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From "Sylvain Lebresne (JIRA)" <j...@apache.org>
Subject [jira] [Updated] (CASSANDRA-4321) stackoverflow building interval tree & possible sstable corruptions
Date Thu, 28 Jun 2012 17:54:46 GMT

     [ https://issues.apache.org/jira/browse/CASSANDRA-4321?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
]

Sylvain Lebresne updated CASSANDRA-4321:
----------------------------------------

    Attachment: 0004-Add-manifest-integrity-check-v7.txt
                0003-Create-standalone-scrub-v7.txt
                0002-Scrub-detects-and-repair-outOfOrder-rows-v7.txt
                0001-Fix-overlapping-computation-v7.txt

Alright, so I'm pretty sure I've found the root cause of all this. On top of the Range->Bound
problem we were not correctly computing the set of overlapping sstable in L1 when compacting
multiple L0 files. Citing the comment of the attached fix (where sstables = 'sstables in L0
to compact' and candidates = 'sstable in L1'):
{noformat}
/*
 * Note that picking each sstable from candidates that overlap one of the sstable of sstables
is not enough
 * because you could have the following situation:
 *   sstables = [ s1(a, c), s2(m, z) ]
 *   candidates = [ s3(e, g) ]
 * In that case, s2 overlaps none of s1 or s2, but if we compact s1 with s2, the resulting
sstable will be
 * overlapping s3, so we must return s3.
 */
{noformat}

So I'm attaching a v7 of the patches with the fix for that in the first patch. The last patch
(the integrity tests) was also breaking the offline scrub so that's fix in v7 too. Though
I note that the integrity tests of the last patch is probably overkill and I didn't really
intended to commit it (i.e. the integrity check that is in trunk is probably enough).
                
> stackoverflow building interval tree & possible sstable corruptions
> -------------------------------------------------------------------
>
>                 Key: CASSANDRA-4321
>                 URL: https://issues.apache.org/jira/browse/CASSANDRA-4321
>             Project: Cassandra
>          Issue Type: Bug
>          Components: Core
>    Affects Versions: 1.1.1
>            Reporter: Anton Winter
>            Assignee: Sylvain Lebresne
>             Fix For: 1.1.2
>
>         Attachments: 0001-Fix-overlapping-computation-v7.txt, 0002-Scrub-detects-and-repair-outOfOrder-rows-v7.txt,
0003-Create-standalone-scrub-v7.txt, 0004-Add-manifest-integrity-check-v7.txt, ooyala-hastur-stacktrace.txt
>
>
> After upgrading to 1.1.1 (from 1.1.0) I have started experiencing StackOverflowError's
resulting in compaction backlog and failure to restart. 
> The ring currently consists of 6 DC's and 22 nodes using LCS & compression.  This
issue was first noted on 2 nodes in one DC and then appears to have spread to various other
nodes in the other DC's.  
> When the first occurrence of this was found I restarted the instance but it failed to
start so I cleared its data and treated it as a replacement node for the token it was previously
responsible for.  This node successfully streamed all the relevant data back but failed again
a number of hours later with the same StackOverflowError and again was unable to restart.

> The initial stack overflow error on a running instance looks like this:
> ERROR [CompactionExecutor:314] 2012-06-07 09:59:43,017 AbstractCassandraDaemon.java (line
134) Exception in thread Thread[CompactionExecutor:314,1,main]
> java.lang.StackOverflowError
>         at java.util.Arrays.mergeSort(Arrays.java:1157)
>         at java.util.Arrays.sort(Arrays.java:1092)
>         at java.util.Collections.sort(Collections.java:134)
>         at org.apache.cassandra.utils.IntervalTree.IntervalNode.findMinMedianMax(IntervalNode.java:114)
>         at org.apache.cassandra.utils.IntervalTree.IntervalNode.<init>(IntervalNode.java:49)
>         at org.apache.cassandra.utils.IntervalTree.IntervalNode.<init>(IntervalNode.java:62)
>         at org.apache.cassandra.utils.IntervalTree.IntervalNode.<init>(IntervalNode.java:62)
>         at org.apache.cassandra.utils.IntervalTree.IntervalNode.<init>(IntervalNode.java:62)
> [snip - this repeats until stack overflow.  Compactions stop from this point onwards]
> I restarted this failing instance with DEBUG logging enabled and it throws the following
exception part way through startup:
> ERROR 11:37:51,046 Exception in thread Thread[OptionalTasks:1,5,main]
> java.lang.StackOverflowError
>         at org.slf4j.helpers.MessageFormatter.safeObjectAppend(MessageFormatter.java:307)
>         at org.slf4j.helpers.MessageFormatter.deeplyAppendParameter(MessageFormatter.java:276)
>         at org.slf4j.helpers.MessageFormatter.arrayFormat(MessageFormatter.java:230)
>         at org.slf4j.helpers.MessageFormatter.format(MessageFormatter.java:124)
>         at org.slf4j.impl.Log4jLoggerAdapter.debug(Log4jLoggerAdapter.java:228)
>         at org.apache.cassandra.utils.IntervalTree.IntervalNode.<init>(IntervalNode.java:45)
>         at org.apache.cassandra.utils.IntervalTree.IntervalNode.<init>(IntervalNode.java:62)
>         at org.apache.cassandra.utils.IntervalTree.IntervalNode.<init>(IntervalNode.java:62)
> [snip - this repeats until stack overflow]
>         at org.apache.cassandra.utils.IntervalTree.IntervalNode.<init>(IntervalNode.java:62)
>         at org.apache.cassandra.utils.IntervalTree.IntervalNode.<init>(IntervalNode.java:64)
>         at org.apache.cassandra.utils.IntervalTree.IntervalNode.<init>(IntervalNode.java:62)
>         at org.apache.cassandra.utils.IntervalTree.IntervalNode.<init>(IntervalNode.java:62)
>         at org.apache.cassandra.utils.IntervalTree.IntervalNode.<init>(IntervalNode.java:64)
>         at org.apache.cassandra.utils.IntervalTree.IntervalNode.<init>(IntervalNode.java:62)
>         at org.apache.cassandra.utils.IntervalTree.IntervalNode.<init>(IntervalNode.java:62)
>         at org.apache.cassandra.utils.IntervalTree.IntervalNode.<init>(IntervalNode.java:64)
>         at org.apache.cassandra.utils.IntervalTree.IntervalNode.<init>(IntervalNode.java:62)
>         at org.apache.cassandra.utils.IntervalTree.IntervalNode.<init>(IntervalNode.java:62)
>         at org.apache.cassandra.utils.IntervalTree.IntervalNode.<init>(IntervalNode.java:62)
>         at org.apache.cassandra.utils.IntervalTree.IntervalTree.<init>(IntervalTree.java:39)
>         at org.apache.cassandra.db.DataTracker.buildIntervalTree(DataTracker.java:560)
>         at org.apache.cassandra.db.DataTracker$View.replace(DataTracker.java:617)
>         at org.apache.cassandra.db.DataTracker.replace(DataTracker.java:320)
>         at org.apache.cassandra.db.DataTracker.addInitialSSTables(DataTracker.java:259)
>         at org.apache.cassandra.db.ColumnFamilyStore.<init>(ColumnFamilyStore.java:234)
>         at org.apache.cassandra.db.ColumnFamilyStore.createColumnFamilyStore(ColumnFamilyStore.java:331)
>         at org.apache.cassandra.db.ColumnFamilyStore.createColumnFamilyStore(ColumnFamilyStore.java:309)
>         at org.apache.cassandra.db.Table.initCf(Table.java:367)
>         at org.apache.cassandra.db.Table.<init>(Table.java:299)
>         at org.apache.cassandra.db.Table.open(Table.java:114)
>         at org.apache.cassandra.db.Table.open(Table.java:97)
>         at org.apache.cassandra.db.Table$2.apply(Table.java:574)
>         at org.apache.cassandra.db.Table$2.apply(Table.java:571)
>         at com.google.common.collect.Iterators$8.next(Iterators.java:751)
>         at org.apache.cassandra.db.ColumnFamilyStore.all(ColumnFamilyStore.java:1625)
>         at org.apache.cassandra.db.MeteredFlusher.countFlushingBytes(MeteredFlusher.java:118)
>         at org.apache.cassandra.db.MeteredFlusher.run(MeteredFlusher.java:45)
>         at org.apache.cassandra.concurrent.DebuggableScheduledThreadPoolExecutor$UncomplainingRunnable.run(DebuggableScheduledThreadPoolExecutor.java:79)
>         at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
>         at java.util.concurrent.FutureTask$Sync.innerRunAndReset(FutureTask.java:351)
>         at java.util.concurrent.FutureTask.runAndReset(FutureTask.java:178)
>         at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$201(ScheduledThreadPoolExecutor.java:165)
>         at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:267)
>         at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1110)
>         at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:603)
>         at java.lang.Thread.run(Thread.java:636)
> DEBUG 11:37:51,052 Initializing ksU.cfS
> And then finally fails with the following:
> DEBUG 11:49:03,752 Creating IntervalNode from [Interval(DecoratedKey(104860264640932324846851821824650966808,
4fcc88eb0218216164673394), DecoratedKey(93975306025956344620001177071135439009, 4fc8fb042c98458c7a58bc3b)),
Interval(DecoratedKey(104860264640932324846851821824650966808, 4fcc88eb0218216164673394),
DecoratedKey(93975306025956344620001177071135439009, 4fc8fb042c98458c7a58bc3b)), Interval(DecoratedKey(104860264640932324846851821824650966808,
4fcc88eb0218216164673394), DecoratedKey(93975306025956344620001177071135439009, 4fc8fb042c98458c7a58bc3b)),
Interval(DecoratedKey(104860264640932324846851821824650966808, 4fcc88eb0218216164673394),
DecoratedKey(93975306025956344620001177071135439009, 4fc8fb042c98458c7a58bc3b)), Interval(DecoratedKey(104860264640932324846851821824650966808,
4fcc88eb0218216164673394), DecoratedKey(93975306025956344620001177071135439009, 4fc8fb042c98458c7a58bc3b)),
Interval(DecoratedKey(104860264640932324846851821824650966808, 4fcc88eb0218216164673394),
DecoratedKey(93975306025956344620001177071135439009, 4fc8fb042c98458c7a58bc3b))]
> java.lang.reflect.InvocationTargetException
> DEBUG 11:49:03,753 Configured datacenter replicas are dc1:2, dc2:2, dc3:2, dc4:2, dc5:0,
dc6:2, dc7:0, dc8:0, dc9:2
>         at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
>         at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
>         at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
>         at java.lang.reflect.Method.invoke(Method.java:616)
>         at org.apache.commons.daemon.support.DaemonLoader.load(DaemonLoader.java:160)
> Caused by: java.lang.StackOverflowError
>         at org.slf4j.helpers.MessageFormatter.safeObjectAppend(MessageFormatter.java:307)
>         at org.slf4j.helpers.MessageFormatter.deeplyAppendParameter(MessageFormatter.java:276)
>         at org.slf4j.helpers.MessageFormatter.arrayFormat(MessageFormatter.java:230)
>         at org.slf4j.helpers.MessageFormatter.format(MessageFormatter.java:124)
>         at org.slf4j.impl.Log4jLoggerAdapter.debug(Log4jLoggerAdapter.java:228)
>         at org.apache.cassandra.utils.IntervalTree.IntervalNode.<init>(IntervalNode.java:45)
>         at org.apache.cassandra.utils.IntervalTree.IntervalNode.<init>(IntervalNode.java:62)
>         at org.apache.cassandra.utils.IntervalTree.IntervalNode.<init>(IntervalNode.java:62)
> [snip - this repeats until stack overflow]
>         at org.apache.cassandra.utils.IntervalTree.IntervalNode.<init>(IntervalNode.java:62)
>         at org.apache.cassandra.utils.IntervalTree.IntervalNode.<init>(IntervalNode.java:62)
>         at org.apache.cassandra.utils.IntervalTree.IntervalNode.<init>(IntervalNode.java:62)
>         at org.apache.cassandra.utils.IntervalTree.IntervalNode.<init>(IntervalNode.java:64)
>         at org.apache.cassandra.utils.IntervalTree.IntervalNode.<init>(IntervalNode.java:62)
>         at org.apache.cassandra.utils.IntervalTree.IntervalNode.<init>(IntervalNode.java:62)
>         at org.apache.cassandra.utils.IntervalTree.IntervalNode.<init>(IntervalNode.java:64)
>         at org.apache.cassandra.utils.IntervalTree.IntervalNode.<init>(IntervalNode.java:62)
>         at org.apache.cassandra.utils.IntervalTree.IntervalNode.<init>(IntervalNode.java:62)
>         at org.apache.cassandra.utils.IntervalTree.IntervalNode.<init>(IntervalNode.java:64)
>         at org.apache.cassandra.utils.IntervalTree.IntervalNode.<init>(IntervalNode.java:62)
>         at org.apache.cassandra.utils.IntervalTree.IntervalNode.<init>(IntervalNode.java:62)
>         at org.apache.cassandra.utils.IntervalTree.IntervalNode.<init>(IntervalNode.java:62)
>         at org.apache.cassandra.utils.IntervalTree.IntervalTree.<init>(IntervalTree.java:39)
>         at org.apache.cassandra.db.DataTracker.buildIntervalTree(DataTracker.java:560)
>         at org.apache.cassandra.db.DataTracker$View.replace(DataTracker.java:617)
>         at org.apache.cassandra.db.DataTracker.replace(DataTracker.java:320)
>         at org.apache.cassandra.db.DataTracker.addInitialSSTables(DataTracker.java:259)
>         at org.apache.cassandra.db.ColumnFamilyStore.<init>(ColumnFamilyStore.java:234)
>         at org.apache.cassandra.db.ColumnFamilyStore.createColumnFamilyStore(ColumnFamilyStore.java:331)
>         at org.apache.cassandra.db.ColumnFamilyStore.createColumnFamilyStore(ColumnFamilyStore.java:309)
>         at org.apache.cassandra.db.Table.initCf(Table.java:367)
>         at org.apache.cassandra.db.Table.<init>(Table.java:299)
>         at org.apache.cassandra.db.Table.open(Table.java:114)
>         at org.apache.cassandra.db.Table.open(Table.java:97)
>         at org.apache.cassandra.service.AbstractCassandraDaemon.setup(AbstractCassandraDaemon.java:204)
>         at org.apache.cassandra.service.AbstractCassandraDaemon.init(AbstractCassandraDaemon.java:254)
>         ... 5 more
> Cannot load daemon
> Service exit with a return value of 3
> Running with assertions enabled allows me to start the instance but when doing so I get
errors such as:
> ERROR 01:22:22,753 Exception in thread Thread[SSTableBatchOpen:2,5,main]java.lang.AssertionError:
SSTable first key DecoratedKey(100294972947100949193477090306072672386, 4fcf051ef5067d7f17d9fc35)
> last key DecoratedKey(90250429663386465697464050082134975058, 4fce996e3c1eed8c4b17dd66)
> at org.apache.cassandra.io.sstable.SSTableReader.load(SSTableReader.java:412)
> at org.apache.cassandra.io.sstable.SSTableReader.open(SSTableReader.java:187)
> at org.apache.cassandra.io.sstable.SSTableReader$1.run(SSTableReader.java:225)
> at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
> at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334)
> at java.util.concurrent.FutureTask.run(FutureTask.java:166)
> at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1110)
> at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:603)
> at java.lang.Thread.run(Thread.java:636)
> and:
> ERROR 01:27:58,946 Exception in thread Thread[CompactionExecutor:9,1,main]
> java.lang.AssertionError: Last written key DecoratedKey(81958437188197992567937826278457419048,
4fa1aebad23f81e4321d344d) >= current key DecoratedKey(64546479828744423263742604083767363606,
4fcafc0f19f6a8092d4d4f94) writing into /var/lib/XX/data/cassandra/ks1/cf1/ks1-cf1-tmp-hd-657317-Data.db
>         at org.apache.cassandra.io.sstable.SSTableWriter.beforeAppend(SSTableWriter.java:134)
>         at org.apache.cassandra.io.sstable.SSTableWriter.append(SSTableWriter.java:153)
>         at org.apache.cassandra.db.compaction.CompactionTask.execute(CompactionTask.java:159)
>         at org.apache.cassandra.db.compaction.LeveledCompactionTask.execute(LeveledCompactionTask.java:50)
>         at org.apache.cassandra.db.compaction.CompactionManager$1.runMayThrow(CompactionManager.java:150)
>         at org.apache.cassandra.utils.WrappedRunnable.run(WrappedRunnable.java:30)
>         at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
>         at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334)
>         at java.util.concurrent.FutureTask.run(FutureTask.java:166)
>         at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1110)
>         at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:603)
>         at java.lang.Thread.run(Thread.java:636)
> Just like the initial errors compactions appear to stop occurring after this point. 

> Given the above this looks like sstables are getting corrupted.  By restarting nodes
I am able to identify several hundred sstables exhibiting the same problem and this appears
to be growing.
> I have tried scrubbing those affected nodes but the problem continues to occur.  If this
is due to sstable corruptions is there another way of validating sstables for correctness?
 Given that it has spread to various servers in other DC's it looks like this is directly
related to the 1.1.1 upgrade recently performed on the ring.

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