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From Ted Yu <yuzhih...@gmail.com>
Subject Re: spark there is no space on the disk
Date Thu, 19 Mar 2015 21:24:06 GMT
For YARN, possibly this one ?

    <property>
      <name>yarn.nodemanager.local-dirs</name>
      <value>/hadoop/yarn/local</value>
    </property>

Cheers

On Thu, Mar 19, 2015 at 2:21 PM, Marcelo Vanzin <vanzin@cloudera.com> wrote:

> IIRC you have to set that configuration on the Worker processes (for
> standalone). The app can't override it (only for a client-mode
> driver). YARN has a similar configuration, but I don't know the name
> (shouldn't be hard to find, though).
>
> On Thu, Mar 19, 2015 at 11:56 AM, Davies Liu <davies@databricks.com>
> wrote:
> > Is it possible that `spark.local.dir` is overriden by others? The docs
> say:
> >
> >     NOTE: In Spark 1.0 and later this will be overriden by
> > SPARK_LOCAL_DIRS (Standalone, Mesos) or LOCAL_DIRS (YARN)
> >
> > On Sat, Mar 14, 2015 at 5:29 PM, Peng Xia <sparkpengxia@gmail.com>
> wrote:
> >> Hi Sean,
> >>
> >> Thank very much for your reply.
> >> I tried to config it from below code:
> >>
> >> sf = SparkConf().setAppName("test").set("spark.executor.memory",
> >> "45g").set("spark.cores.max", 62),set("spark.local.dir", "C:\\tmp")
> >>
> >> But still get the error.
> >> Do you know how I can config this?
> >>
> >>
> >> Thanks,
> >> Best,
> >> Peng
> >>
> >>
> >> On Sat, Mar 14, 2015 at 3:41 AM, Sean Owen <sowen@cloudera.com> wrote:
> >>>
> >>> It means pretty much what it says. You ran out of space on an executor
> >>> (not driver), because the dir used for serialization temp files is
> >>> full (not all volumes). Set spark.local.dirs to something more
> >>> appropriate and larger.
> >>>
> >>> On Sat, Mar 14, 2015 at 2:10 AM, Peng Xia <sparkpengxia@gmail.com>
> wrote:
> >>> > Hi
> >>> >
> >>> >
> >>> > I was running a logistic regression algorithm on a 8 nodes spark
> >>> > cluster,
> >>> > each node has 8 cores and 56 GB Ram (each node is running a windows
> >>> > system).
> >>> > And the spark installation driver has 1.9 TB capacity. The dataset
I
> was
> >>> > training on are has around 40 million records with around 6600
> features.
> >>> > But
> >>> > I always get this error during the training process:
> >>> >
> >>> > Py4JJavaError: An error occurred while calling
> >>> > o70.trainLogisticRegressionModelWithLBFGS.
> >>> > : org.apache.spark.SparkException: Job aborted due to stage failure:
> >>> > Task
> >>> > 2709 in stage 3.0 failed 4 times, most recent failure: Lost task
> 2709.3
> >>> > in
> >>> > stage 3.0 (TID 2766,
> >>> > workernode0.rbaHdInsightCluster5.b6.internal.cloudapp.net):
> >>> > java.io.IOException: There is not enough space on the disk
> >>> >         at java.io.FileOutputStream.writeBytes(Native Method)
> >>> >         at java.io.FileOutputStream.write(FileOutputStream.java:345)
> >>> >         at
> >>> > java.io.BufferedOutputStream.write(BufferedOutputStream.java:122)
> >>> >         at
> >>> >
> >>> >
> org.xerial.snappy.SnappyOutputStream.dumpOutput(SnappyOutputStream.java:300)
> >>> >         at
> >>> >
> >>> >
> org.xerial.snappy.SnappyOutputStream.rawWrite(SnappyOutputStream.java:247)
> >>> >         at
> >>> >
> org.xerial.snappy.SnappyOutputStream.write(SnappyOutputStream.java:107)
> >>> >         at
> >>> >
> >>> >
> java.io.ObjectOutputStream$BlockDataOutputStream.drain(ObjectOutputStream.java:1876)
> >>> >         at
> >>> >
> >>> >
> java.io.ObjectOutputStream$BlockDataOutputStream.writeByte(ObjectOutputStream.java:1914)
> >>> >         at
> >>> >
> >>> >
> java.io.ObjectOutputStream.writeFatalException(ObjectOutputStream.java:1575)
> >>> >         at
> >>> > java.io.ObjectOutputStream.writeObject(ObjectOutputStream.java:350)
> >>> >         at
> >>> >
> >>> >
> org.apache.spark.serializer.JavaSerializationStream.writeObject(JavaSerializer.scala:42)
> >>> >         at
> >>> >
> >>> >
> org.apache.spark.serializer.SerializationStream.writeAll(Serializer.scala:110)
> >>> >         at
> >>> >
> >>> >
> org.apache.spark.storage.BlockManager.dataSerializeStream(BlockManager.scala:1177)
> >>> >         at
> >>> > org.apache.spark.storage.DiskStore.putIterator(DiskStore.scala:78)
> >>> >         at
> >>> > org.apache.spark.storage.BlockManager.doPut(BlockManager.scala:787)
> >>> >         at
> >>> >
> >>> >
> org.apache.spark.storage.BlockManager.putIterator(BlockManager.scala:638)
> >>> >         at
> >>> >
> org.apache.spark.CacheManager.putInBlockManager(CacheManager.scala:145)
> >>> >         at
> >>> > org.apache.spark.CacheManager.getOrCompute(CacheManager.scala:70)
> >>> >         at org.apache.spark.rdd.RDD.iterator(RDD.scala:243)
> >>> >         at
> >>> > org.apache.spark.rdd.FilteredRDD.compute(FilteredRDD.scala:34)
> >>> >         at
> >>> > org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:278)
> >>> >         at org.apache.spark.rdd.RDD.iterator(RDD.scala:245)
> >>> >         at
> >>> > org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:61)
> >>> >         at org.apache.spark.scheduler.Task.run(Task.scala:56)
> >>> >         at
> >>> > org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:200)
> >>> >         at
> >>> >
> >>> >
> java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
> >>> >         at
> >>> >
> >>> >
> java.util.concurrent.ThreadPoolExecutor$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$$failJobAndIndependentStages(DAGScheduler.scala:1214)
> >>> >         at
> >>> >
> >>> >
> org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1203)
> >>> >         at
> >>> >
> >>> >
> org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1202)
> >>> >         at
> >>> >
> >>> >
> scala.collection.mutable.ResizableArray$class.foreach(ResizableArray.scala:59)
> >>> >         at
> >>> > scala.collection.mutable.ArrayBuffer.foreach(ArrayBuffer.scala:47)
> >>> >         at
> >>> >
> >>> >
> org.apache.spark.scheduler.DAGScheduler.abortStage(DAGScheduler.scala:1202)
> >>> >         at
> >>> >
> >>> >
> org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:696)
> >>> >         at
> >>> >
> >>> >
> org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:696)
> >>> >         at scala.Option.foreach(Option.scala:236)
> >>> >         at
> >>> >
> >>> >
> org.apache.spark.scheduler.DAGScheduler.handleTaskSetFailed(DAGScheduler.scala:696)
> >>> >         at
> >>> >
> >>> >
> org.apache.spark.scheduler.DAGSchedulerEventProcessActor$$anonfun$receive$2.applyOrElse(DAGScheduler.scala:1420)
> >>> >         at akka.actor.Actor$class.aroundReceive(Actor.scala:465)
> >>> >         at
> >>> >
> >>> >
> org.apache.spark.scheduler.DAGSchedulerEventProcessActor.aroundReceive(DAGScheduler.scala:1375)
> >>> >         at akka.actor.ActorCell.receiveMessage(ActorCell.scala:516)
> >>> >         at akka.actor.ActorCell.invoke(ActorCell.scala:487)
> >>> >         at akka.dispatch.Mailbox.processMailbox(Mailbox.scala:238)
> >>> >         at akka.dispatch.Mailbox.run(Mailbox.scala:220)
> >>> >         at
> >>> >
> >>> >
> akka.dispatch.ForkJoinExecutorConfigurator$AkkaForkJoinTask.exec(AbstractDispatcher.scala:393)
> >>> >         at
> >>> > scala.concurrent.forkjoin.ForkJoinTask.doExec(ForkJoinTask.java:260)
> >>> >         at
> >>> >
> >>> >
> scala.concurrent.forkjoin.ForkJoinPool$WorkQueue.runTask(ForkJoinPool.java:1339)
> >>> >         at
> >>> >
> scala.concurrent.forkjoin.ForkJoinPool.runWorker(ForkJoinPool.java:1979)
> >>> >         at
> >>> >
> >>> >
> scala.concurrent.forkjoin.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:107)
> >>> >
> >>> > The code is below:
> >>> >
> >>> > from pyspark.mllib.regression import LabeledPoint
> >>> > from pyspark.mllib.classification import LogisticRegressionWithSGD
> >>> > from numpy import array
> >>> > from sklearn.feature_extraction import FeatureHasher
> >>> > from pyspark import SparkContext
> >>> > sf = SparkConf().setAppName("test").set("spark.executor.memory",
> >>> > "45g").set("spark.cores.max", 62)
> >>> > sc = SparkContext(conf=sf)
> >>> > training_file = sc.textFile("train_small.txt")
> >>> > def hash_feature(line):
> >>> >     values = [0, dict()]
> >>> >     for index, x in enumerate(line.strip("\n").split('\t')):
> >>> >         if index == 0:
> >>> >             values[0] = float(x)
> >>> >         else:
> >>> >             values[1][str(index)+"_"+x] = 1
> >>> >     return values
> >>> > n_feature = 2**14
> >>> > hasher = FeatureHasher(n_features=n_feature)
> >>> > training_file_hashed = training_file.map(lambda line:
> >>> > [hash_feature(line)[0], hasher.transform([hash_feature(line)[1]])])
> >>> > def build_lable_points(line):
> >>> >     values = [0.0] * n_feature
> >>> >     for index, value in zip(line[1].indices, line[1].data):
> >>> >         values[index] = value
> >>> >     return LabeledPoint(line[0], values)
> >>> > parsed_training_data = training_file_hashed.map(lambda line:
> >>> > build_lable_points(line))
> >>> > model = LogisticRegressionWithSGD.train(parsed_training_data)
> >>> >
> >>> > Can anyone share any experience on this?
> >>
> >>
> >
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> >
>
>
>
> --
> Marcelo
>
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>

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