On Fri, Jun 17, 2011 at 1:51 PM, Dominic Williams <dwilli...@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 <sylv...@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 >> <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 > >
