Lessons Learned From Running 1800 Clusters (Brooke Jensen, Instaclustr) | Cassandra Summit 2016

Brooke Jensen
VP Technical Operations & Customer Services
Instaclustr
Lessons learned from running over 1800 2000 clusters

Instaclustr
• Launched at 2014 Summit.
• Now 25+ staff in 4 countries.
• Engineering (dev & ops) from Canberra, AU
• Cassandra as a service (CaaS)
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“Globally unique perspective of Cassandra.”
• Our customer base:
• Diverse. From early stage start-ups to large well-
known global enterprises.
• Education, Retail, Marketing, Advertising, Finance,
Insurance, Health, Social, Research
• All use cases: Messaging, IoT, eCommerce, Analytics,
Recommendations, Security.
• Small development clusters to large scale production
deployments requiring 100% uptime.
• Nodes under management:
• 700+ active nodes under management,
• All versions from Cassandra 2.0.11 - Cassandra 3.7

About Me
Brooke Jensen
VP Technical Operations, Customer Services / Cassandra MVP
• Previous: Senior Software Engineer, Instaclustr
• Education: Bachelor Software Engineering
• Life before Instaclustr:
• 11+ years Software Engineering.
• Specialized in performance optimization of large enterprise systems (e.g. Australian Customs, Taxation
Office, Department of Finance, Deutsche Bank)
• Extensive experience managing and resolving major system incidents and outages.
• Lives: Canberra, Au

Talk Overview
• Collection of common problems we see and manage on a daily basis.
• Examples and war stories from the field.
• HOWTOs, tips and tricks.
• Covering:
• Cluster Design
• Managing compactions
• Large partitions
• Disk usage and management
• Tombstones and Deletes
• Common sense advice

Cluster Design Basics – Racks & RF
• For production we recommend (minimum): 3 nodes in 3 racks with RF3.
 Make racks a multiple of RF.
• Use logical racks and map to physical racks.
• Each rack will contain a full copy of the data.
• Can survive the loss of nodes without losing QUORUM (strong consistency)
• Use NetworkTopologyStrategy. It’s not just for multi-DC, but is also “rack aware”
ALTER KEYSPACE <keyspace> WITH replication = {'class': 'NetworkTopologyStrategy','DC1': '3'}
Getting this right upfront will make
management of the cluster much
easier in the future.
R2
R2
R2
R1
R1
R1
R3
R3
R3

The case for single racks
• Datastax docs suggest not to use racks?
• “It’s hard to set up”
• “Expanding is difficult” – not if using vnodes (default from 2.0.9)
• Spending the time to set up is WORTH IT!
• Minimizes downtime during upgrades and maintenance
• Can perform upgrades/restarts rack-by-rack
• Can (technically) lose a whole rack without downtime
• We go one further and map racks to AWS AZ:

Setting it up
yaml:
endpoint_snitch: GossipingPropertyFileSnitch
cassandra-rackdc.properties:
Executing 'cat /etc/cassandra/cassandra-rackdc.properties' on 52.37.XXX.XXX
Host 52.37.XXX.XXX response:
#Generated by Instaclustr
#Mon Mar 28 19:22:21 UTC 2016
dc=US_WEST_2
prefer_local=true
rack=us-west-2b

Compactions – the basics
• Regular compactions are an integral part of any healthy Cassandra cluster.
• Occur periodically to purge tombstones, merge disparate row data into new SSTables to reclaim
disk space and keep read operations optimized.
• Can have a significant disk, memory (GC), cpu, IO overhead.
• Are often the cause of “unexplained” latency or IO issues in the cluster
• Ideally, get the compaction strategy right at table creation time. You can change it later, but that
may force a re-write all of the data in that CF using the new Compaction Strategy
• STCS – Insert heavy and general workloads
• LCS – Read heavy workloads, or more updates than inserts
• DTCS – Not where there are updates to old data or inserts that are out of order.

Monitoring Compactions
$ nodetool compactionstats -H
pending tasks: 130
compaction type keyspace table completed total unit progress
Compaction instametrics events_raw 1.35 GB 1.6 GB bytes 84.77%
Compaction instametrics events_raw 1.28 GB 1.6 GB bytes 80.21%
Active compaction remaining time : 0h00m33s
• Not uncommon for large compactions to get “stuck” or fall behind.
• On 2.0 in particular. Significantly improved in 2.1, even better in 3
• A single node doing compactions can cause latency issues across
the whole cluster, as it will become slow to respond to queries.
• Heap pressure will cause frequent flushing of Memtables to disk.
=> many small SSTables => many compactions

Compactions: other things to check

Managing Compactions
Few things you can do if compactions are causing issues (e.g. latency)
Throttle: nodetool setcompactionthroughput 16
Stop and disable : nodetool stop COMPACTION
Take the node out (and unthrottle):
nodetool disablebinary && nodetool disablegossip && nodetool disablethrift && nodetool setcompactionthroughput 0
Set until C* is restarted. On 2.1 applies to NEW
compactions, on 2.2.5+ applies instantly
Other nodes will mark this node as down,
So need to complete within HH window (3h)
Case is important!
Stops currently active compactions only.
Compaction starts
Node taken out

Large Partitions
• One of the biggest problems we deal with. Root cause of many other issues, and a PITA to manage.
• We recommend to keep them 100MB or less.
Creates issues with:
Compactions
In 2.0, compactions of partitions > 64MB were considerably slower. Partitions >2GB often getting stuck.
Improved in 2.1 and confirmed we observe less of these problems in upgraded clusters.
Adding, replacing nodes – streaming will often fail.
Querying large partitions is considerably slower. The whole partition is stored on every replica node,
leading to hotspots.
Can be hard to get rid of.

Checking partition sizes
~ $ nodetool cfstats -H keyspace.columnfamily
…
Compacted partition minimum bytes: 125 bytes
Compacted partition maximum bytes: 11.51 GB
Compacted partition mean bytes: 844 bytes
$ nodetool cfhistograms keyspace columnfamily
Percentile SSTables Write Latency Read Latency Partition Size Cell Count
(micros) (micros) (bytes)
50% 1.00 14.00 124.00 372 2
75% 1.00 14.00 1916.00 372 2
95% 3.00 24.00 17084.00 1597 12
98% 4.00 35.00 17084.00 3311 24
99% 5.00 50.00 20501.00 4768 42
Min 0.00 4.00 51.00 125 0
Max 5.00 446.00 20501.00 12359319162 129557750
Huge delta between 99th percentile and
Max indicates most data (bytes) is in
one partition.

Disk Usage
• As a guide, maintain nodes under 70% (50% for STCS).
• At 80% take action.
• Why so much headroom?
• Compactions will cause a temporary increase in disk usage while both sets of SSTables exist, but
once complete will free up space that was occupied by old SSTables.
• FYI, repair requests a snapshot before execution.
• Recovering from a filled disk can be a pain, and you CAN LOSE DATA.
• C* won’t start, for a start.
• Nodes out of the cluster during recovery >3 hours will require repair.
Sep 08 05:38:15 cassandra[17118]: at java.lang.Thread.run(Thread.java:745) ~[na:1.8.0_91]
Sep 08 05:38:15 cassandra[17118]: Caused by: java.io.IOException: No configured data directory contains
enough space to write 99 bytes
Sep 08 05:38:16 systemd[1]: cassandra.service: Main process exited, code=exited,
Sep 08 05:38:16 systemd[1]: cassandra.service: Unit entered failed state.

Try this first: stop writing data.

Can’t stop? Won’t stop?
Quick win: clearing snapshots.
nodetool cfstats or nodetool listsnapshots will show if you have any snapshots to clear:
nodetool clearsnapshot

Finding data to remove
I like to look at the data folders on disk – easier to identify than with cfstats.
Note also: might not just be your data. Space can commonly be consumed by snapshots or even system keyspaces.
• We’ve had nodes nearly fill up because of stored hints.

Tip: Removing data
DELETE - creates tombstones which will not be purged by compactions until after gc_grace_seconds
• Default is 10 days, but you can ALTER it and it is effective immediately.
• Make sure all nodes are UP before changing gc_grace.
TRUNCATE or DROP – only creates a snapshot as a backup before removing all the data.
• The disk space is released as soon as the snapshot is cleared
• Preferred where possible.

Disk Usage – Other Actions to try
• Add Nodes + run cleanups
• After all new nodes are running, run nodetool cleanup on each of the previously existing nodes to remove
the keys that no longer belong to those nodes.
• If on AWS, add EBS (requires restart).
• Disable autocompactions (will negatively effect read latency so not recommended)
Tip: JOINING (adding) nodes
• When you add nodes to a cluster, they will typically overstream data initially using more disk space than you expect. Duplicates will be
compacted away eventually.
• Disable compaction throttling while the node is JOINING.
• If streaming/joining fails and you have to restart it, the node will restream ALL SSTables again from the beginning, potentially filling up the
disks. ‘rm’ cassandra data folder before restarting.

Compaction spikes
• Compactions, particularly large ones, will cause spikes in disk usage while both sets of SSTables
exist.
• Ideally, you want the compaction(s) to complete and free up space, but how can you assess
whether that is possible?
Unlikely.

Compaction spikes
1. Find the tmp SSTable associated with the current compaction. From this, together with %
complete in compactionstats you can get a feel for how much more space you need:
$ -rw-r--r-- find /var/lib/cassandra/data/ -name "*tmp*Data.db" | xargs ls –lh
1 root root 4.5G Sep 1 14:56 keyspace1/posts/keyspace1-posts-tmp-ka-118955-Data.db
2. Keep a very close eye the disk, compaction and size of tmp file:
watch –n30 'df -h; ls -lh keyspace1-posts-tmp-ka-118955-Data.db; nodetool compactionstats –H’
Filesystem Size Used Avail Use% Mounted on
/dev/md127 787G 746G 506M 100% /var/lib/cassandra

Case study: Yesterday’s drama
Scene:
• 15 node production cluster, 12 * m4xl-1600 nodes + 3 * m4xl-800 nodes (ie 3 with half storage)
• Keyspace is RF 2 and application requires QUORUM
• (sum_of_replication_factors / 2) + 1 = 2 (ie both replicas)
• Therefore can’t take nodes out (or let them die) as it will cause application outage.
• Peak processing time is 8am-6pm.
• Need to keep the node up until the end of the day.
• Write heavy workload

09:33:
~ $ df –h
/dev/md127 787G 777G 10G 99% /var/lib/cassandra
11:03:
/dev/md127 787G 781G 5.9G 100% /var/lib/cassandra
12:37:
~ $ nodetool disableautocompaction
~ $ df –h

13:40:
Crap.

Solution was to move one CF to EBS in the background before the disk fills up.
~ $ du -hs /var/lib/cassandra/data/prod/*
89G /var/lib/cassandra/data/prod/cf-39153090119811e693793df4078eeb99
38G /var/lib/cassandra/data/prod/cf_one_min-e17256f091a011e5a5c327b05b4cd3f4
~ $ rsync -aOHh /var/lib/cassandra/data/prod/cf_one_min-e17256f091a011e5a5c327b05b4cd3f4 /mnt/ebs/
Meanwhile:
/dev/md127 787G 746G 906M 100% /var/lib/cassandra
/dev/xvdp 79G 37G 39G 49% /mnt/ebs
Now just mount bind it, and restart Cassandra:
/dev/xvdp on /lib/cassandra/data/prod/cf_one_min-e17256f091a011e5a5c327b05b4cd3f4

Monitoring – how we detect problems
• Client read and write latency
• Local CF read and write latency
• Number of reads or writes deviating from average
• Outlier nodes
• Down nodes
• Disk usage
• Pending compactions
• Check for large partitions (data model issues)
• In the logs:
• Large batch warnings
• Tombstone warnings
• Excessive GC and/or long pauses

Case study: Don’t break your cluster.
WARNING! It is possible to get your cluster into a state from which you are unable to recover
without significant downtime or data loss.

“This happened during normal operations at night, so I don't think any of us were doing anything
abnormal. We've been doing some processing that creates pretty heavy load over the last few weeks...”
Orly?

Unthrottled data load
• Load average of 56, on 8 core machines.
• Nodes were saturated and exhausted heap space.
• Regular GC pauses of 12000ms - 17000ms
• Memtables are frequently flushed to disk.
• This resulted in over 120,000 small SSTables being created on some nodes.
• Data was spread across thousands of SSTables, so read latency skyrocketed.
• Was using paxos writes (LWT), which require a read before every write. This caused writes to fail
because as reads were timing out.
• Compactions could not keep up, and added additional load to the already overloaded nodes.
• C* eventually crashed on most nodes, leaving some corrupt SSTables.

17 second GC pauses. Nice.
Aug 16 15:51:58 INFO o.a.cassandra.service.GCInspector ConcurrentMarkSweep GC in 12416ms. CMS
Old Gen: 6442450872 -> 6442450912; Par Eden Space: 1718091776 -> 297543768; Par Survivor Space:
214695856 -> 0
Aug 16 15:52:20 INFO o.a.cassandra.service.GCInspector ConcurrentMarkSweep GC in 17732ms. CMS
Old Gen: 6442450912 -> 6442450864; Par Eden Space: 1718091776 -> 416111040; Par Survivor Space:
214671752 -> 0
Heap pressure causes C* to flush memtables to disk. This created >120,000 Memtables on some
nodes.
 3+ days just to catch up on compactions, which were continually failing because of:
Aug 18 22:11:43 java.io.FileNotFoundException: /var/lib/cassandra/data/keyspace/cf-
f4683d90f88111e586b7e962b0d85be3/keyspace-cf-ka-1243722-Data.db (Too many open files)
java.lang.RuntimeException: java.io.FileNotFoundException: /var/lib/cassandra/data/keyspace/cf-
f4683d90f88111e586b7e962b0d85be3/keyspace-cf-ka-1106806-Data.db (No such file or directory)

1. Once we got C* stable and caught up on compactions, there were still corrupt SSTables present and
nodes were in an inconsistent state.
2. Couldn’t fix with repairs:
ERROR o.apache.cassandra.repair.Validator Failed creating a merkle tree for [repair #21be1ac0-6809-11e6-a098-
b377cb035d78 on keyspace/cf, (-227556542627198517,-225096881583623998]], /52.XXX.XXX.XXX (see log for details)
ERROR o.a.c.service.CassandraDaemon Exception in thread Thread[ValidationExecutor:708,1,main]
java.lang.NullPointerException: null
3. Have deleted corrupt SSSTables on some nodes. This is ok, presume there are other copies of the data
in the cluster. We’ll have to repair later.
4. Run online scrubs on each node to identify corrupt SSTables, and fix (rewrite) where possible.
5. For nodes where online scrub does not complete, take the node offline and attempt an offline scrub of
identified corrupt SSTables.
6. If offline scrub fails to rewrite any SSTables a node, delete those remaining corrupt SSTables.
7. Run a repair across the cluster to make data consistent across all nodes.
@ 8th September, 3 weeks after the initial data load and the cluster is STILL in an inconsistent state
with corrupt SSTables and queries occasionally failing.
Long road to recovery

Some final tips
• When making major changes to the cluster (expanding, migrating, decomissioning), GO SLOW.
• It takes longer to recover from errors than just doing it right the first time.
• Things I’ve seen customers do:
• Rebuild 16 nodes in a new DC concurrently
• Decommission multiple nodes at once
• Unthrrotled data loads
• Keep C* up to date, but not too up to date.
• 2.0 has troubles with large compactions
• Currently investigating segfaults with MV in 3.7
• Read the source code.
• It is the most thorough and up to date documentation.

Lessons Learned From Running 1800 Clusters (Brooke Jensen, Instaclustr) | Cassandra Summit 2016

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