java.io.IOException: Stream is closed! Error in HDInsight with ADLS Gen 2

EagleByte 1 Reputation point
2020-06-29T14:55:04.947+00:00

I am currently using Hail for the pyspark library to perform varying operations on Genomic data in ADLS Gen 2 with an HDInsight 4.0, Spark 2.4 cluster.

I have been in touch with the development team regarding this error I have been getting when running a command to write a table to ADLS. The team has looked through the source code on their end and confirmed that they have a safe method of avoiding double closures of streams, by checking if it has closed prior to closing one, and are suggesting it may be an issue from within AbfsOutputStream.java within the Hadoop libraries or that this error is disguising a deeper issue.

Any help would be greatly appreciated. It doesn't appear that this should be happening, according to the code on both ends.

Below is the error I am experiencing:

IOException: Stream is closed!

Java stack trace:
java.lang.RuntimeException: error while applying lowering 'InterpretNonCompilable'
    at is.hail.expr.ir.lowering.LoweringPipeline$$anonfun$apply$1.apply(LoweringPipeline.scala:26)
    at is.hail.expr.ir.lowering.LoweringPipeline$$anonfun$apply$1.apply(LoweringPipeline.scala:18)
    at scala.collection.IndexedSeqOptimized$class.foreach(IndexedSeqOptimized.scala:33)
    at scala.collection.mutable.WrappedArray.foreach(WrappedArray.scala:35)
    at is.hail.expr.ir.lowering.LoweringPipeline.apply(LoweringPipeline.scala:18)
    at is.hail.expr.ir.CompileAndEvaluate$._apply(CompileAndEvaluate.scala:28)
    at is.hail.backend.spark.SparkBackend.is$hail$backend$spark$SparkBackend$$_execute(SparkBackend.scala:317)
    at is.hail.backend.spark.SparkBackend$$anonfun$execute$1.apply(SparkBackend.scala:304)
    at is.hail.backend.spark.SparkBackend$$anonfun$execute$1.apply(SparkBackend.scala:303)
    at is.hail.expr.ir.ExecuteContext$$anonfun$scoped$1.apply(ExecuteContext.scala:20)
    at is.hail.expr.ir.ExecuteContext$$anonfun$scoped$1.apply(ExecuteContext.scala:18)
    at is.hail.utils.package$.using(package.scala:601)
    at is.hail.annotations.Region$.scoped(Region.scala:18)
    at is.hail.expr.ir.ExecuteContext$.scoped(ExecuteContext.scala:18)
    at is.hail.backend.spark.SparkBackend.withExecuteContext(SparkBackend.scala:229)
    at is.hail.backend.spark.SparkBackend.execute(SparkBackend.scala:303)
    at is.hail.backend.spark.SparkBackend.executeJSON(SparkBackend.scala:323)
    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:282)
    at py4j.commands.AbstractCommand.invokeMethod(AbstractCommand.java:132)
    at py4j.commands.CallCommand.execute(CallCommand.java:79)
    at py4j.GatewayConnection.run(GatewayConnection.java:238)
    at java.lang.Thread.run(Thread.java:748)

org.apache.spark.SparkException: Job aborted due to stage failure: Task 0 in stage 1.0 failed 4 times, most recent failure: Lost task 0.3 in stage 1.0 (TID 4, wn5-iqviae.euwjv10e4raexden0li12nxlvc.cx.internal.cloudapp.net, executor 2): java.io.IOException: Stream is closed!
    at org.apache.hadoop.fs.azurebfs.services.AbfsOutputStream.close(AbfsOutputStream.java:244)
    at org.apache.hadoop.fs.FSDataOutputStream$PositionCache.close(FSDataOutputStream.java:72)
    at org.apache.hadoop.fs.FSDataOutputStream.close(FSDataOutputStream.java:101)
    at is.hail.io.fs.HadoopFS$$anon$1.close(HadoopFS.scala:39)
    at java.io.FilterOutputStream.close(FilterOutputStream.java:159)
    at is.hail.utils.richUtils.ByteTrackingOutputStream.close(ByteTrackingOutputStream.scala:23)
    at is.hail.io.StreamBlockOutputBuffer.close(OutputBuffers.scala:287)
    at is.hail.io.LZ4OutputBlockBuffer.close(OutputBuffers.scala:307)
    at is.hail.io.BlockingOutputBuffer.close(OutputBuffers.scala:201)
    at is.hail.io.LEB128OutputBuffer.close(OutputBuffers.scala:139)
    at is.hail.io.CompiledEncoder.close(Encoder.scala:27)
    at is.hail.utils.package$.using(package.scala:603)
    at is.hail.io.RichContextRDDRegionValue$$anonfun$2.apply(RichContextRDDRegionValue.scala:101)
    at is.hail.io.RichContextRDDRegionValue$$anonfun$2.apply(RichContextRDDRegionValue.scala:99)
    at is.hail.utils.package$.using(package.scala:601)
    at is.hail.io.RichContextRDDRegionValue$.writeSplitRegion(RichContextRDDRegionValue.scala:99)
    at is.hail.rvd.RVD$$anonfun$27.apply(RVD.scala:938)
    at is.hail.rvd.RVD$$anonfun$27.apply(RVD.scala:936)
    at is.hail.sparkextras.ContextRDD$$anonfun$cmapPartitionsWithIndex$1$$anonfun$apply$18.apply(ContextRDD.scala:248)
    at is.hail.sparkextras.ContextRDD$$anonfun$cmapPartitionsWithIndex$1$$anonfun$apply$18.apply(ContextRDD.scala:248)
    at is.hail.utils.richUtils.RichContextRDD$$anonfun$cleanupRegions$1$$anonfun$1.apply(RichContextRDD.scala:22)
    at is.hail.utils.richUtils.RichContextRDD$$anonfun$cleanupRegions$1$$anonfun$1.apply(RichContextRDD.scala:22)
    at scala.collection.Iterator$$anon$12.nextCur(Iterator.scala:435)
    at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:441)
    at is.hail.utils.richUtils.RichContextRDD$$anonfun$cleanupRegions$1$$anon$1.hasNext(RichContextRDD.scala:31)
    at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
    at scala.collection.Iterator$class.foreach(Iterator.scala:891)
    at scala.collection.AbstractIterator.foreach(Iterator.scala:1334)
    at scala.collection.generic.Growable$class.$plus$plus$eq(Growable.scala:59)
    at scala.collection.mutable.ArrayBuffer.$plus$plus$eq(ArrayBuffer.scala:104)
    at scala.collection.mutable.ArrayBuffer.$plus$plus$eq(ArrayBuffer.scala:48)
    at scala.collection.TraversableOnce$class.to(TraversableOnce.scala:310)
    at scala.collection.AbstractIterator.to(Iterator.scala:1334)
    at scala.collection.TraversableOnce$class.toBuffer(TraversableOnce.scala:302)
    at scala.collection.AbstractIterator.toBuffer(Iterator.scala:1334)
    at scala.collection.TraversableOnce$class.toArray(TraversableOnce.scala:289)
    at scala.collection.AbstractIterator.toArray(Iterator.scala:1334)
    at org.apache.spark.rdd.RDD$$anonfun$collect$1$$anonfun$13.apply(RDD.scala:945)
    at org.apache.spark.rdd.RDD$$anonfun$collect$1$$anonfun$13.apply(RDD.scala:945)
    at org.apache.spark.SparkContext$$anonfun$runJob$5.apply(SparkContext.scala:2101)
    at org.apache.spark.SparkContext$$anonfun$runJob$5.apply(SparkContext.scala:2101)
    at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:90)
    at org.apache.spark.scheduler.Task.run(Task.scala:121)
    at org.apache.spark.executor.Executor$TaskRunner$$anonfun$10.apply(Executor.scala:402)
    at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1360)
    at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:408)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
    at java.util.concurrent.ThreadPoolExecutor$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$$failJobAndIndependentStages(DAGScheduler.scala:1889)
    at org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1877)
    at org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1876)
    at scala.collection.mutable.ResizableArray$class.foreach(ResizableArray.scala:59)
    at scala.collection.mutable.ArrayBuffer.foreach(ArrayBuffer.scala:48)
    at org.apache.spark.scheduler.DAGScheduler.abortStage(DAGScheduler.scala:1876)
    at org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:926)
    at org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:926)
    at scala.Option.foreach(Option.scala:257)
    at org.apache.spark.scheduler.DAGScheduler.handleTaskSetFailed(DAGScheduler.scala:926)
    at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.doOnReceive(DAGScheduler.scala:2110)
    at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:2059)
    at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:2048)
    at org.apache.spark.util.EventLoop$$anon$1.run(EventLoop.scala:49)
    at org.apache.spark.scheduler.DAGScheduler.runJob(DAGScheduler.scala:737)
    at org.apache.spark.SparkContext.runJob(SparkContext.scala:2061)
    at org.apache.spark.SparkContext.runJob(SparkContext.scala:2082)
    at org.apache.spark.SparkContext.runJob(SparkContext.scala:2101)
    at org.apache.spark.SparkContext.runJob(SparkContext.scala:2126)
    at org.apache.spark.rdd.RDD$$anonfun$collect$1.apply(RDD.scala:945)
    at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151)
    at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:112)
    at org.apache.spark.rdd.RDD.withScope(RDD.scala:363)
    at org.apache.spark.rdd.RDD.collect(RDD.scala:944)
    at is.hail.sparkextras.ContextRDD.collect(ContextRDD.scala:166)
    at is.hail.rvd.RVD.writeRowsSplit(RVD.scala:953)
    at is.hail.expr.ir.MatrixValue.write(MatrixValue.scala:224)
    at is.hail.expr.ir.MatrixNativeWriter.apply(MatrixWriter.scala:41)
    at is.hail.expr.ir.WrappedMatrixWriter.apply(MatrixWriter.scala:25)
    at is.hail.expr.ir.Interpret$.run(Interpret.scala:726)
    at is.hail.expr.ir.Interpret$.alreadyLowered(Interpret.scala:53)
    at is.hail.expr.ir.InterpretNonCompilable$.interpretAndCoerce$1(InterpretNonCompilable.scala:16)
    at is.hail.expr.ir.InterpretNonCompilable$.is$hail$expr$ir$InterpretNonCompilable$$rewrite$1(InterpretNonCompilable.scala:53)
    at is.hail.expr.ir.InterpretNonCompilable$.apply(InterpretNonCompilable.scala:58)
    at is.hail.expr.ir.lowering.InterpretNonCompilablePass$.transform(LoweringPass.scala:50)
    at is.hail.expr.ir.lowering.LoweringPass$$anonfun$apply$3$$anonfun$1.apply(LoweringPass.scala:15)
    at is.hail.expr.ir.lowering.LoweringPass$$anonfun$apply$3$$anonfun$1.apply(LoweringPass.scala:15)
    at is.hail.utils.ExecutionTimer.time(ExecutionTimer.scala:69)
    at is.hail.expr.ir.lowering.LoweringPass$$anonfun$apply$3.apply(LoweringPass.scala:15)
    at is.hail.expr.ir.lowering.LoweringPass$$anonfun$apply$3.apply(LoweringPass.scala:13)
    at is.hail.utils.ExecutionTimer.time(ExecutionTimer.scala:69)
    at is.hail.expr.ir.lowering.LoweringPass$class.apply(LoweringPass.scala:13)
    at is.hail.expr.ir.lowering.InterpretNonCompilablePass$.apply(LoweringPass.scala:45)
    at is.hail.expr.ir.lowering.LoweringPipeline$$anonfun$apply$1.apply(LoweringPipeline.scala:20)
    at is.hail.expr.ir.lowering.LoweringPipeline$$anonfun$apply$1.apply(LoweringPipeline.scala:18)
    at scala.collection.IndexedSeqOptimized$class.foreach(IndexedSeqOptimized.scala:33)
    at scala.collection.mutable.WrappedArray.foreach(WrappedArray.scala:35)
    at is.hail.expr.ir.lowering.LoweringPipeline.apply(LoweringPipeline.scala:18)
    at is.hail.expr.ir.CompileAndEvaluate$._apply(CompileAndEvaluate.scala:28)
    at is.hail.backend.spark.SparkBackend.is$hail$backend$spark$SparkBackend$$_execute(SparkBackend.scala:317)
    at is.hail.backend.spark.SparkBackend$$anonfun$execute$1.apply(SparkBackend.scala:304)
    at is.hail.backend.spark.SparkBackend$$anonfun$execute$1.apply(SparkBackend.scala:303)
    at is.hail.expr.ir.ExecuteContext$$anonfun$scoped$1.apply(ExecuteContext.scala:20)
    at is.hail.expr.ir.ExecuteContext$$anonfun$scoped$1.apply(ExecuteContext.scala:18)
    at is.hail.utils.package$.using(package.scala:601)
    at is.hail.annotations.Region$.scoped(Region.scala:18)
    at is.hail.expr.ir.ExecuteContext$.scoped(ExecuteContext.scala:18)
    at is.hail.backend.spark.SparkBackend.withExecuteContext(SparkBackend.scala:229)
    at is.hail.backend.spark.SparkBackend.execute(SparkBackend.scala:303)
    at is.hail.backend.spark.SparkBackend.executeJSON(SparkBackend.scala:323)
    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:282)
    at py4j.commands.AbstractCommand.invokeMethod(AbstractCommand.java:132)
    at py4j.commands.CallCommand.execute(CallCommand.java:79)
    at py4j.GatewayConnection.run(GatewayConnection.java:238)
    at java.lang.Thread.run(Thread.java:748)

java.io.IOException: Stream is closed!
    at org.apache.hadoop.fs.azurebfs.services.AbfsOutputStream.close(AbfsOutputStream.java:244)
    at org.apache.hadoop.fs.FSDataOutputStream$PositionCache.close(FSDataOutputStream.java:72)
    at org.apache.hadoop.fs.FSDataOutputStream.close(FSDataOutputStream.java:101)
    at is.hail.io.fs.HadoopFS$$anon$1.close(HadoopFS.scala:39)
    at java.io.FilterOutputStream.close(FilterOutputStream.java:159)
    at is.hail.utils.richUtils.ByteTrackingOutputStream.close(ByteTrackingOutputStream.scala:23)
    at is.hail.io.StreamBlockOutputBuffer.close(OutputBuffers.scala:287)
    at is.hail.io.LZ4OutputBlockBuffer.close(OutputBuffers.scala:307)
    at is.hail.io.BlockingOutputBuffer.close(OutputBuffers.scala:201)
    at is.hail.io.LEB128OutputBuffer.close(OutputBuffers.scala:139)
    at is.hail.io.CompiledEncoder.close(Encoder.scala:27)
    at is.hail.utils.package$.using(package.scala:603)
    at is.hail.io.RichContextRDDRegionValue$$anonfun$2.apply(RichContextRDDRegionValue.scala:101)
    at is.hail.io.RichContextRDDRegionValue$$anonfun$2.apply(RichContextRDDRegionValue.scala:99)
    at is.hail.utils.package$.using(package.scala:601)
    at is.hail.io.RichContextRDDRegionValue$.writeSplitRegion(RichContextRDDRegionValue.scala:99)
    at is.hail.rvd.RVD$$anonfun$27.apply(RVD.scala:938)
    at is.hail.rvd.RVD$$anonfun$27.apply(RVD.scala:936)
    at is.hail.sparkextras.ContextRDD$$anonfun$cmapPartitionsWithIndex$1$$anonfun$apply$18.apply(ContextRDD.scala:248)
    at is.hail.sparkextras.ContextRDD$$anonfun$cmapPartitionsWithIndex$1$$anonfun$apply$18.apply(ContextRDD.scala:248)
    at is.hail.utils.richUtils.RichContextRDD$$anonfun$cleanupRegions$1$$anonfun$1.apply(RichContextRDD.scala:22)
    at is.hail.utils.richUtils.RichContextRDD$$anonfun$cleanupRegions$1$$anonfun$1.apply(RichContextRDD.scala:22)
    at scala.collection.Iterator$$anon$12.nextCur(Iterator.scala:435)
    at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:441)
    at is.hail.utils.richUtils.RichContextRDD$$anonfun$cleanupRegions$1$$anon$1.hasNext(RichContextRDD.scala:31)
    at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
    at scala.collection.Iterator$class.foreach(Iterator.scala:891)
    at scala.collection.AbstractIterator.foreach(Iterator.scala:1334)
    at scala.collection.generic.Growable$class.$plus$plus$eq(Growable.scala:59)
    at scala.collection.mutable.ArrayBuffer.$plus$plus$eq(ArrayBuffer.scala:104)
    at scala.collection.mutable.ArrayBuffer.$plus$plus$eq(ArrayBuffer.scala:48)
    at scala.collection.TraversableOnce$class.to(TraversableOnce.scala:310)
    at scala.collection.AbstractIterator.to(Iterator.scala:1334)
    at scala.collection.TraversableOnce$class.toBuffer(TraversableOnce.scala:302)
    at scala.collection.AbstractIterator.toBuffer(Iterator.scala:1334)
    at scala.collection.TraversableOnce$class.toArray(TraversableOnce.scala:289)
    at scala.collection.AbstractIterator.toArray(Iterator.scala:1334)
    at org.apache.spark.rdd.RDD$$anonfun$collect$1$$anonfun$13.apply(RDD.scala:945)
    at org.apache.spark.rdd.RDD$$anonfun$collect$1$$anonfun$13.apply(RDD.scala:945)
    at org.apache.spark.SparkContext$$anonfun$runJob$5.apply(SparkContext.scala:2101)
    at org.apache.spark.SparkContext$$anonfun$runJob$5.apply(SparkContext.scala:2101)
    at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:90)
    at org.apache.spark.scheduler.Task.run(Task.scala:121)
    at org.apache.spark.executor.Executor$TaskRunner$$anonfun$10.apply(Executor.scala:402)
    at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1360)
    at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:408)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
    at java.lang.Thread.run(Thread.java:748)





Hail version: 0.2.47-d9e1f3a110c8
Error summary: IOException: Stream is closed!
Traceback (most recent call last):
  File "</usr/bin/anaconda/envs/hail/lib/python3.7/site-packages/decorator.py:decorator-gen-1213>", line 2, in write
  File "/usr/bin/anaconda/envs/hail/lib/python3.7/site-packages/hail/typecheck/check.py", line 614, in wrapper
    return __original_func(*args_, **kwargs_)
  File "/usr/bin/anaconda/envs/hail/lib/python3.7/site-packages/hail/matrixtable.py", line 2524, in write
    Env.backend().execute(ir.MatrixWrite(self._mir, writer))
  File "/usr/bin/anaconda/envs/hail/lib/python3.7/site-packages/hail/backend/spark_backend.py", line 296, in execute
    result = json.loads(self._jhc.backend().executeJSON(jir))
  File "/usr/hdp/current/spark2-client/python/lib/py4j-0.10.7-src.zip/py4j/java_gateway.py", line 1257, in __call__
    answer, self.gateway_client, self.target_id, self.name)
  File "/usr/bin/anaconda/envs/hail/lib/python3.7/site-packages/hail/backend/spark_backend.py", line 41, in deco
    'Error summary: %s' % (deepest, full, hail.__version__, deepest)) from None
hail.utils.java.FatalError: IOException: Stream is closed!

Java stack trace:
java.lang.RuntimeException: error while applying lowering 'InterpretNonCompilable'
    at is.hail.expr.ir.lowering.LoweringPipeline$$anonfun$apply$1.apply(LoweringPipeline.scala:26)
    at is.hail.expr.ir.lowering.LoweringPipeline$$anonfun$apply$1.apply(LoweringPipeline.scala:18)
    at scala.collection.IndexedSeqOptimized$class.foreach(IndexedSeqOptimized.scala:33)
    at scala.collection.mutable.WrappedArray.foreach(WrappedArray.scala:35)
    at is.hail.expr.ir.lowering.LoweringPipeline.apply(LoweringPipeline.scala:18)
    at is.hail.expr.ir.CompileAndEvaluate$._apply(CompileAndEvaluate.scala:28)
    at is.hail.backend.spark.SparkBackend.is$hail$backend$spark$SparkBackend$$_execute(SparkBackend.scala:317)
    at is.hail.backend.spark.SparkBackend$$anonfun$execute$1.apply(SparkBackend.scala:304)
    at is.hail.backend.spark.SparkBackend$$anonfun$execute$1.apply(SparkBackend.scala:303)
    at is.hail.expr.ir.ExecuteContext$$anonfun$scoped$1.apply(ExecuteContext.scala:20)
    at is.hail.expr.ir.ExecuteContext$$anonfun$scoped$1.apply(ExecuteContext.scala:18)
    at is.hail.utils.package$.using(package.scala:601)
    at is.hail.annotations.Region$.scoped(Region.scala:18)
    at is.hail.expr.ir.ExecuteContext$.scoped(ExecuteContext.scala:18)
    at is.hail.backend.spark.SparkBackend.withExecuteContext(SparkBackend.scala:229)
    at is.hail.backend.spark.SparkBackend.execute(SparkBackend.scala:303)
    at is.hail.backend.spark.SparkBackend.executeJSON(SparkBackend.scala:323)
    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:282)
    at py4j.commands.AbstractCommand.invokeMethod(AbstractCommand.java:132)
    at py4j.commands.CallCommand.execute(CallCommand.java:79)
    at py4j.GatewayConnection.run(GatewayConnection.java:238)
    at java.lang.Thread.run(Thread.java:748)

org.apache.spark.SparkException: Job aborted due to stage failure: Task 0 in stage 1.0 failed 4 times, most recent failure: Lost task 0.3 in stage 1.0 (TID 4, wn5-iqviae.euwjv10e4raexden0li12nxlvc.cx.internal.cloudapp.net, executor 2): java.io.IOException: Stream is closed!
    at org.apache.hadoop.fs.azurebfs.services.AbfsOutputStream.close(AbfsOutputStream.java:244)
    at org.apache.hadoop.fs.FSDataOutputStream$PositionCache.close(FSDataOutputStream.java:72)
    at org.apache.hadoop.fs.FSDataOutputStream.close(FSDataOutputStream.java:101)
    at is.hail.io.fs.HadoopFS$$anon$1.close(HadoopFS.scala:39)
    at java.io.FilterOutputStream.close(FilterOutputStream.java:159)
    at is.hail.utils.richUtils.ByteTrackingOutputStream.close(ByteTrackingOutputStream.scala:23)
    at is.hail.io.StreamBlockOutputBuffer.close(OutputBuffers.scala:287)
    at is.hail.io.LZ4OutputBlockBuffer.close(OutputBuffers.scala:307)
    at is.hail.io.BlockingOutputBuffer.close(OutputBuffers.scala:201)
    at is.hail.io.LEB128OutputBuffer.close(OutputBuffers.scala:139)
    at is.hail.io.CompiledEncoder.close(Encoder.scala:27)
    at is.hail.utils.package$.using(package.scala:603)
    at is.hail.io.RichContextRDDRegionValue$$anonfun$2.apply(RichContextRDDRegionValue.scala:101)
    at is.hail.io.RichContextRDDRegionValue$$anonfun$2.apply(RichContextRDDRegionValue.scala:99)
    at is.hail.utils.package$.using(package.scala:601)
    at is.hail.io.RichContextRDDRegionValue$.writeSplitRegion(RichContextRDDRegionValue.scala:99)
    at is.hail.rvd.RVD$$anonfun$27.apply(RVD.scala:938)
    at is.hail.rvd.RVD$$anonfun$27.apply(RVD.scala:936)
    at is.hail.sparkextras.ContextRDD$$anonfun$cmapPartitionsWithIndex$1$$anonfun$apply$18.apply(ContextRDD.scala:248)
    at is.hail.sparkextras.ContextRDD$$anonfun$cmapPartitionsWithIndex$1$$anonfun$apply$18.apply(ContextRDD.scala:248)
    at is.hail.utils.richUtils.RichContextRDD$$anonfun$cleanupRegions$1$$anonfun$1.apply(RichContextRDD.scala:22)
    at is.hail.utils.richUtils.RichContextRDD$$anonfun$cleanupRegions$1$$anonfun$1.apply(RichContextRDD.scala:22)
    at scala.collection.Iterator$$anon$12.nextCur(Iterator.scala:435)
    at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:441)
    at is.hail.utils.richUtils.RichContextRDD$$anonfun$cleanupRegions$1$$anon$1.hasNext(RichContextRDD.scala:31)
    at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
    at scala.collection.Iterator$class.foreach(Iterator.scala:891)
    at scala.collection.AbstractIterator.foreach(Iterator.scala:1334)
    at scala.collection.generic.Growable$class.$plus$plus$eq(Growable.scala:59)
    at scala.collection.mutable.ArrayBuffer.$plus$plus$eq(ArrayBuffer.scala:104)
    at scala.collection.mutable.ArrayBuffer.$plus$plus$eq(ArrayBuffer.scala:48)
    at scala.collection.TraversableOnce$class.to(TraversableOnce.scala:310)
    at scala.collection.AbstractIterator.to(Iterator.scala:1334)
    at scala.collection.TraversableOnce$class.toBuffer(TraversableOnce.scala:302)
    at scala.collection.AbstractIterator.toBuffer(Iterator.scala:1334)
    at scala.collection.TraversableOnce$class.toArray(TraversableOnce.scala:289)
    at scala.collection.AbstractIterator.toArray(Iterator.scala:1334)
    at org.apache.spark.rdd.RDD$$anonfun$collect$1$$anonfun$13.apply(RDD.scala:945)
    at org.apache.spark.rdd.RDD$$anonfun$collect$1$$anonfun$13.apply(RDD.scala:945)
    at org.apache.spark.SparkContext$$anonfun$runJob$5.apply(SparkContext.scala:2101)
    at org.apache.spark.SparkContext$$anonfun$runJob$5.apply(SparkContext.scala:2101)
    at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:90)
    at org.apache.spark.scheduler.Task.run(Task.scala:121)
    at org.apache.spark.executor.Executor$TaskRunner$$anonfun$10.apply(Executor.scala:402)
    at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1360)
    at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:408)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
    at java.util.concurrent.ThreadPoolExecutor$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$$failJobAndIndependentStages(DAGScheduler.scala:1889)
    at org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1877)
    at org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1876)
    at scala.collection.mutable.ResizableArray$class.foreach(ResizableArray.scala:59)
    at scala.collection.mutable.ArrayBuffer.foreach(ArrayBuffer.scala:48)
    at org.apache.spark.scheduler.DAGScheduler.abortStage(DAGScheduler.scala:1876)
    at org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:926)
    at org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:926)
    at scala.Option.foreach(Option.scala:257)
    at org.apache.spark.scheduler.DAGScheduler.handleTaskSetFailed(DAGScheduler.scala:926)
    at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.doOnReceive(DAGScheduler.scala:2110)
    at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:2059)
    at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:2048)
    at org.apache.spark.util.EventLoop$$anon$1.run(EventLoop.scala:49)
    at org.apache.spark.scheduler.DAGScheduler.runJob(DAGScheduler.scala:737)
    at org.apache.spark.SparkContext.runJob(SparkContext.scala:2061)
    at org.apache.spark.SparkContext.runJob(SparkContext.scala:2082)
    at org.apache.spark.SparkContext.runJob(SparkContext.scala:2101)
    at org.apache.spark.SparkContext.runJob(SparkContext.scala:2126)
    at org.apache.spark.rdd.RDD$$anonfun$collect$1.apply(RDD.scala:945)
    at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151)
    at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:112)
    at org.apache.spark.rdd.RDD.withScope(RDD.scala:363)
    at org.apache.spark.rdd.RDD.collect(RDD.scala:944)
    at is.hail.sparkextras.ContextRDD.collect(ContextRDD.scala:166)
    at is.hail.rvd.RVD.writeRowsSplit(RVD.scala:953)
    at is.hail.expr.ir.MatrixValue.write(MatrixValue.scala:224)
    at is.hail.expr.ir.MatrixNativeWriter.apply(MatrixWriter.scala:41)
    at is.hail.expr.ir.WrappedMatrixWriter.apply(MatrixWriter.scala:25)
    at is.hail.expr.ir.Interpret$.run(Interpret.scala:726)
    at is.hail.expr.ir.Interpret$.alreadyLowered(Interpret.scala:53)
    at is.hail.expr.ir.InterpretNonCompilable$.interpretAndCoerce$1(InterpretNonCompilable.scala:16)
    at is.hail.expr.ir.InterpretNonCompilable$.is$hail$expr$ir$InterpretNonCompilable$$rewrite$1(InterpretNonCompilable.scala:53)
    at is.hail.expr.ir.InterpretNonCompilable$.apply(InterpretNonCompilable.scala:58)
    at is.hail.expr.ir.lowering.InterpretNonCompilablePass$.transform(LoweringPass.scala:50)
    at is.hail.expr.ir.lowering.LoweringPass$$anonfun$apply$3$$anonfun$1.apply(LoweringPass.scala:15)
    at is.hail.expr.ir.lowering.LoweringPass$$anonfun$apply$3$$anonfun$1.apply(LoweringPass.scala:15)
    at is.hail.utils.ExecutionTimer.time(ExecutionTimer.scala:69)
    at is.hail.expr.ir.lowering.LoweringPass$$anonfun$apply$3.apply(LoweringPass.scala:15)
    at is.hail.expr.ir.lowering.LoweringPass$$anonfun$apply$3.apply(LoweringPass.scala:13)
    at is.hail.utils.ExecutionTimer.time(ExecutionTimer.scala:69)
    at is.hail.expr.ir.lowering.LoweringPass$class.apply(LoweringPass.scala:13)
    at is.hail.expr.ir.lowering.InterpretNonCompilablePass$.apply(LoweringPass.scala:45)
    at is.hail.expr.ir.lowering.LoweringPipeline$$anonfun$apply$1.apply(LoweringPipeline.scala:20)
    at is.hail.expr.ir.lowering.LoweringPipeline$$anonfun$apply$1.apply(LoweringPipeline.scala:18)
    at scala.collection.IndexedSeqOptimized$class.foreach(IndexedSeqOptimized.scala:33)
    at scala.collection.mutable.WrappedArray.foreach(WrappedArray.scala:35)
    at is.hail.expr.ir.lowering.LoweringPipeline.apply(LoweringPipeline.scala:18)
    at is.hail.expr.ir.CompileAndEvaluate$._apply(CompileAndEvaluate.scala:28)
    at is.hail.backend.spark.SparkBackend.is$hail$backend$spark$SparkBackend$$_execute(SparkBackend.scala:317)
    at is.hail.backend.spark.SparkBackend$$anonfun$execute$1.apply(SparkBackend.scala:304)
    at is.hail.backend.spark.SparkBackend$$anonfun$execute$1.apply(SparkBackend.scala:303)
    at is.hail.expr.ir.ExecuteContext$$anonfun$scoped$1.apply(ExecuteContext.scala:20)
    at is.hail.expr.ir.ExecuteContext$$anonfun$scoped$1.apply(ExecuteContext.scala:18)
    at is.hail.utils.package$.using(package.scala:601)
    at is.hail.annotations.Region$.scoped(Region.scala:18)
    at is.hail.expr.ir.ExecuteContext$.scoped(ExecuteContext.scala:18)
    at is.hail.backend.spark.SparkBackend.withExecuteContext(SparkBackend.scala:229)
    at is.hail.backend.spark.SparkBackend.execute(SparkBackend.scala:303)
    at is.hail.backend.spark.SparkBackend.executeJSON(SparkBackend.scala:323)
    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:282)
    at py4j.commands.AbstractCommand.invokeMethod(AbstractCommand.java:132)
    at py4j.commands.CallCommand.execute(CallCommand.java:79)
    at py4j.GatewayConnection.run(GatewayConnection.java:238)
    at java.lang.Thread.run(Thread.java:748)

java.io.IOException: Stream is closed!
    at org.apache.hadoop.fs.azurebfs.services.AbfsOutputStream.close(AbfsOutputStream.java:244)
    at org.apache.hadoop.fs.FSDataOutputStream$PositionCache.close(FSDataOutputStream.java:72)
    at org.apache.hadoop.fs.FSDataOutputStream.close(FSDataOutputStream.java:101)
    at is.hail.io.fs.HadoopFS$$anon$1.close(HadoopFS.scala:39)
    at java.io.FilterOutputStream.close(FilterOutputStream.java:159
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