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sparkhail's Issues

ClassNotFoundException: sparkhail.CreateOption with Spark3.5

I was trying to use sparkhail. This version works with spark2.4, but not Spark3.5.

sc <- spark_connect(master = "local", config = hail_config())

  • Using Spark: 3.5.0
    Warning message:
    In normalizePath(unlist(unique(all_jars))) :
    path[1]="": No such file or directory
    Connected to your session in progress, last started 2023-Nov-06 20:45:00 UTC (1 hour ago)

hl <- hail_context(sc)
Error: java.lang.ClassNotFoundException: sparkhail.CreateOption
at java.base/java.net.URLClassLoader.findClass(URLClassLoader.java:476)
at java.base/java.lang.ClassLoader.loadClass(ClassLoader.java:594)
at java.base/java.lang.ClassLoader.loadClass(ClassLoader.java:527)
at java.base/java.lang.Class.forName0(Native Method)
at java.base/java.lang.Class.forName(Class.java:315)
at sparklyr.StreamHandler.handleMethodCall(stream.scala:111)
at sparklyr.StreamHandler.read(stream.scala:62)
at sparklyr.BackendHandler.$anonfun$channelRead0$1(handler.scala:60)
at scala.util.control.Breaks.breakable(Breaks.scala:42)
at sparklyr.BackendHandler.channelRead0(handler.scala:41)
at sparklyr.BackendHandler.channelRead0(handler.scala:14)
at io.netty.channel.SimpleChannelInboundHandler.channelRead(SimpleChannelInboundHandler.java:99)
at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:444)
at io.netty.channel.AbstractChannelHandlerContext.invok

SparkException: Failed to register classes with Kryo

Hello,
I'm very new to spark and hail.
But I installed sparklyr and sparkhail as the documentation, and I also installed spark 2.1.0 following sparklyr website. when I tried connecting to spark, I got this error message:

> sc <- spark_connect(master = "local[*]", version = "2.1.0", config = hail_config())
Warning message:
In normalizePath(unlist(unique(all_jars))) :
  path[1]="": No such file or directory
Error: org.apache.spark.SparkException: Job aborted due to stage failure: Task serialization failed: org.apache.spark.SparkException: Failed to register classes with Kryo
org.apache.spark.SparkException: Failed to register classes with Kryo
	at org.apache.spark.serializer.KryoSerializer.newKryo(KryoSerializer.scala:138)
	at org.apache.spark.serializer.KryoSerializerInstance.borrowKryo(KryoSerializer.scala:289)
	at org.apache.spark.serializer.KryoSerializerInstance.<init>(KryoSerializer.scala:274)
	at org.apache.spark.serializer.KryoSerializer.newInstance(KryoSerializer.scala:184)
	at org.apache.spark.broadcast.TorrentBroadcast$.blockifyObject(TorrentBroadcast.scala:265)
	at org.apache.spark.broadcast.TorrentBroadcast.writeBlocks(TorrentBroadcast.scala:126)
	at org.apache.spark.broadcast.TorrentBroadcast.<init>(TorrentBroadcast.scala:88)
	at org.apache.spark.broadcast.TorrentBroadcastFactory.newBroadcast(TorrentBroadcastFactory.scala:34)
	at org.apache.spark.broadcast.BroadcastManager.newBroadcast(BroadcastManager.scala:56)
	at org.apache.spark.SparkContext.broadcast(SparkContext.scala:1411)
	at org.apache.spark.scheduler.DAGScheduler.submitMissingTasks(DAGScheduler.scala:996)
	at org.apache.spark.scheduler.DAGScheduler.org$apache$spark$scheduler$DAGScheduler$$submitStage(DAGScheduler.scala:918)
	at org.apache.spark.scheduler.DAGScheduler$$anonfun$org$apache$spark$scheduler$DAGScheduler$$submitStage$4.apply(DAGScheduler.scala:921)
	at org.apache.spark.scheduler.DAGScheduler$$anonfun$org$apache$spark$scheduler$DAGScheduler$$submitStage$4.apply(DAGScheduler.scala:920)
	at scala.collection.immutable.List.foreach(List.scala:381)
	at org.apache.spark.scheduler.DAGScheduler.org$apache$spark$scheduler$DAGScheduler$$submitStage(DAGScheduler.scala:920)
	at org.apache.spark.scheduler.DAGScheduler.handleJobSubmitted(DAGScheduler.scala:862)
	at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.doOnReceive(DAGScheduler.scala:1613)
	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$$anon$1.run(EventLoop.scala:48)
Caused by: java.lang.ClassNotFoundException: is.hail.kryo.HailKryoRegistrator
	at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
	at java.lang.Class.forName0(Native Method)
	at java.lang.Class.forName(Class.java:348)
	at org.apache.spark.serializer.KryoSerializer$$anonfun$newKryo$5.apply(KryoSerializer.scala:133)
	at org.apache.spark.serializer.KryoSerializer$$anonfun$newKryo$5.apply(KryoSerializer.scala:133)
	at scala.collection.TraversableLike$$anonfun$map$1.apply(TraversableLike.scala:234)
	at scala.collection.TraversableLike$$anonfun$map$1.apply(TraversableLike.scala:234)
	at scala.collection.IndexedSeqOptimized$class.foreach(IndexedSeqOptimized.scala:33)
	at scala.collection.mutable.ArrayOps$ofRef.foreach(ArrayOps.scala:186)
	at scala.collection.TraversableLike$class.map(TraversableLike.scala:234)
	at scala.collection.mutable.ArrayOps$ofRef.map(ArrayOps.scala:186)
	at org.apache.spark.serializer.KryoSerializer.newKryo(KryoSerializer.scala:133)
	... 20 more

	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$$anonfun$abortStage$1.apply(DAGScheduler.scala:1422)
	at scala.collection.mutable.ResizableArray$class.foreach(ResizableArray.scala:59)
	at scala.collection.mutable.ArrayBuffer.foreach(ArrayBuffer.scala:48)
	at org.apache.spark.scheduler.DAGScheduler.abortStage(DAGScheduler.scala:1422)
	at org.apache.spark.scheduler.DAGScheduler.submitMissingTasks(DAGScheduler.scala:1006)
	at org.apache.spark.scheduler.DAGScheduler.org$apache$spark$scheduler$DAGScheduler$$submitStage(DAGScheduler.scala:918)
	at org.apache.spark.scheduler.DAGScheduler$$anonfun$org$apache$spark$scheduler$DAGScheduler$$submitStage$4.apply(DAGScheduler.scala:921)
	at org.apache.spark.scheduler.DAGScheduler$$anonfun$org$apache$spark$scheduler$DAGScheduler$$submitStage$4.apply(DAGScheduler.scala:920)
	at scala.collection.immutable.List.foreach(List.scala:381)
	at org.apache.spark.scheduler.DAGScheduler.org$apache$spark$scheduler$DAGScheduler$$submitStage(DAGScheduler.scala:920)
	at org.apache.spark.scheduler.DAGScheduler.handleJobSubmitted(DAGScheduler.scala:862)
	at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.doOnReceive(DAGScheduler.scala:1613)
	at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:1605)
	at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:1594)
	at org.apache.spark.util.EventLoop$$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:1944)
	at org.apache.spark.SparkContext.runJob(SparkContext.scala:1958)
	at org.apache.spark.rdd.RDD$$anonfun$collect$1.apply(RDD.scala:935)
	at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151)
	at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:112)
	at org.apache.spark.rdd.RDD.withScope(RDD.scala:362)
	at org.apache.spark.rdd.RDD.collect(RDD.scala:934)
	at org.apache.spark.sql.execution.SparkPlan.executeCollect(SparkPlan.scala:275)
	at org.apache.spark.sql.Dataset$$anonfun$org$apache$spark$sql$Dataset$$execute$1$1.apply(Dataset.scala:2371)
	at org.apache.spark.sql.execution.SQLExecution$.withNewExecutionId(SQLExecution.scala:57)
	at org.apache.spark.sql.Dataset.withNewExecutionId(Dataset.scala:2765)
	at org.apache.spark.sql.Dataset.org$apache$spark$sql$Dataset$$execute$1(Dataset.scala:2370)
	at org.apache.spark.sql.Dataset.org$apache$spark$sql$Dataset$$collect(Dataset.scala:2377)
	at org.apache.spark.sql.Dataset$$anonfun$count$1.apply(Dataset.scala:2405)
	at org.apache.spark.sql.Dataset$$anonfun$count$1.apply(Dataset.scala:2404)
	at org.apache.spark.sql.Dataset.withCallback(Dataset.scala:2778)
	at org.apache.spark.sql.Dataset.count(Dataset.scala:2404)
	at sparklyr.Utils$.collect(utils.scala:24)
	at sparklyr.Utils.collect(utils.scala)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:497)
	at sparklyr.Invoke.invoke(invoke.scala:161)
	at sparklyr.StreamHandler.handleMethodCall(stream.scala:141)
	at sparklyr.StreamHandler.read(stream.scala:62)
	at sparklyr.BackendHandler$$anonfun$channelRead0$1.apply$mcV$sp(handler.scala:60)
	at scala.util.control.Breaks.breakable(Breaks.scala:38)
	at sparklyr.BackendHandler.channelRead0(handler.scala:40)
	at sparklyr.BackendHandler.channelRead0(handler.scala:14)
	at io.netty.channel.SimpleChannelInboundHandler.channelRead(SimpleChannelInboundHandler.java:105)
	at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:367)
	at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:353)
	at io.netty.channel.AbstractChannelHandlerContext.fireChannelRead(AbstractChannelHandlerContext.java:346)
	at io.netty.handler.codec.MessageToMessageDecoder.channelRead(MessageToMessageDecoder.java:102)
	at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:367)
	at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerCo

But if I run sc <- spark_connect(master = "local[*]", version = "2.1.0"), there is error message.

I appreciate any help!
Thanks!

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