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https://issues.apache.org/jira/browse/CASSANDRA-3592?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=13168473#comment-13168473
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Jonathan Ellis commented on CASSANDRA-3592:
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Can you try the CASSANDRA-3618 patch?
> 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
> Labels: compaction
>
> 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 IO 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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