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From Sylvain Lebresne <sylv...@datastax.com>
Subject Re: SSTable corruption blocking compaction and scrub can't fix it
Date Fri, 17 Jun 2011 11:12:05 GMT
Scrub apparently dies because it cannot acquire a file descriptor. Scrub does
not correctly closes files
(https://issues.apache.org/jira/browse/CASSANDRA-2669)
so that may be part of why that happens. However, a simple fix is probably to
raise up the file descriptor limit.

--
Sylvain


On Fri, Jun 17, 2011 at 11:31 AM, Dominic Williams
<dwilliams@system7.co.uk> wrote:
> Hi all,
> Anyone experiencing this..?
> I noticed one of my 7.6-2 nodes had inexplicable and consistently high cpu
> usage. Checking the log I found that there was a some kind of SSTable
> corruption that was stopping a bunch of files from compacting (first trace
> copied below).
> I then tried scrub (before anyone asks it had been run when upgrading, but I
> was just trying to find out if this fixed it) but that failed with "Too many
> open files" even though node should be using mem map (second trace copied
> below).
> Current plan is to snapshot, decommission & bootstrap but not what should be
> happening. Only factor I can think of that might have caused problem is we
> are currently running huge GCGraceSeconds because we can't run repair (we
> are hanging on for 8.1 as CASSANDRA-2280 causes repair to consume all disk
> space and fail)
>  INFO [NonPeriodicTasks:1] 2011-06-16 22:43:45,232 SSTable.java (line 147)
> Deleted /var/opt/cassandra/data/FightMyMonster/Users_CisIndex-f-5922
>  INFO [MutationStage:7989] 2011-06-16 22:49:57,852 ColumnFamilyStore.java
> (line 1065) Enqueuing flush of Memtable-UserMonsters@423965881(34471 bytes,
> 322112 operations)
>  INFO [FlushWriter:1176] 2011-06-16 22:49:57,917 Memtable.java (line 157)
> Writing Memtable-UserMonsters@423965881(34471 bytes, 322112 operations)
>  INFO [FlushWriter:1176] 2011-06-16 22:50:01,087 Memtable.java (line 172)
> Completed flushing
> /var/opt/cassandra/data/FightMyMonster/UserMonsters-f-7614-Data.db (7250239
> bytes)
>  INFO [CompactionExecutor:1] 2011-06-16 22:50:01,090 CompactionManager.java
> (line 395) Compacting
> [SSTableReader(path='/var/opt/cassandra/data/FightMyMonster/UserMonsters-f-6993-Data.db'),SSTableReader(
> path='/var/opt/cassandra/data/FightMyMonster/UserMonsters-f-6994-Data.db'),SSTableReader(path='/var/opt/cassandra/data/FightMyMonster/UserMonsters-f-6995-Data.db'),SSTableReader(path='/var/opt/cassandra
> /data/FightMyMonster/UserMonsters-f-6996-Data.db'),SSTableReader(path='/var/opt/cassandra/data/FightMyMonster/UserMonsters-f-6998-Data.db'),SSTableReader(path='/var/opt/cassandra/data/FightMyMonster/Use
> rMonsters-f-7000-Data.db'),SSTableReader(path='/var/opt/cassandra/data/FightMyMonster/UserMonsters-f-7002-Data.db'),SSTableReader(path='/var/opt/cassandra/data/FightMyMonster/UserMonsters-f-7004-Data.db
> '),SSTableReader(path='/var/opt/cassandra/data/FightMyMonster/UserMonsters-f-7006-Data.db'),SSTableReader(path='/var/opt/cassandra/data/FightMyMonster/UserMonsters-f-7008-Data.db'),SSTableReader(path='/
> var/opt/cassandra/data/FightMyMonster/UserMonsters-f-7010-Data.db'),SSTableReader(path='/var/opt/cassandra/data/FightMyMonster/UserMonsters-f-7012-Data.db'),SSTableReader(path='/var/opt/cassandra/data/F
> ightMyMonster/UserMonsters-f-7014-Data.db'),SSTableReader(path='/var/opt/cassandra/data/FightMyMonster/UserMonsters-f-7016-Data.db'),SSTableReader(path='/var/opt/cassandra/data/FightMyMonster/UserMonste
> rs-f-7018-Data.db'),SSTableReader(path='/var/opt/cassandra/data/FightMyMonster/UserMonsters-f-7020-Data.db'),SSTableReader(path='/var/opt/cassandra/data/FightMyMonster/UserMonsters-f-7022-Data.db'),SSTa
> bleReader(path='/var/opt/cassandra/data/FightMyMonster/UserMonsters-f-7024-Data.db'),SSTableReader(path='/var/opt/cassandra/data/FightMyMonster/UserMonsters-f-7026-Data.db'),SSTableReader(path='/var/opt
> /cassandra/data/FightMyMonster/UserMonsters-f-7028-Data.db'),SSTableReader(path='/var/opt/cassandra/data/FightMyMonster/UserMonsters-f-7030-Data.db'),SSTableReader(path='/var/opt/cassandra/data/FightMyM
> onster/UserMonsters-f-7032-Data.db'),SSTableReader(path='/var/opt/cassandra/data/FightMyMonster/UserMonsters-f-7034-Data.db'),SSTableReader(path='/var/opt/cassandra/data/FightMyMonster/UserMonsters-f-70
> 36-Data.db'),SSTableReader(path='/var/opt/cassandra/data/FightMyMonster/UserMonsters-f-7038-Data.db'),SSTableReader(path='/var/opt/cassandra/data/FightMyMonster/UserMonsters-f-7040-Data.db'),SSTableRead
> er(path='/var/opt/cassandra/data/FightMyMonster/UserMonsters-f-7042-Data.db'),SSTableReader(path='/var/opt/cassandra/data/FightMyMonster/UserMonsters-f-7044-Data.db'),SSTableReader(path='/var/opt/cassan
> dra/data/FightMyMonster/UserMonsters-f-7046-Data.db'),SSTableReader(path='/var/opt/cassandra/data/FightMyMonster/UserMonsters-f-7048-Data.db'),SSTableReader(path='/var/opt/cassandra/data/FightMyMonster/
> UserMonsters-f-7050-Data.db'),SSTableReader(path='/var/opt/cassandra/data/FightMyMonster/UserMonsters-f-7052-Data.db')]
>  INFO [NonPeriodicTasks:1] 2011-06-16 22:50:02,399 ColumnFamilyStore.java
> (line 1065) Enqueuing flush of Memtable-Monsters@562380513(497561 bytes,
> 13860 operations)
>  INFO [FlushWriter:1176] 2011-06-16 22:50:02,399 Memtable.java (line 157)
> Writing Memtable-Monsters@562380513(497561 bytes, 13860 operations)
>  INFO [FlushWriter:1176] 2011-06-16 22:50:02,580 Memtable.java (line 172)
> Completed flushing
> /var/opt/cassandra/data/FightMyMonster/Monsters-f-7160-Data.db (471100
> bytes)
> ERROR [CompactionExecutor:1] 2011-06-16 22:50:37,776
> AbstractCassandraDaemon.java (line 114) Fatal exception in thread
> Thread[CompactionExecutor:1,1,main]
> java.io.IOError: java.io.IOException: Corrupt (negative) value length
> encountered
>         at
> org.apache.cassandra.io.util.ColumnIterator.deserializeNext(ColumnSortedMap.java:252)
>         at
> org.apache.cassandra.io.util.ColumnIterator.next(ColumnSortedMap.java:268)
>         at
> org.apache.cassandra.io.util.ColumnIterator.next(ColumnSortedMap.java:227)
>         at
> java.util.concurrent.ConcurrentSkipListMap.buildFromSorted(ConcurrentSkipListMap.java:1493)
>         at
> java.util.concurrent.ConcurrentSkipListMap.<init>(ConcurrentSkipListMap.java:1443)
>         at
> org.apache.cassandra.db.SuperColumnSerializer.deserialize(SuperColumn.java:379)
>         at
> org.apache.cassandra.db.SuperColumnSerializer.deserialize(SuperColumn.java:362)
>         at
> org.apache.cassandra.db.SuperColumnSerializer.deserialize(SuperColumn.java:322)
>         at
> org.apache.cassandra.db.ColumnFamilySerializer.deserializeColumns(ColumnFamilySerializer.java:129)
>         at
> org.apache.cassandra.io.sstable.SSTableIdentityIterator.getColumnFamilyWithColumns(SSTableIdentityIterator.java:201)
>         at
> org.apache.cassandra.io.PrecompactedRow.<init>(PrecompactedRow.java:78)
>         at
> org.apache.cassandra.io.CompactionIterator.getCompactedRow(CompactionIterator.java:154)
>         at
> org.apache.cassandra.io.CompactionIterator.getReduced(CompactionIterator.java:110)
>        at
> org.apache.cassandra.io.CompactionIterator.getReduced(CompactionIterator.java:45)
>        at
> org.apache.cassandra.utils.ReducingIterator.computeNext(ReducingIterator.java:74)
>         at
> com.google.common.collect.AbstractIterator.tryToComputeNext(AbstractIterator.java:136)
>        at
> com.google.common.collect.AbstractIterator.hasNext(AbstractIterator.java:131)
>         at
> org.apache.commons.collections.iterators.FilterIterator.setNextObject(FilterIterator.java:183)
>         at
> org.apache.commons.collections.iterators.FilterIterator.hasNext(FilterIterator.java:94)
>         at
> org.apache.cassandra.db.CompactionManager.doCompaction(CompactionManager.java:448)
>         at
> org.apache.cassandra.db.CompactionManager$1.call(CompactionManager.java:124)
>         at
> org.apache.cassandra.db.CompactionManager$1.call(CompactionManager.java:94)
>         at
> java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)
>         at java.util.concurrent.FutureTask.run(FutureTask.java:138)
>         at
> java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886)
>         at
> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908)
>         at java.lang.Thread.run(Thread.java:619)
> Caused by: java.io.IOException: Corrupt (negative) value length encountered
>         at
> org.apache.cassandra.utils.ByteBufferUtil.readWithLength(ByteBufferUtil.java:315)
>         at
> org.apache.cassandra.db.ColumnSerializer.deserialize(ColumnSerializer.java:99)
>         at
> org.apache.cassandra.io.util.ColumnIterator.deserializeNext(ColumnSortedMap.java:248)
>         ... 26 more
>  INFO [CompactionExecutor:1] 2011-06-16 22:50:37,794 CompactionManager.java
> (line 395) Compacting
> [SSTableReader(path='/var/opt/cassandra/data/FightMyMonster/Monsters-f-7157-Data.db'),SSTableReader(path
> ='/var/opt/cassandra/data/FightMyMonster/Monsters-f-7158-Data.db'),SSTableReader(path='/var/opt/cassandra/data/FightMyMonster/Monsters-f-7159-Data.db'),SSTableReader(path='/var/opt/cassandra/data/FightM
> yMonster/Monsters-f-7160-Data.db')]
>
>  INFO [CompactionExecutor:1] 2011-06-17 00:46:24,756 CompactionManager.java
> (line 652) Scrub of
> SSTableReader(path='/var/opt/cassandra/data/FightMyMonster/UserMonsters-f-7554-Data.db')
> complete: 244 rows in new sstable and 0 empty (tombstoned) rows dropped
>  INFO [CompactionExecutor:1] 2011-06-17 00:46:24,756 CompactionManager.java
> (line 511) Scrubbing
> SSTableReader(path='/var/opt/cassandra/data/FightMyMonster/UserMonsters-f-7446-Data.db')
>  INFO [CompactionExecutor:1] 2011-06-17 00:46:26,115 CompactionManager.java
> (line 652) Scrub of
> SSTableReader(path='/var/opt/cassandra/data/FightMyMonster/UserMonsters-f-7446-Data.db')
> complete: 493 rows in new sstable and 0 empty (tombstoned) rows dropped
>  INFO [CompactionExecutor:1] 2011-06-17 00:46:26,115 CompactionManager.java
> (line 511) Scrubbing
> SSTableReader(path='/var/opt/cassandra/data/FightMyMonster/UserMonsters-f-7018-Data.db')
>  INFO [CompactionExecutor:1] 2011-06-17 00:46:26,225 CompactionManager.java
> (line 652) Scrub of
> SSTableReader(path='/var/opt/cassandra/data/FightMyMonster/UserMonsters-f-7018-Data.db')
> complete: 275 rows in new sstable and 0 empty (tombstoned) rows dropped
>  INFO [CompactionExecutor:1] 2011-06-17 00:46:26,226 CompactionManager.java
> (line 511) Scrubbing
> SSTableReader(path='/var/opt/cassandra/data/FightMyMonster/UserMonsters-f-7580-Data.db')
>  INFO [CompactionExecutor:1] 2011-06-17 00:46:28,383 CompactionManager.java
> (line 652) Scrub of
> SSTableReader(path='/var/opt/cassandra/data/FightMyMonster/UserMonsters-f-7580-Data.db')
> complete: 297 rows in new sstable and 0 empty (tombstoned) rows dropped
>  INFO [CompactionExecutor:1] 2011-06-17 00:46:28,384 CompactionManager.java
> (line 511) Scrubbing
> SSTableReader(path='/var/opt/cassandra/data/FightMyMonster/UserMonsters-f-7574-Data.db')
>  INFO [CompactionExecutor:1] 2011-06-17 00:46:29,300 CompactionManager.java
> (line 652) Scrub of
> SSTableReader(path='/var/opt/cassandra/data/FightMyMonster/UserMonsters-f-7574-Data.db')
> complete: 347 rows in new sstable and 0 empty (tombstoned) rows dropped
>  INFO [CompactionExecutor:1] 2011-06-17 00:46:29,300 CompactionManager.java
> (line 511) Scrubbing
> SSTableReader(path='/var/opt/cassandra/data/FightMyMonster/UserMonsters-f-7010-Data.db')
> ERROR [CompactionExecutor:1] 2011-06-17 00:46:29,374
> AbstractCassandraDaemon.java (line 114) Fatal exception in thread
> Thread[CompactionExecutor:1,1,main]
> java.io.FileNotFoundException:
> /var/opt/cassandra/data/FightMyMonster/UserMonsters-tmp-f-7823-Data.db (Too
> many open files)
>         at java.io.RandomAccessFile.open(Native Method)
>         at java.io.RandomAccessFile.<init>(RandomAccessFile.java:212)
>         at
> org.apache.cassandra.io.util.BufferedRandomAccessFile.<init>(BufferedRandomAccessFile.java:113)
>         at
> org.apache.cassandra.io.sstable.SSTableWriter.<init>(SSTableWriter.java:78)
>         at
> org.apache.cassandra.db.ColumnFamilyStore.createCompactionWriter(ColumnFamilyStore.java:2243)
>         at
> org.apache.cassandra.db.CompactionManager.maybeCreateWriter(CompactionManager.java:794)
>         at
> org.apache.cassandra.db.CompactionManager.doScrub(CompactionManager.java:534)
>         at
> org.apache.cassandra.db.CompactionManager.access$600(CompactionManager.java:56)
>         at
> org.apache.cassandra.db.CompactionManager$3.call(CompactionManager.java:195)
>         at
> java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)
>         at java.util.concurrent.FutureTask.run(FutureTask.java:138)
>         at
> java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886)
>         at
> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908)
>         at java.lang.Thread.run(Thread.java:619)
> Dominic

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