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should explicitly kill the child if interrupted? #144

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yarikoptic opened this issue Dec 10, 2020 · 0 comments
Open

should explicitly kill the child if interrupted? #144

yarikoptic opened this issue Dec 10, 2020 · 0 comments
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@yarikoptic
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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?

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