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  1. Core Server
  2. SERVER-6141

can't successfully replicate our shards anymore. replication isn't using memory efficiently and linux is invoking oom_killer to kill mongod. servers replicated earlier on same config (with smaller data sets) are still working fine...

    • Type: Icon: Bug Bug
    • Resolution: Duplicate
    • Priority: Icon: Blocker - P1 Blocker - P1
    • None
    • Affects Version/s: 2.0.6
    • Component/s: Replication
    • None
    • Environment:
      centos 6
    • Linux

      We have an issue with replication that is preventing us from successfully adding any new nodes to the replica sets in our main mongo sharded (4 shards) cluster... the team here is evaluating moving to a different db platform but I'm hoping that there's a patch or workaround that will allow us to continue growing the cluster without needing to boot up new boxes with double the RAM just to successfully replicate.

      From a new box (dual Core 8gb vm instance on Joyentcloud running centos 6), we installed the latest mongo 2.0.6 and started replication for the shard... the external sort finished but then mongo eventually crashed... here's the end of the mongo log from /var/log/mongo/mongod.log .

      (Note how fast it was going initially and then how slow it got near the end. took 23 minutes to get to 80% and then 3 hours or so to get from 80% to 89% before it crashed.)

      Wed Jun 20 02:04:51 [rsSync] external sort used : 113 files in 728 secs
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      Wed Jun 20 02:09:54 [FileAllocator] allocating new datafile /data/mongo/chartboost.23, filling with zeroes...
      Wed Jun 20 02:09:54 [FileAllocator] done allocating datafile /data/mongo/chartboost.23, size: 2047MB, took 0.022 secs
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      Wed Jun 20 02:13:53 [conn2] command admin.$cmd command:

      { writebacklisten: ObjectId('4fcf6f27fb0b7403c30c7021') }

      ntoreturn:1 reslen:44 300000ms
      40792200/111903891 36%
      Wed Jun 20 02:14:02 [conn22] command admin.$cmd command:

      { writebacklisten: ObjectId('4fcf6ee0c637de224e7ecb5d') }

      ntoreturn:1 reslen:44 300000ms
      Wed Jun 20 02:14:03 [conn23] command admin.$cmd command:

      { writebacklisten: ObjectId('4fbc4fe47fc06f85f192440a') }

      ntoreturn:1 reslen:44 300000ms
      41561700/111903891 37%
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      Wed Jun 20 02:14:26 [rsSync] old journal file will be removed: /data/mongo/journal/j._19
      43119100/111903891 38%
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      Wed Jun 20 02:15:25 [FileAllocator] allocating new datafile /data/mongo/chartboost.24, filling with zeroes...
      Wed Jun 20 02:15:25 [FileAllocator] done allocating datafile /data/mongo/chartboost.24, size: 2047MB, took 0.017 secs
      47653800/111903891 42%
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      Wed Jun 20 02:18:53 [conn2] command admin.$cmd command:

      { writebacklisten: ObjectId('4fcf6f27fb0b7403c30c7021') }

      ntoreturn:1 reslen:44 300001ms
      62555700/111903891 55%
      Wed Jun 20 02:19:02 [conn22] command admin.$cmd command:

      { writebacklisten: ObjectId('4fcf6ee0c637de224e7ecb5d') }

      ntoreturn:1 reslen:44 300000ms
      Wed Jun 20 02:19:03 [conn23] command admin.$cmd command:

      { writebacklisten: ObjectId('4fbc4fe47fc06f85f192440a') }

      ntoreturn:1 reslen:44 300000ms
      63141000/111903891 56%
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      Wed Jun 20 02:19:44 [FileAllocator] allocating new datafile /data/mongo/chartboost.25, filling with zeroes...
      Wed Jun 20 02:19:44 [FileAllocator] done allocating datafile /data/mongo/chartboost.25, size: 2047MB, took 0.039 secs
      65603700/111903891 58%
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      Wed Jun 20 02:21:57 [rsSync] old journal file will be removed: /data/mongo/journal/j._20
      Wed Jun 20 02:21:57 [rsSync] old journal file will be removed: /data/mongo/journal/j._21
      73429700/111903891 65%
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      Wed Jun 20 02:23:53 [conn2] command admin.$cmd command:

      { writebacklisten: ObjectId('4fcf6f27fb0b7403c30c7021') }

      ntoreturn:1 reslen:44 300000ms
      80812700/111903891 72%
      Wed Jun 20 02:24:02 [conn22] command admin.$cmd command:

      { writebacklisten: ObjectId('4fcf6ee0c637de224e7ecb5d') }

      ntoreturn:1 reslen:44 300000ms
      Wed Jun 20 02:24:03 [conn23] command admin.$cmd command:

      { writebacklisten: ObjectId('4fbc4fe47fc06f85f192440a') }

      ntoreturn:1 reslen:44 300000ms
      81429300/111903891 72%
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      82644800/111903891 73%
      Wed Jun 20 02:24:31 [FileAllocator] allocating new datafile /data/mongo/chartboost.26, filling with zeroes...
      Wed Jun 20 02:24:31 [FileAllocator] done allocating datafile /data/mongo/chartboost.26, size: 2047MB, took 0.036 secs
      83297000/111903891 74%
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      Wed Jun 20 02:26:53 [PeriodicTask::Runner] task: WriteBackManager::cleaner took: 8ms
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      Wed Jun 20 02:27:58 [FileAllocator] allocating new datafile /data/mongo/chartboost.27, filling with zeroes...
      Wed Jun 20 02:27:58 [FileAllocator] done allocating datafile /data/mongo/chartboost.27, size: 2047MB, took 0.022 secs
      94167700/111903891 84%
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      Wed Jun 20 02:28:53 [conn2] command admin.$cmd command:

      { writebacklisten: ObjectId('4fcf6f27fb0b7403c30c7021') }

      ntoreturn:1 reslen:44 300024ms
      Wed Jun 20 02:29:00 [rsSync] old journal file will be removed: /data/mongo/journal/j._22
      96491100/111903891 86%
      Wed Jun 20 02:29:02 [conn22] command admin.$cmd command:

      { writebacklisten: ObjectId('4fcf6ee0c637de224e7ecb5d') }

      ntoreturn:1 reslen:44 300001ms
      Wed Jun 20 02:29:03 [conn23] command admin.$cmd command:

      { writebacklisten: ObjectId('4fbc4fe47fc06f85f192440a') }

      ntoreturn:1 reslen:44 300001ms
      96751100/111903891 86%
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      Wed Jun 20 02:33:53 [conn2] command admin.$cmd command:

      { writebacklisten: ObjectId('4fcf6f27fb0b7403c30c7021') }

      ntoreturn:1 reslen:44 300001ms
      98441300/111903891 87%
      Wed Jun 20 02:34:02 [conn22] command admin.$cmd command:

      { writebacklisten: ObjectId('4fcf6ee0c637de224e7ecb5d') }

      ntoreturn:1 reslen:44 300001ms
      Wed Jun 20 02:34:03 [conn23] command admin.$cmd command:

      { writebacklisten: ObjectId('4fbc4fe47fc06f85f192440a') }

      ntoreturn:1 reslen:44 300001ms
      98441800/111903891 87%
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      Wed Jun 20 02:38:53 [conn2] command admin.$cmd command:

      { writebacklisten: ObjectId('4fcf6f27fb0b7403c30c7021') }

      ntoreturn:1 reslen:44 300001ms
      98481600/111903891 88%
      Wed Jun 20 02:39:02 [conn22] command admin.$cmd command:

      { writebacklisten: ObjectId('4fcf6ee0c637de224e7ecb5d') }

      ntoreturn:1 reslen:44 300001ms
      Wed Jun 20 02:39:03 [conn23] command admin.$cmd command:

      { writebacklisten: ObjectId('4fbc4fe47fc06f85f192440a') }

      ntoreturn:1 reslen:44 300001ms
      98484300/111903891 88%
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      Wed Jun 20 02:43:53 [conn2] command admin.$cmd command:

      { writebacklisten: ObjectId('4fcf6f27fb0b7403c30c7021') }

      ntoreturn:1 reslen:44 300001ms
      98541800/111903891 88%
      Wed Jun 20 02:44:02 [conn22] command admin.$cmd command:

      { writebacklisten: ObjectId('4fcf6ee0c637de224e7ecb5d') }

      ntoreturn:1 reslen:44 300001ms
      Wed Jun 20 02:44:03 [conn23] command admin.$cmd command:

      { writebacklisten: ObjectId('4fbc4fe47fc06f85f192440a') }

      ntoreturn:1 reslen:44 300001ms
      98546300/111903891 88%
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      Wed Jun 20 02:48:53 [conn2] command admin.$cmd command:

      { writebacklisten: ObjectId('4fcf6f27fb0b7403c30c7021') }

      ntoreturn:1 reslen:44 300000ms
      Wed Jun 20 02:49:02 [conn22] command admin.$cmd command:

      { writebacklisten: ObjectId('4fcf6ee0c637de224e7ecb5d') }

      ntoreturn:1 reslen:44 300001ms
      Wed Jun 20 02:49:03 [conn23] command admin.$cmd command:

      { writebacklisten: ObjectId('4fbc4fe47fc06f85f192440a') }

      ntoreturn:1 reslen:44 300001ms
      98573100/111903891 88%
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      Wed Jun 20 02:53:53 [conn2] command admin.$cmd command:

      { writebacklisten: ObjectId('4fcf6f27fb0b7403c30c7021') }

      ntoreturn:1 reslen:44 300000ms
      98594400/111903891 88%
      Wed Jun 20 02:54:02 [conn22] command admin.$cmd command:

      { writebacklisten: ObjectId('4fcf6ee0c637de224e7ecb5d') }

      ntoreturn:1 reslen:44 300001ms
      Wed Jun 20 02:54:03 [conn23] command admin.$cmd command:

      { writebacklisten: ObjectId('4fbc4fe47fc06f85f192440a') }

      ntoreturn:1 reslen:44 300001ms
      98595100/111903891 88%
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      98597100/111903891 88%

      etc etc... and 4 hours later it's now up to ... 89%:

      Wed Jun 20 05:39:03 [conn23] command admin.$cmd command:

      { writebacklisten: ObjectId('4fbc4fe47fc06f85f192440a') }

      ntoreturn:1 reslen:44 300001ms
      99588700/111903891 88%
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      Checking the /var/log/messages file, we saw that the linux oom_killer was being invoked and killing mongod.

      when mongo adds to a new member of a replica set, the data seems to transfer over just fine but then it runs out of memory when it is building its indexes & sort tables etc...

      We have other members of the replica set running with 8GB RAM / 1GB swap drive just fine...

      I've only experienced oom_killer being invoked once or twice ever, and it's only when stuff is REALLY bad on the server, and always always something configured wrong and running out of disk space and ram.

      mongo docs declare that mongo isn't supposed to do this.

      we aren't booting up small boxes here... this failure is happening on a dual core machine with 8GB ram and a 1GB swap disk.

      Mongo Docs

      http://www.mongodb.org/display/DOCS/Production+Notes#ProductionNotes-Swap

      "Swap

      It is useful for the linux kernel to have swap space to use in emergencies. Because of the way MongoDB memory maps the database files none of this data will ever end up in swap; this means that on a healthy system the swap space will rarely be used on a system only running MongoDB. Having swap can keep the kernel from killing MongoDB when physical memory limits are reached."

      http://www.mongodb.org/display/DOCS/The+Linux+Out+of+Memory+OOM+Killer

      "You may also want to look at using something which compresses swap/memory like compcache.

      MongoDB uses memory mapped files. The entire data is mapped. Over time, if there is no memory pressure, the mongod resident bytes may approach total memory, as the resident bytes includes file system cache bytes for the file pages open and touched by mongod."

      /var/log/messages

      and the oom info in the /var/log/messages file:

      Jun 20 08:05:36 c4fabbdf-f958-4e1f-b159-c6ff18df2020 kernel: [286991.177205] mongod invoked oom-killer: gfp_mask=0x201da, order=0, oom_adj=0, oom_score_adj=0
      Jun 20 08:05:36 c4fabbdf-f958-4e1f-b159-c6ff18df2020 kernel: [286991.178669] mongod cpuset=/ mems_allowed=0
      Jun 20 08:05:36 c4fabbdf-f958-4e1f-b159-c6ff18df2020 kernel: [286991.179406] Pid: 11935, comm: mongod Not tainted 3.1.10joyent-centos-6-opt #1
      Jun 20 08:05:36 c4fabbdf-f958-4e1f-b159-c6ff18df2020 kernel: [286991.180830] Call Trace:
      Jun 20 08:05:36 c4fabbdf-f958-4e1f-b159-c6ff18df2020 kernel: [286991.181467] [<ffffffff810a16a4>] dump_header+0x84/0x1e0
      Jun 20 08:05:36 c4fabbdf-f958-4e1f-b159-c6ff18df2020 kernel: [286991.182273] [<ffffffff810a13aa>] ? find_lock_task_mm+0x2a/0x70
      Jun 20 08:05:36 c4fabbdf-f958-4e1f-b159-c6ff18df2020 kernel: [286991.183125] [<ffffffff810a1c5d>] oom_kill_process+0x7d/0x270
      Jun 20 08:05:36 c4fabbdf-f958-4e1f-b159-c6ff18df2020 kernel: [286991.183926] [<ffffffff810a2058>] out_of_memory+0x208/0x3a0
      Jun 20 08:05:36 c4fabbdf-f958-4e1f-b159-c6ff18df2020 kernel: [286991.184715] [<ffffffff810a5eb7>] __alloc_pages_nodemask+0x787/0x7a0
      Jun 20 08:05:36 c4fabbdf-f958-4e1f-b159-c6ff18df2020 kernel: [286991.185548] [<ffffffff810d54c0>] alloc_pages_current+0xa0/0x100
      Jun 20 08:05:36 c4fabbdf-f958-4e1f-b159-c6ff18df2020 kernel: [286991.186367] [<ffffffff8109eabf>] __page_cache_alloc+0x7f/0x90
      Jun 20 08:05:36 c4fabbdf-f958-4e1f-b159-c6ff18df2020 kernel: [286991.187178] [<ffffffff8109e589>] ? find_get_page+0x19/0xa0
      Jun 20 08:05:36 c4fabbdf-f958-4e1f-b159-c6ff18df2020 kernel: [286991.187966] [<ffffffff8109f71b>] filemap_fault+0x1ab/0x4d0
      Jun 20 08:05:36 c4fabbdf-f958-4e1f-b159-c6ff18df2020 kernel: [286991.188755] [<ffffffff810bd084>] __do_fault+0x74/0x510
      Jun 20 08:05:36 c4fabbdf-f958-4e1f-b159-c6ff18df2020 kernel: [286991.189522] [<ffffffff810bd59f>] handle_pte_fault+0x7f/0xa70
      Jun 20 08:05:36 c4fabbdf-f958-4e1f-b159-c6ff18df2020 kernel: [286991.190404] [<ffffffff810e184c>] ? mem_cgroup_count_vm_event+0x1c/0x50
      Jun 20 08:05:36 c4fabbdf-f958-4e1f-b159-c6ff18df2020 kernel: [286991.191307] [<ffffffff810be0ce>] handle_mm_fault+0x13e/0x250
      Jun 20 08:05:36 c4fabbdf-f958-4e1f-b159-c6ff18df2020 kernel: [286991.192142] [<ffffffff81025c9d>] do_page_fault+0x12d/0x3b0
      Jun 20 08:05:36 c4fabbdf-f958-4e1f-b159-c6ff18df2020 kernel: [286991.192972] [<ffffffff81001037>] ? __switch_to+0x227/0x2f0
      Jun 20 08:05:36 c4fabbdf-f958-4e1f-b159-c6ff18df2020 kernel: [286991.193806] [<ffffffff8157ad85>] ? __schedule+0x375/0x7c0
      Jun 20 08:05:36 c4fabbdf-f958-4e1f-b159-c6ff18df2020 kernel: [286991.194613] [<ffffffff8157d62f>] page_fault+0x1f/0x30
      Jun 20 08:05:36 c4fabbdf-f958-4e1f-b159-c6ff18df2020 kernel: [286991.195403] Mem-Info:
      Jun 20 08:05:36 c4fabbdf-f958-4e1f-b159-c6ff18df2020 kernel: [286991.196022] Node 0 DMA per-cpu:
      Jun 20 08:05:36 c4fabbdf-f958-4e1f-b159-c6ff18df2020 kernel: [286991.196720] CPU 0: hi: 0, btch: 1 usd: 0
      Jun 20 08:05:36 c4fabbdf-f958-4e1f-b159-c6ff18df2020 kernel: [286991.197481] CPU 1: hi: 0, btch: 1 usd: 0
      Jun 20 08:05:36 c4fabbdf-f958-4e1f-b159-c6ff18df2020 kernel: [286991.198255] Node 0 DMA32 per-cpu:
      Jun 20 08:05:36 c4fabbdf-f958-4e1f-b159-c6ff18df2020 kernel: [286991.198962] CPU 0: hi: 186, btch: 31 usd: 82
      Jun 20 08:05:36 c4fabbdf-f958-4e1f-b159-c6ff18df2020 kernel: [286991.199727] CPU 1: hi: 186, btch: 31 usd: 153
      Jun 20 08:05:36 c4fabbdf-f958-4e1f-b159-c6ff18df2020 kernel: [286991.200558] Node 0 Normal per-cpu:
      Jun 20 08:05:36 c4fabbdf-f958-4e1f-b159-c6ff18df2020 kernel: [286991.201260] CPU 0: hi: 186, btch: 31 usd: 175
      Jun 20 08:05:36 c4fabbdf-f958-4e1f-b159-c6ff18df2020 kernel: [286991.202059] CPU 1: hi: 186, btch: 31 usd: 32
      Jun 20 08:05:36 c4fabbdf-f958-4e1f-b159-c6ff18df2020 kernel: [286991.202891] active_anon:1665611 inactive_anon:301926 isolated_anon:0
      Jun 20 08:05:36 c4fabbdf-f958-4e1f-b159-c6ff18df2020 kernel: [286991.202893] active_file:11 inactive_file:1308 isolated_file:31
      Jun 20 08:05:36 c4fabbdf-f958-4e1f-b159-c6ff18df2020 kernel: [286991.202894] unevictable:0 dirty:0 writeback:0 unstable:0
      Jun 20 08:05:36 c4fabbdf-f958-4e1f-b159-c6ff18df2020 kernel: [286991.202896] free:11493 slab_reclaimable:679 slab_unreclaimable:1676
      Jun 20 08:05:36 c4fabbdf-f958-4e1f-b159-c6ff18df2020 kernel: [286991.202897] mapped:98 shmem:1 pagetables:37659 bounce:0
      Jun 20 08:05:36 c4fabbdf-f958-4e1f-b159-c6ff18df2020 kernel: [286991.207035] Node 0 DMA free:15908kB min:20kB low:24kB high:28kB active_anon:0kB inactive_anon:0kB active_file:0kB inactive_file:0kB unevictable:0kB isolated(anon):0kB isolated(file):0kB present:15652kB mlocked:0kB dirty:0kB writeback:0kB mapped:0kB shmem:0kB slab_reclaimable:0kB slab_unreclaimable:0kB kernel_stack:0kB pagetables:0kB unstable:0kB bounce:0kB writeback_tmp:0kB pages_scanned:0 all_unreclaimable? yes
      Jun 20 08:05:36 c4fabbdf-f958-4e1f-b159-c6ff18df2020 kernel: [286991.212201] lowmem_reserve[]: 0 3504 8040 8040
      Jun 20 08:05:36 c4fabbdf-f958-4e1f-b159-c6ff18df2020 kernel: [286991.213231] Node 0 DMA32 free:23140kB min:4996kB low:6244kB high:7492kB active_anon:2913228kB inactive_anon:582760kB active_file:72kB inactive_file:0kB unevictable:0kB isolated(anon):0kB isolated(file):0kB present:3588340kB mlocked:0kB dirty:0kB writeback:0kB mapped:4kB shmem:4kB slab_reclaimable:364kB slab_unreclaimable:336kB kernel_stack:16kB pagetables:57444kB unstable:0kB bounce:0kB writeback_tmp:0kB pages_scanned:2864 all_unreclaimable? yes
      Jun 20 08:05:36 c4fabbdf-f958-4e1f-b159-c6ff18df2020 kernel: [286991.218476] lowmem_reserve[]: 0 0 4536 4536
      Jun 20 08:05:36 c4fabbdf-f958-4e1f-b159-c6ff18df2020 kernel: [286991.219331] Node 0 Normal free:6924kB min:6468kB low:8084kB high:9700kB active_anon:3749216kB inactive_anon:624944kB active_file:0kB inactive_file:5104kB unevictable:0kB isolated(anon):0kB isolated(file):124kB present:4644864kB mlocked:0kB dirty:0kB writeback:0kB mapped:560kB shmem:0kB slab_reclaimable:2352kB slab_unreclaimable:6368kB kernel_stack:800kB pagetables:93192kB unstable:0kB bounce:0kB writeback_tmp:0kB pages_scanned:157 all_unreclaimable? no
      Jun 20 08:05:36 c4fabbdf-f958-4e1f-b159-c6ff18df2020 kernel: [286991.224709] lowmem_reserve[]: 0 0 0 0
      Jun 20 08:05:36 c4fabbdf-f958-4e1f-b159-c6ff18df2020 kernel: [286991.225523] Node 0 DMA: 1*4kB 0*8kB 0*16kB 1*32kB 2*64kB 1*128kB 1*256kB 0*512kB 1*1024kB 1*2048kB 3*4096kB = 15908kB

            Assignee:
            schwerin@mongodb.com Andy Schwerin
            Reporter:
            cb_john John Albietz
            Votes:
            1 Vote for this issue
            Watchers:
            8 Start watching this issue

              Created:
              Updated:
              Resolved: