[ACCUMULO-3783] Unexpected Filesystem Closed exceptions

• Type: Bug
• Status: Resolved
• Priority: Major
• Resolution: Cannot Reproduce
• Affects Version/s: 1.7.0
• Component/s: master, start, tserver
• Assignee: Josh Elser
• Reporter: Josh Elser
• Created: 08/May/15 05:04
• Updated: 30/Jun/15 19:12
• Resolved: 30/Jun/15 19:09

Description

Noticed this in testing 1.7.0 on my laptop tonight. Started two tservers, one continuous ingest client and would kill/restart one of the tservers occasionally.

Failed to close map file
	java.io.IOException: Filesystem closed
		at org.apache.hadoop.hdfs.DFSClient.checkOpen(DFSClient.java:795)
		at org.apache.hadoop.hdfs.DFSInputStream.close(DFSInputStream.java:629)
		at java.io.FilterInputStream.close(FilterInputStream.java:181)
		at org.apache.accumulo.core.file.blockfile.impl.CachableBlockFile$Reader.close(CachableBlockFile.java:409)
		at org.apache.accumulo.core.file.rfile.RFile$Reader.close(RFile.java:921)
		at org.apache.accumulo.tserver.tablet.Compactor.compactLocalityGroup(Compactor.java:391)
		at org.apache.accumulo.tserver.tablet.Compactor.call(Compactor.java:214)
		at org.apache.accumulo.tserver.tablet.Tablet._majorCompact(Tablet.java:1981)
		at org.apache.accumulo.tserver.tablet.Tablet.majorCompact(Tablet.java:2098)
		at org.apache.accumulo.tserver.tablet.CompactionRunner.run(CompactionRunner.java:44)
		at org.apache.htrace.wrappers.TraceRunnable.run(TraceRunnable.java:57)
		at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
		at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
		at org.apache.accumulo.fate.util.LoggingRunnable.run(LoggingRunnable.java:35)
		at java.lang.Thread.run(Thread.java:745)

null
	java.nio.channels.ClosedChannelException
		at org.apache.hadoop.hdfs.DFSOutputStream.checkClosed(DFSOutputStream.java:1622)
		at org.apache.hadoop.fs.FSOutputSummer.write(FSOutputSummer.java:104)
		at org.apache.hadoop.fs.FSDataOutputStream$PositionCache.write(FSDataOutputStream.java:58)
		at java.io.DataOutputStream.write(DataOutputStream.java:107)
		at org.apache.accumulo.core.file.rfile.bcfile.SimpleBufferedOutputStream.flushBuffer(SimpleBufferedOutputStream.java:39)
		at org.apache.accumulo.core.file.rfile.bcfile.SimpleBufferedOutputStream.flush(SimpleBufferedOutputStream.java:68)
		at org.apache.hadoop.io.compress.CompressionOutputStream.flush(CompressionOutputStream.java:69)
		at org.apache.accumulo.core.file.rfile.bcfile.Compression$FinishOnFlushCompressionStream.flush(Compression.java:66)
		at java.io.BufferedOutputStream.flush(BufferedOutputStream.java:141)
		at org.apache.accumulo.core.file.rfile.bcfile.BCFile$Writer$WBlockState.finish(BCFile.java:233)
		at org.apache.accumulo.core.file.rfile.bcfile.BCFile$Writer$BlockAppender.close(BCFile.java:320)
		at org.apache.accumulo.core.file.blockfile.impl.CachableBlockFile$BlockWrite.close(CachableBlockFile.java:121)
		at org.apache.accumulo.core.file.rfile.RFile$Writer.closeBlock(RFile.java:398)
		at org.apache.accumulo.core.file.rfile.RFile$Writer.append(RFile.java:382)
		at org.apache.accumulo.tserver.tablet.Compactor.compactLocalityGroup(Compactor.java:356)
		at org.apache.accumulo.tserver.tablet.Compactor.call(Compactor.java:214)
		at org.apache.accumulo.tserver.tablet.Tablet._majorCompact(Tablet.java:1981)
		at org.apache.accumulo.tserver.tablet.Tablet.majorCompact(Tablet.java:2098)
		at org.apache.accumulo.tserver.tablet.CompactionRunner.run(CompactionRunner.java:44)
		at org.apache.htrace.wrappers.TraceRunnable.run(TraceRunnable.java:57)
		at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
		at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
		at org.apache.accumulo.fate.util.LoggingRunnable.run(LoggingRunnable.java:35)
		at java.lang.Thread.run(Thread.java:745)

Filesystem closed
	java.io.IOException: Filesystem closed
		at org.apache.hadoop.hdfs.DFSClient.checkOpen(DFSClient.java:795)
		at org.apache.hadoop.hdfs.DFSClient.delete(DFSClient.java:1927)
		at org.apache.hadoop.hdfs.DistributedFileSystem$12.doCall(DistributedFileSystem.java:638)
		at org.apache.hadoop.hdfs.DistributedFileSystem$12.doCall(DistributedFileSystem.java:634)
		at org.apache.hadoop.fs.FileSystemLinkResolver.resolve(FileSystemLinkResolver.java:81)
		at org.apache.hadoop.hdfs.DistributedFileSystem.delete(DistributedFileSystem.java:634)
		at org.apache.accumulo.server.fs.VolumeManagerImpl.deleteRecursively(VolumeManagerImpl.java:193)
		at org.apache.accumulo.tserver.tablet.Compactor.call(Compactor.java:255)
		at org.apache.accumulo.tserver.tablet.Tablet._majorCompact(Tablet.java:1981)
		at org.apache.accumulo.tserver.tablet.Tablet.majorCompact(Tablet.java:2098)
		at org.apache.accumulo.tserver.tablet.CompactionRunner.run(CompactionRunner.java:44)
		at org.apache.htrace.wrappers.TraceRunnable.run(TraceRunnable.java:57)
		at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
		at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
		at org.apache.accumulo.fate.util.LoggingRunnable.run(LoggingRunnable.java:35)
		at java.lang.Thread.run(Thread.java:745)

MinC failed (null) to create hdfs://localhost:8020/accumulo17/tables/2/t-0000011/F00000yd.rf_tmp retrying ...

MajC Failed, extent = 2;5;45
	java.io.IOException: Filesystem closed
		at org.apache.hadoop.hdfs.DFSClient.checkOpen(DFSClient.java:795)
		at org.apache.hadoop.hdfs.DFSClient.create(DFSClient.java:1651)
		at org.apache.hadoop.hdfs.DFSClient.create(DFSClient.java:1593)
		at org.apache.hadoop.hdfs.DistributedFileSystem$6.doCall(DistributedFileSystem.java:397)
		at org.apache.hadoop.hdfs.DistributedFileSystem$6.doCall(DistributedFileSystem.java:393)
		at org.apache.hadoop.fs.FileSystemLinkResolver.resolve(FileSystemLinkResolver.java:81)
		at org.apache.hadoop.hdfs.DistributedFileSystem.create(DistributedFileSystem.java:393)
		at org.apache.hadoop.hdfs.DistributedFileSystem.create(DistributedFileSystem.java:337)
		at org.apache.hadoop.fs.FileSystem.create(FileSystem.java:908)
		at org.apache.hadoop.fs.FileSystem.create(FileSystem.java:889)
		at org.apache.accumulo.core.file.rfile.RFileOperations.openWriter(RFileOperations.java:126)
		at org.apache.accumulo.core.file.rfile.RFileOperations.openWriter(RFileOperations.java:106)
		at org.apache.accumulo.core.file.DispatchingFileFactory.openWriter(DispatchingFileFactory.java:78)
		at org.apache.accumulo.tserver.tablet.Compactor.call(Compactor.java:192)
		at org.apache.accumulo.tserver.tablet.Tablet._majorCompact(Tablet.java:1981)
		at org.apache.accumulo.tserver.tablet.Tablet.majorCompact(Tablet.java:2098)
		at org.apache.accumulo.tserver.tablet.CompactionRunner.run(CompactionRunner.java:44)
		at org.apache.htrace.wrappers.TraceRunnable.run(TraceRunnable.java:57)
		at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
		at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
		at org.apache.accumulo.fate.util.LoggingRunnable.run(LoggingRunnable.java:35)
		at java.lang.Thread.run(Thread.java:745)

MajC Failed, extent = 2;45;4
	java.io.IOException: Filesystem closed
		at org.apache.hadoop.hdfs.DFSClient.checkOpen(DFSClient.java:795)
		at org.apache.hadoop.hdfs.DFSClient.create(DFSClient.java:1651)
		at org.apache.hadoop.hdfs.DFSClient.create(DFSClient.java:1593)
		at org.apache.hadoop.hdfs.DistributedFileSystem$6.doCall(DistributedFileSystem.java:397)
		at org.apache.hadoop.hdfs.DistributedFileSystem$6.doCall(DistributedFileSystem.java:393)
		at org.apache.hadoop.fs.FileSystemLinkResolver.resolve(FileSystemLinkResolver.java:81)
		at org.apache.hadoop.hdfs.DistributedFileSystem.create(DistributedFileSystem.java:393)
		at org.apache.hadoop.hdfs.DistributedFileSystem.create(DistributedFileSystem.java:337)
		at org.apache.hadoop.fs.FileSystem.create(FileSystem.java:908)
		at org.apache.hadoop.fs.FileSystem.create(FileSystem.java:889)
		at org.apache.accumulo.core.file.rfile.RFileOperations.openWriter(RFileOperations.java:126)
		at org.apache.accumulo.core.file.rfile.RFileOperations.openWriter(RFileOperations.java:106)
		at org.apache.accumulo.core.file.DispatchingFileFactory.openWriter(DispatchingFileFactory.java:78)
		at org.apache.accumulo.tserver.tablet.Compactor.call(Compactor.java:192)
		at org.apache.accumulo.tserver.tablet.Tablet._majorCompact(Tablet.java:1981)
		at org.apache.accumulo.tserver.tablet.Tablet.majorCompact(Tablet.java:2098)
		at org.apache.accumulo.tserver.tablet.CompactionRunner.run(CompactionRunner.java:44)
		at org.apache.htrace.wrappers.TraceRunnable.run(TraceRunnable.java:57)
		at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
		at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
		at org.apache.accumulo.fate.util.LoggingRunnable.run(LoggingRunnable.java:35)
		at java.lang.Thread.run(Thread.java:745)

MajC Failed, extent = 2;35;3
	java.io.IOException: Filesystem closed
		at org.apache.hadoop.hdfs.DFSClient.checkOpen(DFSClient.java:795)
		at org.apache.hadoop.hdfs.DFSClient.create(DFSClient.java:1651)
		at org.apache.hadoop.hdfs.DFSClient.create(DFSClient.java:1593)
		at org.apache.hadoop.hdfs.DistributedFileSystem$6.doCall(DistributedFileSystem.java:397)
		at org.apache.hadoop.hdfs.DistributedFileSystem$6.doCall(DistributedFileSystem.java:393)
		at org.apache.hadoop.fs.FileSystemLinkResolver.resolve(FileSystemLinkResolver.java:81)
		at org.apache.hadoop.hdfs.DistributedFileSystem.create(DistributedFileSystem.java:393)
		at org.apache.hadoop.hdfs.DistributedFileSystem.create(DistributedFileSystem.java:337)
		at org.apache.hadoop.fs.FileSystem.create(FileSystem.java:908)
		at org.apache.hadoop.fs.FileSystem.create(FileSystem.java:889)
		at org.apache.accumulo.core.file.rfile.RFileOperations.openWriter(RFileOperations.java:126)
		at org.apache.accumulo.core.file.rfile.RFileOperations.openWriter(RFileOperations.java:106)
		at org.apache.accumulo.core.file.DispatchingFileFactory.openWriter(DispatchingFileFactory.java:78)
		at org.apache.accumulo.tserver.tablet.Compactor.call(Compactor.java:192)
		at org.apache.accumulo.tserver.tablet.Tablet._majorCompact(Tablet.java:1981)
		at org.apache.accumulo.tserver.tablet.Tablet.majorCompact(Tablet.java:2098)
		at org.apache.accumulo.tserver.tablet.CompactionRunner.run(CompactionRunner.java:44)
		at org.apache.htrace.wrappers.TraceRunnable.run(TraceRunnable.java:57)
		at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
		at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
		at org.apache.accumulo.fate.util.LoggingRunnable.run(LoggingRunnable.java:35)
		at java.lang.Thread.run(Thread.java:745)

Filesystem closed
	java.io.IOException: Filesystem closed
		at org.apache.hadoop.hdfs.DFSClient.checkOpen(DFSClient.java:795)
		at org.apache.hadoop.hdfs.DFSClient.create(DFSClient.java:1651)
		at org.apache.hadoop.hdfs.DFSClient.create(DFSClient.java:1593)
		at org.apache.hadoop.hdfs.DistributedFileSystem$6.doCall(DistributedFileSystem.java:397)
		at org.apache.hadoop.hdfs.DistributedFileSystem$6.doCall(DistributedFileSystem.java:393)
		at org.apache.hadoop.fs.FileSystemLinkResolver.resolve(FileSystemLinkResolver.java:81)
		at org.apache.hadoop.hdfs.DistributedFileSystem.create(DistributedFileSystem.java:393)
		at org.apache.hadoop.hdfs.DistributedFileSystem.create(DistributedFileSystem.java:337)
		at org.apache.hadoop.fs.FileSystem.create(FileSystem.java:908)
		at org.apache.hadoop.fs.FileSystem.create(FileSystem.java:889)
		at org.apache.accumulo.core.file.rfile.RFileOperations.openWriter(RFileOperations.java:126)
		at org.apache.accumulo.core.file.rfile.RFileOperations.openWriter(RFileOperations.java:106)
		at org.apache.accumulo.core.file.DispatchingFileFactory.openWriter(DispatchingFileFactory.java:78)
		at org.apache.accumulo.tserver.tablet.Compactor.call(Compactor.java:192)
		at org.apache.accumulo.tserver.tablet.Tablet._majorCompact(Tablet.java:1981)
		at org.apache.accumulo.tserver.tablet.Tablet.majorCompact(Tablet.java:2098)
		at org.apache.accumulo.tserver.tablet.CompactionRunner.run(CompactionRunner.java:44)
		at org.apache.htrace.wrappers.TraceRunnable.run(TraceRunnable.java:57)
		at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
		at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
		at org.apache.accumulo.fate.util.LoggingRunnable.run(LoggingRunnable.java:35)
		at java.lang.Thread.run(Thread.java:745)

This reminded me of something that bills ran into and tried to get to the bottom of.

My hunch was that somethign registered a shutdown hook which closed the filesystem object. I also remembered that FileSystem instances are cached.

Bill pointed out that he thought this might still be a VFS related issue (despite having nothign to do with VFS). After I noticed a shutdown hook in our VFS usage, I think it's unsafe to be sharing FileSystem instances with VFS code that might also be used by Accumulo for important things like writing to files.

We should get a unique FileSystem instance to provide to any VFS code. We can do this by:

1. Setting fs.hdfs.impl.disable.cache in the Hadoop Configuration we provide to FileSystem.get(Configuration)
2. Call FileSystem.newInstance(URI, Configuration).

Either seem to do what we want – the latter possibly having more reliable semantics than just a configuration value.

Issue Links

• is related to: ACCUMULO-3923 bootstrap_hdfs.sh does not copy correct jars to hdfs
• is related to: HADOOP-4829 Allow FileSystem shutdown hook to be disabled