Docker container refuses to get killed after run command turns into a zombie

Question

first thing first. my system info and versions:

$ lsb_release -a
No LSB modules are available.
Distributor ID: Ubuntu
Description:    Ubuntu 13.04
Release:    13.04
Codename:   raring

$ sudo docker version
Client version: 0.9.0
Go version (client): go1.2.1
Git commit (client): 2b3fdf2
Server version: 0.9.0
Git commit (server): 2b3fdf2
Go version (server): go1.2.1

$ lxc-version
lxc version: 0.9.0

$ uname -a
Linux ip-10-0-2-86 3.8.0-19-generic #29-Ubuntu SMP Wed Apr 17 18:16:28 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux

I am not able to stop a container after the process inside of it becomes a zombie. After upgrading to to docker 0.9.0 I was seeing tons of zombies on my server. example:

$ ps axo stat,ppid,pid,comm | grep -w defunct
Zl   25327 25332 node <defunct>

$ pstree -p
init(1)─┬
        ├─sh(819)───docker(831)─┬
                                ├─lxc-start(25327)───node(25332)───{node}(25378)

I can see that lxc-start(25327) not calling wait() on the node process 25332 keeping to zombie alive. So I checked what it was doing with strace and it seemed to be stuck on a epoll_wait. stract actually gets stuck at first and just shows this:

$sudo strace -ir -ttt -T -v -p 25327
Process 25327 attached - interrupt to quit (when asked to kill)
     0.000103 [    7fe59b9d34b3] epoll_wait(8, 

but after I run a sudo docker kill 3da5764b7bc9358 I get more output:

 0.000103 [    7fe59b9d34b3] epoll_wait(8, {{EPOLLIN, {u32=21673408, u64=21673408}}}, 10, 4294967295) = 1 <8.935002>
 8.935097 [    7fe59bcaff60] accept(4, 0, NULL) = 9 <0.000035>
 0.000095 [    7fe59bcafeb3] fcntl(9, F_SETFD, FD_CLOEXEC) = 0 <0.000027>
 0.000083 [    7fe59b9d401a] setsockopt(9, SOL_SOCKET, SO_PASSCRED, [1], 4) = 0 <0.000027>
 0.000089 [    7fe59b9d347a] epoll_ctl(8, EPOLL_CTL_ADD, 9, {EPOLLIN, {u32=21673472, u64=21673472}}) = 0 <0.000023>
 0.000087 [    7fe59b9d34b3] epoll_wait(8, {{EPOLLIN, {u32=21673472, u64=21673472}}}, 10, 4294967295) = 1 <0.000026>
 0.000090 [    7fe59bcb0130] recvmsg(9, {msg_name(0)=NULL, msg_iov(1)=[{"\3\0\0\0\0\0\0\0", 8}], msg_controllen=32, {cmsg_len=28, cmsg_level=SOL_SOCKET, cmsg_type=SCM_CREDENTIALS{pid=773, uid=0, gid=0}}, msg_flags=0}, 0) = 8 <0.000034>
 0.000128 [    7fe59bcb019d] sendto(9, "\0\0\0\0\0\0\0\0\364b\0\0\0\0\0\0\0\0\0\0\0\0\0\0", 24, 0, NULL, 0) = 24 <0.000029>
 0.000090 [    7fe59b9d34b3] epoll_wait(8, {{EPOLLIN|EPOLLHUP, {u32=21673472, u64=21673472}}}, 10, 4294967295) = 1 <0.000018>
 0.000091 [    7fe59bcb0130] recvmsg(9, {msg_name(0)=NULL, msg_iov(1)=[{"\3\0\0\0\0\0\0\0", 8}], msg_controllen=32, {cmsg_len=28, cmsg_level=SOL_SOCKET, cmsg_type=SCM_CREDENTIALS{pid=0, uid=0, gid=0}}, msg_flags=0}, 0) = 0 <0.000026>
 0.000122 [    7fe59b9d347a] epoll_ctl(8, EPOLL_CTL_DEL, 9, NULL) = 0 <0.000037>
 0.000084 [    7fe59bcafd00] close(9) = 0 <0.000048>
 0.000103 [    7fe59b9d34b3] epoll_wait(8, {{EPOLLIN, {u32=21673408, u64=21673408}}}, 10, 4294967295) = 1 <1.091839>
 1.091916 [    7fe59bcaff60] accept(4, 0, NULL) = 9 <0.000035>
 0.000093 [    7fe59bcafeb3] fcntl(9, F_SETFD, FD_CLOEXEC) = 0 <0.000027>
 0.000083 [    7fe59b9d401a] setsockopt(9, SOL_SOCKET, SO_PASSCRED, [1], 4) = 0 <0.000026>
 0.000090 [    7fe59b9d347a] epoll_ctl(8, EPOLL_CTL_ADD, 9, {EPOLLIN, {u32=21673504, u64=21673504}}) = 0 <0.000032>
 0.000100 [    7fe59b9d34b3] epoll_wait(8, {{EPOLLIN, {u32=21673504, u64=21673504}}}, 10, 4294967295) = 1 <0.000028>
 0.000088 [    7fe59bcb0130] recvmsg(9, {msg_name(0)=NULL, msg_iov(1)=[{"\3\0\0\0\0\0\0\0", 8}], msg_controllen=32, {cmsg_len=28, cmsg_level=SOL_SOCKET, cmsg_type=SCM_CREDENTIALS{pid=774, uid=0, gid=0}}, msg_flags=0}, 0) = 8 <0.000030>
 0.000125 [    7fe59bcb019d] sendto(9, "\0\0\0\0\0\0\0\0\364b\0\0\0\0\0\0\0\0\0\0\0\0\0\0", 24, 0, NULL, 0) = 24 <0.000032>
 0.000119 [    7fe59b9d34b3] epoll_wait(8, {{EPOLLIN|EPOLLHUP, {u32=21673504, u64=21673504}}}, 10, 4294967295) = 1 <0.000071>
 0.000139 [    7fe59bcb0130] recvmsg(9, {msg_name(0)=NULL, msg_iov(1)=[{"\3\0\0\0\0\0\0\0", 8}], msg_controllen=32, {cmsg_len=28, cmsg_level=SOL_SOCKET, cmsg_type=SCM_CREDENTIALS{pid=0, uid=0, gid=0}}, msg_flags=0}, 0) = 0 <0.000018>
 0.000112 [    7fe59b9d347a] epoll_ctl(8, EPOLL_CTL_DEL, 9, NULL) = 0 <0.000028>
 0.000076 [    7fe59bcafd00] close(9) = 0 <0.000027>
 0.000096 [    7fe59b9d34b3] epoll_wait(8,

then I looked at what epoll_wait was waiting which looks like file 8 (i am guessing this from epoll_wait(8, {{EPOLLIN, {u32=21673408, u64=21673408}}}, 10, 4294967295) = 1 <8.935002> which is of the form int epoll_wait(int epfd, struct epoll_event *events, int maxevents, int timeout);

$ cat /proc/25327/fdinfo/8
pos:    0
flags:  02000002
tfd:        7 events:       19 data:          14ab830
tfd:        4 events:       19 data:          14ab5c0

also adding 7 and 4 based on tfd above (not sure what tfd really means)

$ cat /proc/25327/fdinfo/4
pos:    0
flags:  02000002
$ cat /proc/25327/fdinfo/7
pos:    0
flags:  02000002
sigmask:    fffffffe7ffbfab7
$ cd /proc/25327/fd
$ ls -al
lr-x------ 1 root root 64 Mar 13 22:28 0 -> /dev/null
lrwx------ 1 root root 64 Mar 13 22:28 1 -> /dev/pts/17
lrwx------ 1 root root 64 Mar 13 22:28 2 -> /dev/pts/17
l-wx------ 1 root root 64 Mar 13 22:28 3 -> /var/log/lxc/3da5764b7bc935896a72abc9371ce68d4d658d8c70b56e1090aacb631080ec0e.log
lrwx------ 1 root root 64 Mar 13 22:28 4 -> socket:[48415]
lrwx------ 1 root root 64 Mar 14 00:03 5 -> /dev/ptmx
lrwx------ 1 root root 64 Mar 14 00:03 6 -> /dev/pts/18
lrwx------ 1 root root 64 Mar 14 00:03 7 -> anon_inode:[signalfd]
lrwx------ 1 root root 64 Mar 14 00:03 8 -> anon_inode:[eventpoll]

info about socket:

$ sudo netstat -anp | grep 48415
Proto RefCnt Flags       Type       State         I-Node   PID/Program name    Path
unix  2      [ ACC ]     STREAM     LISTENING     48415    25327/lxc-start     @/var/lib/lxc/3da5764b7bc935896a72abc9371ce68d4d658d8c70b56e1090aacb631080ec0e/command

there does seem to be a common pattern in the docker.log all containers that do not stop have this signature:

2014/03/16 16:33:15 Container beb71548b3b23ba3337ca30c6c2efcbfcaf19d4638cf3d5ec5b8a3e4c5f1059a failed to exit within 0 seconds of SIGTERM - using the force
2014/03/16 16:33:25 Container SIGKILL failed to exit within 10 seconds of lxc-kill beb71548b3b2 - trying direct SIGKILL

At this point I have no idea what to do next. any suggestions on how I can find out what is causing these containers not exit? Any other data I should collect? I also sent a SIGCHLD to this process with no avail.

more data: added log to end of the node process we start using the start command in the container:

Mon Mar 17 2014 20:52:52 GMT+0000 (UTC) process: main process = exit code: 0

and here are logs from docker:

2014/03/17 20:52:52 Container f8a3d55e0f... failed to exit within 0 seconds of SIGTERM - using the force
2014/03/17 20:53:02 Container SIGKILL failed to exit within 10 seconds of lxc-kill f8a3d55e0fd8 - trying direct SIGKILL

timestamps show process exited @ 20:52:52

This happens using both native and lxc docker drivers.

EDIT: REPRO STEPS!

turn this into a bash script and run and watch almost 50% of the containers turn into zombies!

CNT=0
while true
do 
  echo $CNT
  DOCK=$(sudo docker run -d -t anandkumarpatel/zombie_bug ./node index.js)
  sleep 60 && sudo docker stop $DOCK > out.log &
  sleep 1
  CNT=$(($CNT+1))
  if [[ "$CNT" == "50" ]]; then
    exit
  fi
done

Answer 1

changing to latest kernel fixes the issue

found exact kernel difference:
REPRO: linux-image-3.8.0-31-generic
NO REPRO: linux-image-3.8.0-32-generic

I think this is the fix:

+++ linux-3.8.0/kernel/pid_namespace.c
@@ -181,6 +181,7 @@
    int nr;
    int rc;
    struct task_struct *task, *me = current;
+   int init_pids = thread_group_leader(me) ? 1 : 2;

    /* Don't allow any more processes into the pid namespace */
    disable_pid_allocation(pid_ns);
@@ -230,7 +231,7 @@
     */
    for (;;) {
        set_current_state(TASK_UNINTERRUPTIBLE);
-       if (pid_ns->nr_hashed == 1)
+       if (pid_ns->nr_hashed == init_pids)
            break;
        schedule();
    }

which came from here: https://groups.google.com/forum/#!msg/fa.linux.kernel/u4b3n4oYDQ4/GuLrXfDIYggJ

going to upgrade all our servers which repro this and see if it still occurs.

Answer 2

Observing not killable Docker container on SLES 12 SP 1 (was running since 3 weeks)

On docker exec -it command following error message:

rpc error: code = 13 desc = invalid header field value "oci runtime error: exec failed: container_linux.go:247: starting container process caused \"process_linux.go:83: executing setns process caused \\"exit status 16\\"\"\n"

Linux kernel: 3.12.62-60.64.8-default

Docker version 1.12.2, build 8eab29e