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From "Stefano Ortolani (JIRA)" <j...@apache.org>
Subject [jira] [Commented] (CASSANDRA-11906) Unstable JVM due too many files when anticompacting big LCS tables
Date Sat, 20 Aug 2016 21:15:21 GMT

    [ https://issues.apache.org/jira/browse/CASSANDRA-11906?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=15429513#comment-15429513
] 

Stefano Ortolani commented on CASSANDRA-11906:
----------------------------------------------

Now that I think of it, it might be related to the fact that repairs are ran with the -pr
option on each node sequentially.
Since the the repair command returns way before all anticompactions are done, the crashing
node might do so because of anticompaction sessions induced by the repairs of more than one
node.

> Unstable JVM due too many files when anticompacting big LCS tables
> ------------------------------------------------------------------
>
>                 Key: CASSANDRA-11906
>                 URL: https://issues.apache.org/jira/browse/CASSANDRA-11906
>             Project: Cassandra
>          Issue Type: Bug
>            Reporter: Stefano Ortolani
>            Assignee: Sean McCarthy
>             Fix For: 3.0.x
>
>
> I have recently moved from C* 2.1.x to C* 3.0.6. The setup is quite 
> heavy:
> 	- 13 nodes with spinning disks
> 	- ~120 GB of data per node
> 	- 50% of CFs are LCS and have quite wide rows.
> 	- 2/3 CFs with LCS have more than 200 SStables
> Incremental repairs do not seem to play really well with that.
> I have been running some tests node by node by using the -pr option:
> {code:xml}
> nodetool -h localhost repair -pr keyscheme
> {code}
> and to my surprise the whole process takes quite some time (1 hour
> minimum, 8 hours if I haven't been repairing for 5/6 days).
> Yesterday I tried to run the command with the -seq option so to 
> decrease the number of simultanoues compactions. After a while
> the node on which I was running the repair simply died during
> the anticompaction phase with the following
> exception in the logs.
> {code:xml}
> ERROR [metrics-graphite-reporter-1-thread-1] 2016-05-25 21:54:21,868 ScheduledReporter.java:119
- RuntimeException thrown from GraphiteReporter#report. Exception was suppressed.
> java.lang.RuntimeException: Failed to list files in /data/cassandra/data/keyschema/columnfamily-3996ce80b7ac11e48a9b6776bf484396
> 	at org.apache.cassandra.db.lifecycle.LogAwareFileLister.list(LogAwareFileLister.java:57)
~[apache-cassandra-3.0.6.jar:3.0.6]
> 	at org.apache.cassandra.db.lifecycle.LifecycleTransaction.getFiles(LifecycleTransaction.java:547)
~[apache-cassandra-3.0.6.jar:3.0.6]
> 	at org.apache.cassandra.db.Directories$SSTableLister.filter(Directories.java:691) ~[apache-cassandra-3.0.6.jar:3.0.6]
> 	at org.apache.cassandra.db.Directories$SSTableLister.listFiles(Directories.java:662)
~[apache-cassandra-3.0.6.jar:3.0.6]
> 	at org.apache.cassandra.db.Directories$TrueFilesSizeVisitor.<init>(Directories.java:981)
~[apache-cassandra-3.0.6.jar:3.0.6]
> 	at org.apache.cassandra.db.Directories.getTrueAllocatedSizeIn(Directories.java:893)
~[apache-cassandra-3.0.6.jar:3.0.6]
> 	at org.apache.cassandra.db.Directories.trueSnapshotsSize(Directories.java:883) ~[apache-cassandra-3.0.6.jar:3.0.6]
> 	at org.apache.cassandra.db.ColumnFamilyStore.trueSnapshotsSize(ColumnFamilyStore.java:2332)
~[apache-cassandra-3.0.6.jar:3.0.6]
> 	at org.apache.cassandra.metrics.TableMetrics$32.getValue(TableMetrics.java:637) ~[apache-cassandra-3.0.6.jar:3.0.6]
> 	at org.apache.cassandra.metrics.TableMetrics$32.getValue(TableMetrics.java:634) ~[apache-cassandra-3.0.6.jar:3.0.6]
> 	at com.codahale.metrics.graphite.GraphiteReporter.reportGauge(GraphiteReporter.java:281)
~[metrics-graphite-3.1.0.jar:3.1.0]
> 	at com.codahale.metrics.graphite.GraphiteReporter.report(GraphiteReporter.java:158)
~[metrics-graphite-3.1.0.jar:3.1.0]
> 	at com.codahale.metrics.ScheduledReporter.report(ScheduledReporter.java:162) ~[metrics-core-3.1.0.jar:3.1.0]
> 	at com.codahale.metrics.ScheduledReporter$1.run(ScheduledReporter.java:117) ~[metrics-core-3.1.0.jar:3.1.0]
> 	at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511) [na:1.8.0_91]
> 	at java.util.concurrent.FutureTask.runAndReset(FutureTask.java:308) [na:1.8.0_91]
> 	at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$301(ScheduledThreadPoolExecutor.java:180)
[na:1.8.0_91]
> 	at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:294)
[na:1.8.0_91]
> 	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) [na:1.8.0_91]
> 	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) [na:1.8.0_91]
> 	at java.lang.Thread.run(Thread.java:745) [na:1.8.0_91]
> Caused by: java.lang.RuntimeException: java.nio.file.FileSystemException: /data/cassandra/data/keyschema/columnfamily-3996ce80b7ac11e48a9b6776bf484396/ma_txn_anticompactionafterrepair_f20b50d0-22bd-11e6-970f-6f22464f4624.log:
Too many open files
> 	at org.apache.cassandra.io.util.FileUtils.readLines(FileUtils.java:622) ~[apache-cassandra-3.0.6.jar:3.0.6]
> 	at java.util.stream.Collectors.lambda$toMap$58(Collectors.java:1321) ~[na:1.8.0_91]
> 	at java.util.stream.ReduceOps$3ReducingSink.accept(ReduceOps.java:169) ~[na:1.8.0_91]
> 	at java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:193) ~[na:1.8.0_91]
> 	at java.util.Iterator.forEachRemaining(Iterator.java:116) ~[na:1.8.0_91]
> 	at java.util.Spliterators$IteratorSpliterator.forEachRemaining(Spliterators.java:1801)
~[na:1.8.0_91]
> 	at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:481) ~[na:1.8.0_91]
> 	at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:471) ~[na:1.8.0_91]
> 	at java.util.stream.ReduceOps$ReduceOp.evaluateSequential(ReduceOps.java:708) ~[na:1.8.0_91]
> 	at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234) ~[na:1.8.0_91]
> 	at java.util.stream.ReferencePipeline.collect(ReferencePipeline.java:499) ~[na:1.8.0_91]
> 	at org.apache.cassandra.db.lifecycle.LogReplicaSet.readRecords(LogReplicaSet.java:105)
~[apache-cassandra-3.0.6.jar:3.0.6]
> 	at org.apache.cassandra.db.lifecycle.LogFile.verify(LogFile.java:132) ~[apache-cassandra-3.0.6.jar:3.0.6]
> 	at org.apache.cassandra.db.lifecycle.LogAwareFileLister.readTxnLog(LogAwareFileLister.java:113)
~[apache-cassandra-3.0.6.jar:3.0.6]
> 	at org.apache.cassandra.db.lifecycle.LogAwareFileLister.classifyFiles(LogAwareFileLister.java:106)
~[apache-cassandra-3.0.6.jar:3.0.6]
> 	at java.util.stream.ForEachOps$ForEachOp$OfRef.accept(ForEachOps.java:184) ~[na:1.8.0_91]
> 	at java.util.stream.ReferencePipeline$2$1.accept(ReferencePipeline.java:175) ~[na:1.8.0_91]
> 	at java.util.ArrayList$ArrayListSpliterator.forEachRemaining(ArrayList.java:1374) ~[na:1.8.0_91]
> 	at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:481) ~[na:1.8.0_91]
> 	at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:471) ~[na:1.8.0_91]
> 	at java.util.stream.ForEachOps$ForEachOp.evaluateSequential(ForEachOps.java:151) ~[na:1.8.0_91]
> 	at java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(ForEachOps.java:174)
~[na:1.8.0_91]
> 	at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234) ~[na:1.8.0_91]
> 	at java.util.stream.ReferencePipeline.forEach(ReferencePipeline.java:418) ~[na:1.8.0_91]
> 	at org.apache.cassandra.db.lifecycle.LogAwareFileLister.innerList(LogAwareFileLister.java:75)
~[apache-cassandra-3.0.6.jar:3.0.6]
> 	at org.apache.cassandra.db.lifecycle.LogAwareFileLister.list(LogAwareFileLister.java:53)
~[apache-cassandra-3.0.6.jar:3.0.6]
> 	... 20 common frames omitted
> Caused by: java.nio.file.FileSystemException: /data/cassandra/data/keyschema/columnfamily-3996ce80b7ac11e48a9b6776bf484396/ma_txn_anticompactionafterrepair_f20b50d0-22bd-11e6-970f-6f22464f4624.log:
Too many open files
> 	at sun.nio.fs.UnixException.translateToIOException(UnixException.java:91) ~[na:1.8.0_91]
> 	at sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:102) ~[na:1.8.0_91]
> 	at sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:107) ~[na:1.8.0_91]
> 	at sun.nio.fs.UnixFileSystemProvider.newByteChannel(UnixFileSystemProvider.java:214)
~[na:1.8.0_91]
> 	at java.nio.file.Files.newByteChannel(Files.java:361) ~[na:1.8.0_91]
> 	at java.nio.file.Files.newByteChannel(Files.java:407) ~[na:1.8.0_91]
> 	at java.nio.file.spi.FileSystemProvider.newInputStream(FileSystemProvider.java:384)
~[na:1.8.0_91]
> 	at java.nio.file.Files.newInputStream(Files.java:152) ~[na:1.8.0_91]
> 	at java.nio.file.Files.newBufferedReader(Files.java:2784) ~[na:1.8.0_91]
> 	at java.nio.file.Files.readAllLines(Files.java:3202) ~[na:1.8.0_91]
> 	at org.apache.cassandra.io.util.FileUtils.readLines(FileUtils.java:615) ~[apache-cassandra-3.0.6.jar:3.0.6]
> 	... 45 common frames omitted
> WARN  [HintsWriteExecutor:1] 2016-05-25 21:54:28,389 CLibrary.java:256 - open(/var/lib/cassandra/hints,
O_RDONLY) failed, errno (24).
> ERROR [CompactionExecutor:2660] 2016-05-25 21:54:29,915 JVMStabilityInspector.java:139
- JVM state determined to be unstable.  Exiting forcefully due to:
> java.io.FileNotFoundException: /data/cassandra/data/keyschema/columnfamily-3996ce80b7ac11e48a9b6776bf484396/ma-92661-big-Filter.db
(Too many open files)
> 	at java.io.FileOutputStream.open0(Native Method) ~[na:1.8.0_91]
> 	at java.io.FileOutputStream.open(FileOutputStream.java:270) ~[na:1.8.0_91]
> 	at java.io.FileOutputStream.<init>(FileOutputStream.java:213) ~[na:1.8.0_91]
> 	at java.io.FileOutputStream.<init>(FileOutputStream.java:101) ~[na:1.8.0_91]
> 	at org.apache.cassandra.io.sstable.format.big.BigTableWriter$IndexWriter.flushBf(BigTableWriter.java:431)
~[apache-cassandra-3.0.6.jar:3.0.6]
> 	at org.apache.cassandra.io.sstable.format.big.BigTableWriter$IndexWriter.doPrepare(BigTableWriter.java:461)
~[apache-cassandra-3.0.6.jar:3.0.6]
> 	at org.apache.cassandra.utils.concurrent.Transactional$AbstractTransactional.prepareToCommit(Transactional.java:173)
~[apache-cassandra-3.0.6.jar:3.0.6]
> 	at org.apache.cassandra.io.sstable.format.big.BigTableWriter$TransactionalProxy.doPrepare(BigTableWriter.java:303)
~[apache-cassandra-3.0.6.jar:3.0.6]
> 	at org.apache.cassandra.utils.concurrent.Transactional$AbstractTransactional.prepareToCommit(Transactional.java:173)
~[apache-cassandra-3.0.6.jar:3.0.6]
> 	at org.apache.cassandra.io.sstable.format.SSTableWriter.prepareToCommit(SSTableWriter.java:229)
~[apache-cassandra-3.0.6.jar:3.0.6]
> 	at org.apache.cassandra.io.sstable.SSTableRewriter.doPrepare(SSTableRewriter.java:357)
~[apache-cassandra-3.0.6.jar:3.0.6]
> 	at org.apache.cassandra.utils.concurrent.Transactional$AbstractTransactional.prepareToCommit(Transactional.java:173)
~[apache-cassandra-3.0.6.jar:3.0.6]
> 	at org.apache.cassandra.db.compaction.CompactionManager.antiCompactGroup(CompactionManager.java:1303)
[apache-cassandra-3.0.6.jar:3.0.6]
> 	at org.apache.cassandra.db.compaction.CompactionManager.doAntiCompaction(CompactionManager.java:1232)
[apache-cassandra-3.0.6.jar:3.0.6]
> 	at org.apache.cassandra.db.compaction.CompactionManager.performAnticompaction(CompactionManager.java:569)
[apache-cassandra-3.0.6.jar:3.0.6]
> 	at org.apache.cassandra.db.compaction.CompactionManager$7.runMayThrow(CompactionManager.java:479)
[apache-cassandra-3.0.6.jar:3.0.6]
> 	at org.apache.cassandra.utils.WrappedRunnable.run(WrappedRunnable.java:28) [apache-cassandra-3.0.6.jar:3.0.6]
> 	at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511) [na:1.8.0_91]
> 	at java.util.concurrent.FutureTask.run(FutureTask.java:266) [na:1.8.0_91]
> 	at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511) [na:1.8.0_91]
> 	at java.util.concurrent.FutureTask.run(FutureTask.java:266) [na:1.8.0_91]
> 	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) [na:1.8.0_91]
> 	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) [na:1.8.0_91]
> 	at java.lang.Thread.run(Thread.java:745) [na:1.8.0_91]
> {code}
> Seems like that by using the -seq option, C* just opened wat too 
> many files. The limits are currently quite ok though, as showed below:
> {code:xml}
> root@node3:/# cat /etc/security/limits.d/cassandra.conf 
> # Provided by the cassandra package
> cassandra  -  memlock  unlimited
> cassandra  -  nofile   100000
> cassandra  -  as       unlimited
> cassandra  -  nproc    8096
> {code}
> Today I checked the number of file opened by C* (admittedly while running 
> another repair without the -seq option):
> {code:xml}
> pssh --inline-stdout -h cassandra-hosts.txt -l root -t 0 "lsof -n | grep java | grep
cassandra | wc -l"
> [1] 14:29:43 [SUCCESS] node3 (where the repair is taking place)
> 25452
> [2] 14:29:43 [SUCCESS] node4
> 46779
> pssh --inline-stdout -h cassandra-hosts.txt -l root -t 0 "lsof -n | grep java | grep
cassandra | grep 'REG' | wc -l"
> [1] 14:26:40 [SUCCESS] node3 (where the repair is taking place)
> 24020
> [2] 14:26:41 [SUCCESS] node4
> 4050
> {code}
> Looks like that during a repair, lots of file descriptors on the repairing node 
> relate to regular files, while on all others the stark majority relate to memory 
> mapped files.
> Nevertheless 25K is still way less then 100K (still high though). 
> (To be honest, when I started the repair nodetool logged it with "Starting repair 
> command #2". I didn't pay that much attention to that as the previous repair
> had returned already for quite some time, but it might have been the case that 
> another repair was still lingering (weird if that was the case).
> In conclusion, is this behavior normal? Shall I increase the limits, or is 
> AntiCompaction really playing badly with incremental repairs and LCS 
> (and quite overloaded to be honest) tables?



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