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Bigun
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Joined: 21 Sep 2003
Posts: 2154

PostPosted: Thu Mar 30, 2017 10:04 am    Post subject: Keep running out of memory (solved) Reply with quote

Let me preface this whole post with this statement: This has only become a problem in the last few months, before that, this system has ran like a top for the last 5 years or so. With that, I'll move on.

For whatever reason, after about 7 to 18 days, the machine will start running out of memory and start killing off random processes to make RAM. From what I can tell, swap is hardly even being touched.

Code:
# swapon
NAME       TYPE        SIZE USED PRIO
/dev/md125 partition 956.9M   1M   -1


I'd give you dmesg info, but I only got the command to work once before it started closing my SSH session when I ran it.

Here's all the info I can give.

Code:
 # cat /proc/meminfo
MemTotal:        8230396 kB
MemFree:          137596 kB
MemAvailable:    7574380 kB
Buffers:               4 kB
Cached:          7261372 kB
SwapCached:           32 kB
Active:          6293844 kB
Inactive:         975316 kB
Active(anon):       7528 kB
Inactive(anon):     5904 kB
Active(file):    6286316 kB
Inactive(file):   969412 kB
Unevictable:           0 kB
Mlocked:               0 kB
HighTotal:       7401664 kB
HighFree:         128368 kB
LowTotal:         828732 kB
LowFree:            9228 kB
SwapTotal:        979836 kB
SwapFree:         978780 kB
Dirty:                 0 kB
Writeback:             0 kB
AnonPages:          7768 kB
Mapped:             6120 kB
Shmem:              5648 kB
Slab:             543296 kB
SReclaimable:     476480 kB
SUnreclaim:        66816 kB
KernelStack:        1304 kB
PageTables:          560 kB
NFS_Unstable:          0 kB
Bounce:                0 kB
WritebackTmp:          0 kB
CommitLimit:     5095032 kB
Committed_AS:      70112 kB
VmallocTotal:     122880 kB
VmallocUsed:           0 kB
VmallocChunk:          0 kB
HugePages_Total:       0
HugePages_Free:        0
HugePages_Rsvd:        0
HugePages_Surp:        0
Hugepagesize:       2048 kB
DirectMap4k:       10232 kB
DirectMap2M:      901120 kB


Code:
# ps -A
  PID TTY          TIME CMD
    1 ?        00:00:04 init
    2 ?        00:00:00 kthreadd
    3 ?        00:00:23 ksoftirqd/0
    7 ?        00:01:03 rcu_sched
    8 ?        00:00:00 rcu_bh
    9 ?        00:00:00 migration/0
   10 ?        00:00:00 lru-add-drain
   11 ?        00:00:00 cpuhp/0
   12 ?        00:00:00 cpuhp/1
   13 ?        00:00:00 migration/1
   14 ?        00:00:00 ksoftirqd/1
   17 ?        00:00:00 kdevtmpfs
   18 ?        00:00:00 netns
  384 ?        00:00:00 oom_reaper
  385 ?        00:00:00 writeback
  387 ?        00:00:00 crypto
  388 ?        00:00:00 bioset
  390 ?        00:00:00 kblockd
  565 ?        00:00:00 ata_sff
  585 ?        00:00:00 md
  593 ?        00:00:00 cfg80211
  688 ?        00:00:00 rpciod
  689 ?        00:00:00 xprtiod
  701 ?        00:02:28 kswapd0
  723 ?        00:00:00 vmstat
  802 ?        00:00:00 nfsiod
  811 ?        00:00:00 cifsiod
  821 ?        00:00:00 bioset
  829 ?        00:00:00 xfsalloc
  830 ?        00:00:00 xfs_mru_cache
  897 ?        00:00:00 acpi_thermal_pm
  915 ?        00:00:00 i915/signal:0
  916 ?        00:00:00 i915/signal:1
  917 ?        00:00:00 i915/signal:2
  934 ?        00:00:00 bioset
  935 ?        00:00:00 bioset
  936 ?        00:00:00 bioset
  937 ?        00:00:00 bioset
  938 ?        00:00:00 bioset
  939 ?        00:00:00 bioset
  940 ?        00:00:00 bioset
  941 ?        00:00:00 bioset
  942 ?        00:00:00 bioset
  943 ?        00:00:00 bioset
  944 ?        00:00:00 bioset
  945 ?        00:00:00 bioset
  946 ?        00:00:00 bioset
  947 ?        00:00:00 bioset
  948 ?        00:00:00 bioset
  949 ?        00:00:00 bioset
  984 ?        00:00:00 bioset
  988 ?        00:00:00 bioset
  991 ?        00:00:00 bioset
  994 ?        00:00:00 bioset
  997 ?        00:00:00 bioset
 1000 ?        00:00:00 bioset
 1003 ?        00:00:00 bioset
 1006 ?        00:00:00 bioset
 1018 ?        00:00:00 iscsi_eh
 1041 ?        00:00:00 scsi_eh_0
 1042 ?        00:00:00 scsi_tmf_0
 1045 ?        00:00:00 scsi_eh_1
 1046 ?        00:00:00 scsi_tmf_1
 1049 ?        00:00:00 scsi_eh_2
 1050 ?        00:00:00 scsi_tmf_2
 1053 ?        00:00:00 scsi_eh_3
 1054 ?        00:00:00 scsi_tmf_3
 1057 ?        00:00:00 scsi_eh_4
 1058 ?        00:00:00 scsi_tmf_4
 1061 ?        00:00:00 scsi_eh_5
 1062 ?        00:00:00 scsi_tmf_5
 1066 ?        00:00:00 scsi_eh_6
 1068 ?        00:00:00 scsi_tmf_6
 1071 ?        00:00:00 scsi_eh_7
 1072 ?        00:00:00 scsi_tmf_7
 1146 ?        00:00:00 raid5wq
 1187 ?        00:00:00 bioset
 1195 ?        00:00:00 bioset
 1204 ?        00:00:00 bioset
 1212 ?        00:00:00 bioset
 1222 ?        00:00:08 kworker/1:2
 1232 ?        00:00:00 bioset
 1245 ?        00:00:00 bioset
 1257 ?        00:00:00 bioset
 1261 ?        00:00:00 bioset
 1265 ?        00:00:00 bioset
 1266 ?        00:00:17 md126_raid1
 1268 ?        00:00:00 bioset
 1272 ?        00:00:00 bioset
 1273 ?        00:00:00 md125_raid1
 1275 ?        00:00:00 bioset
 1279 ?        00:00:00 bioset
 1280 ?        00:00:00 md124_raid1
 1283 ?        00:00:00 xfs-buf/md126
 1284 ?        00:00:00 xfs-data/md126
 1285 ?        00:00:00 xfs-conv/md126
 1286 ?        00:00:00 xfs-cil/md126
 1287 ?        00:00:00 xfs-reclaim/md1
 1288 ?        00:00:00 xfs-log/md126
 1289 ?        00:00:00 xfs-eofblocks/m
 1290 ?        00:02:13 xfsaild/md126
 1698 ?        00:00:00 systemd-udevd
 2763 ?        00:00:00 syslog-ng
 2764 ?        00:00:01 syslog-ng
 2821 ?        00:00:00 rpcbind
 2847 ?        00:00:00 rpc.statd
 2897 ?        00:00:00 rpc.idmapd
 2928 ?        00:00:00 rpc.mountd
 2932 ?        00:00:00 nfsd4_callbacks
 2933 ?        00:00:00 lockd
 2935 ?        00:00:00 nfsd
 2936 ?        00:00:00 nfsd
 2937 ?        00:00:00 nfsd
 2938 ?        00:00:00 nfsd
 2939 ?        00:00:00 nfsd
 2940 ?        00:00:00 nfsd
 2941 ?        00:00:00 nfsd
 2942 ?        00:00:00 nfsd
 3081 ?        00:00:42 avahi-daemon
 3082 ?        00:00:00 avahi-daemon
 3166 ?        00:00:00 smartd
 3196 ?        00:00:00 sshd
 3221 ?        00:00:00 cron
 3252 tty1     00:00:00 agetty
 3253 tty2     00:00:00 agetty
 3254 tty3     00:00:00 agetty
 3255 tty4     00:00:00 agetty
 3256 tty5     00:00:00 agetty
 3257 tty6     00:00:00 agetty
 3456 ?        00:00:00 bioset
 3463 ?        00:00:00 bioset
 3464 ?        00:00:12 md127_raid5
 3482 ?        00:00:00 xfs-buf/md127
 3483 ?        00:00:00 xfs-data/md127
 3484 ?        00:00:00 xfs-conv/md127
 3485 ?        00:00:00 xfs-cil/md127
 3486 ?        00:00:00 xfs-reclaim/md1
 3487 ?        00:00:00 xfs-log/md127
 3488 ?        00:00:00 xfs-eofblocks/m
 3489 ?        00:00:05 xfsaild/md127
 3548 ?        00:02:14 cifsd
 9814 ?        00:00:24 kworker/0:0
16183 ?        00:00:00 kworker/1:1H
19416 ?        00:00:00 kworker/0:2H
19782 ?        00:00:00 kworker/0:2
19812 ?        00:00:00 kworker/1:0
19818 ?        00:00:00 kworker/0:1H
19819 ?        00:00:00 sshd
19825 ?        00:00:00 sshd
19830 pts/0    00:00:00 bash
19833 ?        00:00:00 kworker/u4:1
19859 ?        00:00:00 kworker/0:1
19861 pts/0    00:00:00 su
19864 pts/0    00:00:00 bash
19871 ?        00:00:00 kworker/0:0H
19873 pts/0    00:00:00 ps
23190 ?        00:00:00 kworker/1:0H
24797 ?        00:00:00 kworker/u4:0


Code:
# tail -n 100 /var/log/messages

Mar 30 05:56:31 projector sshd[19819]: pam_unix(sshd:session): session closed for user bigun
Mar 30 05:56:31 projector kernel: dmesg invoked oom-killer: gfp_mask=0x24040c0(GFP_KERNEL|__GFP_COMP), nodemask=0, order=2, oom_score_adj=0
Mar 30 05:56:31 projector kernel: COMPACTION is disabled!!!
Mar 30 05:56:31 projector kernel: dmesg cpuset=/ mems_allowed=0
Mar 30 05:56:31 projector kernel: CPU: 0 PID: 19874 Comm: dmesg Not tainted 4.9.6-gentoo-r1 #1
Mar 30 05:56:31 projector kernel: Hardware name: Gigabyte Technology Co., Ltd. To be filled by O.E.M./H61M-DS2H, BIOS F5 04/02/2012
Mar 30 05:56:31 projector kernel:  d526bcb0 c12ecd91 d526bd7c c18faa90 d526bcd8 c10e4e7b 00000000 f0ebc380
Mar 30 05:56:31 projector kernel:  00000206 d526bcd8 c12f0f42 f0b4b600 c18faa90 00000000 d526bcfc c10b5714
Mar 30 05:56:31 projector kernel:  c10b5566 00000000 00000000 d526bd7c d526bd7c c19ee700 c19ee9d4 d526bd18
Mar 30 05:56:31 projector kernel: Call Trace:
Mar 30 05:56:31 projector kernel:  [<c12ecd91>] dump_stack+0x47/0x5b
Mar 30 05:56:31 projector kernel:  [<c10e4e7b>] dump_header.isra.13+0x6e/0x179
Mar 30 05:56:31 projector kernel:  [<c12f0f42>] ? ___ratelimit+0xa1/0xab
Mar 30 05:56:31 projector kernel:  [<c10b5714>] oom_kill_process+0x66/0x2fe
Mar 30 05:56:31 projector kernel:  [<c10b5566>] ? oom_badness+0xc5/0xfc
Mar 30 05:56:31 projector kernel:  [<c10b5d01>] out_of_memory+0x254/0x28b
Mar 30 05:56:31 projector kernel:  [<c10b882f>] __alloc_pages_nodemask+0x828/0x8db
Mar 30 05:56:31 projector kernel:  [<c10c84e6>] kmalloc_order+0x16/0x28
Mar 30 05:56:31 projector kernel:  [<c106b164>] devkmsg_open+0x39/0xc6
Mar 30 05:56:31 projector kernel:  [<c1341fbb>] memory_open+0x48/0x4c
Mar 30 05:56:31 projector kernel:  [<c10eaa27>] chrdev_open+0x10c/0x12a
Mar 30 05:56:31 projector kernel:  [<c10e55ca>] do_dentry_open+0x193/0x272
Mar 30 05:56:31 projector kernel:  [<c10ea91b>] ? cdev_put+0x1a/0x1a
Mar 30 05:56:31 projector kernel:  [<c10e6388>] vfs_open+0x45/0x4e
Mar 30 05:56:31 projector kernel:  [<c10f2af1>] path_openat+0xae7/0xcb2
Mar 30 05:56:31 projector kernel:  [<c10f2ced>] do_filp_open+0x31/0x77
Mar 30 05:56:31 projector kernel:  [<c10fc3e1>] ? __alloc_fd+0x72/0x10f
Mar 30 05:56:31 projector kernel:  [<c10e6687>] do_sys_open+0x12d/0x1a6
Mar 30 05:56:31 projector kernel:  [<c10e6718>] SyS_open+0x18/0x1a
Mar 30 05:56:31 projector kernel:  [<c1001023>] do_fast_syscall_32+0x8b/0xf6
Mar 30 05:56:31 projector kernel:  [<c16cb6eb>] sysenter_past_esp+0x40/0x6a
Mar 30 05:56:31 projector kernel: Mem-Info:
Mar 30 05:56:31 projector kernel: active_anon:1888 inactive_anon:1476 isolated_anon:0\x0a active_file:1571579 inactive_file:242353 isolated_file:0\x0a unevictable:0 dirty:0 writeback:0 unstable:0\x0a slab_reclaimable:119120 slab_unreclaimable:16703\x0a mapped:1559 shmem:1412 pagetables:140 bounce:0\x0a free:34401 free_pcp:583 free_cma:0
Mar 30 05:56:31 projector kernel: Node 0 active_anon:7552kB inactive_anon:5904kB active_file:6286316kB inactive_file:969412kB unevictable:0kB isolated(anon):0kB isolated(file):0kB mapped:6236kB dirty:0kB writeback:0kB shmem:5648kB writeback_tmp:0kB unstable:0kB pages_scanned:0 all_unreclaimable? no
Mar 30 05:56:31 projector kernel: DMA free:3204kB min:64kB low:80kB high:96kB active_anon:0kB inactive_anon:0kB active_file:0kB inactive_file:0kB unevictable:0kB writepending:0kB present:15976kB managed:15360kB mlocked:0kB slab_reclaimable:10372kB slab_unreclaimable:664kB kernel_stack:0kB pagetables:0kB bounce:0kB free_pcp:0kB local_pcp:0kB free_cma:0kB
Mar 30 05:56:31 projector kernel: lowmem_reserve[]: 0 793 8021 8021
Mar 30 05:56:31 projector kernel: Normal free:6032kB min:3572kB low:4464kB high:5356kB active_anon:0kB inactive_anon:68kB active_file:4kB inactive_file:88kB unevictable:0kB writepending:0kB present:894968kB managed:813372kB mlocked:0kB slab_reclaimable:466108kB slab_unreclaimable:66148kB kernel_stack:1296kB pagetables:0kB bounce:0kB free_pcp:1280kB local_pcp:592kB free_cma:0kB
Mar 30 05:56:31 projector kernel: lowmem_reserve[]: 0 0 57825 57825
Mar 30 05:56:31 projector kernel: HighMem free:128368kB min:512kB low:8644kB high:16776kB active_anon:7552kB inactive_anon:5836kB active_file:6286312kB inactive_file:969324kB unevictable:0kB writepending:0kB present:7401664kB managed:7401664kB mlocked:0kB slab_reclaimable:0kB slab_unreclaimable:0kB kernel_stack:0kB pagetables:560kB bounce:0kB free_pcp:1052kB local_pcp:580kB free_cma:0kB
Mar 30 05:56:31 projector kernel: lowmem_reserve[]: 0 0 0 0
Mar 30 05:56:31 projector kernel: DMA: 19*4kB (UE) 3*8kB (U) 2*16kB (UE) 2*32kB (UE) 1*64kB (U) 1*128kB (E) 7*256kB (UE) 2*512kB (U) 0*1024kB 0*2048kB 0*4096kB = 3204kB
Mar 30 05:56:31 projector kernel: Normal: 1488*4kB (UME) 9*8kB (ME) 0*16kB 0*32kB 0*64kB 0*128kB 0*256kB 0*512kB 0*1024kB 0*2048kB 0*4096kB = 6024kB
Mar 30 05:56:31 projector kernel: HighMem: 11650*4kB (UM) 3061*8kB (M) 480*16kB (UM) 276*32kB (UM) 175*64kB (M) 63*128kB (UM) 16*256kB (M) 14*512kB (UM) 4*1024kB (M) 3*2048kB (UM) 0*4096kB = 128368kB
Mar 30 05:56:31 projector kernel: Node 0 hugepages_total=0 hugepages_free=0 hugepages_surp=0 hugepages_size=2048kB
Mar 30 05:56:31 projector kernel: 1815352 total pagecache pages
Mar 30 05:56:31 projector kernel: 8 pages in swap cache
Mar 30 05:56:31 projector kernel: Swap cache stats: add 784, delete 776, find 11/15
Mar 30 05:56:31 projector kernel: Free swap  = 978780kB
Mar 30 05:56:31 projector kernel: Total swap = 979836kB
Mar 30 05:56:31 projector kernel: 2078152 pages RAM
Mar 30 05:56:31 projector kernel: 1850416 pages HighMem/MovableOnly
Mar 30 05:56:31 projector kernel: 20553 pages reserved
Mar 30 05:56:31 projector kernel: [ pid ]   uid  tgid total_vm      rss nr_ptes nr_pmds swapents oom_score_adj name
Mar 30 05:56:31 projector kernel: [ 1698]     0  1698     2685      587       6       3        0         -1000 systemd-udevd
Mar 30 05:56:31 projector kernel: [ 2763]     0  2763     1703      103       7       3        0             0 syslog-ng
Mar 30 05:56:31 projector kernel: [ 2764]     0  2764     6470      546      10       3        0             0 syslog-ng
Mar 30 05:56:31 projector kernel: [ 2821]     0  2821      613       39       5       3        0             0 rpcbind
Mar 30 05:56:31 projector kernel: [ 2847]     0  2847      730      402       5       3        0             0 rpc.statd
Mar 30 05:56:31 projector kernel: [ 2897]     0  2897      692       43       5       3        0             0 rpc.idmapd
Mar 30 05:56:31 projector kernel: [ 2928]     0  2928      817      124       5       3        0             0 rpc.mountd
Mar 30 05:56:31 projector kernel: [ 3081]   104  3081      748      362       4       3        0             0 avahi-daemon
Mar 30 05:56:31 projector kernel: [ 3082]   104  3082      748       51       4       3        0             0 avahi-daemon
Mar 30 05:56:31 projector kernel: [ 3166]     0  3166     1098      128       5       3        0             0 smartd
Mar 30 05:56:31 projector kernel: [ 3196]     0  3196     1355      547       6       3        0         -1000 sshd
Mar 30 05:56:31 projector kernel: [ 3221]     0  3221      600      389       5       3        0             0 cron
Mar 30 05:56:31 projector kernel: [ 3252]     0  3252     1096      315       6       3        0             0 agetty
Mar 30 05:56:31 projector kernel: [ 3253]     0  3253     1096      298       6       3        0             0 agetty
Mar 30 05:56:31 projector kernel: [ 3254]     0  3254     1096      316       6       3        0             0 agetty
Mar 30 05:56:31 projector kernel: [ 3255]     0  3255     1096      294       6       3        0             0 agetty
Mar 30 05:56:31 projector kernel: [ 3256]     0  3256     1096      317       6       3        0             0 agetty
Mar 30 05:56:31 projector kernel: [ 3257]     0  3257     1096      314       6       3        0             0 agetty
Mar 30 05:56:31 projector kernel: [19819]     0 19819     2086     1121       7       3        0             0 sshd
Mar 30 05:56:31 projector kernel: [19825]  1000 19825    10412      981      10       3        0             0 sshd
Mar 30 05:56:31 projector kernel: [19830]  1000 19830      925      727       5       3        0             0 bash
Mar 30 05:56:31 projector kernel: [19861]  1000 19861      755      577       5       3        0             0 su
Mar 30 05:56:31 projector kernel: [19864]     0 19864      925      752       5       3        0             0 bash
Mar 30 05:56:31 projector kernel: [19874]     0 19874      563      169       5       3        0             0 dmesg
Mar 30 05:56:31 projector kernel: Out of memory: Kill process 19819 (sshd) score 0 or sacrifice child
Mar 30 05:56:31 projector kernel: Killed process 19825 (sshd) total-vm:41648kB, anon-rss:604kB, file-rss:3320kB, shmem-rss:0kB
Mar 30 05:56:31 projector su[19861]: pam_unix(su:session): session closed for user root
Mar 30 05:57:03 projector sshd[19877]: SSH: Server;Ltype: Version;Remote: 192.168.0.104-5081;Protocol: 2.0;Client: PuTTY_Release_0.66
Mar 30 05:57:03 projector sshd[19877]: SSH: Server;Ltype: Kex;Remote: 192.168.0.104-5081;Enc: aes256-ctr;MAC: hmac-sha2-256;Comp: none [preauth]
Mar 30 05:57:08 projector sshd[19877]: Accepted keyboard-interactive/pam for bigun from 192.168.0.104 port 5081 ssh2
Mar 30 05:57:08 projector sshd[19877]: pam_unix(sshd:session): session opened for user bigun by (uid=0)
Mar 30 05:57:08 projector sshd[19883]: SSH: Server;Ltype: Kex;Remote: 192.168.0.104-5081;Enc: aes256-ctr;MAC: hmac-sha2-256;Comp: none
Mar 30 05:57:23 projector su[19892]: Successful su for root by bigun
Mar 30 05:57:23 projector su[19892]: + /dev/pts/0 bigun:root
Mar 30 05:57:23 projector su[19892]: pam_unix(su:session): session opened for user root by bigun(uid=1000)
Mar 30 05:59:01 projector cron[19901]: (root) CMD (rm -f /var/spool/cron/lastrun/cron.hourly)
Mar 30 06:00:01 projector cron[19905]: (root) CMD (test -x /usr/sbin/run-crons && /usr/sbin/run-crons)
Mar 30 06:02:18 projector su[19892]: pam_unix(su:session): session closed for user root
Mar 30 06:03:16 projector su[19930]: Successful su for root by bigun
Mar 30 06:03:16 projector su[19930]: + /dev/pts/0 bigun:root
Mar 30 06:03:16 projector su[19930]: pam_unix(su:session): session opened for user root by bigun(uid=1000)


I don't even know where to start. Going to reboot the server now to get it usable.
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Last edited by Bigun on Mon Apr 17, 2017 4:11 pm; edited 1 time in total
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PostPosted: Thu Mar 30, 2017 10:20 am    Post subject: Reply with quote

my opinion

your kernel is outdated. 4.9.16 is stable for amd64.
+ experimental software like systemd + xfs

Quote:
Mar 30 05:56:31 projector kernel: [ pid ] uid tgid total_vm rss nr_ptes nr_pmds swapents oom_score_adj name
Mar 30 05:56:31 projector kernel: [ 1698] 0 1698 2685 587 6 3 0 -1000 systemd-udevd


not sure if i have read that correctly.

total_vm => total virtual memory? => 2685 MB? process systemd-udevd

--

if that was my box, i would use top regularly before it dies and check myself these processes with big memory usage.

have you checked /var/log/messages ?

Quote:
Mar 30 05:56:31 projector kernel: [ 2763] 0 2763 1703 103 7 3 0 0 syslog-ng
Mar 30 05:56:31 projector kernel: [ 2764] 0 2764 6470 546 10 3 0 0 syslog-ng


--

Easiest way to do something is first to update your kernel. than monitor with top regularly how the memory consumption is

--

There was a way to enalbe swap, swapon?, and also to lower the pirority of swap, so swap will be more used.
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PostPosted: Thu Mar 30, 2017 10:32 am    Post subject: Reply with quote

Roman_Gruber wrote:
my opinion

your kernel is outdated. 4.9.16 is stable for amd64.
+ experimental software like systemd + xfs

Quote:
Mar 30 05:56:31 projector kernel: [ pid ] uid tgid total_vm rss nr_ptes nr_pmds swapents oom_score_adj name
Mar 30 05:56:31 projector kernel: [ 1698] 0 1698 2685 587 6 3 0 -1000 systemd-udevd



I'll get the server on the latest kernel.



Roman_Gruber wrote:
if that was my box, i would use top regularly before it dies and check myself these processes with big memory usage.

have you checked /var/log/messages ?

Quote:
Mar 30 05:56:31 projector kernel: [ 2763] 0 2763 1703 103 7 3 0 0 syslog-ng
Mar 30 05:56:31 projector kernel: [ 2764] 0 2764 6470 546 10 3 0 0 syslog-ng



The last snippet of code in my OP was from /var/log/messages



Roman_Gruber wrote:
There was a way to enalbe swap, swapon?, and also to lower the pirority of swap, so swap will be more used.


Swap is enabled AFAICT. There's even a code snippet from the command in my OP.
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PostPosted: Thu Mar 30, 2017 10:35 am    Post subject: Reply with quote

Also, this box is running a 32 bit kernel.

Code:
 # uname -a
Linux projector 4.9.6-gentoo-r1 #1 SMP Thu Feb 23 06:50:25 EST 2017 i686 Intel(R) Celeron(R) CPU G530 @ 2.40GHz GenuineIntel GNU/Linux


There isn't a stable 4.9.16 version available yet.
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PostPosted: Thu Mar 30, 2017 10:45 am    Post subject: Reply with quote

Well i Know its very off topic

https://www.cnet.com/products/gigabyte-ga-h61m-ds2h-2-1-motherboard-micro-atx-lga1155-socket-h61/specs/

Any reason why you run 32bit on 64bit capable box?

It may be that you run in a not very well tested issue, bug. I assue most of the guys these days use amd64. Running the platform with more users may cause less issues in the long run => amd64, ext4, openrc / eudev

--

Only thing to ask is what you do with your server? Check regularly with top to see what causes this issue

Some software like google chrome have a memory hole since years ...
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PostPosted: Thu Mar 30, 2017 11:06 am    Post subject: Reply with quote

Roman_Gruber wrote:
Well i Know its very off topic

https://www.cnet.com/products/gigabyte-ga-h61m-ds2h-2-1-motherboard-micro-atx-lga1155-socket-h61/specs/

Any reason why you run 32bit on 64bit capable box?


The original thinking when I set up this box was "stability" (ironically enough)

But now-a-days, you're absolutely right. If I ever redid the box, it would be 64-bit.

Roman_Gruber wrote:
Only thing to ask is what you do with your server? Check regularly with top to see what causes this issue

Some software like google chrome have a memory hole since years ...


It's a headless box with no GUI components installed, so those kinds of things aren't a factor.

This box does five things:

1) Host torrents via rtorrent
2) Hosts a file share via Samba for workstations around the house
3) Get's a daily backup of the webserver via unison
4) Pushes offsite backup via SSH tunnel to a Raspberry Pi
5) Plays media via Plex Media Server
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PostPosted: Thu Mar 30, 2017 11:34 am    Post subject: Reply with quote

I'd use something like https://github.com/pixelb/ps_mem to see where the memory goes and what is swapping (the -S option to it) things out (suggesting potential memory leaks or at least unused memory for a long while). I believe the ps_mem.py file can be used indepdently without dealing with the whole repo.
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PostPosted: Thu Mar 30, 2017 12:00 pm    Post subject: Reply with quote

Leio wrote:
I'd use something like https://github.com/pixelb/ps_mem to see where the memory goes and what is swapping (the -S option to it) things out (suggesting potential memory leaks or at least unused memory for a long while). I believe the ps_mem.py file can be used indepdently without dealing with the whole repo.


Grabbed the script, time to monitor:

Code:
 # ~/ps_mem.py -S
 Private  +   Shared  =  RAM used   Swap used   Program

 96.0 KiB +  32.0 KiB = 128.0 KiB         0.0 KiB     0.0 KiB   sleep
120.0 KiB +  38.0 KiB = 158.0 KiB         0.0 KiB     0.0 KiB   init
172.0 KiB +  63.5 KiB = 235.5 KiB         0.0 KiB     0.0 KiB   cron
232.0 KiB + 119.0 KiB = 351.0 KiB         0.0 KiB     0.0 KiB   rpcbind
376.0 KiB + 141.0 KiB = 517.0 KiB         0.0 KiB     0.0 KiB   su
476.0 KiB +  48.5 KiB = 524.5 KiB         0.0 KiB     0.0 KiB   rpc.idmapd
184.0 KiB + 514.0 KiB = 698.0 KiB         0.0 KiB     0.0 KiB   start_pms (2)
696.0 KiB + 107.0 KiB = 803.0 KiB         0.0 KiB     0.0 KiB   rpc.mountd
688.0 KiB + 124.0 KiB = 812.0 KiB         0.0 KiB     0.0 KiB   rpc.statd
412.0 KiB + 551.5 KiB = 963.5 KiB         0.0 KiB     0.0 KiB   avahi-daemon [deleted] (2)
916.0 KiB + 129.0 KiB =   1.0 MiB         0.0 KiB     0.0 KiB   smartd
908.0 KiB + 164.0 KiB =   1.0 MiB         0.0 KiB     0.0 KiB   screen
908.0 KiB + 197.0 KiB =   1.1 MiB         0.0 KiB     0.0 KiB   pglcmd.wd
792.0 KiB + 422.0 KiB =   1.2 MiB         0.0 KiB     0.0 KiB   agetty (6)
700.0 KiB + 681.0 KiB =   1.3 MiB         0.0 KiB     0.0 KiB   bash (2)
  1.3 MiB + 399.5 KiB =   1.6 MiB         0.0 KiB     0.0 KiB   Plex Relay
  1.2 MiB + 564.5 KiB =   1.8 MiB         0.0 KiB     0.0 KiB   nmbd
  1.7 MiB + 120.0 KiB =   1.9 MiB         0.0 KiB     0.0 KiB   systemd-udevd
  1.5 MiB + 971.0 KiB =   2.5 MiB         0.0 KiB     0.0 KiB   syslog-ng (2)
  1.4 MiB +   2.2 MiB =   3.6 MiB         0.0 KiB     0.0 KiB   sshd (3)
  5.7 MiB +   1.6 MiB =   7.3 MiB         0.0 KiB     0.0 KiB   Plex Tuner Service
  2.9 MiB +   8.7 MiB =  11.5 MiB         0.0 KiB     0.0 KiB   smbd (4)
 10.6 MiB +   3.8 MiB =  14.3 MiB         0.0 KiB     0.0 KiB   Plex DLNA Server
 18.3 MiB + 153.5 KiB =  18.4 MiB         0.0 KiB     0.0 KiB   Plex Transcoder
 20.0 MiB +  60.5 KiB =  20.1 MiB         0.0 KiB     0.0 KiB   pgld
 22.6 MiB + 840.0 KiB =  23.5 MiB         0.0 KiB     0.0 KiB   rtorrent main
 64.2 MiB +   4.3 MiB =  68.5 MiB         0.0 KiB     0.0 KiB   Plex Media Server
125.3 MiB +   7.9 MiB = 133.2 MiB         0.0 KiB     0.0 KiB   Plex Script Host (7)
-------------------------------------------------------------
                        318.9 MiB         0.0 KiB     0.0 KiB
=============================================================

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Last edited by Bigun on Thu Mar 30, 2017 12:09 pm; edited 1 time in total
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PostPosted: Thu Mar 30, 2017 12:09 pm    Post subject: Reply with quote

I doubt this issue is the age of your kernel. 4.9 is plenty recent.

I see no reference in your dmesg that /dev/md125 is being used for swap. This could be a kernel setting or an fstab issue

Code:
root@hypoid-2 [3] 1 /root # zgrep SWAP /proc/config.gz
CONFIG_SWAP=y
CONFIG_MEMCG_SWAP=y
# CONFIG_MEMCG_SWAP_ENABLED is not set
CONFIG_ARCH_USE_BUILTIN_BSWAP=y
CONFIG_FRONTSWAP=y
# CONFIG_ZSWAP is not set
# CONFIG_NFS_SWAP is not set

root@hypoid-2 [3] 2 /root # grep -i swap /var/log/kern.log
Mar  5 21:52:47 hypoid-2 kernel: Adding 8185112k swap on /dev/sda5.  Priority:-1 extents:1 across:8185112k SSFS

root@hypoid-2 [3] 3 /root # grep -i swap /etc/fstab
/dev/sda5               none            swap            sw                      0 3


Edit to add: I see the reference to /dev/md125 in your swapon output. You and I are running the exact same kernel, 4.9.6-r1, and my kern.log and dmesg log report the use of swap quite differently compared with the report from your kernel. On boot, my kernel reports "Adding swap on [device]"

Not to say your system or some app doesn't have a memory leak, but the "not swapping before crashing out with fully consumed memory" is a solvable problem. Also, FWIW, I run a 64 bit kernel on a 32 bit system on a 64 bit machine. It works fine. It worked fine with a 32 bit kernel too.

Edit to add, I get a similar reference to the swap device in dmesg

Code:
[    4.418379] Adding 8388604k swap on /dev/sda5.  Priority:-1 extents:1 across:8388604k SSFS


Last edited by cboldt on Thu Mar 30, 2017 12:22 pm; edited 1 time in total
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PostPosted: Thu Mar 30, 2017 12:12 pm    Post subject: Reply with quote

cboldt wrote:
I doubt this issue is the age of your kernel. 4.9 is plenty recent.

I see no reference in your dmesg that /dev/md125 is being used for swap. This could be a kernel setting or an fstab issue

Code:
root@hypoid-2 [3] 1 /root # zgrep SWAP /proc/config.gz
CONFIG_SWAP=y
CONFIG_MEMCG_SWAP=y
# CONFIG_MEMCG_SWAP_ENABLED is not set
CONFIG_ARCH_USE_BUILTIN_BSWAP=y
CONFIG_FRONTSWAP=y
# CONFIG_ZSWAP is not set
# CONFIG_NFS_SWAP is not set

root@hypoid-2 [3] 2 /root # grep -i swap /var/log/kern.log
Mar  5 21:52:47 hypoid-2 kernel: Adding 8185112k swap on /dev/sda5.  Priority:-1 extents:1 across:8185112k SSFS

root@hypoid-2 [3] 3 /root # grep -i swap /etc/fstab
/dev/sda5               none            swap            sw                      0 3


Not to say your system or some app doesn't have a memory leak, but the "not swapping before crashing out with fully consumed memory" is a solvable problem. Also, FWIW, I run a 64 bit kernel on a 32 bit system on a 64 bit machine. It works fine. It worked fine with a 32 bit kernel too.


Code:
 # cat /usr/src/linux/.config | grep SWAP
CONFIG_SWAP=y
CONFIG_ARCH_USE_BUILTIN_BSWAP=y
# CONFIG_FRONTSWAP is not set
# CONFIG_NFS_SWAP is not set


AFAIK, using the swapon command should show you the mounted swap partitions. I always though as long as it was mounted as swap, it would be used.

And yeah, there may be a memory leak somewhere, but activating swap if it isn't should slow down the crashing process.
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PostPosted: Thu Mar 30, 2017 12:30 pm    Post subject: Reply with quote

Yes, swapon will show what is available. I get similar report here, with `swapon` and `swapon -s`. And in your case that command does refer to the device /dev/md125.

But your kernel boot log does not refer to the device at all, while my kernel boot log does, and reports adding it.

Could be just a difference in logging. My swap is a normal partition. Something is resisting paging out to SWAP, in favor of dropping information from RAM.

I don't know enough off the top of my head to say whether our kernel config differences re:SWAP have a role.
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PostPosted: Thu Mar 30, 2017 12:33 pm    Post subject: Reply with quote

What do you get on `stat /dev/md125`

For comparison purposes, here are the relevant specifications on my swap space, /dev/sda5

Code:
root@hypoid-2 [3] 8 /root # stat /dev/sda5
  File: '/dev/sda5'
  Size: 0               Blocks: 0          IO Block: 4096   block special file
Device: 6h/6d   Inode: 1162        Links: 1     Device type: 8,5
Access: (0660/brw-rw----)  Uid: (    0/    root)   Gid: (    6/    disk)
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PostPosted: Thu Mar 30, 2017 12:38 pm    Post subject: Reply with quote

For anybody curious, the (8 Gb) size of my swap space is only because /dev/sda5 on this machine was created with an eye to using it for hibernate space, if I ever get around to working on that project. Other machines under my watchful eye have much less swap space, and swap space is barely touched on any machine, even after hundreds of days of uptime.

Edit to add, just to be the first to jump on "useless use of cat" -- you can grep the contents of .config directly
`grep SWAP /usr/src/linux/.config` works fine, and skips a pipeline.
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PostPosted: Thu Mar 30, 2017 12:52 pm    Post subject: Reply with quote

You aren't the only one, but this supposedly was fixed for 4.9 kernel

http://unix.stackexchange.com/questions/300106/why-is-the-oom-killer-killing-processes-when-swap-is-hardly-used
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PostPosted: Thu Mar 30, 2017 12:56 pm    Post subject: Reply with quote

Bigun,

swap can't be used for everything. Its only used for dynamically allocated RAM.
If something in RAM has a permanent home on your HDD, it won't be swapped to swap.
Dirty buffers will be written, so that the RAM they use can be freed.
Code or other read only data will be dropped. Next time its needed, you get a page fault and its reloaded form HDD.
It is swapping - just not using the swap space, which is why you should always have some swap.

When the kernel needs to invoke the OOM manager. Its done all of the above and has nowhere to go.
Its kill something or panic. That it choose sshd is unfortunate.

The usual cause in a memory leak, however, memory leaks come from dynamically allocated RAM that is not deallocated.
If turn, that means you can usually watch swap fill up before the OOM manager kicks in.

Your log shows
Code:
Mar 30 05:56:31 projector kernel: COMPACTION is disabled!!!
Maybe you have lots of free RAM but its fragmented, so the kernel cannot get a contiguous allocation the size it needs. Its worth trying a kernel with the memory compaction option enabled.
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PostPosted: Thu Mar 30, 2017 1:07 pm    Post subject: Reply with quote

cboldt wrote:
What do you get on `stat /dev/md125`

For comparison purposes, here are the relevant specifications on my swap space, /dev/sda5

Code:
root@hypoid-2 [3] 8 /root # stat /dev/sda5
  File: '/dev/sda5'
  Size: 0               Blocks: 0          IO Block: 4096   block special file
Device: 6h/6d   Inode: 1162        Links: 1     Device type: 8,5
Access: (0660/brw-rw----)  Uid: (    0/    root)   Gid: (    6/    disk)


Code:
# stat /dev/md125
  File: '/dev/md125'
  Size: 0               Blocks: 0          IO Block: 4096   block special file
Device: 6h/6d   Inode: 147         Links: 1     Device type: 9,7d
Access: (0660/brw-rw----)  Uid: (    0/    root)   Gid: (    6/    disk)
Access: 2017-03-30 08:11:30.318037522 -0400
Modify: 2017-03-30 06:06:36.329000062 -0400
Change: 2017-03-30 06:06:36.329000062 -0400
 Birth: -

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PostPosted: Thu Mar 30, 2017 1:11 pm    Post subject: Reply with quote

New toys! I never looked into the oom killer, but it is configurable. You can protect sshd if you want ...

http://www.oracle.com/technetwork/articles/servers-storage-dev/oom-killer-1911807.html

In short, /proc/PID/oom_adj is available, and takes values from -16 (preserved) to +15 (vulnerable), and even recognizes a value of -17, which allows the protected app to commit suicide by bringing down the kernel.
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PostPosted: Thu Mar 30, 2017 1:12 pm    Post subject: Reply with quote

NeddySeagoon wrote:
...
The usual cause in a memory leak, however, memory leaks come from dynamically allocated RAM that is not deallocated.
If turn, that means you can usually watch swap fill up before the OOM manager kicks in.

Your log shows
Code:
Mar 30 05:56:31 projector kernel: COMPACTION is disabled!!!
Maybe you have lots of free RAM but its fragmented, so the kernel cannot get a contiguous allocation the size it needs. Its worth trying a kernel with the memory compaction option enabled.


Pleasure as always Neddy.

I'll be adding the option and recompiling. Get back with you in weeks coming to see what happens.
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PostPosted: Thu Mar 30, 2017 1:14 pm    Post subject: Reply with quote

cboldt wrote:
New toys! I never looked into the oom killer, but it is configurable. You can protect sshd if you want ...

http://www.oracle.com/technetwork/articles/servers-storage-dev/oom-killer-1911807.html

In short, /proc/PID/oom_adj is available, and takes values from -16 (preserved) to +15 (vulnerable), and even recognizes a value of -17, which allows the protected app to commit suicide by bringing down the kernel.


If this keeps up, I'll be making that change post-haste. ;)
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PostPosted: Thu Mar 30, 2017 1:19 pm    Post subject: Reply with quote

Code:
CONFIG_COMPACTION:
  │ 
  │ Compaction is the only memory management component to form 
  │ high order (larger physically contiguous) memory blocks
  │ reliably. The page allocator relies on compaction heavily and
  │ the lack of the feature can lead to unexpected OOM killer
  │ invocations for high order memory requests. You shouldn't
  │ disable this option unless there really is a strong reason for
  │ it and then we would be really interested to hear about that at
  │ linux-mm@kvack.org.
  │
  │ Symbol: COMPACTION [=y] 
  │ Type  : boolean
  │ Prompt: Allow for memory compaction
  │   Location:
  │     -> Processor type and features
  │   Defined at mm/Kconfig:259
  │   Depends on: MMU [=y]
  │   Selects: MIGRATION [=y]
  │   Selected by: TRANSPARENT_HUGEPAGE [=y] && HAVE_ARCH_TRANSPARENT_HUGEPAGE [=y]


I never would have caught that. Neddy to the rescue ... again!
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PostPosted: Thu Mar 30, 2017 1:25 pm    Post subject: Reply with quote

cboldt wrote:
Code:
CONFIG_COMPACTION:
  │ 
  │ Compaction is the only memory management component to form 
  │ high order (larger physically contiguous) memory blocks
  │ reliably. The page allocator relies on compaction heavily and
  │ the lack of the feature can lead to unexpected OOM killer
  │ invocations for high order memory requests. You shouldn't
  │ disable this option unless there really is a strong reason for
  │ it and then we would be really interested to hear about that at
  │ linux-mm@kvack.org.
  │
  │ Symbol: COMPACTION [=y] 
  │ Type  : boolean
  │ Prompt: Allow for memory compaction
  │   Location:
  │     -> Processor type and features
  │   Defined at mm/Kconfig:259
  │   Depends on: MMU [=y]
  │   Selects: MIGRATION [=y]
  │   Selected by: TRANSPARENT_HUGEPAGE [=y] && HAVE_ARCH_TRANSPARENT_HUGEPAGE [=y]


I never would have caught that. Neddy to the rescue ... again!


Honestly, as useful a feature as that is, you would think it would be suggested to be turned on in the Gentoo handbook.
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cboldt
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PostPosted: Thu Mar 30, 2017 1:50 pm    Post subject: Reply with quote

I suspect compaction is "naturally" turned on by other selections, or kernel default, but maybe not. In my case, it is turned on by other configuration options. It (compaction) has the -*- indicator next to it. It can't be toggled directly.

The kernel has tons of "weird" options and pitfalls. I chased "why does my system show a loadavg close to 1.0 with no CPU cycles?" for a few days, and found quite by accident that the loadavg calculation is greatly affected by high precision timers. I bet there are literally hundreds of interactions like that, and yours with oom-killer. It's tough enough to get the average computer user into a working system without scaring the crap out of them with so many issues and options.
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PostPosted: Thu Mar 30, 2017 2:21 pm    Post subject: Reply with quote

cboldt wrote:
I suspect compaction is "naturally" turned on by other selections, or kernel default, but maybe not. In my case, it is turned on by other configuration options. It (compaction) has the -*- indicator next to it. It can't be toggled directly.

The kernel has tons of "weird" options and pitfalls. I chased "why does my system show a loadavg close to 1.0 with no CPU cycles?" for a few days, and found quite by accident that the loadavg calculation is greatly affected by high precision timers. I bet there are literally hundreds of interactions like that, and yours with oom-killer. It's tough enough to get the average computer user into a working system without scaring the crap out of them with so many issues and options.


My TRANSPARENT_HUGEPAGE wasn't on, so it was never turned on. But if the Gentoo team was worried about overwhelming the user, then that ship sailed 12 pages into the handhook, what's one more line?
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NeddySeagoon
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PostPosted: Thu Mar 30, 2017 2:46 pm    Post subject: Reply with quote

Bigun,

You have the choice of forcing COMPACTION on by choosing
Code:
Selected by: TRANSPARENT_HUGEPAGE [=y] && HAVE_ARCH_TRANSPARENT_HUGEPAGE [=y]

or selecting it manually.

Actually, HAVE_ARCH_TRANSPARENT_HUGEPAGE will be a hidden symbol forced by your choice of ARCH. The default setting for ARCH is defined in the environment. The only time you would change it is if you were cross compiling a kernel.
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cboldt
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PostPosted: Thu Mar 30, 2017 2:59 pm    Post subject: Reply with quote

The kernel default is CONFIG_COMPACTION=y (just tested with `make defconfig`)
Some kernel `make` options turn comapaction off. `make tinyconfig` results in "# CONFIG_COMPACTION is not set"

I don't know what genkernel does, or what the "Gentoo helpers" toggle does vs. COMPACTION

I think Bigun has a good point. If COMPACTION isn't the most likely outcome due to other causes (like genkernel, or start with default kernel, of "on" via the Gentoo switch, etc.), then a mention in the kernel config part of the handbook ought to be created.
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