AWS - EC2 - MongoDB replica set time sync issue - NTP - replication lag - linux

Question

We are encountering clock drift issues with our MongoDB replica set running on AWS. This just seemed to start happening recently after we added additional data to the set, before then we did not really notice this issue unless the system was under heavy load. The following error is logged in the mongod.log file sporadically and the system is not under load.
To test this we have isolated a set of machines with the same dataset and not in use by our web application though the error is still occurring;
2014-12-12T13:33:51.333+0000 [rsBackgroundSync] changing sync target
because current sync target's most recent OpTime is Dec 12 13:32:42:c
which is more than 30 seconds behind member mongo1:27017 whose most
recent OpTime is 1418391230
From the above the time stamp shows that one of the mongodb replica set members is over a minute behind. The worst we have seen is 12 minutes out of sync.
This error in turn causes replication lag and we receive the notification about this from the Mongo Monitoring Service although it does correct itself.
The setup is 3 x r3.xlarge AWS Linux instances, 1 in each availability zone of the EU-West-1A region. The machines have been setup using the Mongo recommended settings with a Raid array and the cloud formation scripts provided by Mongo. The data is around 4GB in size.
We think the issue is related to the NTP sync, by default on the AWS Linux Amazon Machine Image the ntpd service is configured to go to a pool of aws ntp servers hosted on www.pool.ntp.org.
To try and rule this out we setup our own NTP server on AWS that the MongoDB servers could sync to. The issue still occurred so we changed the maxpoll and minpoll time for the ntpd service on the mongo machines to sync the time every 16 seconds from the NTP server but the error is still occurring.
We increased the MongoDB OpLog size as well to see if that would make any difference but it didn’t.
Does anyone else encounter this type of issue? Is there something we are missing?
Cheers,
Colin.
ps -ef |grep ntp;
mongodb1
ntp 5163 1 0 Dec11 ? 00:00:00 ntpd -u ntp:ntp -p /var/run/ntpd.pid -g
ec2-user 15865 15839 0 09:31 pts/2 00:00:00 grep ntp
mongodb2
ntp 4834 1 0 Dec11 ? 00:00:00 ntpd -u ntp:ntp -p /var/run/ntpd.pid -g
ec2-user 19056 19029 0 09:31 pts/0 00:00:00 grep ntp
mongodb3
ntp 5795 1 0 Dec11 ? 00:00:00 ntpd -u ntp:ntp -p /var/run/ntpd.pid -g
ec2-user 26199 26173 0 09:31 pts/0 00:00:00 grep ntp
cat /etc/ntp.conf;
# For more information about this file, see the man pages
# ntp.conf(5), ntp_acc(5), ntp_auth(5), ntp_clock(5), ntp_misc(5), ntp_mon(5).
driftfile /var/lib/ntp/drift
# Permit time synchronization with our time source, but do not
# permit the source to query or modify the service on this system.
restrict default kod nomodify notrap nopeer noquery
restrict -6 default kod nomodify notrap nopeer noquery
# Permit all access over the loopback interface. This could
# be tightened as well, but to do so would effect some of
# the administrative functions.
restrict 127.0.0.1
restrict -6 ::1
# Hosts on local network are less restricted.
#restrict 192.168.1.0 mask 255.255.255.0 nomodify notrap
# Use public servers from the pool.ntp.org project.
# Please consider joining the pool (http://www.pool.ntp.org/join.html).
#server 0.amazon.pool.ntp.org iburst dynamic
#server 1.amazon.pool.ntp.org iburst dynamic
#server 2.amazon.pool.ntp.org iburst dynamic
#server 3.amazon.pool.ntp.org iburst dynamic
server time-server.domain.com iburst
#broadcast 192.168.1.255 autokey # broadcast server
#broadcastclient # broadcast client
#broadcast 224.0.1.1 autokey # multicast server
#multicastclient 224.0.1.1 # multicast client
#manycastserver 239.255.254.254 # manycast server
#manycastclient 239.255.254.254 autokey # manycast client
# Enable public key cryptography.
#crypto
includefile /etc/ntp/crypto/pw
# Key file containing the keys and key identifiers used when operating
# with symmetric key cryptography.
keys /etc/ntp/keys
# Specify the key identifiers which are trusted.
#trustedkey 4 8 42
# Specify the key identifier to use with the ntpdc utility.
#requestkey 8
# Specify the key identifier to use with the ntpq utility.
#controlkey 8
# Enable writing of statistics records.
#statistics clockstats cryptostats loopstats peerstats
# Enable additional logging.
logconfig =clockall =peerall =sysall =syncall
# Listen only on the primary network interface.
interface listen eth0
interface ignore ipv6
ntpq -npcrv;
remote refid st t when poll reach delay offset jitter
==============================================================================
*172.31.14.137 91.*.*.* 3 u 557 1024 377 1.121 -0.264 0.161
associd=0 status=0615 leap_none, sync_ntp, 1 event, clock_sync,
version="ntpd 4.2.6p5#1.2349-o Sat Mar 23 00:37:31 UTC 2013 (1)",
processor="x86_64", system="Linux/3.14.23-22.44.amzn1.x86_64", leap=00,
stratum=4, precision=-23, rootdelay=23.597, rootdisp=109.962,
refid=172.31.14.137,
reftime=d83a757a.175b5fa1 Tue, Dec 16 2014 9:10:18.091,
clock=d83a77a7.82431efa Tue, Dec 16 2014 9:19:35.508, peer=27361,
tc=10, mintc=3, offset=-0.264, frequency=-13.994, sys_jitter=0.000,
clk_jitter=0.358, clk_wander=0.053

Answer 1

After upgrading to MongoDB 3 using the WiredTiger storage engine we do not see this issue any more.