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java.io.IOException: java.io.IOException: Could not seek StoreFileScanner[org.apache.hadoop.hbase.io

java.io.IOException: java.io.IOException: Could not seek StoreFileScanner[org.apache.hadoop.hbase.io

New Contributor

Hi All,

 

We are using Hbase Version 1.2.0. While external application trying to access triple using sparql-query we are getting below error.

 

Can you please suggest possible reasons / ways to troubleshoot this issue asap.

 

javax.servlet.ServletException: com.daedafusion.knowledge.trinity.QueryException: org.apache.hadoop.hbase.client.RetriesExhaustedException: Failed after attempts=5, exceptions:
Mon Nov 21 02:20:25 CST 2016, RpcRetryingCaller{globalStartTime=1479716425959, pause=1000, retries=5}, java.io.IOException: java.io.IOException: Could not seek StoreFileScanner[org.apache.hadoop.hbase.io.HalfStoreFileReader$1@6008d9e9, cur=null] to key jh\xC7&\xD5Av\xA1\x16\x96\xEE\xBFS\xAD\x9A\x12\xA1\x13\xA7\xC7\x9B@:\x87v\xA1P\xB1pH\x01\xB8\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00/r:/LATEST_TIMESTAMP/DeleteFamily/vlen=0/seqid=0
	at org.apache.hadoop.hbase.regionserver.StoreFileScanner.seek(StoreFileScanner.java:217)
	at org.apache.hadoop.hbase.regionserver.StoreScanner.seekScanners(StoreScanner.java:343)
	at org.apache.hadoop.hbase.regionserver.StoreScanner.<init>(StoreScanner.java:198)
	at org.apache.hadoop.hbase.regionserver.HStore.createScanner(HStore.java:2106)
	at org.apache.hadoop.hbase.regionserver.HStore.getScanner(HStore.java:2096)
	at org.apache.hadoop.hbase.regionserver.HRegion$RegionScannerImpl.<init>(HRegion.java:5543)
	at org.apache.hadoop.hbase.regionserver.HRegion.instantiateRegionScanner(HRegion.java:2568)
	at org.apache.hadoop.hbase.regionserver.HRegion.getScanner(HRegion.java:2554)
	at org.apache.hadoop.hbase.regionserver.HRegion.getScanner(HRegion.java:2535)
	at org.apache.hadoop.hbase.regionserver.RSRpcServices.scan(RSRpcServices.java:2411)
	at org.apache.hadoop.hbase.protobuf.generated.ClientProtos$ClientService$2.callBlockingMethod(ClientProtos.java:33648)
	at org.apache.hadoop.hbase.ipc.RpcServer.call(RpcServer.java:2170)
	at org.apache.hadoop.hbase.ipc.CallRunner.run(CallRunner.java:109)
	at org.apache.hadoop.hbase.ipc.RpcExecutor.consumerLoop(RpcExecutor.java:133)
	at org.apache.hadoop.hbase.ipc.RpcExecutor$1.run(RpcExecutor.java:108)
	at java.lang.Thread.run(Thread.java:745)
Caused by: java.io.IOException: On-disk size without header provided is 114569, but block header contains 0. Block offset: 912709265, data starts with: \xF0\xD5\xFAJ\xCA\xFBG\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x01ras\x00\x00\x01X6
	at org.apache.hadoop.hbase.io.hfile.HFileBlock.validateOnDiskSizeWithoutHeader(HFileBlock.java:521)
	at org.apache.hadoop.hbase.io.hfile.HFileBlock.access$700(HFileBlock.java:88)
	at org.apache.hadoop.hbase.io.hfile.HFileBlock$FSReaderImpl.readBlockDataInternal(HFileBlock.java:1665)
	at org.apache.hadoop.hbase.io.hfile.HFileBlock$FSReaderImpl.readBlockData(HFileBlock.java:1532)
	at org.apache.hadoop.hbase.io.hfile.HFileReaderV2.readBlock(HFileReaderV2.java:445)
	at org.apache.hadoop.hbase.io.hfile.HFileBlockIndex$BlockIndexReader.loadDataBlockWithScanInfo(HFileBlockIndex.java:261)
	at org.apache.hadoop.hbase.io.hfile.HFileReaderV2$AbstractScannerV2.seekTo(HFileReaderV2.java:642)
	at org.apache.hadoop.hbase.io.hfile.HFileReaderV2$AbstractScannerV2.seekTo(HFileReaderV2.java:592)
	at org.apache.hadoop.hbase.io.HalfStoreFileReader$1.seekTo(HalfStoreFileReader.java:265)
	at org.apache.hadoop.hbase.regionserver.StoreFileScanner.seekAtOrAfter(StoreFileScanner.java:294)
	at org.apache.hadoop.hbase.regionserver.StoreFileScanner.seek(StoreFileScanner.java:199)
	... 15 more

 

1 REPLY 1
Highlighted

Re: java.io.IOException: java.io.IOException: Could not seek StoreFileScanner[org.apache.hadoop.hbas

Expert Contributor

looks similar to this bug: https://issues.apache.org/jira/browse/HBASE-13830

 

If that is not the issue like there is maybe something wrong/corrupted with one of the HFileblocks for that HFile?  does the hfile tool reveal anything? here is the hfile tool doc: 

http://archive.cloudera.com/cdh/unstable/hbase-0.90.1-CDH3B4/ch10s02.html#hfile_tool

 

code responsible for the ultimate issue is here: 

https://hbase.apache.org/1.2/xref/org/apache/hadoop/hbase/io/hfile/HFileBlock.html

 

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