Long lasting MM bug when swap is smaller than RAM

Long lasting MM bug when swap is smaller than RAM

[Attila Kinali]

Moin,

There has been a bug back in the 2.4.17 days that is somehow
triggered by swap being smaller than RAM, which i thought had
been fixed long ago, reappeared on one of the machines i manage.

<history>
Back in 2002, i had a few machines, running 2.4.x kernels, which
i upgraded heavily from some 16-64MB RAM to a couple 100MB
(changing mainboards at times, but keeping the harddisks).
Due to the upgrade of RAM, the swap size became a lot smaller
than RAM size, sometimes not even half as much.
Under most conditions these machines worked fine, but sometimes,
they showed a strange behavior: At times, the swap use would grow
(depending on the machine and its use faster or slower, sometimes
at 1MB/minute) until it was full. I couldnt figure out what filled
swap back then, couldnt find any programm that used a lot of memory.
And even more, the RAM portion that was used as cache and buffers
was most times still very large, ie it didnt seem like something using
a lot of memory.
After swap was full, nothing happend. No programms crashing, no errors
in the logs, nothing.... Until later (between hours and a few weeks),
the OOM would suddenly start to kick in and kill applications. This
time, something would use a lot of memory, but i couldn't figure out
what. None of the applications running would use more than usual.
And even killing the usual culprits (Mozilla, X11,...) wouldnt help.
The only cure was to reboot.

All the machines back then were running Debian, a vanilla kernel,
and had more RAM than swap and were x86 boxes. Other than that,
they didnt had much in common. One was a machine with an Adaptec
2940UW, others had IDE, one had a K6-III CPU, others were Intel.
Some had a lot of disk, others very little. Machine usage was
fileserver, firewall/router, desktop, laptop.

I reported this bug back then but never got an answer, so i used
the only fix i had available back then: disable swap completely.
</history>

Now, 7 years later, i have a machine that shows the same behavior.

Some data:

We have a HP DL380 G4 currently running a 2.6.29.4 vanilla kernel,
compiled for x86 32 bit.
It was originaly purchased in 2005 with 2GB RAM and a few weeks
ago upgraded to 6GB (no other changes beside this and a kernel upgrade).
The machine, being the MPlayer main server, runs a lighttpd, svnserve,
mailman, postfix, bind. Ie nothing unusual and the applications didn't
change in the last months (since the update from debian/etch to lenny).

---
root@natsuki:/home/attila# uname -a
Linux natsuki 2.6.29.4 #1 SMP Sun May 31 22:13:21 CEST 2009 i686 GNU/Linux
root@natsuki:/home/attila# uptime
 11:41:07 up 29 days, 13:17,  5 users,  load average: 0.15, 0.36, 0.54
root@natsuki:/home/attila# free -m
             total       used       free     shared    buffers     cached
Mem:          6023       5919        103          0        415       3873
-/+ buffers/cache:       1630       4393
Swap:         3812        879       2932
---

I want to point your attention at the fact that the machine has now
more RAM installed than it previously had RAM+Swap (ie before the upgrade).
Ie there is no reason it would need to swap out, at least not so much.

What is even more interesting is the amount of swap used over time.
Sampled every day at 10:00 CEST:

---
Date: Wed, 17 Jun 2009 10:00:01 +0200 (CEST)
Mem:          6023       5893        130          0        405       3834
Swap:         3812        190       3622

Date: Thu, 18 Jun 2009 10:00:01 +0200 (CEST)
Mem:          6023       5793        229          0        340       3939
Swap:         3812        225       3586

Date: Fri, 19 Jun 2009 10:00:01 +0200 (CEST)
Mem:          6023       5820        203          0        341       3899
Swap:         3812        275       3536

Date: Sun, 21 Jun 2009 10:00:01 +0200 (CEST)
Mem:          6023       5264        758          0        459       3181
Swap:         3812        325       3486

Date: Sat, 20 Jun 2009 10:00:01 +0200 (CEST)
Mem:          6023       5761        262          0        348       3865
Swap:         3812        297       3514

Date: Mon, 22 Jun 2009 10:00:01 +0200 (CEST)
Mem:          6023       5875        147          0        397       3681
Swap:         3812        353       3458

Date: Tue, 23 Jun 2009 10:00:01 +0200 (CEST)
Mem:          6023       5748        275          0        193       3949
Swap:         3812        415       3396

Date: Wed, 24 Jun 2009 10:00:01 +0200 (CEST)
Mem:          6023       5779        244          0        176       3924
Swap:         3812        519       3292

Date: Thu, 25 Jun 2009 10:00:01 +0200 (CEST)
Mem:          6023       5812        210          0        345       3856
Swap:         3812        611       3200

Date: Fri, 26 Jun 2009 10:00:01 +0200 (CEST)
Mem:          6023       5830        192          0        431       3688
Swap:         3812        682       3129

Date: Sat, 27 Jun 2009 10:00:01 +0200 (CEST)
Mem:          6023       5697        326          0        442       3621
Swap:         3812        719       3093

Date: Sun, 28 Jun 2009 10:00:02 +0200 (CEST)
Mem:          6023       5890        132          0        402       3886
Swap:         3812        784       3028

Date: Mon, 29 Jun 2009 10:00:01 +0200 (CEST)
Mem:          6023       5388        635          0        425       3321
Swap:         3812        826       2985
---

As you can see, although memory usage didnt change much over time,
swap usage increased from 190MB to 826MB in about two weeks.

As i'm pretty much clueless when it commes to how the linux VM works,
i would appreciate it if someone could give me some pointers on how
to figure out what causes this bug so that it could be fixed finally.

Thanks a lot in advance

			Attila Kinali

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Re: Long lasting MM bug when swap is smaller than RAM

[Hugh Dickins]

On Tue, 30 Jun 2009, Attila Kinali wrote:
> 
> There has been a bug back in the 2.4.17 days that is somehow
> triggered by swap being smaller than RAM, which i thought had
> been fixed long ago, reappeared on one of the machines i manage.

Snipped <history>, which I hope won't be repeated to the point of OOM.

> 
> Now, 7 years later, i have a machine that shows the same behavior.
> 
> Some data:
> 
> We have a HP DL380 G4 currently running a 2.6.29.4 vanilla kernel,
> compiled for x86 32 bit.
> It was originaly purchased in 2005 with 2GB RAM and a few weeks
> ago upgraded to 6GB (no other changes beside this and a kernel upgrade).
> The machine, being the MPlayer main server, runs a lighttpd, svnserve,
> mailman, postfix, bind. Ie nothing unusual and the applications didn't
> change in the last months (since the update from debian/etch to lenny).
> 
> ---
> root@natsuki:/home/attila# uname -a
> Linux natsuki 2.6.29.4 #1 SMP Sun May 31 22:13:21 CEST 2009 i686 GNU/Linux
> root@natsuki:/home/attila# uptime
>  11:41:07 up 29 days, 13:17,  5 users,  load average: 0.15, 0.36, 0.54
> root@natsuki:/home/attila# free -m
>              total       used       free     shared    buffers     cached
> Mem:          6023       5919        103          0        415       3873
> -/+ buffers/cache:       1630       4393
> Swap:         3812        879       2932
> ---
> 
> I want to point your attention at the fact that the machine has now
> more RAM installed than it previously had RAM+Swap (ie before the upgrade).
> Ie there is no reason it would need to swap out, at least not so much.
> 
> What is even more interesting is the amount of swap used over time.
> Sampled every day at 10:00 CEST:
> 
> ---
> Date: Wed, 17 Jun 2009 10:00:01 +0200 (CEST)
> Mem:          6023       5893        130          0        405       3834
> Swap:         3812        190       3622
> 
> Date: Thu, 18 Jun 2009 10:00:01 +0200 (CEST)
> Mem:          6023       5793        229          0        340       3939
> Swap:         3812        225       3586
> 
...
> 
> Date: Sun, 28 Jun 2009 10:00:02 +0200 (CEST)
> Mem:          6023       5890        132          0        402       3886
> Swap:         3812        784       3028
> 
> Date: Mon, 29 Jun 2009 10:00:01 +0200 (CEST)
> Mem:          6023       5388        635          0        425       3321
> Swap:         3812        826       2985
> ---
> 
> As you can see, although memory usage didnt change much over time,
> swap usage increased from 190MB to 826MB in about two weeks.
> 
> As i'm pretty much clueless when it commes to how the linux VM works,
> i would appreciate it if someone could give me some pointers on how
> to figure out what causes this bug so that it could be fixed finally.

I'm not sure that there's any problem here at all.  Beyond hibernation
to disk wanting enough swapspace to write its image, I can't think of
any reason why the kernel would misbehave if your swapspace is smaller
than your RAM.

One possibility is that this steady rise in swap usage just reflects
memory pressure (a nightly cron job?) pushing pages out to swap,
slightly different choices each time, and what's not modified later
gets left with a copy on swap.  That would tend to rise (at a slower
and slower rate) until swap is 50% full, then other checks should
keep it around that level.

If you do see it at more than 50% full in the morning, then yes,
I think you do have a leak: but it's more likely to be an
application than the kernel itself.  When kernel leaks occur,
they're often of "Slab:" memory - is that rising in /proc/meminfo?

Are you sure this steady rise in swap usage wasn't happening before
you added that RAM?  It's possible that you have an application which
decides how much memory to use, based on the amount of RAM in the
machine, itself assuming there's more than that of swap.

Do you have unwanted temporary files accumulating in a tmpfs?
Their pages get pushed out to swap.  Or a leak in shared memory:
does ipcs show increasing usage of shared memory?

Hugh

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Re: Long lasting MM bug when swap is smaller than RAM

[Attila Kinali]

Good morning,

On Tue, 30 Jun 2009 18:58:29 +0100 (BST)
Hugh Dickins <hugh.dickins@tiscali.co.uk> wrote:

> One possibility is that this steady rise in swap usage just reflects
> memory pressure (a nightly cron job?) pushing pages out to swap,

That might be true, if we wouldn't have now a lot more RAM than
swap+RAM before. Ie if we now would have memory pressure, then
we would have run out of swap space before and hence triggered the OOM
which didnt happen.

Tough, i did enable logging of the memory usage and swap space in
mrtg: http://natsuki.mplayerhq.hu/cgi-bin/mrtg-rrd.cgi/localmem.html
(blue is free mem w/o buffers/cache, red is used swap space).
The daily/weekly/monthly cron jobs are run between 6:25 and 7:00
but we dont have any increase in memory usage then.
What is interesting is the step at 4:10, which is exactly the time
when an rsync based backup of the mailman archives (lot of small files)
is started. But swap usage didnt increase at that time.
What is strange though, is that the backup takes about 13 minutes.
Most of that time is spend on traversing the directory tree and
stat'ing files. But the increase in memory usage is a sharp step
at the beginning only.

> slightly different choices each time, and what's not modified later
> gets left with a copy on swap.  That would tend to rise (at a slower
> and slower rate) until swap is 50% full, then other checks should
> keep it around that level.

I don't want to wait that long.

> 
> If you do see it at more than 50% full in the morning, then yes,
> I think you do have a leak: but it's more likely to be an
> application than the kernel itself.  When kernel leaks occur,
> they're often of "Slab:" memory - is that rising in /proc/meminfo?

I havent monitored /proc/meminfo yet.

> Are you sure this steady rise in swap usage wasn't happening before
> you added that RAM?  

Yes. I semi-regularly checked memory usage by hand and we never had
more than a couple MB of swap used.

> It's possible that you have an application which
> decides how much memory to use, based on the amount of RAM in the
> machine, itself assuming there's more than that of swap.

I dont think we have any application that does this. As I said, it's only a
web/mail/dns/svn server. There isnt anything fancy running.
Even the webpages are static only (beside the mailman interface).
The number of users on the machine is limited and none runs anything
directly on the machine (they are all just maintenance accounts).

> Do you have unwanted temporary files accumulating in a tmpfs?
> Their pages get pushed out to swap.  Or a leak in shared memory:
> does ipcs show increasing usage of shared memory?

/tmp is on a hard disk and thus doesnt add to memory usage.
The two tmpfs mounts (/dev/shm and /lib/init/rw) are completely
unused and empty.


			Attila Kinali

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Re: Long lasting MM bug when swap is smaller than RAM

[Robert Hancock]

On 06/30/2009 03:58 AM, Attila Kinali wrote:
> Moin,
>
> There has been a bug back in the 2.4.17 days that is somehow
> triggered by swap being smaller than RAM, which i thought had
> been fixed long ago, reappeared on one of the machines i manage.
>
> <history>

It's quite unlikely what you are seeing is at all related to that 
problem. The VM subsystem has been hugely changed since then.

> root@natsuki:/home/attila# free -m
>               total       used       free     shared    buffers     cached
> Mem:          6023       5919        103          0        415       3873
> -/+ buffers/cache:       1630       4393
> Swap:         3812        879       2932
> ---
>
> I want to point your attention at the fact that the machine has now
> more RAM installed than it previously had RAM+Swap (ie before the upgrade).
> Ie there is no reason it would need to swap out, at least not so much.
>
> What is even more interesting is the amount of swap used over time.
> Sampled every day at 10:00 CEST:
>
> ---
> Date: Wed, 17 Jun 2009 10:00:01 +0200 (CEST)
> Mem:          6023       5893        130          0        405       3834
> Swap:         3812        190       3622

..

> As you can see, although memory usage didnt change much over time,
> swap usage increased from 190MB to 826MB in about two weeks.
>
> As i'm pretty much clueless when it commes to how the linux VM works,
> i would appreciate it if someone could give me some pointers on how
> to figure out what causes this bug so that it could be fixed finally.

You didn't post what the swap usage history before the upgrade was. But 
swapping does not only occur if memory is running low. If disk usage is 
high then non-recently used data may be swapped out to make more room 
for disk caching.

Also, by increasing memory from 2GB to 6GB on a 32-bit kernel, some 
memory pressure may actually be increased since many kernel data 
structures can only be in low memory (the bottom 896MB). The more that 
the system memory is increased the more the pressure on low memory can 
become. Using a 64-bit kernel avoids this problem.

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Re: Long lasting MM bug when swap is smaller than RAM

[Attila Kinali]

On Tue, 30 Jun 2009 19:36:15 -0600
Robert Hancock <hancockrwd@gmail.com> wrote:

> On 06/30/2009 03:58 AM, Attila Kinali wrote:
> > Moin,
> >
> > There has been a bug back in the 2.4.17 days that is somehow
> > triggered by swap being smaller than RAM, which i thought had
> > been fixed long ago, reappeared on one of the machines i manage.
> >
> > <history>
> 
> It's quite unlikely what you are seeing is at all related to that 
> problem. The VM subsystem has been hugely changed since then.

That's why i thought this problem was fixed.

> You didn't post what the swap usage history before the upgrade was. 

Because i don't have any hard data on this. I checked it by hand
from time to time and we never had more than a few MB of swap used.

> But 
> swapping does not only occur if memory is running low. If disk usage is 
> high then non-recently used data may be swapped out to make more room 
> for disk caching.

Hmm..I didn't know this.. thanks!

 
> Also, by increasing memory from 2GB to 6GB on a 32-bit kernel, some 
> memory pressure may actually be increased since many kernel data 
> structures can only be in low memory (the bottom 896MB).

Interesting. But shouldnt memory be "swapped" to highmem first
before going out onto disk?

> The more that 
> the system memory is increased the more the pressure on low memory can 
> become. Using a 64-bit kernel avoids this problem.

Unfortunately, the CPU we have is still a pure 32bit CPU, so this option
cannot be used.

			Attila Kinali

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Re: Long lasting MM bug when swap is smaller than RAM

[Attila Kinali]

On Wed, 1 Jul 2009 10:04:32 +0200
Attila Kinali <attila@kinali.ch> wrote:

> > But 
> > swapping does not only occur if memory is running low. If disk usage is 
> > high then non-recently used data may be swapped out to make more room 
> > for disk caching.
> 
> Hmm..I didn't know this.. thanks!

This was the cause of the problem!

I just restarted svnserv, clamav and bind (the three applications
using most memory) and suddenly swap cleared up.

Now the question is, why did they accumulate so much used swap
space, while before the RAM upgrade, we hardly used the swap space at all?

		Attila Kinali

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Re: Long lasting MM bug when swap is smaller than RAM

[Zan Lynx]

Attila Kinali wrote:
> On Wed, 1 Jul 2009 10:04:32 +0200
> Attila Kinali <attila@kinali.ch> wrote:
> 
>>> But 
>>> swapping does not only occur if memory is running low. If disk usage is 
>>> high then non-recently used data may be swapped out to make more room 
>>> for disk caching.
>> Hmm..I didn't know this.. thanks!
> 
> This was the cause of the problem!
> 
> I just restarted svnserv, clamav and bind (the three applications
> using most memory) and suddenly swap cleared up.
> 
> Now the question is, why did they accumulate so much used swap
> space, while before the RAM upgrade, we hardly used the swap space at all?

I do not know about the others, but ClamAV suffers from pretty serious 
memory fragmentation.  What it does is load the updated signatures into 
a new memory allocation, verify them, then free the old signature 
allocation.  This results in a large hole in glibc's malloc structures 
and because of ClamAV's allocation pattern, this hole is difficult to 
reclaim.  This ClamAV memory fragmentation will continue to grow worse 
until the daemon is completely restarted.

Under memory pressure the kernel pushes least used pages out to swap, 
and these unused but still allocated pages of ClamAV are never again 
used, so out to swap they go.

I know this because the company I work for tried to fix the memory 
allocation fragmentation of ClamAV, but they did not like our patch and 
preferred to continue allowing the memory allocator to fragment in 
exchange for simpler code.

-- 
Zan Lynx
zlynx@acm.org

"Knowledge is Power.  Power Corrupts.  Study Hard.  Be Evil."

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Re: Long lasting MM bug when swap is smaller than RAM

[Wu Fengguang]

On Tue, Jun 30, 2009 at 11:58:19AM +0200, Attila Kinali wrote:
> Moin,
> 
> There has been a bug back in the 2.4.17 days that is somehow
> triggered by swap being smaller than RAM, which i thought had
> been fixed long ago, reappeared on one of the machines i manage.
> 
> <history>
> Back in 2002, i had a few machines, running 2.4.x kernels, which
> i upgraded heavily from some 16-64MB RAM to a couple 100MB
> (changing mainboards at times, but keeping the harddisks).
> Due to the upgrade of RAM, the swap size became a lot smaller
> than RAM size, sometimes not even half as much.
> Under most conditions these machines worked fine, but sometimes,
> they showed a strange behavior: At times, the swap use would grow
> (depending on the machine and its use faster or slower, sometimes
> at 1MB/minute) until it was full. I couldnt figure out what filled
> swap back then, couldnt find any programm that used a lot of memory.
> And even more, the RAM portion that was used as cache and buffers
> was most times still very large, ie it didnt seem like something using
> a lot of memory.
> After swap was full, nothing happend. No programms crashing, no errors
> in the logs, nothing.... Until later (between hours and a few weeks),
> the OOM would suddenly start to kick in and kill applications. This
> time, something would use a lot of memory, but i couldn't figure out
> what. None of the applications running would use more than usual.
> And even killing the usual culprits (Mozilla, X11,...) wouldnt help.
> The only cure was to reboot.
> 
> All the machines back then were running Debian, a vanilla kernel,
> and had more RAM than swap and were x86 boxes. Other than that,
> they didnt had much in common. One was a machine with an Adaptec
> 2940UW, others had IDE, one had a K6-III CPU, others were Intel.
> Some had a lot of disk, others very little. Machine usage was
> fileserver, firewall/router, desktop, laptop.
> 
> I reported this bug back then but never got an answer, so i used
> the only fix i had available back then: disable swap completely.
> </history>
> 
> Now, 7 years later, i have a machine that shows the same behavior.
> 
> Some data:
> 
> We have a HP DL380 G4 currently running a 2.6.29.4 vanilla kernel,
> compiled for x86 32 bit.
> It was originaly purchased in 2005 with 2GB RAM and a few weeks
> ago upgraded to 6GB (no other changes beside this and a kernel upgrade).
> The machine, being the MPlayer main server, runs a lighttpd, svnserve,
> mailman, postfix, bind. Ie nothing unusual and the applications didn't
> change in the last months (since the update from debian/etch to lenny).
> 
> ---
> root@natsuki:/home/attila# uname -a
> Linux natsuki 2.6.29.4 #1 SMP Sun May 31 22:13:21 CEST 2009 i686 GNU/Linux
> root@natsuki:/home/attila# uptime
>  11:41:07 up 29 days, 13:17,  5 users,  load average: 0.15, 0.36, 0.54
> root@natsuki:/home/attila# free -m
>              total       used       free     shared    buffers     cached
> Mem:          6023       5919        103          0        415       3873
> -/+ buffers/cache:       1630       4393
> Swap:         3812        879       2932
> ---

Hi Attila, 

What's your /proc/meminfo and/or /proc/vmstat contents?
Are you making use of tmpfs, or intel graphics devices with drm?

Thanks,
Fengguang

> I want to point your attention at the fact that the machine has now
> more RAM installed than it previously had RAM+Swap (ie before the upgrade).
> Ie there is no reason it would need to swap out, at least not so much.
> 
> What is even more interesting is the amount of swap used over time.
> Sampled every day at 10:00 CEST:
> 
> ---
> Date: Wed, 17 Jun 2009 10:00:01 +0200 (CEST)
> Mem:          6023       5893        130          0        405       3834
> Swap:         3812        190       3622
> 
> Date: Thu, 18 Jun 2009 10:00:01 +0200 (CEST)
> Mem:          6023       5793        229          0        340       3939
> Swap:         3812        225       3586
> 
> Date: Fri, 19 Jun 2009 10:00:01 +0200 (CEST)
> Mem:          6023       5820        203          0        341       3899
> Swap:         3812        275       3536
> 
> Date: Sun, 21 Jun 2009 10:00:01 +0200 (CEST)
> Mem:          6023       5264        758          0        459       3181
> Swap:         3812        325       3486
> 
> Date: Sat, 20 Jun 2009 10:00:01 +0200 (CEST)
> Mem:          6023       5761        262          0        348       3865
> Swap:         3812        297       3514
> 
> Date: Mon, 22 Jun 2009 10:00:01 +0200 (CEST)
> Mem:          6023       5875        147          0        397       3681
> Swap:         3812        353       3458
> 
> Date: Tue, 23 Jun 2009 10:00:01 +0200 (CEST)
> Mem:          6023       5748        275          0        193       3949
> Swap:         3812        415       3396
> 
> Date: Wed, 24 Jun 2009 10:00:01 +0200 (CEST)
> Mem:          6023       5779        244          0        176       3924
> Swap:         3812        519       3292
> 
> Date: Thu, 25 Jun 2009 10:00:01 +0200 (CEST)
> Mem:          6023       5812        210          0        345       3856
> Swap:         3812        611       3200
> 
> Date: Fri, 26 Jun 2009 10:00:01 +0200 (CEST)
> Mem:          6023       5830        192          0        431       3688
> Swap:         3812        682       3129
> 
> Date: Sat, 27 Jun 2009 10:00:01 +0200 (CEST)
> Mem:          6023       5697        326          0        442       3621
> Swap:         3812        719       3093
> 
> Date: Sun, 28 Jun 2009 10:00:02 +0200 (CEST)
> Mem:          6023       5890        132          0        402       3886
> Swap:         3812        784       3028
> 
> Date: Mon, 29 Jun 2009 10:00:01 +0200 (CEST)
> Mem:          6023       5388        635          0        425       3321
> Swap:         3812        826       2985
> ---
> 
> As you can see, although memory usage didnt change much over time,
> swap usage increased from 190MB to 826MB in about two weeks.
> 
> As i'm pretty much clueless when it commes to how the linux VM works,
> i would appreciate it if someone could give me some pointers on how
> to figure out what causes this bug so that it could be fixed finally.
> 
> Thanks a lot in advance
> 
> 			Attila Kinali
> 
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