54

I use mongodb 3.0 and I find a warning:

MongoDB shell version: 3.0.0
connecting to: test
Server has startup warnings: 
2015-03-13T16:28:29.405+0800 I CONTROL  [initandlisten] 
2015-03-13T16:28:29.406+0800 I CONTROL  [initandlisten] ** WARNING: /sys/kernel/mm/transparent_hugepage/enabled is 'always'.
2015-03-13T16:28:29.406+0800 I CONTROL  [initandlisten] **        We suggest setting it to 'never'
2015-03-13T16:28:29.406+0800 I CONTROL  [initandlisten] 
2015-03-13T16:28:29.407+0800 I CONTROL  [initandlisten] ** WARNING: /sys/kernel/mm/transparent_hugepage/defrag is 'always'.
2015-03-13T16:28:29.407+0800 I CONTROL  [initandlisten] **        We suggest setting it to 'never'
2015-03-13T16:28:29.407+0800 I CONTROL  [initandlisten]

~# cat /sys/kernel/mm/transparent_hugepage/enabled
[always] madvise never

~# cat /sys/kernel/mm/transparent_hugepage/defrag
[always] madvise never

I try to use echo, but it's not permanent, after reboot it will be reset.

echo never > /sys/kernel/mm/transparent_hugepage/defrag

How do I modify /sys/kernel/mm/transparent_hugepage/enabled permanently?

Mark Stosberg
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Feng Yu
  • 857

7 Answers7

77

You can

  1. install the sysfsutils package:

    sudo apt install sysfsutils

  2. and append a line with that setting to /etc/sysfs.conf:

    kernel/mm/transparent_hugepage/enabled = never

This is the cleanest solution, because it keeps all the sysfs configuration in one place instead of relying on custom start-up scripts. The other answers, with the scripts and conditional expressions, are suitable if you don't know through which path the kernel will expose that setting, i. e. if you don't even have a rough idea of the kernel version running on the affected machine.

David Foerster
  • 36,890
  • 56
  • 97
  • 151
26

The MongoDB docs have a few suggestions. http://docs.mongodb.org/manual/reference/transparent-huge-pages/

The "preferred" way is to edit /etc/default/grub and append transparent_hugepage=never to GRUB_CMDLINE_LINUX_DEFAULT then run update-grub to rebuild the GRUB configuration.

The following two-liner will do just that. Make sure to verify the output!

sed -r 's/GRUB_CMDLINE_LINUX_DEFAULT="[a-zA-Z0-9_= ]*/& transparent_hugepage=never/' /etc/default/grub | sudo tee /etc/default/grub
sudo update-grub

Note that update-grub is a wrapper for grub-mkconfig. grub-mkconfig will clobber entries in /etc/default/grub with those from /etc/default/grub.d/*. If by chance you are running on AWS, you will need to instead edit /etc/default/grub.d/50-cloudimg-settings.cfg.

The "alternate" method is to edit /etc/rc.local and add the following before exit 0:

if test -f /sys/kernel/mm/transparent_hugepage/khugepaged/defrag; then
  echo 0 > /sys/kernel/mm/transparent_hugepage/khugepaged/defrag
fi
if test -f /sys/kernel/mm/transparent_hugepage/defrag; then
  echo never > /sys/kernel/mm/transparent_hugepage/defrag
fi
if test -f /sys/kernel/mm/transparent_hugepage/enabled; then
  echo never > /sys/kernel/mm/transparent_hugepage/enabled
fi

Personally, I ended up doing both the "preferred" and "alternate" methods since they aren't mutually exclusive and it eliminates the warning about defrag.

* Worked for me on Ubuntu 14.04, MongoDB 3.0.2, and AWS.

clayzermk1
  • 361
17

Here's a solution that has been tested to work on Ubuntu 16.04 on AWS EC2. Ubuntu 16.04 uses the systemd init system, and this config file expresses that these settings should be changed before MongoDB boots up.

Create a file named /etc/systemd/system/mongodb-hugepage-fix.service and add the following content:

[Unit]
Description="Disable Transparent Hugepage before MongoDB boots"
#WARN: check service name on your system
# If you are using MongoDB Cloud, service name is "mongodb-mms-automation-agent.service"
Before=mongodb.service      

[Service]
Type=oneshot
ExecStart=/bin/bash -c 'echo never > /sys/kernel/mm/transparent_hugepage/enabled'
ExecStart=/bin/bash -c 'echo never > /sys/kernel/mm/transparent_hugepage/defrag'

[Install]
#WARN: check service name on your system
# If you are using MongoDB Cloud, service name is "mongodb-mms-automation-agent.service"
RequiredBy=mongodb.service

To load the file into systemd:

systemctl daemon-reload

To activate the file as a boot-time dependency of MongoDB

systemctl enable mongodb-hugepage-fix

If you want to activate the changes immediately (before the next boot)

systemctl start mongodb-hugepage-fix
systemctl restart mongod

This solution is not suitable for Ubuntu 14.04, which uses the Upstart init solution instead of systemd.

Mark Stosberg
  • 3,447
7

Append the following lines below into of /etc/rc.local.

if test -f /sys/kernel/mm/transparent_hugepage/enabled; then
  echo never > /sys/kernel/mm/transparent_hugepage/enabled
fi

if test -f /sys/kernel/mm/transparent_hugepage/defrag; then
   echo never > /sys/kernel/mm/transparent_hugepage/defrag
fi

This will run when you reboot the server.

PKumar
  • 3,182
1

Since we are deploying machines with Ansible I don't like modifying rc files.

I tried using sysfsutils / sysfs.conf but ran into timing issues when starting the services on fast (or slow machines). It looked like sometimes mongod was started before sysfsutils. Sometimes it worked, sometimes it did not.

Since mongod is an upstart process I found that the cleanest solution was to add the file /etc/mongo_vm_settings.conf with the following content:

# Ubuntu upstart file at /etc/init/mongod_vm_settings.conf
#
#   This file will set the correct kernel VM settings for MongoDB
#   This file is maintained in Ansible

start on (starting mongod)
script
  echo "never" > /sys/kernel/mm/transparent_hugepage/enabled
  echo "never" > /sys/kernel/mm/transparent_hugepage/defrag
end script

This will run the script just before mongod will be started. Restart mongod (sudo service mongod restart) and done.

Whyhankee
  • 111
1

After reading a little bit in the warning log I've added these two lines in /etc/sysfs.conf y voilá

kernel/mm/transparent_hugepage/enabled = never
kernel/mm/transparent_hugepage/defrag = never

Reboot the machine after applying these changes.

Community
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Ulv3r
  • 11
0

GRUB will change after upgrade, and rc.local will run only after mongo is started, so maybe we should add service mongo restart at the end of rc.local like this 

if test -f /sys/kernel/mm/transparent_hugepage/enabled; then
  echo never > /sys/kernel/mm/transparent_hugepage/enabled
fi

if test -f /sys/kernel/mm/transparent_hugepage/defrag; then
   echo never > /sys/kernel/mm/transparent_hugepage/defrag
fi

wait 1 && servie mongod restart

or maybe someone successfully added the lines above to init script in Ubuntu 14.04?

Edik Mkoyan
  • 349