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Date

[Bug 1013807] Re: transparent hugepages and thrashing on amd64

To: kernel-packages@xxxxxxxxxxxxxxxxxxx
From: garyr <1013807@xxxxxxxxxxxxxxxxxx>
Date: Fri, 11 Dec 2015 23:07:22 -0000
Reply-to: Bug 1013807 <1013807@xxxxxxxxxxxxxxxxxx>
Sender: bounces@xxxxxxxxxxxxx

apport information

** Tags added: apport-collected wily

** Description changed:

I seem to have found a solution to a severe thrashing/swapping/freezing
problem that I've been having for months now. I guess the real question
is - should I turn it into a bug report and what would be useful data to
include if so.

This is a quad core AMD Phaeom system with 4G of ram, dual monitors and
a single 1TB WD caviar black HD. It had been behaving normally until
something broke sometime late in the 11.x release cycle and continues in
the current 12.04 LTS. The symptoms are running a moderate load of apps
(firefox with ~8 tabs, a terminal or 2, and aisleriot solitaire for
example) and experiencing system freezes where the entire UI becomes
totally unresponsive for 20 seconds - 5 minutes with solid disk
activity. Trying to figure out what was going on via iotop and top show
jbd2 and kswapd accounting for the largest load, but since it freezes
iotop like everything else I can't tell what's going during the worst
storms. Googling around shows a fair number of other people with
similar problems, most of them with multi core amd64 systems.

The other day I spotted this report on opensuse that looked similar but
not identical:

http://lists.opensuse.org/opensuse/2012-03/msg00657.html

I booted with the grub parameter transparent_hugepage=never yesterday
and the problem went and away and hasn't come back. I've streesed the
system by running a bunch of flash/java tabs in firefox, running a
large java based stock app (ThinkorSwim) in another workspace and
playing a 1080p 60fps movie in a third workspace. This certainly causes
swapping, but not freezing or stumbling. It actually did a bit of
swapping a minute ago while I was typing and it managed to make Pandora
radio stumble for a moment - but that's orders of magnitude better than
it has been.

I think there may be a fundamental problem with how transparent
hugepages are handled with some AMD CPUs. I think this problem started
when this feature was implemented and enabled by default. The manpage
for madvise() says this was added in 2.6.38, but I don't know if it was
enabled by default at that point.

Hre's a partial list of things that haven't worked well in the past:

Playing with the swappiness value: setting swappiness to very low values
makes the problem take longer to surface, but (unsurprisinglly) makes it
even worse once it does.

swapoff-a ; swapon-a: this makes it go away for a while. A potentially
interesting thing is that as soon as I can get the system to act on the
swapoff -a the system becomes responsive again. It pegs once CPU core at
100% and the HD grinds like crazy but it stops freezing right away.

Moving swap from the HD to a USB thumb drive: Obviously I didn't expect
that to be faster but wanted to see if segregating swap to a different
device on a different bus would make it swap more smoothly - it didn't.

Playing with nice and ionice priorities for jdb2, kswapd. The fact that
running these processes at a lower priority than anything else on the
system makes no difference leads me to think they were just symptoms and
not at the root of the problem.

I think this may be a tip of the iceberg and there may be a lot of other
having this problem. Looking around I see a fair number of reports,
most of them unsolved. Some may have been fixed by just adding enough
RAM that dirty hugepages just don't collect. Some may have been fixed
by chaanging filesystems - ext4 seems like something a lot of people
with this problem have in common.

Workaround:
hold down the spacebar during boot in order to bring up the grub menu, edit the command line and add
transparent_hugepage=never

If this fixes the problem you can make it permanent by editing
/etc/default/grub and adding the ransparent_hugepage=never to the
GRUB_CMDLINE_LINUX_DEFAULT line and then running update-grub

Problems with this workaround:
1) transparent hugepages should work. This may cause a small performance hit in some situations and a larger hit in others.
2) If you do this you will probably never know when or if it actually gets fixed.

PS: Lars Müller [ˈlaː(r)z ˈmʏlɐ]
Samba Team
SUSE Linux, Maxfeldstraße 5, 90409 Nürnberg, Germany

is looking for bugzilla reports on this too.
+ ---
+ ApportVersion: 2.19.1-0ubuntu5
+ Architecture: amd64
+ AudioDevicesInUse:
+ USER PID ACCESS COMMAND
+ /dev/snd/controlC0: garyrich 2339 F.... pulseaudio
+ /dev/snd/controlC1: garyrich 2339 F.... pulseaudio
+ CurrentDesktop: Unity
+ DistroRelease: Ubuntu 15.10
+ EcryptfsInUse: Yes
+ HibernationDevice: RESUME=UUID=5b22d42d-33c8-435c-bea0-c1fbba7f88bf
+ InstallationDate: Installed on 2010-01-22 (2149 days ago)
+ InstallationMedia: Ubuntu 9.10 "Karmic Koala" - Release amd64 (20091027)
+ IwConfig:
+ eth0 no wireless extensions.
+
+ lo no wireless extensions.
+ MachineType: System manufacturer System Product Name
+ Package: linux (not installed)
+ ProcFB: 0 radeondrmfb
+ ProcKernelCmdLine: BOOT_IMAGE=/boot/vmlinuz-4.2.0-19-generic root=UUID=ab3cda85-2125-40b3-a1d0-f27222cc9ff6 ro quiet splash elevator=cfq vt.handoff=7
+ ProcVersionSignature: Ubuntu 4.2.0-19.23-generic 4.2.6
+ RelatedPackageVersions:
+ linux-restricted-modules-4.2.0-19-generic N/A
+ linux-backports-modules-4.2.0-19-generic N/A
+ linux-firmware 1.149.3
+ RfKill:
+
+ Tags: wily
+ Uname: Linux 4.2.0-19-generic x86_64
+ UpgradeStatus: No upgrade log present (probably fresh install)
+ UserGroups: adm admin audio cdrom debian-tor dialout dip fax fuse games lpadmin messagebus netdev plugdev sambashare ssh staff syslog tape users video
+ _MarkForUpload: True
+ dmi.bios.date: 04/13/2011
+ dmi.bios.vendor: American Megatrends Inc.
+ dmi.bios.version: 3503
+ dmi.board.asset.tag: To Be Filled By O.E.M.
+ dmi.board.name: M4A78T-E
+ dmi.board.vendor: ASUSTeK Computer INC.
+ dmi.board.version: Rev 1.xx
+ dmi.chassis.asset.tag: Asset-1234567890
+ dmi.chassis.type: 3
+ dmi.chassis.vendor: Chassis Manufacture
+ dmi.chassis.version: Chassis Version
+ dmi.modalias: dmi:bvnAmericanMegatrendsInc.:bvr3503:bd04/13/2011:svnSystemmanufacturer:pnSystemProductName:pvrSystemVersion:rvnASUSTeKComputerINC.:rnM4A78T-E:rvrRev1.xx:cvnChassisManufacture:ct3:cvrChassisVersion:
+ dmi.product.name: System Product Name
+ dmi.product.version: System Version
+ dmi.sys.vendor: System manufacturer

** Attachment added: "AlsaInfo.txt"
https://bugs.launchpad.net/bugs/1013807/+attachment/4533433/+files/AlsaInfo.txt

--
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https://bugs.launchpad.net/bugs/1013807

Title:
transparent hugepages and thrashing on amd64

Status in linux package in Ubuntu:
Incomplete

Bug description:
I seem to have found a solution to a severe
thrashing/swapping/freezing problem that I've been having for months
now. I guess the real question is - should I turn it into a bug
report and what would be useful data to include if so.

This is a quad core AMD Phaeom system with 4G of ram, dual monitors
and a single 1TB WD caviar black HD. It had been behaving normally
until something broke sometime late in the 11.x release cycle and
continues in the current 12.04 LTS. The symptoms are running a
moderate load of apps (firefox with ~8 tabs, a terminal or 2, and
aisleriot solitaire for example) and experiencing system freezes where
the entire UI becomes totally unresponsive for 20 seconds - 5 minutes
with solid disk activity. Trying to figure out what was going on via
iotop and top show jbd2 and kswapd accounting for the largest load,
but since it freezes iotop like everything else I can't tell what's
going during the worst storms. Googling around shows a fair number of
other people with similar problems, most of them with multi core amd64
systems.

The other day I spotted this report on opensuse that looked similar
but not identical:

http://lists.opensuse.org/opensuse/2012-03/msg00657.html

I booted with the grub parameter transparent_hugepage=never yesterday
and the problem went and away and hasn't come back. I've streesed the
system by running a bunch of flash/java tabs in firefox, running a
large java based stock app (ThinkorSwim) in another workspace and
playing a 1080p 60fps movie in a third workspace. This certainly
causes swapping, but not freezing or stumbling. It actually did a bit
of swapping a minute ago while I was typing and it managed to make
Pandora radio stumble for a moment - but that's orders of magnitude
better than it has been.

I think there may be a fundamental problem with how transparent
hugepages are handled with some AMD CPUs. I think this problem
started when this feature was implemented and enabled by default. The
manpage for madvise() says this was added in 2.6.38, but I don't know
if it was enabled by default at that point.

Hre's a partial list of things that haven't worked well in the past:

Playing with the swappiness value: setting swappiness to very low
values makes the problem take longer to surface, but (unsurprisinglly)
makes it even worse once it does.

swapoff-a ; swapon-a: this makes it go away for a while. A
potentially interesting thing is that as soon as I can get the system
to act on the swapoff -a the system becomes responsive again. It pegs
once CPU core at 100% and the HD grinds like crazy but it stops
freezing right away.

Moving swap from the HD to a USB thumb drive: Obviously I didn't
expect that to be faster but wanted to see if segregating swap to a
different device on a different bus would make it swap more smoothly -
it didn't.

Playing with nice and ionice priorities for jdb2, kswapd. The fact
that running these processes at a lower priority than anything else on
the system makes no difference leads me to think they were just
symptoms and not at the root of the problem.

I think this may be a tip of the iceberg and there may be a lot of
other having this problem. Looking around I see a fair number of
reports, most of them unsolved. Some may have been fixed by just
adding enough RAM that dirty hugepages just don't collect. Some may
have been fixed by chaanging filesystems - ext4 seems like something a
lot of people with this problem have in common.

Workaround:
hold down the spacebar during boot in order to bring up the grub menu, edit the command line and add
transparent_hugepage=never

If this fixes the problem you can make it permanent by editing
/etc/default/grub and adding the ransparent_hugepage=never to the
GRUB_CMDLINE_LINUX_DEFAULT line and then running update-grub

PS: Lars Müller [ˈlaː(r)z ˈmʏlɐ]
Samba Team
SUSE Linux, Maxfeldstraße 5, 90409 Nürnberg, Germany

is looking for bugzilla reports on this too.
---
ApportVersion: 2.19.1-0ubuntu5
Architecture: amd64
AudioDevicesInUse:
USER PID ACCESS COMMAND
/dev/snd/controlC0: garyrich 2339 F.... pulseaudio
/dev/snd/controlC1: garyrich 2339 F.... pulseaudio
CurrentDesktop: Unity
DistroRelease: Ubuntu 15.10
EcryptfsInUse: Yes
HibernationDevice: RESUME=UUID=5b22d42d-33c8-435c-bea0-c1fbba7f88bf
InstallationDate: Installed on 2010-01-22 (2149 days ago)
InstallationMedia: Ubuntu 9.10 "Karmic Koala" - Release amd64 (20091027)
IwConfig:
eth0 no wireless extensions.

lo no wireless extensions.
MachineType: System manufacturer System Product Name
Package: linux (not installed)
ProcFB: 0 radeondrmfb
ProcKernelCmdLine: BOOT_IMAGE=/boot/vmlinuz-4.2.0-19-generic root=UUID=ab3cda85-2125-40b3-a1d0-f27222cc9ff6 ro quiet splash elevator=cfq vt.handoff=7
ProcVersionSignature: Ubuntu 4.2.0-19.23-generic 4.2.6
RelatedPackageVersions:
linux-restricted-modules-4.2.0-19-generic N/A
linux-backports-modules-4.2.0-19-generic N/A
linux-firmware 1.149.3
RfKill:

Tags: wily
Uname: Linux 4.2.0-19-generic x86_64
UpgradeStatus: No upgrade log present (probably fresh install)
UserGroups: adm admin audio cdrom debian-tor dialout dip fax fuse games lpadmin messagebus netdev plugdev sambashare ssh staff syslog tape users video
_MarkForUpload: True
dmi.bios.date: 04/13/2011
dmi.bios.vendor: American Megatrends Inc.
dmi.bios.version: 3503
dmi.board.asset.tag: To Be Filled By O.E.M.
dmi.board.name: M4A78T-E
dmi.board.vendor: ASUSTeK Computer INC.
dmi.board.version: Rev 1.xx
dmi.chassis.asset.tag: Asset-1234567890
dmi.chassis.type: 3
dmi.chassis.vendor: Chassis Manufacture
dmi.chassis.version: Chassis Version
dmi.modalias: dmi:bvnAmericanMegatrendsInc.:bvr3503:bd04/13/2011:svnSystemmanufacturer:pnSystemProductName:pvrSystemVersion:rvnASUSTeKComputerINC.:rnM4A78T-E:rvrRev1.xx:cvnChassisManufacture:ct3:cvrChassisVersion:
dmi.product.name: System Product Name
dmi.product.version: System Version
dmi.sys.vendor: System manufacturer

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