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Merge branch 'master' of ssh://git-annex.branchable.com

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Joey Hess 2021-11-19 09:20:07 -04:00
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doc/forum/git-annex_causing_zombie_git_processes_to_build_up/comment_8_02c5903bf4de4b94e6db84bc43b3b3d8._comment Normal file
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[[!comment format=mdwn
username="yarikoptic"
avatar="http://cdn.libravatar.org/avatar/f11e9c84cb18d26a1748c33b48c924b4"
subject="god bless search"
date="2021-11-17T21:03:29Z"
content="""
found this issue which was not `done`.
I have ran into it again: on initial occasion I could not even ssh to that host because ~4000 `[git] <defunct>` processes forbid any other process to start according to the policy.
Updated git-annex to standalone build from conda (8.20211012-geb95ed486), repeated again (on http://datasets.datalad.org/labs/hasson/narratives/derivatives/fmriprep/.git
) with a plain `git annex get -J5 .` -- had to interrupt it when I saw that reached 1k of those. Here is dump of annexy config variables so - no retries
```
(datalad) [d31548v@discovery7 fmriprep]$ git config --list | grep annex
annex.pidlock=true
remote.origin.annex-bare=false
remote.origin.annex-uuid=348d8bd8-1142-4de1-b52e-6b9899faa1d5
annex.uuid=75d12ed4-e3e4-4ad0-ba7e-ec11538966d2
annex.version=8
filter.annex.smudge=git-annex smudge -- %f
filter.annex.clean=git-annex smudge --clean -- %f
remote.fcp-indi.annex-s3=true
remote.fcp-indi.annex-uuid=bf6f56f3-f6b7-4df8-9898-a4226dc71400
```
I wish Nick_P has shared the script -- I could try to bisect... otherwise someone needs to write one ;-)
"""]]

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doc/forum/git-annex_causing_zombie_git_processes_to_build_up/comment_9_b6780a99d7a175d2ff3e33e198c28a9d._comment Normal file
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[[!comment format=mdwn
username="yarikoptic"
avatar="http://cdn.libravatar.org/avatar/f11e9c84cb18d26a1748c33b48c924b4"
subject="bisection"
date="2021-11-18T02:29:01Z"
content="""
if I bisected it right (didn't doublecheck manually), it is due to [8.20210127-107-gdd39e9e25 AKA 8.20210223~41](https://git.kitenet.net/index.cgi/git-annex.git/commit/?id=dd39e9e255a5684824ea75861f48f658eaaba288)
<details>
<summary>bisection script</summary>
```
#!/bin/bash
set -u
u=http://datasets.datalad.org/labs/hasson/narratives/derivatives/fmriprep/.git
d=/mnt/scrap/tmp/fmriprep
[ -e \"$d\" ] || datalad clone \"$u\" \"$d\"
cd \"$d\"
git annex drop --all
git annex get -J5 . >/dev/null &
p=$! # use pstree?
for i in {1..200}; do # 200 sec seems to be enough
np=$(ps auxw | grep $USER | grep '\[git\] <defunct>' | wc -l)
echo -n \"$i $np \"
if [ $np -gt 10 ]; then { kill $p; exit 1; } fi
sleep 1
done
kill \"$p\"
echo done
```
</details>
"""]]