diff --git a/doc/bugs/git-annex_precommit_.__gets_stuck_after_likely_interrupted___96__annex_add__96___call/comment_2_f5e21a674c54c5dc4c8474ce1b4ffaf1._comment b/doc/bugs/git-annex_precommit_.__gets_stuck_after_likely_interrupted___96__annex_add__96___call/comment_2_f5e21a674c54c5dc4c8474ce1b4ffaf1._comment new file mode 100644 index 0000000000..11b33946ab --- /dev/null +++ b/doc/bugs/git-annex_precommit_.__gets_stuck_after_likely_interrupted___96__annex_add__96___call/comment_2_f5e21a674c54c5dc4c8474ce1b4ffaf1._comment @@ -0,0 +1,21 @@ +[[!comment format=mdwn + username="yarikoptic" + avatar="http://cdn.libravatar.org/avatar/f11e9c84cb18d26a1748c33b48c924b4" + subject="reporting back" + date="2019-03-19T17:01:10Z" + content=""" +Removing .lck, setting `annex.pidlock=true` worked! got just one complaint from git: + +[[!format sh \"\"\" +$ git commit -m 'Committing staged changes after annex process was killed +> +> Also removed stale .git/annex/*.lck and now set annex.pidlock=True for the repo' +(recording state in git...) +git-annex: .git/annex/journal/e64_e4a_MD5E-s55076--a7352bf6fd37902fc1dfb6228f2e8a53.log: removeLink: does not exist (No such file or directory) + +\"\"\"]] +I found that file (via `find * -lname *MD5E-s55076--a7352bf6fd37902fc1dfb6228f2e8a53*` FTR), it was not known to git yet, so I am now running `annex add` on it (takes awhile -- I guess repo is indeed got large + NFS) -- will report back when done/if there is more. + + + +"""]] diff --git a/doc/bugs/git-annex_precommit_.__gets_stuck_after_likely_interrupted___96__annex_add__96___call/comment_3_028eca36967a89e5f479802499232a90._comment b/doc/bugs/git-annex_precommit_.__gets_stuck_after_likely_interrupted___96__annex_add__96___call/comment_3_028eca36967a89e5f479802499232a90._comment new file mode 100644 index 0000000000..3f8c80b6c9 --- /dev/null +++ b/doc/bugs/git-annex_precommit_.__gets_stuck_after_likely_interrupted___96__annex_add__96___call/comment_3_028eca36967a89e5f479802499232a90._comment @@ -0,0 +1,33 @@ +[[!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] +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] +15650 pts/50 Z+ 0:00 \_ [git] +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? + +"""]]