Kernel v4.7-rc5 - performance degradation upto 40% after disabling and re-enabling a core

[Jirka Hladky]

Hello,

on NUMA enabled server equipped with 4 Intel E5-4610 v2 CPUs we
observe following performance degradation:

Runtime to run "lu.C.x" test from NAS Parallel Benchmarks after
booting the kernel:

real  1m57.834s
user  113m51.520s

Then we disable and re-enable one core:

echo 0 > /sys/devices/system/cpu/cpu1/online
echo 1 > /sys/devices/system/cpu/cpu1/online

and rerun the same test. Runtime is now degraded (by 40% for user time
and by 30% for the real (wall-clock) time) using all 64 cores

real 2m47.746s
user 160m46.109s

The issue was first reported in "The Linux Scheduler: a Decade of
Wasted Cores" paper
http://www.ece.ubc.ca/~sasha/papers/eurosys16-final29.pdf
https://github.com/jplozi/wastedcores/issues/1

How to reproduce the issue:

A) Get benchmark and compile it:

1) wget http://www.nas.nasa.gov/assets/npb/NPB3.3.1.tar.gz
2) tar zxvf NPB3.3.1.tar.gz
3) cd ~/NPB3.3.1/NPB3.3-OMP/config/
4) ln -sf NAS.samples/make.def.gcc_x86 make.def (assuming using gcc compiler)
5) ln -sf NAS.samples/suite.def.lu suite.def
6) cd ~/NPB3.3.1/NPB3.3-OMP
7) make suite
8) You should have now in directory ~/NPB3.3.1/NPB3.3-OMP/bin
benchmarks  lu.*. The binaries are alphabetically sorted by runtime
with  "lu.A.x" having the shortest runtime.

B) Reproducing the issue (see also attached script)

Remark: we have done the tests with autogroup disabled
sysctl -w kernel.sched_autogroup_enabled=0
to avoid this issue on 4.7 kernel:
https://bugzilla.kernel.org/show_bug.cgi?id=120481

The test was conducted on NUMA server with 4 nodes and using all
available 64 cores.

1) (time bin/lu.C.x) |& tee $(uname
-r)_lu.C.x.log_before_reenable_kernel.sched_autogroup_enabled=0

2) disable and re-enable one core
echo 0 > /sys/devices/system/cpu/cpu1/online
echo 1 > /sys/devices/system/cpu/cpu1/online

3) (time bin/lu.C.x) |& tee $(uname
-r)_lu.C.x.log_after_reenable_kernel.sched_autogroup_enabled=0

grep "real\|user" *lu.C*

You will see significant difference in both real and user time.

Regarding to the authors of the paper the root cause of the problem is
a missing call to regenerate domains inside NUMA nodes after
re-enabling CPU. The problem was introduced in 3.19 kernel. The
authors of paper has proposed a patch which applies to 4.1 kernel.
Here is the link:
https://github.com/jplozi/wastedcores/blob/master/patches/missing_sched_domains_linux_4.1.patch

===========For the completeness here are the results with 4.6 kernel===========

AFTER BOOT
real    1m31.639s
user    89m24.657s

AFTER core has been disabled and re-enabled
real    2m44.566s
user    157m59.814s

Please notice that 4.6 kernel problem is much more visible than with
4.7 rc5 kernel.

At the same time, 4.6 kernel delivers much better performance after
boot than 4.7 rc5 kernel which might indicate that another problem is
in play.
=================================================================

I have also tested kernel provided by Peter Zijlstra on Friday, June
24th which provides fix for
https://bugzilla.kernel.org/show_bug.cgi?id=120481. It does not fix
this issue and kernel right after boot performs worse than 4.6 kernel
right after boot so we may in fact face two problems here.

========Results with 4.7.0-02548776ded1185e6e16ad0a475481e982741ee9 kernel=====
git://git.kernel.org/pub/scm/linux/kernel/git/peterz/queue.git sched/urgent
$ git rev-parse HEAD
02548776ded1185e6e16ad0a475481e982741ee9

 AFTER BOOT
real        1m58.549s
user        113m31.448s

AFTER core has been disabled and re-enabled
real 2m35.930s
user 148m20.795s
=================================================================

Thanks a lot!
Jirka

PS: I have opened this BZ to track this issue
Bug 121121 - Kernel v4.7-rc5 - performance degradation upto 40% after
disabling and re-enabling a core
https://bugzilla.kernel.org/show_bug.cgi?id=121121

Attachment: reproduce.sh
Description: Bourne shell script