Fails while running on OSX
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Assessment
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Newbie friendliness
- 35/100
- Issue type
- Bug
- Clarity
- Mostly clear
- Activity status
- Stale
- Tech stack
- docker, macos, python
- Domain
- devops, operating-systems
Research direction
Start by reproducing the walkthrough's containers-run step on macOS with the versions and command shown. Inspect MRIQC's mriqc/cli/run.py and the Python multiprocessing forkserver traceback; done means the walkthrough command completes successfully on macOS without the Invalid argument error.
Written by the indexing model from the issue text.
Description
Hi, intrepid user here. Running through the 'walkthrough'; in the 'containers-run' step I get the following error:
(base) kennedyd@MCSMLS065401 ds000003-qc % datalad containers-run
--container-name bids-mriqc
--input sourcedata
--output .
'{inputs}' '{outputs}' participant --participant-label sub-02 -w workdir
[INFO ] Making sure inputs are available (this may take some time)
get(ok): containers/images/bids/bids-mriqc--0.16.0.sing (file) [from origin...]
[INFO ] == Command start (output follows) =====
240523-20:51:23,365 cli IMPORTANT:Running MRIQC version 0.16.0: * BIDS dataset path: /Users/kennedyd/my-experiments/ds000003-qc/sourcedata. * Output folder: /Users/kennedyd/my-experiments/ds000003-qc. * Analysis levels: ['participant'].You are using MRIQC v0.16.0, and a newer version is available: 24.0.0.
Traceback (most recent call last):
File "/usr/local/miniconda/bin/mriqc", line 10, in
sys.exit(main())
File "/usr/local/miniconda/lib/python3.7/site-packages/mriqc/cli/run.py", line 37, in main
with Manager() as mgr:
File "/usr/local/miniconda/lib/python3.7/multiprocessing/context.py", line 56, in Manager
m.start()
File "/usr/local/miniconda/lib/python3.7/multiprocessing/managers.py", line 543, in start
self._process.start()
File "/usr/local/miniconda/lib/python3.7/multiprocessing/process.py", line 112, in start
self._popen = self._Popen(self)
File "/usr/local/miniconda/lib/python3.7/multiprocessing/context.py", line 291, in _Popen
return Popen(process_obj)
File "/usr/local/miniconda/lib/python3.7/multiprocessing/popen_forkserver.py", line 35, in init
super().init(process_obj)
File "/usr/local/miniconda/lib/python3.7/multiprocessing/popen_fork.py", line 20, in init
self._launch(process_obj)
File "/usr/local/miniconda/lib/python3.7/multiprocessing/popen_forkserver.py", line 51, in _launch
self.sentinel, w = forkserver.connect_to_new_process(self._fds)
File "/usr/local/miniconda/lib/python3.7/multiprocessing/forkserver.py", line 64, in connect_to_new_process
self.ensure_running()
File "/usr/local/miniconda/lib/python3.7/multiprocessing/forkserver.py", line 118, in ensure_running
listener.bind(address)
OSError: [Errno 22] Invalid argument
[INFO ] == Command exit (modification check follows) =====
run(error): /Users/kennedyd/my-experiments/ds000003-qc (dataset) [./containers/scripts/singularity_cmd run...]
action summary:
get (notneeded: 2, ok: 1)
run (error: 1)
save (notneeded: 3)
I'm running on a Mac: 14.1 (23B74)
Docker: 4.28.0 (139021)
Engine: Engine: 25.0.3
- Dominant language
- Python
- Stars
- 32
- Forks
- 17
- Avg merge
- 12h 2m
- Merged PRs (30d)
- 3
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