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Joey Hess 2024-05-30 13:26:44 -04:00
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### Please describe the problem.
Trying to get fresh data from a server but `annex get` is just stuck without any output. Here is how it looks with `--debug`:
```
yoh@typhon:/mnt/DATA/data/yoh/1076_spacetop$ git annex get --debug sub-0002/ses-01/dwi/sub-0002_ses-01_acq-96dirX6b0Xmb_dwi.nii.gz
[2024-05-29 14:08:30.203689795] (Utility.Process) process [3922981] read: git ["--git-dir=.git","--work-tree=.","--literal-pathspecs","-c","annex.debug=true","ls-files","--stage","-z","--error-unmatch","--","sub-0002/ses-01/dwi/sub-0002_ses-01_acq-96dirX6b0Xmb_dwi.nii.gz"]
[2024-05-29 14:08:30.204159722] (Utility.Process) process [3922982] chat: git ["--git-dir=.git","--work-tree=.","--literal-pathspecs","-c","annex.debug=true","cat-file","--batch-check=%(objectname) %(objecttype) %(objectsize)","--buffer"]
[2024-05-29 14:08:30.204574378] (Utility.Process) process [3922983] chat: git ["--git-dir=.git","--work-tree=.","--literal-pathspecs","-c","annex.debug=true","cat-file","--batch=%(objectname) %(objecttype) %(objectsize)","--buffer"]
[2024-05-29 14:08:30.205075804] (Utility.Process) process [3922984] read: git ["--git-dir=.git","--work-tree=.","--literal-pathspecs","-c","annex.debug=true","show-ref","git-annex"]
[2024-05-29 14:08:30.207328301] (Utility.Process) process [3922984] done ExitSuccess
[2024-05-29 14:08:30.207536385] (Utility.Process) process [3922985] read: git ["--git-dir=.git","--work-tree=.","--literal-pathspecs","-c","annex.debug=true","show-ref","--hash","refs/heads/git-annex"]
[2024-05-29 14:08:30.209355606] (Utility.Process) process [3922985] done ExitSuccess
[2024-05-29 14:08:30.209800913] (Utility.Process) process [3922986] chat: git ["--git-dir=.git","--work-tree=.","--literal-pathspecs","-c","annex.debug=true","cat-file","--batch=%(objectname) %(objecttype) %(objectsize)","--buffer"]
get sub-0002/ses-01/dwi/sub-0002_ses-01_acq-96dirX6b0Xmb_dwi.nii.gz [2024-05-29 14:08:30.215082484] (Utility.Process) process [3922987] chat: git ["--git-dir=.git","--work-tree=.","--literal-pathspecs","-c","annex.debug=true","cat-file","--batch"]
(from origin...)
[2024-05-29 14:08:30.225575902] (Utility.Process) process [3922988] read: ssh ["-O","stop","-S","bids@rolando.cns.dartmouth.edu","-o","ControlMaster=auto","-o","ControlPersist=yes","localhost"] in ".git/annex/ssh/"
[2024-05-29 14:08:30.230512383] (Utility.Process) process [3922988] done ExitSuccess
[2024-05-29 14:08:30.231078838] (Utility.Process) process [3922989] read: ssh ["-o","BatchMode=true","-S",".git/annex/ssh/bids@rolando.cns.dartmouth.edu","-o","ControlMaster=auto","-o","ControlPersist=yes","-n","-T","bids@rolando.cns.dartmouth.edu","true"]
[2024-05-29 14:08:31.042361711] (Utility.Process) process [3922989] done ExitSuccess
[2024-05-29 14:08:31.043219566] (Utility.Process) process [3923085] chat: ssh ["bids@rolando.cns.dartmouth.edu","-S",".git/annex/ssh/bids@rolando.cns.dartmouth.edu","-o","ControlMaster=auto","-o","ControlPersist=yes","-T","git-annex-shell 'p2pstdio' '/inbox/BIDS/Wager/Wager/1076_spacetop' '--debug' '97b6f5e4-4642-43a7-988a-c483caf553c5' --uuid 590b4fd0-0142-4e9d-8964-d1158c242c6a"]
[2024-05-29 14:08:31.540468659] (P2P.IO) [ThreadId 4] P2P > AUTH-SUCCESS 590b4fd0-0142-4e9d-8964-d1158c242c6a
[2024-05-29 14:08:31.539643152] (P2P.IO) [ssh connection Just 3923085] [ThreadId 4] P2P < AUTH-SUCCESS 590b4fd0-0142-4e9d-8964-d1158c242c6a
[2024-05-29 14:08:31.539846045] (P2P.IO) [ssh connection Just 3923085] [ThreadId 4] P2P > VERSION 1
[2024-05-29 14:08:31.542774097] (P2P.IO) [ThreadId 4] P2P < VERSION 1
[2024-05-29 14:08:31.543007073] (P2P.IO) [ThreadId 4] P2P > VERSION 1
[2024-05-29 14:08:31.541288127] (P2P.IO) [ssh connection Just 3923085] [ThreadId 4] P2P < VERSION 1
[2024-05-29 14:08:31.541362199] (P2P.IO) [ssh connection Just 3923085] [ThreadId 4] P2P > GET 0 sub-0002/ses-01/dwi/sub-0002_ses-01_acq-96dirX6b0Xmb_dwi.nii.gz MD5E-s239384952--c3aaaebbed3ef5932b4390ddb47d2150.nii.gz
[2024-05-29 14:08:31.544298446] (P2P.IO) [ThreadId 4] P2P < GET 0 sub-0002/ses-01/dwi/sub-0002_ses-01_acq-96dirX6b0Xmb_dwi.nii.gz MD5E-s239384952--c3aaaebbed3ef5932b4390ddb47d2150.nii.gz
```
and on the server it looks like ( I killed one, client reinitiated, this is current one)
```
bids 27577 0.3 0.0 1074226428 11120 ? Ssl 14:10 0:00 /data/home/bids/git-annexes/10.20231129+git83-g86dbe9a825/usr/lib/git-annex.linux/exe/git-annex-shell --library-path /data/home/bids/git-annexes/10.20231129+git83-g86dbe9a825/usr/lib/git-annex.linux//lib/x86_64-linux-gnu: /data/home/bids/git-annexes/10.20231129+git83-g86dbe9a825/usr/lib/git-annex.linux/shimmed/git-annex-shell/git-annex-shell p2pstdio /inbox/BIDS/Wager/Wager/1076_spacetop.git --debug 97b6f5e4-4642-43a7-988a-c483caf553c5 --uuid 40795e62-527c-4d26-ae8c-af42a6e2da5a
```
and on server config is
```
[annex]
sshcaching = false
autoupgraderepository = false
pidlock = true
[safe]
directory = /inbox/BIDS
```
and that directory `/inbox/BIDS` is NFS mounted.
Not sure what nobs to turn to help diagnose the issue.
The git-annex on client side is `10.20240129-1~ndall+1`
[[!meta author=yoh]]
[[!tag projects/repronim]]
### What steps will reproduce the problem?
### What version of git-annex are you using? On what operating system?
### Please provide any additional information below.
[[!format sh """
# If you can, paste a complete transcript of the problem occurring here.
# If the problem is with the git-annex assistant, paste in .git/annex/daemon.log
# End of transcript or log.
"""]]
### Have you had any luck using git-annex before? (Sometimes we get tired of reading bug reports all day and a lil' positive end note does wonders)

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[[!comment format=mdwn
username="yarikoptic"
avatar="http://cdn.libravatar.org/avatar/f11e9c84cb18d26a1748c33b48c924b4"
subject="odd odd odd"
date="2024-05-29T18:25:11Z"
content="""
and I cannot copy from the server to the client:
```
[bids@rolando 1076_spacetop.git] > git annex copy --debug --to typhon --fast --not --in typhon
yoh@typhon.dartmouth.edu's password:
[2024-05-29 14:21:40.601369476] (Utility.Process) process [28828] read: git [\"--git-dir=.\",\"--literal-pathspecs\",\"-c\",\"annex.debug=true\",\"ls-tree\",\"--full-tree\",\"-z\",\"-r\",\"--\",\"refs/heads/git-annex\"]
[2024-05-29 14:21:40.602439011] (Utility.Process) process [28829] chat: git [\"--git-dir=.\",\"--literal-pathspecs\",\"-c\",\"annex.debug=true\",\"cat-file\",\"--batch=%(objectname) %(objecttype) %(objectsize)\",\"--buffer\"]
[2024-05-29 14:21:40.775458494] (Messages.explain) [ MD5E-s292602526--2069b86f10e1a39bda5a6ed8996078d4.nii.gz does not match:not in=typhon[TRUE] ]
[2024-05-29 14:21:40.793913739] (Messages.explain) [ MD5E-s2615170--589b64f4cd3067f468408d809c7f1037.nii.gz does not match:not in=typhon[TRUE] ]
[2024-05-29 14:21:40.811856562] (Messages.explain) [ MD5E-s597779--1108c4d91a2386573c50c251a0e967c2.tgz matches:not in=typhon[FALSE] ]
copy MD5E-s597779--1108c4d91a2386573c50c251a0e967c2.tgz (to typhon...) [2024-05-29 14:21:40.974993044] (Utility.Process) process [28817] done ExitSuccess
[2024-05-29 14:21:40.975527841] (Utility.Process) process [28816] done ExitSuccess
You have enabled concurrency, but git-annex is not able to use ssh connection caching. This may result in multiple ssh processes prompting for passwords at the same time.
annex.sshcaching is not set to true
[2024-05-29 14:21:40.977267402] (Utility.Process) process [28831] chat: ssh [\"yoh@typhon.dartmouth.edu\",\"-T\",\"git-annex-shell 'p2pstdio' '/mnt/DATA/data/yoh/1076_spacetop' '--debug' '40795e62-527c-4d26-ae8c-af42a6e2da5a' --uuid 97b6f5e4-4642-43a7-988a-c483caf553c5\"]
yoh@typhon.dartmouth.edu's password:
[2024-05-29 14:21:57.87732028] (P2P.IO) [ThreadId 4] P2P > AUTH-SUCCESS 97b6f5e4-4642-43a7-988a-c483caf553c5
[2024-05-29 14:21:57.879974047] (P2P.IO) [ssh connection Just 28831] [ThreadId 4] P2P < AUTH-SUCCESS 97b6f5e4-4642-43a7-988a-c483caf553c5
[2024-05-29 14:21:57.880228709] (P2P.IO) [ssh connection Just 28831] [ThreadId 4] P2P > VERSION 1
[2024-05-29 14:21:57.878927215] (P2P.IO) [ThreadId 4] P2P < VERSION 1
[2024-05-29 14:21:57.878991142] (P2P.IO) [ThreadId 4] P2P > VERSION 1
[2024-05-29 14:21:57.881305277] (P2P.IO) [ssh connection Just 28831] [ThreadId 4] P2P < VERSION 1
[2024-05-29 14:21:57.881487685] (P2P.IO) [ssh connection Just 28831] [ThreadId 4] P2P > PUT MD5E-s597779--1108c4d91a2386573c50c251a0e967c2.tgz
[2024-05-29 14:21:57.880214299] (P2P.IO) [ThreadId 4] P2P < PUT MD5E-s597779--1108c4d91a2386573c50c251a0e967c2.tgz
[2024-05-29 14:21:57.880467298] (P2P.IO) [ThreadId 4] P2P > PUT-FROM 0
[2024-05-29 14:21:57.882841829] (P2P.IO) [ssh connection Just 28831] [ThreadId 4] P2P < PUT-FROM 0
```
NB we had issue with a recent 10GB switch update which was worked around by me reducing MTU on my servers from Jumbo frames to regular 1500 . But it manifested that scp did not work. Here scp worked (I did scp on typhon from rolando). And for heejung it does not work to `pull` data from roland to discovery.
"""]]

43
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[[!comment format=mdwn
username="yarikoptic"
avatar="http://cdn.libravatar.org/avatar/f11e9c84cb18d26a1748c33b48c924b4"
subject="odd odd odd"
date="2024-05-29T18:25:23Z"
content="""
and I cannot copy from the server to the client:
```
[bids@rolando 1076_spacetop.git] > git annex copy --debug --to typhon --fast --not --in typhon
yoh@typhon.dartmouth.edu's password:
[2024-05-29 14:21:40.601369476] (Utility.Process) process [28828] read: git [\"--git-dir=.\",\"--literal-pathspecs\",\"-c\",\"annex.debug=true\",\"ls-tree\",\"--full-tree\",\"-z\",\"-r\",\"--\",\"refs/heads/git-annex\"]
[2024-05-29 14:21:40.602439011] (Utility.Process) process [28829] chat: git [\"--git-dir=.\",\"--literal-pathspecs\",\"-c\",\"annex.debug=true\",\"cat-file\",\"--batch=%(objectname) %(objecttype) %(objectsize)\",\"--buffer\"]
[2024-05-29 14:21:40.775458494] (Messages.explain) [ MD5E-s292602526--2069b86f10e1a39bda5a6ed8996078d4.nii.gz does not match:not in=typhon[TRUE] ]
[2024-05-29 14:21:40.793913739] (Messages.explain) [ MD5E-s2615170--589b64f4cd3067f468408d809c7f1037.nii.gz does not match:not in=typhon[TRUE] ]
[2024-05-29 14:21:40.811856562] (Messages.explain) [ MD5E-s597779--1108c4d91a2386573c50c251a0e967c2.tgz matches:not in=typhon[FALSE] ]
copy MD5E-s597779--1108c4d91a2386573c50c251a0e967c2.tgz (to typhon...) [2024-05-29 14:21:40.974993044] (Utility.Process) process [28817] done ExitSuccess
[2024-05-29 14:21:40.975527841] (Utility.Process) process [28816] done ExitSuccess
You have enabled concurrency, but git-annex is not able to use ssh connection caching. This may result in multiple ssh processes prompting for passwords at the same time.
annex.sshcaching is not set to true
[2024-05-29 14:21:40.977267402] (Utility.Process) process [28831] chat: ssh [\"yoh@typhon.dartmouth.edu\",\"-T\",\"git-annex-shell 'p2pstdio' '/mnt/DATA/data/yoh/1076_spacetop' '--debug' '40795e62-527c-4d26-ae8c-af42a6e2da5a' --uuid 97b6f5e4-4642-43a7-988a-c483caf553c5\"]
yoh@typhon.dartmouth.edu's password:
[2024-05-29 14:21:57.87732028] (P2P.IO) [ThreadId 4] P2P > AUTH-SUCCESS 97b6f5e4-4642-43a7-988a-c483caf553c5
[2024-05-29 14:21:57.879974047] (P2P.IO) [ssh connection Just 28831] [ThreadId 4] P2P < AUTH-SUCCESS 97b6f5e4-4642-43a7-988a-c483caf553c5
[2024-05-29 14:21:57.880228709] (P2P.IO) [ssh connection Just 28831] [ThreadId 4] P2P > VERSION 1
[2024-05-29 14:21:57.878927215] (P2P.IO) [ThreadId 4] P2P < VERSION 1
[2024-05-29 14:21:57.878991142] (P2P.IO) [ThreadId 4] P2P > VERSION 1
[2024-05-29 14:21:57.881305277] (P2P.IO) [ssh connection Just 28831] [ThreadId 4] P2P < VERSION 1
[2024-05-29 14:21:57.881487685] (P2P.IO) [ssh connection Just 28831] [ThreadId 4] P2P > PUT MD5E-s597779--1108c4d91a2386573c50c251a0e967c2.tgz
[2024-05-29 14:21:57.880214299] (P2P.IO) [ThreadId 4] P2P < PUT MD5E-s597779--1108c4d91a2386573c50c251a0e967c2.tgz
[2024-05-29 14:21:57.880467298] (P2P.IO) [ThreadId 4] P2P > PUT-FROM 0
[2024-05-29 14:21:57.882841829] (P2P.IO) [ssh connection Just 28831] [ThreadId 4] P2P < PUT-FROM 0
```
NB we had issue with a recent 10GB switch update which was worked around by me reducing MTU on my servers from Jumbo frames to regular 1500 . But it manifested that scp did not work. Here scp worked (I did scp on typhon from rolando). And for heejung it does not work to `pull` data from roland to discovery.
"""]]

18
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[[!comment format=mdwn
username="yarikoptic"
avatar="http://cdn.libravatar.org/avatar/f11e9c84cb18d26a1748c33b48c924b4"
subject="comment 3"
date="2024-05-29T18:31:16Z"
content="""
might be (part of) mystery resolved -- dmesg on server shows bunch of
```
[Wed May 29 14:12:32 2024] lockd: server dbic-mrinbox not responding, still trying
[Wed May 29 14:12:32 2024] lockd: server dbic-mrinbox not responding, still trying
[Wed May 29 14:21:33 2024] lockd: server dbic-mrinbox not responding, still trying
[Wed May 29 14:23:34 2024] lockd: server dbic-mrinbox not responding, still trying
[Wed May 29 14:26:34 2024] lockd: server dbic-mrinbox not responding, still trying
```
although I can still read content just fine, so it is more specifically about locking I guess (despite using pidlock?)?
"""]]

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[[!comment format=mdwn
username="yarikoptic"
avatar="http://cdn.libravatar.org/avatar/f11e9c84cb18d26a1748c33b48c924b4"
subject="comment 7"
date="2024-05-30T14:29:43Z"
content="""
fixed in [10.20240129-86-g3475b09c3e AKA 10.20240227~29](https://git.kitenet.net/index.cgi/git-annex.git/commit/?id=3475b09c3e93ae7e5f21de02e7ada8f460e490a4) --[[yarikoptic]]
"""]]

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[[!comment format=mdwn
username="yarikoptic"
avatar="http://cdn.libravatar.org/avatar/f11e9c84cb18d26a1748c33b48c924b4"
subject="comment 8"
date="2024-05-30T14:34:32Z"
content="""
FWIW the trick with `.git/last-commit-msg` did not really work for me in direct use of git-annex as I guess annex introduces changes to git-annex when I do `git-annex add` first, so it takes then PRIOR commit message:
```
❯ git annex add random2
(recording state in git...)
add random2
ok
(recording state in git...)
❯ git commit -a
[master 16107604] Will be committing changes to following files: random2
1 file changed, 1 insertion(+)
create mode 120000 random2
❯ git show git-annex
commit dfb41b9b170e4d504e1e494538362e20bd73943a (git-annex)
Author: Yaroslav Halchenko <debian@onerussian.com>
Date: Thu May 30 10:31:46 2024 -0400
Will be committing changes to following files: random
diff --git a/a37/1c8/MD5E-s1000--288b6b2b44800acf433b76dc5889695c.log b/a37/1c8/MD5E-s1000--288b6b2b44800acf433b76dc5889695c.log
new file mode 100644
index 00000000..4a3787e6
--- /dev/null
+++ b/a37/1c8/MD5E-s1000--288b6b2b44800acf433b76dc5889695c.log
@@ -0,0 +1 @@
+1717079506s 1 fff52b70-2aa4-4d16-8377-97fee7b2de1c
❯ cat .git/last-commit-msg
Will be committing changes to following files: random2
❯ git lg HEAD^^..HEAD
* 16107604 - (HEAD -> master) Will be committing changes to following files: random2 (3 minutes ago) [Yaroslav Halchenko]
* d4840167 - Will be committing changes to following files: random (4 minutes ago) [Yaroslav Halchenko]
```
"""]]