Can't create dplyr src backed by SparkSQL in d

Question

Recently I found out about great dplyr.spark.hive package that enables dplyr frontend operations with spark or hive backend .

There is an information on how to install this package in package's README :

options(repos = c("http://r.piccolboni.info", unlist(options("repos"))))
install.packages("dplyr.spark.hive")

and there are also many examples on how to work with dplyr.spark.hive when one is already connected to hiveServer - check this.

But I am not able to connect to hiveServer, so I can not benefit from the great power of this package...

I've tried such commands, but they did not work out. Does anyone have any solution or comment on what am I doing wrong?

> library(dplyr.spark.hive, 
+         lib.loc = '/opt/wpusers/mkosinski/R/x86_64-redhat-linux-gnu-library/3.1')
Warning: changing locked binding for ‘over’ in ‘dplyr’ whilst loading ‘dplyr.spark.hive’
Warning: changing locked binding for ‘partial_eval’ in ‘dplyr’ whilst loading ‘dplyr.spark.hive’
Warning: changing locked binding for ‘default_op’ in ‘dplyr’ whilst loading ‘dplyr.spark.hive’
Warning messages:
1: replacing previous import by ‘purrr::%>%’ when loading ‘dplyr.spark.hive’ 
2: replacing previous import by ‘purrr::order_by’ when loading ‘dplyr.spark.hive’ 
> 
> Sys.setenv(SPARK_HOME = "/opt/spark-1.5.0-bin-hadoop2.4")
> Sys.setenv(HIVE_SERVER2_THRIFT_BIND_HOST = 'tools-1.hadoop.srv')
> Sys.setenv(HIVE_SERVER2_THRIFT_PORT = '10000')
> 
> my_db = src_SparkSQL()
Error in .jfindClass(as.character(driverClass)[1]) : class not found
> 
> my_db = src_SparkSQL(host = 'jdbc:hive2://tools-1.hadoop.srv:10000/loghost;auth=noSasl',
+                      port = 10000)
Error in .jfindClass(as.character(driverClass)[1]) : class not found
> 
> my_db = src_SparkSQL(start.server = TRUE)
Error in start.server() : 
  Couldn't start thrift server:org.apache.spark.sql.hive.thriftserver.HiveThriftServer2 running as process 37580.  Stop it first.
In addition: Warning message:
running command 'cd /opt/tech/prj_bdc/pmozie_status/user_topics;/opt/spark-1.5.0-bin-hadoop2.4/sbin/start-thriftserver.sh ' had status 1 
> 
> my_db = src_SparkSQL(start.server = TRUE,
+                      list(spark.num.executors='5', spark.executor.cores='5', master="yarn-client"))
Error in start.server() : 
  Couldn't start thrift server:org.apache.spark.sql.hive.thriftserver.HiveThriftServer2 running as process 37580.  Stop it first.
In addition: Warning message:
running command 'cd /opt/tech/prj_bdc/pmozie_status/user_topics;/opt/spark-1.5.0-bin-hadoop2.4/sbin/start-thriftserver.sh ' had status 1 

EDIT 2

I have set more paths to system variables like this but now I receive a warning telling me that some kind of Java logging-configuration is not specified bu I think it is

> library(dplyr.spark.hive, 
+         lib.loc = '/opt/wpusers/mkosinski/R/x86_64-redhat-linux-gnu-library/3.1')
Warning messages:
1: replacing previous import by ‘purrr::%>%’ when loading ‘dplyr.spark.hive’ 
2: replacing previous import by ‘purrr::order_by’ when loading ‘dplyr.spark.hive’ 
3: package ‘SparkR’ was built under R version 3.2.1 
> 
> Sys.setenv(SPARK_HOME = "/opt/spark-1.5.0-bin-hadoop2.4")
> Sys.setenv(HIVE_SERVER2_THRIFT_BIND_HOST = 'tools-1.hadoop.srv')
> Sys.setenv(HIVE_SERVER2_THRIFT_PORT = '10000')
> Sys.setenv(HADOOP_JAR = "/opt/spark-1.5.0-bin-hadoop2.4/lib/spark-assembly-1.5.0-hadoop2.4.0.jar")
> Sys.setenv(HADOOP_HOME="/usr/share/hadoop")
> Sys.setenv(HADOOP_CONF_DIR="/etc/hadoop")
> Sys.setenv(PATH='/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/share/hadoop/bin:/opt/hive/bin')
> 
> 
> my_db = src_SparkSQL()
log4j:WARN No appenders could be found for logger (org.apache.hive.jdbc.Utils).
log4j:WARN Please initialize the log4j system properly.
log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for more info.

My log properties are not empty.

-bash-4.2$ wc /etc/hadoop/log4j.properties 
 179  432 6581 /etc/hadoop/log4j.properties

EDIT 3

My exact call to the scr_SparkSQL() is

> detach("package:SparkR", unload=TRUE)
Warning message:
package ‘SparkR’ was built under R version 3.2.1 
> detach("package:dplyr", unload=TRUE)
> library(dplyr.spark.hive, lib.loc = '/opt/wpusers/mkosinski/R/x86_64-redhat-linux-gnu-library/3.1')
Warning: changing locked binding for ‘over’ in ‘dplyr’ whilst loading ‘dplyr.spark.hive’
Warning: changing locked binding for ‘partial_eval’ in ‘dplyr’ whilst loading ‘dplyr.spark.hive’
Warning: changing locked binding for ‘default_op’ in ‘dplyr’ whilst loading ‘dplyr.spark.hive’
Warning messages:
1: replacing previous import by ‘purrr::%>%’ when loading ‘dplyr.spark.hive’ 
2: replacing previous import by ‘purrr::order_by’ when loading ‘dplyr.spark.hive’ 
> Sys.setenv(HADOOP_JAR = "/opt/spark-1.5.0-bin-hadoop2.4/lib/spark-assembly-1.5.0-hadoop2.4.0.jar")
> Sys.setenv(HIVE_SERVER2_THRIFT_BIND_HOST = 'tools-1.hadoop.srv')
> Sys.setenv(HIVE_SERVER2_THRIFT_PORT = '10000')
> my_db = src_SparkSQL()
log4j:WARN No appenders could be found for logger (org.apache.hive.jdbc.Utils).
log4j:WARN Please initialize the log4j system properly.
log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for more info.

And then the proces does not stop (never). Where those settings work for beeline with such params:

beeline  -u "jdbc:hive2://tools-1.hadoop.srv:10000/loghost;auth=noSasl" -n mkosinski --outputformat=tsv --incremental=true -f sql_statement.sql > sql_output

but I am not able to pass user name and dbname to src_SparkSQL() so I have tried to manual use the code from inside that function but I receive the sam problem that the below code also does not finish

host = 'tools-1.hadoop.srv'
port = 10000
driverclass = "org.apache.hive.jdbc.HiveDriver"
Sys.setenv(HADOOP_JAR = "/opt/spark-1.5.0-bin-hadoop2.4/lib/spark-assembly-1.5.0-hadoop2.4.0.jar")
library(RJDBC)
dr = JDBC(driverclass, Sys.getenv("HADOOP_JAR"))
url = paste0("jdbc:hive2://", host, ":", port)
class = "Hive"
con.class = paste0(class, "Connection") # class = "Hive"
# dbConnect_retry =
#   function(dr, url, retry){
#     if(retry > 0)
#       tryCatch(
#         dbConnect(drv = dr, url = url),
#         error =
#           function(e) {
#             Sys.sleep(0.1)
#             dbConnect_retry(dr = dr, url = url, retry - 1)})
#     else dbConnect(drv = dr, url = url)}
#################
##con = new(con.class, dbConnect_retry(dr, url, retry = 100))
#################
con = new(con.class, dbConnect(dr, url, user = "mkosinski", dbname = "loghost"))

Maybe the url should containg also /loghost - the dbname?

Answer 1

I now see that you tried multiple things with multiple errors. Let me comment error by error.

my_db = src_SparkSQL() Error in .jfindClass(as.character(driverClass)[1]) : class not found

The RJDBC object could not be created. Unless we solve this, nothing else will work, workarounds or not. Have you set HADOOP_JAR with, for instance, Sys.setenv(HADOOP_JAR = "../spark/assembly/target/scala-2.10/spark-assembly-1.5.0-hadoop2.6.0.jar"). Sorry I seem to have skipped this in the instructions. Will fix.

my_db = src_SparkSQL(host = 'jdbc:hive2://tools-1.hadoop.srv:10000/loghost;auth=noSasl', + port = 10000) Error in .jfindClass(as.character(driverClass)[1]) : class not found

Same problem. Please note host port argument do not accept URL syntax, just host and port. URL is formed internally.

my_db = src_SparkSQL(start.server = TRUE) Error in start.server() : Couldn't start thrift server:org.apache.spark.sql.hive.thriftserver.HiveThriftServer2 running as process 37580. Stop it first. In addition: Warning message: running command 'cd /opt/tech/prj_bdc/pmozie_status/user_topics;/opt/spark-1.5.0-bin-hadoop2.4/sbin/start-thriftserver.sh ' had status 1

Stop thriftserver first or connect to existing one, but you still have to fix the class not found problem.

my_db = src_SparkSQL(start.server = TRUE, + list(spark.num.executors='5', spark.executor.cores='5', master="yarn-client")) Error in start.server() : Couldn't start thrift server:org.apache.spark.sql.hive.thriftserver.HiveThriftServer2 running as process 37580. Stop it first. In addition: Warning message: running command 'cd /opt/tech/prj_bdc/pmozie_status/user_topics;/opt/spark-1.5.0-bin-hadoop2.4/sbin/start-thriftserver.sh ' had status 1

Same as above.

Plan:

• Set HADOOP_JAR. Find host and port of running thriftserver, if not default. Try src_SparkSQL with start.server = FALSE. If happy quit, else goto step 2
• Stop existing thriftserver. Try again src_SparkSQL with start.server = TRUE

Let me know how things go.

Answer 2

There was a problem that I did't specify the proper classPath that was needed inside JDBC function that created a driver. Parameters to classPath in dplyr.spark.hive package are passed via HADOOP_JAR global variable.

To use JDBC as a driver to hiveServer2 (through the Thrift protocol) one need to add at least those 3 .jars with Java classes to create a proper driver

• hive-jdbc-1.0.0-standalone.jar
• hadoop/common/lib/commons-configuration-1.6.jar
• hadoop/common/hadoop-common-2.4.1.jar

versions are arbitrary and should be compatible with the installed version of local hive, hadoop and hiveServer2.

They need to be set with the .Platform$path.sep (as described here)

classPath = c("system_path1_to_hive/hive/lib/hive-jdbc-1.0.0-standalone.jar",
                  "system_path1_to_hadoop/hadoop/common/lib/commons-configuration-1.6.jar",
                   "system_path1_to_hadoop/hadoop/common/hadoop-common-2.4.1.jar")
Sys.setenv(HADOOP_JAR= paste0(classPath, collapse=.Platform$path.sep)

Then when HADOOP_JAR is set one have to be carefull with hiveServer2 url. In my case it had to be

host = 'tools-1.hadoop.srv'
port = 10000
url = paste0("jdbc:hive2://", host, ":", port, "/loghost;auth=noSasl")

and finally the proper connection with hiveServer2 using RJDBC package is

Sys.setenv(HADOOP_HOME="/usr/share/hadoop/share/hadoop/common/")
Sys.setenv(HIVE_HOME = '/opt/hive/lib/')
host = 'tools-1.hadoop.srv'
port = 10000
url = paste0("jdbc:hive2://", host, ":", port, "/loghost;auth=noSasl")
driverclass = "org.apache.hive.jdbc.HiveDriver"
library(RJDBC)
.jinit()
dr2 = JDBC(driverclass,
           classPath = c("/opt/hive/lib/hive-jdbc-1.0.0-standalone.jar",
                         #"/opt/hive/lib/commons-configuration-1.6.jar",
                         "/usr/share/hadoop/share/hadoop/common/lib/commons-configuration-1.6.jar",
                         "/usr/share/hadoop/share/hadoop/common/hadoop-common-2.4.1.jar"),
           identifier.quote = "`")

url = paste0("jdbc:hive2://", host, ":", port, "/loghost;auth=noSasl")
dbConnect(dr2, url, username = "mkosinski") -> cont