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yarikoptic 2018-11-12 16:48:08 +00:00 • committed by admin
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doc/bugs/multiple_ssh_prompts__44___and_thread_blocked_indefinitely_in_an___63____63____63___transaction/comment_4_817a9d27a0b15798671f4dc5cd661164._comment Normal file
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[[!comment format=mdwn
username="yarikoptic"
avatar="http://cdn.libravatar.org/avatar/f11e9c84cb18d26a1748c33b48c924b4"
subject="reply on the issue "
date="2018-11-12T16:48:08Z"
content="""
> (can't tell from your version string due to the git rev not being one from the git-annex repo)
patch for my \"custom\" version is now (if was not before) sent out -- needs adjustment in standalone patch
> As Andrew noted, the multiple ssh password prompt issue is expected if you are using GIT_SSH or GIT_SSH_COMMAND. From discussion in https://github.com/datalad/datalad/issues/2988 it seems like you might be?
in [a comment on that issue](https://github.com/datalad/datalad/issues/2988#issuecomment-437088252) I call `git annex` directly, so I think I did not have any custom env settings set... Moreover as I [commented further](https://github.com/datalad/datalad/issues/2988#issuecomment-437095621) nothing changed when I set `GIT_ANNEX_USE_GIT_SSH=1` which I guess should have counteracted?
I have tried now with `6.20170815+gitg22da64d0f-1~ndall+1` -- provides a single prompt.
Here is again output now also checking for SSH variables:
[[!format sh \"\"\"
[yhalchen@discovery7 QA]$ export | grep GIT
[yhalchen@discovery7 QA]$ git annex version | head -n 1
git-annex version: 6.20180926-gc906aaf
[yhalchen@discovery7 QA]$ git annex get -J2 sub-qa/
get sub-qa/ses-20161128/dwi/sub-qa_ses-20161128_acq-DTIX30Xp2Xs4_dwi.nii.gz get sub-qa/ses-20161128/dwi/sub-qa_ses-20161128_acq-DTIX30Xp2_dwi.nii.gz (from origin...)
(from origin...)
yoh@falkor.datalad.org's password: yoh@falkor.datalad.org's password:
\"\"\"]]
> ... suggests they you have annex.pidlock set locally. It would be good to know about this or other configuration.
smth like?
[[!format sh \"\"\"
[yhalchen@discovery7 QA]$ git config annex.pidlock
false
\"\"\"]]
I also no longer see that \"transfer already in progress...\" - may be I changed config since then:
[[!format sh \"\"\"
[yhalchen@discovery7 QA]$ git annex version | head -n1 ; git annex get -J2 sub-qa/
git-annex version: 7.20181105+git22-g4c7236c58-1~ndall+1
get sub-qa/ses-20161128/dwi/sub-qa_ses-20161128_acq-DTIX30Xp2Xs4_dwi.nii.gz get sub-qa/ses-20161128/dwi/sub-qa_ses-20161128_acq-DTIX30Xp2_dwi.nii.gz (from origin...)
(from origin...)
thread blocked indefinitely in an STM transaction
thread blocked indefinitely in an MVar operation
Unable to access these remotes: origin
Unable to access these remotes: origin
Try making some of these repositories available:
Try making some of these repositories available:
6384a551-a41d-4290-b186-9258befede97 -- bids@rolando:/inbox/BIDS/dbic/QA
6384a551-a41d-4290-b186-9258befede97 -- bids@rolando:/inbox/BIDS/dbic/QA
7d9ed214-3e5f-4cc8-ac88-f397145b2d4c -- yoh@falkor:/srv/datasets.datalad.org/www/dbic/QA [origin]
ba8f2cea-f229-422c-82be-6580e5e07ed5 -- yoh@smaug:/mnt/datasets/datalad/crawl/dbic/QA
7d9ed214-3e5f-4cc8-ac88-f397145b2d4c -- yoh@falkor:/srv/datasets.datalad.org/www/dbic/QA [origin]
failed
ba8f2cea-f229-422c-82be-6580e5e07ed5 -- yoh@smaug:/mnt/datasets/datalad/crawl/dbic/QA
failed
git-annex: thread blocked indefinitely in an STM transaction
\"\"\"]]
FWIW, I have now ran `git annex test` with TMPDIR on that partition, with
[[!format sh \"\"\"
157 out of 293 tests failed (686.03s)
\"\"\"]]
as the result. [HEre is the full log](http://www.onerussian.com/tmp/annex-test-7.20181105+git22-g4c7236c58.txt) -- may be it would give you some hints.
"""]]