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#1 2018-05-13 11:40:15

gandolin
Member
Registered: 2018-05-10
Posts: 9

Is this a kernel memory leak (kernel 4.16.7-1)?

Recently I noticed that an abnormal amount of RAM was being used on my Arch machine. This seems very abnormal because I have a machine with 64GB of RAM, and I'm consuming 61GB. The incident has happened multiple times for me after a couple of days. No RAM intensive applications were running. While trying to figure out where my RAM was going, I ran into the "linux ate my RAM" page. The buff/cache being consumed on the computer is significantly less that what's being used, so I don't think that's the reason for the high memory usage. Is this a kernel memory leak? Would I need to compile a new kernel to debug this?

This is my kernel version:
4.16.7-1-ARCH #1 SMP PREEMPT Wed May 2 21:12:36 UTC 2018 x86_64 GNU/Linux

Top below shows that I'm using 61GB/64GB. I've sorted on memory usage, and it can be seen that the total memory consumption of the applications I'm running gets nowhere near 95%. The buff/cache is 1GB, and the available memory is 2GB...

Output of Top:

top - 07:15:28 up 2 days, 12:00,  0 users,  load average: 0.20, 0.61, 0.76
Tasks: 284 total,   1 running, 280 sleeping,   2 stopped,   1 zombie
%Cpu(s):  0.2 us,  0.1 sy,  0.0 ni, 99.7 id,  0.0 wa,  0.0 hi,  0.0 si,  0.0 st
MiB Mem :  64333.2 total,   1344.4 free,  61932.7 used,   1056.0 buff/cache
MiB Swap:  32676.0 total,  32676.0 free,      0.0 used.   2279.3 avail Mem

  PID USER      PR  NI    VIRT    RES    SHR S  %CPU  %MEM     TIME+ COMMAND
  894 thor      20   0 1418376 853896  18648 S   0.0   1.3  79:20.52 xfdesktop
 1095 thor      20   0 2418612 727480  89704 S   0.0   1.1   2:00.04 Web Content
  666 root      20   0 1651552 715948 101448 S   2.0   1.1  55:43.37 Xorg
 1029 thor      20   0 2697284 658716 172180 S   0.0   1.0   9:24.63 firefox
 6328 thor      20   0 3320972 380496 131388 S   0.0   0.6   6:11.75 python
 6404 thor      20   0 2009496 348972 141784 S   0.0   0.5   1:18.34 Web Content
 2940 thor      20   0 1977672 307556  88520 S   0.0   0.5   1:32.44 Web Content
 1377 thor      20   0 1994868 303436  89176 S   0.0   0.5   1:19.97 Web Content
  909 thor      20   0 1185424 218460  42284 S   0.0   0.3   0:50.85 polkit-gnome-au
  902 thor      20   0 1204800 217672  41316 S   0.0   0.3   0:51.64 xfce4-power-man
  912 thor      20   0 1203876 217420  41996 S   0.0   0.3   0:53.84 xfce4-power-man
 5153 thor      20   0  730696 175844  29264 S   2.0   0.3   0:58.82 xfce4-terminal
  375 root      20   0  191876  72232  71488 S   0.0   0.1   0:06.05 systemd-journal
24633 thor      30  10  844336  57604  46944 T   0.0   0.1   0:04.34 starwars
 5352 thor      30  10  844336  57564  46912 T   0.0   0.1   0:02.02 starwars
  890 thor      20   0  368488  51232  23600 S   0.0   0.1   6:00.87 xfce4-panel
  848 thor      20   0  225512  42684  18456 S   0.0   0.1   3:02.87 xfwm4
  892 thor      20   0  330472  37464  13712 S   0.0   0.1   1:30.74 xfsettingsd
  905 thor      20   0  212612  36016  16020 S   0.0   0.1   0:31.23 panel-2-actions
  772 thor      20   0  364604  34920  14052 S   0.0   0.1   1:36.50 xfce4-session
  900 thor      20   0  209088  33304  13748 S   0.0   0.1   0:31.31 panel-6-systray
  883 thor      20   0  213704  32776  13324 S   0.0   0.0   0:30.55 Thunar
 6340 thor      20   0   99788  30100   7188 S   0.0   0.0   0:00.64 python2.7
  775 polkitd   20   0 2915456  20076  14836 S   0.0   0.0   0:00.42 polkitd
 6341 thor      20   0   58988  17884   5860 S   0.0   0.0   0:00.32 python3
 5351 thor      20   0  146892  12192   5572 S   0.0   0.0   0:02.80 python2.7
    1 root      20   0  234472   8736   6724 S   0.0   0.0   0:01.37 systemd
  954 root      20   0  310044   8572   7120 S   0.0   0.0   0:00.12 upowerd

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#2 2018-05-13 12:16:48

seth
Member
Registered: 2012-09-03
Posts: 8,452

Re: Is this a kernel memory leak (kernel 4.16.7-1)?

cat /proc/meminfo

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#3 2018-05-13 12:26:29

gandolin
Member
Registered: 2018-05-10
Posts: 9

Re: Is this a kernel memory leak (kernel 4.16.7-1)?

Output of /proc/meminfo

MemTotal:       65877232 kB
MemFree:         1344968 kB
MemAvailable:    2584672 kB
Buffers:          116524 kB
Cached:           845748 kB
SwapCached:            0 kB
Active:          3904156 kB
Inactive:        1518224 kB
Active(anon):    3574300 kB
Inactive(anon):    62036 kB
Active(file):     329856 kB
Inactive(file):  1456188 kB
Unevictable:          32 kB
Mlocked:              32 kB
SwapTotal:      33460220 kB
SwapFree:       33460220 kB
Dirty:                68 kB
Writeback:             0 kB
AnonPages:       4460204 kB
Mapped:           388212 kB
Shmem:             64660 kB
Slab:             174612 kB
SReclaimable:      95832 kB
SUnreclaim:        78780 kB
KernelStack:       11168 kB
PageTables:        28660 kB
NFS_Unstable:          0 kB
Bounce:                0 kB
WritebackTmp:          0 kB
CommitLimit:    66398836 kB
Committed_AS:    7747508 kB
VmallocTotal:   34359738367 kB
VmallocUsed:           0 kB
VmallocChunk:          0 kB
HardwareCorrupted:     0 kB
AnonHugePages:         0 kB
ShmemHugePages:        0 kB
ShmemPmdMapped:        0 kB
HugePages_Total:       0
HugePages_Free:        0
HugePages_Rsvd:        0
HugePages_Surp:        0
Hugepagesize:       2048 kB
Hugetlb:               0 kB
DirectMap4k:      622932 kB
DirectMap2M:    12914688 kB
DirectMap1G:    55574528 kB

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#4 2018-05-13 12:49:20

seth
Member
Registered: 2012-09-03
Posts: 8,452

Re: Is this a kernel memory leak (kernel 4.16.7-1)?

Yup, the kernel has no explanation for that huge gap.
How fast does this happen (does it take days or weeks to build up or do you get there within minutes/hours after the boot)?
Also "lsmod" output please, for suspicious modules.

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#5 2018-05-13 12:57:13

gandolin
Member
Registered: 2018-05-10
Posts: 9

Re: Is this a kernel memory leak (kernel 4.16.7-1)?

It usually takes a couple of days. In the post above you can see that top reports the uptime as 2 days 12hrs. Yesterday it was consuming significantly less, so I'd say between 1 and 2 days.

lsmod output:

Module                  Size  Used by
fuse                  118784  3
8021q                  36864  0
mrp                    20480  1 8021q
nct6775                65536  0
hwmon_vid              16384  1 nct6775
amdkfd                176128  1
amd_iommu_v2           20480  1 amdkfd
b43                   454656  0
snd_hda_codec_realtek   106496  1
snd_hda_codec_hdmi     57344  1
amdgpu               3158016  18
snd_hda_codec_generic    86016  1 snd_hda_codec_realtek
mac80211              905216  1 b43
intel_rapl             24576  0
x86_pkg_temp_thermal    16384  0
intel_powerclamp       16384  0
coretemp               16384  0
chash                  16384  1 amdgpu
kvm_intel             176128  0
gpu_sched              28672  1 amdgpu
cfg80211              741376  2 b43,mac80211
ttm                   122880  1 amdgpu
kvm                   708608  1 kvm_intel
drm_kms_helper        200704  1 amdgpu
irqbypass              16384  1 kvm
ssb                    86016  1 b43
crct10dif_pclmul       16384  0
crc32_pclmul           16384  0
drm                   466944  15 amdgpu,gpu_sched,ttm,drm_kms_helper
snd_hda_intel          45056  0
ghash_clmulni_intel    16384  0
pcbc                   16384  0
mmc_core              172032  2 b43,ssb
snd_hda_codec         151552  4 snd_hda_intel,snd_hda_codec_hdmi,snd_hda_codec_generic,snd_hda_codec_realtek
mousedev               24576  0
btusb                  53248  0
nls_iso8859_1          16384  1
hid_generic            16384  0
btrtl                  16384  1 btusb
nls_cp437              20480  1
pcmcia                 69632  1 ssb
btbcm                  16384  1 btusb
aesni_intel           188416  0
snd_hda_core           94208  5 snd_hda_intel,snd_hda_codec,snd_hda_codec_hdmi,snd_hda_codec_generic,snd_hda_codec_realtek
agpgart                49152  2 ttm,drm
pcmcia_core            28672  1 pcmcia
syscopyarea            16384  1 drm_kms_helper
eeepc_wmi              16384  0
rng_core               16384  1 b43
aes_x86_64             20480  1 aesni_intel
snd_hwdep              16384  1 snd_hda_codec
btintel                24576  1 btusb
usbhid                 57344  0
asus_wmi               32768  1 eeepc_wmi
sysfillrect            16384  1 drm_kms_helper
vfat                   24576  1
iTCO_wdt               16384  0
crypto_simd            16384  1 aesni_intel
glue_helper            16384  1 aesni_intel
sysimgblt              16384  1 drm_kms_helper
bluetooth             638976  5 btrtl,btintel,btbcm,btusb
fat                    81920  1 vfat
iTCO_vendor_support    16384  1 iTCO_wdt
wmi_bmof               16384  0
e1000e                282624  0
sparse_keymap          16384  1 asus_wmi
intel_wmi_thunderbolt    16384  0
mxm_wmi                16384  0
igb                   241664  0
fb_sys_fops            16384  1 drm_kms_helper
snd_pcm               135168  4 snd_hda_intel,snd_hda_codec,snd_hda_core,snd_hda_codec_hdmi
bcma                   61440  1 b43
hid                   139264  2 hid_generic,usbhid
cryptd                 28672  3 crypto_simd,ghash_clmulni_intel,aesni_intel
raid1                  45056  1
snd_timer              36864  1 snd_pcm
i2c_algo_bit           16384  2 igb,amdgpu
ecdh_generic           24576  1 bluetooth
dca                    16384  1 igb
intel_cstate           16384  0
rfkill                 28672  4 asus_wmi,bluetooth,cfg80211
mei_me                 45056  0
snd                    98304  8 snd_hda_intel,snd_hwdep,snd_hda_codec,snd_timer,snd_hda_codec_hdmi,snd_hda_codec_generic,snd_hda_codec_realtek,snd_pcm
intel_uncore          131072  0
input_leds             16384  0
ptp                    20480  2 igb,e1000e
md_mod                167936  2 raid1
intel_rapl_perf        16384  0
soundcore              16384  1 snd
led_class              16384  3 asus_wmi,b43,input_leds
pcspkr                 16384  0
mei                   102400  1 mei_me
i2c_i801               32768  0
shpchp                 40960  0
pps_core               20480  1 ptp
lpc_ich                28672  0
rtc_cmos               24576  1
wmi                    28672  4 asus_wmi,wmi_bmof,intel_wmi_thunderbolt,mxm_wmi
evdev                  20480  8
mac_hid                16384  0
vboxnetflt             32768  0
vboxnetadp             28672  0
vboxpci                28672  0
vboxdrv               487424  3 vboxnetadp,vboxnetflt,vboxpci
ip_tables              28672  0
x_tables               45056  1 ip_tables
ext4                  716800  2
crc32c_generic         16384  0
crc16                  16384  2 bluetooth,ext4
mbcache                16384  1 ext4
jbd2                  122880  1 ext4
fscrypto               32768  1 ext4
sr_mod                 28672  0
cdrom                  69632  1 sr_mod
sd_mod                 61440  8
serio_raw              16384  0
ahci                   40960  5
atkbd                  32768  0
xhci_pci               16384  0
libps2                 16384  1 atkbd
libahci                40960  1 ahci
ehci_pci               16384  0
xhci_hcd              258048  1 xhci_pci
ehci_hcd               94208  1 ehci_pci
crc32c_intel           24576  2
libata                278528  2 ahci,libahci
usbcore               286720  6 usbhid,ehci_hcd,xhci_pci,btusb,xhci_hcd,ehci_pci
scsi_mod              258048  3 sd_mod,libata,sr_mod
usb_common             16384  1 usbcore
i8042                  32768  0
serio                  28672  4 serio_raw,atkbd,i8042

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#6 2018-05-13 13:01:45

graysky
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From: :wq
Registered: 2008-12-01
Posts: 9,553
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Re: Is this a kernel memory leak (kernel 4.16.7-1)?

I'm seeing the same on Arch ARM (aarch64) for a month or so now; that machine is running the 4.16.x series of kernels.  I do not see it manifesting on my Arch boxes though, just the ODROID-C2.  I haven't been able to track down the cause of it.


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#7 2018-05-13 13:05:34

seth
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Registered: 2012-09-03
Posts: 8,452

Re: Is this a kernel memory leak (kernel 4.16.7-1)?

virtualbox?

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#8 2018-05-13 13:44:40

gandolin
Member
Registered: 2018-05-10
Posts: 9

Re: Is this a kernel memory leak (kernel 4.16.7-1)?

I do have virtualbox installed, but I don't have it open or running anything.

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#9 2018-05-13 14:01:56

seth
Member
Registered: 2012-09-03
Posts: 8,452

Re: Is this a kernel memory leak (kernel 4.16.7-1)?

If you're not using it anyway, I'd suggest trying to unload (and not auto-load) the vbox kernel modules.
And of course it would be interesting to hear whether graysky has vboxdrv loaded as well. (Actual any overlapping kernel modules - should not be that many with an odroid)

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#10 2018-05-13 15:11:47

graysky
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Registered: 2008-12-01
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Re: Is this a kernel memory leak (kernel 4.16.7-1)?

seth wrote:

...And of course it would be interesting to hear whether graysky has vboxdrv loaded as well.

I do not.  The Arch ARM box I have just runs pihole and openvpn... very minimal.  Typically, it's only using 150-175 MB of RAM but ever since aarch64 went to 4.16.x, it has been "leaking" memory very similar to what the OP reported.


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#11 2018-05-13 19:44:06

gandolin
Member
Registered: 2018-05-10
Posts: 9

Re: Is this a kernel memory leak (kernel 4.16.7-1)?

I do have a couple virtual machines and I do want to use them (one of the reasons I have so much RAM), but since I'm not doing anything with them right now I've disabled the virtualbox kernel modules from loading and will see if that has any effect. Given that graysky doesn't have virtualbox kernel modules running, this may not be the issue.

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#12 2018-05-17 20:44:25

graysky
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Re: Is this a kernel memory leak (kernel 4.16.7-1)?

@OP - You ever get to the bottom of the leak?  I did not!


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#13 2018-05-20 20:32:17

gandolin
Member
Registered: 2018-05-10
Posts: 9

Re: Is this a kernel memory leak (kernel 4.16.7-1)?

I have not gotten to the bottom of the leak. It has been ~7 days since I rebooted. My system has not consumed all of my RAM in that time, but it is still consuming more than it should be. 18/64 GB are currently in use. 2GB of the 18GB is being used for buff/cache which leaves 16GB/64GB = 25% used by something else. Top shows that no processes are using anything near 25%. Perhaps unloading the virtual box modules helped a little bit. This time the resources are disappearing much more slowly.

top - 16:16:43 up 7 days,  1:00,  0 users,  load average: 0.26, 0.56, 0.71
Tasks: 274 total,   2 running, 272 sleeping,   0 stopped,   0 zombie
%Cpu(s):  0.1 us,  0.0 sy,  0.0 ni, 99.8 id,  0.0 wa,  0.0 hi,  0.0 si,  0.0 st
MiB Mem :  64333.2 total,  44032.7 free,  18360.9 used,   1939.7 buff/cache
MiB Swap:  32676.0 total,  32676.0 free,      0.0 used.  45873.8 avail Mem 

  PID USER      PR  NI    VIRT    RES    SHR S  %CPU  %MEM     TIME+ COMMAND    
15280 user      20   0 2504856 465484 147504 S   0.0   0.7   5:12.79 firefox    
15347 user      20   0 2172924 353396  87924 S   0.0   0.5   0:13.44 Web Conte+ 
15644 user      20   0 2126068 339892  90812 S   0.7   0.5  45:05.65 Web Conte+ 
  675 root      20   0 1146768 208084  72068 R   2.3   0.3  19:18.32 Xorg       
15412 user      20   0 1805916 142972 112452 S   0.0   0.2   0:03.24 Web Conte+ 
15764 user      20   0 1775328 113948  81916 S   0.0   0.2   0:01.33 Web Conte+ 
15240 user      20   0  616128  56616  18156 S   0.0   0.1   0:47.16 xfdesktop  
15584 user      20   0  597272  41912  29736 S   1.3   0.1   0:02.74 xfce4-ter+ 
  374 root      20   0  120408  28524  27572 S   0.0   0.0   0:09.18 systemd-j+ 
15235 user      20   0  297720  25784  19700 S   0.0   0.0   0:05.74 xfce4-pan+ 
15232 user      20   0  203364  23640  17572 S   0.0   0.0   0:05.01 xfwm4      
15257 user      20   0  334292  21456  15652 S   0.0   0.0   0:00.51 polkit-gn+ 

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#14 2018-05-23 00:07:46

graysky
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Re: Is this a kernel memory leak (kernel 4.16.7-1)?

I can't offer much help since I can't even track what process is consuming the memory on my machine but I will say that for me the bug occurs on aarch64 which runs the 4.16.x kernel (confirmed on odroid-c2 and raspberry pi 3 running aarch64).  When I switch over to armv7h on raspberry pi3  which runs the 4.14.x kernels, I do not see the leak.  Can you try booting in the linux-lts kernel package on x86_64 box?  It too runs the 4.14.x series.


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#15 2018-05-23 01:44:31

gandolin
Member
Registered: 2018-05-10
Posts: 9

Re: Is this a kernel memory leak (kernel 4.16.7-1)?

Sure. I've installed the linux-lts kernel package, booted the kernel, and will post an update in a couple of days once I've allowed for enough time for the RAM usage to go back up.

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#16 2018-05-24 15:46:19

graysky
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Re: Is this a kernel memory leak (kernel 4.16.7-1)?

I did a few tests using an older x86_64 box (Intel E5200), an few aarch64 boxes (ODROID-C2 and Raspberry Pi3), and a a few boxes running armv7h (RPi2 and RPi3).

tl;dr summary:  I see memory "leaks" for the x86_64, and aarch64 boxes, but not for the armv7h boxes.

Details: 
For x86_64, the test was to boot it under 4.16.11 and 4.14.41 and log the mem usage `free --mega | grep Mem | awk '{ print $3 }'` once per hour via a cronjob.  The result was the used memory went up for each kernel with the box just sitting idle (mysqld, kodi, vncserver/lxqt, and openvpn/server all running just sitting idle with no user interaction with the exception of openvpn which has my family hitting it):

Under 4.16.11, used memory over a 24 h period increased in a linear fashion at a rate of approx 6 MB/hour.
Under 4.14.41, used memory over a 24 h period increased in a linear fashion at a rate of approx 5 MB/hour.

For aarch64.ODROID-C2 under kernel 4.16.11, sitting idle with just systemd networking, sshd, and ufw running, memory increased over 24 h at a very low rate of 0.3 MB/hour.
Running pihole and openvpn in lxcs in addition to the base services, memory increased increased in a linear fashion over a 24 h at a rate of 10.5 MB/hour,

Note that, if I let the ODROID-C2 run without a reboot, the free memory will eventually increase to consume the entire free amount.

I also tried running Arch ARM aarch64 on a Raspberry Pi 3.  Measured under kernel 4.16.10.
Running pihole and openvpn in lxcs in addition to the base services, memory increased in a linear fashion over a 36 h at a rate of 9.9 MB/hour.

If I let it run without a reboot, it too will go until there is no free RAM.

In contrast, running armv7h on a Raspberry Pi 2 or 3 (similar results), does not show the memory leak:
I haven't run with the log file (doing it now) but one example is a RPi3 box running 4.14.39.  All it does is runs pihole, nginx, php in an lxc.  It has 13 days of uptime currently and `free --mega` shows 103 used.... when I booted this machine the used memory was 82 so in 13 days (312 hours), the rate of memory use was 0.09 MB/hour... that's over 100 times less than either of the aarch64 boxes hmm

Last edited by graysky (2018-05-24 16:03:57)


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#17 2018-05-29 20:44:16

graysky
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From: :wq
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Re: Is this a kernel memory leak (kernel 4.16.7-1)?

I think the culprit could be systemd-journal.  Right now I am seeing the used memory (free --mega) track linearly with the resident size set (ps --sort -rss -eo pid,pmem,rss,vsz,comm) for systemd-journalctl.  I need to collect more data/will post back.

Last edited by graysky (2018-05-29 20:48:42)


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#18 2018-05-30 11:36:51

gandolin
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Registered: 2018-05-10
Posts: 9

Re: Is this a kernel memory leak (kernel 4.16.7-1)?

It's been about 7 days again for me and I'm not seeing a memory leak with the 4.14 kernel, "4.14.41-1-lts". I started running virtualbox VMs again as can be seen in the output of top. The total memory consumption is about 7GB, and it all seems to be explained by running processes and buff/cache usage.

top - 07:25:56 up 7 days,  6:28,  0 users,  load average: 0.16, 0.13, 0.04
Tasks: 256 total,   1 running, 255 sleeping,   0 stopped,   0 zombie
%Cpu(s):  0.2 us,  0.1 sy,  0.0 ni, 99.7 id,  0.0 wa,  0.0 hi,  0.0 si,  0.0 st
MiB Mem :  64334.1 total,  53802.2 free,   7275.5 used,   3256.4 buff/cache
MiB Swap:  32676.0 total,  32676.0 free,      0.0 used.  56592.9 avail Mem

  PID USER      PR  NI    VIRT    RES    SHR S  %CPU  %MEM     TIME+ COMMAND
16109 thor      20   0 7042960 931628 860584 S   1.0   1.4 173:17.67 VirtualBox
 1016 thor      20   0 2580068 530552 182868 S   0.0   0.8  38:34.30 firefox
14960 thor      20   0 4254468 401640 345400 S   1.3   0.6 162:26.29 VirtualBox
 1205 thor      20   0 2002060 304268 122648 S   0.0   0.5   7:53.79 Web Conte+
 1083 thor      20   0 2032824 270008  91736 S   0.3   0.4  49:36.45 Web Conte+
15024 thor      20   0 2090264 230364 130616 S   0.0   0.3   4:30.90 Web Conte+
 1270 thor      20   0 1986348 212660  97684 S   0.0   0.3 104:06.72 Web Conte+
  628 root      20   0 1053892 135104  87452 S   2.0   0.2  76:11.17 Xorg
14910 thor      20   0 2170444 121568  90236 S   0.0   0.2  25:58.00 VirtualBox
  781 thor      20   0 1019712  55552  40916 S   0.0   0.1   0:00.25 polkit-gn+
  775 thor      20   0 1039064  55056  42108 S   0.0   0.1   0:01.65 xfce4-pow+
  784 thor      20   0 1038936  54196  41296 S   0.0   0.1   0:00.24 xfce4-pow+
  967 thor      20   0  597168  44044  30444 S   1.0   0.1   0:12.18 xfce4-ter+
14938 thor      20   0  968376  38528  17504 S   0.7   0.1  59:30.19 VBoxSVC
  345 root      20   0  128404  32452  31704 S   0.0   0.0   0:00.90 systemd-j+

Are you sure that the memory leak happened with the 4.14 kernel as well on an x86_64?

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#19 2018-05-30 11:45:16

graysky
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From: :wq
Registered: 2008-12-01
Posts: 9,553
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Re: Is this a kernel memory leak (kernel 4.16.7-1)?

Yes, 100% sure both kernels on x86_64.


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