R - Sparklyr :spark_apply函数在集群模式下不起作用

Question

我组合了两个具有不同行数的数据帧。通过qpcR库使用cbind.na函数合并了两个数据帧。它显示了在我的本地机器中使用spark_apply功能在 sparklyr 中的结果。但是，在群集模式下，它显示错误如下。

注意：单个数据帧同时显示集群和本地的结果。

Error : Error: org.apache.spark.SparkException: Job aborted due to stage failure: Task 0 in stage 111.0 failed 4 times, most recent failure: Lost task 0.3 in stage 111.0 (TID 229, 192.168.1.20, executor 1): java.lang.Exception: sparklyr worker rscript failure, check worker logs for details.
    at sparklyr.Rscript.init(rscript.scala:56)
    at sparklyr.WorkerRDD$$anon$2.run(rdd.scala:89)
Driver stacktrace:
    at org.apache.spark.scheduler.DAGScheduler.org$apache$spark$scheduler$DAGScheduler$$failJobAndIndependentStages(DAGScheduler.scala:1499)
    at org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1487)
    at org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1486)
    at scala.collection.mutable.ResizableArray$class.foreach(ResizableArray.scala:59)
    at scala.collection.mutable.ArrayBuffer.foreach(ArrayBuffer.scala:48)
    at org.apache.spark.scheduler.DAGScheduler.abortStage(DAGScheduler.scala:1486)
    at org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:814)
    at org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:814)
    at scala.Option.foreach(Option.scala:257)
    at org.apache.spark.scheduler.DAGScheduler.handleTaskSetFailed(DAGScheduler.scala:814)
    at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.doOnReceive(DAGScheduler.scala:1714)
    at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:1669)
    at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:1658)
    at org.apache.spark.util.EventLoop$$anon$1.run(EventLoop.scala:48)
    at org.apache.spark.scheduler.DAGScheduler.runJob(DAGScheduler.scala:630)
    at org.apache.spark.SparkContext.runJob(SparkContext.scala:2022)
    at org.apache.spark.SparkContext.runJob(SparkContext.scala:2043)
    at org.apache.spark.SparkContext.runJob(SparkContext.scala:2062)
    at org.apache.spark.rdd.RDD$$anonfun$take$1.apply(RDD.scala:1354)
    at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151)
    at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:112)
    at org.apache.spark.rdd.RDD.withScope(RDD.scala:362)
    at org.apache.spark.rdd.RDD.take(RDD.scala:1327)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:498)
    at sparklyr.Invoke$.invoke(invoke.scala:102)
    at sparklyr.StreamHandler$.handleMethodCall(stream.scala:97)
    at sparklyr.StreamHandler$.read(stream.scala:62)
    at sparklyr.BackendHandler.channelRead0(handler.scala:52)
    at sparklyr.BackendHandler.channelRead0(handler.scala:14)
    at io.netty.channel.SimpleChannelInboundHandler.channelRead(SimpleChannelInboundHandler.java:105)
    at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:357)
    at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:343)
    at io.netty.channel.AbstractChannelHandlerContext.fireChannelRead(AbstractChannelHandlerContext.java:336)
    at io.netty.handler.codec.MessageToMessageDecoder.channelRead(MessageToMessageDecoder.java:102)
    at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:357)
    at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:343)
    at io.netty.channel.AbstractChannelHandlerContext.fireChannelRead(AbstractChannelHandlerContext.java:336)
    at io.netty.handler.codec.ByteToMessageDecoder.fireChannelRead(ByteToMessageDecoder.java:293)
    at io.netty.handler.codec.ByteToMessageDecoder.channelRead(ByteToMessageDecoder.java:267)
    at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:357)
    at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:343)
    at io.netty.channel.AbstractChannelHandlerContext.fireChannelRead(AbstractChannelHandlerContext.java:336)
    at io.netty.channel.DefaultChannelPipeline$HeadContext.channelRead(DefaultChannelPipeline.java:1294)
    at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:357)
    at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:343)
    at io.netty.channel.DefaultChannelPipeline.fireChannelRead(DefaultChannelPipeline.java:911)
    at io.netty.channel.nio.AbstractNioByteChannel$NioByteUnsafe.read(AbstractNioByteChannel.java:131)
    at io.netty.channel.nio.NioEventLoop.processSelectedKey(NioEventLoop.java:643)
    at io.netty.channel.nio.NioEventLoop.processSelectedKeysOptimized(NioEventLoop.java:566)
    at io.netty.channel.nio.NioEventLoop.processSelectedKeys(NioEventLoop.java:480)
    at io.netty.channel.nio.NioEventLoop.run(NioEventLoop.java:442)
    at io.netty.util.concurrent.SingleThreadEventExecutor$2.run(SingleThreadEventExecutor.java:131)
    at io.netty.util.concurrent.DefaultThreadFactory$DefaultRunnableDecorator.run(DefaultThreadFactory.java:144)
    at java.lang.Thread.run(Thread.java:748)
Caused by: java.lang.Exception: sparklyr worker rscript failure, check worker logs for details.
    at sparklyr.Rscript.init(rscript.scala:56)
    at sparklyr.WorkerRDD$$anon$2.run(rdd.scala:89)

Answer 1

如果您在Spark Apply中使用qPCR，则可能无法在群集模式下工作，因为本地机器可能是Windows，集群机器可能是linux。最好尝试另一种方法。