[SPARK-14277] Significant amount of CPU is being consumed in SnappyNative arrayCopy method

• Type: Improvement
• Status: Resolved
• Priority: Major
• Resolution: Fixed
• Affects Version/s: 1.6.1
• Fix Version/s: 2.0.0
• Component/s: Shuffle, Spark Core
• Assignee: Sital Kedia
• Reporter: Sital Kedia
• Created: 30/Mar/16 18:13
• Updated: 17/May/20 18:30
• Resolved: 31/Mar/16 23:06

Description

While running a Spark job which is spilling a lot of data in reduce phase, we see that significant amount of CPU is being consumed in native Snappy ArrayCopy method (Please see the stack trace below).

Stack trace -
org.xerial.snappy.SnappyNative.$$YJP$$arrayCopy(Native Method)
org.xerial.snappy.SnappyNative.arrayCopy(SnappyNative.java)
org.xerial.snappy.Snappy.arrayCopy(Snappy.java:85)
org.xerial.snappy.SnappyInputStream.rawRead(SnappyInputStream.java:190)
org.xerial.snappy.SnappyInputStream.read(SnappyInputStream.java:163)
java.io.DataInputStream.readFully(DataInputStream.java:195)
java.io.DataInputStream.readLong(DataInputStream.java:416)
org.apache.spark.util.collection.unsafe.sort.UnsafeSorterSpillReader.loadNext(UnsafeSorterSpillReader.java:71)
org.apache.spark.util.collection.unsafe.sort.UnsafeSorterSpillMerger$2.loadNext(UnsafeSorterSpillMerger.java:79)
org.apache.spark.sql.execution.UnsafeExternalRowSorter$1.next(UnsafeExternalRowSorter.java:136)
org.apache.spark.sql.execution.UnsafeExternalRowSorter$1.next(UnsafeExternalRowSorter.java:123)

The reason for that is the SpillReader does a lot of small reads from the underlying snappy compressed stream and SnappyInputStream invokes native jni ArrayCopy method to copy the data, which is expensive. We should fix Snappy- java to use with non-JNI based System.arrayCopy method in this case.

Issue Links

• links to: [Github] Pull Request #12074 (sitalkedia)
• links to: [Github] Pull Request #12096 (sitalkedia)