[SPARK-26587] Deadlock between SparkUI thread and Driver thread

• Type: Bug
• Status: Resolved
• Priority: Major
• Resolution: Duplicate
• Affects Version/s: 2.2.0
• Component/s: Spark Core

Environment

EMR 5.9.0

• Assignee: Unassigned
• Reporter: Vitaliy Savkin
• Created: 10/Jan/19 11:26
• Updated: 15/Feb/22 06:18
• Resolved: 01/Mar/19 21:56

Description

One time in a month (~1000 runs) one of our spark applications freezes at startup. jstack says that there is a deadlock. Please see locks 0x00000000802c00c0 and 0x000000008271bb98 in stacktraces below.

"Driver":
at java.lang.Package.getSystemPackage(Package.java:540)
- waiting to lock <0x00000000802c00c0> (a java.util.HashMap)
at java.lang.ClassLoader.getPackage(ClassLoader.java:1625)
at java.net.URLClassLoader.getAndVerifyPackage(URLClassLoader.java:394)
at java.net.URLClassLoader.definePackageInternal(URLClassLoader.java:420)
at java.net.URLClassLoader.defineClass(URLClassLoader.java:452)
at java.net.URLClassLoader.access$100(URLClassLoader.java:74)
at java.net.URLClassLoader$1.run(URLClassLoader.java:369)
at java.net.URLClassLoader$1.run(URLClassLoader.java:363)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:362)
at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
- locked <0x0000000082789598> (a org.apache.spark.sql.hive.client.IsolatedClientLoader$$anon$1)
at org.apache.spark.sql.hive.client.IsolatedClientLoader$$anon$1.doLoadClass(IsolatedClientLoader.scala:221)
at org.apache.spark.sql.hive.client.IsolatedClientLoader$$anon$1.loadClass(IsolatedClientLoader.scala:210)
at java.lang.ClassLoader.loadClass(ClassLoader.java:411)
- locked <0x0000000082789540> (a org.apache.spark.sql.internal.NonClosableMutableURLClassLoader)
at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
at java.lang.Class.forName0(Native Method)
at java.lang.Class.forName(Class.java:348)
at java.util.ServiceLoader$LazyIterator.nextService(ServiceLoader.java:370)
at java.util.ServiceLoader$LazyIterator.next(ServiceLoader.java:404)
at java.util.ServiceLoader$1.next(ServiceLoader.java:480)
at javax.xml.parsers.FactoryFinder$1.run(FactoryFinder.java:294)
at java.security.AccessController.doPrivileged(Native Method)
at javax.xml.parsers.FactoryFinder.findServiceProvider(FactoryFinder.java:289)
at javax.xml.parsers.FactoryFinder.find(FactoryFinder.java:267)
at javax.xml.parsers.DocumentBuilderFactory.newInstance(DocumentBuilderFactory.java:120)
at org.apache.hadoop.conf.Configuration.loadResource(Configuration.java:2516)
at org.apache.hadoop.conf.Configuration.loadResources(Configuration.java:2492)
at org.apache.hadoop.conf.Configuration.getProps(Configuration.java:2405)
- locked <0x000000008271bb98> (a org.apache.hadoop.conf.Configuration)
at org.apache.hadoop.conf.Configuration.get(Configuration.java:981)
at org.apache.hadoop.conf.Configuration.getTrimmed(Configuration.java:1031)
at org.apache.hadoop.conf.Configuration.getClass(Configuration.java:2189)
at org.apache.hadoop.fs.FileSystem.getFileSystemClass(FileSystem.java:2702)
at org.apache.hadoop.fs.FsUrlStreamHandlerFactory.createURLStreamHandler(FsUrlStreamHandlerFactory.java:74)
at java.net.URL.getURLStreamHandler(URL.java:1142)
at java.net.URL.<init>(URL.java:599)
at java.net.URL.<init>(URL.java:490)
at java.net.URL.<init>(URL.java:439)
at java.net.JarURLConnection.parseSpecs(JarURLConnection.java:175)
at java.net.JarURLConnection.<init>(JarURLConnection.java:158)
at sun.net.www.protocol.jar.JarURLConnection.<init>(JarURLConnection.java:81)
at sun.net.www.protocol.jar.Handler.openConnection(Handler.java:41)
at java.net.URL.openConnection(URL.java:979)
at java.net.URLClassLoader.getResourceAsStream(URLClassLoader.java:238)
at org.apache.spark.sql.hive.client.IsolatedClientLoader$$anon$1.doLoadClass(IsolatedClientLoader.scala:216)
at org.apache.spark.sql.hive.client.IsolatedClientLoader$$anon$1.loadClass(IsolatedClientLoader.scala:210)
at java.lang.ClassLoader.loadClass(ClassLoader.java:411)
- locked <0x0000000082789540> (a org.apache.spark.sql.internal.NonClosableMutableURLClassLoader)
at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
at org.apache.spark.sql.hive.client.IsolatedClientLoader.createClient(IsolatedClientLoader.scala:262)
at org.apache.spark.sql.hive.HiveUtils$.newClientForMetadata(HiveUtils.scala:362)
at org.apache.spark.sql.hive.HiveUtils$.newClientForMetadata(HiveUtils.scala:266)
at org.apache.spark.sql.hive.HiveExternalCatalog.client$lzycompute(HiveExternalCatalog.scala:66)
- locked <0x000000008302a120> (a org.apache.spark.sql.hive.HiveExternalCatalog)
at org.apache.spark.sql.hive.HiveExternalCatalog.client(HiveExternalCatalog.scala:65)
at org.apache.spark.sql.hive.HiveExternalCatalog$$anonfun$databaseExists$1.apply$mcZ$sp(HiveExternalCatalog.scala:194)
at org.apache.spark.sql.hive.HiveExternalCatalog$$anonfun$databaseExists$1.apply(HiveExternalCatalog.scala:194)
at org.apache.spark.sql.hive.HiveExternalCatalog$$anonfun$databaseExists$1.apply(HiveExternalCatalog.scala:194)
at org.apache.spark.sql.hive.HiveExternalCatalog.withClient(HiveExternalCatalog.scala:97)
- locked <0x000000008302a120> (a org.apache.spark.sql.hive.HiveExternalCatalog)
at org.apache.spark.sql.hive.HiveExternalCatalog.databaseExists(HiveExternalCatalog.scala:193)
at org.apache.spark.sql.internal.SharedState.externalCatalog$lzycompute(SharedState.scala:105)
- locked <0x0000000082d8bb80> (a org.apache.spark.sql.internal.SharedState)
at org.apache.spark.sql.internal.SharedState.externalCatalog(SharedState.scala:93)
at org.apache.spark.sql.hive.HiveSessionStateBuilder.externalCatalog(HiveSessionStateBuilder.scala:39)
at org.apache.spark.sql.hive.HiveSessionStateBuilder.catalog$lzycompute(HiveSessionStateBuilder.scala:54)
- locked <0x000000008302a180> (a org.apache.spark.sql.hive.HiveSessionStateBuilder)
at org.apache.spark.sql.hive.HiveSessionStateBuilder.catalog(HiveSessionStateBuilder.scala:52)
at org.apache.spark.sql.hive.HiveSessionStateBuilder.catalog(HiveSessionStateBuilder.scala:35)
at org.apache.spark.sql.internal.BaseSessionStateBuilder.build(BaseSessionStateBuilder.scala:289)
at org.apache.spark.sql.SparkSession$.org$apache$spark$sql$SparkSession$$instantiateSessionState(SparkSession.scala:1050)
at org.apache.spark.sql.SparkSession$$anonfun$sessionState$2.apply(SparkSession.scala:130)
at org.apache.spark.sql.SparkSession$$anonfun$sessionState$2.apply(SparkSession.scala:130)
at scala.Option.getOrElse(Option.scala:121)
at org.apache.spark.sql.SparkSession.sessionState$lzycompute(SparkSession.scala:129)
- locked <0x0000000082d8bb40> (a org.apache.spark.sql.SparkSession)
at org.apache.spark.sql.SparkSession.sessionState(SparkSession.scala:126)
at org.apache.spark.sql.SparkSession$Builder$$anonfun$getOrCreate$5.apply(SparkSession.scala:938)
at org.apache.spark.sql.SparkSession$Builder$$anonfun$getOrCreate$5.apply(SparkSession.scala:938)
at scala.collection.mutable.HashMap$$anonfun$foreach$1.apply(HashMap.scala:99)
at scala.collection.mutable.HashMap$$anonfun$foreach$1.apply(HashMap.scala:99)
at scala.collection.mutable.HashTable$class.foreachEntry(HashTable.scala:230)
at scala.collection.mutable.HashMap.foreachEntry(HashMap.scala:40)
at scala.collection.mutable.HashMap.foreach(HashMap.scala:99)
at org.apache.spark.sql.SparkSession$Builder.getOrCreate(SparkSession.scala:938)
- locked <0x00000000805d7f48> (a org.apache.spark.sql.SparkSession$)
- locked <0x00000000805d7f68> (a org.apache.spark.sql.SparkSession$Builder)
at com.BatchPartitioner$.run(BatchPartitioner.scala:72)
at com.BatchPartitioner$.main(BatchPartitioner.scala:59)
at com.BatchPartitioner.main(BatchPartitioner.scala)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.apache.spark.deploy.yarn.ApplicationMaster$$anon$2.run(ApplicationMaster.scala:635)

"SparkUI-43":
at org.apache.hadoop.conf.Configuration.getProps(Configuration.java:2401)
- waiting to lock <0x000000008271bb98> (a org.apache.hadoop.conf.Configuration)
at org.apache.hadoop.conf.Configuration.get(Configuration.java:981)
at org.apache.hadoop.conf.Configuration.getTrimmed(Configuration.java:1031)
at org.apache.hadoop.conf.Configuration.getClass(Configuration.java:2189)
at org.apache.hadoop.fs.FileSystem.getFileSystemClass(FileSystem.java:2702)
at org.apache.hadoop.fs.FsUrlStreamHandlerFactory.createURLStreamHandler(FsUrlStreamHandlerFactory.java:74)
at java.net.URL.getURLStreamHandler(URL.java:1142)
at java.net.URL.<init>(URL.java:420)
at java.net.URL.<init>(URL.java:310)
at java.net.URL.<init>(URL.java:333)
at sun.net.www.ParseUtil.fileToEncodedURL(ParseUtil.java:272)
at java.lang.Package$1.run(Package.java:579)
at java.lang.Package$1.run(Package.java:570)
at java.security.AccessController.doPrivileged(Native Method)
at java.lang.Package.defineSystemPackage(Package.java:570)
at java.lang.Package.getSystemPackage(Package.java:546)
- locked <0x00000000802c00c0> (a java.util.HashMap)
at java.lang.Package.getPackage(Package.java:336)
at java.lang.Class.getPackage(Class.java:796)
at com.fasterxml.jackson.databind.introspect.BasicClassIntrospector._isStdJDKCollection(BasicClassIntrospector.java:257)
at com.fasterxml.jackson.databind.introspect.BasicClassIntrospector._findStdJdkCollectionDesc(BasicClassIntrospector.java:277)
at com.fasterxml.jackson.databind.introspect.BasicClassIntrospector.forSerialization(BasicClassIntrospector.java:88)
at com.fasterxml.jackson.databind.introspect.BasicClassIntrospector.forSerialization(BasicClassIntrospector.java:15)
at com.fasterxml.jackson.databind.SerializationConfig.introspect(SerializationConfig.java:789)
at com.fasterxml.jackson.databind.ser.BeanSerializerFactory.createSerializer(BeanSerializerFactory.java:134)
at com.fasterxml.jackson.databind.SerializerProvider._createUntypedSerializer(SerializerProvider.java:1203)
- locked <0x0000000082913c68> (a com.fasterxml.jackson.databind.ser.SerializerCache)
at com.fasterxml.jackson.databind.SerializerProvider._createAndCacheUntypedSerializer(SerializerProvider.java:1157)
at com.fasterxml.jackson.databind.SerializerProvider.findValueSerializer(SerializerProvider.java:481)
at com.fasterxml.jackson.databind.SerializerProvider.findTypedValueSerializer(SerializerProvider.java:679)
at com.fasterxml.jackson.databind.ser.DefaultSerializerProvider.serializeValue(DefaultSerializerProvider.java:107)
at com.fasterxml.jackson.databind.ObjectMapper.writeValue(ObjectMapper.java:2383)
at com.fasterxml.jackson.core.base.GeneratorBase.writeObject(GeneratorBase.java:324)
at com.fasterxml.jackson.core.JsonGenerator.writeObjectField(JsonGenerator.java:1415)
at com.codahale.metrics.json.MetricsModule$MetricRegistrySerializer.serialize(MetricsModule.java:186)
at com.codahale.metrics.json.MetricsModule$MetricRegistrySerializer.serialize(MetricsModule.java:171)
at com.fasterxml.jackson.databind.ser.DefaultSerializerProvider.serializeValue(DefaultSerializerProvider.java:130)
at com.fasterxml.jackson.databind.ObjectMapper._configAndWriteValue(ObjectMapper.java:3559)
at com.fasterxml.jackson.databind.ObjectMapper.writeValueAsString(ObjectMapper.java:2927)
at org.apache.spark.metrics.sink.MetricsServlet.getMetricsSnapshot(MetricsServlet.scala:59)
at org.apache.spark.metrics.sink.MetricsServlet$$anonfun$getHandlers$1.apply(MetricsServlet.scala:54)
at org.apache.spark.metrics.sink.MetricsServlet$$anonfun$getHandlers$1.apply(MetricsServlet.scala:54)
at org.apache.spark.ui.JettyUtils$$anon$3.doGet(JettyUtils.scala:90)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:687)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:790)
at org.spark_project.jetty.servlet.ServletHolder.handle(ServletHolder.java:845)
at org.spark_project.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:583)
at org.spark_project.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:1180)
at org.spark_project.jetty.servlet.ServletHandler.doScope(ServletHandler.java:511)
at org.spark_project.jetty.server.handler.ContextHandler.doScope(ContextHandler.java:1112)
at org.spark_project.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:141)
at org.spark_project.jetty.server.handler.ContextHandlerCollection.handle(ContextHandlerCollection.java:213)
at org.spark_project.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:134)
at org.spark_project.jetty.server.Server.handle(Server.java:524)
at org.spark_project.jetty.server.HttpChannel.handle(HttpChannel.java:319)
at org.spark_project.jetty.server.HttpConnection.onFillable(HttpConnection.java:253)
at org.spark_project.jetty.io.AbstractConnection$ReadCallback.succeeded(AbstractConnection.java:273)
at org.spark_project.jetty.io.FillInterest.fillable(FillInterest.java:95)
at org.spark_project.jetty.io.SelectChannelEndPoint$2.run(SelectChannelEndPoint.java:93)
at org.spark_project.jetty.util.thread.strategy.ExecuteProduceConsume.executeProduceConsume(ExecuteProduceConsume.java:303)
at org.spark_project.jetty.util.thread.strategy.ExecuteProduceConsume.produceConsume(ExecuteProduceConsume.java:148)
at org.spark_project.jetty.util.thread.strategy.ExecuteProduceConsume.run(ExecuteProduceConsume.java:136)
at org.spark_project.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:671)
at org.spark_project.jetty.util.thread.QueuedThreadPool$2.run(QueuedThreadPool.java:589)
at java.lang.Thread.run(Thread.java:748)

It happens only with an application working with Hive. Others seem to be not affected.

Issue Links

• duplicates: SPARK-26961 Found Java-level deadlock in Spark Driver
• is related to: SPARK-26961 Found Java-level deadlock in Spark Driver