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reporting on SQLite3 problem rendering pidlocked system unusable

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yarikoptic 2020-06-05 02:31:21 +00:00 • committed by admin
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doc/bugs/crippled_fs___40__pidlock__41___leads_to_git-annex__58___SQLite3_returned_ErrorIO_while_attempting_to_perform_prepare___34__PRAGMA_journal__95__mode__61__WAL__59____34____58___disk_I__47__O_error.mdwn Normal file
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### Please describe the problem.
It was a long journey... ;-) First I had ran `git annex test` which resulted in `437 out of 834 tests failed` and saw bunch of those failures - [full log](http://www.onerussian.com/tmp/git-annex-test-log-8.20200502-g55acb2e52-2.log) ... Then I got to "troubleshoot" too long of pidlock detection [filed separately](https://git-annex.branchable.com/todo/faster___40__took_2_min__41___way_to_realize_the_need_in_pidlock__63__/?updated), where a complete run of `annex get` finally crashed with
[[!format sh """
[2020-06-04 22:16:49.683393126] process done ExitSuccess
git-annex: SQLite3 returned ErrorIO while attempting to perform prepare "PRAGMA journal_mode=WAL;": disk I/O error
[yhalchen@discovery7 containers]$ echo $?
1
"""]]
<details>
<summary>A full log:</summary>
```shell
*[yhalchen@discovery7 containers]$ git annex --debug get --from origin images/bids/bids-fmriprep--20.1.0.sing
[2020-06-04 22:14:49.036738929] read: git ["--git-dir=.git","--work-tree=.","--literal-pathspecs","show-ref","git-annex"]
[2020-06-04 22:14:49.053892561] process done ExitSuccess
[2020-06-04 22:14:49.054443458] read: git ["--git-dir=.git","--work-tree=.","--literal-pathspecs","show-ref","--hash","refs/heads/git-annex"]
[2020-06-04 22:14:49.066856316] process done ExitFailure 1
[2020-06-04 22:14:49.06701345] call: git ["--git-dir=.git","--work-tree=.","--literal-pathspecs","show-ref","--verify","-q","origin/git-annex"]
[2020-06-04 22:14:49.07703984] process done ExitFailure 1
[2020-06-04 22:14:49.079889542] read: git ["--git-dir=.git","--work-tree=.","--literal-pathspecs","write-tree"]
[2020-06-04 22:14:49.097069694] process done ExitSuccess
[2020-06-04 22:14:49.097233049] chat: git ["--git-dir=.git","--work-tree=.","--literal-pathspecs","commit-tree","4b825dc642cb6eb9a060e54bf8d69288fbee4904","--no-gpg-sign"]
[2020-06-04 22:14:49.131741755] process done ExitSuccess
[2020-06-04 22:14:49.131910038] call: git ["--git-dir=.git","--work-tree=.","--literal-pathspecs","update-ref","refs/heads/git-annex","8cab5728da95189f68c785bd4bb59ca754e133fd"]
[2020-06-04 22:14:49.153852043] process done ExitSuccess
[2020-06-04 22:14:49.159730902] call: git ["--git-dir=.git","--work-tree=.","--literal-pathspecs","config","annex.uuid","fd97689f-716d-4e82-87ce-5b96c2421dd6"]
[2020-06-04 22:14:49.175319685] process done ExitSuccess
[2020-06-04 22:14:49.175479616] read: git ["config","--null","--list"]
[2020-06-04 22:14:49.184803048] process done ExitSuccess
Detected a filesystem without POSIX fcntl lock support.
Enabling annex.pidlock.
[2020-06-04 22:16:49.25775881] call: git ["--git-dir=.git","--work-tree=.","--literal-pathspecs","config","annex.pidlock","true"]
[2020-06-04 22:16:49.28355608] process done ExitSuccess
[2020-06-04 22:16:49.283718998] read: git ["config","--null","--list"]
[2020-06-04 22:16:49.294520291] process done ExitSuccess
[2020-06-04 22:16:49.319943516] read: git ["--git-dir=.git","--work-tree=.","--literal-pathspecs","show-ref","git-annex"]
[2020-06-04 22:16:49.337681756] process done ExitSuccess
[2020-06-04 22:16:49.337851772] read: git ["--git-dir=.git","--work-tree=.","--literal-pathspecs","show-ref","--hash","refs/heads/git-annex"]
[2020-06-04 22:16:49.350699481] process done ExitSuccess
[2020-06-04 22:16:49.351471951] read: git ["--git-dir=.git","--work-tree=.","--literal-pathspecs","log","refs/heads/git-annex..8cab5728da95189f68c785bd4bb59ca754e133fd","--pretty=%H","-n1"]
[2020-06-04 22:16:49.364911775] process done ExitSuccess
[2020-06-04 22:16:49.365042588] read: git ["--git-dir=.git","--work-tree=.","--literal-pathspecs","log","refs/heads/git-annex..e3361f4b81727323f8ea01f390de1013fc970fe0","--pretty=%H","-n1"]
[2020-06-04 22:16:49.382315188] process done ExitSuccess
[2020-06-04 22:16:49.39123874] chat: git ["--git-dir=.git","--work-tree=.","--literal-pathspecs","cat-file","--batch"]
[2020-06-04 22:16:49.392177285] chat: git ["--git-dir=.git","--work-tree=.","--literal-pathspecs","cat-file","--batch-check=%(objectname) %(objecttype) %(objectsize)"]
(merging origin/git-annex into git-annex...)
[2020-06-04 22:16:49.403384458] chat: git ["--git-dir=.git","--work-tree=.","--literal-pathspecs","hash-object","-w","--stdin-paths","--no-filters"]
[2020-06-04 22:16:49.404525057] feed: git ["--git-dir=.git","--work-tree=.","--literal-pathspecs","update-index","-z","--index-info"]
[2020-06-04 22:16:49.405361559] read: git ["--git-dir=.git","--work-tree=.","--literal-pathspecs","diff-index","--raw","-z","-r","--no-renames","-l0","--cached","e3361f4b81727323f8ea01f390de1013fc970fe0","--"]
[2020-06-04 22:16:49.419146962] process done ExitSuccess
[2020-06-04 22:16:49.423309792] process done ExitSuccess
[2020-06-04 22:16:49.424375953] read: git ["--git-dir=.git","--work-tree=.","--literal-pathspecs","log","e3361f4b81727323f8ea01f390de1013fc970fe0..refs/heads/git-annex","--pretty=%H","-n1"]
[2020-06-04 22:16:49.437440657] process done ExitSuccess
(recording state in git...)
[2020-06-04 22:16:49.438388893] read: git ["--git-dir=.git","--work-tree=.","--literal-pathspecs","write-tree"]
[2020-06-04 22:16:49.455648835] process done ExitSuccess
[2020-06-04 22:16:49.455794606] chat: git ["--git-dir=.git","--work-tree=.","--literal-pathspecs","commit-tree","1e2019e8261920b3331694be7582e576f48f98ce","--no-gpg-sign","-p","refs/heads/git-annex","-p","e3361f4b81727323f8ea01f390de1013fc970fe0"]
[2020-06-04 22:16:49.474057462] process done ExitSuccess
[2020-06-04 22:16:49.474203707] call: git ["--git-dir=.git","--work-tree=.","--literal-pathspecs","update-ref","refs/heads/git-annex","40ec653567414f60bb5a8fcecbf35e445329d19c"]
[2020-06-04 22:16:49.496182398] process done ExitSuccess
[2020-06-04 22:16:49.510323334] call: git ["--git-dir=.git","--work-tree=.","--literal-pathspecs","config","annex.version","8"]
[2020-06-04 22:16:49.52428458] process done ExitSuccess
[2020-06-04 22:16:49.524446647] read: git ["config","--null","--list"]
[2020-06-04 22:16:49.53479347] process done ExitSuccess
[2020-06-04 22:16:49.534979055] read: git ["--git-dir=.git","--work-tree=.","--literal-pathspecs","status","--porcelain"]
[2020-06-04 22:16:49.616544919] process done ExitSuccess
[2020-06-04 22:16:49.616691354] call: git ["--git-dir=.git","--work-tree=.","--literal-pathspecs","config","filter.annex.smudge","git-annex smudge -- %f"]
[2020-06-04 22:16:49.631712464] process done ExitSuccess
[2020-06-04 22:16:49.631878376] read: git ["config","--null","--list"]
[2020-06-04 22:16:49.642378001] process done ExitSuccess
[2020-06-04 22:16:49.642543068] call: git ["--git-dir=.git","--work-tree=.","--literal-pathspecs","config","filter.annex.clean","git-annex smudge --clean -- %f"]
[2020-06-04 22:16:49.656618605] process done ExitSuccess
[2020-06-04 22:16:49.65676469] read: git ["config","--null","--list"]
[2020-06-04 22:16:49.667352993] process done ExitSuccess
(scanning for unlocked files...)
[2020-06-04 22:16:49.671201261] read: git ["--git-dir=.git","--work-tree=.","--literal-pathspecs","show-ref","--head"]
[2020-06-04 22:16:49.683393126] process done ExitSuccess
git-annex: SQLite3 returned ErrorIO while attempting to perform prepare "PRAGMA journal_mode=WAL;": disk I/O error
```
</details>
File system details:
[[!format sh """
[yhalchen@discovery7 containers]$ df -h .
Filesystem Type Size Used Avail Use% Mounted on
isilon.hpcc.dartmouth.edu:/ifs/home nfs 51G 23G 28G 45% /ihome
[yhalchen@discovery7 containers]$ mount | grep /ifs/home
isilon.hpcc.dartmouth.edu:/ifs/home on /ihome type nfs (rw,relatime,vers=3,rsize=131072,wsize=524288,namlen=255,hard,proto=tcp,timeo=600,retrans=2,sec=sys,mountaddr=10.232.???.???,mountvers=3,mountport=300,mountproto=udp,local_lock=none,addr=10.232.???.???)
"""]]
[[!format sh """
git-annex version: 8.20200502-g55acb2e52
build flags: Assistant Webapp Pairing S3 WebDAV Inotify DBus DesktopNotify TorrentParser MagicMime Feeds Testsuite
dependency versions: aws-0.20 bloomfilter-2.0.1.0 cryptonite-0.25 DAV-1.3.3 feed-1.0.1.0 ghc-8.6.5 http-client-0.5.14 persistent-sqlite-2.9.3 torrent-10000.1.1 uuid-1.3.13 yesod-1.6.0
key/value backends: SHA256E SHA256 SHA512E SHA512 SHA224E SHA224 SHA384E SHA384 SHA3_256E SHA3_256 SHA3_512E SHA3_512 SHA3_224E SHA3_224 SHA3_384E SHA3_384 SKEIN256E SKEIN256 SKEIN512E SKEIN512 BLAKE2B256E BLAKE2B256 BLAKE2B512E BLAKE2B512 BLAKE2B160E BLAKE2B160 BLAKE2B224E BLAKE2B224 BLAKE2B384E BLAKE2B384 BLAKE2BP512E BLAKE2BP512 BLAKE2S256E BLAKE2S256 BLAKE2S160E BLAKE2S160 BLAKE2S224E BLAKE2S224 BLAKE2SP256E BLAKE2SP256 BLAKE2SP224E BLAKE2SP224 SHA1E SHA1 MD5E MD5 WORM URL
remote types: git gcrypt p2p S3 bup directory rsync web bittorrent webdav adb tahoe glacier ddar git-lfs hook external
operating system: linux x86_64
supported repository versions: 8
upgrade supported from repository versions: 0 1 2 3 4 5 6 7
local repository version: 8
"""]]
I think I should look at some point to establish similar setup within https://github.com/datalad/datalad-extensions to run released and freshly built annex tests also on a crippled FS.