It looks likes due to R could not be found. Try to set zeppelin.R.cmd to
where R you installed in interpreter setting.
Roger Sherman <roger.sher...@quantium.com.au>于2017年6月2日周五 上午7:03写道：
> Hello there!
>
> I'm trying to get SparkR running on Zeppelin. I'm using Spark 2.0.2 (built
> with Scala 2.11), R 3.4.0, and Zeppelin 0.6.2, on a MapR cluster, and
> having very little success. I'm having a difficult time googling the
> errors, as it seems a lot of people get these errors when the SPARK_HOME
> isn't set, but in my case it is.
>
> The error in question is as follows:
>
> org.apache.commons.exec.ExecuteException: Execution failed (Exit value:
> -559038737. Caused by java.io.IOException: Cannot run program "R" (in
> directory "."): error=2, No such file or directory)
> at
> org.apache.commons.exec.DefaultExecutor$1.run(DefaultExecutor.java:205)
> at java.lang.Thread.run(Thread.java:745)
> Caused by: java.io.IOException: Cannot run program "R" (in directory "."):
> error=2, No such file or directory
> at java.lang.ProcessBuilder.start(ProcessBuilder.java:1047)
> at java.lang.Runtime.exec(Runtime.java:617)
> at
> org.apache.commons.exec.launcher.Java13CommandLauncher.exec(Java13CommandLauncher.java:61)
> at
> org.apache.commons.exec.DefaultExecutor.launch(DefaultExecutor.java:279)
> at
> org.apache.commons.exec.DefaultExecutor.executeInternal(DefaultExecutor.java:336)
> at
> org.apache.commons.exec.DefaultExecutor.access$200(DefaultExecutor.java:48)
> at
> org.apache.commons.exec.DefaultExecutor$1.run(DefaultExecutor.java:200)
> ... 1 more
> Caused by: java.io.IOException: error=2, No such file or directory
> at java.lang.UNIXProcess.forkAndExec(Native Method)
> at java.lang.UNIXProcess.<init>(UNIXProcess.java:187)
> at java.lang.ProcessImpl.start(ProcessImpl.java:130)
> at java.lang.ProcessBuilder.start(ProcessBuilder.java:1028)
> ... 7 more
>
>
> I have r-base and r-base-dev installed across the cluster, on bare metal
> (running Ubuntu 14.04), across the cluster, If I
> fire up just a sparkR shell, it works fine, and I can see the distributed job
> working in YARN.
>
> Here's the env output:
>
> SPARK_EXECUTOR_TIMEOUT=300
> HOSTNAME=zeppelin-test5285.platform-dev.company.com.au
> SPARK_HOME=/apps/spark/spark-2.0.2-bin-mapr5.1.0_yarn_fat_j7_2.11
> ZEPPELIN_MEM=-Xms1024m -Xmx1024m -XX:MaxPermSize=512m
> TERM=unknown
> HOST=node.company.com.au.local
> ZEPPELIN_INTERPRETER_DIR=/zeppelin/interpreter
> JAVA_INTP_OPTS= -Dfile.encoding=UTF-8
> -Dlog4j.configuration=file:///projects/platform-dev/apps/platform-dev-zeppelin-test5285/conf/log4j.properties
>
> -Dzeppelin.log.file=/zeppelin/logs/zeppelin-interpreter-sh-rsherman-zeppelin-test5285.platform-dev.company.com.au.log
> HADOOP_HOME=/opt/mapr/hadoop/hadoop-2.7.0
> SPARK_DRIVER_MEMORY=6g
> PORT0=31399
> APP_NAME=platform-dev-zeppelin-test5285
> MESOS_TASK_ID=platform-dev-zeppelin-test5285.ce9d43e1-466a-11e7-8ff4-0242ac1f3802
> ZEPPELIN_INTP_MEM=-Xms1024m -Xmx1024m -XX:MaxPermSize=512m
> SPARK_CONF_DIR=/projects/platform-dev/apps/platform-dev-zeppelin-test5285/conf/spark
> SPARK_EXECUTOR_MEMORY=12g
> JAVA_OPTS= -Dfile.encoding=UTF-8 -Xms1024m -Xmx1024m -XX:MaxPermSize=512m
> -Dlog4j.configuration=file:///projects/platform-dev/apps/platform-dev-zeppelin-test5285/conf/log4j.properties
>
> -Dzeppelin.log.file=/zeppelin/logs/zeppelin-rsherman-zeppelin-test5285.platform-company.com.au.log
> -Dfile.encoding=UTF-8 -Xms1024m -Xmx1024m -XX:MaxPermSize=512m
> -Dlog4j.configuration=file:///projects/platform-dev/apps/platform-dev-zeppelin-test5285/conf/log4j.properties
> USER=rsherman
> SUDO_USER=root
> ZEPPELIN_NOTEBOOK_DIR=/projects/platform-dev/apps/platform-dev-zeppelin-test5285/data/notebook
> SUDO_UID=0
> INITRD=no
> APP_USERNAME=rsherman
> SCALABLE=false
> MAPR_TICKETFILE_LOCATION=/home/rsherman/.maprticket
> ZEPPELIN_HOME=/zeppelin
> ZEPPELIN_RUNNER=java
> ZEPPELIN_WAR=/zeppelin/zeppelin-web/dist
> ZEPPELIN_PID_DIR=/zeppelin/run
> USERNAME=rsherman
> APP_REVISION=10
>
> Here are the flags set at build time:
>
> $make_distro --mvn ${MAVEN_HOME}/bin/mvn --name ${ARTIFACT_NAME} --tgz -Pyarn
> -Phadoop-${HADOOP_VERSION} -Phive -Psparkr -Phive-thriftserver
> -Pspark-ganglia-lgpl ${HADOOP_PROVIDED_OPTION}
> -Dhadoop.version=2.7.0-mapr-1602 -Dyarn.version=2.7.0-mapr-1602
> -Dzookeeper.version=3.4.5-mapr-1503 -Dscala-${SCALA_VERSION} -DskipTests -e
>
> And finally, here is the full stacktrace leading up to the failure:
>
> 17/06/01 02:22:06 INFO SchedulerFactory: Job
> paragraph_1496283119069_1363557346 started by scheduler
> org.apache.zeppelin.interpreter.remote.RemoteInterpretershared_session900607537
> 17/06/01 02:22:06 INFO Paragraph: run paragraph 20170601-021159_529838667
> using spark.r org.apache.zeppelin.interpreter.LazyOpenInterpreter@52a4904f
> 17/06/01 02:22:06 INFO SchedulerFactory: Job remoteInterpretJob_1496283726813
> started by scheduler org.apache.zeppelin.spark.SparkRInterpreter936853935
> 17/06/01 02:22:06 INFO ZeppelinR: File
> /tmp/zeppelin_sparkr-2889736965928624810.R created
> 17/06/01 02:22:06 ERROR ZeppelinR: Execution failed (Exit value: -559038737.
> Caused by java.io.IOException: Cannot run program "R" (in directory "."):
> error=2, No such file or directory)
> org.apache.commons.exec.ExecuteException: Execution failed (Exit value:
> -559038737. Caused by java.io.IOException: Cannot run program "R" (in
> directory "."): error=2, No such file or directory)
> at
> org.apache.commons.exec.DefaultExecutor$1.run(DefaultExecutor.java:205)
> at java.lang.Thread.run(Thread.java:745)
> Caused by: java.io.IOException: Cannot run program "R" (in directory "."):
> error=2, No such file or directory
> at java.lang.ProcessBuilder.start(ProcessBuilder.java:1047)
> at java.lang.Runtime.exec(Runtime.java:617)
> at
> org.apache.commons.exec.launcher.Java13CommandLauncher.exec(Java13CommandLauncher.java:61)
> at
> org.apache.commons.exec.DefaultExecutor.launch(DefaultExecutor.java:279)
> at
> org.apache.commons.exec.DefaultExecutor.executeInternal(DefaultExecutor.java:336)
> at
> org.apache.commons.exec.DefaultExecutor.access$200(DefaultExecutor.java:48)
> at
> org.apache.commons.exec.DefaultExecutor$1.run(DefaultExecutor.java:200)
> ... 1 more
> Caused by: java.io.IOException: error=2, No such file or directory
> at java.lang.UNIXProcess.forkAndExec(Native Method)
> at java.lang.UNIXProcess.<init>(UNIXProcess.java:187)
> at java.lang.ProcessImpl.start(ProcessImpl.java:130)
> at java.lang.ProcessBuilder.start(ProcessBuilder.java:1028)
> ... 7 more
> 17/06/01 02:22:07 ERROR Job: Job failed
> org.apache.zeppelin.interpreter.InterpreterException: sparkr is not responding
> at
> org.apache.zeppelin.spark.ZeppelinR.waitForRScriptInitialized(ZeppelinR.java:295)
> at org.apache.zeppelin.spark.ZeppelinR.request(ZeppelinR.java:235)
> at org.apache.zeppelin.spark.ZeppelinR.eval(ZeppelinR.java:183)
> at org.apache.zeppelin.spark.ZeppelinR.open(ZeppelinR.java:172)
> at
> org.apache.zeppelin.spark.SparkRInterpreter.open(SparkRInterpreter.java:85)
> at
> org.apache.zeppelin.interpreter.LazyOpenInterpreter.open(LazyOpenInterpreter.java:69)
> at
> org.apache.zeppelin.interpreter.LazyOpenInterpreter.interpret(LazyOpenInterpreter.java:93)
> at
> org.apache.zeppelin.interpreter.remote.RemoteInterpreterServer$InterpretJob.jobRun(RemoteInterpreterServer.java:341)
> at org.apache.zeppelin.scheduler.Job.run(Job.java:176)
> at
> org.apache.zeppelin.scheduler.FIFOScheduler$1.run(FIFOScheduler.java:139)
> at
> java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
> at java.util.concurrent.FutureTask.run(FutureTask.java:262)
> at
> java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$201(ScheduledThreadPoolExecutor.java:178)
> at
> java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:292)
> 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)
> 17/06/01 02:22:07 INFO SchedulerFactory: Job remoteInterpretJob_1496283726813
> finished by scheduler org.apache.zeppelin.spark.SparkRInterpreter936853935
> 17/06/01 02:22:07 INFO ZeppelinR: File
> /tmp/zeppelin_sparkr-5775729319721689200.R created
> 17/06/01 02:22:07 INFO NotebookServer: Job 20170601-021159_529838667 is
> finished
> 17/06/01 02:22:07 ERROR ZeppelinR: Execution failed (Exit value: -559038737.
> Caused by java.io.IOException: Cannot run program "R" (in directory "."):
> error=2, No such file or directory)
> org.apache.commons.exec.ExecuteException: Execution failed (Exit value:
> -559038737. Caused by java.io.IOException: Cannot run program "R" (in
> directory "."): error=2, No such file or directory)
> at
> org.apache.commons.exec.DefaultExecutor$1.run(DefaultExecutor.java:205)
> at java.lang.Thread.run(Thread.java:745)
> Caused by: java.io.IOException: Cannot run program "R" (in directory "."):
> error=2, No such file or directory
> at java.lang.ProcessBuilder.start(ProcessBuilder.java:1047)
> at java.lang.Runtime.exec(Runtime.java:617)
> at
> org.apache.commons.exec.launcher.Java13CommandLauncher.exec(Java13CommandLauncher.java:61)
> at
> org.apache.commons.exec.DefaultExecutor.launch(DefaultExecutor.java:279)
> at
> org.apache.commons.exec.DefaultExecutor.executeInternal(DefaultExecutor.java:336)
> at
> org.apache.commons.exec.DefaultExecutor.access$200(DefaultExecutor.java:48)
> at
> org.apache.commons.exec.DefaultExecutor$1.run(DefaultExecutor.java:200)
> ... 1 more
> Caused by: java.io.IOException: error=2, No such file or directory
> at java.lang.UNIXProcess.forkAndExec(Native Method)
> at java.lang.UNIXProcess.<init>(UNIXProcess.java:187)
> at java.lang.ProcessImpl.start(ProcessImpl.java:130)
> at java.lang.ProcessBuilder.start(ProcessBuilder.java:1028)
> ... 7 more
> 17/06/01 02:22:07 INFO SchedulerFactory: Job
> paragraph_1496283119069_1363557346 finished by scheduler
> org.apache.zeppelin.interpreter.remote.RemoteInterpretershared_session900607537
> 17/06/01 02:22:08 ERROR TThreadPoolServer: Error occurred during processing
> of message.
> org.apache.zeppelin.interpreter.InterpreterException: sparkr is not responding
> at
> org.apache.zeppelin.spark.ZeppelinR.waitForRScriptInitialized(ZeppelinR.java:295)
> at org.apache.zeppelin.spark.ZeppelinR.request(ZeppelinR.java:235)
> at org.apache.zeppelin.spark.ZeppelinR.eval(ZeppelinR.java:183)
> at org.apache.zeppelin.spark.ZeppelinR.open(ZeppelinR.java:172)
> at
> org.apache.zeppelin.spark.SparkRInterpreter.open(SparkRInterpreter.java:85)
> at
> org.apache.zeppelin.interpreter.LazyOpenInterpreter.open(LazyOpenInterpreter.java:69)
> at
> org.apache.zeppelin.interpreter.LazyOpenInterpreter.getProgress(LazyOpenInterpreter.java:110)
> at
> org.apache.zeppelin.interpreter.remote.RemoteInterpreterServer.getProgress(RemoteInterpreterServer.java:404)
> at
> org.apache.zeppelin.interpreter.thrift.RemoteInterpreterService$Processor$getProgress.getResult(RemoteInterpreterService.java:1509)
> at
> org.apache.zeppelin.interpreter.thrift.RemoteInterpreterService$Processor$getProgress.getResult(RemoteInterpreterService.java:1494)
> at org.apache.thrift.ProcessFunction.process(ProcessFunction.java:39)
> at org.apache.thrift.TBaseProcessor.process(TBaseProcessor.java:39)
> at
> org.apache.thrift.server.TThreadPoolServer$WorkerProcess.run(TThreadPoolServer.java:285)
> at
> java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
> at
> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
> at java.lang.Thread.run(Thread.java:745)
> 17/06/01 02:22:08 ERROR JobProgressPoller: Can not get or update progress
> org.apache.zeppelin.interpreter.InterpreterException:
> org.apache.thrift.transport.TTransportException
> at
> org.apache.zeppelin.interpreter.remote.RemoteInterpreter.getProgress(RemoteInterpreter.java:373)
> at
> org.apache.zeppelin.interpreter.LazyOpenInterpreter.getProgress(LazyOpenInterpreter.java:111)
> at org.apache.zeppelin.notebook.Paragraph.progress(Paragraph.java:237)
> at
> org.apache.zeppelin.scheduler.JobProgressPoller.run(JobProgressPoller.java:51)
> Caused by: org.apache.thrift.transport.TTransportException
> at
> org.apache.thrift.transport.TIOStreamTransport.read(TIOStreamTransport.java:132)
> at org.apache.thrift.transport.TTransport.readAll(TTransport.java:86)
> at
> org.apache.thrift.protocol.TBinaryProtocol.readAll(TBinaryProtocol.java:429)
> at
> org.apache.thrift.protocol.TBinaryProtocol.readI32(TBinaryProtocol.java:318)
> at
> org.apache.thrift.protocol.TBinaryProtocol.readMessageBegin(TBinaryProtocol.java:219)
> at org.apache.thrift.TServiceClient.receiveBase(TServiceClient.java:69)
> at
> org.apache.zeppelin.interpreter.thrift.RemoteInterpreterService$Client.recv_getProgress(RemoteInterpreterService.java:296)
> at
> org.apache.zeppelin.interpreter.thrift.RemoteInterpreterService$Client.getProgress(RemoteInterpreterService.java:281)
> at
> org.apache.zeppelin.interpreter.remote.RemoteInterpreter.getProgress(RemoteInterpreter.java:370)
> ... 3 more
>
>
> It's probably obvious that I don't have much experience with Zeppelin, so if
> I've left out anything obvious, just let me know and I'll be happy to add it.
> anyone could point me in the right direction, it would be greatly
> appreciated.
>
>
> Best Regards,
>
> Roger Sherman
>
>
