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

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Joey Hess 2020-06-05 10:41:30 -04:00
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115
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.

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[[!comment format=mdwn
username="git-annex@17927e6dc041ab425c14217a97a685adf3ecf44f"
nickname="git-annex"
avatar="http://cdn.libravatar.org/avatar/66e5c6e044d726597ce5a0ad68f86fe4"
subject="content expression is standard"
date="2020-06-04T20:28:01Z"
content="""
Yes - it is set to standard.
"""]]

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doc/forum/dropped_files_keep_coming_back/comment_3_1a2ee19bfb3d56a2e2641dbcd89d8be2._comment Normal file
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[[!comment format=mdwn
username="git-annex@17927e6dc041ab425c14217a97a685adf3ecf44f"
nickname="git-annex"
avatar="http://cdn.libravatar.org/avatar/66e5c6e044d726597ce5a0ad68f86fe4"
subject="Actually they were not standard"
date="2020-06-04T21:05:30Z"
content="""
The 'git annex wanted .' on the manual node returned nothing - so default. I would have thought that that was 'standard'. However, when setting it to standard, the files stopped rebounding.
Christopher
"""]]

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doc/forum/dropped_files_keep_coming_back/comment_4_02a6e3591acfa410ed7c7917dc573663._comment Normal file
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[[!comment format=mdwn
username="git-annex@17927e6dc041ab425c14217a97a685adf3ecf44f"
nickname="git-annex"
avatar="http://cdn.libravatar.org/avatar/66e5c6e044d726597ce5a0ad68f86fe4"
subject="Actually they were not standard"
date="2020-06-04T21:05:48Z"
content="""
The 'git annex wanted .' on the manual node returned nothing - so default. I would have thought that that was 'standard'. However, when setting it to standard, the files stopped rebounding.
Christopher
"""]]

8
doc/forum/standalone_tarballs_for_specific_versions/comment_8_74875c799f20d051739227e2b79de18f._comment Normal file
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[[!comment format=mdwn
username="Ilya_Shlyakhter"
avatar="http://cdn.libravatar.org/avatar/1647044369aa7747829c38b9dcc84df0"
subject="correct standalone tarball for git-annex-8.20200522"
date="2020-06-05T06:21:07Z"
content="""
The current standalone tarball at [https://downloads.kitenet.net/git-annex/linux/current/git-annex-standalone-amd64.tar.gz](https://downloads.kitenet.net/git-annex/linux/current/git-annex-standalone-amd64.tar.gz) displays 8.20200502 on 'git-annex version', although the git commit message suggests it should be 8.20200522 . Which is correct?
"""]]

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<details>
<summary>full log</summary>
```shell
[yhalchen@discovery7 tmp]$ ( PS4='[$(date)] > '; set -x; mkdir test; cd test; git init; git annex --debug init; cat .git/config; )
[Thu Jun 4 22:03:14 EDT 2020] > mkdir test
[Thu Jun 4 22:03:14 EDT 2020] > cd test
[Thu Jun 4 22:03:14 EDT 2020] > git init
Initialized empty Git repository in /ihome/yhalchen/tmp/test/.git/
[Thu Jun 4 22:03:15 EDT 2020] > git annex --debug init
init [2020-06-04 22:03:15.148337333] read: git ["--git-dir=.git","--work-tree=.","--literal-pathspecs","show-ref","--hash","refs/heads/git-annex"]
[2020-06-04 22:03:15.160519651] process done ExitFailure 1
[2020-06-04 22:03:15.160710842] call: git ["--git-dir=.git","--work-tree=.","--literal-pathspecs","show-ref","--verify","-q","origin/git-annex"]
[2020-06-04 22:03:15.170626699] process done ExitFailure 1
[2020-06-04 22:03:15.173741089] read: git ["--git-dir=.git","--work-tree=.","--literal-pathspecs","write-tree"]
[2020-06-04 22:03:15.193985902] process done ExitSuccess
[2020-06-04 22:03:15.194151767] chat: git ["--git-dir=.git","--work-tree=.","--literal-pathspecs","commit-tree","4b825dc642cb6eb9a060e54bf8d69288fbee4904","--no-gpg-sign"]
[2020-06-04 22:03:15.211084581] process done ExitSuccess
[2020-06-04 22:03:15.211219476] call: git ["--git-dir=.git","--work-tree=.","--literal-pathspecs","update-ref","refs/heads/git-annex","c2a44ece57b7a7c9105efec702a3fcd5118c16a5"]
[2020-06-04 22:03:15.251272209] process done ExitSuccess
[2020-06-04 22:03:15.257790738] call: git ["--git-dir=.git","--work-tree=.","--literal-pathspecs","config","annex.uuid","17782290-31aa-4bdf-a18d-7808ffe7c977"]
[2020-06-04 22:03:15.272462579] process done ExitSuccess
[2020-06-04 22:03:15.272624366] read: git ["config","--null","--list"]
[2020-06-04 22:03:15.283187109] process done ExitSuccess
Detected a filesystem without POSIX fcntl lock support.
Enabling annex.pidlock.
[2020-06-04 22:05:15.34524884] call: git ["--git-dir=.git","--work-tree=.","--literal-pathspecs","config","annex.pidlock","true"]
[2020-06-04 22:05:15.372408603] process done ExitSuccess
[2020-06-04 22:05:15.372568858] read: git ["config","--null","--list"]
[2020-06-04 22:05:15.382733867] process done ExitSuccess
[2020-06-04 22:05:15.409269066] read: git ["--git-dir=.git","--work-tree=.","--literal-pathspecs","show-ref","git-annex"]
[2020-06-04 22:05:15.422429606] process done ExitSuccess
[2020-06-04 22:05:15.422580683] read: git ["--git-dir=.git","--work-tree=.","--literal-pathspecs","show-ref","--hash","refs/heads/git-annex"]
[2020-06-04 22:05:15.433488294] process done ExitSuccess
[2020-06-04 22:05:15.434294861] read: git ["--git-dir=.git","--work-tree=.","--literal-pathspecs","log","refs/heads/git-annex..c2a44ece57b7a7c9105efec702a3fcd5118c16a5","--pretty=%H","-n1"]
[2020-06-04 22:05:15.447151633] process done ExitSuccess
[2020-06-04 22:05:15.448153606] chat: git ["--git-dir=.git","--work-tree=.","--literal-pathspecs","cat-file","--batch"]
[2020-06-04 22:05:15.449404288] chat: git ["--git-dir=.git","--work-tree=.","--literal-pathspecs","cat-file","--batch-check=%(objectname) %(objecttype) %(objectsize)"]
[2020-06-04 22:05:15.45912651] call: git ["--git-dir=.git","--work-tree=.","--literal-pathspecs","config","annex.version","8"]
[2020-06-04 22:05:15.473144196] process done ExitSuccess
[2020-06-04 22:05:15.473323633] read: git ["config","--null","--list"]
[2020-06-04 22:05:15.484002445] process done ExitSuccess
[2020-06-04 22:05:15.484194067] read: git ["--git-dir=.git","--work-tree=.","--literal-pathspecs","status","--porcelain"]
[2020-06-04 22:05:15.500626848] process done ExitSuccess
[2020-06-04 22:05:15.500774482] call: git ["--git-dir=.git","--work-tree=.","--literal-pathspecs","config","filter.annex.smudge","git-annex smudge -- %f"]
[2020-06-04 22:05:15.514966575] process done ExitSuccess
[2020-06-04 22:05:15.515111682] read: git ["config","--null","--list"]
[2020-06-04 22:05:15.525620475] process done ExitSuccess
[2020-06-04 22:05:15.526092889] call: git ["--git-dir=.git","--work-tree=.","--literal-pathspecs","config","filter.annex.clean","git-annex smudge --clean -- %f"]
[2020-06-04 22:05:15.540331882] process done ExitSuccess
[2020-06-04 22:05:15.540500706] read: git ["config","--null","--list"]
[2020-06-04 22:05:15.550791736] process done ExitSuccess
(scanning for unlocked files...)
[2020-06-04 22:05:15.554116957] read: git ["--git-dir=.git","--work-tree=.","--literal-pathspecs","show-ref","--head"]
[2020-06-04 22:05:15.564970531] process done ExitSuccess
[2020-06-04 22:05:15.579478389] read: git ["--git-dir=.git","--work-tree=.","--literal-pathspecs","symbolic-ref","-q","HEAD"]
[2020-06-04 22:05:15.589809596] process done ExitSuccess
[2020-06-04 22:05:15.589951516] read: git ["--git-dir=.git","--work-tree=.","--literal-pathspecs","show-ref","refs/heads/master"]
[2020-06-04 22:05:15.601255052] process done ExitFailure 1
[2020-06-04 22:05:15.601424674] read: git ["--git-dir=.git","--work-tree=.","--literal-pathspecs","symbolic-ref","-q","HEAD"]
[2020-06-04 22:05:15.611496747] process done ExitSuccess
[2020-06-04 22:05:15.611639271] read: git ["--git-dir=.git","--work-tree=.","--literal-pathspecs","show-ref","--hash","refs/heads/master"]
[2020-06-04 22:05:15.622536266] process done ExitFailure 1
[2020-06-04 22:05:15.622929217] call: git ["--git-dir=.git","--work-tree=.","--literal-pathspecs","checkout","-q","-B","master"]
[2020-06-04 22:05:15.638313905] process done ExitSuccess
[2020-06-04 22:05:15.645385428] read: uname ["-n"]
[2020-06-04 22:05:15.651959283] process done ExitSuccess
ok
[2020-06-04 22:05:15.704393232] chat: git ["--git-dir=.git","--work-tree=.","--literal-pathspecs","hash-object","-w","--stdin-paths","--no-filters"]
[2020-06-04 22:05:15.705996303] feed: git ["--git-dir=.git","--work-tree=.","--literal-pathspecs","update-index","-z","--index-info"]
[2020-06-04 22:05:15.72599264] process done ExitSuccess
[2020-06-04 22:05:15.726142726] read: git ["--git-dir=.git","--work-tree=.","--literal-pathspecs","show-ref","--hash","refs/heads/git-annex"]
[2020-06-04 22:05:15.737436564] process done ExitSuccess
(recording state in git...)
[2020-06-04 22:05:15.737859056] read: git ["--git-dir=.git","--work-tree=.","--literal-pathspecs","write-tree"]
[2020-06-04 22:05:15.758832639] process done ExitSuccess
[2020-06-04 22:05:15.758982175] chat: git ["--git-dir=.git","--work-tree=.","--literal-pathspecs","commit-tree","1767824d19ab44b9b0f2a156663e4f3bc37e902f","--no-gpg-sign","-p","refs/heads/git-annex"]
[2020-06-04 22:05:15.777364836] process done ExitSuccess
[2020-06-04 22:05:15.777525965] call: git ["--git-dir=.git","--work-tree=.","--literal-pathspecs","update-ref","refs/heads/git-annex","6dc63f68c7036fbef7a4afeead658ab42433ad55"]
[2020-06-04 22:05:15.797354413] process done ExitSuccess
[2020-06-04 22:05:15.828091917] process done ExitSuccess
[2020-06-04 22:05:15.828520537] process done ExitSuccess
[2020-06-04 22:05:15.828968133] process done ExitSuccess
[Thu Jun 4 22:05:15 EDT 2020] > cat .git/config
[core]
repositoryformatversion = 0
filemode = true
bare = false
logallrefupdates = true
[annex]
uuid = 17782290-31aa-4bdf-a18d-7808ffe7c977
pidlock = true
version = 8
[filter "annex"]
smudge = git-annex smudge -- %f
clean = git-annex smudge --clean -- %f
[yhalchen@discovery7 tmp]$ git annex version
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
```
</details>
the excerpt for running `git-annex init` of 8.20200502-g55acb2e52 on an NFS mounted isilon volume:
[[!format sh """
[2020-06-04 22:03:15.283187109] process done ExitSuccess
Detected a filesystem without POSIX fcntl lock support.
Enabling annex.pidlock.
[2020-06-04 22:05:15.34524884] call: git ["--git-dir=.git","--work-tree=.","--literal-pathspecs","config","annex.pidlock","true"]
"""]]
so - 2 minutes. Running with `strace -f` showed a long flood of `[pid 2890] read(4, "\1\0\0\0\0\0\0\0", 8) = 8`
<details>
<summary>here is an excerpt where it begins with timing stamps</summary>
```shell
[pid 7661] 22:12:42.464620 futex(0x2abd17039ad0, FUTEX_WAKE_PRIVATE, 1) = 0
[pid 7661] 22:12:42.464705 openat(AT_FDCWD, "./.noannex", O_RDONLY|O_NOCTTY|O_NONBLOCK) = -1 ENOENT (No such file or directory)
[pid 7661] 22:12:42.464828 getcwd("/ihome/yhalchen/tmp/test", 4096) = 25
[pid 7661] 22:12:42.464913 getcwd("/ihome/yhalchen/tmp/test", 4096) = 25
[pid 7661] 22:12:42.465045 mkdir(".git/annex/misctmp", 0777) = 0
[pid 7661] 22:12:42.466273 unlink(".git/annex/misctmp/lockprobe") = -1 ENOENT (No such file or directory)
[pid 7661] 22:12:42.466699 openat(AT_FDCWD, ".git/annex/misctmp/lockprobe", O_RDWR|O_CREAT, 0666) = 11
[pid 7661] 22:12:42.467692 fcntl(11, F_GETFD) = 0
[pid 7661] 22:12:42.467768 fcntl(11, F_SETFD, FD_CLOEXEC) = 0
[pid 7661] 22:12:42.467841 fcntl(11, F_SETLKW, {l_type=F_WRLCK, l_whence=SEEK_SET, l_start=0, l_len=0} <unfinished ...>
[pid 7703] 22:12:42.473082 <... read resumed>"\1\0\0\0\0\0\0\0", 8) = 8
[pid 7703] 22:12:42.473137 read(4, "\1\0\0\0\0\0\0\0", 8) = 8
[pid 7703] 22:12:42.483143 read(4, "\1\0\0\0\0\0\0\0", 8) = 8
[pid 7703] 22:12:42.493202 read(4, "\1\0\0\0\0\0\0\0", 8) = 8
[pid 7703] 22:12:42.503215 read(4, "\1\0\0\0\0\0\0\0", 8) = 8
[pid 7703] 22:12:42.513202 read(4, "\1\0\0\0\0\0\0\0", 8) = 8
[pid 7703] 22:12:42.523178 read(4, "\1\0\0\0\0\0\0\0", 8) = 8
[pid 7703] 22:12:42.533202 read(4, "\1\0\0\0\0\0\0\0", 8) = 8
[pid 7703] 22:12:42.543191 read(4, "\1\0\0\0\0\0\0\0", 8) = 8
[pid 7703] 22:12:42.553186 read(4, "\1\0\0\0\0\0\0\0", 8) = 8
[pid 7703] 22:12:42.563219 read(4, "\1\0\0\0\0\0\0\0", 8) = 8
[pid 7703] 22:12:42.573212 read(4, "\1\0\0\0\0\0\0\0", 8) = 8
[pid 7703] 22:12:42.583215 read(4, "\1\0\0\0\0\0\0\0", 8) = 8
[pid 7703] 22:12:42.593206 read(4, "\1\0\0\0\0\0\0\0", 8) = 8
[pid 7703] 22:12:42.603168 read(4, "\1\0\0\0\0\0\0\0", 8) = 8
[pid 7703] 22:12:42.613209 read(4, "\1\0\0\0\0\0\0\0", 8) = 8
[pid 7703] 22:12:42.623150 read(4, "\1\0\0\0\0\0\0\0", 8) = 8
[pid 7703] 22:12:42.633193 read(4, "\1\0\0\0\0\0\0\0", 8) = 8
[pid 7703] 22:12:42.643242 read(4, "\1\0\0\0\0\0\0\0", 8) = 8
[pid 7703] 22:12:42.653170 read(4, "\1\0\0\0\0\0\0\0", 8) = 8
[pid 7703] 22:12:42.663189 read(4, "\1\0\0\0\0\0\0\0", 8) = 8
[pid 7703] 22:12:42.673182 read(4, "\1\0\0\0\0\0\0\0", 8) = 8
[pid 7703] 22:12:42.683183 read(4, "\1\0\0\0\0\0\0\0", 8) = 8
[pid 7703] 22:12:42.693190 read(4, "\1\0\0\0\0\0\0\0", 8) = 8
[pid 7703] 22:12:42.703184 read(4, "\1\0\0\0\0\0\0\0", 8) = 8
[pid 7703] 22:12:42.713203 read(4, "\1\0\0\0\0\0\0\0", 8) = 8
[pid 7703] 22:12:42.723212 read(4, "\1\0\0\0\0\0\0\0", 8) = 8
[pid 7703] 22:12:42.733202 read(4, "\1\0\0\0\0\0\0\0", 8) = 8
[pid 7703] 22:12:42.743181 read(4, "\1\0\0\0\0\0\0\0", 8) = 8
[pid 7703] 22:12:42.753220 read(4, "\1\0\0\0\0\0\0\0", 8) = 8
[pid 7703] 22:12:42.763179 read(4, "\1\0\0\0\0\0\0\0", 8) = 8
[pid 7703] 22:12:42.773207 read(4, "\1\0\0\0\0\0\0\0", 8) = 8
[pid 7703] 22:12:42.783204 write(10, "\377\0\0\0\0\0\0\0", 8) = 8
[pid 7705] 22:12:42.783323 <... poll resumed>) = 1 ([{fd=10, revents=POLLIN}])
[pid 7703] 22:12:42.783367 read(4, <unfinished ...>
[pid 7705] 22:12:42.783441 futex(0x2abd17039cbc, FUTEX_WAIT_PRIVATE, 0, NULL <unfinished ...>
[pid 7703] 22:12:42.793162 <... read resumed>"\1\0\0\0\0\0\0\0", 8) = 8
[pid 7703] 22:12:42.793241 read(4, "\1\0\0\0\0\0\0\0", 8) = 8
[pid 7703] 22:12:42.803209 read(4, "\1\0\0\0\0\0\0\0", 8) = 8
[pid 7703] 22:12:42.813218 read(4, "\1\0\0\0\0\0\0\0", 8) = 8
[pid 7703] 22:12:42.823185 read(4, "\1\0\0\0\0\0\0\0", 8) = 8
[pid 7703] 22:12:42.833206 read(4, "\1\0\0\0\0\0\0\0", 8) = 8
[pid 7703] 22:12:42.843189 read(4, "\1\0\0\0\0\0\0\0", 8) = 8
```
</details>
I wonder if there is a way to "speed up" pidlock detection?
At least adding some debug message before running the detection could be of help, it could help troubleshoot what I thought was some "ssh" stall since it just got stuck at
<details>
<summary>with the last line just saying "process done ExitSuccess" for that long and I kept killing it impatiently</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
# here I kept killing it but then eventually it shows that it is enabling pidlock
```
</details>
[[!meta author=yoh]]
[[!tag projects/datalad]]