[Bug 1928744] Re: Disk IO very slow on kernel 4.15.0-142-generic

2021-07-21 Thread Zahid Bukhari
This bug is also affecting us.  We're on Xenial but use this kernel for
HWE. Basically for our monitoring, the leader to all this shows as dirty
memory and or filesystem writeback.

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[Bug 1928744] Re: Disk IO very slow on kernel 4.15.0-142-generic

2021-07-08 Thread Leon van Heerden
I have also been running 4.15.0-144-generic for three weeks so far
without the issue occurring.

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[Bug 1928744] Re: Disk IO very slow on kernel 4.15.0-142-generic

2021-07-05 Thread Mariusz
John - thanks for finding ==> 
https://bugs.launchpad.net/ubuntu/+source/linux/+bug/1926081
There is a great testing work done there.

For this thread I have been running kernel 4.15.0-144-generic for the
last 3 weeks and haven't seen the issue.

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[Bug 1928744] Re: Disk IO very slow on kernel 4.15.0-142-generic

2021-07-05 Thread John McDonnell
I note it is possible this is a duplicate of
https://bugs.launchpad.net/ubuntu/+source/linux/+bug/1926081

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[Bug 1928744] Re: Disk IO very slow on kernel 4.15.0-142-generic

2021-06-29 Thread Paul Krizak
We were directed to this bug by our Portworx support team, and believe
we're seeing the same thing.

We are running Ubuntu 16.04 with the hardware enablement kernel.  Most
of our nodes are running 4.15.0-140, and like Peter notes above, the I/O
performance problem does not show up right away, but takes a few days to
appear.  When it gets bad, we see exactly the same behavior when looking
at `iotop`, where any processes doing more than trivial I/O show as
99.9% IOWAIT time.  The system performs sluggishly (notably the
container runtime) and a reboot "fixes" the problem.

Our strategy at the moment is roll back to the -136 kernel on all of our
bare metal Kubernetes nodes, and hopefully get upgraded to Ubuntu 20.04
by the end of the year.

If any further testing is requested please let us know and we can try
things out on our dev systems.

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[Bug 1928744] Re: Disk IO very slow on kernel 4.15.0-142-generic

2021-06-23 Thread Peter Jönsson
Hi!

We are running some large (100+) kubernetes clusters on bare metal
machines also running a LSI MegaRAID controller and we are experiencing
these exact problems since about a week (cluster being in production
since early june).

We run with this controller:

# lspci | grep -i mega
59:00.0 RAID bus controller: LSI Logic / Symbios Logic MegaRAID Tri-Mode 
SAS3516 (rev 01)


After being in operation and taking production traffic (we are very IO intense) 
for less month both clusters started behaving weirdly with timeouts between 
processes on different nodes. After much debugging we found that basically IO 
performance had ground to a halt. Here is a quick summary of what we found 
together with our external partner (developer of our software defined storage 
solution):

We analyzed a small subset of nodes encountering the issue. Based on our
initial diagnosis, here are the findings:

- The CPU and IO utilization were low but all systems reported high load 
averages.
- All disks looked fine - root and data disks. The IO load was very small with 
no visible spikes in latencies. None of the devices were unresponsive/stuck.
- All user space processes looked fine, none were blocked.
- The systems were slow in general. i.e. Installing packages and writing even 
to the root disk was very slow.
- A kernel thread dump showed a lot of them in D state, all stuck on writing to 
the page cache.
- We used dd to write a small 1M file on the host (NOT on px device), requiring 
no disk io and it showed the same symptoms.
- System dirty threshold settings do not show anything out of the ordinary.
- All the affected nodes another common symptom is that the page cache drain 
appeared to be slow/stuck. Amount of pages in the writeback list is high but no 
writeback appeared to be happening.

These clusters all run a 18.04 LTS but have different kernels depending
on their patch level:

Cluster A:

 228 4.15.0-140-generic
  74 4.15.0-142-generic
   7 4.15.0-143-generic


Cluster B:

 418 4.15.0-136-generic
  22 4.15.0-144-generic
  12 4.15.0-143-generic
   9 4.15.0-142-generic


Cluster A is the one with the worst performance. Cluster B have had similar 
problems but since the majority of the nodes are on 136 it has not been so 
badly hit.

Our only remedy for now have been to downgrade to 136 and/or rebooting
the machines. Rebooting the machines but staying on the problematic
kernel works for now, but most likely we will see the same behavior in a
week or so of taking production traffic.

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[Bug 1928744] Re: Disk IO very slow on kernel 4.15.0-142-generic

2021-06-21 Thread Mariusz
Hey,

We experienced the performance issue on different hardware servers:

LENOVO System x3650 M5
Lenovo ThinkSystem SR650

with the following kernels:

4.15.0-137-generic: disk performance issue
4.15.0-139-generic: disk performance issue
4.15.0-140-generic: disk performance issue
4.15.0-142-generic: disk performance issue

I haven't seen this issue on virtual machines (VMware VMs Ubuntu 18/20).
At the moment, I'm testing "4.15.0-144-generic". To early to say it is free of 
the bug - I will come back in a week.

Thanks
Mariusz

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[Bug 1928744] Re: Disk IO very slow on kernel 4.15.0-142-generic

2021-06-18 Thread Leon van Heerden
Hi, 
We think we are affected by the same bug. 
We were on version 4.15.0-139 and upgraded to 144 before finding this post. 
Is there any confirmation that this issue also occurs in 4.15.0-144? 

I have have installed version 4.15.0-136 in the meantime to allow us to
reboot and select that kernel, incase the issue is present.

Hope to see a fix for this issue soon.

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  Disk IO very slow on kernel 4.15.0-142-generic

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[Bug 1928744] Re: Disk IO very slow on kernel 4.15.0-142-generic

2021-06-18 Thread Launchpad Bug Tracker
Status changed to 'Confirmed' because the bug affects multiple users.

** Changed in: linux (Ubuntu Bionic)
   Status: New => Confirmed

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[Bug 1928744] Re: Disk IO very slow on kernel 4.15.0-142-generic

2021-06-08 Thread Mariusz
Hi Khaled,

I have finished testing the kernels - it took more time than I expected
but the results are:

4.15.0-136-generic: no issues
4.15.0-137-generic: disk performance issue
4.15.0-139-generic: disk performance issue
4.15.0-140-generic: disk performance issue
4.15.0-142-generic: disk performance issue

Each kernel was running for minimum 7 days. Those which have disk
performance issue start to break after few days of normal workload.

Here is an example of "iotop -a", when our disk operations are
throttled:

Actual DISK READ:   0.00 B/s | Actual DISK WRITE:   0.00 B/s
  TID  PRIO  USER DISK READ  DISK WRITE  SWAPIN IO>COMMAND  

   
10908 be/4 barman0.00 B144.00 K  0.00 % 99.99 % pg_receivewal 
--dbname=dbname=replication host=XX replication=~o-password 
--directory=/data/barman/X/streaming --slot=barman
 9494 be/4 barman0.00 B144.00 K  0.00 % 99.99 % rsync --server 
-logDtpre.iLsfxC . /data/barman/XX/incoming/0001318300ED
10907 be/4 barman0.00 B144.00 K  0.00 % 99.99 % pg_receivewal 
--dbname=dbname=replication host=XX replication~-password 
--directory=/data/barman/XXX/streaming --slot=barman
 7148 be/4 barman0.00 B144.00 K  0.00 % 99.99 % rsync --server 
-logDtpre.iLsfxC . /data/barman/XX/incoming/0001D2E90043
11144 be/4 barman0.00 B144.00 K  0.00 % 99.99 % pg_receivewal 
--dbname=dbname=replication host=X replication=~o-password 
--directory=/data/barman/X/streaming --slot=barman
17724 be/3 root  0.00 B  8.00 K  0.00 % 99.99 % auditd
11217 be/4 root  0.00 B  8.00 K  0.00 % 99.99 % syslog-ng -F
10003 be/4 barman0.00 B 96.00 K  0.00 % 99.99 % gpg -e -r 
BarmanBackup
10219 be/4 barman0.00 B 96.00 K  0.00 % 99.99 % gpg -e -r 
BarmanBackup
 9247 be/4 barman0.00 B140.00 K  0.00 % 98.62 % rsync --server 
-logDtpre.iLsfxC . 
/data/barman/mel-attn-hostdb/incoming/00014CE00083
11391 be/4 barman0.00 B140.00 K  0.00 % 98.60 % pg_receivewal 
--dbname=dbname=replication host=XXX replication=~o-password 
--directory=/data/barmanXXX/streaming --slot=barman
 9556 be/4 barman0.00 B 92.00 K  0.00 % 98.53 % gpg -e -r 
BarmanBackup
 4381 be/4 root  0.00 B  8.00 K  0.00 % 57.53 % sadc -F -L -S DISK 
60 /var/log/sysstat
10959 be/4 root  0.00 B  4.00 K  0.00 % 26.29 % sadc -F -L -S DISK 
60 /var/log/sysstat
15626 be/4 root  0.00 B  4.00 K  0.00 %  8.22 % sadc -F -L -S DISK 
60 /var/log/sysstat


So, I think it is ok to say that the problem was introduced with 
4.15.0-137-generic.


We will try to see the latest kernel in our next patching window. However, 
based on the fact that kernels 137,139,140,142 are not working correctly, could 
this be related to some tuning changes? In our case, we haven't done any 
changes to e.g. sysctl after patching.

Many thanks for your help so far!

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[Bug 1928744] Re: Disk IO very slow on kernel 4.15.0-142-generic

2021-06-08 Thread Khaled El Mously
Thanks for the extensive testing, Mariusz. (I assume -137 doesn't have
the performance problem?)

So, for comment #9 - the difference in loaded modules comes down to 20
additional modules that were loaded when performance was bad:

-ip6_tables 28672 0
-iptable_filter 16384 0
-ip_tables 28672 1 iptable_filter
-x_tables 40960 3 iptable_filter,ip6_tables,ip_tables
-tcp_diag 16384 0
-udp_diag 16384 0
-inet_diag 24576 2 tcp_diag,udp_diag
-cpuid 16384 0
-btrfs 1155072 0
-zstd_compress 163840 1 btrfs
-xor 24576 1 btrfs
-raid6_pq 114688 1 btrfs
-ufs 77824 0
-qnx4 16384 0
-minix 32768 0
-ntfs 102400 0
-msdos 20480 0
-jfs 188416 0
-xfs 1204224 0
-libcrc32c 16384 1 xfs


Seems they are mostly filesystem modules and iptables modules. It is possible 
that this could affect performance - though unlikely to cause performance 
issues simply by them being loaded. If they are causing the performance hit it 
would probably mean that some thing else is running not just additional modules 
loaded in memory.

So, if I understand correctly, -140 seemed initially fine, but after
some time, performance degrades. That makes things a bit more
interesting. Do you see those additional modules loaded when performance
is degraded? Note that all those additional modules don't seem to have
any external dependencies other than themselves - they depend only on
each other. So it should be easily possible to unload them and see if
that "fixes" the performance issue.

By the way, kernels -143 and -144 have been released since this bug was
created. Maybe it is worthwhile to also try those kernels?

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[Bug 1928744] Re: Disk IO very slow on kernel 4.15.0-142-generic

2021-05-30 Thread Mariusz
Hi,

I have done longer testing of kernel 140 and it has performance
degradation issue as well. It took a couple of days to fully max out
disk IOs on that kernel with the same load. Therefore, I came back to
testing the other kernels in longer time-window.

At the moment, I'm running kernel 4.15.0-137-generic. Will leave it
running for the next few days to see if there is any difference.

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[Bug 1928744] Re: Disk IO very slow on kernel 4.15.0-142-generic

2021-05-23 Thread Mariusz
Hi,

In the last 3 days, I have been testing the other kernels. The steps
which I took:

1. Boot to kernel-4.15.0-136.
2. Install kernel X, where X = 136,137,139,140:

sudo apt-get install linux-image-4.15.0-X-generic 
linux-headers-4.15.0-X-generic linux-modules-4.15.0-X-generic 
linux-modules-extra-4.15.0-X-generic

3. Boot to kernel X.

4. Manually run:
sudo depmod

5. Reboot.

4. Run the server's normal workload and see how it was performing.

I haven't seen disk performance issues with those kernels.
But there is one difference, which I don't know how to explain.

Before I raised this bug, we had the same disk performance issues on 
kernel-4.15.0-140. 
I collected the list of kernel modules running on that kernel at that time:

Module  Size  Used by
joydev 24576  0
input_leds 16384  0
hid_generic16384  0
usbhid 49152  0
hid   122880  2 usbhid,hid_generic
ip6_tables 28672  0
iptable_filter 16384  0
ip_tables  28672  1 iptable_filter
x_tables   40960  3 iptable_filter,ip6_tables,ip_tables
tcp_diag   16384  0
udp_diag   16384  0
inet_diag  24576  2 tcp_diag,udp_diag
cpuid  16384  0
btrfs1155072  0
zstd_compress 163840  1 btrfs
xor24576  1 btrfs
raid6_pq  114688  1 btrfs
ufs77824  0
qnx4   16384  0
minix  32768  0
ntfs  102400  0
msdos  20480  0
jfs   188416  0
xfs  1204224  0
libcrc32c  16384  1 xfs
intel_rapl 20480  0
sb_edac24576  0
x86_pkg_temp_thermal16384  0
intel_powerclamp   16384  0
coretemp   16384  0
kvm_intel 217088  0
kvm   614400  1 kvm_intel
ipmi_ssif  32768  0
irqbypass  16384  1 kvm
crct10dif_pclmul   16384  0
crc32_pclmul   16384  0
ghash_clmulni_intel16384  0
pcbc   16384  0
aesni_intel   188416  0
aes_x86_64 20480  1 aesni_intel
cdc_ether  16384  0
usbnet 45056  1 cdc_ether
mii16384  1 usbnet
crypto_simd16384  1 aesni_intel
glue_helper16384  1 aesni_intel
cryptd 24576  3 crypto_simd,ghash_clmulni_intel,aesni_intel
intel_cstate   20480  0
intel_rapl_perf16384  0
ipmi_si57344  0
ipmi_devintf   20480  0
ipmi_msghandler53248  3 ipmi_devintf,ipmi_si,ipmi_ssif
shpchp 36864  0
mei_me 40960  0
mei94208  1 mei_me
lpc_ich24576  0
acpi_power_meter   20480  0
acpi_pad  180224  0
mac_hid16384  0
bonding   163840  0
lp 20480  0
parport49152  1 lp
autofs440960  2
mgag20045056  1
i2c_algo_bit   16384  1 mgag200
ttm   106496  1 mgag200
drm_kms_helper172032  1 mgag200
syscopyarea16384  1 drm_kms_helper
sysfillrect16384  1 drm_kms_helper
tg3   167936  0
sysimgblt  16384  1 drm_kms_helper
fb_sys_fops16384  1 drm_kms_helper
ptp20480  1 tg3
drm   401408  4 drm_kms_helper,mgag200,ttm
pps_core   20480  1 ptp
megaraid_sas  143360  12
mxm_wmi16384  0
wmi24576  1 mxm_wmi


Now, after the testing we are running on kernel-4.15.0-140 (again) and this 
time I don't see the issue. 
But the list of kernel module is different:
lsmod
Module  Size  Used by
intel_rapl 20480  0
sb_edac24576  0
x86_pkg_temp_thermal16384  0
intel_powerclamp   16384  0
coretemp   16384  0
kvm_intel 217088  0
ipmi_ssif  32768  0
kvm   614400  1 kvm_intel
irqbypass  16384  1 kvm
crct10dif_pclmul   16384  0
crc32_pclmul   16384  0
ghash_clmulni_intel16384  0
pcbc   16384  0
aesni_intel   188416  0
aes_x86_64 20480  1 aesni_intel
crypto_simd16384  1 aesni_intel
glue_helper16384  1 aesni_intel
cryptd 24576  3 crypto_simd,ghash_clmulni_intel,aesni_intel
intel_cstate   20480  0
cdc_ether  16384  0
usbnet 45056  1 cdc_ether
input_leds 16384  0
joydev 24576  0
mii16384  1 usbnet
intel_rapl_perf16384  0
ipmi_si57344  0
ipmi_devintf   20480  0
ipmi_msghandler53248  3 ipmi_devintf,ipmi_si,ipmi_ssif
mei_me 40960  0
mei94208  1 mei_me
lpc_ich

[Bug 1928744] Re: Disk IO very slow on kernel 4.15.0-142-generic

2021-05-20 Thread Mariusz
Cool cool, I will try to do what you have suggested - that make sense.
Will get back once I have some details.

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[Bug 1928744] Re: Disk IO very slow on kernel 4.15.0-142-generic

2021-05-20 Thread Khaled El Mously
Hi @Mariusz - thank you for the bug report. That certainly sounds like a
kernel bug based on your description.

Doing a kernel bisect is probably the fastest approach to identifying
the offending change. There are 392 changes between -136 and -142 so it
could take up to 9 tests for a full bisect.

@Mariusz, is it possible to find out which (if any) of the intermediate
kernels between -136 and -142 are affected ?

If you don't have any of the intermediate kernels installed already, you
can install them with a command like this one:

sudo apt-get install linux-image-4.15.0-137-generic linux-
headers-4.15.0-137-generic linux-modules-4.15.0-137-generic linux-
modules-extra-4.15.0-137-generic

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[Bug 1928744] Re: Disk IO very slow on kernel 4.15.0-142-generic

2021-05-20 Thread Juerg Haefliger
** Also affects: linux (Ubuntu Bionic)
   Importance: Undecided
   Status: New

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[Bug 1928744] Re: Disk IO very slow on kernel 4.15.0-142-generic

2021-05-19 Thread Mariusz
Hi,

I have done another test and compared the same server running on
4.15.0-136-generic and kernel 4.15.0-142-generic. Collected zabbix CPU
utilization graph which is showing the problem from the performance
point of view. On 4.15.0-136-generic, the server works normal and there
are no processes stuck on 99% iowait. On 4.15.0-142-generic it is not
working at all and rsync, pg_receivewal or dd processes are hanging with
iowait 99%. I attached the zabbix graph to this bug.

** Attachment added: "kernel_issue.png"
   
https://bugs.launchpad.net/ubuntu/+source/linux/+bug/1928744/+attachment/5498858/+files/kernel_issue.png

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[Bug 1928744] Re: Disk IO very slow on kernel 4.15.0-142-generic

2021-05-18 Thread Mariusz
Unable to run apport-collect 1928744 command.

** Changed in: linux (Ubuntu)
   Status: Incomplete => Confirmed

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Title:
  Disk IO very slow on kernel 4.15.0-142-generic

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[Bug 1928744] Re: Disk IO very slow on kernel 4.15.0-142-generic

2021-05-18 Thread Chris Guiver
changed HWE to linux as I see no reference to a HWE (5.4) kernel

** Package changed: linux-signed-hwe (Ubuntu) => linux (Ubuntu)

** Tags added: bionic

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Title:
  Disk IO very slow on kernel 4.15.0-142-generic

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[Bug 1928744] Re: Disk IO very slow on kernel 4.15.0-142-generic

2021-05-18 Thread Mariusz
Thanks a lot for coming back to me. I couldn't run apport-collect as we
don't have python-launchpadlib installed. I did check (apt install
python3-launchpadlib) and in my case it would install quite a lot of
dependent packages - we would like to avoid that due to the nature of
our server.

But I did collect a bug report with "ubuntu-bug  linux-image-generic"
and attached to this case. Hope this will be helpful.

** Attachment added: "apport.linux-image-generic.zrvzpzar.apport"
   
https://bugs.launchpad.net/ubuntu/+source/linux-signed-hwe/+bug/1928744/+attachment/5498602/+files/apport.linux-image-generic.zrvzpzar.apport

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Title:
  Disk IO very slow on kernel 4.15.0-142-generic

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[Bug 1928744] Re: Disk IO very slow on kernel 4.15.0-142-generic

2021-05-18 Thread Chris Guiver
Thank you for taking the time to report this bug and helping to make
Ubuntu better. Please execute the following command only once, as it
will automatically gather debugging information, in a terminal:

apport-collect 1928744

When reporting bugs in the future please use apport by using 'ubuntu-
bug' and the name of the package affected. You can learn more about this
functionality at https://wiki.ubuntu.com/ReportingBugs.

Note: you may have issues with this, as you've changed the package to
the HWE kernel (kernel 5.4 for 18.04) but your details imply you're
using 18.04's GA kernel of 4.15 (Ubuntu 16.04 using HWE uses the 4.15
kernel)

If you have issues; please change the package to 'linux' then try
apport-collect again.

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Title:
  Disk IO very slow on kernel 4.15.0-142-generic

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[Bug 1928744] Re: Disk IO very slow on kernel 4.15.0-142-generic

2021-05-18 Thread Mariusz
** Package changed: ubuntu => linux-signed-hwe (Ubuntu)

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Title:
  Disk IO very slow on kernel 4.15.0-142-generic

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