Please describe the problem.
I have spotted that git annex drop was at time quite slow. I thought it was testing the remote(s) but ended up being not that: e.g.
git annex drop --debug sub-440958/sub-440958_ses-20190213T115547_behavior+ecephys+image+ogen.nwb
has
[2025-03-06 17:17:27.142370501] (Utility.Process) process [3058825] chat: git ["--git-dir=.git","--work-tree=.","--literal-pathspecs","-c","annex.debug=true","cat-file","--batch"]
[2025-03-06 17:17:27.147619069] (Annex.Perms) thawing content directory .git/annex/objects/Q2/6g/SHA256E-s458941350881--40f2a2dd11d2f5f5572b32f654d0c92557f2a390fe1434e70caecd44fd3225c9.nwb
[2025-03-06 17:17:27.147915521] (Annex.Perms) freezing content directory .git/annex/objects/Q2/6g/SHA256E-s458941350881--40f2a2dd11d2f5f5572b32f654d0c92557f2a390fe1434e70caecd44fd3225c9.nwb
[2025-03-06 17:17:27.196116156] (Utility.Url) Request {
host = "dandiarchive.s3.amazonaws.com"
port = 443
secure = True
requestHeaders = [("Accept-Encoding",""),("User-Agent","git-annex/10.20250115+git160-g93fb1ba536-1~ndall+1")]
path = "/blobs/227/91d/22791d80-26dc-4495-b4c0-651fe10e3298"
queryString = "?versionId=mnU_QOZwfaLCY7kSeUX_lcNGHUjjbeU2"
method = "HEAD"
proxy = Nothing
rawBody = False
redirectCount = 10
responseTimeout = ResponseTimeoutDefault
requestVersion = HTTP/1.1
proxySecureMode = ProxySecureWithConnect
}
[2025-03-06 17:17:27.388964083] (Command.Drop) Dropping from here proof: Just (SafeDropProof (NumCopies 1) (MinCopies 1) [RecentlyVerifiedCopy UUID "00000000-0000-0000-0000-000000000001"] Nothing (Just (ContentRemovalLock (MkKey {keyData = Key {keyName = "40f2a2dd11d2f5f5572b32f654d0c92557f2a390fe1434e70caecd44fd3225c9.nwb", keyVariety = SHA2Key (HashSize 256) (HasExt True), keySize = Just 458941350881, keyMtime = Nothing, keyChunkSize = Nothing, keyChunkNum = Nothing}, keySerialization = "SHA256E-s458941350881--40f2a2dd11d2f5f5572b32f654d0c92557f2a390fe1434e70caecd44fd3225c9.nwb"}))))
[2025-03-06 17:17:27.389404507] (Annex.Perms) thawing content directory .git/annex/objects/Q2/6g/SHA256E-s458941350881--40f2a2dd11d2f5f5572b32f654d0c92557f2a390fe1434e70caecd44fd3225c9.nwb
[2025-03-06 17:19:16.06748192] (Annex.Perms) thawing content directory .git/annex/objects/Q2/6g/SHA256E-s458941350881--40f2a2dd11d2f5f5572b32f654d0c92557f2a390fe1434e70caecd44fd3225c9.nwb
[2025-03-06 17:19:16.068644724] (Annex.Branch) read a22/51b/SHA256E-s458941350881--40f2a2dd11d2f5f5572b32f654d0c92557f2a390fe1434e70caecd44fd3225c9.nwb.log
[2025-03-06 17:19:16.070244398] (Annex.Branch) set a22/51b/SHA256E-s458941350881--40f2a2dd11d2f5f5572b32f654d0c92557f2a390fe1434e70caecd44fd3225c9.nwb.log
so - it has actually 3 (not two) log lines on thawing and 1st one comes even before testing remote URL. - it takes almost two minutes between 2nd and 3rd thawing lines (without any output inbetween)
repository is quite light in number of files (not size though)
annexed files in working tree: 174
size of annexed files in working tree: 65.7 terabytes
and could be cloned from https://github.com/dandisets/000363 .
Interestingly, looking at other not yet dropped files there -- those folders are not even write-protected! (actual key files are):
dandi@drogon:/mnt/backup/dandi/dandisets/000363$ git annex find --in here sub-440* | while read f; do ccd=$(readlink -f "$f"|xargs dirname); ls -ld "$ccd"; done
drwxr-sr-x 1 dandi dandi 182 Mar 3 23:21 /mnt/backup/dandi/dandisets/000363/.git/annex/objects/v7/W1/SHA256E-s446084260431--0c66c1f84686ab5838353fe42630c35d5b9c255e3ebf92a82d1d1adfa8a7fedf.nwb
drwxr-sr-x 1 dandi dandi 182 Mar 3 23:24 /mnt/backup/dandi/dandisets/000363/.git/annex/objects/G7/zQ/SHA256E-s440859400651--7364c08d63b04a92b8cbe82a506733ff4e7ba36e78060ca1aa06b32111622a78.nwb
drwxr-sr-x 1 dandi dandi 176 Mar 3 23:25 /mnt/backup/dandi/dandisets/000363/.git/annex/objects/6J/wk/SHA256E-s159195870--66243f8b55567671400b14da186518293a76d406f0b1c979cc9d97ecb254d9ae.nwb
drwxr-sr-x 1 dandi dandi 182 Mar 3 23:25 /mnt/backup/dandi/dandisets/000363/.git/annex/objects/6K/V6/SHA256E-s480007274147--da636994efc2d9c53f4f2261d04dd0f98f56d6626088bf77aa393a0090d8fb63.nwb
drwxr-sr-x 1 dandi dandi 182 Mar 3 23:25 /mnt/backup/dandi/dandisets/000363/.git/annex/objects/jP/mJ/SHA256E-s296110873457--68d9d40d3d356183b3d2a433fabffc5ed19d04f2057e2121d7b7c9c5372ebe44.nwb
drwxr-sr-x 1 dandi dandi 182 Mar 3 23:21 /mnt/backup/dandi/dandisets/000363/.git/annex/objects/51/pP/SHA256E-s372184652945--5bdbb5e06e77c714d0c2460a961bf95753623618e1e5c83073fb7f0a3cb8f0b8.nwb
drwxr-sr-x 1 dandi dandi 182 Mar 3 23:25 /mnt/backup/dandi/dandisets/000363/.git/annex/objects/02/mz/SHA256E-s359721690048--7e90fae4aa4808f2c4d85361dd57a8e188bf349b9c88993e74beb6f54719ae8e.nwb
drwxr-sr-x 1 dandi dandi 182 Mar 3 23:25 /mnt/backup/dandi/dandisets/000363/.git/annex/objects/QM/j4/SHA256E-s274399228635--8833b0c1024b4130e9ce389a76c0241cd0cf3c4a7ded74d23b2fd151aaffe311.nwb
and repo is not 'shared' AFAIK
dandi@drogon:/mnt/backup/dandi/dandisets/000363$ grep share .git/config
dandi@drogon:/mnt/backup/dandi/dandisets/000363$
What version of git-annex are you using? On what operating system?
detected with earlier version but was investigating further with "bleeding edge"
dandi@drogon:/mnt/backup/dandi/dandisets/000363$ git annex version
git-annex version: 10.20250115+git160-g93fb1ba536-1~ndall+1
build flags: Assistant Webapp Pairing Inotify DBus DesktopNotify TorrentParser MagicMime Servant Benchmark Feeds Testsuite S3 WebDAV
dependency versions: aws-0.22.1 bloomfilter-2.0.1.0 cryptonite-0.29 DAV-1.3.4 feed-1.3.2.1 ghc-9.0.2 http-client-0.7.13.1 persistent-sqlite-2.13.1.0 torrent-10000.1.1 uuid-1.3.15 yesod-1.6.2.1
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 GITBUNDLE GITMANIFEST VURL X*
remote types: git gcrypt p2p S3 bup directory rsync web bittorrent webdav adb tahoe glacier ddar git-lfs httpalso borg rclone hook external
operating system: linux x86_64
supported repository versions: 8 9 10
upgrade supported from repository versions: 0 1 2 3 4 5 6 7 8 9 10
local repository version: 10
I do not think custom threeze/thaw configured here
dandi@drogon:/mnt/backup/dandi/dandisets/000363$ git config -l | grep annex
alias.annexdiff=!GIT_EXTERNAL_DIFF='git-annex diffdriver -- git-annex-diff-wrapper --' git diff
annex.stalldetection=1KB/120s
annex.autoupgraderepository=false
annex.uuid=1ce3e7b7-edf2-4907-ad29-610e9a46315f
annex.version=10
filter.annex.smudge=git-annex smudge -- %f
filter.annex.clean=git-annex smudge --clean -- %f
filter.annex.process=git-annex filter-process
remote.dandi-dandisets-dropbox.annex-externaltype=rclone
remote.dandi-dandisets-dropbox.annex-uuid=727f466f-60c3-4778-90b2-b2332856c2f8
remote.dandi-dandisets-dropbox.annex-cost=200.0
remote.dandi-dandisets-dropbox.annex-availability=GloballyAvailable
remote.github.annex-ignore=true
remote.dandiapi.annex-web=true
remote.dandiapi.annex-uuid=00000000-0000-0000-0000-000000000001
remote.dandiapi.annex-config-uuid=f80ff5ab-efbc-4b0b-aaf7-bfbed92e4c29
file system is BTRFS and quite "busy" but I would not expect 2 minutes on chmod call there... unclear why 3 log lines as well
Seems to be chronic but not all the time -- seems one run had it go fast albeit with 3 log lines as well
dandi@drogon:/mnt/backup/dandi/dandisets/000363$ grep 'thawing content directory' .duct/logs/2025.03.*
.duct/logs/2025.03.04T09.19.20-178850_stderr:[2025-03-04 09:19:20.914767806] (Annex.Perms) thawing content directory .git/annex/objects/zg/F6/SHA256E-s424900914587--0f859aca43eaf7fb3a12de068b667ffd1b836d8edcd7574547c1e8782cd1f04e.nwb
.duct/logs/2025.03.04T09.19.20-178850_stderr:[2025-03-04 09:19:21.187113505] (Annex.Perms) thawing content directory .git/annex/objects/zg/F6/SHA256E-s424900914587--0f859aca43eaf7fb3a12de068b667ffd1b836d8edcd7574547c1e8782cd1f04e.nwb
.duct/logs/2025.03.04T09.19.20-178850_stderr:[2025-03-04 09:22:28.320213649] (Annex.Perms) thawing content directory .git/annex/objects/zg/F6/SHA256E-s424900914587--0f859aca43eaf7fb3a12de068b667ffd1b836d8edcd7574547c1e8782cd1f04e.nwb
.duct/logs/2025.03.06T17.08.02-3042067_stderr:[2025-03-06 17:08:03.059666572] (Annex.Perms) thawing content directory .git/annex/objects/M2/5j/SHA256E-s296808899160--b2c4f356904a6a034ef8630a34508950958cfda4bf7969662f1a1ee3ad682cfc.nwb
.duct/logs/2025.03.06T17.08.02-3042067_stderr:[2025-03-06 17:08:03.356505174] (Annex.Perms) thawing content directory .git/annex/objects/M2/5j/SHA256E-s296808899160--b2c4f356904a6a034ef8630a34508950958cfda4bf7969662f1a1ee3ad682cfc.nwb
.duct/logs/2025.03.06T17.08.02-3042067_stderr:[2025-03-06 17:09:25.985686417] (Annex.Perms) thawing content directory .git/annex/objects/M2/5j/SHA256E-s296808899160--b2c4f356904a6a034ef8630a34508950958cfda4bf7969662f1a1ee3ad682cfc.nwb
.duct/logs/2025.03.06T17.17.16-3058713_stderr:[2025-03-06 17:17:16.437911131] (Annex.Perms) thawing content directory .git/annex/objects/Zx/gm/SHA256E-s190766322--419f317867cae557e0cf72460d981dafed54eb5a2136fecf25e7650db3bec944.nwb
.duct/logs/2025.03.06T17.17.16-3058713_stderr:[2025-03-06 17:17:16.693636236] (Annex.Perms) thawing content directory .git/annex/objects/Zx/gm/SHA256E-s190766322--419f317867cae557e0cf72460d981dafed54eb5a2136fecf25e7650db3bec944.nwb
.duct/logs/2025.03.06T17.17.16-3058713_stderr:[2025-03-06 17:17:16.804165428] (Annex.Perms) thawing content directory .git/annex/objects/Zx/gm/SHA256E-s190766322--419f317867cae557e0cf72460d981dafed54eb5a2136fecf25e7650db3bec944.nwb
.duct/logs/2025.03.06T17.17.26-3058787_stderr:[2025-03-06 17:17:27.147619069] (Annex.Perms) thawing content directory .git/annex/objects/Q2/6g/SHA256E-s458941350881--40f2a2dd11d2f5f5572b32f654d0c92557f2a390fe1434e70caecd44fd3225c9.nwb
.duct/logs/2025.03.06T17.17.26-3058787_stderr:[2025-03-06 17:17:27.389404507] (Annex.Perms) thawing content directory .git/annex/objects/Q2/6g/SHA256E-s458941350881--40f2a2dd11d2f5f5572b32f654d0c92557f2a390fe1434e70caecd44fd3225c9.nwb
.duct/logs/2025.03.06T17.17.26-3058787_stderr:[2025-03-06 17:19:16.06748192] (Annex.Perms) thawing content directory .git/annex/objects/Q2/6g/SHA256E-s458941350881--40f2a2dd11d2f5f5572b32f654d0c92557f2a390fe1434e70caecd44fd3225c9.nwb