Develop Reference

beanshell - Deadlock issue

Has anyone got any experience of having deadlocks with beanshell? This is something we have been encountering recently in our production system where script execution is blocking other threads, due to it's lock on classloading via tomcat. The following is the stacktrace for the lock owner in thread dump:
"Thread-64" : 150 : BLOCKED : cpu=37812500000 : cpuLoad= 0.0
BlockedCount:93354 BlockedTime:-1 LockName:java.lang.Object#219d66b6 LockOwnerID:151 LockOwnerName:Thread-65
WaitedCount:13 WaitedTime:-1 InNative:false IsSuspended:false at org.apache.catalina.webresources.AbstractSingleArchiveResourceSet.getArchiveEntries(AbstractSingleArchiveResourceSet.java:66)
at org.apache.catalina.webresources.AbstractArchiveResourceSet.getResource(AbstractArchiveResourceSet.java:262)
at org.apache.catalina.webresources.StandardRoot.getResourceInternal(StandardRoot.java:281)
at org.apache.catalina.webresources.Cache.getResource(Cache.java:62)
at org.apache.catalina.webresources.StandardRoot.getResource(StandardRoot.java:216)
at org.apache.catalina.webresources.StandardRoot.getClassLoaderResource(StandardRoot.java:225)
at org.apache.catalina.loader.WebappClassLoaderBase.findClassInternal(WebappClassLoaderBase.java:2173)
at org.apache.catalina.loader.WebappClassLoaderBase.findClass(WebappClassLoaderBase.java:811)
at org.apache.catalina.loader.WebappClassLoaderBase.loadClass(WebappClassLoaderBase.java:1260)
at org.apache.catalina.loader.WebappClassLoaderBase.loadClass(WebappClassLoaderBase.java:1119)
at java.lang.Class.forName0(Class.java:-2)
at java.lang.Class.forName(Class.java:348)
at bsh.classpath.ClassManagerImpl.classForName(null:-1)
at bsh.NameSpace.classForName(null:-1)
at bsh.NameSpace.getImportedClassImpl(null:-1)
at bsh.NameSpace.getClassImpl(null:-1)
at bsh.NameSpace.getClass(null:-1)
at bsh.Name.consumeNextObjectField(null:-1)
at bsh.Name.toObject(null:-1)
at bsh.BSHAmbiguousName.toObject(null:-1)
at bsh.BSHAmbiguousName.toObject(null:-1)
at bsh.BSHPrimaryExpression.eval(null:-1)
at bsh.BSHPrimaryExpression.eval(null:-1)
at bsh.BSHVariableDeclarator.eval(null:-1)
at bsh.BSHTypedVariableDeclaration.eval(null:-1)
at bsh.Interpreter.eval(null:-1)
at bsh.Interpreter.eval(null:-1)
at bsh.Interpreter.eval(null:-1)
at my.package.MyClassFile(MyClassFile:2332)
I see that Groovy is a more popular choice for Java scripting, but I haven't seen many posts where it says that bsh can cause deadlocks.
It would be good to get some ideas from SO users.
Regards,

There's a fix for one dead lock in GUI does not start in Java 8 found in Beanshell (almost latest) version 2.0b5.
You can open a new issue in Beanshell project.
It may be connected to ClassManagerImpl:
Bsh has a multi-tiered class loading architecture. No class loader is
created unless/until a class is generated, the classpath is modified,
or a class is reloaded.
Note: we may need some synchronization in here

Spark possible race condition in driver

I have a Spark job that processes several folders on S3 per run and stores its state on DynamoDB. In other words, we're running the job once per day, it looks for new folders added by another job, transforms them one-by-one and writes state to DynamoDB. Here's rough pseudocode:
object App {
val allFolders = S3Folders.list()
val foldersToProcess = DynamoDBState.getFoldersToProcess(allFolders)
Transformer.run(foldersToProcess)
}
object Transformer {
def run(folders: List[String]): Unit = {
val sc = new SparkContext()
folders.foreach(process(sc, _))
}
def process(sc: SparkContext, folder: String): Unit = ??? // transform and write to S3
}
This approach works well if S3Folders.list() returns relatively small amount of folders (up to few thousands), if it returns more (4-8K) very often we see following error (that in first glance has nothing to do with Spark):
17/10/31 08:38:20 ERROR ApplicationMaster: User class threw exception: shadeaws.SdkClientException: Failed to sanitize XML document destined for handler class shadeaws.services.s3.model.transform.XmlResponses
SaxParser$ListObjectsV2Handler
shadeaws.SdkClientException: Failed to sanitize XML document destined for handler class shadeaws.services.s3.model.transform.XmlResponsesSaxParser$ListObjectsV2Handler
at shadeaws.services.s3.model.transform.XmlResponsesSaxParser.sanitizeXmlDocument(XmlResponsesSaxParser.java:214)
at shadeaws.services.s3.model.transform.XmlResponsesSaxParser.parseListObjectsV2Response(XmlResponsesSaxParser.java:315)
at shadeaws.services.s3.model.transform.Unmarshallers$ListObjectsV2Unmarshaller.unmarshall(Unmarshallers.java:88)
at shadeaws.services.s3.model.transform.Unmarshallers$ListObjectsV2Unmarshaller.unmarshall(Unmarshallers.java:77)
at shadeaws.services.s3.internal.S3XmlResponseHandler.handle(S3XmlResponseHandler.java:62)
at shadeaws.services.s3.internal.S3XmlResponseHandler.handle(S3XmlResponseHandler.java:31)
at shadeaws.http.response.AwsResponseHandlerAdapter.handle(AwsResponseHandlerAdapter.java:70)
at shadeaws.http.AmazonHttpClient$RequestExecutor.handleResponse(AmazonHttpClient.java:1553)
at shadeaws.http.AmazonHttpClient$RequestExecutor.executeOneRequest(AmazonHttpClient.java:1271)
at shadeaws.http.AmazonHttpClient$RequestExecutor.executeHelper(AmazonHttpClient.java:1055)
at shadeaws.http.AmazonHttpClient$RequestExecutor.doExecute(AmazonHttpClient.java:743)
at shadeaws.http.AmazonHttpClient$RequestExecutor.executeWithTimer(AmazonHttpClient.java:717)
at shadeaws.http.AmazonHttpClient$RequestExecutor.execute(AmazonHttpClient.java:699)
at shadeaws.http.AmazonHttpClient$RequestExecutor.access$500(AmazonHttpClient.java:667)
at shadeaws.http.AmazonHttpClient$RequestExecutionBuilderImpl.execute(AmazonHttpClient.java:649)
at shadeaws.http.AmazonHttpClient.execute(AmazonHttpClient.java:513)
at shadeaws.services.s3.AmazonS3Client.invoke(AmazonS3Client.java:4247)
at shadeaws.services.s3.AmazonS3Client.invoke(AmazonS3Client.java:4194)
at shadeaws.services.s3.AmazonS3Client.invoke(AmazonS3Client.java:4188)
at shadeaws.services.s3.AmazonS3Client.listObjectsV2(AmazonS3Client.java:865)
at me.chuwy.transform.S3Folders$.com$chuwy$transform$S3Folders$$isGlacierified(S3Folders.scala:136)
at scala.collection.TraversableLike$$anonfun$filterImpl$1.apply(TraversableLike.scala:248)
at scala.collection.immutable.List.foreach(List.scala:381)
at scala.collection.TraversableLike$class.filterImpl(TraversableLike.scala:247)
at scala.collection.TraversableLike$class.filterNot(TraversableLike.scala:267)
at scala.collection.AbstractTraversable.filterNot(Traversable.scala:104)
at me.chuwy.transform.S3Folders$.list(S3Folders.scala:112)
at me.chuwy.transform.Main$.main(Main.scala:22)
at me.chuwy.transform.Main.main(Main.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:637)
Caused by: shadeaws.AbortedException:
at shadeaws.internal.SdkFilterInputStream.abortIfNeeded(SdkFilterInputStream.java:53)
at shadeaws.internal.SdkFilterInputStream.read(SdkFilterInputStream.java:81)
at shadeaws.event.ProgressInputStream.read(ProgressInputStream.java:180)
at sun.nio.cs.StreamDecoder.readBytes(StreamDecoder.java:284)
at sun.nio.cs.StreamDecoder.implRead(StreamDecoder.java:326)
at sun.nio.cs.StreamDecoder.read(StreamDecoder.java:178)
at java.io.InputStreamReader.read(InputStreamReader.java:184)
at java.io.BufferedReader.read1(BufferedReader.java:210)
at java.io.BufferedReader.read(BufferedReader.java:286)
at java.io.Reader.read(Reader.java:140)
at shadeaws.services.s3.model.transform.XmlResponsesSaxParser.sanitizeXmlDocument(XmlResponsesSaxParser.java:186)
... 36 more
For big amount of folders (~20K) this happens all the time and job cannot start.
Previously we had very similar, but much more frequent error when getFoldersToProcess did GetItem for every folder from allFolders and therefore took much longer:
17/09/30 14:46:07 ERROR ApplicationMaster: User class threw exception: shadeaws.AbortedException:
shadeaws.AbortedException:
at shadeaws.internal.SdkFilterInputStream.abortIfNeeded(SdkFilterInputStream.java:51)
at shadeaws.internal.SdkFilterInputStream.read(SdkFilterInputStream.java:71)
at shadeaws.event.ProgressInputStream.read(ProgressInputStream.java:180)
at com.fasterxml.jackson.core.json.ByteSourceJsonBootstrapper.ensureLoaded(ByteSourceJsonBootstrapper.java:489)
at com.fasterxml.jackson.core.json.ByteSourceJsonBootstrapper.detectEncoding(ByteSourceJsonBootstrapper.java:126)
at com.fasterxml.jackson.core.json.ByteSourceJsonBootstrapper.constructParser(ByteSourceJsonBootstrapper.java:215)
at com.fasterxml.jackson.core.JsonFactory._createParser(JsonFactory.java:1240)
at com.fasterxml.jackson.core.JsonFactory.createParser(JsonFactory.java:802)
at shadeaws.http.JsonResponseHandler.handle(JsonResponseHandler.java:109)
at shadeaws.http.JsonResponseHandler.handle(JsonResponseHandler.java:43)
at shadeaws.http.response.AwsResponseHandlerAdapter.handle(AwsResponseHandlerAdapter.java:70)
at shadeaws.http.AmazonHttpClient$RequestExecutor.handleResponse(AmazonHttpClient.java:1503)
at shadeaws.http.AmazonHttpClient$RequestExecutor.executeOneRequest(AmazonHttpClient.java:1226)
at shadeaws.http.AmazonHttpClient$RequestExecutor.executeHelper(AmazonHttpClient.java:1030)
at shadeaws.http.AmazonHttpClient$RequestExecutor.doExecute(AmazonHttpClient.java:742)
at shadeaws.http.AmazonHttpClient$RequestExecutor.executeWithTimer(AmazonHttpClient.java:716)
at shadeaws.http.AmazonHttpClient$RequestExecutor.execute(AmazonHttpClient.java:699)
at shadeaws.http.AmazonHttpClient$RequestExecutor.access$500(AmazonHttpClient.java:667)
at shadeaws.http.AmazonHttpClient$RequestExecutionBuilderImpl.execute(AmazonHttpClient.java:649)
at shadeaws.http.AmazonHttpClient.execute(AmazonHttpClient.java:513)
at shadeaws.services.dynamodbv2.AmazonDynamoDBClient.doInvoke(AmazonDynamoDBClient.java:2089)
at shadeaws.services.dynamodbv2.AmazonDynamoDBClient.invoke(AmazonDynamoDBClient.java:2065)
at shadeaws.services.dynamodbv2.AmazonDynamoDBClient.executeGetItem(AmazonDynamoDBClient.java:1173)
at shadeaws.services.dynamodbv2.AmazonDynamoDBClient.getItem(AmazonDynamoDBClient.java:1149)
at me.chuwy.tranform.sdk.Manifest$.contains(Manifest.scala:179)
at me.chuwy.tranform.DynamoDBState$$anonfun$getUnprocessed$1.apply(ProcessManifest.scala:44)
at scala.collection.TraversableLike$$anonfun$filterImpl$1.apply(TraversableLike.scala:248)
at scala.collection.immutable.List.foreach(List.scala:381)
at scala.collection.TraversableLike$class.filterImpl(TraversableLike.scala:247)
at scala.collection.TraversableLike$class.filterNot(TraversableLike.scala:267)
at scala.collection.AbstractTraversable.filterNot(Traversable.scala:104)
at me.chuwy.transform.DynamoDBState$.getFoldersToProcess(DynamoDBState.scala:44)
at me.chuwy.transform.Main$.main(Main.scala:19)
at me.chuwy.transform.Main.main(Main.scala)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.apache.spark.deploy.yarn.ApplicationMaster$$anon$2.run(ApplicationMaster.scala:637)
I believe that current error has nothing to do with XML parsing or invalid response, but originate from some race condition inside Spark, because:
There's clear connection between amount of time "state-fetching" takes and chance of failure
Tracebacks have underlying AbortedException, which AFAIK caused by swallowed InterruptedException, which can mean something inside JVM (spark-submit or even YARN) calls Thread.sleep for main thread.
Right now I'm using EMR AMI 5.5.0, Spark 2.1.0 and shaded AWS SDK 1.11.208, but had similar error with AWS SDK 1.10.75.
I'm deploying this job on EMR via command-runner.jar spark-submit --deploy-mode cluster --class ....
Does anyone have any idea where does this exception originate from and how to fix it?

foreach does not guarantee orderly computations and it applies the operation(s) to each element of an RDD, meaning that it will instantiate for every element which, in turn, may overwhelm the executor.

The problem was that getFoldersToProcess is a blocking (and very long) operation, which prevents SparkContext from being instantiated. SpackContext itself should signal about own instantiation to YARN and if it doesn't help in a certain amount of time - YARN assumes that driver node has fallen off and kills the whole cluster.

Getting errors leasing tasks

When I try to lease tasks from a pull queue in my application, I get the error below. This didn't happen previously with my code, so something has changed. I suspect that it's a threading issue - these calls are made in a separate thread (created using ThreadManager.createThreadForCurrentRequest) - has that recently been disallowed?
uk.org.jaggard.myapp.BlahBlahBlahRunnable run: Exception leasing tasks. Already tried 0 times.
com.google.apphosting.api.ApiProxy$CancelledException: The API call taskqueue.QueryAndOwnTasks() was explicitly cancelled.
at com.google.apphosting.runtime.ApiProxyImpl.doSyncCall(ApiProxyImpl.java:218)
at com.google.apphosting.runtime.ApiProxyImpl.access$000(ApiProxyImpl.java:68)
at com.google.apphosting.runtime.ApiProxyImpl$1.run(ApiProxyImpl.java:182)
at com.google.apphosting.runtime.ApiProxyImpl$1.run(ApiProxyImpl.java:180)
at java.security.AccessController.doPrivileged(Native Method)
at com.google.apphosting.runtime.ApiProxyImpl.makeSyncCall(ApiProxyImpl.java:180)
at com.google.apphosting.runtime.ApiProxyImpl.makeSyncCall(ApiProxyImpl.java:68)
at com.google.appengine.tools.appstats.Recorder.makeSyncCall(Recorder.java:323)
at com.googlecode.objectify.cache.TriggerFutureHook.makeSyncCall(TriggerFutureHook.java:154)
at com.google.apphosting.api.ApiProxy.makeSyncCall(ApiProxy.java:105)
at com.google.appengine.api.taskqueue.QueueApiHelper.makeSyncCall(QueueApiHelper.java:44)
at com.google.appengine.api.taskqueue.QueueImpl.leaseTasksInternal(QueueImpl.java:709)
at com.google.appengine.api.taskqueue.QueueImpl.leaseTasks(QueueImpl.java:731)
at uk.org.jaggard.myapp.BlahBlahBlahRunnable.run(BlahBlahBlahRunnable.java:53)
at com.google.apphosting.runtime.ApiProxyImpl$CurrentRequestThreadFactory$1$1.run(ApiProxyImpl.java:997)
at java.security.AccessController.doPrivileged(Native Method)
at com.google.apphosting.runtime.ApiProxyImpl$CurrentRequestThreadFactory$1.run(ApiProxyImpl.java:994)
at java.lang.Thread.run(Thread.java:679)
at com.google.apphosting.runtime.ApiProxyImpl$CurrentRequestThreadFactory$2$1.run(ApiProxyImpl.java:1031)

I suspect the warnings in your application's logs will contain
"Thread was interrupted, throwing CancelledException."
Java's InterruptedException is discussed in
http://www.ibm.com/developerworks/java/library/j-jtp05236/index.html
and the book "Java Concurrency in Practice".

Exception Caught Too Early

Background: Hibernate connects to a database using a username and password entered into a GUI. Upon failure, instead of propagating the error up as an exception, it comes out as a stack trace in the logger. I don't know where the exception is being caught at. Also a tiny bit troubling is the following block:
if (reason != null) {
println("getConnection failed: " + reason);
throw reason;
}
My breakpoint is set at the throw line (and successfully triggers), but the println statement never generates output (MySQL is using some sort of logger setup I can't find an open file hand for). Any sort of trick for locating where an exception is caught?
EDIT 1:
I call
sessionFactory = /*AnnotationConfiguration*/ ac.buildSessionFactory();
The exception is caught by Hibernate somewhere between the java.sql.DriverManager class and my HibernateUtil class. I presume we can blame Hibernate deciding that I don't really want to see the exception. I want to convince hibernate to let me see the exception.
EDIT 2:
My stack is this:
java.sql.SQLException: Access denied for user 'user'#'machine' (using password: YES)
at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:1055)
at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:956)
at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3491)
at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3423)
at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:910)
at com.mysql.jdbc.MysqlIO.secureAuth411(MysqlIO.java:3923)
at com.mysql.jdbc.MysqlIO.doHandshake(MysqlIO.java:1273)
at com.mysql.jdbc.ConnectionImpl.createNewIO(ConnectionImpl.java:2031)
at com.mysql.jdbc.ConnectionImpl.<init>(ConnectionImpl.java:718)
at com.mysql.jdbc.JDBC4Connection.<init>(JDBC4Connection.java:46)
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:39)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27)
at java.lang.reflect.Constructor.newInstance(Constructor.java:513)
at com.mysql.jdbc.Util.handleNewInstance(Util.java:406)
at com.mysql.jdbc.ConnectionImpl.getInstance(ConnectionImpl.java:302)
at com.mysql.jdbc.NonRegisteringDriver.connect(NonRegisteringDriver.java:282)
/* Exception is thrown on the next line (1st code block in original post). */
at java.sql.DriverManager.getConnection(DriverManager.java:582)
at java.sql.DriverManager.getConnection(DriverManager.java:154)
/* Begin hidden source calls */
at org.hibernate.connection.DriverManagerConnectionProvider.getConnection(DriverManagerConnectionProvider.java:110)
at org.hibernate.cfg.SettingsFactory.buildSettings(SettingsFactory.java:84)
at org.hibernate.cfg.Configuration.buildSettings(Configuration.java:2009)
at org.hibernate.cfg.Configuration.buildSessionFactory(Configuration.java:1292)
at org.hibernate.cfg.AnnotationConfiguration.buildSessionFactory(AnnotationConfiguration.java:859)
/* End hidden source calls */
at com.****.****.util.HibernateUtil.initialize(HibernateUtil.java:34)
I can't get the debugger to look at any point above the stack beyond DriverManager.java:582. Everything in the stack beyond that is not visible in the debugger.

First of all, as you mention that there is a logger, you should replace all println statements with log calls.
You can also add further log messages to identify what happens inside the app. Alternatively (or in combination with the above), you can step through the critical code part in the debugger to see where the exception actually happens.

Here's the end result: Line 116 of org.hibernate.cfg.SettingsFactory catches the sql exception and forces it to a log. No configuration is available to change this. It appears I'll be unable to tell my end-user why their connection fails unless I make use of the logs.
Netbeans, for some annoying reason after I gave it the source for Hibernate still wanted to call all of this "hidden source calls." Some time with VIM and reading the line numbers later, I've got it cleared up.

Set a breakpoint for the exception thrown, and when the debugger starts single step to see what happens. You Will probably only need a few steps before the print happens.

An exception is encountered java.lang.UNIXProcess.forkAndExec

Anyone knows what is the reason for encountering this exception?
An exception is encountered during the processing. The stack track is below:
java.lang.UNIXProcess.forkAndExec(Native Method)
java.lang.UNIXProcess.<init>(UNIXProcess.java:53)
java.lang.ProcessImpl.start(ProcessImpl.java:65)
java.lang.ProcessBuilder.start(ProcessBuilder.java:451)
java.lang.Runtime.exec(Runtime.java:591)
java.lang.Runtime.exec(Runtime.java:464)
....
org.springframework.util.MethodInvoker.invoke(MethodInvoker.java:248)
org.springframework.scheduling.quartz.MethodInvokingJobDetailFactoryBean$MethodInvokingJob.executeInternal(MethodInvokingJobDetailFactoryBean.java:198)
org.springframework.scheduling.quartz.QuartzJobBean.execute(QuartzJobBean.java:90)
org.quartz.core.JobRunShell.run(JobRunShell.java:202)
org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:529)

If the exception is being thrown from the start() method, then the OS isn't able to fork/exec the process. So the problem isn't the subprocess dying, but that it's not being launched.
So are you specifying this correctly ? Are you relying on PATH settings ? Are the execute permissions correct ?
It would be useful to see the code that you use to initialise the ProcessBuilder. i.e. the invocation parameters.