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 <dwilli...@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
