[CentOS] Memory leak - how to investigate

Mon Feb 3 13:43:16 UTC 2014
Jussi Hirvi <listmember at greenspot.fi>

My web & name server runs out of memory from time to time, to the point 
where it's completely unresponsive to anything. At that point reset is 
the only alternative. (Or, as this is a virtual guest, I just say "virsh 
destroy").

But why this happens - I would like to know.

The host in question is a KVM guest, and runs CentOS 6.4.

 From "top" (situation now):
Mem:   1361564k total,  1264324k used,    97240k free,     8428k buffers
Swap:  3014648k total,    64852k used,  2949796k free,   358676k cached

At or before the last crash I got a long error message on the console. 
"Oom-killer" was called repeatedly by httpd and named.

I paste below the first error message, which is long. There were several 
long entries like this. I

- Jussi

[root at ns1 ~]# httpd invoked oom-killer: gfp_mask=0x280da, order=0, 
oom_adj=0, oom_score_adj=0
httpd cpuset=/ mems_allowed=0
Pid: 2962, comm: httpd Not tainted 2.6.32-358.23.2.el6.x86_64 #1
Call Trace:
  [<ffffffff810cb641>] ? cpuset_print_task_mems_allowed+0x91/0xb0
  [<ffffffff8111ce40>] ? dump_header+0x90/0x1b0
  [<ffffffff810e930e>] ? __delayacct_freepages_end+0x2e/0x30
  [<ffffffff8121d4ec>] ? security_real_capable_noaudit+0x3c/0x70
  [<ffffffff8111d2c2>] ? oom_kill_process+0x82/0x2a0
  [<ffffffff8111d201>] ? select_bad_process+0xe1/0x120
  [<ffffffff8111d700>] ? out_of_memory+0x220/0x3c0
  [<ffffffff8112c3dc>] ? __alloc_pages_nodemask+0x8ac/0x8d0
  [<ffffffff81160d6a>] ? alloc_pages_vma+0x9a/0x150
  [<ffffffff81143f0b>] ? handle_pte_fault+0x76b/0xb50
  [<ffffffffa00c60f9>] ? ext4_check_acl+0x29/0x90 [ext4]
  [<ffffffff81075887>] ? current_fs_time+0x27/0x30
  [<ffffffff8114452a>] ? handle_mm_fault+0x23a/0x310
  [<ffffffff810474e9>] ? __do_page_fault+0x139/0x480
  [<ffffffff8114aaba>] ? do_mmap_pgoff+0x33a/0x380
  [<ffffffff81513bfe>] ? do_page_fault+0x3e/0xa0
  [<ffffffff81510fb5>] ? page_fault+0x25/0x30
Mem-Info:
Node 0 DMA per-cpu:
CPU    0: hi:    0, btch:   1 usd:   0
Node 0 DMA32 per-cpu:
CPU    0: hi:  186, btch:  31 usd:  89
active_anon:201535 inactive_anon:68173 isolated_anon:3424
  active_file:130 inactive_file:284 isolated_file:160
  unevictable:0 dirty:0 writeback:245 unstable:0
  free:14234 slab_reclaimable:2891 slab_unreclaimable:13218
  mapped:239 shmem:14 pagetables:28858 bounce:0
Node 0 DMA free:8252kB min:340kB low:424kB high:508kB active_anon:2168kB 
inactive_anon:4624kB active_file:4kB inactive_file:144kB unevictable:0kB 
isolated(anon):0kB isolated(file):0kB present:15348kB mlocked:0kB 
dirty:0kB writeback:28kB mapped:8kB shmem:0kB slab_reclaimable:12kB 
slab_unreclaimable:128kB kernel_stack:8kB pagetables:376kB unstable:0kB 
bounce:0kB writeback_tmp:0kB pages_scanned:1424 all_unreclaimable? no
lowmem_reserve[]: 0 1956 1956 1956
Node 0 DMA32 free:48684kB min:44712kB low:55888kB high:67068kB 
active_anon:803972kB inactive_anon:268068kB active_file:516kB 
inactive_file:992kB unevictable:0kB isolated(anon):13696kB 
isolated(file):640kB present:2003828kB mlocked:0kB dirty:0kB 
writeback:888kB mapped:948kB shmem:56kB slab_reclaimable:11552kB 
slab_unreclaimable:52744kB kernel_stack:3344kB pagetables:115056kB 
unstable:0kB bounce:0kB writeback_tmp:0kB pages_scanned:7552 
all_unreclaimable? no
lowmem_reserve[]: 0 0 0 0
Node 0 DMA: 25*4kB 11*8kB 6*16kB 3*32kB 9*64kB 3*128kB 1*256kB 3*512kB 
1*1024kB 2*2048kB 0*4096kB = 8252kB
Node 0 DMA32: 977*4kB 401*8kB 320*16kB 179*32kB 58*64kB 63*128kB 
32*256kB 7*512kB 3*1024kB 0*2048kB 1*4096kB = 48684kB
21463 total pagecache pages
20882 pages in swap cache
Swap cache stats: add 1523887, delete 1503005, find 201987/297332
Free swap  = 0kB
Total swap = 3014648kB
511996 pages RAM
43605 pages reserved
66036 pages shared
446256 pages non-shared
[ pid ]   uid  tgid total_vm      rss cpu oom_adj oom_score_adj name
[  449]     0   449     2675        0   0     -17         -1000 udevd
[ 1080]     0  1080     6909        6   0     -17         -1000 auditd
[ 1105]     0  1105    62271        1   0       0             0 rsyslogd
[ 1142]    25  1142    40455      262   0       0             0 named
[ 1184]     0  1184    16563        0   0     -17         -1000 sshd
[ 1195]     0  1195    13036        0   0       0             0 vsftpd
[ 1231]     0  1231    27041        1   0       0             0 mysqld_safe
[ 1333]    27  1333   187111     4825   0       0             0 mysqld
[ 1430]     0  1430    20216       21   0       0             0 master
[ 1438]    89  1438    20236       18   0       0             0 pickup
[ 1439]    89  1439    20279       22   0       0             0 qmgr
[ 1440]     0  1440    79250      368   0       0             0 httpd
[ 1448]     0  1448    29313       34   0       0             0 crond
[ 1459]    48  1459    88738      727   0       0             0 httpd
[ 1460]    48  1460    89244      494   0       0             0 httpd
[ 1461]    48  1461    89729      803   0       0             0 httpd
[ 1462]    48  1462    88987     1055   0       0             0 httpd
[ 1463]    48  1463    89796     2560   0       0             0 httpd
[ 1464]    48  1464    91371     3558   0       0             0 httpd
[ 1465]    48  1465    88596     1283   0       0             0 httpd
[ 1466]    48  1466    90794     1253   0       0             0 httpd
[ 1469]     0  1469   106619      198   0       0             0 
fail2ban-server
[ 1497]     0  1497     1015        1   0       0             0 mingetty
[ 1499]     0  1499     1015        1   0       0             0 mingetty
[ 1501]     0  1501     1015        1   0       0             0 mingetty
[ 1503]     0  1503     1015        1   0       0             0 mingetty
[ 1505]     0  1505     1015        1   0       0             0 mingetty
[ 1507]     0  1507     1015        1   0       0             0 mingetty
[ 1512]     0  1512     2674        0   0     -17         -1000 udevd
[ 1513]     0  1513     2674        0   0     -17         -1000 udevd
[ 1514]     0  1514    14249        1   0       0             0 login
[ 1520]    48  1520    89586     1139   0       0             0 httpd
[ 1522]    48  1522    90606      773   0       0             0 httpd
[ 1523]    48  1523    88343     2527   0       0             0 httpd
[ 1524]     0  1524    27075        1   0       0             0 bash
[ 1549]    48  1549    88937     1738   0       0             0 httpd
[ 1550]    48  1550    89721     1736   0       0             0 httpd
[ 1579]    48  1579    91106      600   0       0             0 httpd
[ 1581]    48  1581    88218     1491   0       0             0 httpd
[ 1582]    48  1582    88559      595   0       0             0 httpd
[ 1755]    48  1755    88115     1716   0       0             0 httpd
[ 2376]    48  2376    90860     1318   0       0             0 httpd
[ 2562]    48  2562    89680     2348   0       0             0 httpd
[ 2697]    48  2697    87846     2082   0       0             0 httpd
[ 2709]    48  2709    86589     3201   0       0             0 httpd
[ 2710]    48  2710    86056     2467   0       0             0 httpd
[ 2713]    48  2713    84422     1068   0       0             0 httpd
[ 2714]    48  2714    85544     2688   0       0             0 httpd
[ 2715]    48  2715    84748     1505   0       0             0 httpd
[ 2716]    48  2716    84569     1318   0       0             0 httpd
[ 2721]    48  2721    84815     1718   0       0             0 httpd
[ 2722]    48  2722    84502     1256   0       0             0 httpd
[ 2723]    48  2723    87014     4123   0       0             0 httpd
[ 2724]    48  2724    84502     1246   0       0             0 httpd
[ 2725]    48  2725    84420     1203   0       0             0 httpd
[ 2726]    48  2726    86782     4034   0       0             0 httpd
[ 2727]    48  2727    84502     1262   0       0             0 httpd
[ 2728]    48  2728    86054     2340   0       0             0 httpd
[ 2737]    48  2737    84815     1743   0       0             0 httpd
[ 2738]    48  2738    84748     1639   0       0             0 httpd
[ 2739]    48  2739    86589     3300   0       0             0 httpd
[ 2740]    48  2740    85202     2201   0       0             0 httpd
[ 2741]    48  2741    86054     1742   0       0             0 httpd
[ 2742]    48  2742    87014     4231   0       0             0 httpd
[ 2743]    48  2743    84301      711   0       0             0 httpd
[ 2744]    48  2744    84502     1233   0       0             0 httpd
[ 2745]    48  2745    84815     1614   0       0             0 httpd
[ 2746]    48  2746    84420     1113   0       0             0 httpd
[ 2747]    48  2747    84432      913   0       0             0 httpd
[ 2748]    48  2748    84301      724   0       0             0 httpd
[ 2749]    48  2749    86251     3541   0       0             0 httpd
[ 2750]    48  2750    84301      764   0       0             0 httpd
[ 2751]    48  2751    84422     1004   0       0             0 httpd
[ 2752]    48  2752    84291      588   0       0             0 httpd
[ 2758]    48  2758    84301      687   0       0             0 httpd
[ 2759]    48  2759    84301      725   0       0             0 httpd
[ 2760]    48  2760    84432      890   0       0             0 httpd
[ 2761]    48  2761    84301      788   0       0             0 httpd
[ 2765]    48  2765    84420      930   0       0             0 httpd
[ 2766]    48  2766    84430      868   0       0             0 httpd
[ 2769]    48  2769    84432      946   0       0             0 httpd
[ 2770]    48  2770    87526     8319   0       0             0 httpd
[ 2774]    48  2774    84291      582   0       0             0 httpd
[ 2775]    48  2775    84430      897   0       0             0 httpd
[ 2779]    48  2779    84301      692   0       0             0 httpd
[ 2780]    48  2780    84301      659   0       0             0 httpd
[ 2781]    48  2781    84430     1098   0       0             0 httpd
[ 2782]    48  2782    84420     2692   0       0             0 httpd
[ 2783]    48  2783    84430      823   0       0             0 httpd
[ 2784]    48  2784    84422     1062   0       0             0 httpd
[ 2785]    48  2785    84432      899   0       0             0 httpd
[ 2786]    48  2786    84502     1259   0       0             0 httpd
[ 2787]    48  2787    84301      733   0       0             0 httpd
[ 2788]    48  2788    84434      906   0       0             0 httpd
[ 2789]    48  2789    84432     1000   0       0             0 httpd
[ 2790]    48  2790    87526     8311   0       0             0 httpd
[ 2791]    48  2791    84430     1067   0       0             0 httpd
[ 2792]    48  2792    84504     1259   0       0             0 httpd
[ 2793]    48  2793    84301      749   0       0             0 httpd
[ 2794]    48  2794    84422      935   0       0             0 httpd
[ 2795]    48  2795    84303      740   0       0             0 httpd
[ 2796]    48  2796    84560     1417   0       0             0 httpd
[ 2797]    48  2797    84420     1091   0       0             0 httpd
[ 2798]    48  2798    84420     1023   0       0             0 httpd
[ 2799]    48  2799    84301      678   0       0             0 httpd
[ 2800]    48  2800    84301      643   0       0             0 httpd
[ 2809]    48  2809    84422     1017   0       0             0 httpd
[ 2811]    48  2811    84301      643   0       0             0 httpd
[ 2812]    48  2812    84301      620   0       0             0 httpd
[ 2813]    48  2813    84432      958   0       0             0 httpd
[ 2814]    48  2814    84432      928   0       0             0 httpd
[ 2815]    48  2815    84420     1126   0       0             0 httpd
[ 2816]    48  2816    87014     7940   0       0             0 httpd
[ 2817]    48  2817    84301      725   0       0             0 httpd
[ 2818]    48  2818    84301      695   0       0             0 httpd
[ 2819]    48  2819    84432      800   0       0             0 httpd
[ 2820]    48  2820    84420     1209   0       0             0 httpd
[ 2821]    48  2821    84502     1351   0       0             0 httpd
[ 2822]    48  2822    84815     1684   0       0             0 httpd
[ 2823]    48  2823    84301      702   0       0             0 httpd
[ 2824]    48  2824    84430     1416   0       0             0 httpd
[ 2825]    48  2825    84432      824   0       0             0 httpd
[ 2826]    48  2826    84432      899   0       0             0 httpd
[ 2827]    48  2827    84432      884   0       0             0 httpd
[ 2828]    48  2828    84301      794   0       0             0 httpd
[ 2829]    48  2829    84301      723   0       0             0 httpd
[ 2830]    48  2830    84301     1413   0       0             0 httpd
[ 2831]    48  2831    85331     3528   0       0             0 httpd
[ 2832]    48  2832    84420     3300   0       0             0 httpd
[ 2833]    48  2833    84430     1353   0       0             0 httpd
[ 2834]    48  2834    84432      897   0       0             0 httpd
[ 2835]    48  2835    84291      572   0       0             0 httpd
[ 2836]    48  2836    85460     3295   0       0             0 httpd
[ 2852]    48  2852    83773     4497   0       0             0 httpd
[ 2853]    48  2853    84814     2177   0       0             0 httpd
[ 2857]    48  2857    84420     1140   0       0             0 httpd
[ 2858]    48  2858    84432      925   0       0             0 httpd
[ 2859]    48  2859    84485     1568   0       0             0 httpd
[ 2860]    48  2860    84552     1749   0       0             0 httpd
[ 2861]    48  2861    84291      582   0       0             0 httpd
[ 2862]    48  2862    84420     3627   0       0             0 httpd
[ 2868]    48  2868    84301      804   0       0             0 httpd
[ 2869]    48  2869    84487     1268   0       0             0 httpd
[ 2870]    48  2870    84301      803   0       0             0 httpd
[ 2874]    48  2874    84422     1033   0       0             0 httpd
[ 2875]    48  2875    84301      718   0       0             0 httpd
[ 2876]    48  2876    84485     1125   0       0             0 httpd
[ 2877]    48  2877    84420      924   0       0             0 httpd
[ 2878]    48  2878    84748     2217   0       0             0 httpd
[ 2885]    48  2885    84301     2638   0       0             0 httpd
[ 2886]    48  2886    84420      905   0       0             0 httpd
[ 2887]    48  2887    84420     1558   0       0             0 httpd
[ 2888]    48  2888    84301      697   0       0             0 httpd
[ 2889]    48  2889    84502     1228   0       0             0 httpd
[ 2904]    48  2904    84430      791   0       0             0 httpd
[ 2915]    48  2915    84748     1518   0       0             0 httpd
[ 2916]    48  2916    85331     3691   0       0             0 httpd
[ 2917]    48  2917    84569     1634   0       0             0 httpd
[ 2918]    48  2918    84239     4498   0       0             0 httpd
[ 2919]    48  2919    84502     2969   0       0             0 httpd
[ 2920]    48  2920    86763     4460   0       0             0 httpd
[ 2921]    48  2921    84420     1133   0       0             0 httpd
[ 2922]    48  2922    86381     5779   0       0             0 httpd
[ 2928]    48  2928    84502     2436   0       0             0 httpd
[ 2938]    48  2938    85208     2426   0       0             0 httpd
[ 2939]    48  2939    86055     5438   0       0             0 httpd
[ 2940]    48  2940    84487     4186   0       0             0 httpd
[ 2944]    48  2944    84432     2877   0       0             0 httpd
[ 2945]    48  2945    84291     1446   0       0             0 httpd
[ 2946]    48  2946    84818     3977   0       0             0 httpd
[ 2960]    48  2960    84239     4311   0       0             0 httpd
[ 2961]    48  2961    89636     9983   0       0             0 httpd
[ 2962]    48  2962    87955     8183   0       0             0 httpd
[ 2970]    48  2970    84241     4777   0       0             0 httpd
[ 2973]    48  2973    84239     4759   0       0             0 httpd
[ 2974]    48  2974    80053     1296   0       0             0 httpd
[ 2975]    48  2975    80012     1410   0       0             0 httpd
[ 2976]    48  2976    80185     1606   0       0             0 httpd
[ 2978]    48  2978    79284      414   0       0             0 httpd
[ 2980]    48  2980    80185     1387   0       0             0 httpd
[ 2981]    48  2981    80021     1076   0       0             0 httpd
[ 2982]    48  2982    80181     1383   0       0             0 httpd
[ 2983]    48  2983    80138     1348   0       0             0 httpd
[ 2984]    48  2984    80202     1273   0       0             0 httpd
[ 2985]    48  2985    80010      418   0       0             0 httpd
[ 2986]    48  2986    79990     1409   0       0             0 httpd
[ 2988]    48  2988    80202     1540   0       0             0 httpd
[ 2989]    48  2989    79996      756   0       0             0 httpd
[ 2990]    48  2990    80010     1412   0       0             0 httpd
[ 2991]    48  2991    79986      789   0       0             0 httpd
[ 2992]    48  2992    79284      401   0       0             0 httpd
[ 2993]    48  2993    80189     1562   0       0             0 httpd
[ 2994]    48  2994    80119     1316   0       0             0 httpd
[ 3010]    48  3010    79283      425   0       0             0 httpd
[ 3013]    48  3013    80046     1291   0       0             0 httpd
[ 3016]    48  3016    79250      412   0       0             0 httpd
[ 3018]    48  3018    79283      451   0       0             0 httpd
[ 3022]     0  3022    33480       63   0       0             0 crond
Out of memory: Kill process 1333 (mysqld) score 12 or sacrifice child
Killed process 1333, UID 27, (mysqld) total-vm:748444kB, 
anon-rss:19232kB, file-rss:68kB