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[[!comment format=mdwn
username="yarikoptic"
avatar="http://cdn.libravatar.org/avatar/f11e9c84cb18d26a1748c33b48c924b4"
subject="comment 2"
date="2022-05-24T20:35:58Z"
content="""
FWIW, I have added
```
(base) dandi@drogon:/mnt/backup/dandi/dandisets$ git config annex.stalldetection
1KB/120s
```
and I see 4 days old (now it is `Tue 24 May 2022 04:34:33 PM EDT`)
```
dandi 1682561 0.0 0.1 173328 73808 ? S May20 0:02 python -m tools.backups2datalad -l DEBUG -J 5 --target /mnt/backup/dandi/dandisets populate dandi-dandisets-dropbox
dandi 1683786 0.0 0.0 1075306796 61632 ? Sl May20 2:49 git-annex get -c annex.retry=3 --jobs 5 --from=web --not --in dandi-dandisets-dropbox --and --not --in here
dandi 1683813 0.4 0.0 1074200772 46872 ? Sl May20 26:18 /home/dandi/miniconda3/envs/dandisets/bin/git-annex transferrer -c annex.retry=3
dandi 1683820 0.0 0.0 109896 2504 ? S May20 0:00 git --git-dir=.git --work-tree=. --literal-pathspecs -c annex.retry=3 cat-file --batch
dandi 1683819 0.4 0.0 1074200772 48152 ? Sl May20 24:56 /home/dandi/miniconda3/envs/dandisets/bin/git-annex transferrer -c annex.retry=3
dandi 1683826 0.0 0.0 109896 2320 ? S May20 0:00 git --git-dir=.git --work-tree=. --literal-pathspecs -c annex.retry=3 cat-file --batch
dandi 1683830 0.4 0.0 1074200772 47092 ? Sl May20 26:27 /home/dandi/miniconda3/envs/dandisets/bin/git-annex transferrer -c annex.retry=3
dandi 1683843 0.0 0.0 109896 2288 ? S May20 0:00 git --git-dir=.git --work-tree=. --literal-pathspecs -c annex.retry=3 cat-file --batch
dandi 1683846 0.4 0.0 1074200804 47932 ? Sl May20 25:12 /home/dandi/miniconda3/envs/dandisets/bin/git-annex transferrer -c annex.retry=3
dandi 1683852 0.0 0.0 109896 2460 ? S May20 0:00 git --git-dir=.git --work-tree=. --literal-pathspecs -c annex.retry=3 cat-file --batch
dandi 1683863 0.0 0.0 1074127072 47300 ? Sl May20 0:26 /home/dandi/miniconda3/envs/dandisets/bin/git-annex transferrer -c annex.retry=3
dandi 1683869 0.0 0.0 109896 3244 ? S May20 0:00 git --git-dir=.git --work-tree=. --literal-pathspecs -c annex.retry=3 cat-file --batch
```
which smells like stuck... looking at open files, I see the stderr to be redirected and looking into it:
```
(base) dandi@drogon:/mnt/backup/dandi/dandisets$ tail /mnt/backup/dandi/dandisets/.git/tmp/stderr
(Delaying 1s before retrying....)
ok
get rawdata/sub-I46/ses-SPIM/micr/sub-I46_ses-SPIM_sample-MotorCortexS08_stain-Calretinin_chunk-00_SPIM.ome.tif (from web...)
thread blocked indefinitely in an MVar operation
(Delaying 1s before retrying....)
ok
get rawdata/sub-I46/ses-SPIM/micr/sub-I46_ses-SPIM_sample-MotorCortexS08_stain-Nuclei_chunk-05_SPIM.ome.tif (from web...)
thread blocked indefinitely in an MVar operation
(Delaying 1s before retrying....)
ok
```
and I do not think that file saw any updates (`tail -f ` is silent):
```
(base) dandi@drogon:/mnt/backup/dandi/dandisets$ stat /mnt/backup/dandi/dandisets/.git/tmp/stderr
File: /mnt/backup/dandi/dandisets/.git/tmp/stderr
Size: 28944 Blocks: 64 IO Block: 4096 regular file
Device: 28h/40d Inode: 34338261 Links: 1
Access: (0644/-rw-r--r--) Uid: ( 1001/ dandi) Gid: ( 1015/ dandi)
Access: 2021-12-16 17:10:51.838720227 -0500
Modify: 2022-05-20 21:10:19.383226789 -0400
Change: 2022-05-20 21:10:19.383226789 -0400
Birth: 2021-12-16 17:10:51.838720227 -0500
```
NB I got a bit surprised that we dump to such possibly shared stderr file, but it is done within `tools/backups2datalad-cron` which we guard with flock to not run more than 1 instance so it is ok.
Would you recommend to look at anything specific or may be `thread blocked indefinitely in an MVar operation` is giving ideas? (FTR: I believe the annex is `10.20220322-g7b64dea`)
"""]]