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  1. Core Server
  2. SERVER-20159

Out of memory on index build during initial sync even with low cacheSize parameter

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    • Type: Icon: Bug Bug
    • Resolution: Done
    • Priority: Icon: Critical - P2 Critical - P2
    • 3.0.7, 3.1.9
    • Affects Version/s: 3.0.6
    • Component/s: WiredTiger
    • Environment:
      Debian Wheezy (7.7)
    • Fully Compatible
    • Linux

      When we try to rebuild a 3.0.6 replicaSet member the process mongod is killed by OOMKiller.

      • Reconstruction started at:
        2015/08/26-23h44: /etc/init.d/mongodb-rsm-uniq start
      • It stoped at 2015/08/27-07h21:

      /var/log/syslog:

      Aug 27 07:21:39 mongo-uniq1 kernel: mongod invoked oom-killer: gfp_mask=0x201da, order=0, oom_score_adj=0
Aug 27 07:21:39 mongo-uniq1 kernel: mongod cpuset=/ mems_allowed=0
Aug 27 07:21:39 mongo-uniq1 kernel: CPU: 7 PID: 4521 Comm: mongod Not tainted 3.10.23-xxxx-std-ipv6-64 #1
Aug 27 07:21:39 mongo-uniq1 kernel: Hardware name: Supermicro X9SRH-7F/7TF/X9SRH-7F/7TF, BIOS 3.00 07/05/2013
Aug 27 07:21:39 mongo-uniq1 kernel: 0000000000000000 ffff881fc3bb1918 ffffffff81d38724 ffff881fc3bb1998
Aug 27 07:21:39 mongo-uniq1 kernel: ffffffff81d328a8 ffff881fc3bb1998 ffff881fd02936e0 ffff881fd02936f8
Aug 27 07:21:39 mongo-uniq1 kernel: 0000000000000202 ffff881f00000000 0000000000000206 ffff881fc3bb1998
Aug 27 07:21:39 mongo-uniq1 kernel: Call Trace:
Aug 27 07:21:39 mongo-uniq1 kernel: [<ffffffff81d38724>] dump_stack+0x19/0x1b
Aug 27 07:21:39 mongo-uniq1 kernel: [<ffffffff81d328a8>] dump_header+0x75/0x1b9
Aug 27 07:21:39 mongo-uniq1 kernel: [<ffffffff81602326>] ? ___ratelimit+0x96/0x110
Aug 27 07:21:39 mongo-uniq1 kernel: [<ffffffff8112641f>] oom_kill_process+0x1bf/0x310
Aug 27 07:21:39 mongo-uniq1 kernel: [<ffffffff810c7422>] ? has_ns_capability_noaudit+0x12/0x20
Aug 27 07:21:39 mongo-uniq1 kernel: [<ffffffff81126b65>] out_of_memory+0x415/0x450
Aug 27 07:21:39 mongo-uniq1 kernel: [<ffffffff8112bad5>] __alloc_pages_nodemask+0x645/0x840
Aug 27 07:21:39 mongo-uniq1 kernel: [<ffffffff81159777>] alloc_pages_current+0xb7/0x180
Aug 27 07:21:39 mongo-uniq1 kernel: [<ffffffff81122f47>] __page_cache_alloc+0xa7/0xc0
Aug 27 07:21:39 mongo-uniq1 kernel: [<ffffffff81123b12>] filemap_fault+0x292/0x460
Aug 27 07:21:39 mongo-uniq1 kernel: [<ffffffff8113f90f>] __do_fault+0x6f/0x4c0
Aug 27 07:21:39 mongo-uniq1 kernel: [<ffffffff8114243b>] handle_pte_fault+0x8b/0x9f0
Aug 27 07:21:39 mongo-uniq1 kernel: [<ffffffff81182441>] ? set_fd_set+0x21/0x30
Aug 27 07:21:39 mongo-uniq1 kernel: [<ffffffff811831ed>] ? core_sys_select+0x23d/0x2f0
Aug 27 07:21:39 mongo-uniq1 kernel: [<ffffffff81143047>] handle_mm_fault+0x147/0x1e0
Aug 27 07:21:39 mongo-uniq1 kernel: [<ffffffff8106c391>] __do_page_fault+0x151/0x4b0
Aug 27 07:21:39 mongo-uniq1 kernel: [<ffffffff810e4f45>] ? check_preempt_curr+0x75/0xa0
Aug 27 07:21:39 mongo-uniq1 kernel: [<ffffffff810f18a7>] ? ktime_get_ts+0x47/0xe0
Aug 27 07:21:39 mongo-uniq1 kernel: [<ffffffff811823cc>] ? poll_select_copy_remaining+0xec/0x140
Aug 27 07:21:39 mongo-uniq1 kernel: [<ffffffff8106c719>] do_page_fault+0x9/0x10
Aug 27 07:21:39 mongo-uniq1 kernel: [<ffffffff81d41172>] page_fault+0x22/0x30
Aug 27 07:21:39 mongo-uniq1 kernel: Mem-Info:
Aug 27 07:21:39 mongo-uniq1 kernel: Node 0 DMA per-cpu:
Aug 27 07:21:39 mongo-uniq1 kernel: CPU    0: hi:    0, btch:   1 usd:   0
Aug 27 07:21:39 mongo-uniq1 kernel: CPU    1: hi:    0, btch:   1 usd:   0
Aug 27 07:21:39 mongo-uniq1 kernel: CPU    2: hi:    0, btch:   1 usd:   0
Aug 27 07:21:39 mongo-uniq1 kernel: CPU    3: hi:    0, btch:   1 usd:   0
Aug 27 07:21:39 mongo-uniq1 kernel: CPU    4: hi:    0, btch:   1 usd:   0
Aug 27 07:21:39 mongo-uniq1 kernel: CPU    5: hi:    0, btch:   1 usd:   0
Aug 27 07:21:39 mongo-uniq1 kernel: CPU    6: hi:    0, btch:   1 usd:   0
Aug 27 07:21:39 mongo-uniq1 kernel: CPU    7: hi:    0, btch:   1 usd:   0
Aug 27 07:21:39 mongo-uniq1 kernel: CPU    8: hi:    0, btch:   1 usd:   0
Aug 27 07:21:39 mongo-uniq1 kernel: CPU    9: hi:    0, btch:   1 usd:   0
Aug 27 07:21:39 mongo-uniq1 kernel: CPU   10: hi:    0, btch:   1 usd:   0
Aug 27 07:21:39 mongo-uniq1 kernel: CPU   11: hi:    0, btch:   1 usd:   0
Aug 27 07:21:39 mongo-uniq1 kernel: CPU   12: hi:    0, btch:   1 usd:   0
Aug 27 07:21:39 mongo-uniq1 kernel: CPU   13: hi:    0, btch:   1 usd:   0
Aug 27 07:21:39 mongo-uniq1 kernel: CPU   14: hi:    0, btch:   1 usd:   0
Aug 27 07:21:39 mongo-uniq1 kernel: CPU   15: hi:    0, btch:   1 usd:   0
Aug 27 07:21:39 mongo-uniq1 kernel: Node 0 DMA32 per-cpu:
Aug 27 07:21:39 mongo-uniq1 kernel: CPU    0: hi:  186, btch:  31 usd:   0
Aug 27 07:21:39 mongo-uniq1 kernel: CPU    1: hi:  186, btch:  31 usd:   0
Aug 27 07:21:39 mongo-uniq1 kernel: CPU    2: hi:  186, btch:  31 usd:   0
Aug 27 07:21:39 mongo-uniq1 kernel: CPU    3: hi:  186, btch:  31 usd:   0
Aug 27 07:21:39 mongo-uniq1 kernel: CPU    4: hi:  186, btch:  31 usd:   0
Aug 27 07:21:39 mongo-uniq1 kernel: CPU    5: hi:  186, btch:  31 usd:   0
Aug 27 07:21:39 mongo-uniq1 kernel: CPU    6: hi:  186, btch:  31 usd:   0
Aug 27 07:21:39 mongo-uniq1 kernel: CPU    7: hi:  186, btch:  31 usd:   0
Aug 27 07:21:39 mongo-uniq1 kernel: CPU    8: hi:  186, btch:  31 usd:   0
Aug 27 07:21:39 mongo-uniq1 kernel: CPU    9: hi:  186, btch:  31 usd:   0
Aug 27 07:21:39 mongo-uniq1 kernel: CPU   10: hi:  186, btch:  31 usd:   0
Aug 27 07:21:39 mongo-uniq1 kernel: CPU   11: hi:  186, btch:  31 usd:   0
Aug 27 07:21:39 mongo-uniq1 kernel: CPU   12: hi:  186, btch:  31 usd:   0
Aug 27 07:21:39 mongo-uniq1 kernel: CPU   13: hi:  186, btch:  31 usd:   0
Aug 27 07:21:39 mongo-uniq1 kernel: CPU   14: hi:  186, btch:  31 usd:   0
Aug 27 07:21:39 mongo-uniq1 kernel: CPU   15: hi:  186, btch:  31 usd:   0
Aug 27 07:21:39 mongo-uniq1 kernel: Node 0 Normal per-cpu:
Aug 27 07:21:39 mongo-uniq1 kernel: CPU    0: hi:  186, btch:  31 usd:   0
Aug 27 07:21:39 mongo-uniq1 kernel: CPU    1: hi:  186, btch:  31 usd:   0
Aug 27 07:21:39 mongo-uniq1 kernel: CPU    2: hi:  186, btch:  31 usd:   0
Aug 27 07:21:39 mongo-uniq1 kernel: CPU    3: hi:  186, btch:  31 usd:   0
Aug 27 07:21:39 mongo-uniq1 kernel: CPU    4: hi:  186, btch:  31 usd:   0
Aug 27 07:21:39 mongo-uniq1 kernel: CPU    5: hi:  186, btch:  31 usd:   0
Aug 27 07:21:39 mongo-uniq1 kernel: CPU    6: hi:  186, btch:  31 usd:   0
Aug 27 07:21:39 mongo-uniq1 kernel: CPU    7: hi:  186, btch:  31 usd:   0
Aug 27 07:21:39 mongo-uniq1 kernel: CPU    8: hi:  186, btch:  31 usd:   0
Aug 27 07:21:39 mongo-uniq1 kernel: CPU    9: hi:  186, btch:  31 usd:   0
Aug 27 07:21:39 mongo-uniq1 kernel: CPU   10: hi:  186, btch:  31 usd:   0
Aug 27 07:21:39 mongo-uniq1 kernel: CPU   11: hi:  186, btch:  31 usd:   0
Aug 27 07:21:39 mongo-uniq1 kernel: CPU   12: hi:  186, btch:  31 usd:   0
Aug 27 07:21:39 mongo-uniq1 kernel: CPU   13: hi:  186, btch:  31 usd:   0
Aug 27 07:21:39 mongo-uniq1 kernel: CPU   14: hi:  186, btch:  31 usd:   0
Aug 27 07:21:39 mongo-uniq1 kernel: CPU   15: hi:  186, btch:  31 usd:   0
Aug 27 07:21:39 mongo-uniq1 kernel: active_anon:31550706 inactive_anon:1013370 isolated_anon:128
Aug 27 07:21:39 mongo-uniq1 kernel: active_file:134 inactive_file:0 isolated_file:0
Aug 27 07:21:39 mongo-uniq1 kernel: unevictable:0 dirty:0 writeback:7 unstable:0
Aug 27 07:21:39 mongo-uniq1 kernel: free:142436 slab_reclaimable:5981 slab_unreclaimable:15205
Aug 27 07:21:39 mongo-uniq1 kernel: mapped:254 shmem:0 pagetables:69074 bounce:0
Aug 27 07:21:39 mongo-uniq1 kernel: free_cma:0
Aug 27 07:21:39 mongo-uniq1 kernel: Node 0 DMA free:15892kB min:4kB low:4kB high:4kB active_anon:0kB inactive_anon:0kB active_file:0kB inactive_file:0kB unevictable:0k
B isolated(anon):0kB isolated(file):0kB present:15976kB managed:15892kB mlocked:0kB dirty:0kB writeback:0kB mapped:0kB shmem:0kB slab_reclaimable:0kB slab_unreclaimabl
e:0kB kernel_stack:0kB pagetables:0kB unstable:0kB bounce:0kB free_cma:0kB writeback_tmp:0kB pages_scanned:0 all_unreclaimable? yes
Aug 27 07:21:39 mongo-uniq1 kernel: lowmem_reserve[]: 0 1978 128952 128952
Aug 27 07:21:39 mongo-uniq1 kernel: Node 0 DMA32 free:508600kB min:704kB low:880kB high:1056kB active_anon:1133036kB inactive_anon:377844kB active_file:0kB inactive_fi
le:0kB unevictable:0kB isolated(anon):0kB isolated(file):0kB present:2046684kB managed:2026228kB mlocked:0kB dirty:0kB writeback:0kB mapped:0kB shmem:0kB slab_reclaima
ble:1076kB slab_unreclaimable:3512kB kernel_stack:16kB pagetables:2944kB unstable:0kB bounce:0kB free_cma:0kB writeback_tmp:0kB pages_scanned:0 all_unreclaimable? yes
Aug 27 07:21:39 mongo-uniq1 kernel: lowmem_reserve[]: 0 0 126974 126974
Aug 27 07:21:39 mongo-uniq1 kernel: Node 0 Normal free:45252kB min:45252kB low:56564kB high:67876kB active_anon:125069788kB inactive_anon:3675636kB active_file:540kB i
nactive_file:0kB unevictable:0kB isolated(anon):512kB isolated(file):0kB present:132120576kB managed:130021460kB mlocked:0kB dirty:0kB writeback:28kB mapped:1020kB shm
em:0kB slab_reclaimable:22848kB slab_unreclaimable:57308kB kernel_stack:2888kB pagetables:273352kB unstable:0kB bounce:0kB free_cma:0kB writeback_tmp:0kB pages_scanned
:1881 all_unreclaimable? yes
Aug 27 07:21:39 mongo-uniq1 kernel: lowmem_reserve[]: 0 0 0 0
Aug 27 07:21:39 mongo-uniq1 kernel: Node 0 DMA: 1*4kB (U) 0*8kB 1*16kB (U) 0*32kB 2*64kB (U) 1*128kB (U) 1*256kB (U) 0*512kB 1*1024kB (U) 1*2048kB (U) 3*4096kB (MR) =
15892kB
Aug 27 07:21:39 mongo-uniq1 kernel: Node 0 DMA32: 101*4kB (UEM) 42*8kB (UEM) 49*16kB (UE) 167*32kB (UE) 110*64kB (UEM) 69*128kB (UEM) 46*256kB (UE) 36*512kB (UE) 31*10
24kB (UE) 23*2048kB (UE) 92*4096kB (UEMR) = 508628kB
Aug 27 07:21:39 mongo-uniq1 kernel: Node 0 Normal: 9505*4kB (UEM) 81*8kB (EM) 19*16kB (M) 25*32kB (MR) 9*64kB (MR) 8*128kB (R) 2*256kB (R) 1*512kB (R) 0*1024kB 0*2048k
B 1*4096kB (R) = 46492kB
Aug 27 07:21:39 mongo-uniq1 kernel: 10662 total pagecache pages
Aug 27 07:21:39 mongo-uniq1 kernel: 10178 pages in swap cache
Aug 27 07:21:39 mongo-uniq1 kernel: Swap cache stats: add 21060325, delete 21050147, find 47193946/47244483
Aug 27 07:21:39 mongo-uniq1 kernel: Free swap  = 0kB
Aug 27 07:21:39 mongo-uniq1 kernel: Total swap = 9789436kB
Aug 27 07:21:39 mongo-uniq1 kernel: 33554431 pages RAM
Aug 27 07:21:39 mongo-uniq1 kernel: 538296 pages reserved
Aug 27 07:21:39 mongo-uniq1 kernel: 4190101 pages shared
Aug 27 07:21:39 mongo-uniq1 kernel: 32870580 pages non-shared
Aug 27 07:21:39 mongo-uniq1 kernel: [ pid ]   uid  tgid total_vm      rss nr_ptes swapents oom_score_adj name
Aug 27 07:21:39 mongo-uniq1 kernel: [ 2700]     0  2700 5360        1      15      165         -1000 udevd
Aug 27 07:21:39 mongo-uniq1 kernel: [ 4455]     0  4455 50367      570      36      740             0 rsyslogd
Aug 27 07:21:39 mongo-uniq1 kernel: [ 4521]   106  4521 121313      559      90     7851             0 mongod
Aug 27 07:21:39 mongo-uniq1 kernel: [ 4598]     0  4598 3248        0      10       36             0 mdadm
Aug 27 07:21:39 mongo-uniq1 kernel: [ 4637]   103  4637 9769       29      23      132             0 ntpd
Aug 27 07:21:39 mongo-uniq1 kernel: [ 4646]     0  4646 5129       52      14       25             0 irqbalance
Aug 27 07:21:39 mongo-uniq1 kernel: [ 4660]   101  4660 78549      481      71     7365             0 named
Aug 27 07:21:39 mongo-uniq1 kernel: [ 4664]     0  4664 12484       27      26      124         -1000 sshd
Aug 27 07:21:39 mongo-uniq1 kernel: [ 4838]     0  4838 5224       22      14       40             0 cron
Aug 27 07:21:39 mongo-uniq1 kernel: [ 4925]     0  4925 1030        0       7       36             0 acpid
Aug 27 07:21:39 mongo-uniq1 kernel: [ 4974]     0  4974 37265      452      33     1045             0 fail2ban-server
Aug 27 07:21:39 mongo-uniq1 kernel: [ 4994]     0  4994 12283      307      27     1545             0 munin-node
Aug 27 07:21:39 mongo-uniq1 kernel: [ 5055]     0  5055 5987      104      16      412             0 gam_server
Aug 27 07:21:39 mongo-uniq1 kernel: [ 5308]     0  5308 4186        0      12       39             0 getty
Aug 27 07:21:39 mongo-uniq1 kernel: [ 5309]     0  5309 4186        0      13       38             0 getty
Aug 27 07:21:39 mongo-uniq1 kernel: [ 5310]     0  5310 4186        0      12       38             0 getty
Aug 27 07:21:39 mongo-uniq1 kernel: [ 5311]     0  5311 4186        0      12       38             0 getty
Aug 27 07:21:39 mongo-uniq1 kernel: [ 5312]     0  5312 4186        0      12       38             0 getty
Aug 27 07:21:39 mongo-uniq1 kernel: [ 5313]     0  5313 4186        0      12       38             0 getty
Aug 27 07:21:39 mongo-uniq1 kernel: [ 5315]     0  5315 5359        0      14      165         -1000 udevd
Aug 27 07:21:39 mongo-uniq1 kernel: [ 5316]     0  5316 5359        0      14      165         -1000 udevd
Aug 27 07:21:39 mongo-uniq1 kernel: [16237]   106 16237    58006 13576      85    10814             0 mongos
Aug 27 07:21:39 mongo-uniq1 kernel: [19001]   106 19001   221422 1667     144     6120             0 mongod
Aug 27 07:21:39 mongo-uniq1 kernel: [ 2001]   107  2001 6332        8      16      122             0 nrpe
Aug 27 07:21:39 mongo-uniq1 kernel: [11628]     0 11628 17816       28      38      179             0 sshd
Aug 27 07:21:39 mongo-uniq1 kernel: [11630]     0 11630 5103        1      13      255             0 bash
Aug 27 07:21:39 mongo-uniq1 kernel: [ 2912]     0  2912 1530       11       7       16             0 tail
Aug 27 07:21:39 mongo-uniq1 kernel: [22462]   106 22462 35077302 32535764   68347  2410259             0 mongod
Aug 27 07:21:39 mongo-uniq1 kernel: Out of memory: Kill process 22462 (mongod) score 987 or sacrifice child
Aug 27 07:21:39 mongo-uniq1 kernel: Killed process 22462 (mongod) total-vm:140309208kB, anon-rss:130143056kB, file-rss:0kB

      /var/log/syslog:

      [...]
2015-08-27T07:21:01.010+0200 I -        [rsSync]   Index Build: 3580500/15695121 22%
2015-08-27T07:21:01.463+0200 I NETWORK  [conn2376] end connection 172.16.21.2:55126 (4 connections now open)
2015-08-27T07:21:01.472+0200 I NETWORK  [initandlisten] connection accepted from 172.16.21.2:55128 #2378 (5 connections now open)
2015-08-27T07:21:04.007+0200 I -        [rsSync]   Index Build: 3613100/15695121 23%
2015-08-27T07:21:07.006+0200 I -        [rsSync]   Index Build: 3647100/15695121 23%
2015-08-27T07:21:10.007+0200 I -        [rsSync]   Index Build: 3680300/15695121 23%
2015-08-27T07:21:13.015+0200 I -        [rsSync]   Index Build: 3710300/15695121 23%
2015-08-27T07:21:16.015+0200 I -        [rsSync]   Index Build: 3736700/15695121 23%
2015-08-27T07:21:19.007+0200 I -        [rsSync]   Index Build: 3764300/15695121 23%
2015-08-27T07:21:19.214+0200 I NETWORK  [initandlisten] connection accepted from 172.16.21.3:53807 #2379 (6 connections now open)
2015-08-27T07:21:19.218+0200 I NETWORK  [conn2377] end connection 172.16.21.3:53803 (5 connections now open)
2015-08-27T07:21:22.021+0200 I -        [rsSync]   Index Build: 3790300/15695121 24%
2015-08-27T07:21:25.035+0200 I -        [rsSync]   Index Build: 3805100/15695121 24%
2015-08-27T07:21:25.418+0200 I COMMAND  [conn2379] command admin.$cmd command: replSetHeartbeat { replSetHeartbeat: "uniq", pv: 1, v: 7, from: "172.16.21.3:27020", fromId: 2, checkEmpty: false } ntoreturn:1 keyUpdates:0 writeConflicts:0 numYields:0 reslen:149 locks:{} 184ms
2015-08-27T07:21:28.012+0200 I -        [rsSync]   Index Build: 3827600/15695121 24%
2015-08-27T07:21:31.011+0200 I -        [rsSync]   Index Build: 3850500/15695121 24%
2015-08-27T07:21:31.877+0200 I NETWORK  [initandlisten] connection accepted from 172.16.21.2:55130 #2380 (6 connections now open)
2015-08-27T07:21:31.884+0200 I NETWORK  [conn2378] end connection 172.16.21.2:55128 (5 connections now open)
2015-08-27T07:21:34.007+0200 I -        [rsSync]   Index Build: 3873400/15695121 24%
2015-08-27T07:21:37.016+0200 I -        [rsSync]   Index Build: 3897400/15695121 24%
(END)

      /var/log/mongodb/mongodb.log:

      mongo-wt.conf we use:

$ cat /etc/mongod-wt.conf
storage:
   dbPath: /var/lib/mongodb
   engine: wiredTiger
   wiredTiger.engineConfig.cacheSizeGB: 1

systemLog:
   destination: file
   path: /var/log/mongodb/mongodb.log
   logAppend: true


net:
   bindIp: 172.16.21.1
   http:
      enabled: false

      We use:

      • Debian Wheezy 7.7.
      • MongoDB 3.0.6

      I've attached a RAM graph to this thread.
      We can see Mongod using 1GB at first, and then saturate the available memory (128GB).

        1. mongodb_crash.tar.gz
          3.91 MB
          Anthony Pastor
        2. RAM_Graph_MongoDB.png
          62 kB
          Anthony Pastor
        3. spike.png
          148 kB
          Ramon Fernandez Marina
        4. stats.html
          427 kB
          Ramon Fernandez Marina
        5. WiredTigerStat.11.15.gz
          109 kB
          Ramon Fernandez Marina

            Assignee:
            michael.cahill@mongodb.com Michael Cahill (Inactive)
            Reporter:
            anthony@stickyads.tv Anthony Pastor
            Votes:
            0 Vote for this issue
            Watchers:
            13 Start watching this issue

              Created:
              Updated:
              Resolved: