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From Aaron Davidson <ilike...@gmail.com>
Subject Re: Reproducible deadlock in 1.0.1, possibly related to Spark-1097
Date Mon, 14 Jul 2014 23:46:10 GMT
The patch won't solve the problem where two people try to add a
configuration option at the same time, but I think there is currently an
issue where two people can try to initialize the Configuration at the same
time and still run into a ConcurrentModificationException. This at least
reduces (slightly) the scope of the exception although eliminating it may
not be possible.


On Mon, Jul 14, 2014 at 4:35 PM, Gary Malouf <malouf.gary@gmail.com> wrote:

> We'll try to run a build tomorrow AM.
>
>
> On Mon, Jul 14, 2014 at 7:22 PM, Patrick Wendell <pwendell@gmail.com>
> wrote:
>
> > Andrew and Gary,
> >
> > Would you guys be able to test
> > https://github.com/apache/spark/pull/1409/files and see if it solves
> > your problem?
> >
> > - Patrick
> >
> > On Mon, Jul 14, 2014 at 4:18 PM, Andrew Ash <andrew@andrewash.com>
> wrote:
> > > I observed a deadlock here when using the AvroInputFormat as well. The
> > > short of the issue is that there's one configuration object per JVM,
> but
> > > multiple threads, one for each task. If each thread attempts to add a
> > > configuration option to the Configuration object at once you get issues
> > > because HashMap isn't thread safe.
> > >
> > > More details to come tonight. Thanks!
> > > On Jul 14, 2014 4:11 PM, "Nishkam Ravi" <nravi@cloudera.com> wrote:
> > >
> > >> HI Patrick, I'm not aware of another place where the access happens,
> but
> > >> it's possible that it does. The original fix synchronized on the
> > >> broadcastConf object and someone reported the same exception.
> > >>
> > >>
> > >> On Mon, Jul 14, 2014 at 3:57 PM, Patrick Wendell <pwendell@gmail.com>
> > >> wrote:
> > >>
> > >> > Hey Nishkam,
> > >> >
> > >> > Aaron's fix should prevent two concurrent accesses to getJobConf
> (and
> > >> > the Hadoop code therein). But if there is code elsewhere that tries
> to
> > >> > mutate the configuration, then I could see how we might still have
> the
> > >> > ConcurrentModificationException.
> > >> >
> > >> > I looked at your patch for HADOOP-10456 and the only example you
> give
> > >> > is of the data being accessed inside of getJobConf. Is it accessed
> > >> > somewhere else too from Spark that you are aware of?
> > >> >
> > >> > https://issues.apache.org/jira/browse/HADOOP-10456
> > >> >
> > >> > - Patrick
> > >> >
> > >> > On Mon, Jul 14, 2014 at 3:28 PM, Nishkam Ravi <nravi@cloudera.com>
> > >> wrote:
> > >> > > Hi Aaron, I'm not sure if synchronizing on an arbitrary lock
> object
> > >> would
> > >> > > help. I suspect we will start seeing the
> > >> ConcurrentModificationException
> > >> > > again. The right fix has gone into Hadoop through 10456.
> > >> Unfortunately, I
> > >> > > don't have any bright ideas on how to synchronize this at the
> Spark
> > >> level
> > >> > > without the risk of deadlocks.
> > >> > >
> > >> > >
> > >> > > On Mon, Jul 14, 2014 at 3:07 PM, Aaron Davidson <
> ilikerps@gmail.com
> > >
> > >> > wrote:
> > >> > >
> > >> > >> The full jstack would still be useful, but our current working
> > theory
> > >> is
> > >> > >> that this is due to the fact that Configuration#loadDefaults
goes
> > >> > through
> > >> > >> every Configuration object that was ever created (via
> > >> > >> Configuration.REGISTRY) and locks it, thus introducing a
> dependency
> > >> from
> > >> > >> new Configuration to old, otherwise unrelated, Configuration
> > objects
> > >> > that
> > >> > >> our locking did not anticipate.
> > >> > >>
> > >> > >> I have created https://github.com/apache/spark/pull/1409
to
> > hopefully
> > >> > fix
> > >> > >> this bug.
> > >> > >>
> > >> > >>
> > >> > >> On Mon, Jul 14, 2014 at 2:44 PM, Patrick Wendell <
> > pwendell@gmail.com>
> > >> > >> wrote:
> > >> > >>
> > >> > >> > Hey Cody,
> > >> > >> >
> > >> > >> > This Jstack seems truncated, would you mind giving the
entire
> > stack
> > >> > >> > trace? For the second thread, for instance, we can't
see where
> > the
> > >> > >> > lock is being acquired.
> > >> > >> >
> > >> > >> > - Patrick
> > >> > >> >
> > >> > >> > On Mon, Jul 14, 2014 at 1:42 PM, Cody Koeninger
> > >> > >> > <cody.koeninger@mediacrossing.com> wrote:
> > >> > >> > > Hi all, just wanted to give a heads up that we're
seeing a
> > >> > reproducible
> > >> > >> > > deadlock with spark 1.0.1 with 2.3.0-mr1-cdh5.0.2
> > >> > >> > >
> > >> > >> > > If jira is a better place for this, apologies in
advance -
> > figured
> > >> > >> > talking
> > >> > >> > > about it on the mailing list was friendlier than
randomly
> > >> > (re)opening
> > >> > >> > jira
> > >> > >> > > tickets.
> > >> > >> > >
> > >> > >> > > I know Gary had mentioned some issues with 1.0.1
on the
> mailing
> > >> > list,
> > >> > >> > once
> > >> > >> > > we got a thread dump I wanted to follow up.
> > >> > >> > >
> > >> > >> > > The thread dump shows the deadlock occurs in the
synchronized
> > >> block
> > >> > of
> > >> > >> > code
> > >> > >> > > that was changed in HadoopRDD.scala, for the Spark-1097
issue
> > >> > >> > >
> > >> > >> > > Relevant portions of the thread dump are summarized
below, we
> > can
> > >> > >> provide
> > >> > >> > > the whole dump if it's useful.
> > >> > >> > >
> > >> > >> > > Found one Java-level deadlock:
> > >> > >> > > =============================
> > >> > >> > > "Executor task launch worker-1":
> > >> > >> > >   waiting to lock monitor 0x00007f250400c520 (object
> > >> > >> 0x00000000fae7dc30,
> > >> > >> > a
> > >> > >> > > org.apache.hadoop.co
> > >> > >> > > nf.Configuration),
> > >> > >> > >   which is held by "Executor task launch worker-0"
> > >> > >> > > "Executor task launch worker-0":
> > >> > >> > >   waiting to lock monitor 0x00007f2520495620 (object
> > >> > >> 0x00000000faeb4fc8,
> > >> > >> > a
> > >> > >> > > java.lang.Class),
> > >> > >> > >   which is held by "Executor task launch worker-1"
> > >> > >> > >
> > >> > >> > >
> > >> > >> > > "Executor task launch worker-1":
> > >> > >> > >         at
> > >> > >> > >
> > >> > >> >
> > >> > >>
> > >> >
> > >>
> >
> org.apache.hadoop.conf.Configuration.reloadConfiguration(Configuration.java:791)
> > >> > >> > >         - waiting to lock <0x00000000fae7dc30>
(a
> > >> > >> > > org.apache.hadoop.conf.Configuration)
> > >> > >> > >         at
> > >> > >> > >
> > >> > >> >
> > >> > >>
> > >> >
> > >>
> >
> org.apache.hadoop.conf.Configuration.addDefaultResource(Configuration.java:690)
> > >> > >> > >         - locked <0x00000000faca6ff8> (a
java.lang.Class for
> > >> > >> > > org.apache.hadoop.conf.Configurati
> > >> > >> > > on)
> > >> > >> > >         at
> > >> > >> > >
> > >> > >> >
> > >> > >>
> > >> >
> > >>
> >
> org.apache.hadoop.hdfs.HdfsConfiguration.<clinit>(HdfsConfiguration.java:34)
> > >> > >> > >         at
> > >> > >> > >
> > >> > >> >
> > >> > >>
> > >> >
> > >>
> >
> org.apache.hadoop.hdfs.DistributedFileSystem.<clinit>(DistributedFileSystem.java:110
> > >> > >> > > )
> > >> > >> > >         at
> > >> > >> sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native
> > >> > >> > > Method)
> > >> > >> > >         at
> > >> > >> > >
> > >> > >> >
> > >> > >>
> > >> >
> > >>
> >
> sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.
> > >> > >> > > java:57)
> > >> > >> > >         at
> > >> > >> sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native
> > >> > >> > > Method)
> > >> > >> > >         at
> > >> > >> > >
> > >> > >> >
> > >> > >>
> > >> >
> > >>
> >
> sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.
> > >> > >> > > java:57)
> > >> > >> > >         at
> > >> > >> > >
> > >> > >> >
> > >> > >>
> > >> >
> > >>
> >
> sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAcces
> > >> > >> > > sorImpl.java:45)
> > >> > >> > >         at
> > >> > >> > java.lang.reflect.Constructor.newInstance(Constructor.java:525)
> > >> > >> > >         at java.lang.Class.newInstance0(Class.java:374)
> > >> > >> > >         at java.lang.Class.newInstance(Class.java:327)
> > >> > >> > >         at
> > >> > >> >
> java.util.ServiceLoader$LazyIterator.next(ServiceLoader.java:373)
> > >> > >> > >         at
> > java.util.ServiceLoader$1.next(ServiceLoader.java:445)
> > >> > >> > >         at
> > >> > >> > >
> > >> >
> org.apache.hadoop.fs.FileSystem.loadFileSystems(FileSystem.java:2364)
> > >> > >> > >         - locked <0x00000000faeb4fc8> (a
java.lang.Class for
> > >> > >> > > org.apache.hadoop.fs.FileSystem)
> > >> > >> > >         at
> > >> > >> > >
> > >> > >>
> > >>
> org.apache.hadoop.fs.FileSystem.getFileSystemClass(FileSystem.java:2375)
> > >> > >> > >         at
> > >> > >> > >
> > >> >
> org.apache.hadoop.fs.FileSystem.createFileSystem(FileSystem.java:2392)
> > >> > >> > >         at
> > >> > >> org.apache.hadoop.fs.FileSystem.access$200(FileSystem.java:89)
> > >> > >> > >         at
> > >> > >> > >
> > >> >
> > org.apache.hadoop.fs.FileSystem$Cache.getInternal(FileSystem.java:2431)
> > >> > >> > >         at
> > >> > >> > org.apache.hadoop.fs.FileSystem$Cache.get(FileSystem.java:2413)
> > >> > >> > >         at
> > >> org.apache.hadoop.fs.FileSystem.get(FileSystem.java:368)
> > >> > >> > >         at
> > >> org.apache.hadoop.fs.FileSystem.get(FileSystem.java:167)
> > >> > >> > >         at
> > >> > >> > >
> > >> >
> org.apache.hadoop.mapred.JobConf.getWorkingDirectory(JobConf.java:587)
> > >> > >> > >         at
> > >> > >> > >
> > >> > >> >
> > >> > >>
> > >> >
> > >>
> >
> org.apache.hadoop.mapred.FileInputFormat.setInputPaths(FileInputFormat.java:315)
> > >> > >> > >         at
> > >> > >> > >
> > >> > >> >
> > >> > >>
> > >> >
> > >>
> >
> org.apache.hadoop.mapred.FileInputFormat.setInputPaths(FileInputFormat.java:288)
> > >> > >> > >         at
> > >> > >> > >
> > >> >
> > org.apache.spark.SparkContext$$anonfun$22.apply(SparkContext.scala:546)
> > >> > >> > >         at
> > >> > >> > >
> > >> >
> > org.apache.spark.SparkContext$$anonfun$22.apply(SparkContext.scala:546)
> > >> > >> > >         at
> > >> > >> > >
> > >> > >> >
> > >> > >>
> > >> >
> > >>
> >
> org.apache.spark.rdd.HadoopRDD$$anonfun$getJobConf$1.apply(HadoopRDD.scala:145)
> > >> > >> > >
> > >> > >> > >
> > >> > >> > >
> > >> > >> > > ...elided...
> > >> > >> > >
> > >> > >> > >
> > >> > >> > > "Executor task launch worker-0" daemon prio=10
> > >> > tid=0x0000000001e71800
> > >> > >> > > nid=0x2d97 waiting for monitor entry [0x00007f24d2bf1000]
> > >> > >> > >    java.lang.Thread.State: BLOCKED (on object monitor)
> > >> > >> > >         at
> > >> > >> > >
> > >> >
> org.apache.hadoop.fs.FileSystem.loadFileSystems(FileSystem.java:2362)
> > >> > >> > >         - waiting to lock <0x00000000faeb4fc8>
(a
> > java.lang.Class
> > >> > for
> > >> > >> > > org.apache.hadoop.fs.FileSystem)
> > >> > >> > >         at
> > >> > >> > >
> > >> > >>
> > >>
> org.apache.hadoop.fs.FileSystem.getFileSystemClass(FileSystem.java:2375)
> > >> > >> > >         at
> > >> > >> > >
> > >> >
> org.apache.hadoop.fs.FileSystem.createFileSystem(FileSystem.java:2392)
> > >> > >> > >         at
> > >> > >> org.apache.hadoop.fs.FileSystem.access$200(FileSystem.java:89)
> > >> > >> > >         at
> > >> > >> > >
> > >> >
> > org.apache.hadoop.fs.FileSystem$Cache.getInternal(FileSystem.java:2431)
> > >> > >> > >         at
> > >> > >> > org.apache.hadoop.fs.FileSystem$Cache.get(FileSystem.java:2413)
> > >> > >> > >         at
> > >> org.apache.hadoop.fs.FileSystem.get(FileSystem.java:368)
> > >> > >> > >         at
> > >> org.apache.hadoop.fs.FileSystem.get(FileSystem.java:167)
> > >> > >> > >         at
> > >> > >> > >
> > >> >
> org.apache.hadoop.mapred.JobConf.getWorkingDirectory(JobConf.java:587)
> > >> > >> > >         at
> > >> > >> > >
> > >> > >> >
> > >> > >>
> > >> >
> > >>
> >
> org.apache.hadoop.mapred.FileInputFormat.setInputPaths(FileInputFormat.java:315)
> > >> > >> > >         at
> > >> > >> > >
> > >> > >> >
> > >> > >>
> > >> >
> > >>
> >
> org.apache.hadoop.mapred.FileInputFormat.setInputPaths(FileInputFormat.java:288)
> > >> > >> > >         at
> > >> > >> > >
> > >> >
> > org.apache.spark.SparkContext$$anonfun$22.apply(SparkContext.scala:546)
> > >> > >> > >         at
> > >> > >> > >
> > >> >
> > org.apache.spark.SparkContext$$anonfun$22.apply(SparkContext.scala:546)
> > >> > >> > >         at
> > >> > >> > >
> > >> > >> >
> > >> > >>
> > >> >
> > >>
> >
> org.apache.spark.rdd.HadoopRDD$$anonfun$getJobConf$1.apply(HadoopRDD.scala:145)
> > >> > >> >
> > >> > >>
> > >> >
> > >>
> >
>

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