T020: CI fails for MacOS runs

Question

T020: CI fails for MacOS runs

mbackenkoehler opened this issue 2 years ago · 5 comments

Answer 1 · 2023-05-24T08:45:09.000Z

Answer 2 · 2023-05-24T08:49:20.000Z

Thanks—to clarify: the notebook works under macos locally just fine, only crashes in the CI. Will add more context on this issue tonight.

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On Wed 24. May 2023 at 09:45, Michael Backenköhler ***@***.***> wrote: @dominiquesydow <https://github.com/dominiquesydow> as discussed :) — Reply to this email directly, view it on GitHub <#364 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABW7RNLAECFWSSGGCKIKET3XHXDCBANCNFSM6AAAAAAYM6OEN4> . You are receiving this because you were mentioned.Message ID: ***@***.***>

Answer 3 · 2023-05-24T08:51:28.000Z

Great! Then we probably can forgo a disclaimer in the notebook.

Answer 4 · 2023-05-24T11:13:37.000Z

There might be more at play here. Now T021 breaks in the macOS CI. And if I get the output below correctly, everything after fails, as well.

Answer 5 · 2023-05-24T11:24:47.000Z

I think T019 might actually cause the problems, since there we have the first failure and after that, everything has a dead kernel.

2023-05-24T10:01:21.5627080Z FAILED teachopencadd/talktorials/T019_md_simulation/talktorial.ipynb::Cell 3
2023-05-24T10:01:21.5627380Z FAILED teachopencadd/talktorials/T019_md_simulation/talktorial.ipynb::Cell 12
2023-05-24T10:01:21.5627680Z FAILED teachopencadd/talktorials/T019_md_simulation/talktorial.ipynb::Cell 14
2023-05-24T10:01:21.5627990Z FAILED teachopencadd/talktorials/T019_md_simulation/talktorial.ipynb::Cell 15
2023-05-24T10:01:21.5628290Z FAILED teachopencadd/talktorials/T019_md_simulation/talktorial.ipynb::Cell 17
2023-05-24T10:01:21.5628580Z FAILED teachopencadd/talktorials/T019_md_simulation/talktorial.ipynb::Cell 18
2023-05-24T10:01:21.5628870Z FAILED teachopencadd/talktorials/T019_md_simulation/talktorial.ipynb::Cell 19
2023-05-24T10:01:21.5629160Z FAILED teachopencadd/talktorials/T019_md_simulation/talktorial.ipynb::Cell 20
2023-05-24T10:01:21.5629470Z FAILED teachopencadd/talktorials/T019_md_simulation/talktorial.ipynb::Cell 21
2023-05-24T10:01:21.5629770Z FAILED teachopencadd/talktorials/T019_md_simulation/talktorial.ipynb::Cell 22
2023-05-24T10:01:21.5630070Z FAILED teachopencadd/talktorials/T019_md_simulation/talktorial.ipynb::Cell 23
2023-05-24T10:01:21.5630410Z FAILED teachopencadd/talktorials/T018_automated_cadd_pipeline/talktorial.ipynb::Cell 44
2023-05-24T10:01:21.5631120Z ERROR teachopencadd/talktorials/T021_one_hot_encoding/talktorial.ipynb::Cell 0 - RuntimeError: Kernel died before replying to kernel_info
2023-05-24T10:01:21.5632260Z ERROR teachopencadd/talktorials/T021_one_hot_encoding/talktorial.ipynb::Cell 1 - RuntimeError: Kernel died before replying to kernel_info
2023-05-24T10:01:21.5633260Z ERROR teachopencadd/talktorials/T021_one_hot_encoding/talktorial.ipynb::Cell 2 - RuntimeError: Kernel died before replying to kernel_info
2023-05-24T10:01:21.5633950Z ERROR teachopencadd/talktorials/T021_one_hot_encoding/talktorial.ipynb::Cell 3 - RuntimeError: Kernel died before replying to kernel_info
2023-05-24T10:01:21.5634620Z ERROR teachopencadd/talktorials/T021_one_hot_encoding/talktorial.ipynb::Cell 4 - RuntimeError: Kernel died before replying to kernel_info
2023-05-24T10:01:21.5635290Z ERROR teachopencadd/talktorials/T021_one_hot_encoding/talktorial.ipynb::Cell 5 - RuntimeError: Kernel died before replying to kernel_info
2023-05-24T10:01:21.5635960Z ERROR teachopencadd/talktorials/T021_one_hot_encoding/talktorial.ipynb::Cell 6 - RuntimeError: Kernel died before replying to kernel_info
2023-05-24T10:01:21.5637080Z ERROR teachopencadd/talktorials/T021_one_hot_encoding/talktorial.ipynb::Cell 7 - RuntimeError: Kernel died before replying to kernel_info
2023-05-24T10:01:21.5638180Z ERROR teachopencadd/talktorials/T021_one_hot_encoding/talktorial.ipynb::Cell 8 - RuntimeError: Kernel died before replying to kernel_info
2023-05-24T10:01:21.5638870Z ERROR teachopencadd/talktorials/T021_one_hot_encoding/talktorial.ipynb::Cell 9 - RuntimeError: Kernel died before replying to kernel_info

In T019 the command from openff.toolkit.topology import Molecule, Topology fails with CalledProcessError: Command '['antechamber', '-L']' died with <Signals.SIGKILL: 9>.