hive spark yarn-cluster job fails with: “ClassNotFoundException: org.datanucleus.api.jdo.JDOPersistenceManagerFactory”

Question

I'm attempting to run a pyspark script on BigInsights on Cloud 4.2 Enterprise that accesses a Hive table.

First I create the hive table:

[biadmin@bi4c-xxxxx-mastermanager ~]$ hive
hive> CREATE TABLE pokes (foo INT, bar STRING);
OK
Time taken: 2.147 seconds
hive> LOAD DATA LOCAL INPATH '/usr/iop/4.2.0.0/hive/doc/examples/files/kv1.txt' OVERWRITE INTO TABLE pokes;
Loading data to table default.pokes
Table default.pokes stats: [numFiles=1, numRows=0, totalSize=5812, rawDataSize=0]
OK
Time taken: 0.49 seconds
hive> 

Then I create a simple pyspark script:

[biadmin@bi4c-xxxxxx-mastermanager ~]$ cat test_pokes.py
from pyspark import SparkContext

sc = SparkContext()

from pyspark.sql import HiveContext
hc = HiveContext(sc)

pokesRdd = hc.sql('select * from pokes')
print( pokesRdd.collect() )

I attempt to execute with:

spark-submit --master yarn-cluster test_pokes.py

However, I encounter the error:

You must build Spark with Hive. Export 'SPARK_HIVE=true' and run build/sbt assembly
Traceback (most recent call last):
  File "test_pokes.py", line 8, in <module>
    pokesRdd = hc.sql('select * from pokes')
  File "/disk2/local/usercache/biadmin/appcache/application_1477084339086_0476/container_e09_1477084339086_0476_02_000001/pyspark.zip/pyspark/sql/context.py", line 580, in sql
  File "/disk2/local/usercache/biadmin/appcache/application_1477084339086_0476/container_e09_1477084339086_0476_02_000001/pyspark.zip/pyspark/sql/context.py", line 683, in _ssql_ctx
  File "/disk2/local/usercache/biadmin/appcache/application_1477084339086_0476/container_e09_1477084339086_0476_02_000001/pyspark.zip/pyspark/sql/context.py", line 692, in _get_hive_ctx
  File "/disk2/local/usercache/biadmin/appcache/application_1477084339086_0476/container_e09_1477084339086_0476_02_000001/py4j-0.9-src.zip/py4j/java_gateway.py", line 1064, in __call__
  File "/disk2/local/usercache/biadmin/appcache/application_1477084339086_0476/container_e09_1477084339086_0476_02_000001/pyspark.zip/pyspark/sql/utils.py", line 45, in deco
  File "/disk2/local/usercache/biadmin/appcache/application_1477084339086_0476/container_e09_1477084339086_0476_02_000001/py4j-0.9-src.zip/py4j/protocol.py", line 308, in get_return_value
py4j.protocol.Py4JJavaError: An error occurred while calling None.org.apache.spark.sql.hive.HiveContext.
: java.lang.RuntimeException: java.lang.RuntimeException: Unable to instantiate org.apache.hadoop.hive.ql.metadata.SessionHiveMetaStoreClient
    at org.apache.hadoop.hive.ql.session.SessionState.start(SessionState.java:522)
    ...
    ...
Caused by: javax.jdo.JDOFatalUserException: Class org.datanucleus.api.jdo.JDOPersistenceManagerFactory was not found.
NestedThrowables:
java.lang.ClassNotFoundException: org.datanucleus.api.jdo.JDOPersistenceManagerFactory
    ...
    ...
    at javax.jdo.JDOHelper.forName(JDOHelper.java:2015)
    at javax.jdo.JDOHelper.invokeGetPersistenceManagerFactoryOnImplementation(JDOHelper.java:1162)

I have seen a number of similar posts for other Hadoop distributions, but not for BigInsights on Cloud.

Answer 1

The solution to this error was to add the jars:

[biadmin@bi4c-xxxxxx-mastermanager ~]$ spark-submit \
    --master yarn-cluster \
    --deploy-mode cluster \
    --jars /usr/iop/4.2.0.0/hive/lib/datanucleus-api-jdo-3.2.6.jar, \
           /usr/iop/4.2.0.0/hive/lib/datanucleus-core-3.2.10.jar, \
           /usr/iop/4.2.0.0/hive/lib/datanucleus-rdbms-3.2.9.jar \
    test_pokes.py

However, I then get a different error:

pyspark.sql.utils.AnalysisException: u'Table not found: pokes; line 1 pos 14'

I've added the other question here: Spark Hive reporting pyspark.sql.utils.AnalysisException: u'Table not found: XXX' when run on yarn cluster

The final solution is captured here: https://stackoverflow.com/a/41272260/1033422