Enough memory but OOM killer invoked?

MikeSkril asked:

It has been a long time since my old friend the OOM killer came to visit me. Now it is coming by once a week and I cannot figure out why it’s triggered. It doesn’t seem that I’m missing memory. What is causing that and what can be done to prevent that?

Kernel: 3.13.0-49-generic #83-Ubuntu SMP

Right before the OOM killer was triggered:

Fri Nov 16 01:45:01 EST 2018                                                                                                  
COMMAND         %MEM                                                                                                          
mysqld          17.2                                                                                                          
apache2          7.2                                                                                                          
spamd child      7.0                                                                                                          
apache2          7.0                                                                                                          
apache2          6.9                                                                                                          
apache2          6.8                                                                                                          
apache2          6.8                                                                                                          
apache2          6.6                                                                                                          
apache2          6.6                                                                                                          
apache2          6.4                                                                                                          
apache2          6.4                                                                                                          
/usr/sbin/spamd  6.4                                                                                                          
spamd child      6.2                                                                                                          
apache2          5.6                                                                                                          
opendkim         0.6                                                                                                          
horde-alarms     0.5                                                                                                          
fail2ban-server  0.5                                                                                                          
apache2          0.4                                                                                                          
munin-node       0.2                                                                                                          
pickup           0.1                                                                                                          
cron             0.1                                                                                                          
cron             0.1                                                                                                          
cron             0.1                                                                                                          
mem.sh           0.1                                                                                                          
init             0.1                                                                                                          
ps               0.1                                                                                                          
config           0.0                                                                                                          
tlsmgr           0.0         
ntpd             0.0                                                                                                          
qmgr             0.0                                                                                                          
sh               0.0                                                                                                          
sh               0.0                                                                                                          
sh               0.0                                                                                                          
systemd-logind   0.0                                                                                                          
dovecot          0.0                                                                                                          
auth             0.0                                                                                                          
whoopsie         0.0                                                                                                          
rsyslogd         0.0                                                                                                          
log              0.0                                                                                                          
vnstatd          0.0                                                                                                          
master           0.0                                                                                                          
dbus-daemon      0.0                                                                                                          
anvil            0.0                                                                                                          
cron             0.0                                                                                                          
upstart-file-br  0.0                                                                                                          
php5-fpm         0.0                                                                                                          
upstart-socket-  0.0                                                                                                          
upstart-udev-br  0.0                                                                                                          
memcached        0.0                                                                                                          
sshd             0.0                                                                                                          
shellinaboxd     0.0                                                                                                          
getty            0.0                                                                                                          
getty            0.0                                                                                                          
getty            0.0                                                                                                          
getty            0.0                                                                                                          
getty            0.0                                                                                                          
php5-fpm         0.0                                                                                                          
php5-fpm         0.0
/usr/sbin/postg  0.0                                                                                                          
getty            0.0                                                                                                          
systemd-udevd    0.0                                                                                                          
acpid            0.0                                                                                                          
opendkim         0.0                                                                                                          
kthreadd         0.0                                                                                                          
ksoftirqd/0      0.0                                                                                                          
kworker/0:0H     0.0                                                                                                          
rcu_sched        0.0                                                                                                          
rcuos/0          0.0                                                                                                          
rcu_bh           0.0                                                                                                          
rcuob/0          0.0                                                                                                          
migration/0      0.0                                                                                                          
watchdog/0       0.0                                                                                                          
khelper          0.0                                                                                                          
kdevtmpfs        0.0                                                                                                          
netns            0.0                                                                                                          
writeback        0.0                                                                                                          
kintegrityd      0.0                                                                                                          
bioset           0.0                                                                                                          
kworker/u3:0     0.0                                                                                                          
kblockd          0.0                                                                                                          
ata_sff          0.0                                                                                                          
khubd            0.0                                                                                                          
md               0.0                                                                                                          
devfreq_wq       0.0                                                                                                          
kworker/0:1      0.0                                                                                                          
khungtaskd       0.0                                                                                                          
kswapd0          0.0                                                                                                          
ksmd             0.0                                                                                                          
khugepaged       0.0                                                                                                          
fsnotify_mark    0.0
ecryptfs-kthrea  0.0                                                                                                          
crypto           0.0                                                                                                          
kthrotld         0.0                                                                                                          
vballoon         0.0                                                                                                          
scsi_eh_0        0.0                                                                                                          
scsi_eh_1        0.0                                                                                                          
deferwq          0.0                                                                                                          
charger_manager  0.0                                                                                                          
scsi_eh_2        0.0                                                                                                          
kpsmoused        0.0                                                                                                          
kworker/0:2      0.0                                                                                                          
ttm_swap         0.0                                                                                                          
qxl_gc           0.0                                                                                                          
jbd2/vda1-8      0.0                                                                                                          
ext4-rsv-conver  0.0                                                                                                          
kvm-irqfd-clean  0.0                                                                                                          
atd              0.0                                                                                                          
shellinaboxd     0.0                                                                                                          
managesieve-log  0.0                                                                                                          
kworker/u3:1     0.0                                                                                                          
kauditd          0.0                                                                                                          
kworker/u2:2     0.0                                                                                                          
kworker/u2:0     0.0                                                                                                          
Memory Space Details                                                                                                          
Total Memory space : 2018 MB                                                                                                  
Used Memory Space : 1055 MB                                                                                                   
Free Memory : 962 MB                                                                                                          
Swap memory Details                                                                                                           
Total Swap space : 1023 MB                                                                                                    
Used Swap Space : 164 MB                                                                                                      
Free Swap : 859 MB         
Node 0, zone      DMA      9     12      6      8      7      4      1      2      2      0      0                            
Node 0, zone    DMA32   2202    535    425    464    304     89     26     24     12      1      0 

Syslog:

Nov 16 01:46:34 foobar kernel: [2269670.312226] apache2 invoked oom-killer: gfp_mask=0x200da, order=0, oom_score_adj=0
Nov 16 01:46:34 foobar kernel: [2269670.312231] apache2 cpuset=/ mems_allowed=0
Nov 16 01:46:34 foobar kernel: [2269670.312234] CPU: 0 PID: 14040 Comm: apache2 Not tainted 3.13.0-49-generic #83-Ubuntu
Nov 16 01:46:34 foobar kernel: [2269670.312235] Hardware name: DigitalOcean Droplet, BIOS 20171212 12/12/2017
Nov 16 01:46:34 foobar kernel: [2269670.312237]  0000000000000000 ffff880003f3b988 ffffffff81721b36 ffff8800041f1800
Nov 16 01:46:34 foobar kernel: [2269670.312240]  ffff880003f3ba10 ffffffff8171c3f1 ffffffff81067996 ffff880003f3b9e8
Nov 16 01:46:34 foobar kernel: [2269670.312242]  ffffffff810c75dc 0000000000000000 ffff88003fff7e28 0000000000000000
Nov 16 01:46:34 foobar kernel: [2269670.312244] Call Trace:
Nov 16 01:46:34 foobar kernel: [2269670.312250]  [<ffffffff81721b36>] dump_stack+0x45/0x56
Nov 16 01:46:34 foobar kernel: [2269670.312257]  [<ffffffff8171c3f1>] dump_header+0x7f/0x1f1
Nov 16 01:46:34 foobar kernel: [2269670.312262]  [<ffffffff81067996>] ? put_online_cpus+0x56/0x80
Nov 16 01:46:34 foobar kernel: [2269670.312273]  [<ffffffff810c75dc>] ? rcu_oom_notify+0xcc/0xf0
Nov 16 01:46:34 foobar kernel: [2269670.312276]  [<ffffffff811529ce>] oom_kill_process+0x1ce/0x330
Nov 16 01:46:34 foobar kernel: [2269670.312280]  [<ffffffff812d75f5>] ? security_capable_noaudit+0x15/0x20
Nov 16 01:46:34 foobar kernel: [2269670.312282]  [<ffffffff81153104>] out_of_memory+0x414/0x450
Nov 16 01:46:34 foobar kernel: [2269670.312285]  [<ffffffff81159470>] __alloc_pages_nodemask+0xa60/0xb80
Nov 16 01:46:34 foobar kernel: [2269670.312289]  [<ffffffff81199dda>] alloc_pages_vma+0x9a/0x140
Nov 16 01:46:34 foobar kernel: [2269670.312292]  [<ffffffff8118c5ab>] read_swap_cache_async+0xeb/0x160
Nov 16 01:46:34 foobar kernel: [2269670.312294]  [<ffffffff8118c6b8>] swapin_readahead+0x98/0xe0
Nov 16 01:46:34 foobar kernel: [2269670.312297]  [<ffffffff8117a536>] handle_mm_fault+0xa76/0xf10
Nov 16 01:46:34 foobar kernel: [2269670.312301]  [<ffffffff8172db74>] __do_page_fault+0x184/0x570
Nov 16 01:46:34 foobar kernel: [2269670.312305]  [<ffffffff811ceb6f>] ? user_path_at_empty+0x5f/0x90
Nov 16 01:46:34 foobar kernel: [2269670.312308]  [<ffffffff810a02c5>] ? set_next_entity+0x95/0xb0
Nov 16 01:46:34 foobar kernel: [2269670.312312]  [<ffffffff8101260b>] ? __switch_to+0x16b/0x4d0
Nov 16 01:46:34 foobar kernel: [2269670.312314]  [<ffffffff8172df7a>] do_page_fault+0x1a/0x70
Nov 16 01:46:34 foobar kernel: [2269670.312316]  [<ffffffff8172d5e9>] do_async_page_fault+0x29/0xe0
Nov 16 01:46:34 foobar kernel: [2269670.312320] Mem-Info:
Nov 16 01:46:34 foobar kernel: [2269670.312321] Node 0 DMA per-cpu:
Nov 16 01:46:34 foobar kernel: [2269670.312323] CPU    0: hi:    0, btch:   1 usd:   0
Nov 16 01:46:34 foobar kernel: [2269670.312324] Node 0 DMA32 per-cpu:
Nov 16 01:46:34 foobar kernel: [2269670.312325] CPU    0: hi:  186, btch:  31 usd:  93
Nov 16 01:46:34 foobar kernel: [2269670.312329] active_anon:101755 inactive_anon:101941 isolated_anon:208
Nov 16 01:46:34 foobar kernel: [2269670.312329]  active_file:294 inactive_file:309 isolated_file:64
Nov 16 01:46:34 foobar kernel: [2269670.312329]  unevictable:0 dirty:0 writeback:63 unstable:0
Nov 16 01:46:34 foobar kernel: [2269670.312329]  free:12210 slab_reclaimable:2743 slab_unreclaimable:8287
Nov 16 01:46:34 foobar kernel: [2269670.312329]  mapped:2580 shmem:6561 pagetables:20656 bounce:0
Nov 16 01:46:34 foobar kernel: [2269670.312329]  free_cma:0
Nov 16 01:46:34 foobar kernel: [2269670.312331] Node 0 DMA free:4596kB min:704kB low:880kB high:1056kB active_anon:4844kB i
nactive_anon:5424kB active_file:0kB inactive_file:0kB unevictable:0kB isolated(anon):0kB isolated(file):0kB present:15992kB ma
naged:15908kB mlocked:0kB dirty:0kB writeback:0kB mapped:92kB shmem:96kB slab_reclaimable:64kB slab_unreclaimable:232kB kernel
_stack:40kB pagetables:684kB unstable:0kB bounce:0kB free_cma:0kB writeback_tmp:0kB pages_scanned:0 all_unreclaimable? yes
Nov 16 01:46:34 foobar kernel: [2269670.312336] lowmem_reserve[]: 0 975 975 975
Nov 16 01:46:34 foobar kernel: [2269670.312338] Node 0 DMA32 free:44244kB min:44348kB low:55432kB high:66520kB active_anon:
402176kB inactive_anon:402340kB active_file:1176kB inactive_file:1236kB unevictable:0kB isolated(anon):832kB isolated(file):25
6kB present:1032172kB managed:1001956kB mlocked:0kB dirty:0kB writeback:252kB mapped:10228kB shmem:26148kB slab_reclaimable:10
908kB slab_unreclaimable:32916kB kernel_stack:2520kB pagetables:81940kB unstable:0kB bounce:0kB free_cma:0kB writeback_tmp:0kB
 pages_scanned:10612 all_unreclaimable? yes
Nov 16 01:46:34 foobar kernel: [2269670.312342] lowmem_reserve[]: 0 0 0 0
Nov 16 01:46:34 foobar kernel: [2269670.312343] Node 0 DMA: 3*4kB (EM) 3*8kB (EM) 3*16kB (UE) 3*32kB (EM) 3*64kB (UMR) 3*12
8kB (UE) 3*256kB (UEM) 2*512kB (EM) 2*1024kB (EM) 0*2048kB 0*4096kB = 4596kB
Nov 16 01:46:34 foobar kernel: [2269670.312351] Node 0 DMA32: 297*4kB (EM) 610*8kB (UEM) 406*16kB (UEM) 234*32kB (UEM) 130*
64kB (UEM) 56*128kB (UEM) 20*256kB (UEM) 3*512kB (E) 0*1024kB 1*2048kB (R) 0*4096kB = 44244kB
Nov 16 01:46:34 foobar kernel: [2269670.312362] Node 0 hugepages_total=0 hugepages_free=0 hugepages_surp=0 hugepages_size=2
048kB
Nov 16 01:46:34 foobar kernel: [2269670.312363] 14604 total pagecache pages
Nov 16 01:46:34 foobar kernel: [2269670.312365] 7377 pages in swap cache
Nov 16 01:46:34 foobar kernel: [2269670.312366] Swap cache stats: add 2208965, delete 2201588, find 55272636/55445769
Nov 16 01:46:34 foobar kernel: [2269670.312367] Free swap  = 0kB
Nov 16 01:46:34 foobar kernel: [2269670.312367] Total swap = 1048572kB
Nov 16 01:46:34 foobar kernel: [2269670.312368] 262041 pages RAM
Nov 16 01:46:34 foobar kernel: [2269670.312369] 0 pages HighMem/MovableOnly
Nov 16 01:46:34 foobar kernel: [2269670.312370] 7554 pages reserved

Nov 16 01:46:34 foobar kernel: [2269670.312610] Out of memory: Kill process 1047 (mysqld) score 115 or sacrifice child
Nov 16 01:46:34 foobar kernel: [2269670.312637] Killed process 1047 (mysqld) total-vm:896532kB, anon-rss:103356kB, file-rss
:0kB
Nov 16 01:46:34 foobar kernel: [2269670.554632] init: mysql main process (1047) killed by KILL signal
Nov 16 01:46:34 foobar kernel: [2269670.554653] init: mysql main process ended, respawning
Nov 16 01:46:34 foobar kernel: [2269670.602286] audit_printk_skb: 9 callbacks suppressed
Nov 16 01:46:34 foobar kernel: [2269670.602290] type=1400 audit(1542350794.977:14): apparmor="STATUS" operation="profile_re
place" profile="unconfined" name="/usr/sbin/mysqld" pid=14117 comm="apparmor_parser"
Nov 16 01:46:37 foobar /etc/mysql/debian-start[14200]: Upgrading MySQL tables if necessary.
Nov 16 01:46:37 foobar /etc/mysql/debian-start[14204]: /usr/bin/mysql_upgrade: the '--basedir' option is always ignored
Nov 16 01:46:37 foobar /etc/mysql/debian-start[14204]: Looking for 'mysql' as: /usr/bin/mysql
Nov 16 01:46:37 foobar /etc/mysql/debian-start[14204]: Looking for 'mysqlcheck' as: /usr/bin/mysqlcheck
Nov 16 01:46:37 foobar /etc/mysql/debian-start[14204]: This installation of MySQL is already upgraded to 5.5.61, use --forc
e if you still need to run mysql_upgrade                                                                                      
Nov 16 01:46:37 foobar /etc/mysql/debian-start[14217]: Checking for insecure root accounts.
Nov 16 01:46:37 foobar /etc/mysql/debian-start[14223]: Triggering myisam-recover for all MyISAM tables
Nov 16 01:46:51 foobar kernel: [2269686.979583] apache2 invoked oom-killer: gfp_mask=0x200da, order=0, oom_score_adj=0
Nov 16 01:46:51 foobar kernel: [2269686.979588] apache2 cpuset=/ mems_allowed=0

My answer:


There’s a bunch of things you need to do here.

First, the OOM killer was triggered by apache2 asking for more memory than was available, not by mysqld. But because the mysqld process was using the most memory at the time, it was the process that got killed.

Consider setting the sysctl vm.oom_kill_allocating_task, which will cause the process that asked for the memory to be killed instead.

Second, you most likely have configured Apache with mpm_prefork and are running PHP as an Apache module. This setup is slow, underperforming, not thread safe, and when PHP fails, the failure gets blamed on other components because PHP is well hidden inside of Apache. Modern web server setups use php-fpm and either nginx or Apache with mpm_event. This will give you better performance and visibility into what PHP is doing (as it is most likely what is eating up all your memory).

Finally, your droplet appears to have 1GB RAM and 1GB swap. If you’re routinely running out, then your VM just may be too small. Consider adding RAM.


View the full question and any other answers on Server Fault.

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