[[!comment format=mdwn
 username="joey"
 subject="""comment 7"""
 date="2019-03-20T15:52:45Z"
 content="""
Hard to see for sure from this strace tail end, but the fd number sequence
suggests it first took the pid lock:

lrwx------ 1 USER GROUP 64 Mar 19 17:03 11 -> /dev/shm/cd6281f9a8c5f62e1da78a60ca9ca1b4D_fmriprep001_.git_annex_pidlock.lck

And since it then seems to have proceeded to start to write to this file,
the pid lock is apparently not the hang point.

lrwx------ 1 USER GROUP 64 Mar 19 17:03 12 -> /zfs1/GROUP/USER/R03/WM-R03/DIAMOND/fmriprep001/.git/annex/misctmp/jlog15565-2

So stageJournal is running, after openjlog. That does not involve any
further locks, and would not normally take a long time unless 
.git/annex/journal/ has an unusual number of files in it. It seems to have
stalled for some reason. It should have started a git update-index process
and fed data into it.

Do you know if this process had a child git update-index running 
at this point? It could be that child is what is stalled, somehow.

The number of lines in the jlog15565-2 file would also be a clue to how far
 it got before it got stuck.

But I think a full strace may be needed to find the sticking point.
"""]]
