Failed to merge indices Elasticsearch - java

I have big problem with ES :(
When i insert bulk (size = 20) a lot of document to ES, ES server throw below exception.
I find many topic discuss about this, but nothing. :sosad: , Any help me, what actually happened ??? Thks so much.
Sr for my bad english.
I using ES 2.3 , client Transport 2.2.1.
Server config
http.port: 9200
http.max_content_length: 100mb
node.name: "es_test"
nod.master: true
node.data: true
index.store.type: niofs
index.number_of_shards: 5
index.number_of_replicas: 0
discovery.zen.ping.multicast.enabled: false
script.inline: on
script.indexed: on
bootstrap.mlockall: true
Erros1
[2016-03-31 07:45:02,601][ERROR][index.engine ] [es_test] [my_index][1] failed to merge
java.io.EOFException: read past EOF: NIOFSIndexInput(path="/data/es_test/data/es_test/nodes/0/indices/my_index/1/index/_190.fnm")
at org.apache.lucene.store.BufferedIndexInput.refill(BufferedIndexInput.java:336)
at org.apache.lucene.store.BufferedIndexInput.readByte(BufferedIndexInput.java:54)
at org.apache.lucene.store.BufferedChecksumIndexInput.readByte(BufferedChecksumIndexInput.java:41)
at org.apache.lucene.store.DataInput.readInt(DataInput.java:101)
at org.apache.lucene.codecs.CodecUtil.checkHeader(CodecUtil.java:195)
at org.apache.lucene.codecs.CodecUtil.checkIndexHeader(CodecUtil.java:256)
at org.apache.lucene.codecs.lucene50.Lucene50FieldInfosFormat.read(Lucene50FieldInfosFormat.java:115)
at org.apache.lucene.index.SegmentCoreReaders.<init>(SegmentCoreReaders.java:99)
at org.apache.lucene.index.SegmentReader.<init>(SegmentReader.java:65)
at org.apache.lucene.index.ReadersAndUpdates.getReader(ReadersAndUpdates.java:145)
at org.apache.lucene.index.IndexWriter.mergeMiddle(IndexWriter.java:4233)
at org.apache.lucene.index.IndexWriter.merge(IndexWriter.java:3664)
at org.apache.lucene.index.ConcurrentMergeScheduler.doMerge(ConcurrentMergeScheduler.java:588)
at org.elasticsearch.index.engine.ElasticsearchConcurrentMergeScheduler.doMerge(ElasticsearchConcurrentMergeScheduler.java:94)
at org.apache.lucene.index.ConcurrentMergeScheduler$MergeThread.run(ConcurrentMergeScheduler.java:626)
Suppressed: org.apache.lucene.index.CorruptIndexException: checksum status indeterminate: remaining=0, please run checkindex for more details (resource=BufferedChecksumIndexInput(NIOFSIndexInput(path="/data/es_test/data/es_test/nodes/0/indices/my_index/1/index/_190.fnm")))
at org.apache.lucene.codecs.CodecUtil.checkFooter(CodecUtil.java:371)
at org.apache.lucene.codecs.lucene50.Lucene50FieldInfosFormat.read(Lucene50FieldInfosFormat.java:164)
... 8 more
[2016-03-31 07:45:02,608][WARN ][index.engine ] [es_test] [my_index][1] failed engine [already closed by tragic event on the index writer]
java.io.EOFException: read past EOF: NIOFSIndexInput(path="/data/es_test/data/es_test/nodes/0/indices/my_index/1/index/_190.fnm")
at org.apache.lucene.store.BufferedIndexInput.refill(BufferedIndexInput.java:336)
at org.apache.lucene.store.BufferedIndexInput.readByte(BufferedIndexInput.java:54)
at org.apache.lucene.store.BufferedChecksumIndexInput.readByte(BufferedChecksumIndexInput.java:41)
at org.apache.lucene.store.DataInput.readInt(DataInput.java:101)
at org.apache.lucene.codecs.CodecUtil.checkHeader(CodecUtil.java:195)
at org.apache.lucene.codecs.CodecUtil.checkIndexHeader(CodecUtil.java:256)
at org.apache.lucene.codecs.lucene50.Lucene50FieldInfosFormat.read(Lucene50FieldInfosFormat.java:115)
at org.apache.lucene.index.SegmentCoreReaders.<init>(SegmentCoreReaders.java:99)
at org.apache.lucene.index.SegmentReader.<init>(SegmentReader.java:65)
at org.apache.lucene.index.ReadersAndUpdates.getReader(ReadersAndUpdates.java:145)
at org.apache.lucene.index.IndexWriter.mergeMiddle(IndexWriter.java:4233)
at org.apache.lucene.index.IndexWriter.merge(IndexWriter.java:3664)
at org.apache.lucene.index.ConcurrentMergeScheduler.doMerge(ConcurrentMergeScheduler.java:588)
at org.elasticsearch.index.engine.ElasticsearchConcurrentMergeScheduler.doMerge(ElasticsearchConcurrentMergeScheduler.java:94)
at org.apache.lucene.index.ConcurrentMergeScheduler$MergeThread.run(ConcurrentMergeScheduler.java:626)
Suppressed: org.apache.lucene.index.CorruptIndexException: checksum status indeterminate: remaining=0, please run checkindex for more details (resource=BufferedChecksumIndexInput(NIOFSIndexInput(path="/data/es_test/data/es_test/nodes/0/indices/my_index/1/index/_190.fnm")))
at org.apache.lucene.codecs.CodecUtil.checkFooter(CodecUtil.java:371)
at org.apache.lucene.codecs.lucene50.Lucene50FieldInfosFormat.read(Lucene50FieldInfosFormat.java:164)
... 8 more
[2016-03-31 07:45:02,609][ERROR][index.engine ] [es_test] [my_index][4] failed to merge
java.io.EOFException: read past EOF: NIOFSIndexInput(path="/data/es_test/data/es_test/nodes/0/indices/my_index/4/index/_190.fdx")
at org.apache.lucene.store.BufferedIndexInput.refill(BufferedIndexInput.java:336)
at org.apache.lucene.store.BufferedIndexInput.readByte(BufferedIndexInput.java:54)
at org.apache.lucene.store.BufferedChecksumIndexInput.readByte(BufferedChecksumIndexInput.java:41)
at org.apache.lucene.store.DataInput.readInt(DataInput.java:101)
at org.apache.lucene.codecs.CodecUtil.checkHeader(CodecUtil.java:195)
at org.apache.lucene.codecs.CodecUtil.checkIndexHeader(CodecUtil.java:256)
at org.apache.lucene.codecs.compressing.CompressingStoredFieldsReader.<init>(CompressingStoredFieldsReader.java:133)
at org.apache.lucene.codecs.compressing.CompressingStoredFieldsFormat.fieldsReader(CompressingStoredFieldsFormat.java:121)
at org.apache.lucene.codecs.lucene50.Lucene50StoredFieldsFormat.fieldsReader(Lucene50StoredFieldsFormat.java:173)
at org.apache.lucene.index.SegmentCoreReaders.<init>(SegmentCoreReaders.java:117)
at org.apache.lucene.index.SegmentReader.<init>(SegmentReader.java:65)
at org.apache.lucene.index.ReadersAndUpdates.getReader(ReadersAndUpdates.java:145)
at org.apache.lucene.index.IndexWriter.mergeMiddle(IndexWriter.java:4233)
at org.apache.lucene.index.IndexWriter.merge(IndexWriter.java:3664)
at org.apache.lucene.index.ConcurrentMergeScheduler.doMerge(ConcurrentMergeScheduler.java:588)
at org.elasticsearch.index.engine.ElasticsearchConcurrentMergeScheduler.doMerge(ElasticsearchConcurrentMergeScheduler.java:94)
at org.apache.lucene.index.ConcurrentMergeScheduler$MergeThread.run(ConcurrentMergeScheduler.java:626)
Suppressed: org.apache.lucene.index.CorruptIndexException: checksum status indeterminate: remaining=0, please run checkindex for more details (resource=BufferedChecksumIndexInput(NIOFSIndexInput(path="/data/es_test/data/es_test/nodes/0/indices/my_index/4/index/_190.fdx")))
at org.apache.lucene.codecs.CodecUtil.checkFooter(CodecUtil.java:371)
at org.apache.lucene.codecs.compressing.CompressingStoredFieldsReader.<init>(CompressingStoredFieldsReader.java:140)
... 10 more
Erros2
[2016-03-31 20:04:07,419][DEBUG][action.admin.cluster.node.stats] [es_test] failed to execute on node [mplUA6JET92RPgmNx-DPMA]
RemoteTransportException[[es_test][ip:9300][cluster:monitor/nodes/stats[n]]]; nested: AlreadyClosedException[this IndexReader is closed];
Caused by: org.apache.lucene.store.AlreadyClosedException: this IndexReader is closed
at org.apache.lucene.index.IndexReader.ensureOpen(IndexReader.java:274)
at org.apache.lucene.index.CompositeReader.getContext(CompositeReader.java:101)
at org.apache.lucene.index.CompositeReader.getContext(CompositeReader.java:55)
at org.apache.lucene.index.IndexReader.leaves(IndexReader.java:438)
at org.elasticsearch.search.suggest.completion.Completion090PostingsFormat.completionStats(Completion090PostingsFormat.java:330)
at org.elasticsearch.index.shard.IndexShard.completionStats(IndexShard.java:765)
at org.elasticsearch.action.admin.indices.stats.CommonStats.<init>(CommonStats.java:164)
at org.elasticsearch.indices.IndicesService.stats(IndicesService.java:253)
at org.elasticsearch.node.service.NodeService.stats(NodeService.java:157)
at org.elasticsearch.action.admin.cluster.node.stats.TransportNodesStatsAction.nodeOperation(TransportNodesStatsAction.java:82)
at org.elasticsearch.action.admin.cluster.node.stats.TransportNodesStatsAction.nodeOperation(TransportNodesStatsAction.java:44)
at org.elasticsearch.action.support.nodes.TransportNodesAction.nodeOperation(TransportNodesAction.java:92)
at org.elasticsearch.action.support.nodes.TransportNodesAction$NodeTransportHandler.messageReceived(TransportNodesAction.java:230)
at org.elasticsearch.action.support.nodes.TransportNodesAction$NodeTransportHandler.messageReceived(TransportNodesAction.java:226)
at org.elasticsearch.transport.RequestHandlerRegistry.processMessageReceived(RequestHandlerRegistry.java:75)
at org.elasticsearch.transport.TransportService$4.doRun(TransportService.java:376)
at org.elasticsearch.common.util.concurrent.AbstractRunnable.run(AbstractRunnable.java:37)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)

I suggest that you receive the error, since upgrading to ES 2.3?
The cause is most likely that your transport client version is older than your clusters version.
When using the transport Client, the versions have to be compatible.

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I wrote a mapreduce job to scan an hbase table for a certain time range to count certain elements we need for analysis.
Mappers in the MR job keeps failing but I don't know why. Seems like each time I run the job, a different number of mappers fail. The YARN log (see below) from Cloudera manager isn't helpful in pointing what the problem is, although, someone said I might be running out of memory.
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Below is a log from YARN for one of the mappers that failed.
Error: org.apache.hadoop.hbase.client.RetriesExhaustedException:
Failed after attempts=36, exceptions: Thu Jun 15 16:26:57 PDT 2017,
null, java.net.SocketTimeoutException: callTimeout=60000,
callDuration=60301: row '152_p3401.db161139.sjc102.dbi_1496271480' on
table 'dbi_based_data' at
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at
org.apache.hadoop.hbase.client.ScannerCallableWithReplicas.call(ScannerCallableWithReplicas.java:207)
at
org.apache.hadoop.hbase.client.ScannerCallableWithReplicas.call(ScannerCallableWithReplicas.java:60)
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at
org.apache.hadoop.hbase.client.ClientScanner.loadCache(ClientScanner.java:403)
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org.apache.hadoop.mapred.MapTask$NewTrackingRecordReader.nextKeyValue(MapTask.java:556)
at
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at
org.apache.hadoop.mapreduce.lib.map.WrappedMapper$Context.nextKeyValue(WrappedMapper.java:91)
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at
java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
at
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
at java.lang.Thread.run(Thread.java:745) Caused by:
java.io.IOException: Call to
hslave35118.ams9.mysecretdomain.com/10.216.35.118:60020 failed on
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org.apache.hadoop.hbase.ipc.AbstractRpcClient.callBlockingMethod(AbstractRpcClient.java:226)
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org.apache.hadoop.hbase.ipc.AbstractRpcClient$BlockingRpcChannelImplementation.callBlockingMethod(AbstractRpcClient.java:331)
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org.apache.hadoop.hbase.client.ScannerCallableWithReplicas$RetryingRPC.call(ScannerCallableWithReplicas.java:334)
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org.apache.hadoop.hbase.ipc.CallTimeoutException: Call id=12,
waitTime=60001, operationTimeout=60000 expired. at
org.apache.hadoop.hbase.ipc.Call.checkAndSetTimeout(Call.java:73) at
org.apache.hadoop.hbase.ipc.RpcClientImpl.call(RpcClientImpl.java:1246)
... 13 more
So it looks like for my case I needed to extend the timeout setting. In my Java program I had to add the following lines to make the exception go away:
conf.set("hbase.rpc.timeout","90000");
conf.set("hbase.client.scanner.timeout.period","90000");
The answer was found on this link on Cloudera's site

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Here is the stack trace:
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... 13 common frames omitted
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...
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at java.io.PipedInputStream.read(PipedInputStream.java:378)
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at org.apache.camel.processor.CamelInternalProcessor.process(CamelInternalProcessor.java:191)
at org.apache.camel.processor.Pipeline.process(Pipeline.java:118)
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at org.apache.camel.management.InstrumentationProcessor.process(InstrumentationProcessor.java:77)
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at org.apache.camel.processor.Pipeline.process(Pipeline.java:118)
at org.apache.camel.processor.Pipeline.process(Pipeline.java:80)
at org.apache.camel.util.AsyncProcessorHelper.process(AsyncProcessorHelper.java:109)
at org.apache.camel.processor.Pipeline.process(Pipeline.java:60)
at org.apache.camel.processor.CamelInternalProcessor.process(CamelInternalProcessor.java:166)
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at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:293)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
at java.lang.Thread.run(Thread.java:744)
I have set redelivery so it re attempts the download. The reattempt happens for the last file and as per the logs the file is downloaded. But when i check the folder the file size is 0 and even the .done file is created, the actual file size on remote server is 28 KB.
For rest of the files i get the below error for each file and none of the file is downloaded:
WARN 04/11/15 07:49:58,877 org.slf4j.helpers.MarkerIgnoringBase :Error processing file RemoteFile[/User/User01/File02.csv] due to Cannot retrieve file: /User/User01/File02.csv. Caused by: [org.apache.camel.component.file.GenericFileOperationFailedException - Cannot retrieve file: /User/User01/File02.csv]
org.apache.camel.component.file.GenericFileOperationFailedException: Cannot retrieve file: /User/User01/File02.csv
at org.apache.camel.component.file.remote.SftpOperations.retrieveFileToStreamInBody(SftpOperations.java:651)
at org.apache.camel.component.file.remote.SftpOperations.retrieveFile(SftpOperations.java:594)
at org.apache.camel.component.file.GenericFileConsumer.processExchange(GenericFileConsumer.java:396)
at org.apache.camel.component.file.remote.RemoteFileConsumer.processExchange(RemoteFileConsumer.java:137)
at org.apache.camel.component.file.GenericFileConsumer.processBatch(GenericFileConsumer.java:211)
at org.apache.camel.component.file.GenericFileConsumer.poll(GenericFileConsumer.java:175)
at org.apache.camel.impl.ScheduledPollConsumer.doRun(ScheduledPollConsumer.java:174)
at org.apache.camel.impl.ScheduledPollConsumer.run(ScheduledPollConsumer.java:101)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
at java.util.concurrent.FutureTask.runAndReset(FutureTask.java:304)
at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$301(ScheduledThreadPoolExecutor.java:178)
at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:293)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
at java.lang.Thread.run(Thread.java:744)
Caused by: 4:
at com.jcraft.jsch.ChannelSftp.get(ChannelSftp.java:1513)
at com.jcraft.jsch.ChannelSftp.get(ChannelSftp.java:1266)
at org.apache.camel.component.file.remote.SftpOperations.retrieveFileToStreamInBody(SftpOperations.java:636)
... 14 more
Caused by: java.io.IOException: Pipe closed
at java.io.PipedInputStream.read(PipedInputStream.java:308)
at com.jcraft.jsch.Channel$MyPipedInputStream.updateReadSide(Channel.java:362)
at com.jcraft.jsch.ChannelSftp.get(ChannelSftp.java:1287)
... 16 more
I tried using both disconnect=true and false, the issue is happening in both the cases.
Any suggestions what could be wrong?
You had used both initial delay which is the delay before polling for a file by the consumer and delay which is before the next poll. Both creates a time buffer which is
Initialdelay+DownloadTime+Delay+WriteDestinationDirectoryTime
Try using only "delay".
Try appending a timestamp to the file being stored in destination.
Try camel-ftp2

SSTable loader streaming failed giving java.io.IOException: Connection reset by peer

I am trying to use sstableloader to stream data to a Cassandra database, which is in fact in the same node. It used to work when i was using DSE 2.2 but when i upgraded it to DSE 4.5 and made all the relevant changes in the cassandra.yaml file, it stopped working and now it is throwing an error like this:
Established connection to initial hosts
Opening sstables and calculating sections to stream
Streaming relevant part of demo/test_yale/demo-test_yale-jb-2-Data.db demo/test_yale/demo-test_yale-jb-1-Data.db to [/127.0.0.1]
Streaming session ID: 02225ef0-1c17-11e4-a1ea-5f2d4f6a32c1
progress: [/127.0.0.1 1/2 (88%)] [total: 88% - 2147483647MB/s (avg: 14MB/s)]ERROR 16:36:29,029 [Stream #02225ef0-1c17-11e4-a1ea-5f2d4f6a32c1] Streaming error occurred
java.io.IOException: Connection reset by peer
at sun.nio.ch.FileDispatcherImpl.write0(Native Method)
at sun.nio.ch.SocketDispatcher.write(SocketDispatcher.java:47)
at sun.nio.ch.IOUtil.writeFromNativeBuffer(IOUtil.java:93)
at sun.nio.ch.IOUtil.write(IOUtil.java:65)
at sun.nio.ch.SocketChannelImpl.write(SocketChannelImpl.java:487)
at java.nio.channels.Channels.writeFullyImpl(Channels.java:78)
at java.nio.channels.Channels.writeFully(Channels.java:98)
at java.nio.channels.Channels.access$000(Channels.java:61)
at java.nio.channels.Channels$1.write(Channels.java:174)
at com.ning.compress.lzf.LZFChunk.writeCompressedHeader(LZFChunk.java:77)
at com.ning.compress.lzf.ChunkEncoder.encodeAndWriteChunk(ChunkEncoder.java:132)
at com.ning.compress.lzf.LZFOutputStream.writeCompressedBlock(LZFOutputStream.java:203)
at com.ning.compress.lzf.LZFOutputStream.write(LZFOutputStream.java:97)
at org.apache.cassandra.streaming.StreamWriter.write(StreamWriter.java:151)
at org.apache.cassandra.streaming.StreamWriter.write(StreamWriter.java:101)
at org.apache.cassandra.streaming.messages.OutgoingFileMessage$1.serialize(OutgoingFileMessage.java:59)
at org.apache.cassandra.streaming.messages.OutgoingFileMessage$1.serialize(OutgoingFileMessage.java:42)
at org.apache.cassandra.streaming.messages.StreamMessage.serialize(StreamMessage.java:45)
at org.apache.cassandra.streaming.ConnectionHandler$OutgoingMessageHandler.sendMessage(ConnectionHandler.java:383)
at org.apache.cassandra.streaming.ConnectionHandler$OutgoingMessageHandler.run(ConnectionHandler.java:363)
at java.lang.Thread.run(Thread.java:745)
WARN 16:36:29,032 [Stream #02225ef0-1c17-11e4-a1ea-5f2d4f6a32c1] Stream failed
Streaming to the following hosts failed:
[/127.0.0.1]
java.util.concurrent.ExecutionException: org.apache.cassandra.streaming.StreamException: Stream failed
I have even tried assigning actual ip address of the node for the listen_address, broadcast_address, and rpc_address in the cassandra.yaml file but the same error occurs.
Can anyone be of assistance please?
It's worth looking at your system.log as specified in cassandra/conf/logback.xml, as suggested by Zanson.
In my case the issue was simply with exhausting disk space on the node:
ERROR [STREAM-IN-/xx.xx.xx.xx] 2016-08-02 10:50:31,125 StreamSession.java:505 - [Stream #8420bfa0-589c-11e6-9512-235b1f79cf1b] Streaming error occurred
java.io.IOException: No space left on device
at java.io.RandomAccessFile.writeBytes(Native Method) ~[na:1.8.0_101]
at java.io.RandomAccessFile.write(RandomAccessFile.java:525) ~[na:1.8.0_101]

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