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Added a comment: another/different? stall

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yarikoptic 2022-05-26 14:31:33 +00:00 • committed by admin
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[[!comment format=mdwn
username="yarikoptic"
avatar="http://cdn.libravatar.org/avatar/f11e9c84cb18d26a1748c33b48c924b4"
subject="another/different? stall"
date="2022-05-26T14:31:33Z"
content="""
next one stalled at the end at
```
get sub-dt15/sub-dt15_ses-dt15_6705um_200213_091923_ecephys.nwb (from web...) ok
get sub-bruce/sub-bruce_ses-bruce_0um_210115_155615_ecephys.nwb (from web...) ok
get sub-bruce/sub-bruce_ses-bruce_0um_210110_171041_ecephys.nwb (from web...) ok
get sub-ros/sub-ros_ses-ros_210320_091833_ecephys.nwb (from web...) ok
(recording state in git...)
```
with recent `gets` not complaining about being unable to lock, only some longer before did, e.g.
```
get sub-CGM49/sub-CGM49_ses-CGM49_512um_210227_093748_ecephys.nwb (from web...)
failed to commit changes to sqlite database: Just SQLite3 returned ErrorBusy while attempting to perform step: database is locked
CallStack (from HasCallStack):
error, called at ./Database/Handle.hs:91:26 in main:Database.Handle
(Delaying 1s before retrying....)
44% 9.58 GiB 57 MiB/s 3m36s
get sub-CGM52/sub-CGM52_ses-CGM52_0um_210216_144320_ecephys.nwb (from web...)
```
```
dandi 2013903 0.0 0.0 5492 0 pts/1 S+ May25 0:00 flock -E 0 -e -n /home/dandi/.run/backup2datalad-cron.lock bash -c /mnt/backup/dandi/dandisets/tools/backups2datalad-cron
dandi 2013904 0.0 0.0 7024 1892 pts/1 S+ May25 0:00 /bin/bash /mnt/backup/dandi/dandisets/tools/backups2datalad-cron
dandi 2013933 0.0 0.0 7024 1520 pts/1 S+ May25 0:00 /bin/bash /mnt/backup/dandi/dandisets/tools/backups2datalad-cron
dandi 2113421 0.0 0.0 321448 3140 pts/1 S+ May25 0:04 python -m tools.backups2datalad -l DEBUG -J 5 --target /mnt/backup/dandi/dandisets populate dandi-dandisets-dropbox
dandi 2151114 0.8 0.0 1075306800 32416 pts/1 Sl+ May25 9:39 git-annex get -c annex.retry=3 --jobs 5 --from=web --not --in dandi-dandisets-dropbox --and --not --in here
dandi 2151142 11.6 0.0 1074200808 37352 pts/1 Sl May25 138:50 /home/dandi/miniconda3/envs/dandisets/bin/git-annex transferrer -c annex.retry=3
dandi 2151170 0.0 0.0 10640 1260 pts/1 S May25 0:00 git --git-dir=.git --work-tree=. --literal-pathspecs -c annex.retry=3 cat-file --batch
dandi 2151143 12.9 0.0 1074200808 36384 pts/1 Sl May25 153:23 /home/dandi/miniconda3/envs/dandisets/bin/git-annex transferrer -c annex.retry=3
dandi 2151158 0.0 0.0 10640 1256 pts/1 S May25 0:00 git --git-dir=.git --work-tree=. --literal-pathspecs -c annex.retry=3 cat-file --batch
dandi 2151147 12.7 0.0 1074127044 35308 pts/1 Sl May25 150:49 /home/dandi/miniconda3/envs/dandisets/bin/git-annex transferrer -c annex.retry=3
dandi 2151160 0.0 0.0 10640 1232 pts/1 S May25 0:00 git --git-dir=.git --work-tree=. --literal-pathspecs -c annex.retry=3 cat-file --batch
dandi 2151148 16.3 0.0 1074200776 35596 pts/1 Sl May25 193:42 /home/dandi/miniconda3/envs/dandisets/bin/git-annex transferrer -c annex.retry=3
dandi 2151168 0.0 0.0 10640 1336 pts/1 S May25 0:00 git --git-dir=.git --work-tree=. --literal-pathspecs -c annex.retry=3 cat-file --batch
dandi 2151161 13.0 0.0 1074200808 32060 pts/1 Sl May25 155:15 /home/dandi/miniconda3/envs/dandisets/bin/git-annex transferrer -c annex.retry=3
dandi 2151177 0.0 0.0 10640 1096 pts/1 S May25 0:00 git --git-dir=.git --work-tree=. --literal-pathspecs -c annex.retry=3 cat-file --batch
```
strace end is
```
[pid 2151125] sched_yield( <unfinished ...>
[pid 2151129] <... sched_yield resumed>) = 0
[pid 2151125] <... sched_yield resumed>) = 0
[pid 2151129] sched_yield() = 0
[pid 2151125] sched_yield( <unfinished ...>
[pid 2151129] sched_yield( <unfinished ...>
[pid 2151125] <... sched_yield resumed>) = 0
[pid 2151129] <... sched_yield resumed>) = 0
[pid 2151137] rt_sigprocmask(SIG_SETMASK, [], <unfinished ...>
[pid 2151126] sched_yield( <unfinished ...>
[pid 2151137] <... rt_sigprocmask resumed>NULL, 8) = 0
[pid 2151129] sched_yield( <unfinished ...>
[pid 2151125] sched_yield( <unfinished ...>
[pid 2151137] futex(0x7fe75c000be8, FUTEX_WAIT_PRIVATE, 0, NULL <unfinished ...>
[pid 2151129] <... sched_yield resumed>) = 0
[pid 2151125] <... sched_yield resumed>) = 0
[pid 2151129] futex(0x7fe740000be8, FUTEX_WAIT_PRIVATE, 0, NULL <unfinished ...>
[pid 2151125] futex(0x52eae6c, FUTEX_WAIT_PRIVATE, 0, NULL <unfinished ...>
[pid 2151126] <... sched_yield resumed>) = 0
[pid 2151126] futex(0x52eb068, FUTEX_WAIT_PRIVATE, 0, NULL <unfinished ...>
[pid 2151115] <... read resumed>\"\1\0\0\0\0\0\0\0\", 8) = 8
[pid 2151115] futex(0x4a4844c, FUTEX_WAIT_PRIVATE, 0, NULL^Cstrace: Process 2151114 detached
strace: Process 2151115 detached
<detached ...>
strace: Process 2151116 detached
strace: Process 2151117 detached
strace: Process 2151119 detached
strace: Process 2151124 detached
strace: Process 2151125 detached
strace: Process 2151126 detached
strace: Process 2151127 detached
strace: Process 2151128 detached
strace: Process 2151129 detached
strace: Process 2151132 detached
strace: Process 2151133 detached
strace: Process 2151136 detached
strace: Process 2151137 detached
strace: Process 2151138 detached
strace: Process 2151139 detached
strace: Process 2151140 detached
strace: Process 2677004 detached
strace: Process 2925046 detached
strace: Process 3026979 detached
strace: Process 3027102 detached
```
I have now killed that `get` process and restarted our backup beastie (should now get to `copy` those `get`ed files into backup)
"""]]