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From Dominic Williams <dwilli...@system7.co.uk>
Subject Re: SSTable corruption blocking compaction and scrub can't fix it
Date Fri, 17 Jun 2011 12:08:53 GMT
Unfortunately I shutdown that node and anyway lsof wasn't installed.

But $ulimit gives
unlimited

On 17 June 2011 13:00, Sylvain Lebresne <sylvain@datastax.com> wrote:

> On Fri, Jun 17, 2011 at 1:51 PM, Dominic Williams
> <dwilliams@system7.co.uk> wrote:
> > As far as scrub goes that could be it. I'm already running unlimited file
> > handles though so ulimit not answer unfortunately
>
> Are you sure ? How many file descriptors are open on the system when
> you get that
> scrub exception ? If you really have unlimited file handles and
> Cassandra uses them
> all, then we have a more serious problem than just CASSANDRA-2669.
>
> --
> Sylvain
>
> > Dominic
> > On 17 June 2011 12:12, Sylvain Lebresne <sylvain@datastax.com> wrote:
> >>
> >> 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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