Stage Failure Error - r

I have the following code:
setwd("C:\\Users\\Anonymous\\Desktop\\Data 2014")
Sys.setenv(SPARK_HOME = "C:\\Users\\Anonymous\\Desktop\\Spark-1.4.1\\spark-1.6.0-bin-hadoop2.6\\spark-1.6.0-bin-hadoop2.6")
Sys.setenv('SPARKR_SUBMIT_ARGS'='"--packages" "com.databricks:spark-csv_2.10:1.3.0" "sparkr-shell"')
.libPaths(c(file.path(Sys.getenv("SPARK_HOME"), "R", "lib"), .libPaths()))
library(SparkR)
library(magrittr)
sc <- sparkR.init(master = "local")
sqlContext <- sparkRSQL.init(sc)
When I run the following:
data <- read.df(sqlContext, "Test.csv", "com.databricks.spark.csv", header="true")
I get the following error:
Error in invokeJava(isStatic = TRUE, className, methodName, ...) :
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): java.lang.NullPointerException
Test.csv is only a 3 x 2 table.

You will get the more details and cause of the error you are getting in the below link. https://databricks.gitbooks.io/databricks-spark-knowledge-base/content/troubleshooting/javaionotserializableexception.html
You have to give the full path of the csv file,if the file in not in your present working directory.I have not much idea. Below I have pasted the code. It is working fine for me you can try it.
Sys.setenv(SPARK_HOME='/home/jayashree/spark-1.5.0') # the path of spark_home dir. Please change it according to your spark home path
.libPaths(c(file.path(Sys.getenv('SPARK_HOME'), 'R', 'lib'), .libPaths()))
library(SparkR)
sc <- sparkR.init(master="local", sparkPackages="com.databricks:spark-csv_2.11:1.2.0")
sqlContext <- sparkRSQL.init(sc)
data <- read.df(sqlContext, "/full_path/to_your/datafile.csv", "com.databricks.spark.csv", header="true")
Are you working on windows?

Related

spark_write_csv doesn't work anymore (with Sparklyr)

spark_write_csv function doesn't work anymore, maybe since I upgraded the Spark version. Could someone help please?
Here is the code example, and the error message below:
library(sparklyr)
library(dplyr)
spark_conn <- spark_connect(master = "local")
iris <- copy_to(spark_conn, iris, overwrite = TRUE)
spark_write_csv(iris, path = "iris.csv")
Error: org.apache.spark.SparkException: Job aborted.
at org.apache.spark.sql.execution.datasources.FileFormatWriter$.write(FileFormatWriter.scala:231)
at org.apache.spark.sql.execution.datasources.InsertIntoHadoopFsRelationCommand.run(InsertIntoHadoopFsRelationCommand.scala:188)
at org.apache.spark.sql.execution.command.DataWritingCommandExec.sideEffectResult$lzycompute(commands.scala:108)
at org.apache.spark.sql.execution.command.DataWritingCommandExec.sideEffectResult(commands.scala:106)
at org.apache.spark.sql.execution.command.DataWritingCommandExec.doExecute(commands.scala:131)
at org.apache.spark.sql.execution.SparkPlan.$anonfun$execute$1(SparkPlan.scala:180)
at org.apache.spark.sql.execution.SparkPlan.$anonfun$executeQuery$1(SparkPlan.scala:218)
at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151)
at org.apache.spark.sql.execution.SparkPlan.executeQuery(SparkPlan.scala:215)
at org.apache.spark.sql.execution.SparkPlan.execute(SparkPlan.scala:176)
at org.apache.spark.sql.execution.QueryExecution.toRdd$lzycompute(QueryExecution.scala:132)

Spark 2.0 pre - CSV parsing error if missing values in date column

Trying to read a CSV file to Spark (using SparkR) containing just this data row:
1|1998-01-01||
Using Spark 1.6.2 (Hadoop 2.6) gives me
> head(sdf)
id d dtwo
1 1 1998-01-01 NA
Spark 2.0 preview (Hadoop 2.7, Rev. 14308) fails with error:
Error in invokeJava(isStatic = TRUE, className, methodName, ...) :
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): java.text.ParseException: Unparseable date: ""
at java.text.DateFormat.parse(DateFormat.java:357)
at org.apache.spark.sql.execution.datasources.csv.CSVTypeCast$.castTo(CSVInferSchema.scala:289)
at org.apache.spark.sql.execution.datasources.csv.CSVRelation$$anonfun$csvParser$3.apply(CSVRelation.scala:98)
at org.apache.spark.sql.execution.datasources.csv.CSVRelation$$anonfun$csvParser$3.apply(CSVRelation.scala:74)
at org.apache.spark.sql.execution.datasources.csv.DefaultSource$$anonfun$buildReader$1$$anonfun$apply$1.apply(DefaultSource.scala:124)
at org.apache.spark.sql.execution.datasources.csv.DefaultSource$$anonfun$buildReader$1$$anonfun$apply$1.apply(DefaultSource.scala:124)
at scala.collection.Iterator$$anon$12.nextCur(Iterator.scala:434)
at scala.collection.Iterator$$anon$12.hasNext(Itera...
The problem seems indeed the NULL value here as with a valid date in the third CSV column it works.
R code:
#Sys.setenv(SPARK_HOME = 'c:/spark/spark-1.6.2-bin-hadoop2.6')
Sys.setenv(SPARK_HOME = 'C:/spark/spark-2.0.0-preview-bin-hadoop2.7')
.libPaths(c(file.path(Sys.getenv("SPARK_HOME"), "R", "lib"), .libPaths()))
library(SparkR)
sc <-
sparkR.init(
master = "local",
sparkPackages = "com.databricks:spark-csv_2.11:1.4.0"
)
sqlContext <- sparkRSQL.init(sc)
st <- structType(structField("id", "integer"), structField("d", "date"), structField("dtwo", "date"))
sdf <- read.df(
sqlContext,
path = "d:/date_test.csv",
source = "com.databricks.spark.csv",
schema = st,
inferSchema = "false",
delimiter = "|",
dateFormat = "yyyy-MM-dd",
nullValue = "",
mode = "PERMISSIVE"
)
head(sdf)
sparkR.stop()
Any idea what the problem is? Should a bug report be opened? (I am rather inexperienced with Spark, so I consider it likely that I am just doing something wrong...)

sparkR : sparkException on createDataFrame

I'm trying to run the sample dataframe example using RStudio.
I have the following code:
Sys.setenv(SPARK_HOME = "C:\\Users\\himanshu.babbar\\Desktop\\Babbar\\Softwares\\spark-1.6.0-bin")
Sys.setenv('SPARKR_SUBMIT_ARGS'='"--packages" "com.databricks:spark-csv_2.11:1.2.0" "sparkr-shell"')
.libPaths(c(file.path(Sys.getenv("SPARK_HOME"), "R", "lib"), .libPaths()))
library(SparkR)
sc <- sparkR.init(master = "local", sparkHome = SPARK_HOME, sparkEnvir = list(spark.driver.memory="512m"))
sqlContext <- sparkRSQL.init(sc)
# Create a simple local data.frame
localDF <- data.frame(name=c("John", "Smith", "Sarah"), age=c(19, 23, 18))
# Convert local data frame to a SparkR DataFrame
df <- createDataFrame(sqlContext, localDF)
On doing this, I'm getting the following exception :
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): java.lang.NullPointerException
at java.lang.ProcessBuilder.start(ProcessBuilder.java:1012)
at org.apache.hadoop.util.Shell.runCommand(Shell.java:482)
at org.apache.hadoop.util.Shell.run(Shell.java:455)
at org.apache.hadoop.util.Shell$ShellCommandExecutor.execute(Shell.java:715)
at org.apache.hadoop.fs.FileUtil.chmod(FileUtil.java:873)
at org.apache.hadoop.fs.FileUtil.chmod(FileUtil.java:853)
at org.apache.spark.util.Utils$.fetchFile(Utils.scala:406)
at org.apache.spark.executor.Executor$$anonfun$org$apache$spark$executor$Executor$$updateDependencies$5.apply(Executor.scala:404)
at org.apache.spark.executor.Executor$$anonfun$org$apache$spark$executor$Executor$$updateDependencies$5.apply(Executor.scala:396)
at scala.collection.TraversableLike$WithFilter$$anonfun$foreach$1.apply(TraversableLike.scala:772)
at scala.collection.mutable.HashMap$$anonfun$foreach$1.apply(HashMap.scala:98)
at scala.collection.mutable.HashMap$$anonfun$foreach$1.apply(HashMap.scala:98)
at scala.collection.mutable.HashTable$class.foreachEntry(HashTable.scala:226)
at scala.collection.mutable.HashMap.foreachEntry(HashMap.scala:39)
at scala.collection.mutable.HashMap.foreach(HashMap.scala:98)
at scala.collection.TraversableLike$WithFilter.foreach(TraversableLike.scala:771)
at org.apache.spark.executor.Executor.org$apache$spark$executor$Executor$$updateDependencies(Executor.scala:396)
at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:192)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
I'm able to run a similar code on my colleagues machine so this could be a configuration thing that i may have been missing. Any pointers here?
You appear to have a Hadoop version and/or libraries mismatch. This may not be "simple" to fix.
Get someone who understands Hadoop installations to take a look at your setup and then ensure the version of Spark you are using supports the Hadoop version on your machine (or the cluster you are connecting to).

SparkR Null Pointer Exception when trying to create a data frame

When trying to create a data frame in sparkR, I get an error regarding a Null Pointer Exception. I have pasted my code, and the error message below. Do I need to install any more packages in order for this code to run?
CODE
SPARK_HOME <- "C:\\Users\\erer\\Downloads\\spark-1.5.2-bin-hadoop2.4\\spark-1.5.2-bin-hadoop2.4"
Sys.setenv('SPARKR_SUBMIT_ARGS'='"--packages" "com.databricks:spark-csv_2.10:1.2.0" "sparkr-shell"')
library(SparkR, lib.loc = "C:\\Users\\erer\\Downloads\\spark-1.5.2-bin-hadoop2.4\\R\\lib")
library(SparkR)
library(rJava)
sc <- sparkR.init(master = "local", sparkHome = SPARK_HOME)
sqlContext <- sparkRSQL.init(sc)
localDF <- data.frame(name=c("John", "Smith", "Sarah"), age=c(19, 23, 18))
df <- createDataFrame(sqlContext, localDF)
ERROR:
Error in invokeJava(isStatic = FALSE, objId$id, methodName, ...) :
org.apache.spark.SparkException: Job aborted due to stage failure: Task 0 in stage 1.0 failed 1 times, most recent failure: Lost task 0.0 in stage 1.0 (TID 1, localhost): java.lang.NullPointerException
at java.lang.ProcessBuilder.start(Unknown Source)
at org.apache.hadoop.util.Shell.runCommand(Shell.java:445)
at org.apache.hadoop.util.Shell.run(Shell.java:418)
at org.apache.hadoop.util.Shell$ShellCommandExecutor.execute(Shell.java:650)
at org.apache.hadoop.fs.FileUtil.chmod(FileUtil.java:873)
at org.apache.hadoop.fs.FileUtil.chmod(FileUtil.java:853)
at org.apache.spark.util.Utils$.fetchFile(Utils.scala:381)
at org.apache.spark.executor.Executor$$anonfun$org$apache$spark$executor$Executor$$updateDependencies$5.apply(Executor.scala:405)
at org.apache.spark.executor.Executor$$anonfun$org$apache$spark$executor$Executor$$updateDependencies$5.apply(Executor.scala:397)
at scala.collection.TraversableLike$WithFilter$$anonfun$foreach$1.apply(TraversableLike.scala:7
You need to point library SparkR to the directory where the local SparkR code is, specified in the lib.loc parameter (if you downloaded a Spark binary, the SPARK_HOME/R/lib will be already populated for you):
`library(SparkR, lib.loc = "/home/kris/spark/spark-1.5.2-bin-hadoop2.6/R/lib")`
See also this tutorial on R-bloggers on how to run Spark from Rstudio: http://www.r-bloggers.com/sparkr-with-rstudio-in-ubuntu-12-04/

SparkR can't load data into R

I followed the exact the same steps from other posts like this one to create a spark dataframe in R.
Sys.setenv(SPARK_HOME = "E:/spark-1.5.0-bin-hadoop2.6")
Sys.setenv('SPARKR_SUBMIT_ARGS'='"--packages" "com.databricks:spark-csv_2.10:1.2.0" "sparkr-shell"')
Sys.setenv(JAVA_HOME="C:/Program Files/Java/jre1.8.0_60")
library(rJava)
library(SparkR, lib.loc = "E:/spark-1.5.0-bin-hadoop2.6/R/lib/")
sc <- sparkR.init(master = "local", sparkHome = "E:/spark-1.5.0-bin-hadoop2.6")
sqlContext <- sparkRSQL.init(sc)
df <- createDataFrame(sqlContext, iris)
However, it keeps giving me the error at the very last step:
Error in invokeJava(isStatic = FALSE, objId$id, methodName, ...) :
org.apache.spark.SparkException: Job aborted due to stage failure: Task 0 in stage 1.0 failed 1 times, most recent failure: Lost task 0.0 in stage 1.0 (TID 1, localhost): java.lang.NullPointerException
at java.lang.ProcessBuilder.start(Unknown Source)
at org.apache.hadoop.util.Shell.runCommand(Shell.java:482)
at org.apache.hadoop.util.Shell.run(Shell.java:455)
at org.apache.hadoop.util.Shell$ShellCommandExecutor.execute(Shell.java:715)
at org.apache.hadoop.fs.FileUtil.chmod(FileUtil.java:873)
at org.apache.hadoop.fs.FileUtil.chmod(FileUtil.java:853)
at org.apache.spark.util.Utils$.fetchFile(Utils.scala:381)
at org.apache.spark.executor.Executor$$anonfun$org$apache$spark$executor$Executor$$updateDependencies$5.apply(Executor.scala:405)
at org.apache.spark.executor.Executor$$anonfun$org$apache$spark$executor$Executor$$updateDependencies$5.apply(Executor.scala:397)
at scala.collection.TraversableLike$WithFilter$$anonfun$foreach$1.apply(TraversableLike.scala:7

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