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From Friso van Vollenhoven <fvanvollenho...@xebia.com>
Subject HBase client hangs after upgrade to 0.20.4 when used from reducer
Date Wed, 12 May 2010 15:31:18 GMT
Hi all,

I am using Hadoop (0.20.2) and HBase to periodically import data (every 15 minutes). There
are a number of import processes, but generally they all create a sequence file on HDFS, which
is then run through a MapReduce job. The MapReduce uses the identity mapper (the input file
is a Hadoop sequence file) and a specialized reducer that does the following:
- Combine the values for a key into one value
- Do a Get from HBase to retrieve existing values for the same key
- Combine the existing value from HBase and the new one into one value again
- Put the final value into HBase under the same key (thus 'overwrite' the existing row; I
keep only one version)

After I upgraded HBase to the 0.20.4 release, the reducers sometimes start hanging on a Get.
When the jobs start, some reducers run to completion fine, but after a while the last reducers
will start to hang. Eventually the reducers are killed of by Hadoop (after 600 secs).

I did a thread dump for one of the hanging reducers. It looks like this:
"main" prio=10 tid=0x0000000048083800 nid=0x4c93 in Object.wait() [0x00000000420ca000]
   java.lang.Thread.State: WAITING (on object monitor)
	at java.lang.Object.wait(Native Method)
	- waiting on <0x00002aaaaeb50d70> (a org.apache.hadoop.hbase.ipc.HBaseClient$Call)
	at java.lang.Object.wait(Object.java:485)
	at org.apache.hadoop.hbase.ipc.HBaseClient.call(HBaseClient.java:721)
	- locked <0x00002aaaaeb50d70> (a org.apache.hadoop.hbase.ipc.HBaseClient$Call)
	at org.apache.hadoop.hbase.ipc.HBaseRPC$Invoker.invoke(HBaseRPC.java:333)
	at $Proxy2.get(Unknown Source)
	at org.apache.hadoop.hbase.client.HTable$4.call(HTable.java:450)
	at org.apache.hadoop.hbase.client.HTable$4.call(HTable.java:448)
	at org.apache.hadoop.hbase.client.HConnectionManager$TableServers.getRegionServerWithRetries(HConnectionManager.java:1050)
	at org.apache.hadoop.hbase.client.HTable.get(HTable.java:447)
	at net.ripe.inrdb.hbase.accessor.real.HBaseTableAccessor.get(HBaseTableAccessor.java:36)
	at net.ripe.inrdb.hbase.store.HBaseStoreUpdater.getExistingRecords(HBaseStoreUpdater.java:101)
	at net.ripe.inrdb.hbase.store.HBaseStoreUpdater.mergeTimelinesWithExistingRecords(HBaseStoreUpdater.java:60)
	at net.ripe.inrdb.hbase.store.HBaseStoreUpdater.doInsert(HBaseStoreUpdater.java:40)
	at net.ripe.inrdb.core.store.SinglePartitionStore$Updater.insert(SinglePartitionStore.java:92)
	at net.ripe.inrdb.core.store.CompositeStore$CompositeStoreUpdater.insert(CompositeStore.java:142)
	at net.ripe.inrdb.importer.StoreInsertReducer.reduce(StoreInsertReducer.java:70)
	at net.ripe.inrdb.importer.StoreInsertReducer.reduce(StoreInsertReducer.java:17)
	at org.apache.hadoop.mapreduce.Reducer.run(Reducer.java:176)
	at org.apache.hadoop.mapred.ReduceTask.runNewReducer(ReduceTask.java:566)
	at org.apache.hadoop.mapred.ReduceTask.run(ReduceTask.java:408)
	at org.apache.hadoop.mapred.Child.main(Child.java:170)

So the client hangs in a wait() call, waiting on a HBaseClient$Call object. I looked at the
code. The wait is in a while() loop and has no time out, so it figures that it never gets
out of there if no notify() gets called on the object. I am not sure for exactly what condition
it is waiting, however.

Meanwhile, after this has happened, I cannot shutdown the master server normally. I have to
kill -9 it, to make it shut down. Normally and before this problem occurs, the master server
shuts down just fine. (Sorry, didn't do a thread dump of the master and now I downgraded to
0.20.3 again.)

I cannot reproduce this error on my local setup (developer machine). It only occurs on our
(currently modest) cluster of one machine running master+NN+Zookeeper and four datanodes which
are all task trackers and region servers as well. The inputs to the periodic MapReduce jobs
are very small (ranging from some Kb to several Mb) and thus contain not so many records.
I know this is not very efficient to do in MapReduce and will be faster when inserted in process
by the importer process because of startup overhead, but we are setting up this architecture
of importers and insertion for anticipated larger loads (up to 80 million records per day).

Does anyone have a clue about what happens? Or where to look for further investigation?

Thanks a lot!


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