We read every piece of feedback, and take your input very seriously.
To see all available qualifiers, see our documentation.
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
I was testing ReproNim/containers#42 and decided to interrupt the invocation:
(git-annex)lena:~/.tmp/repro-6XkWWkE/ds000003-qc[master]git-annex $> REPRONIM_USE_DOCKER=1 datalad containers-run -n containers/bids-mriqc --input sourcedata --output . '{inputs}' '{outputs}' participant group [INFO ] Making sure inputs are available (this may take some time) [INFO ] == Command start (output follows) ===== 2020-12-10 16:17:57,847 mriqc:IMPORTANT Running MRIQC version 0.15.1: * BIDS dataset path: /home/yoh/.tmp/repro-6XkWWkE/ds000003-qc/sourcedata. * Output folder: /home/yoh/.tmp/repro-6XkWWkE/ds000003-qc. * Analysis levels: group, participant. ... N4BiasFieldCorrection -d 3 --input-image /home/yoh/.tmp/repro-6XkWWkE/ds000003-qc/work/workflow_enumerator/anatMRIQCT1w/_in_file_..home..yoh...tmp..repro-6XkWWkE..ds000003-qc..sourcedata..sub-13..anat..sub-13_T1w.nii.gz/conform/sub-13_T1w_conformed.nii.gz --output [ sub-13_T1w_conformed_corrected.nii.gz, sub-13_T1w_conformed_bias.nii.gz ] ^CERROR: Interrupted by user while doing magic: KeyboardInterrupt() [cmd.py:_get_output_online:725]
so the containers-run process quit but underlying script and docker kept going:
yoh 3217993 0.0 0.0 6976 2384 pts/6 S 11:17 0:00 \_ /bin/bash containers/scripts/singularity_cmd run containers/images/bids/bids-mriqc--0.15.1.sing sourcedata participant group yoh 3218011 0.0 0.0 1951776 24620 pts/6 Sl 11:17 0:00 \_ docker run --privileged --rm -e UID=47521 -e GID=47522 -v /home/yoh/.tmp/repro-6XkWWkE/ds000003-qc:/home/yoh/.tmp/repro-6XkWWkE/ds000003-qc ...
so most likely we need an explicit shutdown of a child process in some finally: if it is still alive upon exception?
finally:
The text was updated successfully, but these errors were encountered:
kyleam
No branches or pull requests
I was testing ReproNim/containers#42 and decided to interrupt the invocation:
so the containers-run process quit but underlying script and docker kept going:
so most likely we need an explicit shutdown of a child process in some
finally:
if it is still alive upon exception?The text was updated successfully, but these errors were encountered: