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yarikoptic 2019-03-19 17:41:12 +00:00 • committed by admin
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[[!comment format=mdwn
username="yarikoptic"
avatar="http://cdn.libravatar.org/avatar/f11e9c84cb18d26a1748c33b48c924b4"
subject="comment 3"
date="2019-03-19T17:41:12Z"
content="""
Managed to login to that node again, after hours (>3) of \"running\" `annex add` is still there with current process tree being
[[!format sh \"\"\"
PID TTY STAT TIME COMMAND
22168 pts/50 Ss 0:00 /bin/bash
15560 pts/50 S+ 0:00 \_ git annex add freesurfer/sub-000458/label/lh.BA4p_exvivo.thresh.label
15565 pts/50 Dl+ 0:18 \_ /ihome/crc/install/datalad/python3.7/bin/git-annex add freesurfer/sub-000458/label/lh.BA4p_exvivo.thresh.label
15591 pts/50 Z+ 0:00 \_ [git] <defunct>
15601 pts/50 S+ 0:00 \_ git --git-dir=.git --work-tree=. --literal-pathspecs check-attr -z --stdin annex.backend annex.numcopies annex.largefiles --
15625 pts/50 S+ 0:00 \_ git --git-dir=.git --work-tree=. --literal-pathspecs cat-file --batch
15626 pts/50 S+ 0:00 \_ git --git-dir=.git --work-tree=. --literal-pathspecs cat-file --batch-check=%(objectname) %(objecttype) %(objectsize)
15642 pts/50 Z+ 0:00 \_ [git] <defunct>
15650 pts/50 Z+ 0:00 \_ [git] <defunct>
15703 pts/50 S+ 0:02 \_ git --git-dir=.git --work-tree=. --literal-pathspecs hash-object -w --stdin-paths --no-filters
\"\"\"]]
and all the locks there, and I believe being generated by this `annex add` run:
[[!format sh \"\"\"
$ /bin/ls .git/annex/
index index.lck journal journal.lck misctmp objects pidlock precommit.lck sentinal sentinal.cache
\"\"\"]]
the process 15565 is slowly increasing its seconds (now 19)... is that a good sign (no lockup, just very slow IO) or not (it is locked up, and all the time corresponds just to the periodic querying of the lock)? if to strace -- which particular process? or should I interrupt and run the entire `annex add` under strace?
"""]]