Rong Jialei created SPARK-26961:
-----------------------------------
Summary: Found Java-level deadlock in Spark Driver
Key: SPARK-26961
URL: https://issues.apache.org/jira/browse/SPARK-26961
Project: Spark
Issue Type: Bug
Components: Spark Submit
Affects Versions: 2.3.0
Reporter: Rong Jialei
Our spark job usually will finish in minutes, however, we recently found it
take days to run, and we can only kill it when this happened.
An investigation show all worker container could not connect drive after start,
and driver is hanging, using jstack, we found a Java-level deadlock.
*Jstack output for deadlock part is showing below:*
Found one Java-level deadlock:
=============================
"SparkUI-907":
waiting to lock monitor 0x00007f387761b398 (object 0x00000005c0c1e5e0, a
org.apache.hadoop.conf.Configuration),
which is held by "ForkJoinPool-1-worker-57"
"ForkJoinPool-1-worker-57":
waiting to lock monitor 0x00007f3860574298 (object 0x00000005b7991168, a
org.apache.spark.util.MutableURLClassLoader),
which is held by "ForkJoinPool-1-worker-7"
"ForkJoinPool-1-worker-7":
waiting to lock monitor 0x00007f387761b398 (object 0x00000005c0c1e5e0, a
org.apache.hadoop.conf.Configuration),
which is held by "ForkJoinPool-1-worker-57"
Java stack information for the threads listed above:
===================================================
"SparkUI-907":
at org.apache.hadoop.conf.Configuration.getOverlay(Configuration.java:1328)
- waiting to lock <0x00000005c0c1e5e0> (a org.apache.hadoop.conf.Configuration)
at
org.apache.hadoop.conf.Configuration.handleDeprecation(Configuration.java:684)
at org.apache.hadoop.conf.Configuration.get(Configuration.java:1088)
at org.apache.hadoop.conf.Configuration.getTrimmed(Configuration.java:1145)
at org.apache.hadoop.conf.Configuration.getClass(Configuration.java:2363)
at org.apache.hadoop.fs.FileSystem.getFileSystemClass(FileSystem.java:2840)
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 org.apache.spark.ui.JettyUtils$$anon$4.doRequest(JettyUtils.scala:176)
at org.apache.spark.ui.JettyUtils$$anon$4.doGet(JettyUtils.scala:161)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:687)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:790)
at org.spark_project.jetty.servlet.ServletHolder.handle(ServletHolder.java:848)
at
org.spark_project.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1772)
at
org.apache.hadoop.yarn.server.webproxy.amfilter.AmIpFilter.doFilter(AmIpFilter.java:171)
at
org.spark_project.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1759)
at
org.spark_project.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:582)
at
org.spark_project.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:1180)
at
org.spark_project.jetty.servlet.ServletHandler.doScope(ServletHandler.java:512)
at
org.spark_project.jetty.server.handler.ContextHandler.doScope(ContextHandler.java:1112)
at
org.spark_project.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:141)
at
org.spark_project.jetty.server.handler.gzip.GzipHandler.handle(GzipHandler.java:493)
at
org.spark_project.jetty.server.handler.ContextHandlerCollection.handle(ContextHandlerCollection.java:213)
at
org.spark_project.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:134)
at org.spark_project.jetty.server.Server.handle(Server.java:534)
at org.spark_project.jetty.server.HttpChannel.handle(HttpChannel.java:320)
at
org.spark_project.jetty.server.HttpConnection.onFillable(HttpConnection.java:251)
at
org.spark_project.jetty.io.AbstractConnection$ReadCallback.succeeded(AbstractConnection.java:283)
at org.spark_project.jetty.io.FillInterest.fillable(FillInterest.java:108)
at
org.spark_project.jetty.io.SelectChannelEndPoint$2.run(SelectChannelEndPoint.java:93)
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)
"ForkJoinPool-1-worker-57":
at java.lang.ClassLoader.loadClass(ClassLoader.java:404)
- waiting to lock <0x00000005b7991168> (a
org.apache.spark.util.MutableURLClassLoader)
at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
at org.apache.xerces.parsers.ObjectFactory.findProviderClass(Unknown Source)
at org.apache.xerces.parsers.ObjectFactory.newInstance(Unknown Source)
at org.apache.xerces.parsers.ObjectFactory.createObject(Unknown Source)
at org.apache.xerces.parsers.ObjectFactory.createObject(Unknown Source)
at org.apache.xerces.parsers.DOMParser.<init>(Unknown Source)
at org.apache.xerces.parsers.DOMParser.<init>(Unknown Source)
at org.apache.xerces.jaxp.DocumentBuilderImpl.<init>(Unknown Source)
at
org.apache.xerces.jaxp.DocumentBuilderFactoryImpl.newDocumentBuilder(Unknown
Source)
at org.apache.hadoop.conf.Configuration.loadResource(Configuration.java:2737)
at org.apache.hadoop.conf.Configuration.loadResources(Configuration.java:2696)
at org.apache.hadoop.conf.Configuration.getProps(Configuration.java:2579)
- locked <0x00000005c0c1e5e0> (a org.apache.hadoop.conf.Configuration)
at org.apache.hadoop.conf.Configuration.get(Configuration.java:1091)
at org.apache.hadoop.conf.Configuration.getTrimmed(Configuration.java:1145)
at org.apache.hadoop.conf.Configuration.getClass(Configuration.java:2363)
at org.apache.hadoop.fs.FileSystem.getFileSystemClass(FileSystem.java:2840)
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.URL.openStream(URL.java:1045)
at java.util.ServiceLoader.parse(ServiceLoader.java:304)
at java.util.ServiceLoader.access$200(ServiceLoader.java:185)
at java.util.ServiceLoader$LazyIterator.hasNextService(ServiceLoader.java:357)
at java.util.ServiceLoader$LazyIterator.hasNext(ServiceLoader.java:393)
at java.util.ServiceLoader$1.hasNext(ServiceLoader.java:474)
at
scala.collection.convert.Wrappers$JIteratorWrapper.hasNext(Wrappers.scala:42)
at scala.collection.Iterator$class.foreach(Iterator.scala:893)
at scala.collection.AbstractIterator.foreach(Iterator.scala:1336)
at scala.collection.IterableLike$class.foreach(IterableLike.scala:72)
at scala.collection.AbstractIterable.foreach(Iterable.scala:54)
at scala.collection.TraversableLike$class.filterImpl(TraversableLike.scala:247)
at scala.collection.TraversableLike$class.filter(TraversableLike.scala:259)
at scala.collection.AbstractTraversable.filter(Traversable.scala:104)
at
org.apache.spark.sql.execution.datasources.DataSource$.lookupDataSource(DataSource.scala:614)
at org.apache.spark.sql.DataFrameReader.load(DataFrameReader.scala:190)
at org.apache.spark.sql.DataFrameReader.load(DataFrameReader.scala:174)
at
com.amazon.economics.spark.dq.io.SanjuroDataRegistryData$class.readInstance(SanjuroDataRegistryData.scala:16)
at
com.amazon.economics.spark.dq.metrics.DifferenceRatioMetricSuite.readInstance(DifferenceRatioMetricSuite.scala:19)
at
com.amazon.economics.spark.dq.metrics.ComparisonStandardProvider$class.loadComparisonStandardInstance(ComparisonStandardProvider.scala:21)
at
com.amazon.economics.spark.dq.metrics.DifferenceRatioMetricSuite.loadComparisonStandardInstance(DifferenceRatioMetricSuite.scala:19)
at
com.amazon.economics.spark.dq.metrics.DifferenceRatioMetricSuite.compute(DifferenceRatioMetricSuite.scala:35)
at
com.amazon.economics.spark.dq.MetricsTaskRunner$$anonfun$run$1$$anonfun$1$$anonfun$apply$1$$anonfun$apply$2.apply(MetricsTaskRunner.scala:41)
at
com.amazon.economics.spark.dq.MetricsTaskRunner$$anonfun$run$1$$anonfun$1$$anonfun$apply$1$$anonfun$apply$2.apply(MetricsTaskRunner.scala:39)
at scala.util.Try$.apply(Try.scala:192)
at
com.amazon.economics.spark.dq.MetricsTaskRunner$$anonfun$run$1$$anonfun$1$$anonfun$apply$1.apply(MetricsTaskRunner.scala:39)
at
com.amazon.economics.spark.dq.MetricsTaskRunner$$anonfun$run$1$$anonfun$1$$anonfun$apply$1.apply(MetricsTaskRunner.scala:32)
at
scala.collection.parallel.AugmentedIterableIterator$class.map2combiner(RemainsIterator.scala:115)
at
scala.collection.parallel.immutable.ParVector$ParVectorIterator.map2combiner(ParVector.scala:62)
at
scala.collection.parallel.ParIterableLike$Map.leaf(ParIterableLike.scala:1054)
at
scala.collection.parallel.Task$$anonfun$tryLeaf$1.apply$mcV$sp(Tasks.scala:49)
at scala.collection.parallel.Task$$anonfun$tryLeaf$1.apply(Tasks.scala:48)
at scala.collection.parallel.Task$$anonfun$tryLeaf$1.apply(Tasks.scala:48)
at scala.collection.parallel.Task$class.tryLeaf(Tasks.scala:51)
at
scala.collection.parallel.ParIterableLike$Map.tryLeaf(ParIterableLike.scala:1051)
at
scala.collection.parallel.AdaptiveWorkStealingTasks$WrappedTask$class.compute(Tasks.scala:152)
at
scala.collection.parallel.AdaptiveWorkStealingForkJoinTasks$WrappedTask.compute(Tasks.scala:443)
at scala.concurrent.forkjoin.RecursiveAction.exec(RecursiveAction.java:160)
at scala.concurrent.forkjoin.ForkJoinTask.doExec(ForkJoinTask.java:260)
at
scala.concurrent.forkjoin.ForkJoinPool$WorkQueue.runTask(ForkJoinPool.java:1339)
at scala.concurrent.forkjoin.ForkJoinPool.runWorker(ForkJoinPool.java:1979)
at
scala.concurrent.forkjoin.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:107)
"ForkJoinPool-1-worker-7":
at org.apache.hadoop.conf.Configuration.getOverlay(Configuration.java:1328)
- waiting to lock <0x00000005c0c1e5e0> (a org.apache.hadoop.conf.Configuration)
at
org.apache.hadoop.conf.Configuration.handleDeprecation(Configuration.java:684)
at org.apache.hadoop.conf.Configuration.get(Configuration.java:1088)
at org.apache.hadoop.conf.Configuration.getTrimmed(Configuration.java:1145)
at org.apache.hadoop.conf.Configuration.getClass(Configuration.java:2363)
at org.apache.hadoop.fs.FileSystem.getFileSystemClass(FileSystem.java:2840)
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 sun.misc.URLClassPath$JarLoader.<init>(URLClassPath.java:812)
at sun.misc.URLClassPath$JarLoader$3.run(URLClassPath.java:1094)
at sun.misc.URLClassPath$JarLoader$3.run(URLClassPath.java:1091)
at java.security.AccessController.doPrivileged(Native Method)
at sun.misc.URLClassPath$JarLoader.getResource(URLClassPath.java:1090)
at sun.misc.URLClassPath$JarLoader.getResource(URLClassPath.java:1050)
at sun.misc.URLClassPath.getResource(URLClassPath.java:239)
at java.net.URLClassLoader$1.run(URLClassLoader.java:365)
at java.net.URLClassLoader$1.run(URLClassLoader.java:362)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:361)
at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
- locked <0x00000005b7991168> (a org.apache.spark.util.MutableURLClassLoader)
at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
at java.lang.Class.forName0(Native Method)
at java.lang.Class.forName(Class.java:348)
at
scala.reflect.runtime.JavaMirrors$JavaMirror.javaClass(JavaMirrors.scala:555)
at
scala.reflect.runtime.JavaMirrors$JavaMirror.tryJavaClass(JavaMirrors.scala:559)
at
scala.reflect.runtime.SymbolLoaders$PackageScope$$anonfun$lookupEntry$1.apply(SymbolLoaders.scala:137)
at
scala.reflect.runtime.SymbolLoaders$PackageScope$$anonfun$lookupEntry$1.apply(SymbolLoaders.scala:126)
at scala.reflect.runtime.Gil$class.gilSynchronized(Gil.scala:19)
at scala.reflect.runtime.JavaUniverse.gilSynchronized(JavaUniverse.scala:16)
at
scala.reflect.runtime.SymbolLoaders$PackageScope.syncLockSynchronized(SymbolLoaders.scala:124)
at
scala.reflect.runtime.SymbolLoaders$PackageScope.lookupEntry(SymbolLoaders.scala:126)
at scala.reflect.internal.Types$Type.findDecl(Types.scala:971)
at scala.reflect.internal.Types$Type.decl(Types.scala:566)
at scala.reflect.internal.SymbolTable.openPackageModule(SymbolTable.scala:335)
at
scala.reflect.runtime.SymbolLoaders$LazyPackageType$$anonfun$complete$2.apply$mcV$sp(SymbolLoaders.scala:74)
at
scala.reflect.runtime.SymbolLoaders$LazyPackageType$$anonfun$complete$2.apply(SymbolLoaders.scala:71)
at
scala.reflect.runtime.SymbolLoaders$LazyPackageType$$anonfun$complete$2.apply(SymbolLoaders.scala:71)
at
scala.reflect.internal.SymbolTable.slowButSafeEnteringPhaseNotLaterThan(SymbolTable.scala:263)
at
scala.reflect.runtime.SymbolLoaders$LazyPackageType.complete(SymbolLoaders.scala:71)
at scala.reflect.internal.Symbols$Symbol.info(Symbols.scala:1514)
at
scala.reflect.runtime.SynchronizedSymbols$SynchronizedSymbol$$anon$1.scala$reflect$runtime$SynchronizedSymbols$SynchronizedSymbol$$super$info(SynchronizedSymbols.scala:174)
at
scala.reflect.runtime.SynchronizedSymbols$SynchronizedSymbol$$anonfun$info$1.apply(SynchronizedSymbols.scala:127)
at
scala.reflect.runtime.SynchronizedSymbols$SynchronizedSymbol$$anonfun$info$1.apply(SynchronizedSymbols.scala:127)
at scala.reflect.runtime.Gil$class.gilSynchronized(Gil.scala:19)
at scala.reflect.runtime.JavaUniverse.gilSynchronized(JavaUniverse.scala:16)
at
scala.reflect.runtime.SynchronizedSymbols$SynchronizedSymbol$class.gilSynchronizedIfNotThreadsafe(SynchronizedSymbols.scala:123)
at
scala.reflect.runtime.SynchronizedSymbols$SynchronizedSymbol$$anon$1.gilSynchronizedIfNotThreadsafe(SynchronizedSymbols.scala:174)
at
scala.reflect.runtime.SynchronizedSymbols$SynchronizedSymbol$class.info(SynchronizedSymbols.scala:127)
at
scala.reflect.runtime.SynchronizedSymbols$SynchronizedSymbol$$anon$1.info(SynchronizedSymbols.scala:174)
at scala.reflect.internal.Types$TypeRef.thisInfo(Types.scala:2194)
at scala.reflect.internal.Types$TypeRef.baseClasses(Types.scala:2199)
at
scala.reflect.internal.tpe.FindMembers$FindMemberBase.<init>(FindMembers.scala:17)
at
scala.reflect.internal.tpe.FindMembers$FindMember.<init>(FindMembers.scala:219)
at
scala.reflect.internal.Types$Type.scala$reflect$internal$Types$Type$$findMemberInternal$1(Types.scala:1014)
at scala.reflect.internal.Types$Type.findMember(Types.scala:1016)
at scala.reflect.internal.Types$Type.memberBasedOnName(Types.scala:631)
at scala.reflect.internal.Types$Type.member(Types.scala:600)
at scala.reflect.internal.Mirrors$RootsBase.getModuleOrClass(Mirrors.scala:48)
at scala.reflect.internal.Mirrors$RootsBase.getModuleOrClass(Mirrors.scala:45)
at scala.reflect.internal.Mirrors$RootsBase.getModuleOrClass(Mirrors.scala:45)
at scala.reflect.internal.Mirrors$RootsBase.getModuleOrClass(Mirrors.scala:45)
at scala.reflect.internal.Mirrors$RootsBase.getModuleOrClass(Mirrors.scala:45)
at scala.reflect.internal.Mirrors$RootsBase.getModuleOrClass(Mirrors.scala:66)
at
scala.reflect.internal.Mirrors$RootsBase.staticModuleOrClass(Mirrors.scala:77)
at scala.reflect.internal.Mirrors$RootsBase.staticModule(Mirrors.scala:161)
at scala.reflect.internal.Mirrors$RootsBase.staticModule(Mirrors.scala:22)
at
org.apache.spark.sql.catalyst.ScalaReflection$$anonfun$schemaFor$1$$typecreator48$1.apply(ScalaReflection.scala:726)
at
scala.reflect.api.TypeTags$WeakTypeTagImpl.tpe$lzycompute(TypeTags.scala:232)
- locked <0x00000005c0c47770> (a scala.reflect.api.TypeTags$TypeTagImpl)
at scala.reflect.api.TypeTags$WeakTypeTagImpl.tpe(TypeTags.scala:232)
at
org.apache.spark.sql.catalyst.ScalaReflection$class.localTypeOf(ScalaReflection.scala:839)
at
org.apache.spark.sql.catalyst.ScalaReflection$.localTypeOf(ScalaReflection.scala:39)
at
org.apache.spark.sql.catalyst.ScalaReflection$$anonfun$schemaFor$1.apply(ScalaReflection.scala:726)
at
org.apache.spark.sql.catalyst.ScalaReflection$$anonfun$schemaFor$1.apply(ScalaReflection.scala:715)
at
scala.reflect.internal.tpe.TypeConstraints$UndoLog.undo(TypeConstraints.scala:56)
at
org.apache.spark.sql.catalyst.ScalaReflection$class.cleanUpReflectionObjects(ScalaReflection.scala:824)
at
org.apache.spark.sql.catalyst.ScalaReflection$.cleanUpReflectionObjects(ScalaReflection.scala:39)
at
org.apache.spark.sql.catalyst.ScalaReflection$.schemaFor(ScalaReflection.scala:714)
at
org.apache.spark.sql.catalyst.ScalaReflection$.schemaFor(ScalaReflection.scala:711)
at org.apache.spark.sql.functions$.udf(functions.scala:3356)
at
com.amazon.economics.spark.stata.port.RowTotal$.rowtotalOf(RowTotal.scala:28)
at
com.amazon.economics.spark.stata.port.RowTotal$.rowtotalInt$lzycompute(RowTotal.scala:61)
- locked <0x00000005c0c47858> (a
com.amazon.economics.spark.stata.port.RowTotal$)
at
com.amazon.economics.spark.stata.port.RowTotal$.rowtotalInt(RowTotal.scala:61)
at
com.amazon.economics.spark.stata.port.DataFrameRowtotalOps.<init>(RowTotal.scala:71)
at
com.amazon.economics.spark.stata.port.DataFrameRowtotalOps$.toDataFrameRowTotalOps(RowTotal.scala:140)
at
com.amazon.economics.spark.dq.metrics.DifferenceRatioMetricSuite$$anonfun$1.apply(DifferenceRatioMetricSuite.scala:29)
at
com.amazon.economics.spark.dq.metrics.DifferenceRatioMetricSuite$$anonfun$1.apply(DifferenceRatioMetricSuite.scala:29)
at
scala.collection.LinearSeqOptimized$class.foldLeft(LinearSeqOptimized.scala:124)
at scala.collection.immutable.List.foldLeft(List.scala:84)
at
com.amazon.economics.spark.dq.metrics.DifferenceRatioMetricSuite.compute(DifferenceRatioMetricSuite.scala:29)
at
com.amazon.economics.spark.dq.MetricsTaskRunner$$anonfun$run$1$$anonfun$1$$anonfun$apply$1$$anonfun$apply$2.apply(MetricsTaskRunner.scala:41)
at
com.amazon.economics.spark.dq.MetricsTaskRunner$$anonfun$run$1$$anonfun$1$$anonfun$apply$1$$anonfun$apply$2.apply(MetricsTaskRunner.scala:39)
at scala.util.Try$.apply(Try.scala:192)
at
com.amazon.economics.spark.dq.MetricsTaskRunner$$anonfun$run$1$$anonfun$1$$anonfun$apply$1.apply(MetricsTaskRunner.scala:39)
at
com.amazon.economics.spark.dq.MetricsTaskRunner$$anonfun$run$1$$anonfun$1$$anonfun$apply$1.apply(MetricsTaskRunner.scala:32)
at
scala.collection.parallel.AugmentedIterableIterator$class.map2combiner(RemainsIterator.scala:115)
at
scala.collection.parallel.immutable.ParVector$ParVectorIterator.map2combiner(ParVector.scala:62)
at
scala.collection.parallel.ParIterableLike$Map.leaf(ParIterableLike.scala:1054)
at
scala.collection.parallel.Task$$anonfun$tryLeaf$1.apply$mcV$sp(Tasks.scala:49)
at scala.collection.parallel.Task$$anonfun$tryLeaf$1.apply(Tasks.scala:48)
at scala.collection.parallel.Task$$anonfun$tryLeaf$1.apply(Tasks.scala:48)
at scala.collection.parallel.Task$class.tryLeaf(Tasks.scala:51)
at
scala.collection.parallel.ParIterableLike$Map.tryLeaf(ParIterableLike.scala:1051)
at
scala.collection.parallel.AdaptiveWorkStealingTasks$WrappedTask$class.compute(Tasks.scala:152)
at
scala.collection.parallel.AdaptiveWorkStealingForkJoinTasks$WrappedTask.compute(Tasks.scala:443)
at scala.concurrent.forkjoin.RecursiveAction.exec(RecursiveAction.java:160)
at scala.concurrent.forkjoin.ForkJoinTask.doExec(ForkJoinTask.java:260)
at
scala.concurrent.forkjoin.ForkJoinPool$WorkQueue.runTask(ForkJoinPool.java:1339)
at scala.concurrent.forkjoin.ForkJoinPool.runWorker(ForkJoinPool.java:1979)
at
scala.concurrent.forkjoin.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:107)
Found 1 deadlock.
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