Why does mongodb complain about transparent_hugepage? - linux

Question

A few questions are already asking about how to fix the mongodb warning:
** WARNING: /sys/kernel/mm/transparent_hugepage/defrag is 'always.'
** We suggest setting it to 'never'
But I'm wondering if it should be fixed. I get this warning from MongoDB 3.0.1 on a Ubuntu VM running on Google's Cloud. Should I trust MongoDB that 'never' is better? Or should I trust Google/Ubuntu that they set it to 'always' for a good reason? I imagine there are tradeoffs to be considered and don't know what I'd be trading to keep it or fix it.
Asking how to fix it is fine, but asking whether to fix it seems wiser.

Answer 1

Edit: Mongodb have addressed this issue since I wrote this answer. Their recommendation is at https://docs.mongodb.com/master/tutorial/transparent-huge-pages/ and probably ought to be your go-to solution. My original answer will still work, but I'd consider it a hack now that an official solution is available.
Original answer: According to the MongoDB documentation, http://docs.mongodb.org/manual/reference/transparent-huge-pages/, and support, https://jira.mongodb.org/browse/DOCS-2131, transparent_hugepage (THP) is designed to create fewer large memory blocks rather than many small memory blocks in systems with a lot of memory. This is great if your software needs large contiguous memory accesses. For MongoDB, however, regardless of memory available, it requires numerous smaller memory accesses and therefore performs better with THP disabled.
That makes me think either way will work, but you'll get better mongo (or any database) performance with THP off, giving you smaller bites of memory. If you don't have much memory anyway, THP probably ought to be off no matter what you run.
Several ways to do that are outlined in the link above. The most universally applicable appears to be editing rc.local.
$ sudo nano /etc/rc.local
Insert the following lines before the "exit 0" line.
...
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
exit 0
Note: redhat-based systems may use "redhat_transparent_hugepage" rather than "transparent_hugepage" and can be checked by:
ls /sys/kernel/mm/*transparent_hugepage*/enabled
cat /sys/kernel/mm/*transparent_hugepage*/enabled
To apply the changes, reboot (which will run rc.local) or:
$ sudo su
# source /etc/rc.local
# service mongod restart
# exit
to properly apply the changes made above

Answer 2

For Ubuntu using upstart scripts:
Since we are deploying machines with Ansible I don't like modifying rc files or GRUB configs.
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/init/mongod_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.

Answer 3

In Ubuntu I used the option 'Init Script' of this document: http://docs.mongodb.org/manual/tutorial/transparent-huge-pages/

Answer 4

None of these worked for me on Amazon ec2 instance running Ubuntu 14.04, not even the init.d script recommended by MongoDB. I had to use the hugeadm tool by first installing it via apt-get and then running sudo hugeadm --thp-never, this post pointed me to hugeadm. I'm still trying to figure out how to disable the transparent_hugepage defrag. hugeadm doesn't seem to have an easy way to do that.