Pyspark - Failed to locate the winutils binary in the hadoop binary path [duplicate]

Question

I am trying to integrate pyspark with python 2.7 (Pycharm IDE). I need to run some huge text files.

So this is what i am doing.

Download Spark (2.3.0-bin-hadoop-2.7) and extract it Install JDK

And then i am trying to run this script

spark_home = os.environ.get('SPARK_HOME', None) os.environ["SPARK_HOME"] = "C:\spark-2.3.0-bin-hadoop2.7" import pyspark from pyspark import SparkContext, SparkConf from pyspark.sql import SparkSession

conf = SparkConf()
sc = SparkContext(conf=conf)
spark = SparkSession.builder.config(conf=conf).getOrCreate() 
import pandas as pd
ip = spark.read.format("csv").option("inferSchema","true").option("header","true").load(r"D:\some file.csv")

Pycharm says that no module named Pyspark is found.

I am solving that by adding content roots and pointing to the folders where it is installed.

But the problem is every time i reopen pycharm, i have to add the content roots. How do i fix this?

Next is, when i do manage to run the script it throws up the following error.

2018-06-01 12:20:49 ERROR Shell:397 - Failed to locate the winutils binary in the hadoop binary path
java.io.IOException: Could not locate executable null\bin\winutils.exe in the Hadoop binaries.
    at org.apache.hadoop.util.Shell.getQualifiedBinPath(Shell.java:379)
    at org.apache.hadoop.util.Shell.getWinUtilsPath(Shell.java:394)
    at org.apache.hadoop.util.Shell.<clinit>(Shell.java:387)
    at org.apache.hadoop.util.StringUtils.<clinit>(StringUtils.java:80)
    at org.apache.hadoop.security.SecurityUtil.getAuthenticationMethod(SecurityUtil.java:611)
    at org.apache.hadoop.security.UserGroupInformation.initialize(UserGroupInformation.java:273)
    at org.apache.hadoop.security.UserGroupInformation.ensureInitialized(UserGroupInformation.java:261)
    at org.apache.hadoop.security.UserGroupInformation.loginUserFromSubject(UserGroupInformation.java:791)
    at org.apache.hadoop.security.UserGroupInformation.getLoginUser(UserGroupInformation.java:761)
    at org.apache.hadoop.security.UserGroupInformation.getCurrentUser(UserGroupInformation.java:634)
    at org.apache.spark.util.Utils$$anonfun$getCurrentUserName$1.apply(Utils.scala:2464)
    at org.apache.spark.util.Utils$$anonfun$getCurrentUserName$1.apply(Utils.scala:2464)
    at scala.Option.getOrElse(Option.scala:121)
    at org.apache.spark.util.Utils$.getCurrentUserName(Utils.scala:2464)
    at org.apache.spark.SecurityManager.<init>(SecurityManager.scala:222)
    at org.apache.spark.deploy.SparkSubmit$.secMgr$lzycompute$1(SparkSubmit.scala:393)
    at org.apache.spark.deploy.SparkSubmit$.org$apache$spark$deploy$SparkSubmit$$secMgr$1(SparkSubmit.scala:393)
    at org.apache.spark.deploy.SparkSubmit$$anonfun$prepareSubmitEnvironment$7.apply(SparkSubmit.scala:401)
    at org.apache.spark.deploy.SparkSubmit$$anonfun$prepareSubmitEnvironment$7.apply(SparkSubmit.scala:401)
    at scala.Option.map(Option.scala:146)
    at org.apache.spark.deploy.SparkSubmit$.prepareSubmitEnvironment(SparkSubmit.scala:400)
    at org.apache.spark.deploy.SparkSubmit$.submit(SparkSubmit.scala:170)
    at org.apache.spark.deploy.SparkSubmit$.main(SparkSubmit.scala:136)
    at org.apache.spark.deploy.SparkSubmit.main(SparkSubmit.scala)
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by org.apache.hadoop.security.authentication.util.KerberosUtil (file:/C:/spark-2.3.0-bin-hadoop2.7/jars/hadoop-auth-2.7.3.jar) to method sun.security.krb5.Config.getInstance()
WARNING: Please consider reporting this to the maintainers of org.apache.hadoop.security.authentication.util.KerberosUtil
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
2018-06-01 12:20:49 WARN  NativeCodeLoader:62 - Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
Setting default log level to "WARN".
To adjust logging level use sc.setLogLevel(newLevel). For SparkR, use setLogLevel(newLevel).
2018-06-01 12:20:56 ERROR Executor:91 - Exception in task 0.0 in stage 0.0 (TID 0)
java.lang.ArrayIndexOutOfBoundsException: 63
    at org.apache.spark.unsafe.types.UTF8String.numBytesForFirstByte(UTF8String.java:191)
    at org.apache.spark.unsafe.types.UTF8String.numChars(UTF8String.java:206)
    at org.apache.spark.sql.catalyst.expressions.GeneratedClass$GeneratedIteratorForCodegenStage1.processNext(Unknown Source)
    at org.apache.spark.sql.execution.BufferedRowIterator.hasNext(BufferedRowIterator.java:43)
    at org.apache.spark.sql.execution.WholeStageCodegenExec$$anonfun$10$$anon$1.hasNext(WholeStageCodegenExec.scala:614)
    at org.apache.spark.sql.execution.SparkPlan$$anonfun$2.apply(SparkPlan.scala:253)
    at org.apache.spark.sql.execution.SparkPlan$$anonfun$2.apply(SparkPlan.scala:247)
    at org.apache.spark.rdd.RDD$$anonfun$mapPartitionsInternal$1$$anonfun$apply$25.apply(RDD.scala:830)
    at org.apache.spark.rdd.RDD$$anonfun$mapPartitionsInternal$1$$anonfun$apply$25.apply(RDD.scala:830)
    at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
    at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:324)
    at org.apache.spark.rdd.RDD.iterator(RDD.scala:288)
    at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
    at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:324)
    at org.apache.spark.rdd.RDD.iterator(RDD.scala:288)
    at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:87)
    at org.apache.spark.scheduler.Task.run(Task.scala:109)
    at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:345)
    at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1135)
    at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
    at java.base/java.lang.Thread.run(Thread.java:844)
2018-06-01 12:20:56 WARN  TaskSetManager:66 - Lost task 0.0 in stage 0.0 (TID 0, localhost, executor driver): java.lang.ArrayIndexOutOfBoundsException: 63
    at org.apache.spark.unsafe.types.UTF8String.numBytesForFirstByte(UTF8String.java:191)
    at org.apache.spark.unsafe.types.UTF8String.numChars(UTF8String.java:206)
    at org.apache.spark.sql.catalyst.expressions.GeneratedClass$GeneratedIteratorForCodegenStage1.processNext(Unknown Source)
    at org.apache.spark.sql.execution.BufferedRowIterator.hasNext(BufferedRowIterator.java:43)
    at org.apache.spark.sql.execution.WholeStageCodegenExec$$anonfun$10$$anon$1.hasNext(WholeStageCodegenExec.scala:614)
    at org.apache.spark.sql.execution.SparkPlan$$anonfun$2.apply(SparkPlan.scala:253)
    at org.apache.spark.sql.execution.SparkPlan$$anonfun$2.apply(SparkPlan.scala:247)
    at org.apache.spark.rdd.RDD$$anonfun$mapPartitionsInternal$1$$anonfun$apply$25.apply(RDD.scala:830)
    at org.apache.spark.rdd.RDD$$anonfun$mapPartitionsInternal$1$$anonfun$apply$25.apply(RDD.scala:830)
    at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
    at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:324)
    at org.apache.spark.rdd.RDD.iterator(RDD.scala:288)
    at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
    at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:324)
    at org.apache.spark.rdd.RDD.iterator(RDD.scala:288)
    at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:87)
    at org.apache.spark.scheduler.Task.run(Task.scala:109)
    at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:345)
    at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1135)
    at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
    at java.base/java.lang.Thread.run(Thread.java:844)

2018-06-01 12:20:56 ERROR TaskSetManager:70 - Task 0 in stage 0.0 failed 1 times; aborting job
Traceback (most recent call last):
  File "D:/Microsoft/ThemeSpark.py", line 13, in <module>
    ip = spark.read.format("csv").option("inferSchema","true").option("header","true").load(r"D:\Microsoft\xbox_13.5_26.5\Xbox Family.csv")
  File "C:\spark-2.3.0-bin-hadoop2.7\python\pyspark\sql\readwriter.py", line 166, in load
    return self._df(self._jreader.load(path))
  File "C:\spark-2.3.0-bin-hadoop2.7\python\lib\py4j-0.10.6-src.zip\py4j\java_gateway.py", line 1160, in __call__
  File "C:\spark-2.3.0-bin-hadoop2.7\python\pyspark\sql\utils.py", line 63, in deco
    return f(*a, **kw)
  File "C:\spark-2.3.0-bin-hadoop2.7\python\lib\py4j-0.10.6-src.zip\py4j\protocol.py", line 320, in get_return_value
py4j.protocol.Py4JJavaError: An error occurred while calling o25.load.
: org.apache.spark.SparkException: Job aborted due to stage failure: Task 0 in stage 0.0 failed 1 times, most recent failure: Lost task 0.0 in stage 0.0 (TID 0, localhost, executor driver): java.lang.ArrayIndexOutOfBoundsException: 63
    at org.apache.spark.unsafe.types.UTF8String.numBytesForFirstByte(UTF8String.java:191)
    at org.apache.spark.unsafe.types.UTF8String.numChars(UTF8String.java:206)
    at org.apache.spark.sql.catalyst.expressions.GeneratedClass$GeneratedIteratorForCodegenStage1.processNext(Unknown Source)
    at org.apache.spark.sql.execution.BufferedRowIterator.hasNext(BufferedRowIterator.java:43)
    at org.apache.spark.sql.execution.WholeStageCodegenExec$$anonfun$10$$anon$1.hasNext(WholeStageCodegenExec.scala:614)
    at org.apache.spark.sql.execution.SparkPlan$$anonfun$2.apply(SparkPlan.scala:253)
    at org.apache.spark.sql.execution.SparkPlan$$anonfun$2.apply(SparkPlan.scala:247)
    at org.apache.spark.rdd.RDD$$anonfun$mapPartitionsInternal$1$$anonfun$apply$25.apply(RDD.scala:830)
    at org.apache.spark.rdd.RDD$$anonfun$mapPartitionsInternal$1$$anonfun$apply$25.apply(RDD.scala:830)
    at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
    at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:324)
    at org.apache.spark.rdd.RDD.iterator(RDD.scala:288)
    at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
    at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:324)
    at org.apache.spark.rdd.RDD.iterator(RDD.scala:288)
    at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:87)
    at org.apache.spark.scheduler.Task.run(Task.scala:109)
    at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:345)
    at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1135)
    at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
    at java.base/java.lang.Thread.run(Thread.java:844)

Driver stacktrace:
    at org.apache.spark.scheduler.DAGScheduler.org$apache$spark$scheduler$DAGScheduler$$failJobAndIndependentStages(DAGScheduler.scala:1599)
    at org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1587)
    at org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1586)
    at scala.collection.mutable.ResizableArray$class.foreach(ResizableArray.scala:59)
    at scala.collection.mutable.ArrayBuffer.foreach(ArrayBuffer.scala:48)
    at org.apache.spark.scheduler.DAGScheduler.abortStage(DAGScheduler.scala:1586)
    at org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:831)
    at org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:831)
    at scala.Option.foreach(Option.scala:257)
    at org.apache.spark.scheduler.DAGScheduler.handleTaskSetFailed(DAGScheduler.scala:831)
    at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.doOnReceive(DAGScheduler.scala:1820)
    at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:1769)
    at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:1758)
    at org.apache.spark.util.EventLoop$$anon$1.run(EventLoop.scala:48)
    at org.apache.spark.scheduler.DAGScheduler.runJob(DAGScheduler.scala:642)
    at org.apache.spark.SparkContext.runJob(SparkContext.scala:2027)
    at org.apache.spark.SparkContext.runJob(SparkContext.scala:2048)
    at org.apache.spark.SparkContext.runJob(SparkContext.scala:2067)
    at org.apache.spark.sql.execution.SparkPlan.executeTake(SparkPlan.scala:363)
    at org.apache.spark.sql.execution.CollectLimitExec.executeCollect(limit.scala:38)
    at org.apache.spark.sql.Dataset.org$apache$spark$sql$Dataset$$collectFromPlan(Dataset.scala:3272)
    at org.apache.spark.sql.Dataset$$anonfun$head$1.apply(Dataset.scala:2484)
    at org.apache.spark.sql.Dataset$$anonfun$head$1.apply(Dataset.scala:2484)
    at org.apache.spark.sql.Dataset$$anonfun$52.apply(Dataset.scala:3253)
    at org.apache.spark.sql.execution.SQLExecution$.withNewExecutionId(SQLExecution.scala:77)
    at org.apache.spark.sql.Dataset.withAction(Dataset.scala:3252)
    at org.apache.spark.sql.Dataset.head(Dataset.scala:2484)
    at org.apache.spark.sql.Dataset.take(Dataset.scala:2698)
    at org.apache.spark.sql.execution.datasources.csv.TextInputCSVDataSource$.infer(CSVDataSource.scala:148)
    at org.apache.spark.sql.execution.datasources.csv.CSVDataSource.inferSchema(CSVDataSource.scala:63)
    at org.apache.spark.sql.execution.datasources.csv.CSVFileFormat.inferSchema(CSVFileFormat.scala:57)
    at org.apache.spark.sql.execution.datasources.DataSource$$anonfun$8.apply(DataSource.scala:202)
    at org.apache.spark.sql.execution.datasources.DataSource$$anonfun$8.apply(DataSource.scala:202)
    at scala.Option.orElse(Option.scala:289)
    at org.apache.spark.sql.execution.datasources.DataSource.getOrInferFileFormatSchema(DataSource.scala:201)
    at org.apache.spark.sql.execution.datasources.DataSource.resolveRelation(DataSource.scala:392)
    at org.apache.spark.sql.DataFrameReader.loadV1Source(DataFrameReader.scala:239)
    at org.apache.spark.sql.DataFrameReader.load(DataFrameReader.scala:227)
    at org.apache.spark.sql.DataFrameReader.load(DataFrameReader.scala:174)
    at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.base/java.lang.reflect.Method.invoke(Method.java:564)
    at py4j.reflection.MethodInvoker.invoke(MethodInvoker.java:244)
    at py4j.reflection.ReflectionEngine.invoke(ReflectionEngine.java:357)
    at py4j.Gateway.invoke(Gateway.java:282)
    at py4j.commands.AbstractCommand.invokeMethod(AbstractCommand.java:132)
    at py4j.commands.CallCommand.execute(CallCommand.java:79)
    at py4j.GatewayConnection.run(GatewayConnection.java:214)
    at java.base/java.lang.Thread.run(Thread.java:844)
Caused by: java.lang.ArrayIndexOutOfBoundsException: 63
    at org.apache.spark.unsafe.types.UTF8String.numBytesForFirstByte(UTF8String.java:191)
    at org.apache.spark.unsafe.types.UTF8String.numChars(UTF8String.java:206)
    at org.apache.spark.sql.catalyst.expressions.GeneratedClass$GeneratedIteratorForCodegenStage1.processNext(Unknown Source)
    at org.apache.spark.sql.execution.BufferedRowIterator.hasNext(BufferedRowIterator.java:43)
    at org.apache.spark.sql.execution.WholeStageCodegenExec$$anonfun$10$$anon$1.hasNext(WholeStageCodegenExec.scala:614)
    at org.apache.spark.sql.execution.SparkPlan$$anonfun$2.apply(SparkPlan.scala:253)
    at org.apache.spark.sql.execution.SparkPlan$$anonfun$2.apply(SparkPlan.scala:247)
    at org.apache.spark.rdd.RDD$$anonfun$mapPartitionsInternal$1$$anonfun$apply$25.apply(RDD.scala:830)
    at org.apache.spark.rdd.RDD$$anonfun$mapPartitionsInternal$1$$anonfun$apply$25.apply(RDD.scala:830)
    at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
    at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:324)
    at org.apache.spark.rdd.RDD.iterator(RDD.scala:288)
    at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
    at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:324)
    at org.apache.spark.rdd.RDD.iterator(RDD.scala:288)
    at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:87)
    at org.apache.spark.scheduler.Task.run(Task.scala:109)
    at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:345)
    at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1135)
    at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
    ... 1 mo

I did some research and inferred that it is caused by the absence of the winutils.exefrom the spark folder. I downloaded and placed it in the spark bin. Still this error keeps coming. How do i fixed this?

Answer 1

Spark normally requires a full Hadoop installation. However winutils.exe is a tool created to help if you don't plan to use Hadoop in order to perform distrubite computing, for example because you are only testing Spark locally, on Windows.

Press WIN+PAUSE, go to Advanced Settings and Environment variables.

Set the new environmental variable HADOOP_HOME to a directory of your choice. I recommend C:\winutils and not hadoop since this is not a full hadoop installation.

Create the directory bin inside it, place the file winutils.exe inside bin.

Edit PATH , append %HADOOP_HOME%\ to it.

Now pyspark should work fine, as long as you work locally without distrubuted features.