Currently when running spark on yarn, jars specified with --jars, --packages will be added twice, one is Spark's own file server, another is yarn's distributed cache, this can be seen from log:
./bin/spark-shell --master yarn-client --jars examples/target/scala-2.11/jars/scopt_2.11-3.3.0.jar
If specified the jar to be added is scopt jar, it will added twice:
16/07/14 15:06:48 INFO Server: Started @5603ms
16/07/14 15:06:48 INFO Utils: Successfully started service 'SparkUI' on port 4040.
16/07/14 15:06:48 INFO SparkUI: Bound SparkUI to 0.0.0.0, and started at http://192.168.0.102:4040
16/07/14 15:06:48 INFO SparkContext: Added JAR file:/Users/sshao/projects/apache-spark/examples/target/scala-2.11/jars/scopt_2.11-3.3.0.jar at spark://192.168.0.102:63996/jars/scopt_2.11-3.3.0.jar with timestamp 1468480008637
16/07/14 15:06:49 INFO RMProxy: Connecting to ResourceManager at /0.0.0.0:8032
16/07/14 15:06:49 INFO Client: Requesting a new application from cluster with 1 NodeManagers
16/07/14 15:06:49 INFO Client: Verifying our application has not requested more than the maximum memory capability of the cluster (8192 MB per container)
16/07/14 15:06:49 INFO Client: Will allocate AM container, with 896 MB memory including 384 MB overhead
16/07/14 15:06:49 INFO Client: Setting up container launch context for our AM
16/07/14 15:06:49 INFO Client: Setting up the launch environment for our AM container
16/07/14 15:06:49 INFO Client: Preparing resources for our AM container
16/07/14 15:06:49 WARN Client: Neither spark.yarn.jars nor spark.yarn.archive is set, falling back to uploading libraries under SPARK_HOME.
16/07/14 15:06:50 INFO Client: Uploading resource file:/private/var/folders/tb/8pw1511s2q78mj7plnq8p9g40000gn/T/spark-a446300b-84bf-43ff-bfb1-3adfb0571a42/__spark_libs__6486179704064718817.zip -> hdfs://localhost:8020/user/sshao/.sparkStaging/application_1468468348998_0009/__spark_libs__6486179704064718817.zip
16/07/14 15:06:51 INFO Client: Uploading resource file:/Users/sshao/projects/apache-spark/examples/target/scala-2.11/jars/scopt_2.11-3.3.0.jar -> hdfs://localhost:8020/user/sshao/.sparkStaging/application_1468468348998_0009/scopt_2.11-3.3.0.jar
16/07/14 15:06:51 INFO Client: Uploading resource file:/private/var/folders/tb/8pw1511s2q78mj7plnq8p9g40000gn/T/spark-a446300b-84bf-43ff-bfb1-3adfb0571a42/__spark_conf__326416236462420861.zip -> hdfs://localhost:8020/user/sshao/.sparkStaging/application_1468468348998_0009/__spark_conf__.zip
Actually it is not necessary to add into Spark's file server. This problem exists both in client and cluster modes, and it is introduced in
SPARK-15782 to fix the --packages not work in spark-shell.