AttributeError: 'DataFrame' object has no attribute 'to_spark'

nnekaede · July 22, 2018, 8:01pm

I am trying to covert a Hail table to a pandas dataframe:
kk2 = hl.Table.to_pandas(table1) # convert to pandas
I am not sure why I am getting this error:

---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)
<ipython-input-32-fe9d61b0850f> in <module>()
----> 1 kk2 = hl.Table.to_pandas(table1) # convert to pandas

/home/hail/hail.zip/hail/typecheck/check.py in wrapper(*args, **kwargs)
    545         def wrapper(*args, **kwargs):
    546             args_, kwargs_ = check_all(f, args, kwargs, checkers, is_method=is_method)
--> 547             return f(*args_, **kwargs_)
    548 
    549         update_wrapper(wrapper, f)

/home/hail/hail.zip/hail/table.py in to_pandas(self, flatten)
   2496 
   2497         """
-> 2498         return self.to_spark(flatten).toPandas()
   2499 
   2500     @staticmethod

/opt/conda/lib/python3.6/site-packages/pandas/core/generic.py in __getattr__(self, name)
   4374             if self._info_axis._can_hold_identifiers_and_holds_name(name):
   4375                 return self[name]
-> 4376             return object.__getattribute__(self, name)
   4377 
   4378     def __setattr__(self, name, value):

AttributeError: 'DataFrame' object has no attribute 'to_spark'

tpoterba · July 22, 2018, 11:00pm

ha, that’s a funny error. table1 is already a dataframe. Is it a pandas or spark dataframe?

nnekaede · July 23, 2018, 12:05am

You are right! I reran the cell and didn’t realize.

tpoterba · July 23, 2018, 12:48am

also, ht.to_pandas() is easier (but equivalent to) hl.Table.to_pandas(ht)

cdeniz · July 31, 2018, 10:19pm

Tim,

I’m having an issue with to_pandas(). This is my code:

print(type(vds.cols()))
print(vds.cols().count())

My output:

<class 'hail.table.Table'>
1886

Then I do:

df = vds.cols().to_pandas()

and this is the error:

---------------------------------------------------------------------------
FatalError                                Traceback (most recent call last)
<ipython-input-16-e6ec246e33e1> in <module>()
----> 1 df = vds.cols().to_pandas()

~/hail-python.zip/hail/typecheck/check.py in wrapper(*args, **kwargs)
    545         def wrapper(*args, **kwargs):
    546             args_, kwargs_ = check_all(f, args, kwargs, checkers, is_method=is_method)
--> 547             return f(*args_, **kwargs_)
    548 
    549         update_wrapper(wrapper, f)

~/hail-python.zip/hail/table.py in to_pandas(self, flatten)
   2493 
   2494         """
-> 2495         return self.to_spark(flatten).toPandas()
   2496 
   2497     @staticmethod

~/hail-python.zip/hail/typecheck/check.py in wrapper(*args, **kwargs)
    545         def wrapper(*args, **kwargs):
    546             args_, kwargs_ = check_all(f, args, kwargs, checkers, is_method=is_method)
--> 547             return f(*args_, **kwargs_)
    548 
    549         update_wrapper(wrapper, f)

~/hail-python.zip/hail/table.py in to_spark(self, flatten)
   2470         """
   2471         jt = self._jt
-> 2472         jt = jt.expandTypes()
   2473         if flatten:
   2474             jt = jt.flatten()

/usr/lib/spark/python/lib/py4j-src.zip/py4j/java_gateway.py in __call__(self, *args)
   1131         answer = self.gateway_client.send_command(command)
   1132         return_value = get_return_value(
-> 1133             answer, self.gateway_client, self.target_id, self.name)
   1134 
   1135         for temp_arg in temp_args:

~/hail-python.zip/hail/utils/java.py in deco(*args, **kwargs)
    198             raise FatalError('%s\n\nJava stack trace:\n%s\n'
    199                              'Hail version: %s\n'
--> 200                              'Error summary: %s' % (deepest, full, hail.__version__, deepest)) from None
    201         except pyspark.sql.utils.CapturedException as e:
    202             raise FatalError('%s\n\nJava stack trace:\n%s\n'

FatalError: ConnectionPoolTimeoutException: Timeout waiting for connection from pool

Java stack trace:
org.apache.spark.SparkException: Job aborted due to stage failure: Task 2 in stage 24.0 failed 4 times, most recent failure: Lost task 2.3 in stage 24.0 (TID 1178, ip-172-31-36-114.ec2.internal, executor 1): com.amazon.ws.emr.hadoop.fs.shaded.com.amazonaws.SdkClientException: Unable to execute HTTP request: Timeout waiting for connection from pool
	at com.amazon.ws.emr.hadoop.fs.shaded.com.amazonaws.http.AmazonHttpClient$RequestExecutor.handleRetryableException(AmazonHttpClient.java:1069)
	at com.amazon.ws.emr.hadoop.fs.shaded.com.amazonaws.http.AmazonHttpClient$RequestExecutor.executeHelper(AmazonHttpClient.java:1035)
	at com.amazon.ws.emr.hadoop.fs.shaded.com.amazonaws.http.AmazonHttpClient$RequestExecutor.doExecute(AmazonHttpClient.java:742)
	at com.amazon.ws.emr.hadoop.fs.shaded.com.amazonaws.http.AmazonHttpClient$RequestExecutor.executeWithTimer(AmazonHttpClient.java:716)
	at com.amazon.ws.emr.hadoop.fs.shaded.com.amazonaws.http.AmazonHttpClient$RequestExecutor.execute(AmazonHttpClient.java:699)
	at com.amazon.ws.emr.hadoop.fs.shaded.com.amazonaws.http.AmazonHttpClient$RequestExecutor.access$500(AmazonHttpClient.java:667)
	at com.amazon.ws.emr.hadoop.fs.shaded.com.amazonaws.http.AmazonHttpClient$RequestExecutionBuilderImpl.execute(AmazonHttpClient.java:649)
	at com.amazon.ws.emr.hadoop.fs.shaded.com.amazonaws.http.AmazonHttpClient.execute(AmazonHttpClient.java:513)
	at com.amazon.ws.emr.hadoop.fs.shaded.com.amazonaws.services.s3.AmazonS3Client.invoke(AmazonS3Client.java:4169)
	at com.amazon.ws.emr.hadoop.fs.shaded.com.amazonaws.services.s3.AmazonS3Client.invoke(AmazonS3Client.java:4116)
	at com.amazon.ws.emr.hadoop.fs.shaded.com.amazonaws.services.s3.AmazonS3Client.getObjectMetadata(AmazonS3Client.java:1237)
	at com.amazon.ws.emr.hadoop.fs.s3.lite.call.GetObjectMetadataCall.perform(GetObjectMetadataCall.java:23)
	at com.amazon.ws.emr.hadoop.fs.s3.lite.call.GetObjectMetadataCall.perform(GetObjectMetadataCall.java:9)
	at com.amazon.ws.emr.hadoop.fs.s3.lite.executor.GlobalS3Executor.execute(GlobalS3Executor.java:80)
	at com.amazon.ws.emr.hadoop.fs.s3.lite.AmazonS3LiteClient.invoke(AmazonS3LiteClient.java:176)
	at com.amazon.ws.emr.hadoop.fs.s3.lite.AmazonS3LiteClient.getObjectMetadata(AmazonS3LiteClient.java:94)
	at com.amazon.ws.emr.hadoop.fs.s3.lite.AbstractAmazonS3Lite.getObjectMetadata(AbstractAmazonS3Lite.java:39)
	at com.amazon.ws.emr.hadoop.fs.s3n.Jets3tNativeFileSystemStore.retrieveMetadata(Jets3tNativeFileSystemStore.java:211)
	at sun.reflect.GeneratedMethodAccessor148.invoke(Unknown Source)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at org.apache.hadoop.io.retry.RetryInvocationHandler.invokeMethod(RetryInvocationHandler.java:191)
	at org.apache.hadoop.io.retry.RetryInvocationHandler.invoke(RetryInvocationHandler.java:102)
	at com.sun.proxy.$Proxy30.retrieveMetadata(Unknown Source)
	at com.amazon.ws.emr.hadoop.fs.s3n.S3NativeFileSystem.getFileStatus(S3NativeFileSystem.java:778)
	at com.amazon.ws.emr.hadoop.fs.s3n.S3NativeFileSystem.open(S3NativeFileSystem.java:1206)
	at org.apache.hadoop.fs.FileSystem.open(FileSystem.java:773)
	at com.amazon.ws.emr.hadoop.fs.EmrFileSystem.open(EmrFileSystem.java:166)
	at is.hail.utils.richUtils.RichHadoopConfiguration$.is$hail$utils$richUtils$RichHadoopConfiguration$$open$extension(RichHadoopConfiguration.scala:37)
	at is.hail.utils.richUtils.RichHadoopConfiguration$.unsafeReader$extension(RichHadoopConfiguration.scala:305)
	at is.hail.HailContext$$anon$1.compute(HailContext.scala:544)
	at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323)
	at org.apache.spark.rdd.RDD.iterator(RDD.scala:287)
	at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
	at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323)
	at org.apache.spark.rdd.RDD.iterator(RDD.scala:287)
	at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
	at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323)
	at org.apache.spark.rdd.RDD.iterator(RDD.scala:287)
	at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
	at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323)
	at org.apache.spark.rdd.RDD.iterator(RDD.scala:287)
	at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
	at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323)
	at org.apache.spark.rdd.RDD.iterator(RDD.scala:287)
	at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
	at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323)
	at org.apache.spark.rdd.RDD.iterator(RDD.scala:287)
	at org.apache.spark.rdd.ZippedPartitionsRDD2.compute(ZippedPartitionsRDD.scala:89)
	at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323)
	at org.apache.spark.rdd.RDD.iterator(RDD.scala:287)
	at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
	at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323)
	at org.apache.spark.rdd.RDD.iterator(RDD.scala:287)
	at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
	at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323)
	at org.apache.spark.rdd.RDD.iterator(RDD.scala:287)
	at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
	at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323)
	at org.apache.spark.rdd.RDD.iterator(RDD.scala:287)
	at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
	at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323)
	at org.apache.spark.rdd.RDD.iterator(RDD.scala:287)
	at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:87)
	at org.apache.spark.scheduler.Task.run(Task.scala:108)
	at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:335)
	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)
Caused by: com.amazon.ws.emr.hadoop.fs.shaded.org.apache.http.conn.ConnectionPoolTimeoutException: Timeout waiting for connection from pool
	at com.amazon.ws.emr.hadoop.fs.shaded.org.apache.http.impl.conn.PoolingHttpClientConnectionManager.leaseConnection(PoolingHttpClientConnectionManager.java:286)
	at com.amazon.ws.emr.hadoop.fs.shaded.org.apache.http.impl.conn.PoolingHttpClientConnectionManager$1.get(PoolingHttpClientConnectionManager.java:263)
	at sun.reflect.GeneratedMethodAccessor151.invoke(Unknown Source)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at com.amazon.ws.emr.hadoop.fs.shaded.com.amazonaws.http.conn.ClientConnectionRequestFactory$Handler.invoke(ClientConnectionRequestFactory.java:70)
	at com.amazon.ws.emr.hadoop.fs.shaded.com.amazonaws.http.conn.$Proxy32.get(Unknown Source)
	at com.amazon.ws.emr.hadoop.fs.shaded.org.apache.http.impl.execchain.MainClientExec.execute(MainClientExec.java:190)
	at com.amazon.ws.emr.hadoop.fs.shaded.org.apache.http.impl.execchain.ProtocolExec.execute(ProtocolExec.java:184)
	at com.amazon.ws.emr.hadoop.fs.shaded.org.apache.http.impl.client.InternalHttpClient.doExecute(InternalHttpClient.java:184)
	at com.amazon.ws.emr.hadoop.fs.shaded.org.apache.http.impl.client.CloseableHttpClient.execute(CloseableHttpClient.java:82)
	at com.amazon.ws.emr.hadoop.fs.shaded.org.apache.http.impl.client.CloseableHttpClient.execute(CloseableHttpClient.java:55)
	at com.amazon.ws.emr.hadoop.fs.shaded.com.amazonaws.http.apache.client.impl.SdkHttpClient.execute(SdkHttpClient.java:72)
	at com.amazon.ws.emr.hadoop.fs.shaded.com.amazonaws.http.AmazonHttpClient$RequestExecutor.executeOneRequest(AmazonHttpClient.java:1190)
	at com.amazon.ws.emr.hadoop.fs.shaded.com.amazonaws.http.AmazonHttpClient$RequestExecutor.executeHelper(AmazonHttpClient.java:1030)
	... 67 more

Driver stacktrace:
	at org.apache.spark.scheduler.DAGScheduler.org$apache$spark$scheduler$DAGScheduler$$failJobAndIndependentStages(DAGScheduler.scala:1690)
	at org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1678)
	at org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1677)
	at scala.collection.mutable.ResizableArray$class.foreach(ResizableArray.scala:59)
	at scala.collection.mutable.ArrayBuffer.foreach(ArrayBuffer.scala:48)
	at org.apache.spark.scheduler.DAGScheduler.abortStage(DAGScheduler.scala:1677)
	at org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:855)
	at org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:855)
	at scala.Option.foreach(Option.scala:257)
	at org.apache.spark.scheduler.DAGScheduler.handleTaskSetFailed(DAGScheduler.scala:855)
	at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.doOnReceive(DAGScheduler.scala:1905)
	at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:1860)
	at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:1849)
	at org.apache.spark.util.EventLoop$$anon$1.run(EventLoop.scala:48)
	at org.apache.spark.scheduler.DAGScheduler.runJob(DAGScheduler.scala:671)
	at org.apache.spark.SparkContext.runJob(SparkContext.scala:2022)
	at org.apache.spark.SparkContext.runJob(SparkContext.scala:2119)
	at org.apache.spark.rdd.RDD$$anonfun$reduce$1.apply(RDD.scala:1026)
	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.reduce(RDD.scala:1008)
	at is.hail.sparkextras.ContextRDD.treeAggregate(ContextRDD.scala:276)
	at is.hail.sparkextras.ContextRDD.treeAggregate(ContextRDD.scala:227)
	at is.hail.rvd.RVD$class.treeAggregate(RVD.scala:339)
	at is.hail.rvd.OrderedRVD.treeAggregate(OrderedRVD.scala:32)
	at is.hail.expr.ir.MatrixMapCols.execute(MatrixIR.scala:1505)
	at is.hail.expr.ir.MatrixColsTable.execute(TableIR.scala:765)
	at is.hail.expr.ir.TableMapRows.execute(TableIR.scala:453)
	at is.hail.expr.ir.TableMapRows.execute(TableIR.scala:453)
	at is.hail.table.Table.value$lzycompute(Table.scala:215)
	at is.hail.table.Table.value(Table.scala:213)
	at is.hail.table.Table.x$5$lzycompute(Table.scala:218)
	at is.hail.table.Table.x$5(Table.scala:218)
	at is.hail.table.Table.rvd$lzycompute(Table.scala:218)
	at is.hail.table.Table.rvd(Table.scala:218)
	at is.hail.table.Table.expandTypes(Table.scala:555)
	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)com.amazon.ws.emr.hadoop.fs.shaded.com.amazonaws.SdkClientException: Unable to execute HTTP request: Timeout waiting for connection from pool
	at com.amazon.ws.emr.hadoop.fs.shaded.com.amazonaws.http.AmazonHttpClient$RequestExecutor.handleRetryableException(AmazonHttpClient.java:1069)
	at com.amazon.ws.emr.hadoop.fs.shaded.com.amazonaws.http.AmazonHttpClient$RequestExecutor.executeHelper(AmazonHttpClient.java:1035)
	at com.amazon.ws.emr.hadoop.fs.shaded.com.amazonaws.http.AmazonHttpClient$RequestExecutor.doExecute(AmazonHttpClient.java:742)
	at com.amazon.ws.emr.hadoop.fs.shaded.com.amazonaws.http.AmazonHttpClient$RequestExecutor.executeWithTimer(AmazonHttpClient.java:716)
	at com.amazon.ws.emr.hadoop.fs.shaded.com.amazonaws.http.AmazonHttpClient$RequestExecutor.execute(AmazonHttpClient.java:699)
	at com.amazon.ws.emr.hadoop.fs.shaded.com.amazonaws.http.AmazonHttpClient$RequestExecutor.access$500(AmazonHttpClient.java:667)
	at com.amazon.ws.emr.hadoop.fs.shaded.com.amazonaws.http.AmazonHttpClient$RequestExecutionBuilderImpl.execute(AmazonHttpClient.java:649)
	at com.amazon.ws.emr.hadoop.fs.shaded.com.amazonaws.http.AmazonHttpClient.execute(AmazonHttpClient.java:513)
	at com.amazon.ws.emr.hadoop.fs.shaded.com.amazonaws.services.s3.AmazonS3Client.invoke(AmazonS3Client.java:4169)
	at com.amazon.ws.emr.hadoop.fs.shaded.com.amazonaws.services.s3.AmazonS3Client.invoke(AmazonS3Client.java:4116)
	at com.amazon.ws.emr.hadoop.fs.shaded.com.amazonaws.services.s3.AmazonS3Client.getObjectMetadata(AmazonS3Client.java:1237)
	at com.amazon.ws.emr.hadoop.fs.s3.lite.call.GetObjectMetadataCall.perform(GetObjectMetadataCall.java:23)
	at com.amazon.ws.emr.hadoop.fs.s3.lite.call.GetObjectMetadataCall.perform(GetObjectMetadataCall.java:9)
	at com.amazon.ws.emr.hadoop.fs.s3.lite.executor.GlobalS3Executor.execute(GlobalS3Executor.java:80)
	at com.amazon.ws.emr.hadoop.fs.s3.lite.AmazonS3LiteClient.invoke(AmazonS3LiteClient.java:176)
	at com.amazon.ws.emr.hadoop.fs.s3.lite.AmazonS3LiteClient.getObjectMetadata(AmazonS3LiteClient.java:94)
	at com.amazon.ws.emr.hadoop.fs.s3.lite.AbstractAmazonS3Lite.getObjectMetadata(AbstractAmazonS3Lite.java:39)
	at com.amazon.ws.emr.hadoop.fs.s3n.Jets3tNativeFileSystemStore.retrieveMetadata(Jets3tNativeFileSystemStore.java:211)
	at sun.reflect.GeneratedMethodAccessor148.invoke(Unknown Source)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at org.apache.hadoop.io.retry.RetryInvocationHandler.invokeMethod(RetryInvocationHandler.java:191)
	at org.apache.hadoop.io.retry.RetryInvocationHandler.invoke(RetryInvocationHandler.java:102)
	at com.sun.proxy.$Proxy30.retrieveMetadata(Unknown Source)
	at com.amazon.ws.emr.hadoop.fs.s3n.S3NativeFileSystem.getFileStatus(S3NativeFileSystem.java:778)
	at com.amazon.ws.emr.hadoop.fs.s3n.S3NativeFileSystem.open(S3NativeFileSystem.java:1206)
	at org.apache.hadoop.fs.FileSystem.open(FileSystem.java:773)
	at com.amazon.ws.emr.hadoop.fs.EmrFileSystem.open(EmrFileSystem.java:166)
	at is.hail.utils.richUtils.RichHadoopConfiguration$.is$hail$utils$richUtils$RichHadoopConfiguration$$open$extension(RichHadoopConfiguration.scala:37)
	at is.hail.utils.richUtils.RichHadoopConfiguration$.unsafeReader$extension(RichHadoopConfiguration.scala:305)
	at is.hail.HailContext$$anon$1.compute(HailContext.scala:544)
	at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323)
	at org.apache.spark.rdd.RDD.iterator(RDD.scala:287)
	at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
	at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323)
	at org.apache.spark.rdd.RDD.iterator(RDD.scala:287)
	at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
	at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323)
	at org.apache.spark.rdd.RDD.iterator(RDD.scala:287)
	at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
	at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323)
	at org.apache.spark.rdd.RDD.iterator(RDD.scala:287)
	at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
	at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323)
	at org.apache.spark.rdd.RDD.iterator(RDD.scala:287)
	at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
	at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323)
	at org.apache.spark.rdd.RDD.iterator(RDD.scala:287)
	at org.apache.spark.rdd.ZippedPartitionsRDD2.compute(ZippedPartitionsRDD.scala:89)
	at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323)
	at org.apache.spark.rdd.RDD.iterator(RDD.scala:287)
	at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
	at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323)
	at org.apache.spark.rdd.RDD.iterator(RDD.scala:287)
	at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
	at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323)
	at org.apache.spark.rdd.RDD.iterator(RDD.scala:287)
	at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
	at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323)
	at org.apache.spark.rdd.RDD.iterator(RDD.scala:287)
	at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
	at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323)
	at org.apache.spark.rdd.RDD.iterator(RDD.scala:287)
	at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:87)
	at org.apache.spark.scheduler.Task.run(Task.scala:108)
	at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:335)
	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)com.amazon.ws.emr.hadoop.fs.shaded.org.apache.http.conn.ConnectionPoolTimeoutException: Timeout waiting for connection from pool
	at com.amazon.ws.emr.hadoop.fs.shaded.org.apache.http.impl.conn.PoolingHttpClientConnectionManager.leaseConnection(PoolingHttpClientConnectionManager.java:286)
	at com.amazon.ws.emr.hadoop.fs.shaded.org.apache.http.impl.conn.PoolingHttpClientConnectionManager$1.get(PoolingHttpClientConnectionManager.java:263)
	at sun.reflect.GeneratedMethodAccessor151.invoke(Unknown Source)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at com.amazon.ws.emr.hadoop.fs.shaded.com.amazonaws.http.conn.ClientConnectionRequestFactory$Handler.invoke(ClientConnectionRequestFactory.java:70)
	at com.amazon.ws.emr.hadoop.fs.shaded.com.amazonaws.http.conn.$Proxy32.get(Unknown Source)
	at com.amazon.ws.emr.hadoop.fs.shaded.org.apache.http.impl.execchain.MainClientExec.execute(MainClientExec.java:190)
	at com.amazon.ws.emr.hadoop.fs.shaded.org.apache.http.impl.execchain.ProtocolExec.execute(ProtocolExec.java:184)
	at com.amazon.ws.emr.hadoop.fs.shaded.org.apache.http.impl.client.InternalHttpClient.doExecute(InternalHttpClient.java:184)
	at com.amazon.ws.emr.hadoop.fs.shaded.org.apache.http.impl.client.CloseableHttpClient.execute(CloseableHttpClient.java:82)
	at com.amazon.ws.emr.hadoop.fs.shaded.org.apache.http.impl.client.CloseableHttpClient.execute(CloseableHttpClient.java:55)
	at com.amazon.ws.emr.hadoop.fs.shaded.com.amazonaws.http.apache.client.impl.SdkHttpClient.execute(SdkHttpClient.java:72)
	at com.amazon.ws.emr.hadoop.fs.shaded.com.amazonaws.http.AmazonHttpClient$RequestExecutor.executeOneRequest(AmazonHttpClient.java:1190)
	at com.amazon.ws.emr.hadoop.fs.shaded.com.amazonaws.http.AmazonHttpClient$RequestExecutor.executeHelper(AmazonHttpClient.java:1030)
	at com.amazon.ws.emr.hadoop.fs.shaded.com.amazonaws.http.AmazonHttpClient$RequestExecutor.doExecute(AmazonHttpClient.java:742)
	at com.amazon.ws.emr.hadoop.fs.shaded.com.amazonaws.http.AmazonHttpClient$RequestExecutor.executeWithTimer(AmazonHttpClient.java:716)
	at com.amazon.ws.emr.hadoop.fs.shaded.com.amazonaws.http.AmazonHttpClient$RequestExecutor.execute(AmazonHttpClient.java:699)
	at com.amazon.ws.emr.hadoop.fs.shaded.com.amazonaws.http.AmazonHttpClient$RequestExecutor.access$500(AmazonHttpClient.java:667)
	at com.amazon.ws.emr.hadoop.fs.shaded.com.amazonaws.http.AmazonHttpClient$RequestExecutionBuilderImpl.execute(AmazonHttpClient.java:649)
	at com.amazon.ws.emr.hadoop.fs.shaded.com.amazonaws.http.AmazonHttpClient.execute(AmazonHttpClient.java:513)
	at com.amazon.ws.emr.hadoop.fs.shaded.com.amazonaws.services.s3.AmazonS3Client.invoke(AmazonS3Client.java:4169)
	at com.amazon.ws.emr.hadoop.fs.shaded.com.amazonaws.services.s3.AmazonS3Client.invoke(AmazonS3Client.java:4116)
	at com.amazon.ws.emr.hadoop.fs.shaded.com.amazonaws.services.s3.AmazonS3Client.getObjectMetadata(AmazonS3Client.java:1237)
	at com.amazon.ws.emr.hadoop.fs.s3.lite.call.GetObjectMetadataCall.perform(GetObjectMetadataCall.java:23)
	at com.amazon.ws.emr.hadoop.fs.s3.lite.call.GetObjectMetadataCall.perform(GetObjectMetadataCall.java:9)
	at com.amazon.ws.emr.hadoop.fs.s3.lite.executor.GlobalS3Executor.execute(GlobalS3Executor.java:80)
	at com.amazon.ws.emr.hadoop.fs.s3.lite.AmazonS3LiteClient.invoke(AmazonS3LiteClient.java:176)
	at com.amazon.ws.emr.hadoop.fs.s3.lite.AmazonS3LiteClient.getObjectMetadata(AmazonS3LiteClient.java:94)
	at com.amazon.ws.emr.hadoop.fs.s3.lite.AbstractAmazonS3Lite.getObjectMetadata(AbstractAmazonS3Lite.java:39)
	at com.amazon.ws.emr.hadoop.fs.s3n.Jets3tNativeFileSystemStore.retrieveMetadata(Jets3tNativeFileSystemStore.java:211)
	at sun.reflect.GeneratedMethodAccessor148.invoke(Unknown Source)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at org.apache.hadoop.io.retry.RetryInvocationHandler.invokeMethod(RetryInvocationHandler.java:191)
	at org.apache.hadoop.io.retry.RetryInvocationHandler.invoke(RetryInvocationHandler.java:102)
	at com.sun.proxy.$Proxy30.retrieveMetadata(Unknown Source)
	at com.amazon.ws.emr.hadoop.fs.s3n.S3NativeFileSystem.getFileStatus(S3NativeFileSystem.java:778)
	at com.amazon.ws.emr.hadoop.fs.s3n.S3NativeFileSystem.open(S3NativeFileSystem.java:1206)
	at org.apache.hadoop.fs.FileSystem.open(FileSystem.java:773)
	at com.amazon.ws.emr.hadoop.fs.EmrFileSystem.open(EmrFileSystem.java:166)
	at is.hail.utils.richUtils.RichHadoopConfiguration$.is$hail$utils$richUtils$RichHadoopConfiguration$$open$extension(RichHadoopConfiguration.scala:37)
	at is.hail.utils.richUtils.RichHadoopConfiguration$.unsafeReader$extension(RichHadoopConfiguration.scala:305)
	at is.hail.HailContext$$anon$1.compute(HailContext.scala:544)
	at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323)
	at org.apache.spark.rdd.RDD.iterator(RDD.scala:287)
	at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
	at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323)
	at org.apache.spark.rdd.RDD.iterator(RDD.scala:287)
	at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
	at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323)
	at org.apache.spark.rdd.RDD.iterator(RDD.scala:287)
	at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
	at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323)
	at org.apache.spark.rdd.RDD.iterator(RDD.scala:287)
	at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
	at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323)
	at org.apache.spark.rdd.RDD.iterator(RDD.scala:287)
	at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
	at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323)
	at org.apache.spark.rdd.RDD.iterator(RDD.scala:287)
	at org.apache.spark.rdd.ZippedPartitionsRDD2.compute(ZippedPartitionsRDD.scala:89)
	at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323)
	at org.apache.spark.rdd.RDD.iterator(RDD.scala:287)
	at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
	at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323)
	at org.apache.spark.rdd.RDD.iterator(RDD.scala:287)
	at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
	at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323)
	at org.apache.spark.rdd.RDD.iterator(RDD.scala:287)
	at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
	at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323)
	at org.apache.spark.rdd.RDD.iterator(RDD.scala:287)
	at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
	at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323)
	at org.apache.spark.rdd.RDD.iterator(RDD.scala:287)
	at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:87)
	at org.apache.spark.scheduler.Task.run(Task.scala:108)
	at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:335)
	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: devel-2f56d75b2729
Error summary: ConnectionPoolTimeoutException: Timeout waiting for connection from pool

tpoterba · July 31, 2018, 10:35pm

Can I see the full pipeline? This looks like an AWS-specific Spark configuration problem.

cdeniz · August 1, 2018, 12:16pm

We are using spark 2.2.0. Everything works fine in this script, but the export to pandas:

import hail as hl
hl.init # --> version devel-2f56d75b2729
import numpy as np
import pandas as pd
vds = hl.read_matrix_table("s3://genotype_calls.mt")
table = (hl.import_table('s3://annotations.txt', impute=True,.key_by('Samples'))
type(table) # --> hail.table.Table
vds = vds.annotate_cols(**table[vds.s])
vds = hl.sample_qc(vds) 
df = vds.cols().to_pandas()

tpoterba · August 1, 2018, 12:45pm

One of the most important things to understand about debugging Hail scripts is that errors don’t always appear where you expect them to. Most operations in Hail record the computation, but don’t eagerly execute that computation. Instead, the entire pipeline is optimized, compiled, and executed every time you request that data “leaves Hail” – meaning a write, an aggregation, etc. This is a critical component of scalable systems. Here, the sample_qc and vds.cols().to_pandas() are all executed together in the last line of the script.

I do have one idea – can you try changing s3 to s3a? I believe that will use a different file system API which works much better with Spark.

cdeniz · August 1, 2018, 1:54pm

It didn’t find the s3a file system:

FatalError: ClassNotFoundException: Class org.apache.hadoop.fs.s3a.S3AFileSystem not found

Java stack trace:
java.lang.RuntimeException: java.lang.ClassNotFoundException: Class org.apache.hadoop.fs.s3a.S3AFileSystem not found
	at org.apache.hadoop.conf.Configuration.getClass(Configuration.java:2195)
	at org.apache.hadoop.fs.FileSystem.getFileSystemClass(FileSystem.java:2702)
	at org.apache.hadoop.fs.FileSystem.createFileSystem(FileSystem.java:2715)
	at org.apache.hadoop.fs.FileSystem.access$200(FileSystem.java:93)
	at org.apache.hadoop.fs.FileSystem$Cache.getInternal(FileSystem.java:2751)
	at org.apache.hadoop.fs.FileSystem$Cache.get(FileSystem.java:2733)
	at org.apache.hadoop.fs.FileSystem.get(FileSystem.java:377)
	at org.apache.hadoop.fs.Path.getFileSystem(Path.java:295)
	at is.hail.utils.richUtils.RichHadoopConfiguration$.fileSystem$extension(RichHadoopConfiguration.scala:19)
	at is.hail.utils.richUtils.RichHadoopConfiguration$.isDir$extension(RichHadoopConfiguration.scala:59)
	at is.hail.variant.RelationalSpec$.read(MatrixTable.scala:44)
	at is.hail.expr.ir.MatrixNativeReader.<init>(MatrixIR.scala:208)
	at is.hail.expr.ir.MatrixIR$.read(MatrixIR.scala:24)
	at is.hail.variant.MatrixTable$.read(MatrixTable.scala:129)
	at is.hail.HailContext.read(HailContext.scala:517)
	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: Class org.apache.hadoop.fs.s3a.S3AFileSystem not found
	at org.apache.hadoop.conf.Configuration.getClassByName(Configuration.java:2101)
	at org.apache.hadoop.conf.Configuration.getClass(Configuration.java:2193)
	at org.apache.hadoop.fs.FileSystem.getFileSystemClass(FileSystem.java:2702)
	at org.apache.hadoop.fs.FileSystem.createFileSystem(FileSystem.java:2715)
	at org.apache.hadoop.fs.FileSystem.access$200(FileSystem.java:93)
	at org.apache.hadoop.fs.FileSystem$Cache.getInternal(FileSystem.java:2751)
	at org.apache.hadoop.fs.FileSystem$Cache.get(FileSystem.java:2733)
	at org.apache.hadoop.fs.FileSystem.get(FileSystem.java:377)
	at org.apache.hadoop.fs.Path.getFileSystem(Path.java:295)
	at is.hail.utils.richUtils.RichHadoopConfiguration$.fileSystem$extension(RichHadoopConfiguration.scala:19)
	at is.hail.utils.richUtils.RichHadoopConfiguration$.isDir$extension(RichHadoopConfiguration.scala:59)
	at is.hail.variant.RelationalSpec$.read(MatrixTable.scala:44)
	at is.hail.expr.ir.MatrixNativeReader.<init>(MatrixIR.scala:208)
	at is.hail.expr.ir.MatrixIR$.read(MatrixIR.scala:24)
	at is.hail.variant.MatrixTable$.read(MatrixTable.scala:129)
	at is.hail.HailContext.read(HailContext.scala:517)
	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)

tpoterba · August 1, 2018, 2:07pm

how are you running on AWS? are you using EMR?

cdeniz · August 1, 2018, 2:07pm

Yes, EMR.

tpoterba · August 1, 2018, 2:13pm

https://aws.amazon.com/premiumsupport/knowledge-center/emr-file-system-s3/

try s3n

cdeniz · August 1, 2018, 2:26pm

I reads from s3n but the export to pandas still times out:

FatalError: ConnectionPoolTimeoutException: Timeout waiting for connection from pool

And the table is not that big though:

vds.rows().select().show(3)
output:
+---------------+------------+
| locus         | alleles    |
+---------------+------------+
| locus<GRCh37> | array<str> |
+---------------+------------+
| 1:10472       | ["G","T"]  |
| 1:10482       | ["G","A"]  |
| 1:10483       | ["C","G"]  |
+---------------+------------+

vds.cols().count() # -->1,886

Yes, this might be an amazon issue as I asked someone else to try in Google dataproc and it works.

tpoterba · August 1, 2018, 3:43pm

OK, interesting. We’ll have to read up on how the S3 connection pool works – maybe you just need to increase the connection pool.

tpoterba · August 1, 2018, 3:48pm

There seems to be a lot of weird interplay between Spark / s3 / s3a. I don’t really have time to look into this, but I think you’re looking for something like the spark.hadoop.fs.s3a.connection.maximum configuration parameter, but for s3

cdeniz · August 1, 2018, 3:56pm

I was monitoring the CPU and memory activity and the export task is not demanding a lot of resources. We were wondering yesterday if there is a spark setup to enable memory and cpu use to consume all the resources. I don’t see more than 12GB of RAM used and the CPU goes up to ~65% max.

This is the output I get for s3 and s3n:

FatalError: ConnectionPoolTimeoutException: Timeout waiting for connection from pool

Java stack trace:
org.apache.spark.SparkException: Job aborted due to stage failure: Task 52 in stage 6.0 failed 4 times, most recent failure: Lost task 52.3 in stage 6.0 (TID 112, ip-172-31-36-114.ec2.internal, executor 1): com.amazon.ws.emr.hadoop.fs.shaded.com.amazonaws.SdkClientException: Unable to execute HTTP request: Timeout waiting for connection from pool
	at com.amazon.ws.emr.hadoop.fs.shaded.com.amazonaws.http.AmazonHttpClient$RequestExecutor.handleRetryableException(AmazonHttpClient.java:1069)
	at com.amazon.ws.emr.hadoop.fs.shaded.com.amazonaws.http.AmazonHttpClient$RequestExecutor.executeHelper(AmazonHttpClient.java:1035)
	at com.amazon.ws.emr.hadoop.fs.shaded.com.amazonaws.http.AmazonHttpClient$RequestExecutor.doExecute(AmazonHttpClient.java:742)
	at com.amazon.ws.emr.hadoop.fs.shaded.com.amazonaws.http.AmazonHttpClient$RequestExecutor.executeWithTimer(AmazonHttpClient.java:716)
	at com.amazon.ws.emr.hadoop.fs.shaded.com.amazonaws.http.AmazonHttpClient$RequestExecutor.execute(AmazonHttpClient.java:699)
	at com.amazon.ws.emr.hadoop.fs.shaded.com.amazonaws.http.AmazonHttpClient$RequestExecutor.access$500(AmazonHttpClient.java:667)
	at com.amazon.ws.emr.hadoop.fs.shaded.com.amazonaws.http.AmazonHttpClient$RequestExecutionBuilderImpl.execute(AmazonHttpClient.java:649)
	at com.amazon.ws.emr.hadoop.fs.shaded.com.amazonaws.http.AmazonHttpClient.execute(AmazonHttpClient.java:513)
	at com.amazon.ws.emr.hadoop.fs.shaded.com.amazonaws.services.s3.AmazonS3Client.invoke(AmazonS3Client.java:4169)
	at com.amazon.ws.emr.hadoop.fs.shaded.com.amazonaws.services.s3.AmazonS3Client.invoke(AmazonS3Client.java:4116)
	at com.amazon.ws.emr.hadoop.fs.shaded.com.amazonaws.services.s3.AmazonS3Client.getObjectMetadata(AmazonS3Client.java:1237)
	at com.amazon.ws.emr.hadoop.fs.s3.lite.call.GetObjectMetadataCall.perform(GetObjectMetadataCall.java:23)
	at com.amazon.ws.emr.hadoop.fs.s3.lite.call.GetObjectMetadataCall.perform(GetObjectMetadataCall.java:9)
	at com.amazon.ws.emr.hadoop.fs.s3.lite.executor.GlobalS3Executor.execute(GlobalS3Executor.java:80)
	at com.amazon.ws.emr.hadoop.fs.s3.lite.AmazonS3LiteClient.invoke(AmazonS3LiteClient.java:176)
	at com.amazon.ws.emr.hadoop.fs.s3.lite.AmazonS3LiteClient.getObjectMetadata(AmazonS3LiteClient.java:94)
	at com.amazon.ws.emr.hadoop.fs.s3.lite.AbstractAmazonS3Lite.getObjectMetadata(AbstractAmazonS3Lite.java:39)
	at com.amazon.ws.emr.hadoop.fs.s3n.Jets3tNativeFileSystemStore.retrieveMetadata(Jets3tNativeFileSystemStore.java:211)
	at sun.reflect.GeneratedMethodAccessor130.invoke(Unknown Source)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at org.apache.hadoop.io.retry.RetryInvocationHandler.invokeMethod(RetryInvocationHandler.java:191)
	at org.apache.hadoop.io.retry.RetryInvocationHandler.invoke(RetryInvocationHandler.java:102)
	at com.sun.proxy.$Proxy30.retrieveMetadata(Unknown Source)
	at com.amazon.ws.emr.hadoop.fs.s3n.S3NativeFileSystem.getFileStatus(S3NativeFileSystem.java:778)
	at com.amazon.ws.emr.hadoop.fs.s3n.S3NativeFileSystem.open(S3NativeFileSystem.java:1206)
	at org.apache.hadoop.fs.FileSystem.open(FileSystem.java:773)
	at com.amazon.ws.emr.hadoop.fs.EmrFileSystem.open(EmrFileSystem.java:166)
	at is.hail.utils.richUtils.RichHadoopConfiguration$.is$hail$utils$richUtils$RichHadoopConfiguration$$open$extension(RichHadoopConfiguration.scala:37)
	at is.hail.utils.richUtils.RichHadoopConfiguration$.unsafeReader$extension(RichHadoopConfiguration.scala:305)
	at is.hail.HailContext$$anon$1.compute(HailContext.scala:544)
	at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323)
	at org.apache.spark.rdd.RDD.iterator(RDD.scala:287)
	at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
	at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323)
	at org.apache.spark.rdd.RDD.iterator(RDD.scala:287)
	at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
	at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323)
	at org.apache.spark.rdd.RDD.iterator(RDD.scala:287)
	at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
	at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323)
	at org.apache.spark.rdd.RDD.iterator(RDD.scala:287)
	at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
	at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323)
	at org.apache.spark.rdd.RDD.iterator(RDD.scala:287)
	at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
	at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323)
	at org.apache.spark.rdd.RDD.iterator(RDD.scala:287)
	at org.apache.spark.rdd.ZippedPartitionsRDD2.compute(ZippedPartitionsRDD.scala:89)
	at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323)
	at org.apache.spark.rdd.RDD.iterator(RDD.scala:287)
	at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
	at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323)
	at org.apache.spark.rdd.RDD.iterator(RDD.scala:287)
	at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
	at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323)
	at org.apache.spark.rdd.RDD.iterator(RDD.scala:287)
	at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
	at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323)
	at org.apache.spark.rdd.RDD.iterator(RDD.scala:287)
	at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
	at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323)
	at org.apache.spark.rdd.RDD.iterator(RDD.scala:287)
	at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:87)
	at org.apache.spark.scheduler.Task.run(Task.scala:108)
	at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:335)
	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)
Caused by: com.amazon.ws.emr.hadoop.fs.shaded.org.apache.http.conn.ConnectionPoolTimeoutException: Timeout waiting for connection from pool
	at com.amazon.ws.emr.hadoop.fs.shaded.org.apache.http.impl.conn.PoolingHttpClientConnectionManager.leaseConnection(PoolingHttpClientConnectionManager.java:286)
	at com.amazon.ws.emr.hadoop.fs.shaded.org.apache.http.impl.conn.PoolingHttpClientConnectionManager$1.get(PoolingHttpClientConnectionManager.java:263)
	at sun.reflect.GeneratedMethodAccessor133.invoke(Unknown Source)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at com.amazon.ws.emr.hadoop.fs.shaded.com.amazonaws.http.conn.ClientConnectionRequestFactory$Handler.invoke(ClientConnectionRequestFactory.java:70)
	at com.amazon.ws.emr.hadoop.fs.shaded.com.amazonaws.http.conn.$Proxy32.get(Unknown Source)
	at com.amazon.ws.emr.hadoop.fs.shaded.org.apache.http.impl.execchain.MainClientExec.execute(MainClientExec.java:190)
	at com.amazon.ws.emr.hadoop.fs.shaded.org.apache.http.impl.execchain.ProtocolExec.execute(ProtocolExec.java:184)
	at com.amazon.ws.emr.hadoop.fs.shaded.org.apache.http.impl.client.InternalHttpClient.doExecute(InternalHttpClient.java:184)
	at com.amazon.ws.emr.hadoop.fs.shaded.org.apache.http.impl.client.CloseableHttpClient.execute(CloseableHttpClient.java:82)
	at com.amazon.ws.emr.hadoop.fs.shaded.org.apache.http.impl.client.CloseableHttpClient.execute(CloseableHttpClient.java:55)
	at com.amazon.ws.emr.hadoop.fs.shaded.com.amazonaws.http.apache.client.impl.SdkHttpClient.execute(SdkHttpClient.java:72)
	at com.amazon.ws.emr.hadoop.fs.shaded.com.amazonaws.http.AmazonHttpClient$RequestExecutor.executeOneRequest(AmazonHttpClient.java:1190)
	at com.amazon.ws.emr.hadoop.fs.shaded.com.amazonaws.http.AmazonHttpClient$RequestExecutor.executeHelper(AmazonHttpClient.java:1030)
	... 67 more

Driver stacktrace:
	at org.apache.spark.scheduler.DAGScheduler.org$apache$spark$scheduler$DAGScheduler$$failJobAndIndependentStages(DAGScheduler.scala:1690)
	at org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1678)
	at org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1677)
	at scala.collection.mutable.ResizableArray$class.foreach(ResizableArray.scala:59)
	at scala.collection.mutable.ArrayBuffer.foreach(ArrayBuffer.scala:48)
	at org.apache.spark.scheduler.DAGScheduler.abortStage(DAGScheduler.scala:1677)
	at org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:855)
	at org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:855)
	at scala.Option.foreach(Option.scala:257)
	at org.apache.spark.scheduler.DAGScheduler.handleTaskSetFailed(DAGScheduler.scala:855)
	at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.doOnReceive(DAGScheduler.scala:1905)
	at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:1860)
	at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:1849)
	at org.apache.spark.util.EventLoop$$anon$1.run(EventLoop.scala:48)
	at org.apache.spark.scheduler.DAGScheduler.runJob(DAGScheduler.scala:671)
	at org.apache.spark.SparkContext.runJob(SparkContext.scala:2022)
	at org.apache.spark.SparkContext.runJob(SparkContext.scala:2119)
	at org.apache.spark.rdd.RDD$$anonfun$reduce$1.apply(RDD.scala:1026)
	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.reduce(RDD.scala:1008)
	at is.hail.sparkextras.ContextRDD.treeAggregate(ContextRDD.scala:276)
	at is.hail.sparkextras.ContextRDD.treeAggregate(ContextRDD.scala:227)
	at is.hail.rvd.RVD$class.treeAggregate(RVD.scala:339)
	at is.hail.rvd.OrderedRVD.treeAggregate(OrderedRVD.scala:32)
	at is.hail.expr.ir.MatrixMapCols.execute(MatrixIR.scala:1505)
	at is.hail.expr.ir.MatrixColsTable.execute(TableIR.scala:765)
	at is.hail.expr.ir.TableMapRows.execute(TableIR.scala:453)
	at is.hail.expr.ir.TableMapRows.execute(TableIR.scala:453)
	at is.hail.table.Table.value$lzycompute(Table.scala:215)
	at is.hail.table.Table.value(Table.scala:213)
	at is.hail.table.Table.x$5$lzycompute(Table.scala:218)
	at is.hail.table.Table.x$5(Table.scala:218)
	at is.hail.table.Table.rvd$lzycompute(Table.scala:218)
	at is.hail.table.Table.rvd(Table.scala:218)
	at is.hail.table.Table.expandTypes(Table.scala:555)
	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)com.amazon.ws.emr.hadoop.fs.shaded.com.amazonaws.SdkClientException: Unable to execute HTTP request: Timeout waiting for connection from pool
	at com.amazon.ws.emr.hadoop.fs.shaded.com.amazonaws.http.AmazonHttpClient$RequestExecutor.handleRetryableException(AmazonHttpClient.java:1069)
	at com.amazon.ws.emr.hadoop.fs.shaded.com.amazonaws.http.AmazonHttpClient$RequestExecutor.executeHelper(AmazonHttpClient.java:1035)
	at com.amazon.ws.emr.hadoop.fs.shaded.com.amazonaws.http.AmazonHttpClient$RequestExecutor.doExecute(AmazonHttpClient.java:742)
	at com.amazon.ws.emr.hadoop.fs.shaded.com.amazonaws.http.AmazonHttpClient$RequestExecutor.executeWithTimer(AmazonHttpClient.java:716)
	at com.amazon.ws.emr.hadoop.fs.shaded.com.amazonaws.http.AmazonHttpClient$RequestExecutor.execute(AmazonHttpClient.java:699)
	at com.amazon.ws.emr.hadoop.fs.shaded.com.amazonaws.http.AmazonHttpClient$RequestExecutor.access$500(AmazonHttpClient.java:667)
	at com.amazon.ws.emr.hadoop.fs.shaded.com.amazonaws.http.AmazonHttpClient$RequestExecutionBuilderImpl.execute(AmazonHttpClient.java:649)
	at com.amazon.ws.emr.hadoop.fs.shaded.com.amazonaws.http.AmazonHttpClient.execute(AmazonHttpClient.java:513)
	at com.amazon.ws.emr.hadoop.fs.shaded.com.amazonaws.services.s3.AmazonS3Client.invoke(AmazonS3Client.java:4169)
	at com.amazon.ws.emr.hadoop.fs.shaded.com.amazonaws.services.s3.AmazonS3Client.invoke(AmazonS3Client.java:4116)
	at com.amazon.ws.emr.hadoop.fs.shaded.com.amazonaws.services.s3.AmazonS3Client.getObjectMetadata(AmazonS3Client.java:1237)
	at com.amazon.ws.emr.hadoop.fs.s3.lite.call.GetObjectMetadataCall.perform(GetObjectMetadataCall.java:23)
	at com.amazon.ws.emr.hadoop.fs.s3.lite.call.GetObjectMetadataCall.perform(GetObjectMetadataCall.java:9)
	at com.amazon.ws.emr.hadoop.fs.s3.lite.executor.GlobalS3Executor.execute(GlobalS3Executor.java:80)
	at com.amazon.ws.emr.hadoop.fs.s3.lite.AmazonS3LiteClient.invoke(AmazonS3LiteClient.java:176)
	at com.amazon.ws.emr.hadoop.fs.s3.lite.AmazonS3LiteClient.getObjectMetadata(AmazonS3LiteClient.java:94)
	at com.amazon.ws.emr.hadoop.fs.s3.lite.AbstractAmazonS3Lite.getObjectMetadata(AbstractAmazonS3Lite.java:39)
	at com.amazon.ws.emr.hadoop.fs.s3n.Jets3tNativeFileSystemStore.retrieveMetadata(Jets3tNativeFileSystemStore.java:211)
	at sun.reflect.GeneratedMethodAccessor130.invoke(Unknown Source)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at org.apache.hadoop.io.retry.RetryInvocationHandler.invokeMethod(RetryInvocationHandler.java:191)
	at org.apache.hadoop.io.retry.RetryInvocationHandler.invoke(RetryInvocationHandler.java:102)
	at com.sun.proxy.$Proxy30.retrieveMetadata(Unknown Source)
	at com.amazon.ws.emr.hadoop.fs.s3n.S3NativeFileSystem.getFileStatus(S3NativeFileSystem.java:778)
	at com.amazon.ws.emr.hadoop.fs.s3n.S3NativeFileSystem.open(S3NativeFileSystem.java:1206)
	at org.apache.hadoop.fs.FileSystem.open(FileSystem.java:773)
	at com.amazon.ws.emr.hadoop.fs.EmrFileSystem.open(EmrFileSystem.java:166)
	at is.hail.utils.richUtils.RichHadoopConfiguration$.is$hail$utils$richUtils$RichHadoopConfiguration$$open$extension(RichHadoopConfiguration.scala:37)
	at is.hail.utils.richUtils.RichHadoopConfiguration$.unsafeReader$extension(RichHadoopConfiguration.scala:305)
	at is.hail.HailContext$$anon$1.compute(HailContext.scala:544)
	at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323)
	at org.apache.spark.rdd.RDD.iterator(RDD.scala:287)
	at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
	at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323)
	at org.apache.spark.rdd.RDD.iterator(RDD.scala:287)
	at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
	at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323)
	at org.apache.spark.rdd.RDD.iterator(RDD.scala:287)
	at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
	at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323)
	at org.apache.spark.rdd.RDD.iterator(RDD.scala:287)
	at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
	at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323)
	at org.apache.spark.rdd.RDD.iterator(RDD.scala:287)
	at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
	at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323)
	at org.apache.spark.rdd.RDD.iterator(RDD.scala:287)
	at org.apache.spark.rdd.ZippedPartitionsRDD2.compute(ZippedPartitionsRDD.scala:89)
	at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323)
	at org.apache.spark.rdd.RDD.iterator(RDD.scala:287)
	at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
	at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323)
	at org.apache.spark.rdd.RDD.iterator(RDD.scala:287)
	at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
	at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323)
	at org.apache.spark.rdd.RDD.iterator(RDD.scala:287)
	at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
	at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323)
	at org.apache.spark.rdd.RDD.iterator(RDD.scala:287)
	at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
	at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323)
	at org.apache.spark.rdd.RDD.iterator(RDD.scala:287)
	at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:87)
	at org.apache.spark.scheduler.Task.run(Task.scala:108)
	at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:335)
	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)com.amazon.ws.emr.hadoop.fs.shaded.org.apache.http.conn.ConnectionPoolTimeoutException: Timeout waiting for connection from pool
	at com.amazon.ws.emr.hadoop.fs.shaded.org.apache.http.impl.conn.PoolingHttpClientConnectionManager.leaseConnection(PoolingHttpClientConnectionManager.java:286)
	at com.amazon.ws.emr.hadoop.fs.shaded.org.apache.http.impl.conn.PoolingHttpClientConnectionManager$1.get(PoolingHttpClientConnectionManager.java:263)
	at sun.reflect.GeneratedMethodAccessor133.invoke(Unknown Source)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at com.amazon.ws.emr.hadoop.fs.shaded.com.amazonaws.http.conn.ClientConnectionRequestFactory$Handler.invoke(ClientConnectionRequestFactory.java:70)
	at com.amazon.ws.emr.hadoop.fs.shaded.com.amazonaws.http.conn.$Proxy32.get(Unknown Source)
	at com.amazon.ws.emr.hadoop.fs.shaded.org.apache.http.impl.execchain.MainClientExec.execute(MainClientExec.java:190)
	at com.amazon.ws.emr.hadoop.fs.shaded.org.apache.http.impl.execchain.ProtocolExec.execute(ProtocolExec.java:184)
	at com.amazon.ws.emr.hadoop.fs.shaded.org.apache.http.impl.client.InternalHttpClient.doExecute(InternalHttpClient.java:184)
	at com.amazon.ws.emr.hadoop.fs.shaded.org.apache.http.impl.client.CloseableHttpClient.execute(CloseableHttpClient.java:82)
	at com.amazon.ws.emr.hadoop.fs.shaded.org.apache.http.impl.client.CloseableHttpClient.execute(CloseableHttpClient.java:55)
	at com.amazon.ws.emr.hadoop.fs.shaded.com.amazonaws.http.apache.client.impl.SdkHttpClient.execute(SdkHttpClient.java:72)
	at com.amazon.ws.emr.hadoop.fs.shaded.com.amazonaws.http.AmazonHttpClient$RequestExecutor.executeOneRequest(AmazonHttpClient.java:1190)
	at com.amazon.ws.emr.hadoop.fs.shaded.com.amazonaws.http.AmazonHttpClient$RequestExecutor.executeHelper(AmazonHttpClient.java:1030)
	at com.amazon.ws.emr.hadoop.fs.shaded.com.amazonaws.http.AmazonHttpClient$RequestExecutor.doExecute(AmazonHttpClient.java:742)
	at com.amazon.ws.emr.hadoop.fs.shaded.com.amazonaws.http.AmazonHttpClient$RequestExecutor.executeWithTimer(AmazonHttpClient.java:716)
	at com.amazon.ws.emr.hadoop.fs.shaded.com.amazonaws.http.AmazonHttpClient$RequestExecutor.execute(AmazonHttpClient.java:699)
	at com.amazon.ws.emr.hadoop.fs.shaded.com.amazonaws.http.AmazonHttpClient$RequestExecutor.access$500(AmazonHttpClient.java:667)
	at com.amazon.ws.emr.hadoop.fs.shaded.com.amazonaws.http.AmazonHttpClient$RequestExecutionBuilderImpl.execute(AmazonHttpClient.java:649)
	at com.amazon.ws.emr.hadoop.fs.shaded.com.amazonaws.http.AmazonHttpClient.execute(AmazonHttpClient.java:513)
	at com.amazon.ws.emr.hadoop.fs.shaded.com.amazonaws.services.s3.AmazonS3Client.invoke(AmazonS3Client.java:4169)
	at com.amazon.ws.emr.hadoop.fs.shaded.com.amazonaws.services.s3.AmazonS3Client.invoke(AmazonS3Client.java:4116)
	at com.amazon.ws.emr.hadoop.fs.shaded.com.amazonaws.services.s3.AmazonS3Client.getObjectMetadata(AmazonS3Client.java:1237)
	at com.amazon.ws.emr.hadoop.fs.s3.lite.call.GetObjectMetadataCall.perform(GetObjectMetadataCall.java:23)
	at com.amazon.ws.emr.hadoop.fs.s3.lite.call.GetObjectMetadataCall.perform(GetObjectMetadataCall.java:9)
	at com.amazon.ws.emr.hadoop.fs.s3.lite.executor.GlobalS3Executor.execute(GlobalS3Executor.java:80)
	at com.amazon.ws.emr.hadoop.fs.s3.lite.AmazonS3LiteClient.invoke(AmazonS3LiteClient.java:176)
	at com.amazon.ws.emr.hadoop.fs.s3.lite.AmazonS3LiteClient.getObjectMetadata(AmazonS3LiteClient.java:94)
	at com.amazon.ws.emr.hadoop.fs.s3.lite.AbstractAmazonS3Lite.getObjectMetadata(AbstractAmazonS3Lite.java:39)
	at com.amazon.ws.emr.hadoop.fs.s3n.Jets3tNativeFileSystemStore.retrieveMetadata(Jets3tNativeFileSystemStore.java:211)
	at sun.reflect.GeneratedMethodAccessor130.invoke(Unknown Source)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at org.apache.hadoop.io.retry.RetryInvocationHandler.invokeMethod(RetryInvocationHandler.java:191)
	at org.apache.hadoop.io.retry.RetryInvocationHandler.invoke(RetryInvocationHandler.java:102)
	at com.sun.proxy.$Proxy30.retrieveMetadata(Unknown Source)
	at com.amazon.ws.emr.hadoop.fs.s3n.S3NativeFileSystem.getFileStatus(S3NativeFileSystem.java:778)
	at com.amazon.ws.emr.hadoop.fs.s3n.S3NativeFileSystem.open(S3NativeFileSystem.java:1206)
	at org.apache.hadoop.fs.FileSystem.open(FileSystem.java:773)
	at com.amazon.ws.emr.hadoop.fs.EmrFileSystem.open(EmrFileSystem.java:166)
	at is.hail.utils.richUtils.RichHadoopConfiguration$.is$hail$utils$richUtils$RichHadoopConfiguration$$open$extension(RichHadoopConfiguration.scala:37)
	at is.hail.utils.richUtils.RichHadoopConfiguration$.unsafeReader$extension(RichHadoopConfiguration.scala:305)
	at is.hail.HailContext$$anon$1.compute(HailContext.scala:544)
	at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323)
	at org.apache.spark.rdd.RDD.iterator(RDD.scala:287)
	at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
	at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323)
	at org.apache.spark.rdd.RDD.iterator(RDD.scala:287)
	at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
	at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323)
	at org.apache.spark.rdd.RDD.iterator(RDD.scala:287)
	at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
	at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323)
	at org.apache.spark.rdd.RDD.iterator(RDD.scala:287)
	at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
	at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323)
	at org.apache.spark.rdd.RDD.iterator(RDD.scala:287)
	at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
	at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323)
	at org.apache.spark.rdd.RDD.iterator(RDD.scala:287)
	at org.apache.spark.rdd.ZippedPartitionsRDD2.compute(ZippedPartitionsRDD.scala:89)
	at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323)
	at org.apache.spark.rdd.RDD.iterator(RDD.scala:287)
	at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
	at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323)
	at org.apache.spark.rdd.RDD.iterator(RDD.scala:287)
	at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
	at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323)
	at org.apache.spark.rdd.RDD.iterator(RDD.scala:287)
	at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
	at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323)
	at org.apache.spark.rdd.RDD.iterator(RDD.scala:287)
	at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
	at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323)
	at org.apache.spark.rdd.RDD.iterator(RDD.scala:287)
	at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:87)
	at org.apache.spark.scheduler.Task.run(Task.scala:108)
	at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:335)
	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)

tpoterba · August 1, 2018, 4:01pm

Yeah, this just seems like it’s hitting a max concurrent HTTP connection limit. Probably buried deep in Spark/s3 config

cdeniz · August 1, 2018, 4:05pm

We are using emr-5.10.0 as it has Spark 2.2.0. Have you tried to run Hail on newer versions of spark?

tpoterba · August 1, 2018, 4:07pm

yeah, Hail works (but isn’t automatically tested by our CI server) with Spark 2.3.0. You’d need to compile it yourself though, instead of using one of the deployed jars.

cdeniz · August 1, 2018, 4:08pm

We’ll try with spark 2.3.0, we are compiling our files though.

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AttributeError: 'DataFrame' object has no attribute 'to_spark'

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