I have a lab environment where I deploy about 30 VMs on one physical server and run Linux (Ubuntu 11.10) on all the VMs. Here are the specs of the physical machine:

~ # vsish -e cat /hardware/bios/dmiInfo | head -4
System Information (type1) {
Product Name:Seabream
Vendor Name:InventecESC
Serial Number:P1237010411

~ # vsish -e cat /hardware/cpu/cpuInfo | grep -E 'Number\ of \cores|Number\ of\ CPU'
Number of cores:8
Number of CPUs (threads):8

~ # vsish -e cat /hardware/cpu/cpuModelName
Intel(R) Xeon(R) CPU X5355 @ 2.66GHz

~ # vsish -e cat /memory/comprehensive | head -2
Comprehensive {
Physical memory estimate:8388084 KB

So 8 cores at 2.66GHz and 8GB of RAM, nothing crazy. Each VM has the minimum amount of RAM (192MB) and it actually runs pretty well. I was looking over esxtop and at random period of times, I saw different VMs experiencing high latency. Here is what I saw.


To get to this screen just launch esxtop and hit ‘v’ for “disk VMs”. On ESXi 5.0 the latency is automatically displayed in this view. If you are on 4.x, after selecting ‘v’ you can type in ‘f’ and that will show you a list of available columns, select the latency columns and you will see the same as above. From the above picture we see VM “uaclass39” and “uaclass17” experiencing latency up to 20 milliseconds. At certain times 20 VMs would experience the same issue. I saw this lantency be steady for a couple of minutes. More information regarding latency can be seen at this communities page (Performance Troubleshooting for VMware vSphere™ 4.1”, check out the section entitled ‘7.3.13. Check for Slow or Under-Sized Storage Device’.

I decided to take a look at what the VM is doing and why it was experiencing such high read and write latency. So I ssh’ed over to one of the VMs and I launched top, and here is I saw:Ubuntu_11_10_top

Check out the %wa (it’s 97%). Looking at the man page of ‘top’, I see the following:

wa -- iowait
Amount of time the CPU has been waiting for I/O to complete.

Something is doing a lot of IO and the biggest cpu and memory user is a process called update-apt-xapi. Looking at the man page of ‘ps’, I see the folllowing:

Here are the different values that the s, stat and state output
specifiers (header "STAT" or "S") will display to describe the state of
a process:
D uninterruptible sleep (usually IO)
R running or runnable (on run queue)
S interruptible sleep (waiting for an event to complete)
T stopped, either by a job control signal or because it is being
W paging (not valid since the 2.6.xx kernel)
X dead (should never be seen)
Z defunct ("zombie") process, terminated but not reaped by its

I wanted to check what is in disk IO state, so I ran the below:

root@uaclass39:~# ps -efly | grep ^D
D root 1570 1 3 90 10 137492 58296 sleep_ 16:54 ? 00:00:15 /usr/bin/python /usr/sbin/update-apt-xapian-index --force --quiet

So it looks like the “update-apt-xapian-index” is what’s causing the high disk IO. I then wanted to check how much IO was happening, so I ran the following:

root@uaclass39:~# iostat 1 5 /dev/sda
Linux 3.0.0-17-virtual (uaclass39) 03/29/2012 _x86_64_ (1 CPU)

avg-cpu: %user %nice %system %iowait %steal %idle
1.03 2.09 1.94 44.96 0.00 49.99

Device: tps kB_read/s kB_wrtn/s kB_read kB_wrtn
sda 169.03 5636.54 312.89 7418419 411800

avg-cpu: %user %nice %system %iowait %steal %idle
0.00 1.98 2.97 95.05 0.00 0.00

Device: tps kB_read/s kB_wrtn/s kB_read kB_wrtn
sda 609.90 16419.80 91.09 16584 92

avg-cpu: %user %nice %system %iowait %steal %idle
0.00 2.00 2.00 96.00 0.00 0.00

Device: tps kB_read/s kB_wrtn/s kB_read kB_wrtn
sda 563.00 14884.00 40.00 14884 40

avg-cpu: %user %nice %system %iowait %steal %idle
0.97 1.94 0.97 96.12 0.00 0.00

Device: tps kB_read/s kB_wrtn/s kB_read kB_wrtn
sda 779.61 20749.51 38.83 21372 40

avg-cpu: %user %nice %system %iowait %steal %idle
0.00 7.69 1.92 90.38 0.00 0.00

Device: tps kB_read/s kB_wrtn/s kB_read kB_wrtn
sda 658.65 15638.46 319.23 16264 332

We consistently see very high %iowait and our reads are at ~15-20MB/s. Don’t forget this is on local storage too :) I wanted to find out what this apt-xapian process is, I did some research and I found a bug (363695) from ubuntu. They tried to fix it by throttling the IO by using ionice, my install had that enabled:

root@uaclass39:/etc/cron.weekly# grep -i ionice apt-xapian-index
# ionice should not be called in a virtual environment
egrep -q '(envID|VxID):.*[1-9]' /proc/self/status || IONICE=/usr/bin/ionice
if [ -x "$IONICE" ]
nice -n 19 $IONICE -c 3 $CMD --quiet

but it still caused an issue and it states that ionice should not be used in a virtualized environment. So I decided to just disable it. Since I had setup ssh keys for grading purposes, I wrote this script to disable apt-xapian-index from auto running weekly:


HOSTS="uaclass01 uaclass02 uaclass03 ..."

for i in $HOSTS;do
echo $i
/usr/bin/ssh $i '/bin/chmod 0 /etc/cron.weekly/apt-xapian-index'

A more appropriate fix would be to completely remove the package:

root@uaclass39:~$ dpkg -l | grep apt-xapian
ii apt-xapian-index 0.44ubuntu4 maintenance and search tools for a Xapian index of Debian packages

root@uaclass39:~$ apt-get --purge remove apt-xapian-index
Reading package lists... Done
Building dependency tree
Reading state information... Done
The following packages will be REMOVED:
0 upgraded, 0 newly installed, 1 to remove and 0 not upgraded.
After this operation, 483 kB disk space will be freed.
Do you want to continue [Y/n]? Y
(Reading database ... 28747 files and directories currently installed.)
Removing apt-xapian-index ...
Removing index /var/lib/apt-xapian-index...
Purging configuration files for apt-xapian-index ...
Removing index /var/lib/apt-xapian-index...
Processing triggers for man-db ...

But I didn’t want to do that just yet. Just as an FYI, here are the spec of each VM:

root@uaclass39:~# uname -a
Linux uaclass39 3.0.0-17-virtual #30-Ubuntu SMP Thu Mar 8 23:45:51 UTC 2012 x86_64 x86_64 x86_64 GNU/Linux

root@uaclass39:~# lsb_release -a
No LSB modules are available.
Distributor ID: Ubuntu
Description: Ubuntu 11.10
Release: 11.10
Codename: oneiric

root@uaclass39:~# free -m
total used free shared buffers cached
Mem: 176 167 8 0 10 107
-/+ buffers/cache: 50 126
Swap: 379 35 344

root@uaclass39:~# x86info
x86info v1.25. Dave Jones 2001-2009

Found 1 CPU
EFamily: 0 EModel: 0 Family: 6 Model: 15 Stepping: 7
CPU Model: Core 2 Quad (Kentsfield)
Processor name string: Intel(R) Xeon(R) CPU X5355 @ 2.66GHz
Type: 0 (Original OEM) Brand: 0 (Unsupported)
Number of cores per physical package=1
Number of logical processors per socket=1
Number of logical processors per core=1
APIC ID: 0x0 Package: 0 Core: 0 SMT ID 0

Since the apt-xapian-index just indexes all the aptitude packages, I didn’t really see a problem with disabling it. After I disabled that cron job, I haven’t seen any high latency on any of the VMs.

Published by Karim Elatov

08 April 2012