[HBASE-13329] ArrayIndexOutOfBoundsException in CellComparator#getMinimumMidpointArray

• Type: Bug
• Status: Closed
• Priority: Critical
• Resolution: Fixed
• Affects Version/s: 1.0.1
• Fix Version/s: 1.0.2, 1.2.0, 1.1.2, 2.0.0
• Component/s: regionserver

Environment

linux-debian-jessie
ec2 - t2.micro instances

• Hadoop Flags: Reviewed
• Assignee: Lars Hofhansl
• Reporter: Ruben Aguiar
• Created: 24/Mar/15 19:15
• Updated: 31/Aug/15 22:39
• Resolved: 05/Jul/15 19:32

Description

While trying to benchmark my opentsdb cluster, I've created a script that sends to hbase always the same value (in this case 1). After a few minutes, the whole region server crashes and the region itself becomes impossible to open again (cannot assign or unassign). After some investigation, what I saw on the logs is that when a Memstore flush is called on a large region (128mb) the process errors, killing the regionserver. On restart, replaying the edits generates the same error, making the region unavailable. Tried to manually unassign, assign or close_region. That didn't work because the code that reads/replays it crashes.
From my investigation this seems to be an overflow issue. The logs show that the function getMinimumMidpointArray tried to access index -32743 of an array, extremely close to the minimum short value in Java. Upon investigation of the source code, it seems an index short is used, being incremented as long as the two vectors are the same, probably making it overflow on large vectors with equal data. Changing it to int should solve the problem.
Here follows the hadoop logs of when the regionserver went down. Any help is appreciated. Any other information you need please do tell me:
2015-03-24 18:00:56,187 INFO [regionserver//10.2.0.73:16020.logRoller] wal.FSHLog: Rolled WAL /hbase/WALs/10.2.0.73,16020,1427216382590/10.2.0.73%2C16020%2C1427216382590.default.1427220018516 with entries=143, filesize=134.70 MB; new WAL /hbase/WALs/10.2.0.73,16020,1427216382590/10.2.0.73%2C16020%2C1427216382590.default.1427220056140
2015-03-24 18:00:56,188 INFO [regionserver//10.2.0.73:16020.logRoller] wal.FSHLog: Archiving hdfs://10.2.0.74:8020/hbase/WALs/10.2.0.73,16020,1427216382590/10.2.0.73%2C16020%2C1427216382590.default.1427219987709 to hdfs://10.2.0.74:8020/hbase/oldWALs/10.2.0.73%2C16020%2C1427216382590.default.1427219987709
2015-03-24 18:04:35,722 INFO [MemStoreFlusher.0] regionserver.HRegion: Started memstore flush for tsdb,,1427133969325.52bc1994da0fea97563a4a656a58bec2., current region memstore size 128.04 MB
2015-03-24 18:04:36,154 FATAL [MemStoreFlusher.0] regionserver.HRegionServer: ABORTING region server 10.2.0.73,16020,1427216382590: Replay of WAL required. Forcing server shutdown
org.apache.hadoop.hbase.DroppedSnapshotException: region: tsdb,,1427133969325.52bc1994da0fea97563a4a656a58bec2.
at org.apache.hadoop.hbase.regionserver.HRegion.internalFlushcache(HRegion.java:1999)
at org.apache.hadoop.hbase.regionserver.HRegion.internalFlushcache(HRegion.java:1770)
at org.apache.hadoop.hbase.regionserver.HRegion.flushcache(HRegion.java:1702)
at org.apache.hadoop.hbase.regionserver.MemStoreFlusher.flushRegion(MemStoreFlusher.java:445)
at org.apache.hadoop.hbase.regionserver.MemStoreFlusher.flushRegion(MemStoreFlusher.java:407)
at org.apache.hadoop.hbase.regionserver.MemStoreFlusher.access$800(MemStoreFlusher.java:69)
at org.apache.hadoop.hbase.regionserver.MemStoreFlusher$FlushHandler.run(MemStoreFlusher.java:225)
at java.lang.Thread.run(Thread.java:745)
Caused by: java.lang.ArrayIndexOutOfBoundsException: -32743
at org.apache.hadoop.hbase.CellComparator.getMinimumMidpointArray(CellComparator.java:478)
at org.apache.hadoop.hbase.CellComparator.getMidpoint(CellComparator.java:448)
at org.apache.hadoop.hbase.io.hfile.HFileWriterV2.finishBlock(HFileWriterV2.java:165)
at org.apache.hadoop.hbase.io.hfile.HFileWriterV2.checkBlockBoundary(HFileWriterV2.java:146)
at org.apache.hadoop.hbase.io.hfile.HFileWriterV2.append(HFileWriterV2.java:263)
at org.apache.hadoop.hbase.io.hfile.HFileWriterV3.append(HFileWriterV3.java:87)
at org.apache.hadoop.hbase.regionserver.StoreFile$Writer.append(StoreFile.java:932)
at org.apache.hadoop.hbase.regionserver.StoreFlusher.performFlush(StoreFlusher.java:121)
at org.apache.hadoop.hbase.regionserver.DefaultStoreFlusher.flushSnapshot(DefaultStoreFlusher.java:71)
at org.apache.hadoop.hbase.regionserver.HStore.flushCache(HStore.java:879)
at org.apache.hadoop.hbase.regionserver.HStore$StoreFlusherImpl.flushCache(HStore.java:2128)
at org.apache.hadoop.hbase.regionserver.HRegion.internalFlushcache(HRegion.java:1953)
... 7 more
2015-03-24 18:04:36,156 FATAL [MemStoreFlusher.0] regionserver.HRegionServer: RegionServer abort: loaded coprocessors are: [org.apache.hadoop.hbase.coprocessor.MultiRowMutationEndpoint]

Issue Links

• duplicates: HBASE-14018 RegionServer is aborted when flushing memstore.
• relates to: HBASE-14281 ArrayIndexOutOfBoundsException in CellComparator#getMinimumMidpointArray, part 2