Major Compaction Incredibly Slow
--------------------------------
Key: CASSANDRA-3592
URL: https://issues.apache.org/jira/browse/CASSANDRA-3592
Project: Cassandra
Issue Type: Bug
Components: Core
Affects Versions: 1.0.3
Environment: RHEL6 - 24 core machines 24 GB mem total, 11 GB java heap
java version "1.6.0_26"
6 node cluster (4@0.8.6, 2@1.0.3)
Reporter: Dan Hendry
Twice now (on different nodes), I have observed major compaction for certain
column families take *significantly* longer on 1.0.3 in comparison to 0.8.6.
For example,
On the 0.8.6 node, the post compaction log message:
{noformat}CompactionManager.java (line 608) Compacted to XXX. 339,164,959,170
to 158,825,469,883 (~46% of original) bytes for 25,996 keys. Time:
26,934,317ms.{noformat}
On the 1.0.3 node, the post compaction log message:
{noformat} CompactionTask.java (line 213) Compacted to [XXX]. 222,338,354,529
to 147,751,403,084 (~66% of original) bytes for 26,100 keys at 0.562045MB/s.
Time: 250,703,563ms.{noformat}
So... literally an order of magnitude slower on 1.0.3 in comparison to 0.8.6.
Relevant configuration settings:
* compaction_throughput_mb_per_sec: 0 (why? because the compaction throttling
logic as currently implemented is highly unsuitable for wide rows but thats a
different issue)
* in_memory_compaction_limit_in_mb: 128
Column family characteristics:
* Many wide rows (~5% of rows greater than > 10MB and hundreds of rows greater
than 100 MB, with many small columns).
* Heavy use of expiring columns - each row represents data for a particular
hour so typically all columns in the row will expire together.
* The significant size shrinkage as reported by the log messages is due mainly
to expired data being cleaned up (I typically trigger major compaction when
30-50% of the on disk data has expired which is about once every 3 weeks per
node).
* Perhaps obviously: size tiered compaction and no compression (the schema has
not changed since the partial upgrade to 1.0.x)
* Standard column family
Performance notes during compaction:
* Nice CPU usage and load average is basically the same between 0.8.6 and 1.0.3
- ie, compaction IS running and is not getting stalled or hung up anywhere.
* Compaction is IO bound on the 0.8.6 machines - the disks see heavy, constant
utilization when compaction is running.
* Compaction is uses virtually no CPU on the 1.0.3 machines - disk utilization
is virtually no different when compacting vs not compacting (but at the same
time, CPU usage and load average clearly indicate that compaction IS running).
Finally, I have not had time to profile more thoroughly but jconsole always
shows the following stacktrace for the active compaction thread (for the 1.0.3
machine):
{noformat}
Stack trace:
org.apache.cassandra.db.ColumnFamilyStore.removeDeletedStandard(ColumnFamilyStore.java:851)
org.apache.cassandra.db.ColumnFamilyStore.removeDeletedColumnsOnly(ColumnFamilyStore.java:835)
org.apache.cassandra.db.ColumnFamilyStore.removeDeleted(ColumnFamilyStore.java:826)
org.apache.cassandra.db.compaction.PrecompactedRow.removeDeletedAndOldShards(PrecompactedRow.java:77)
org.apache.cassandra.db.compaction.PrecompactedRow.<init>(PrecompactedRow.java:102)
org.apache.cassandra.db.compaction.CompactionController.getCompactedRow(CompactionController.java:133)
org.apache.cassandra.db.compaction.CompactionIterable$Reducer.getReduced(CompactionIterable.java:102)
org.apache.cassandra.db.compaction.CompactionIterable$Reducer.getReduced(CompactionIterable.java:87)
org.apache.cassandra.utils.MergeIterator$ManyToOne.consume(MergeIterator.java:116)
org.apache.cassandra.utils.MergeIterator$ManyToOne.computeNext(MergeIterator.java:99)
com.google.common.collect.AbstractIterator.tryToComputeNext(AbstractIterator.java:140)
com.google.common.collect.AbstractIterator.hasNext(AbstractIterator.java:135)
com.google.common.collect.Iterators$7.computeNext(Iterators.java:614)
com.google.common.collect.AbstractIterator.tryToComputeNext(AbstractIterator.java:140)
com.google.common.collect.AbstractIterator.hasNext(AbstractIterator.java:135)
org.apache.cassandra.db.compaction.CompactionTask.execute(CompactionTask.java:172)
org.apache.cassandra.db.compaction.CompactionManager$4.call(CompactionManager.java:277)
java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)
java.util.concurrent.FutureTask.run(FutureTask.java:138)
java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886)
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908)
java.lang.Thread.run(Thread.java:662)
{noformat}
I have not really had time to debug the issue further but given the stack trace
and column family characteristics, I suspect some problem with the column
family column iterator .remove() method. If the underlying ISortedColumns
implementation is a ArrayBackedSortedColumns instance, then repeated .remove()
calls could be incredibly inefficient.
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