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rjurney / Agile_Data_Code_2

Code for Agile Data Science 2.0, O'Reilly 2017, Second Edition
http://bit.ly/agile_data_science
MIT License
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[Solved] MongoDB/PySpark not working #35

Closed jwilber closed 7 years ago

jwilber commented 7 years ago

Edit - Solved the issue but will keep up for future use (if that's cool with you). Solution in first comment.

I receive the following (see below) error when running ch02/pyspark_mongodb.py.

The prior examples in chapter 2 ran smoothly. For this example, I ran the following on the ec2 instance in the Agile_Data_Code_2 directory:

>>>pyspark
>>>exec(open("ch02/pyspark_mongodb.py").read())

Which yields this error:

[Stage 2:>                                                          (0 + 2) / 2]17/05/31 08:15:59 ERROR MongoOutputCommitter: Could not write to MongoDB
com.mongodb.MongoTimeoutException: Timed out after 30000 ms while waiting for a server that matches WritableServerSelector. Client view of cluster state is {type=UNKNOWN, servers=[{address=localhost:27017, type=UNKNOWN, state=CONNECTING, exception={com.mongodb.MongoSocketOpenException: Exception opening socket}, caused by {java.net.ConnectException: Connection refused (Connection refused)}}]
    at com.mongodb.connection.BaseCluster.createTimeoutException(BaseCluster.java:369)
    at com.mongodb.connection.BaseCluster.selectServer(BaseCluster.java:101)
    at com.mongodb.binding.ClusterBinding$ClusterBindingConnectionSource.<init>(ClusterBinding.java:75)
    at com.mongodb.binding.ClusterBinding$ClusterBindingConnectionSource.<init>(ClusterBinding.java:71)
    at com.mongodb.binding.ClusterBinding.getWriteConnectionSource(ClusterBinding.java:68)
    at com.mongodb.operation.OperationHelper.withConnection(OperationHelper.java:219)
    at com.mongodb.operation.MixedBulkWriteOperation.execute(MixedBulkWriteOperation.java:168)
    at com.mongodb.operation.MixedBulkWriteOperation.execute(MixedBulkWriteOperation.java:74)
    at com.mongodb.Mongo.execute(Mongo.java:781)
    at com.mongodb.Mongo$2.execute(Mongo.java:764)
    at com.mongodb.DBCollection.executeBulkWriteOperation(DBCollection.java:2195)
    at com.mongodb.DBCollection.executeBulkWriteOperation(DBCollection.java:2188)
    at com.mongodb.BulkWriteOperation.execute(BulkWriteOperation.java:121)
    at com.mongodb.hadoop.output.MongoOutputCommitter.commitTask(MongoOutputCommitter.java:167)
    at com.mongodb.hadoop.output.MongoOutputCommitter.commitTask(MongoOutputCommitter.java:70)
    at org.apache.spark.rdd.PairRDDFunctions$$anonfun$saveAsNewAPIHadoopDataset$1$$anonfun$12.apply(PairRDDFunctions.scala:1132)
    at org.apache.spark.rdd.PairRDDFunctions$$anonfun$saveAsNewAPIHadoopDataset$1$$anonfun$12.apply(PairRDDFunctions.scala:1102)
    at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:87)
    at org.apache.spark.scheduler.Task.run(Task.scala:99)
    at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:282)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:748)
17/05/31 08:15:59 ERROR MongoOutputCommitter: Could not write to MongoDB
com.mongodb.MongoTimeoutException: Timed out after 30000 ms while waiting for a server that matches WritableServerSelector. Client view of cluster state is {type=UNKNOWN, servers=[{address=localhost:27017, type=UNKNOWN, state=CONNECTING, exception={com.mongodb.MongoSocketOpenException: Exception opening socket}, caused by {java.net.ConnectException: Connection refused (Connection refused)}}]
    at com.mongodb.connection.BaseCluster.createTimeoutException(BaseCluster.java:369)
    at com.mongodb.connection.BaseCluster.selectServer(BaseCluster.java:101)
    at com.mongodb.binding.ClusterBinding$ClusterBindingConnectionSource.<init>(ClusterBinding.java:75)
    at com.mongodb.binding.ClusterBinding$ClusterBindingConnectionSource.<init>(ClusterBinding.java:71)
    at com.mongodb.binding.ClusterBinding.getWriteConnectionSource(ClusterBinding.java:68)
    at com.mongodb.operation.OperationHelper.withConnection(OperationHelper.java:219)
    at com.mongodb.operation.MixedBulkWriteOperation.execute(MixedBulkWriteOperation.java:168)
    at com.mongodb.operation.MixedBulkWriteOperation.execute(MixedBulkWriteOperation.java:74)
    at com.mongodb.Mongo.execute(Mongo.java:781)
    at com.mongodb.Mongo$2.execute(Mongo.java:764)
    at com.mongodb.DBCollection.executeBulkWriteOperation(DBCollection.java:2195)
    at com.mongodb.DBCollection.executeBulkWriteOperation(DBCollection.java:2188)
    at com.mongodb.BulkWriteOperation.execute(BulkWriteOperation.java:121)
    at com.mongodb.hadoop.output.MongoOutputCommitter.commitTask(MongoOutputCommitter.java:167)
    at com.mongodb.hadoop.output.MongoOutputCommitter.commitTask(MongoOutputCommitter.java:70)
    at org.apache.spark.rdd.PairRDDFunctions$$anonfun$saveAsNewAPIHadoopDataset$1$$anonfun$12.apply(PairRDDFunctions.scala:1132)
    at org.apache.spark.rdd.PairRDDFunctions$$anonfun$saveAsNewAPIHadoopDataset$1$$anonfun$12.apply(PairRDDFunctions.scala:1102)
    at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:87)
    at org.apache.spark.scheduler.Task.run(Task.scala:99)
    at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:282)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:748)
17/05/31 08:15:59 ERROR Executor: Exception in task 0.0 in stage 2.0 (TID 2)
com.mongodb.MongoTimeoutException: Timed out after 30000 ms while waiting for a server that matches WritableServerSelector. Client view of cluster state is {type=UNKNOWN, servers=[{address=localhost:27017, type=UNKNOWN, state=CONNECTING, exception={com.mongodb.MongoSocketOpenException: Exception opening socket}, caused by {java.net.ConnectException: Connection refused (Connection refused)}}]
    at com.mongodb.connection.BaseCluster.createTimeoutException(BaseCluster.java:369)
    at com.mongodb.connection.BaseCluster.selectServer(BaseCluster.java:101)
    at com.mongodb.binding.ClusterBinding$ClusterBindingConnectionSource.<init>(ClusterBinding.java:75)
    at com.mongodb.binding.ClusterBinding$ClusterBindingConnectionSource.<init>(ClusterBinding.java:71)
    at com.mongodb.binding.ClusterBinding.getWriteConnectionSource(ClusterBinding.java:68)
    at com.mongodb.operation.OperationHelper.withConnection(OperationHelper.java:219)
    at com.mongodb.operation.MixedBulkWriteOperation.execute(MixedBulkWriteOperation.java:168)
    at com.mongodb.operation.MixedBulkWriteOperation.execute(MixedBulkWriteOperation.java:74)
    at com.mongodb.Mongo.execute(Mongo.java:781)
    at com.mongodb.Mongo$2.execute(Mongo.java:764)
    at com.mongodb.DBCollection.executeBulkWriteOperation(DBCollection.java:2195)
    at com.mongodb.DBCollection.executeBulkWriteOperation(DBCollection.java:2188)
    at com.mongodb.BulkWriteOperation.execute(BulkWriteOperation.java:121)
    at com.mongodb.hadoop.output.MongoOutputCommitter.commitTask(MongoOutputCommitter.java:167)
    at com.mongodb.hadoop.output.MongoOutputCommitter.commitTask(MongoOutputCommitter.java:70)
    at org.apache.spark.rdd.PairRDDFunctions$$anonfun$saveAsNewAPIHadoopDataset$1$$anonfun$12.apply(PairRDDFunctions.scala:1132)
    at org.apache.spark.rdd.PairRDDFunctions$$anonfun$saveAsNewAPIHadoopDataset$1$$anonfun$12.apply(PairRDDFunctions.scala:1102)
    at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:87)
    at org.apache.spark.scheduler.Task.run(Task.scala:99)
    at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:282)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:748)
17/05/31 08:15:59 ERROR Executor: Exception in task 1.0 in stage 2.0 (TID 3)
com.mongodb.MongoTimeoutException: Timed out after 30000 ms while waiting for a server that matches WritableServerSelector. Client view of cluster state is {type=UNKNOWN, servers=[{address=localhost:27017, type=UNKNOWN, state=CONNECTING, exception={com.mongodb.MongoSocketOpenException: Exception opening socket}, caused by {java.net.ConnectException: Connection refused (Connection refused)}}]
    at com.mongodb.connection.BaseCluster.createTimeoutException(BaseCluster.java:369)
    at com.mongodb.connection.BaseCluster.selectServer(BaseCluster.java:101)
    at com.mongodb.binding.ClusterBinding$ClusterBindingConnectionSource.<init>(ClusterBinding.java:75)
    at com.mongodb.binding.ClusterBinding$ClusterBindingConnectionSource.<init>(ClusterBinding.java:71)
    at com.mongodb.binding.ClusterBinding.getWriteConnectionSource(ClusterBinding.java:68)
    at com.mongodb.operation.OperationHelper.withConnection(OperationHelper.java:219)
    at com.mongodb.operation.MixedBulkWriteOperation.execute(MixedBulkWriteOperation.java:168)
    at com.mongodb.operation.MixedBulkWriteOperation.execute(MixedBulkWriteOperation.java:74)
    at com.mongodb.Mongo.execute(Mongo.java:781)
    at com.mongodb.Mongo$2.execute(Mongo.java:764)
    at com.mongodb.DBCollection.executeBulkWriteOperation(DBCollection.java:2195)
    at com.mongodb.DBCollection.executeBulkWriteOperation(DBCollection.java:2188)
    at com.mongodb.BulkWriteOperation.execute(BulkWriteOperation.java:121)
    at com.mongodb.hadoop.output.MongoOutputCommitter.commitTask(MongoOutputCommitter.java:167)
    at com.mongodb.hadoop.output.MongoOutputCommitter.commitTask(MongoOutputCommitter.java:70)
    at org.apache.spark.rdd.PairRDDFunctions$$anonfun$saveAsNewAPIHadoopDataset$1$$anonfun$12.apply(PairRDDFunctions.scala:1132)
    at org.apache.spark.rdd.PairRDDFunctions$$anonfun$saveAsNewAPIHadoopDataset$1$$anonfun$12.apply(PairRDDFunctions.scala:1102)
    at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:87)
    at org.apache.spark.scheduler.Task.run(Task.scala:99)
    at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:282)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:748)
17/05/31 08:15:59 WARN TaskSetManager: Lost task 1.0 in stage 2.0 (TID 3, localhost, executor driver): com.mongodb.MongoTimeoutException: Timed out after 30000 ms while waiting for a server that matches WritableServerSelector. Client view of cluster state is {type=UNKNOWN, servers=[{address=localhost:27017, type=UNKNOWN, state=CONNECTING, exception={com.mongodb.MongoSocketOpenException: Exception opening socket}, caused by {java.net.ConnectException: Connection refused (Connection refused)}}]
    at com.mongodb.connection.BaseCluster.createTimeoutException(BaseCluster.java:369)
    at com.mongodb.connection.BaseCluster.selectServer(BaseCluster.java:101)
    at com.mongodb.binding.ClusterBinding$ClusterBindingConnectionSource.<init>(ClusterBinding.java:75)
    at com.mongodb.binding.ClusterBinding$ClusterBindingConnectionSource.<init>(ClusterBinding.java:71)
    at com.mongodb.binding.ClusterBinding.getWriteConnectionSource(ClusterBinding.java:68)
    at com.mongodb.operation.OperationHelper.withConnection(OperationHelper.java:219)
    at com.mongodb.operation.MixedBulkWriteOperation.execute(MixedBulkWriteOperation.java:168)
    at com.mongodb.operation.MixedBulkWriteOperation.execute(MixedBulkWriteOperation.java:74)
    at com.mongodb.Mongo.execute(Mongo.java:781)
    at com.mongodb.Mongo$2.execute(Mongo.java:764)
    at com.mongodb.DBCollection.executeBulkWriteOperation(DBCollection.java:2195)
    at com.mongodb.DBCollection.executeBulkWriteOperation(DBCollection.java:2188)
    at com.mongodb.BulkWriteOperation.execute(BulkWriteOperation.java:121)
    at com.mongodb.hadoop.output.MongoOutputCommitter.commitTask(MongoOutputCommitter.java:167)
    at com.mongodb.hadoop.output.MongoOutputCommitter.commitTask(MongoOutputCommitter.java:70)
    at org.apache.spark.rdd.PairRDDFunctions$$anonfun$saveAsNewAPIHadoopDataset$1$$anonfun$12.apply(PairRDDFunctions.scala:1132)
    at org.apache.spark.rdd.PairRDDFunctions$$anonfun$saveAsNewAPIHadoopDataset$1$$anonfun$12.apply(PairRDDFunctions.scala:1102)
    at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:87)
    at org.apache.spark.scheduler.Task.run(Task.scala:99)
    at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:282)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:748)

17/05/31 08:15:59 ERROR TaskSetManager: Task 1 in stage 2.0 failed 1 times; aborting job
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "<string>", line 14, in <module>
  File "/home/ubuntu/Agile_Data_Code_2/lib/pymongo_spark.py", line 40, in saveToMongoDB
    conf=conf)
  File "/home/ubuntu/spark/python/pyspark/rdd.py", line 1421, in saveAsNewAPIHadoopFile
    keyConverter, valueConverter, jconf)
  File "/home/ubuntu/spark/python/lib/py4j-0.10.4-src.zip/py4j/java_gateway.py", line 1133, in __call__
  File "/home/ubuntu/spark/python/pyspark/sql/utils.py", line 63, in deco
    return f(*a, **kw)
  File "/home/ubuntu/spark/python/lib/py4j-0.10.4-src.zip/py4j/protocol.py", line 319, in get_return_value
py4j.protocol.Py4JJavaError: An error occurred while calling z:org.apache.spark.api.python.PythonRDD.saveAsNewAPIHadoopFile.
: org.apache.spark.SparkException: Job aborted due to stage failure: Task 1 in stage 2.0 failed 1 times, most recent failure: Lost task 1.0 in stage 2.0 (TID 3, localhost, executor driver): com.mongodb.MongoTimeoutException: Timed out after 30000 ms while waiting for a server that matches WritableServerSelector. Client view of cluster state is {type=UNKNOWN, servers=[{address=localhost:27017, type=UNKNOWN, state=CONNECTING, exception={com.mongodb.MongoSocketOpenException: Exception opening socket}, caused by {java.net.ConnectException: Connection refused (Connection refused)}}]
    at com.mongodb.connection.BaseCluster.createTimeoutException(BaseCluster.java:369)
    at com.mongodb.connection.BaseCluster.selectServer(BaseCluster.java:101)
    at com.mongodb.binding.ClusterBinding$ClusterBindingConnectionSource.<init>(ClusterBinding.java:75)
    at com.mongodb.binding.ClusterBinding$ClusterBindingConnectionSource.<init>(ClusterBinding.java:71)
    at com.mongodb.binding.ClusterBinding.getWriteConnectionSource(ClusterBinding.java:68)
    at com.mongodb.operation.OperationHelper.withConnection(OperationHelper.java:219)
    at com.mongodb.operation.MixedBulkWriteOperation.execute(MixedBulkWriteOperation.java:168)
    at com.mongodb.operation.MixedBulkWriteOperation.execute(MixedBulkWriteOperation.java:74)
    at com.mongodb.Mongo.execute(Mongo.java:781)
    at com.mongodb.Mongo$2.execute(Mongo.java:764)
    at com.mongodb.DBCollection.executeBulkWriteOperation(DBCollection.java:2195)
    at com.mongodb.DBCollection.executeBulkWriteOperation(DBCollection.java:2188)
    at com.mongodb.BulkWriteOperation.execute(BulkWriteOperation.java:121)
    at com.mongodb.hadoop.output.MongoOutputCommitter.commitTask(MongoOutputCommitter.java:167)
    at com.mongodb.hadoop.output.MongoOutputCommitter.commitTask(MongoOutputCommitter.java:70)
    at org.apache.spark.rdd.PairRDDFunctions$$anonfun$saveAsNewAPIHadoopDataset$1$$anonfun$12.apply(PairRDDFunctions.scala:1132)
    at org.apache.spark.rdd.PairRDDFunctions$$anonfun$saveAsNewAPIHadoopDataset$1$$anonfun$12.apply(PairRDDFunctions.scala:1102)
    at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:87)
    at org.apache.spark.scheduler.Task.run(Task.scala:99)
    at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:282)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:748)

Driver stacktrace:
    at org.apache.spark.scheduler.DAGScheduler.org$apache$spark$scheduler$DAGScheduler$$failJobAndIndependentStages(DAGScheduler.scala:1435)
    at org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1423)
    at org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1422)
    at scala.collection.mutable.ResizableArray$class.foreach(ResizableArray.scala:59)
    at scala.collection.mutable.ArrayBuffer.foreach(ArrayBuffer.scala:48)
    at org.apache.spark.scheduler.DAGScheduler.abortStage(DAGScheduler.scala:1422)
    at org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:802)
    at org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:802)
    at scala.Option.foreach(Option.scala:257)
    at org.apache.spark.scheduler.DAGScheduler.handleTaskSetFailed(DAGScheduler.scala:802)
    at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.doOnReceive(DAGScheduler.scala:1650)
    at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:1605)
    at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:1594)
    at org.apache.spark.util.EventLoop$$anon$1.run(EventLoop.scala:48)
    at org.apache.spark.scheduler.DAGScheduler.runJob(DAGScheduler.scala:628)
    at org.apache.spark.SparkContext.runJob(SparkContext.scala:1918)
    at org.apache.spark.SparkContext.runJob(SparkContext.scala:1931)
    at org.apache.spark.SparkContext.runJob(SparkContext.scala:1951)
    at org.apache.spark.rdd.PairRDDFunctions$$anonfun$saveAsNewAPIHadoopDataset$1.apply$mcV$sp(PairRDDFunctions.scala:1158)
    at org.apache.spark.rdd.PairRDDFunctions$$anonfun$saveAsNewAPIHadoopDataset$1.apply(PairRDDFunctions.scala:1085)
    at org.apache.spark.rdd.PairRDDFunctions$$anonfun$saveAsNewAPIHadoopDataset$1.apply(PairRDDFunctions.scala:1085)
    at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151)
    at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:112)
    at org.apache.spark.rdd.RDD.withScope(RDD.scala:362)
    at org.apache.spark.rdd.PairRDDFunctions.saveAsNewAPIHadoopDataset(PairRDDFunctions.scala:1085)
    at org.apache.spark.rdd.PairRDDFunctions$$anonfun$saveAsNewAPIHadoopFile$2.apply$mcV$sp(PairRDDFunctions.scala:1005)
    at org.apache.spark.rdd.PairRDDFunctions$$anonfun$saveAsNewAPIHadoopFile$2.apply(PairRDDFunctions.scala:996)
    at org.apache.spark.rdd.PairRDDFunctions$$anonfun$saveAsNewAPIHadoopFile$2.apply(PairRDDFunctions.scala:996)
    at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151)
    at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:112)
    at org.apache.spark.rdd.RDD.withScope(RDD.scala:362)
    at org.apache.spark.rdd.PairRDDFunctions.saveAsNewAPIHadoopFile(PairRDDFunctions.scala:996)
    at org.apache.spark.api.python.PythonRDD$.saveAsNewAPIHadoopFile(PythonRDD.scala:834)
    at org.apache.spark.api.python.PythonRDD.saveAsNewAPIHadoopFile(PythonRDD.scala)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:498)
    at 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)
Caused by: com.mongodb.MongoTimeoutException: Timed out after 30000 ms while waiting for a server that matches WritableServerSelector. Client view of cluster state is {type=UNKNOWN, servers=[{address=localhost:27017, type=UNKNOWN, state=CONNECTING, exception={com.mongodb.MongoSocketOpenException: Exception opening socket}, caused by {java.net.ConnectException: Connection refused (Connection refused)}}]
    at com.mongodb.connection.BaseCluster.createTimeoutException(BaseCluster.java:369)
    at com.mongodb.connection.BaseCluster.selectServer(BaseCluster.java:101)
    at com.mongodb.binding.ClusterBinding$ClusterBindingConnectionSource.<init>(ClusterBinding.java:75)
    at com.mongodb.binding.ClusterBinding$ClusterBindingConnectionSource.<init>(ClusterBinding.java:71)
    at com.mongodb.binding.ClusterBinding.getWriteConnectionSource(ClusterBinding.java:68)
    at com.mongodb.operation.OperationHelper.withConnection(OperationHelper.java:219)
    at com.mongodb.operation.MixedBulkWriteOperation.execute(MixedBulkWriteOperation.java:168)
    at com.mongodb.operation.MixedBulkWriteOperation.execute(MixedBulkWriteOperation.java:74)
    at com.mongodb.Mongo.execute(Mongo.java:781)
    at com.mongodb.Mongo$2.execute(Mongo.java:764)
    at com.mongodb.DBCollection.executeBulkWriteOperation(DBCollection.java:2195)
    at com.mongodb.DBCollection.executeBulkWriteOperation(DBCollection.java:2188)
    at com.mongodb.BulkWriteOperation.execute(BulkWriteOperation.java:121)
    at com.mongodb.hadoop.output.MongoOutputCommitter.commitTask(MongoOutputCommitter.java:167)
    at com.mongodb.hadoop.output.MongoOutputCommitter.commitTask(MongoOutputCommitter.java:70)
    at org.apache.spark.rdd.PairRDDFunctions$$anonfun$saveAsNewAPIHadoopDataset$1$$anonfun$12.apply(PairRDDFunctions.scala:1132)
    at org.apache.spark.rdd.PairRDDFunctions$$anonfun$saveAsNewAPIHadoopDataset$1$$anonfun$12.apply(PairRDDFunctions.scala:1102)
    at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:87)
    at org.apache.spark.scheduler.Task.run(Task.scala:99)
    at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:282)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    ... 1 more

Inspecting my mongodb.log file, I noted the following error:

ERROR: Insufficient free space for journal files
Please make at least 3379MB available in /var/lib/mongodb/journal or use --smallfiles

To attempt to solve this error, I expanded the storage on the server via aws as recommended by this post

Unfortunately, this still yields the same error. Any help would be greatly appreciated!

jwilber commented 7 years ago

Solved Running mongod --smallfiles instead of mongod solved the issue :)