The following error is popping up the new cluster, which was created with the old CloudFormation script (command line works, but this is from the JupyterNotebook)
FatalErrorTraceback (most recent call last)
<ipython-input-8-d61abe05c47a> in <module>()
----> 1 vds.summarize().report()
<decorator-gen-564> in summarize(self)
/mnt/tmp/spark-d192f7e6-76bc-41fd-a898-8e9b4f52b35d/userFiles-c45399eb-18be-4d8a-959f-52d2eeb87c96/hail-python.zip/hail/java.py in handle_py4j(func, *args, **kwargs)
119 raise FatalError('%s\n\nJava stack trace:\n%s\n'
120 'Hail version: %s\n'
--> 121 'Error summary: %s' % (deepest, full, Env.hc().version, deepest))
122 except py4j.protocol.Py4JError as e:
123 if e.args[0].startswith('An error occurred while calling'):
FatalError: ClassNotFoundException: is.hail.sparkextras.ReorderedPartitionsRDDPartition
Java stack trace:
org.apache.spark.SparkException: Job aborted due to stage failure: Task 57 in stage 7.0 failed 4 times, most recent failure: Lost task 57.3 in stage 7.0 (TID 3405, ip-10-6-0-6.ec2.internal, executor 63): java.lang.ClassNotFoundException: is.hail.sparkextras.ReorderedPartitionsRDDPartition
at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
at java.lang.Class.forName0(Native Method)
at java.lang.Class.forName(Class.java:348)
at org.apache.spark.serializer.JavaDeserializationStream$$anon$1.resolveClass(JavaSerializer.scala:67)
at java.io.ObjectInputStream.readNonProxyDesc(ObjectInputStream.java:1826)
at java.io.ObjectInputStream.readClassDesc(ObjectInputStream.java:1713)
at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:2000)
at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1535)
at java.io.ObjectInputStream.defaultReadFields(ObjectInputStream.java:2245)
at java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:2169)
at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:2027)
at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1535)
at java.io.ObjectInputStream.readObject(ObjectInputStream.java:422)
at org.apache.spark.serializer.JavaDeserializationStream.readObject(JavaSerializer.scala:75)
at org.apache.spark.serializer.JavaSerializerInstance.deserialize(JavaSerializer.scala:114)
at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:258)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at java.lang.Thread.run(Thread.java:748)
Driver stacktrace:
at org.apache.spark.scheduler.DAGScheduler.org$apache$spark$scheduler$DAGScheduler$$failJobAndIndependentStages(DAGScheduler.scala:1505)
at org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1493)
at org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1492)
at scala.collection.mutable.ResizableArray$class.foreach(ResizableArray.scala:59)
at scala.collection.mutable.ArrayBuffer.foreach(ArrayBuffer.scala:48)
at org.apache.spark.scheduler.DAGScheduler.abortStage(DAGScheduler.scala:1492)
at org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:803)
at org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:803)
at scala.Option.foreach(Option.scala:257)
at org.apache.spark.scheduler.DAGScheduler.handleTaskSetFailed(DAGScheduler.scala:803)
at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.doOnReceive(DAGScheduler.scala:1720)
at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:1675)
at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:1664)
at org.apache.spark.util.EventLoop$$anon$1.run(EventLoop.scala:48)
at org.apache.spark.scheduler.DAGScheduler.runJob(DAGScheduler.scala:629)
at org.apache.spark.SparkContext.runJob(SparkContext.scala:1918)
at org.apache.spark.SparkContext.runJob(SparkContext.scala:1981)
at org.apache.spark.rdd.RDD$$anonfun$aggregate$1.apply(RDD.scala:1114)
at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151)
at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:112)
at org.apache.spark.rdd.RDD.withScope(RDD.scala:362)
at org.apache.spark.rdd.RDD.aggregate(RDD.scala:1107)
at is.hail.variant.VariantDatasetFunctions$.summarize$extension(VariantDataset.scala:220)
at is.hail.variant.VariantDatasetFunctions.summarize(VariantDataset.scala:221)
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 py4j.reflection.MethodInvoker.invoke(MethodInvoker.java:244)
at py4j.reflection.ReflectionEngine.invoke(ReflectionEngine.java:357)
at py4j.Gateway.invoke(Gateway.java:280)
at py4j.commands.AbstractCommand.invokeMethod(AbstractCommand.java:132)
at py4j.commands.CallCommand.execute(CallCommand.java:79)
at py4j.GatewayConnection.run(GatewayConnection.java:214)
at java.lang.Thread.run(Thread.java:748)java.lang.ClassNotFoundException: is.hail.sparkextras.ReorderedPartitionsRDDPartition
at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
at java.lang.Class.forName0(Native Method)
at java.lang.Class.forName(Class.java:348)
at org.apache.spark.serializer.JavaDeserializationStream$$anon$1.resolveClass(JavaSerializer.scala:67)
at java.io.ObjectInputStream.readNonProxyDesc(ObjectInputStream.java:1826)
at java.io.ObjectInputStream.readClassDesc(ObjectInputStream.java:1713)
at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:2000)
at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1535)
at java.io.ObjectInputStream.defaultReadFields(ObjectInputStream.java:2245)
at java.io.ObjectInputStream.readSerialData(ObjectInputStream.java:2169)
at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:2027)
at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1535)
at java.io.ObjectInputStream.readObject(ObjectInputStream.java:422)
at org.apache.spark.serializer.JavaDeserializationStream.readObject(JavaSerializer.scala:75)
at org.apache.spark.serializer.JavaSerializerInstance.deserialize(JavaSerializer.scala:114)
at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:258)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at java.lang.Thread.run(Thread.java:748)
Hail version: 0.1-74bf1eb
Error summary: ClassNotFoundException: is.hail.sparkextras.ReorderedPartitionsRDDPartition