 39 in _multicall
  File "/opt/miniforge/envs/test-env/lib/python3.8/site-packages/pluggy/_manager.py", line 80 in _hookexec
  File "/opt/miniforge/envs/test-env/lib/python3.8/site-packages/pluggy/_hooks.py", line 265 in __call__
  File "/opt/miniforge/envs/test-env/lib/python3.8/site-packages/_pytest/main.py", line 349 in pytest_runtestloop
  File "/opt/miniforge/envs/test-env/lib/python3.8/site-packages/pluggy/_callers.py", line 39 in _multicall
  File "/opt/miniforge/envs/test-env/lib/python3.8/site-packages/pluggy/_manager.py", line 80 in _hookexec
  File "/opt/miniforge/envs/test-env/lib/python3.8/site-packages/pluggy/_hooks.py", line 265 in __call__
  File "/opt/miniforge/envs/test-env/lib/python3.8/site-packages/_pytest/main.py", line 324 in _main
  File "/opt/miniforge/envs/test-env/lib/python3.8/site-packages/_pytest/main.py", line 270 in wrap_session
  File "/opt/miniforge/envs/test-env/lib/python3.8/site-packages/_pytest/main.py", line 317 in pytest_cmdline_main
  File "/opt/miniforge/envs/test-env/lib/python3.8/site-packages/pluggy/_callers.py", line 39 in _multicall
  File "/opt/miniforge/envs/test-env/lib/python3.8/site-packages/pluggy/_manager.py", line 80 in _hookexec
  File "/opt/miniforge/envs/test-env/lib/python3.8/site-packages/pluggy/_hooks.py", line 265 in __call__
  File "/opt/miniforge/envs/test-env/lib/python3.8/site-packages/_pytest/config/__init__.py", line 167 in main
  File "/opt/miniforge/envs/test-env/lib/python3.8/site-packages/_pytest/config/__init__.py", line 190 in console_main
  File "/opt/miniforge/envs/test-env/bin/pytest", line 10 in <module>
/__w/1/s/.ci/test.sh: line 177:  1664 Bus error               (core dumped) pytest $BUILD_DIRECTORY/tests

I suspect that it's some combination of:

1. conda is pulling in libgomp=12.2.0

   • libgomp conda-forge/linux-64::libgomp-12.2.0-h65d4601_19 None

2. LightGBM is linking to it because conda puts its own libraries on the search path first
   • ref: Python package looks for library in wrong path #5106 (comment)
3. LightGBM is incompatible with OpenMP 12 and 13
   • LightGBM is incompatible with libomp 12 and 13 on macOS #4229

I'll keep experimenting on this branch 😫

[jameslamb]

Maybe it's significant too that it's only Python 3.8 and 3.9 jobs that are failing, not 3.7 or 3.10.

• ❌ regular (Python 3.9)
• ✅ sdist (Python 3.7)
• ❌ bdist (Python 3.8)
• ✅ inference (Python 3.10)
• ❌ mpi_source (Python 3.8)
• ✅ gpu_source (Python 3.10)
• ✅ swig (Python 3.10)

[jameslamb]

Moving this back to draft while I try to figure out these segfaults in the Dask tests 😫

[jameslamb]

I was able to reproduce the test failures in Docker.

It's our old friend,

OSError: dlopen: cannot load any more object with static TLS

I think we should just stop running the Dask tests on the Linux_* jobs (currently Ubuntu 14.04) util we upgrade to a manylinux image with newer GLIBC in #5580.

I'll push a commit here doing that.

[jameslamb]

Even after skipping the Dask tests, the same builds are still failing 😫

https://dev.azure.com/lightgbm-ci/lightgbm-ci/_build/results?buildId=13862&view=logs&j=fb919173-48b9-522d-5342-9a59a13eb10b&t=7fcbeee5-d4c1-571c-8072-1d5874591254

[jameslamb]

Closing this in favor of #5580.

segfaults on the Ubuntu 14.04 job required fixing the CI image for the Linux * jobs and the macOS jobs together.

[github-actions]

This pull request has been automatically locked since there has not been any recent activity since it was closed. To start a new related discussion, open a new issue at https:/microsoft/LightGBM/issues including a reference to this.