Re: Debugging system freezes on filesystem writes

From: Marcus Sundman
Date: Wed Feb 20 2013 - 04:24:42 EST

On 05.12.2012 17:32, Jan Kara wrote:
On Tue 27-11-12 18:14:42, Marcus Sundman wrote:
On 22.11.2012 01:30, Jan Kara wrote:
On Fri 16-11-12 03:11:22, Marcus Sundman wrote:
On 13.11.2012 15:51, Jan Kara wrote:
On Fri 09-11-12 15:12:43, Marcus Sundman wrote:
On 09.11.2012 01:41, Marcus Sundman wrote:
On 07.11.2012 18:17, Jan Kara wrote:
On Fri 02-11-12 04:19:24, Marcus Sundman wrote:
Also, and this might be important, according to iotop there is
almost no disk writing going on during the freeze. (Occasionally
there are a few MB/s, but mostly it's 0-200 kB/s.) Well, at least
when an iotop running on nice -20 hasn't frozen completely, which it
does during the more severe freezes.
OK, it seems as if your machine has some problems with memory
allocations. Can you capture /proc/vmstat before the freeze and
after the
freeze and send them for comparison. Maybe it will show us what is the
system doing.
Here are some more vmstats:

They are from running this:
while true; do cat /proc/vmstat > "vmstat.$(date +%FT%X).txt"; sleep
10; done

There were lots and lots of freezes for almost 20 mins from 14:37:45
onwards, pretty much constantly, but at 14:56:50 the freezes
suddenly stopped and everything went back to how it should be.
I was looking into the data but they didn't show anything problematic.
The machine seems to be writing a lot but there's always some free memory,
even direct reclaim isn't ever entered. Hum, actually you wrote iotop isn't
showing much IO going on but vmstats show there is about 1 GB written
during the freeze. It is not a huge amount given the time span but it
certainly gives a few MB/s of write load.
I didn't watch iotop during this particular freeze. I'll try to keep
an eye on iotop in the future. Is there some particular options I
should run iotop with, or is a "nice -n -20 iotop -od3" fine?
I'm not really familiar with iotop :). Usually I use iostat...
OK, which options for iostat should I use then? :)
I'm back from vacation. Sorry for the delay. You can use
iostat -x 1

Just when you got back I started my pre-vacation work stress and am now ending my post-vacation work-stress.. :)

That iostat -x 1 shows %util as 100 and w_await at 2,000 - 70,000.. like so:

avg-cpu: %user %nice %system %iowait %steal %idle
9.05 0.00 1.51 66.33 0.00 23.12
Device: rrqm/s wrqm/s r/s w/s rkB/s wkB/s avgrq-sz avgqu-sz await r_await w_await svctm %util
sda 0.00 0.00 0.00 1.00 0.00 184.00 368.00 137.08 62199.00 0.00 62199.00 1000.00 100.00

There's surprisingly high number of allocations going on but that may be
due to the IO activity. So let's try something else: Can you switch to
console and when the hang happens press Alt-Sysrq-w (or you can just do
"echo w >/proc/sysrq-trigger" if the machine is live enough to do that).
Then send me the output from dmesg. Thanks!
Sure! Here are two:
Thanks for those and sorry for the delay (I was busy with other stuff).
I had a look into those traces and I have to say I'm not much wiser. In the
first dump there is just kswapd waiting for IO. In the second dump there
are more processes waiting for IO (mostly for reads - nautilus,
thunderbird, opera, ...) but nothing really surprising. So I'm lost what
could cause the hangs you observe.
Yes, mostly it's difficult to trigger the sysrq thingy, because by
the time I manage to switch to the console or running that echo to
proc in a terminal the worst is already over.
I see. Maybe you could have something like
while true; do echo w >/proc/sysrq-trigger; sleep 10; done
running in the background?

Sure, but I suspect it'll take until the worst is over before it manages to load and execute that "echo w".

Recalling you wrote even simple programs
like top hang, maybe it is some CPU scheduling issue? Can you boot with
noautogroup kernel option?
Sure. I've been running with noautogroup for almost a week now, but
no big change one way or the other. (E.g., it's still impossible to
listen to music, because the songs will start skipping/looping
several times during each song even if there isn't any big "hang"
happening. And uncompressing a 100 MB archive (with nice '19' and
ionice 'idle') is still, after a while, followed by a couple of
minutes of superhigh I/O wait causing everything to become really
Hum, I'm starting to wander what's so special about your system that you
see these hangs while noone else seems to be hitting them. Your kernel is a
standard one from Ubuntu so tons of people run it. Your HW doesn't seem to
be too special either.

BTW the fact that you ionice 'tar' doesn't change anything because all the
writes are done in the context of kernel flusher thread (tar just writes
data into cache). But still it shouldn't lock the machine up. What might be
interesting test though is running:
dd if=/dev/zero of=file bs=1M count=200 oflags=direct

Does this trigger any hangs?

Yes, sure. If I run nothing else then it's not so severe, but the system is still quite unusable during the time it runs that dd.

Also, the speeds are closer to an Amiga500-era floppy drive than to an SSD from 2012 which this is:

$ dd if=/dev/zero of=iotest-file bs=1M count=200 oflag=direct
200+0 records in
200+0 records out
209715200 bytes (210 MB) copied, 171.701 s, 1.2 MB/s


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