pyspark saveAsSequenceFile with pyspark.ml.linalg.Vectors

1
votes

I try to save a (huge) list of sparse vectors as a sequence file and I get errors. Below is a dummy code:

#used on pyspark shell
from pyspark.ml.linalg import Vectors
rdd = sc.parallelize([Vectors.sparse(5, {1:1,2:2}), Vectors.sparse(5, {3:3,4:4})])
rdd.zipWithIndex().saveAsSequenceFile("hdfs://master:9000/user/vec.rdd")

16/07/30 09:36:49 ERROR Executor: Exception in task 0.0 in stage 2.0 (TID 5)    
net.razorvine.pickle.PickleException: expected zero arguments for construction of ClassDict (for pyspark.ml.linalg.SparseVector)
    at net.razorvine.pickle.objects.ClassDictConstructor.construct(ClassDictConstructor.java:23)
    at net.razorvine.pickle.Unpickler.load_reduce(Unpickler.java:707)
    at net.razorvine.pickle.Unpickler.dispatch(Unpickler.java:175)
    at net.razorvine.pickle.Unpickler.load(Unpickler.java:99)
    at net.razorvine.pickle.Unpickler.loads(Unpickler.java:112)
    at org.apache.spark.api.python.SerDeUtil$$anonfun$pythonToJava$1$$anonfun$apply$1.apply(SerDeUtil.scala:152)
    at org.apache.spark.api.python.SerDeUtil$$anonfun$pythonToJava$1$$anonfun$apply$1.apply(SerDeUtil.scala:151)
    at scala.collection.Iterator$$anon$12.nextCur(Iterator.scala:434)
    at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:440)
    at scala.collection.Iterator$$anon$10.hasNext(Iterator.scala:389)
    at scala.collection.Iterator$class.foreach(Iterator.scala:893)
    at scala.collection.AbstractIterator.foreach(Iterator.scala:1336)
    at scala.collection.generic.Growable$class.$plus$plus$eq(Growable.scala:59)
    at scala.collection.mutable.ArrayBuffer.$plus$plus$eq(ArrayBuffer.scala:104)
    at scala.collection.mutable.ArrayBuffer.$plus$plus$eq(ArrayBuffer.scala:48)
    at scala.collection.TraversableOnce$class.to(TraversableOnce.scala:310)
    at scala.collection.AbstractIterator.to(Iterator.scala:1336)
    at scala.collection.TraversableOnce$class.toBuffer(TraversableOnce.scala:302)
    at scala.collection.AbstractIterator.toBuffer(Iterator.scala:1336)
    at scala.collection.TraversableOnce$class.toArray(TraversableOnce.scala:289)
    at scala.collection.AbstractIterator.toArray(Iterator.scala:1336)
    at org.apache.spark.rdd.RDD$$anonfun$take$1$$anonfun$29.apply(RDD.scala:1305)
    at org.apache.spark.rdd.RDD$$anonfun$take$1$$anonfun$29.apply(RDD.scala:1305)
    at org.apache.spark.SparkContext$$anonfun$runJob$5.apply(SparkContext.scala:1897)
    at org.apache.spark.SparkContext$$anonfun$runJob$5.apply(SparkContext.scala:1897)
    at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:70)
    at org.apache.spark.scheduler.Task.run(Task.scala:85)
    at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:274)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
    at java.lang.Thread.run(Thread.java:745)
16/07/30 09:36:49 WARN TaskSetManager: Lost task 0.0 in stage 2.0 (TID 5, localhost): net.razorvine.pickle.PickleException: expected zero arguments for construction of ClassDict (for pyspark.ml.linalg.SparseVector)
    at net.razorvine.pickle.objects.ClassDictConstructor.construct(ClassDictConstructor.java:23)
    at net.razorvine.pickle.Unpickler.load_reduce(Unpickler.java:707)
    at net.razorvine.pickle.Unpickler.dispatch(Unpickler.java:175)
    at net.razorvine.pickle.Unpickler.load(Unpickler.java:99)
    at net.razorvine.pickle.Unpickler.loads(Unpickler.java:112)
    at org.apache.spark.api.python.SerDeUtil$$anonfun$pythonToJava$1$$anonfun$apply$1.apply(SerDeUtil.scala:152)
    at org.apache.spark.api.python.SerDeUtil$$anonfun$pythonToJava$1$$anonfun$apply$1.apply(SerDeUtil.scala:151)
    at scala.collection.Iterator$$anon$12.nextCur(Iterator.scala:434)
    at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:440)
    at scala.collection.Iterator$$anon$10.hasNext(Iterator.scala:389)
    at scala.collection.Iterator$class.foreach(Iterator.scala:893)
    at scala.collection.AbstractIterator.foreach(Iterator.scala:1336)
    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$class.to(TraversableOnce.scala:310)
    at scala.collection.AbstractIterator.to(Iterator.scala:1336)
    at scala.collection.TraversableOnce$class.toBuffer(TraversableOnce.scala:302)
    at scala.collection.AbstractIterator.toBuffer(Iterator.scala:1336)
    at scala.collection.TraversableOnce$class.toArray(TraversableOnce.scala:289)
    at scala.collection.AbstractIterator.toArray(Iterator.scala:1336)
    at org.apache.spark.rdd.RDD$$anonfun$take$1$$anonfun$29.apply(RDD.scala:1305)
    at org.apache.spark.rdd.RDD$$anonfun$take$1$$anonfun$29.apply(RDD.scala:1305)
    at org.apache.spark.SparkContext$$anonfun$runJob$5.apply(SparkContext.scala:1897)
    at org.apache.spark.SparkContext$$anonfun$runJob$5.apply(SparkContext.scala:1897)
    at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:70)
    at org.apache.spark.scheduler.Task.run(Task.scala:85)
    at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:274)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
    at java.lang.Thread.run(Thread.java:745)

16/07/30 09:36:49 ERROR TaskSetManager: Task 0 in stage 2.0 failed 1 times; aborting job
Traceback (most recent call last):
  File "", line 1, in 
  File "/home/ubuntu/spark/python/pyspark/rdd.py", line 1450, in saveAsSequenceFile
    path, compressionCodecClass)
  File "/home/ubuntu/spark/python/lib/py4j-0.10.1-src.zip/py4j/java_gateway.py", line 933, 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-0.10.1-src.zip/py4j/protocol.py", line 312, in get_return_value
py4j.protocol.Py4JJavaError: An error occurred while calling z:org.apache.spark.api.python.PythonRDD.saveAsSequenceFile.
: org.apache.spark.SparkException: Job aborted due to stage failure: Task 0 in stage 2.0 failed 1 times, most recent failure: Lost task 0.0 in stage 2.0 (TID 5, localhost): net.razorvine.pickle.PickleException: expected zero arguments for construction of ClassDict (for pyspark.ml.linalg.SparseVector)
    at net.razorvine.pickle.objects.ClassDictConstructor.construct(ClassDictConstructor.java:23)
    at net.razorvine.pickle.Unpickler.load_reduce(Unpickler.java:707)
    at net.razorvine.pickle.Unpickler.dispatch(Unpickler.java:175)
    at net.razorvine.pickle.Unpickler.load(Unpickler.java:99)
    at net.razorvine.pickle.Unpickler.loads(Unpickler.java:112)
    at org.apache.spark.api.python.SerDeUtil$$anonfun$pythonToJava$1$$anonfun$apply$1.apply(SerDeUtil.scala:152)
    at org.apache.spark.api.python.SerDeUtil$$anonfun$pythonToJava$1$$anonfun$apply$1.apply(SerDeUtil.scala:151)
    at scala.collection.Iterator$$anon$12.nextCur(Iterator.scala:434)
    at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:440)
    at scala.collection.Iterator$$anon$10.hasNext(Iterator.scala:389)
    at scala.collection.Iterator$class.foreach(Iterator.scala:893)
    at scala.collection.AbstractIterator.foreach(Iterator.scala:1336)
    at scala.collection.generic.Growable$class.$plus$plus$eq(Growable.scala:59)
    at scala.collection.mutable.ArrayBuffer.$plus$plus$eq(ArrayBuffer.scala:104)
    at scala.collection.mutable.ArrayBuffer.$plus$plus$eq(ArrayBuffer.scala:48)
    at scala.collection.TraversableOnce$class.to(TraversableOnce.scala:310)
    at scala.collection.AbstractIterator.to(Iterator.scala:1336)
    at scala.collection.TraversableOnce$class.toBuffer(TraversableOnce.scala:302)
    at scala.collection.AbstractIterator.toBuffer(Iterator.scala:1336)
    at scala.collection.TraversableOnce$class.toArray(TraversableOnce.scala:289)
    at scala.collection.AbstractIterator.toArray(Iterator.scala:1336)
    at org.apache.spark.rdd.RDD$$anonfun$take$1$$anonfun$29.apply(RDD.scala:1305)
    at org.apache.spark.rdd.RDD$$anonfun$take$1$$anonfun$29.apply(RDD.scala:1305)
    at org.apache.spark.SparkContext$$anonfun$runJob$5.apply(SparkContext.scala:1897)
    at org.apache.spark.SparkContext$$anonfun$runJob$5.apply(SparkContext.scala:1897)
    at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:70)
    at org.apache.spark.scheduler.Task.run(Task.scala:85)
    at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:274)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
    at java.lang.Thread.run(Thread.java:745)

Driver stacktrace:
    at org.apache.spark.scheduler.DAGScheduler.org$apache$spark$scheduler$DAGScheduler$$failJobAndIndependentStages(DAGScheduler.scala:1450)
    at org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1438)
    at org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1437)
    at scala.collection.mutable.ResizableArray$class.foreach(ResizableArray.scala:59)
    at scala.collection.mutable.ArrayBuffer.foreach(ArrayBuffer.scala:48)
    at org.apache.spark.scheduler.DAGScheduler.abortStage(DAGScheduler.scala:1437)
    at org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:811)
    at org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:811)
    at scala.Option.foreach(Option.scala:257)
    at org.apache.spark.scheduler.DAGScheduler.handleTaskSetFailed(DAGScheduler.scala:811)
    at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.doOnReceive(DAGScheduler.scala:1659)
    at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:1618)
    at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:1607)
    at org.apache.spark.util.EventLoop$$anon$1.run(EventLoop.scala:48)
    at org.apache.spark.scheduler.DAGScheduler.runJob(DAGScheduler.scala:632)
    at org.apache.spark.SparkContext.runJob(SparkContext.scala:1871)
    at org.apache.spark.SparkContext.runJob(SparkContext.scala:1884)
    at org.apache.spark.SparkContext.runJob(SparkContext.scala:1897)
    at org.apache.spark.rdd.RDD$$anonfun$take$1.apply(RDD.scala:1305)
    at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151)
    at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:112)
    at org.apache.spark.rdd.RDD.withScope(RDD.scala:358)
    at org.apache.spark.rdd.RDD.take(RDD.scala:1279)
    at org.apache.spark.api.python.SerDeUtil$.pythonToPairRDD(SerDeUtil.scala:233)
    at org.apache.spark.api.python.PythonRDD$.saveAsHadoopFile(PythonRDD.scala:797)
    at org.apache.spark.api.python.PythonRDD$.saveAsSequenceFile(PythonRDD.scala:772)
    at org.apache.spark.api.python.PythonRDD.saveAsSequenceFile(PythonRDD.scala)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:606)
    at py4j.reflection.MethodInvoker.invoke(MethodInvoker.java:237)
    at py4j.reflection.ReflectionEngine.invoke(ReflectionEngine.java:357)
    at py4j.Gateway.invoke(Gateway.java:280)
    at py4j.commands.AbstractCommand.invokeMethod(AbstractCommand.java:128)
    at py4j.commands.CallCommand.execute(CallCommand.java:79)
    at py4j.GatewayConnection.run(GatewayConnection.java:211)
    at java.lang.Thread.run(Thread.java:745)
Caused by: net.razorvine.pickle.PickleException: expected zero arguments for construction of ClassDict (for pyspark.ml.linalg.SparseVector)
    at net.razorvine.pickle.objects.ClassDictConstructor.construct(ClassDictConstructor.java:23)
    at net.razorvine.pickle.Unpickler.load_reduce(Unpickler.java:707)
    at net.razorvine.pickle.Unpickler.dispatch(Unpickler.java:175)
    at net.razorvine.pickle.Unpickler.load(Unpickler.java:99)
    at net.razorvine.pickle.Unpickler.loads(Unpickler.java:112)
    at org.apache.spark.api.python.SerDeUtil$$anonfun$pythonToJava$1$$anonfun$apply$1.apply(SerDeUtil.scala:152)
    at org.apache.spark.api.python.SerDeUtil$$anonfun$pythonToJava$1$$anonfun$apply$1.apply(SerDeUtil.scala:151)
    at scala.collection.Iterator$$anon$12.nextCur(Iterator.scala:434)
    at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:440)
    at scala.collection.Iterator$$anon$10.hasNext(Iterator.scala:389)
    at scala.collection.Iterator$class.foreach(Iterator.scala:893)
    at scala.collection.AbstractIterator.foreach(Iterator.scala:1336)
    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$class.to(TraversableOnce.scala:310)
    at scala.collection.AbstractIterator.to(Iterator.scala:1336)
    at scala.collection.TraversableOnce$class.toBuffer(TraversableOnce.scala:302)
    at scala.collection.AbstractIterator.toBuffer(Iterator.scala:1336)
    at scala.collection.TraversableOnce$class.toArray(TraversableOnce.scala:289)
    at scala.collection.AbstractIterator.toArray(Iterator.scala:1336)
    at org.apache.spark.rdd.RDD$$anonfun$take$1$$anonfun$29.apply(RDD.scala:1305)
    at org.apache.spark.rdd.RDD$$anonfun$take$1$$anonfun$29.apply(RDD.scala:1305)
    at org.apache.spark.SparkContext$$anonfun$runJob$5.apply(SparkContext.scala:1897)
    at org.apache.spark.SparkContext$$anonfun$runJob$5.apply(SparkContext.scala:1897)
    at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:70)
    at org.apache.spark.scheduler.Task.run(Task.scala:85)
    at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:274)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
    ... 1 more

>>> 16/07/30 09:36:49 WARN TaskSetManager: Lost task 2.0 in stage 2.0 (TID 7, localhost): TaskKilled (killed intentionally)

Traceback (most recent call last):
  File "/home/ubuntu/spark/python/pyspark/context.py", line 223, in signal_handler
    raise KeyboardInterrupt()
KeyboardInterrupt
>>> rdd.map(lambda x: (0, x)).saveAsSequenceFile("hdfs://master:9000/user/seq.rdd")
16/07/30 09:38:53 ERROR Executor: Exception in task 2.0 in stage 4.0 (TID 11)
net.razorvine.pickle.PickleException: expected zero arguments for construction of ClassDict (for pyspark.ml.linalg.SparseVector)
    at net.razorvine.pickle.objects.ClassDictConstructor.construct(ClassDictConstructor.java:23)
    at net.razorvine.pickle.Unpickler.load_reduce(Unpickler.java:707)
    at net.razorvine.pickle.Unpickler.dispatch(Unpickler.java:175)
    at net.razorvine.pickle.Unpickler.load(Unpickler.java:99)
    at net.razorvine.pickle.Unpickler.loads(Unpickler.java:112)
    at org.apache.spark.api.python.SerDeUtil$$anonfun$pythonToJava$1$$anonfun$apply$1.apply(SerDeUtil.scala:152)
    at org.apache.spark.api.python.SerDeUtil$$anonfun$pythonToJava$1$$anonfun$apply$1.apply(SerDeUtil.scala:151)
    at scala.collection.Iterator$$anon$12.nextCur(Iterator.scala:434)
    at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:440)
    at scala.collection.Iterator$$anon$10.hasNext(Iterator.scala:389)
    at scala.collection.Iterator$class.foreach(Iterator.scala:893)
    at scala.collection.AbstractIterator.foreach(Iterator.scala:1336)
    at scala.collection.generic.Growable$class.$plus$plus$eq(Growable.scala:59)
    at scala.collection.mutable.ArrayBuffer.$plus$plus$eq(ArrayBuffer.scala:104)
    at scala.collection.mutable.ArrayBuffer.$plus$plus$eq(ArrayBuffer.scala:48)
    at scala.collection.TraversableOnce$class.to(TraversableOnce.scala:310)
    at scala.collection.AbstractIterator.to(Iterator.scala:1336)
    at scala.collection.TraversableOnce$class.toBuffer(TraversableOnce.scala:302)
    at scala.collection.AbstractIterator.toBuffer(Iterator.scala:1336)
    at scala.collection.TraversableOnce$class.toArray(TraversableOnce.scala:289)
    at scala.collection.AbstractIterator.toArray(Iterator.scala:1336)
    at org.apache.spark.rdd.RDD$$anonfun$take$1$$anonfun$29.apply(RDD.scala:1305)
    at org.apache.spark.rdd.RDD$$anonfun$take$1$$anonfun$29.apply(RDD.scala:1305)
    at org.apache.spark.SparkContext$$anonfun$runJob$5.apply(SparkContext.scala:1897)
    at org.apache.spark.SparkContext$$anonfun$runJob$5.apply(SparkContext.scala:1897)
    at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:70)
    at org.apache.spark.scheduler.Task.run(Task.scala:85)
    at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:274)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
    at java.lang.Thread.run(Thread.java:745)
16/07/30 09:38:53 WARN TaskSetManager: Lost task 2.0 in stage 4.0 (TID 11, localhost): net.razorvine.pickle.PickleException: expected zero arguments for construction of ClassDict (for pyspark.ml.linalg.SparseVector)
    at net.razorvine.pickle.objects.ClassDictConstructor.construct(ClassDictConstructor.java:23)
    at net.razorvine.pickle.Unpickler.load_reduce(Unpickler.java:707)
    at net.razorvine.pickle.Unpickler.dispatch(Unpickler.java:175)
    at net.razorvine.pickle.Unpickler.load(Unpickler.java:99)
    at net.razorvine.pickle.Unpickler.loads(Unpickler.java:112)
    at org.apache.spark.api.python.SerDeUtil$$anonfun$pythonToJava$1$$anonfun$apply$1.apply(SerDeUtil.scala:152)
    at org.apache.spark.api.python.SerDeUtil$$anonfun$pythonToJava$1$$anonfun$apply$1.apply(SerDeUtil.scala:151)
    at scala.collection.Iterator$$anon$12.nextCur(Iterator.scala:434)
    at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:440)
    at scala.collection.Iterator$$anon$10.hasNext(Iterator.scala:389)
    at scala.collection.Iterator$class.foreach(Iterator.scala:893)
    at scala.collection.AbstractIterator.foreach(Iterator.scala:1336)
    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$class.to(TraversableOnce.scala:310)
    at scala.collection.AbstractIterator.to(Iterator.scala:1336)
    at scala.collection.TraversableOnce$class.toBuffer(TraversableOnce.scala:302)
    at scala.collection.AbstractIterator.toBuffer(Iterator.scala:1336)
    at scala.collection.TraversableOnce$class.toArray(TraversableOnce.scala:289)
    at scala.collection.AbstractIterator.toArray(Iterator.scala:1336)
    at org.apache.spark.rdd.RDD$$anonfun$take$1$$anonfun$29.apply(RDD.scala:1305)
    at org.apache.spark.rdd.RDD$$anonfun$take$1$$anonfun$29.apply(RDD.scala:1305)
    at org.apache.spark.SparkContext$$anonfun$runJob$5.apply(SparkContext.scala:1897)
    at org.apache.spark.SparkContext$$anonfun$runJob$5.apply(SparkContext.scala:1897)
    at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:70)
    at org.apache.spark.scheduler.Task.run(Task.scala:85)
    at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:274)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
    at java.lang.Thread.run(Thread.java:745)

16/07/30 09:38:53 ERROR TaskSetManager: Task 2 in stage 4.0 failed 1 times; aborting job
16/07/30 09:38:53 WARN TaskSetManager: Lost task 0.0 in stage 4.0 (TID 9, localhost): TaskKilled (killed intentionally)
Traceback (most recent call last):
  File "", line 1, in 
  File "/home/ubuntu/spark/python/pyspark/rdd.py", line 1450, in saveAsSequenceFile
    path, compressionCodecClass)
  File "/home/ubuntu/spark/python/lib/py4j-0.10.1-src.zip/py4j/java_gateway.py", line 933, 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-0.10.1-src.zip/py4j/protocol.py", line 312, in get_return_value
py4j.protocol.Py4JJavaError: An error occurred while calling z:org.apache.spark.api.python.PythonRDD.saveAsSequenceFile.
: org.apache.spark.SparkException: Job aborted due to stage failure: Task 2 in stage 4.0 failed 1 times, most recent failure: Lost task 2.0 in stage 4.0 (TID 11, localhost): net.razorvine.pickle.PickleException: expected zero arguments for construction of ClassDict (for pyspark.ml.linalg.SparseVector)
    at net.razorvine.pickle.objects.ClassDictConstructor.construct(ClassDictConstructor.java:23)
    at net.razorvine.pickle.Unpickler.load_reduce(Unpickler.java:707)
    at net.razorvine.pickle.Unpickler.dispatch(Unpickler.java:175)
    at net.razorvine.pickle.Unpickler.load(Unpickler.java:99)
    at net.razorvine.pickle.Unpickler.loads(Unpickler.java:112)
    at org.apache.spark.api.python.SerDeUtil$$anonfun$pythonToJava$1$$anonfun$apply$1.apply(SerDeUtil.scala:152)
    at org.apache.spark.api.python.SerDeUtil$$anonfun$pythonToJava$1$$anonfun$apply$1.apply(SerDeUtil.scala:151)
    at scala.collection.Iterator$$anon$12.nextCur(Iterator.scala:434)
    at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:440)
    at scala.collection.Iterator$$anon$10.hasNext(Iterator.scala:389)
    at scala.collection.Iterator$class.foreach(Iterator.scala:893)
    at scala.collection.AbstractIterator.foreach(Iterator.scala:1336)
    at scala.collection.generic.Growable$class.$plus$plus$eq(Growable.scala:59)
    at scala.collection.mutable.ArrayBuffer.$plus$plus$eq(ArrayBuffer.scala:104)
    at scala.collection.mutable.ArrayBuffer.$plus$plus$eq(ArrayBuffer.scala:48)
    at scala.collection.TraversableOnce$class.to(TraversableOnce.scala:310)
    at scala.collection.AbstractIterator.to(Iterator.scala:1336)
    at scala.collection.TraversableOnce$class.toBuffer(TraversableOnce.scala:302)
    at scala.collection.AbstractIterator.toBuffer(Iterator.scala:1336)
    at scala.collection.TraversableOnce$class.toArray(TraversableOnce.scala:289)
    at scala.collection.AbstractIterator.toArray(Iterator.scala:1336)
    at org.apache.spark.rdd.RDD$$anonfun$take$1$$anonfun$29.apply(RDD.scala:1305)
    at org.apache.spark.rdd.RDD$$anonfun$take$1$$anonfun$29.apply(RDD.scala:1305)
    at org.apache.spark.SparkContext$$anonfun$runJob$5.apply(SparkContext.scala:1897)
    at org.apache.spark.SparkContext$$anonfun$runJob$5.apply(SparkContext.scala:1897)
    at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:70)
    at org.apache.spark.scheduler.Task.run(Task.scala:85)
    at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:274)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
    at java.lang.Thread.run(Thread.java:745)

Driver stacktrace:
    at org.apache.spark.scheduler.DAGScheduler.org$apache$spark$scheduler$DAGScheduler$$failJobAndIndependentStages(DAGScheduler.scala:1450)
    at org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1438)
    at org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1437)
    at scala.collection.mutable.ResizableArray$class.foreach(ResizableArray.scala:59)
    at scala.collection.mutable.ArrayBuffer.foreach(ArrayBuffer.scala:48)
    at org.apache.spark.scheduler.DAGScheduler.abortStage(DAGScheduler.scala:1437)
    at org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:811)
    at org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:811)
    at scala.Option.foreach(Option.scala:257)
    at org.apache.spark.scheduler.DAGScheduler.handleTaskSetFailed(DAGScheduler.scala:811)
    at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.doOnReceive(DAGScheduler.scala:1659)
    at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:1618)
    at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:1607)
    at org.apache.spark.util.EventLoop$$anon$1.run(EventLoop.scala:48)
    at org.apache.spark.scheduler.DAGScheduler.runJob(DAGScheduler.scala:632)
    at org.apache.spark.SparkContext.runJob(SparkContext.scala:1871)
    at org.apache.spark.SparkContext.runJob(SparkContext.scala:1884)
    at org.apache.spark.SparkContext.runJob(SparkContext.scala:1897)
    at org.apache.spark.rdd.RDD$$anonfun$take$1.apply(RDD.scala:1305)
    at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151)
    at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:112)
    at org.apache.spark.rdd.RDD.withScope(RDD.scala:358)
    at org.apache.spark.rdd.RDD.take(RDD.scala:1279)
    at org.apache.spark.api.python.SerDeUtil$.pythonToPairRDD(SerDeUtil.scala:233)
    at org.apache.spark.api.python.PythonRDD$.saveAsHadoopFile(PythonRDD.scala:797)
    at org.apache.spark.api.python.PythonRDD$.saveAsSequenceFile(PythonRDD.scala:772)
    at org.apache.spark.api.python.PythonRDD.saveAsSequenceFile(PythonRDD.scala)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:606)
    at py4j.reflection.MethodInvoker.invoke(MethodInvoker.java:237)
    at py4j.reflection.ReflectionEngine.invoke(ReflectionEngine.java:357)
    at py4j.Gateway.invoke(Gateway.java:280)
    at py4j.commands.AbstractCommand.invokeMethod(AbstractCommand.java:128)
    at py4j.commands.CallCommand.execute(CallCommand.java:79)
    at py4j.GatewayConnection.run(GatewayConnection.java:211)
    at java.lang.Thread.run(Thread.java:745)
Caused by: net.razorvine.pickle.PickleException: expected zero arguments for construction of ClassDict (for pyspark.ml.linalg.SparseVector)
    at net.razorvine.pickle.objects.ClassDictConstructor.construct(ClassDictConstructor.java:23)
    at net.razorvine.pickle.Unpickler.load_reduce(Unpickler.java:707)
    at net.razorvine.pickle.Unpickler.dispatch(Unpickler.java:175)
    at net.razorvine.pickle.Unpickler.load(Unpickler.java:99)
    at net.razorvine.pickle.Unpickler.loads(Unpickler.java:112)
    at org.apache.spark.api.python.SerDeUtil$$anonfun$pythonToJava$1$$anonfun$apply$1.apply(SerDeUtil.scala:152)
    at org.apache.spark.api.python.SerDeUtil$$anonfun$pythonToJava$1$$anonfun$apply$1.apply(SerDeUtil.scala:151)
    at scala.collection.Iterator$$anon$12.nextCur(Iterator.scala:434)
    at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:440)
    at scala.collection.Iterator$$anon$10.hasNext(Iterator.scala:389)
    at scala.collection.Iterator$class.foreach(Iterator.scala:893)
    at scala.collection.AbstractIterator.foreach(Iterator.scala:1336)
    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$class.to(TraversableOnce.scala:310)
    at scala.collection.AbstractIterator.to(Iterator.scala:1336)
    at scala.collection.TraversableOnce$class.toBuffer(TraversableOnce.scala:302)
    at scala.collection.AbstractIterator.toBuffer(Iterator.scala:1336)
    at scala.collection.TraversableOnce$class.toArray(TraversableOnce.scala:289)
    at scala.collection.AbstractIterator.toArray(Iterator.scala:1336)
    at org.apache.spark.rdd.RDD$$anonfun$take$1$$anonfun$29.apply(RDD.scala:1305)
    at org.apache.spark.rdd.RDD$$anonfun$take$1$$anonfun$29.apply(RDD.scala:1305)
    at org.apache.spark.SparkContext$$anonfun$runJob$5.apply(SparkContext.scala:1897)
    at org.apache.spark.SparkContext$$anonfun$runJob$5.apply(SparkContext.scala:1897)
    at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:70)
    at org.apache.spark.scheduler.Task.run(Task.scala:85)
    at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:274)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
    ... 1 more

Does this problem lie in the hadoop-native library that isn't loaded? because simple types like Integers and Strings work. If it can't be done this way, is there any fast and compact way to serialize a large collection of sparse vectors?

1
pythonapache-sparkpyspark

1 Answers

2
votes

Native Hadoop libraries are not an issue here. The problem here is a SparseVector class itself. ml / mllib vectors heavily use native NumPy structures which cannot be handled by Pyrolite library.

Arguably using sequence files in PySpark to handle anything else than built-in types is just a waste of time. Since custom objects are represented as Map<String, Object> and dict in Java and Python respectively you cannot even seamlessly retrieve saved Python objects. For example object of class Foo:

class Foo(object):
    def __init__(self, x):
        self.x = x

foo = Foo(1)

becomes:

{'__class__': 'foo.Foo', 'x': 1}

in Python and something roughly equivalent to

import scala.collection.mutable.Map
import scala.collection.JavaConverters.mapAsJavaMapConverter

Map[String, Any]("__class__" -> "foo.Foo", "x" -> 1).asJava

on JVM.

If you want to save Vectors in a reliable way you can for example use Parquet:

rdd.zipWithIndex().toDF().write.parquet(...)