The kernel logs sound concerning to me and a cursory google search reveals some kernel bug tickets. Is there a time correlation there?
On Fri, May 10, 2013 at 1:13 PM, Brenden Matthews < [email protected]> wrote: > So after cat'ing around in /proc, I can see that the JVM is blocking on > disk I/O apparently: > > root@i-bde90adc:~# cat /proc/24689/status > > Name: java > > State: D (disk sleep) > > Tgid: 24689 > > Pid: 24689 > > PPid: 24629 > > TracerPid: 0 > > Uid: 997 997 997 997 > > Gid: 997 997 997 997 > > FDSize: 512 > > Groups: > > VmPeak: 2198700 kB > > VmSize: 2196016 kB > > VmLck: 0 kB > > VmPin: 0 kB > > VmHWM: 305276 kB > > VmRSS: 296828 kB > > VmData: 2040128 kB > > VmStk: 156 kB > > VmExe: 4 kB > > VmLib: 32692 kB > > VmPTE: 1292 kB > > VmSwap: 0 kB > > Threads: 104 > > SigQ: 0/180427 > > SigPnd: 0000000000000000 > > ShdPnd: 0000000000000000 > > SigBlk: 0000000000000000 > > SigIgn: 0000000000000000 > > SigCgt: 2000000181005ccf > > CapInh: 0000000000000000 > > CapPrm: 0000000000000000 > > CapEff: 0000000000000000 > > CapBnd: ffffffffffffffff > > Cpus_allowed: ffff > > Cpus_allowed_list: 0-15 > > Mems_allowed: 00000000,00000001 > > Mems_allowed_list: 0 > > voluntary_ctxt_switches: 25 > > nonvoluntary_ctxt_switches: 0 > > > > Mesos looks okay: > > root@i-bde90adc:~# cat /proc/3684/status > > Name: lt-mesos-slave > > State: S (sleeping) > > Tgid: 3684 > > Pid: 3684 > > PPid: 1131 > > TracerPid: 0 > > Uid: 0 0 0 0 > > Gid: 0 0 0 0 > > FDSize: 256 > > Groups: > > VmPeak: 1531868 kB > > VmSize: 1531864 kB > > VmLck: 0 kB > > VmPin: 0 kB > > VmHWM: 15272 kB > > VmRSS: 15272 kB > > VmData: 1402012 kB > > VmStk: 136 kB > > VmExe: 152 kB > > VmLib: 31824 kB > > VmPTE: 416 kB > > VmSwap: 0 kB > > Threads: 20 > > SigQ: 1/180427 > > SigPnd: 0000000000000000 > > ShdPnd: 0000000000000000 > > SigBlk: 0000000000000000 > > SigIgn: 0000000000000000 > > SigCgt: 0000000180000000 > > CapInh: 0000000000000000 > > CapPrm: ffffffffffffffff > > CapEff: ffffffffffffffff > > CapBnd: ffffffffffffffff > > Cpus_allowed: ffff > > Cpus_allowed_list: 0-15 > > Mems_allowed: 00000000,00000001 > > Mems_allowed_list: 0 > > voluntary_ctxt_switches: 69 > > nonvoluntary_ctxt_switches: 0 > > > Is it possible that changing the state of the freezer from thawed -> frozen > causes all disk I/O to stop? I'm not sure where to look to mitigate this. > > > On Fri, May 10, 2013 at 11:58 AM, Brenden Matthews < > [email protected]> wrote: > > > The kernel gives me a bunch of "soft lockup: CPU stuck!" and 'task java > > blocked for more than 120 seconds". I think these are fairly generic > > errors and can be caused by any sort of race condition on the system. > > Strace also isn't helpful, as it doesn't tell me which resource the > > processes are stuck on. > > > > I'll try and check /proc/pid/status next time it happens. Other tools > > like lsof are unable to run. > > > > > > On Fri, May 10, 2013 at 11:49 AM, Vinod Kone <[email protected]> > wrote: > > > >> ---------- Forwarded message ---------- > >> From: Vinod Kone <[email protected]> > >> Date: Fri, May 10, 2013 at 11:25 AM > >> Subject: Re: OOM killer stuck when freezing cgroup > >> To: "[email protected]" <[email protected]> > >> > >> > >> Anything in the kernel logs during this time? > >> > >> > >> @vinodkone > >> > >> > >> On Fri, May 10, 2013 at 11:13 AM, Benjamin Mahler < > >> [email protected] > >> > wrote: > >> > >> > Sorry about that miscommunication, I meant to say "from the kernel OOM > >> > killer", and you're right that the OOM shouldn't be the source of the > >> > problem here (just trying to make a mental note that our accounting is > >> > wrong), OOMs are indeed expected as part of normal operation on the > >> slave. > >> > > >> > It's tough to say what the issue is as I don't have any experience > >> running > >> > on newer kernels like 3.2, I would recommend augmenting the logging in > >> the > >> > cgroups::Freezer to try to nail down at which point the slave is > >> blocking. > >> > In particular, in Freezer::freeze() and Freezer::watchFrozen(). > >> > > >> > Also, do you have /proc/<slave_pid>/status output for the slave when > >> it's > >> > frozen? > >> > > >> > It will be really useful to know if that is consistently the last log > >> line > >> > you see before things lock up as well, as that helps narrow this down. > >> > > >> > > >> > On Fri, May 10, 2013 at 10:44 AM, Brenden Matthews < > >> > [email protected]> wrote: > >> > > >> > > This isn't a kernel OOM. I started the debugger and let it go > >> overnight > >> > > with no luck. It just doesn't want to budge. I'm aware of the > memory > >> > > limit issue, but I don't think that's the real problem here. > >> Regardless > >> > of > >> > > whether we run out of memory, the whole system shouldn't freeze when > >> > trying > >> > > to kill the process. I'm not sure if this is a kernel problem or a > >> Mesos > >> > > problem, but I suspect that the issue isn't with the kernel. > Walking > >> > > through the Mesos code, I can't see anything that is obviously wrong > >> > > either. I'm using my own branch from here: > >> > > https://github.com/airbnb/mesos/tree/testing. > >> > > > >> > > My next step will be to run a bunch of slaves in GDB and then launch > >> some > >> > > tasks. Hopefully I can stop them and get a backtrace. I thought it > >> > might > >> > > be worth asking about it here to see if anyone else has dealt with > >> this > >> > and > >> > > knows what's going on. > >> > > > >> > > These are EC2 instances running the latest Ubuntu Precise AMIs. > >> Here's > >> > the > >> > > `uname -a' from one: > >> > > > >> > > Linux i-b5dbc1d5 3.2.0-41-virtual #66-Ubuntu SMP Thu Apr 25 03:47:17 > >> UTC > >> > > 2013 x86_64 x86_64 x86_64 GNU/Linux > >> > > > >> > > > >> > > > >> > > > >> > > On Fri, May 10, 2013 at 10:21 AM, Benjamin Mahler < > >> > > [email protected] > >> > > > wrote: > >> > > > >> > > > Hey Brenden, what kernel version are you running? What version of > >> the > >> > > code > >> > > > are you running? Are you seeing this on different machines? Can > you > >> > > confirm > >> > > > you're unable to attach to the slave with gdb (that would be the > >> > easiest > >> > > > way to figure out what's blocking in the slave)? Is that always > the > >> > last > >> > > > line in the log before the processes get stuck? > >> > > > > >> > > > As an aside, it looks like we aren't properly setting the JVM heap > >> size > >> > > for > >> > > > TaskTrackers in the MesosScheduler for Hadoop. We try to estimate > >> the > >> > JVM > >> > > > memory overhead, but it was perhaps not enough to avoid kernel > OOMs. > >> > > > > >> > > > > >> > > > On Fri, May 10, 2013 at 9:57 AM, Brenden Matthews < > >> > > > [email protected]> wrote: > >> > > > > >> > > > > Hey folks, > >> > > > > > >> > > > > I'm bumping in to a problem frequently. When an executor > exceeds > >> its > >> > > > > memory limit and the executor is deemed in need of execution, > the > >> > > entire > >> > > > > system becomes stuck (though I'm unsure as to whether it's stuck > >> > before > >> > > > or > >> > > > > after attempting to freeze). Here's what the mesos slave log > >> looks > >> > > like: > >> > > > > > >> > > > > I0510 04:22:37.935608 13622 cgroups_isolator.cpp:1023] OOM > >> notifier > >> > is > >> > > > > > triggered for executor executor_Task_Tracker_446 of framework > >> > > > > > 201305100055-1471680778-5050-18199-0000 with uuid > >> > > > > > 14a21d5a-a670-40fd-91b1-54c42b9a30e0 > >> > > > > > I0510 04:22:37.935925 13622 cgroups_isolator.cpp:1068] OOM > >> detected > >> > > for > >> > > > > > executor executor_Task_Tracker_446 of framework > >> > > > > > 201305100055-1471680778-5050-18199-0000 with uuid > >> > > > > > 14a21d5a-a670-40fd-91b1-54c42b9a30e0 > >> > > > > > I0510 04:22:37.936982 13622 cgroups_isolator.cpp:1109] Memory > >> limit > >> > > > > > exceeded: Requested: 2570MB Used: 2570MB > >> > > > > > MEMORY STATISTICS: > >> > > > > > cache 1682083840 > >> > > > > > rss 1012756480 > >> > > > > > mapped_file 1085440 > >> > > > > > pgpgin 22863635 > >> > > > > > pgpgout 22205715 > >> > > > > > swap 0 > >> > > > > > pgfault 11881912 > >> > > > > > pgmajfault 304 > >> > > > > > inactive_anon 0 > >> > > > > > active_anon 1012756480 > >> > > > > > inactive_file 1065136128 > >> > > > > > active_file 616947712 > >> > > > > > unevictable 0 > >> > > > > > hierarchical_memory_limit 2694840320 > >> > > > > > hierarchical_memsw_limit 9223372036854775807 > >> > > > > > total_cache 1682083840 > >> > > > > > total_rss 1012756480 > >> > > > > > total_mapped_file 1085440 > >> > > > > > total_pgpgin 22863635 > >> > > > > > total_pgpgout 22205715 > >> > > > > > total_swap 0 > >> > > > > > total_pgfault 11881912 > >> > > > > > total_pgmajfault 304 > >> > > > > > total_inactive_anon 0 > >> > > > > > total_active_anon 1012756480 > >> > > > > > total_inactive_file 1065136128 > >> > > > > > total_active_file 616947712 > >> > > > > > total_unevictable 0 > >> > > > > > I0510 04:22:37.965666 13622 cgroups_isolator.cpp:620] Killing > >> > > executor > >> > > > > > executor_Task_Tracker_446 of framework > >> > > > > > 201305100055-1471680778-5050-18199-0000 > >> > > > > > I0510 04:22:37.967418 13621 cgroups.cpp:1175] Trying to freeze > >> > cgroup > >> > > > > > > >> > > > > > >> > > > > >> > > > >> > > >> > /cgroup/mesos/framework_201305100055-1471680778-5050-18199-0000_executor_executor_Task_Tracker_446_tag_14a21d5a-a670-40fd-91b1-54c42b9a30e0 > >> > > > > > >> > > > > > >> > > > > After the last line in the log, both the executing task and the > >> mesos > >> > > > > process are stuck indefinitely. Usually the way to resolve this > >> is > >> > > > > `killall -9 java lt-mesos-slave' or a reboot. > >> > > > > > >> > > > > If I cat /cgroup/mesos/framework.../freezer.state, it shows that > >> it's > >> > > > > freezing. Since the entire system is stuck, I cannot attach a > >> > debugger > >> > > > to > >> > > > > either the JVM or mesos. > >> > > > > > >> > > > > Any ideas? This problem is very frustrating and I'm stuck at > this > >> > > point. > >> > > > > > >> > > > > >> > > > >> > > >> > > > > >
