Package: git-annex
Version: 5.20141024
Severity: normal
I know that the version I have is outdated but it is not a regularly occuring
issue, so decided to investigate/report instead of just
kill/upgrade/restart. I have noted busy fan of the laptop, and saw that
31825 yoh 20 0 678276 53756 37872 S 103.7 0.3 57:26.39 git-annex
which monitors few (two) annex repositories is way too busy.
log file $HOME/annex/.git/annex/daemon.log is not growing with last entry about
inability to connect to remote box:
ssh: connect to host xxx.yyy.dartmouth.edu port 22: Connection timed out
fatal: Could not read from remote repository.
Please make sure you have the correct access rights
and the repository exists.
following files are open:
hopa:/proc/31825/fd
$> ls -l
total 0
lr-x------ 1 yoh yoh 64 Nov 24 08:58 0 -> /dev/null
l-wx------ 1 yoh yoh 64 Nov 24 08:58 1 -> /home/yoh/annex/.git/annex/daemon.log
lr-x------ 1 yoh yoh 64 Nov 24 08:58 10 -> anon_inode:inotify
lr-x------ 1 yoh yoh 64 Nov 24 08:58 11 -> /dev/null
lrwx------ 1 yoh yoh 64 Nov 24 21:31 12 -> socket:[1407919]
l-wx------ 1 yoh yoh 64 Nov 24 08:58 13 -> pipe:[981286]
lrwx------ 1 yoh yoh 64 Nov 24 08:58 14 -> socket:[979402]
lrwx------ 1 yoh yoh 64 Nov 24 08:58 15 -> /home/yoh/annex/.git/annex/daemon.pid
l-wx------ 1 yoh yoh 64 Nov 24 08:58 16 -> pipe:[981054]
lr-x------ 1 yoh yoh 64 Nov 24 08:58 17 -> pipe:[981055]
lrwx------ 1 yoh yoh 64 Nov 24 21:31 18 -> socket:[1411137]
lr-x------ 1 yoh yoh 64 Nov 24 08:58 19 -> anon_inode:inotify
l-wx------ 1 yoh yoh 64 Nov 24 08:58 2 -> /home/yoh/annex/.git/annex/daemon.log
lr-x------ 1 yoh yoh 64 Nov 24 08:58 20 -> anon_inode:inotify
lrwx------ 1 yoh yoh 64 Nov 24 08:58 21 -> socket:[981220]
l-wx------ 1 yoh yoh 64 Nov 24 08:58 22 -> pipe:[981218]
lr-x------ 1 yoh yoh 64 Nov 24 08:58 23 -> pipe:[981219]
lrwx------ 1 yoh yoh 64 Nov 24 08:58 24 -> socket:[981221]
lr-x------ 1 yoh yoh 64 Nov 24 08:58 25 -> anon_inode:inotify
lr-x------ 1 yoh yoh 64 Nov 24 08:58 26 -> pipe:[981287]
l-wx------ 1 yoh yoh 64 Nov 24 08:58 27 -> pipe:[980836]
lr-x------ 1 yoh yoh 64 Nov 24 08:58 28 -> pipe:[980837]
lr-x------ 1 yoh yoh 64 Nov 24 08:58 3 -> /dev/urandom
lrwx------ 1 yoh yoh 64 Nov 24 08:58 4 -> anon_inode:[eventpoll]
lr-x------ 1 yoh yoh 64 Nov 24 08:58 5 -> pipe:[978406]
l-wx------ 1 yoh yoh 64 Nov 24 08:58 6 -> pipe:[978406]
lrwx------ 1 yoh yoh 64 Nov 24 08:58 7 -> anon_inode:[eventfd]
lr-x------ 1 yoh yoh 64 Nov 24 08:58 8 -> /home/yoh/.config/git-annex/autostart
lrwx------ 1 yoh yoh 64 Nov 24 08:58 9 -> socket:[979773]
and according to strace
> strace -f -p 31825 2>&1 | head -100 | xsel -i
Process 31825 attached with 7 threads
[pid 10521] futex(0x7fa65000091c, FUTEX_WAIT_PRIVATE, 1, NULL <unfinished ...>
[pid 32172] futex(0x7fa65c00698c, FUTEX_WAIT_PRIVATE, 11, NULL <unfinished ...>
[pid 31848] futex(0x7fa65800091c, FUTEX_WAIT_PRIVATE, 3023, NULL <unfinished
...>
[pid 31829] futex(0x445e59c, FUTEX_WAIT_PRIVATE, 262485, NULL <unfinished ...>
[pid 31828] futex(0x445e38c, FUTEX_WAIT_PRIVATE, 304773, NULL <unfinished ...>
[pid 31825] futex(0x445e26c, FUTEX_WAIT_PRIVATE, 45, NULL) = ? ERESTARTSYS (To
be restarted if SA_RESTART is set)
[pid 31825] --- SIGVTALRM {si_signo=SIGVTALRM, si_code=SI_TIMER, si_timerid=0,
si_overrun=0, si_value={int=0, ptr=0}} ---
[pid 31825] rt_sigreturn( <unfinished ...>
[pid 31838] futex(0x445e59c, FUTEX_WAKE_OP_PRIVATE, 1, 1, 0x445e598,
{FUTEX_OP_SET, 0, FUTEX_OP_CMP_GT, 1} <unfinished ...>
[pid 31825] <... rt_sigreturn resumed> ) = 202
[pid 31838] <... futex resumed> ) = 1
[pid 31829] <... futex resumed> ) = 0
[pid 31838] futex(0x7fa6600009dc, FUTEX_WAIT_PRIVATE, 181307, NULL <unfinished
...>
[pid 31829] futex(0x445e5c8, FUTEX_WAKE_PRIVATE, 1 <unfinished ...>
[pid 31825] futex(0x445e26c, FUTEX_WAIT_PRIVATE, 45, NULL <unfinished ...>
[pid 31829] <... futex resumed> ) = 0
[pid 31825] <... futex resumed> ) = ? ERESTARTSYS (To be restarted if
SA_RESTART is set)
[pid 31825] --- SIGVTALRM {si_signo=SIGVTALRM, si_code=SI_TIMER, si_timerid=0,
si_overrun=0, si_value={int=0, ptr=0}} ---
[pid 31825] rt_sigreturn() = 202
[pid 31825] futex(0x445e26c, FUTEX_WAIT_PRIVATE, 45, NULL) = ? ERESTARTSYS (To
be restarted if SA_RESTART is set)
[pid 31825] --- SIGVTALRM {si_signo=SIGVTALRM, si_code=SI_TIMER, si_timerid=0,
si_overrun=0, si_value={int=0, ptr=0}} ---
[pid 31825] rt_sigreturn( <unfinished ...>
[pid 31829] futex(0x7fa6600009dc, FUTEX_WAKE_OP_PRIVATE, 1, 1, 0x7fa6600009d8,
{FUTEX_OP_SET, 0, FUTEX_OP_CMP_GT, 1} <unfinished ...>
[pid 31825] <... rt_sigreturn resumed> ) = 202
[pid 31829] <... futex resumed> ) = 1
[pid 31825] futex(0x445e26c, FUTEX_WAIT_PRIVATE, 45, NULL <unfinished ...>
[pid 31829] futex(0x445e59c, FUTEX_WAIT_PRIVATE, 262487, NULL <unfinished ...>
[pid 31838] <... futex resumed> ) = 0
[pid 31838] futex(0x7fa660000a08, FUTEX_WAKE_PRIVATE, 1) = 0
[pid 31825] <... futex resumed> ) = ? ERESTARTSYS (To be restarted if
SA_RESTART is set)
[pid 31825] --- SIGVTALRM {si_signo=SIGVTALRM, si_code=SI_TIMER, si_timerid=0,
si_overrun=0, si_value={int=0, ptr=0}} ---
[pid 31825] rt_sigreturn() = 202
[pid 31825] futex(0x445e26c, FUTEX_WAIT_PRIVATE, 45, NULL) = ? ERESTARTSYS (To
be restarted if SA_RESTART is set)
[pid 31825] --- SIGVTALRM {si_signo=SIGVTALRM, si_code=SI_TIMER, si_timerid=0,
si_overrun=0, si_value={int=0, ptr=0}} ---
[pid 31838] futex(0x445e59c, FUTEX_WAKE_OP_PRIVATE, 1, 1, 0x445e598,
{FUTEX_OP_SET, 0, FUTEX_OP_CMP_GT, 1} <unfinished ...>
[pid 31825] rt_sigreturn( <unfinished ...>
[pid 31838] <... futex resumed> ) = 1
[pid 31829] <... futex resumed> ) = 0
[pid 31838] futex(0x7fa6600009dc, FUTEX_WAIT_PRIVATE, 181309, NULL <unfinished
...>
[pid 31829] futex(0x445e5c8, FUTEX_WAKE_PRIVATE, 1 <unfinished ...>
[pid 31825] <... rt_sigreturn resumed> ) = 202
[pid 31829] <... futex resumed> ) = 0
[pid 31825] futex(0x445e26c, FUTEX_WAIT_PRIVATE, 45, NULL) = ? ERESTARTSYS (To
be restarted if SA_RESTART is set)
[pid 31825] --- SIGVTALRM {si_signo=SIGVTALRM, si_code=SI_TIMER, si_timerid=0,
si_overrun=0, si_value={int=0, ptr=0}} ---
[pid 31825] rt_sigreturn() = 202
[pid 31825] futex(0x445e26c, FUTEX_WAIT_PRIVATE, 45, NULL) = ? ERESTARTSYS (To
be restarted if SA_RESTART is set)
[pid 31825] --- SIGVTALRM {si_signo=SIGVTALRM, si_code=SI_TIMER, si_timerid=0,
si_overrun=0, si_value={int=0, ptr=0}} ---
[pid 31829] futex(0x7fa6600009dc, FUTEX_WAKE_OP_PRIVATE, 1, 1, 0x7fa6600009d8,
{FUTEX_OP_SET, 0, FUTEX_OP_CMP_GT, 1} <unfinished ...>
[pid 31825] rt_sigreturn( <unfinished ...>
[pid 31829] <... futex resumed> ) = 1
[pid 31838] <... futex resumed> ) = 0
[pid 31829] futex(0x445e59c, FUTEX_WAIT_PRIVATE, 262489, NULL <unfinished ...>
[pid 31838] futex(0x7fa660000a08, FUTEX_WAKE_PRIVATE, 1 <unfinished ...>
[pid 31825] <... rt_sigreturn resumed> ) = 202
[pid 31838] <... futex resumed> ) = 0
[pid 31825] futex(0x445e26c, FUTEX_WAIT_PRIVATE, 45, NULL) = ? ERESTARTSYS (To
be restarted if SA_RESTART is set)
[pid 31825] --- SIGVTALRM {si_signo=SIGVTALRM, si_code=SI_TIMER, si_timerid=0,
si_overrun=0, si_value={int=0, ptr=0}} ---
[pid 31825] rt_sigreturn() = 202
[pid 31825] futex(0x445e26c, FUTEX_WAIT_PRIVATE, 45, NULL) = ? ERESTARTSYS (To
be restarted if SA_RESTART is set)
[pid 31825] --- SIGVTALRM {si_signo=SIGVTALRM, si_code=SI_TIMER, si_timerid=0,
si_overrun=0, si_value={int=0, ptr=0}} ---
[pid 31838] futex(0x445e59c, FUTEX_WAKE_OP_PRIVATE, 1, 1, 0x445e598,
{FUTEX_OP_SET, 0, FUTEX_OP_CMP_GT, 1} <unfinished ...>
[pid 31825] rt_sigreturn( <unfinished ...>
[pid 31838] <... futex resumed> ) = 1
[pid 31829] <... futex resumed> ) = 0
[pid 31838] futex(0x7fa6600009dc, FUTEX_WAIT_PRIVATE, 181311, NULL <unfinished
...>
[pid 31829] futex(0x445e5c8, FUTEX_WAKE_PRIVATE, 1 <unfinished ...>
[pid 31825] <... rt_sigreturn resumed> ) = 202
[pid 31829] <... futex resumed> ) = 0
[pid 31825] futex(0x445e26c, FUTEX_WAIT_PRIVATE, 45, NULL) = ? ERESTARTSYS (To
be restarted if SA_RESTART is set)
[pid 31825] --- SIGVTALRM {si_signo=SIGVTALRM, si_code=SI_TIMER, si_timerid=0,
si_overrun=0, si_value={int=0, ptr=0}} ---
[pid 31825] rt_sigreturn() = 202
[pid 31825] futex(0x445e26c, FUTEX_WAIT_PRIVATE, 45, NULL) = ? ERESTARTSYS (To
be restarted if SA_RESTART is set)
[pid 31825] --- SIGVTALRM {si_signo=SIGVTALRM, si_code=SI_TIMER, si_timerid=0,
si_overrun=0, si_value={int=0, ptr=0}} ---
[pid 31829] futex(0x7fa6600009dc, FUTEX_WAKE_OP_PRIVATE, 1, 1, 0x7fa6600009d8,
{FUTEX_OP_SET, 0, FUTEX_OP_CMP_GT, 1} <unfinished ...>
[pid 31825] rt_sigreturn( <unfinished ...>
[pid 31838] <... futex resumed> ) = 0
[pid 31829] <... futex resumed> ) = 1
[pid 31838] futex(0x7fa660000a08, FUTEX_WAIT_PRIVATE, 2, NULL <unfinished ...>
[pid 31829] futex(0x7fa660000a08, FUTEX_WAKE_PRIVATE, 1 <unfinished ...>
[pid 31838] <... futex resumed> ) = -1 EAGAIN (Resource temporarily
unavailable)
[pid 31829] <... futex resumed> ) = 0
[pid 31838] futex(0x7fa660000a08, FUTEX_WAKE_PRIVATE, 1 <unfinished ...>
[pid 31829] futex(0x445e59c, FUTEX_WAIT_PRIVATE, 262491, NULL <unfinished ...>
[pid 31838] <... futex resumed> ) = 0
[pid 31825] <... rt_sigreturn resumed> ) = 202
[pid 31825] futex(0x445e26c, FUTEX_WAIT_PRIVATE, 45, NULL) = ? ERESTARTSYS (To
be restarted if SA_RESTART is set)
[pid 31825] --- SIGVTALRM {si_signo=SIGVTALRM, si_code=SI_TIMER, si_timerid=0,
si_overrun=0, si_value={int=0, ptr=0}} ---
[pid 31825] rt_sigreturn() = 202
[pid 31825] futex(0x445e26c, FUTEX_WAIT_PRIVATE, 45, NULL) = ? ERESTARTSYS (To
be restarted if SA_RESTART is set)
[pid 31825] --- SIGVTALRM {si_signo=SIGVTALRM, si_code=SI_TIMER, si_timerid=0,
si_overrun=0, si_value={int=0, ptr=0}} ---
[pid 31838] futex(0x445e59c, FUTEX_WAKE_OP_PRIVATE, 1, 1, 0x445e598,
{FUTEX_OP_SET, 0, FUTEX_OP_CMP_GT, 1} <unfinished ...>
[pid 31825] rt_sigreturn( <unfinished ...>
[pid 31838] <... futex resumed> ) = 1
[pid 31829] <... futex resumed> ) = 0
[pid 31838] futex(0x7fa6600009dc, FUTEX_WAIT_PRIVATE, 181313, NULL <unfinished
...>
[pid 31829] futex(0x445e5c8, FUTEX_WAKE_PRIVATE, 1 <unfinished ...>
[pid 31825] <... rt_sigreturn resumed> ) = 202
[pid 31829] <... futex resumed> ) = 0
[pid 31825] futex(0x445e26c, FUTEX_WAIT_PRIVATE, 45, NULL) = ? ERESTARTSYS (To
be restarted if SA_RESTART is set)
git annex webapp causes browser to start but there it is stuck at "Starting
webapp..."
here are annexes running (besides reportbug git-annex ;) )
$> ps auxw -H | grep -1 '[ ]git-annex'
yoh 1566 0.0 0.0 21132 3684 ? S Nov11 0:00 git
--git-dir=/home/yoh/annex/.git --work-tree=/home/yoh/annex cat-file --batch
yoh 1578 0.0 0.0 292812 6412 ? S Nov11 0:00 git-annex
assistant --startdelay=5s
yoh 1608 0.1 0.2 519176 43204 ? Sl Nov11 33:01 git-annex
assistant --startdelay=5s
yoh 1619 0.0 0.0 22172 4060 ? S Nov11 0:00 git
--git-dir=/home/yoh/deb/tarballs/.git --work-tree=/home/yoh/deb/tarballs
cat-file --batch
yoh 1696 0.0 0.1 444396 18328 ? SNl Nov11 0:00 git-annex
remotedaemon
yoh 1727 0.0 0.0 21128 3536 ? S Nov11 0:00 git
--git-dir=/home/yoh/deb/tarballs/.git --work-tree=/home/yoh/deb/tarballs
check-ignore -z --stdin --verbose --non-matching
--
yoh 31823 0.0 0.5 2074452 91832 ? Ssl Nov18 0:28
/home/yoh/.dropbox-dist/dropbox-lnx.x86_64-2.10.52/dropbox
yoh 31825 0.7 0.3 678276 53756 ? Sl Nov18 65:38 git-annex
assistant --startdelay=5s
yoh 31865 0.0 0.0 21188 3700 ? S Nov18 0:00 git
--git-dir=/home/yoh/annex/.git --work-tree=/home/yoh/annex cat-file --batch
yoh 32022 0.0 0.1 519152 20720 ? SNl Nov18 0:00 git-annex
remotedaemon
yoh 32171 0.0 0.0 27248 5348 ? SN Nov18 0:00 git
--git-dir=/home/yoh/annex/.git --work-tree=/home/yoh/annex cat-file --batch
I have killed 31825 and then started webapp succesfully which insists that the
beast is " Syncing with xxx.yyy.dartmouth.edu_annex, onerussian.com_annex"
(even if I "Shutdown daemon"). anyway -- CPU is now not 100% loaded so it must
be "ok".
FWIW that xxx.yyy.dartmouth.edu_annex is not reachable atm at all (need
to bring that poor sparc up again manually tomorrow).
-- System Information:
Debian Release: jessie/sid
APT prefers testing
APT policy: (900, 'testing'), (600, 'unstable'), (300, 'experimental')
Architecture: amd64 (x86_64)
Kernel: Linux 3.17-1-amd64 (SMP w/4 CPU cores)
Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash
Versions of packages git-annex depends on:
ii curl 7.38.0-3
ii git 1:2.1.1-1
ii libc6 2.19-12
ii libffi6 3.1-2
ii libgmp10 2:6.0.0+dfsg-6
ii libgnutls-deb0-28 3.3.8-3
ii libgsasl7 1.8.0-6
ii libicu52 52.1-6
ii libidn11 1.29-1
ii libxml2 2.9.1+dfsg1-4
ii libyaml-0-2 0.1.6-2
ii openssh-client 1:6.7p1-3
ii rsync 3.1.1-2+b1
ii wget 1.16-1
ii zlib1g 1:1.2.8.dfsg-2
Versions of packages git-annex recommends:
ii bind9-host 1:9.9.5.dfsg-5
ii git-remote-gcrypt 0.20130908-7
ii gnupg 1.4.18-4
ii lsof 4.86+dfsg-1
ii nocache 0.9-2
ii quvi 0.4.2-2
Versions of packages git-annex suggests:
pn bup <none>
ii graphviz 2.38.0-6
ii libnss-mdns 0.10-6
pn tahoe-lafs <none>
-- no debconf information
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