Pyspark error instantiating 'org.apache.spark.sql.hive.HiveSessionStateBuilder':"

Question

I was trying this code i also found on stackoverflow

from pyspark.mllib.linalg.distributed import RowMatrix
rows = sc.parallelize([(1, 2, 3), (4, 5, 6), (7, 8, 9), (10, 11, 12)])

# Convert to RowMatrix
mat = RowMatrix(rows)

# Calculate exact and approximate similarities
exact = mat.columnSimilarities()
approx = mat.columnSimilarities(0.05)

# Output
exact.entries.collect()
[MatrixEntry(0, 2, 0.991935352214),
 MatrixEntry(1, 2, 0.998441152599),
 MatrixEntry(0, 1, 0.997463284056)]

then when I ran exaxt.entries I got this error

---------------------------------------------------------------------------
IllegalArgumentException                  Traceback (most recent call last)
<ipython-input-3-912f64c8ec62> in <module>()
----> 1 print exact.entries

D:\opt\spark\spark-2.2.0-bin-hadoop2.7\python\pyspark\mllib\linalg\distributed.pyc in entries(self)
    824         # DataFrame on the Scala/Java side. Then we map each Row in
    825         # the DataFrame back to a MatrixEntry on this side.
--> 826         entries_df = callMLlibFunc("getMatrixEntries", self._java_matrix_wrapper._java_model)
    827         entries = entries_df.rdd.map(lambda row: MatrixEntry(row[0], row[1], row[2]))
    828         return entries

D:\opt\spark\spark-2.2.0-bin-hadoop2.7\python\pyspark\mllib\common.pyc in callMLlibFunc(name, *args)
    128     sc = SparkContext.getOrCreate()
    129     api = getattr(sc._jvm.PythonMLLibAPI(), name)
--> 130     return callJavaFunc(sc, api, *args)
    131 
    132 

D:\opt\spark\spark-2.2.0-bin-hadoop2.7\python\pyspark\mllib\common.pyc in callJavaFunc(sc, func, *args)
    121     """ Call Java Function """
    122     args = [_py2java(sc, a) for a in args]
--> 123     return _java2py(sc, func(*args))
    124 
    125 

D:\opt\spark\spark-2.2.0-bin-hadoop2.7\python\lib\py4j-0.10.4-src.zip\py4j\java_gateway.py in __call__(self, *args)
   1131         answer = self.gateway_client.send_command(command)
   1132         return_value = get_return_value(
-> 1133             answer, self.gateway_client, self.target_id, self.name)
   1134 
   1135         for temp_arg in temp_args:

D:\opt\spark\spark-2.2.0-bin-hadoop2.7\python\pyspark\sql\utils.pyc in deco(*a, **kw)
     77                 raise QueryExecutionException(s.split(': ', 1)[1], stackTrace)
     78             if s.startswith('java.lang.IllegalArgumentException: '):
---> 79                 raise IllegalArgumentException(s.split(': ', 1)[1], stackTrace)
     80             raise
     81     return deco

IllegalArgumentException: u"Error while instantiating 'org.apache.spark.sql.hive.HiveSessionStateBuilder':"

I installed Spark on windows10 using this site https://medium.com/@GalarnykMichael/install-spark-on-windows-pyspark-4498a5d8d66c

any fix on this? thanks

*update: additional error from cmd I dont understand the error. there actually exist a metastore_db in my folder

18/02/04 16:48:22 ERROR Schema: Failed initialising database.
Unable to open a test connection to the given database. JDBC url = jdbc:derby:;databaseName=metastore_db;create=true, username = APP. Terminating connection pool (set lazyInit to true if you expect to start your database after your app). Original Exception: ------
java.sql.SQLException: Failed to start database 'metastore_db' with class loader org.apache.spark.sql.hive.client.IsolatedClientLoader$$anon$1@700d488a, see the next exception for details.
        at org.apache.derby.impl.jdbc.SQLExceptionFactory.getSQLException(Unknown Source)
        at org.apache.derby.impl.jdbc.SQLExceptionFactory.getSQLException(Unknown Source)
        at org.apache.derby.impl.jdbc.Util.seeNextException(Unknown Source)
        at org.apache.derby.impl.jdbc.EmbedConnection.bootDatabase(Unknown Source)
        at org.apache.derby.impl.jdbc.EmbedConnection.<init>(Unknown Source)
        at org.apache.derby.jdbc.InternalDriver$1.run(Unknown Source)
        at org.apache.derby.jdbc.InternalDriver$1.run(Unknown Source)
        at java.security.AccessController.doPrivileged(Native Method)
        at org.apache.derby.jdbc.InternalDriver.getNewEmbedConnection(Unknown Source)
        at org.apache.derby.jdbc.InternalDriver.connect(Unknown Source)
        at org.apache.derby.jdbc.InternalDriver.connect(Unknown Source)
        at org.apache.derby.jdbc.AutoloadedDriver.connect(Unknown Source)
        at java.sql.DriverManager.getConnection(Unknown Source)
        at java.sql.DriverManager.getConnection(Unknown Source)
        at com.jolbox.bonecp.BoneCP.obtainRawInternalConnection(BoneCP.java:361)
        at com.jolbox.bonecp.BoneCP.<init>(BoneCP.java:416)
        at com.jolbox.bonecp.BoneCPDataSource.getConnection(BoneCPDataSource.java:120)
        at org.datanucleus.store.rdbms.ConnectionFactoryImpl$ManagedConnectionImpl.getConnection(ConnectionFactoryImpl.java:501)
        at org.datanucleus.store.rdbms.RDBMSStoreManager.<init>(RDBMSStoreManager.java:298)
        at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
        at sun.reflect.NativeConstructorAccessorImpl.newInstance(Unknown Source)
        at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown Source)
        at java.lang.reflect.Constructor.newInstance(Unknown Source)
        at org.datanucleus.plugin.NonManagedPluginRegistry.createExecutableExtension(NonManagedPluginRegistry.java:631)
        at org.datanucleus.plugin.PluginManager.createExecutableExtension(PluginManager.java:301)
        at org.datanucleus.NucleusContext.createStoreManagerForProperties(NucleusContext.java:1187)
        at org.datanucleus.NucleusContext.initialise(NucleusContext.java:356)
        at org.datanucleus.api.jdo.JDOPersistenceManagerFactory.freezeConfiguration(JDOPersistenceManagerFactory.java:775)
        at org.datanucleus.api.jdo.JDOPersistenceManagerFactory.createPersistenceManagerFactory(JDOPersistenceManagerFactory.java:333)
        at org.datanucleus.api.jdo.JDOPersistenceManagerFactory.getPersistenceManagerFactory(JDOPersistenceManagerFactory.java:202)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
        at java.lang.reflect.Method.invoke(Unknown Source)
        at javax.jdo.JDOHelper$16.run(JDOHelper.java:1965)
        at java.security.AccessController.doPrivileged(Native Method)
        at javax.jdo.JDOHelper.invoke(JDOHelper.java:1960)
        at javax.jdo.JDOHelper.invokeGetPersistenceManagerFactoryOnImplementation(JDOHelper.java:1166)
        at javax.jdo.JDOHelper.getPersistenceManagerFactory(JDOHelper.java:808)
        at javax.jdo.JDOHelper.getPersistenceManagerFactory(JDOHelper.java:701)
        at org.apache.hadoop.hive.metastore.ObjectStore.getPMF(ObjectStore.java:365)
        at org.apache.hadoop.hive.metastore.ObjectStore.getPersistenceManager(ObjectStore.java:394)
        at org.apache.hadoop.hive.metastore.ObjectStore.initialize(ObjectStore.java:291)
        at org.apache.hadoop.hive.metastore.ObjectStore.setConf(ObjectStore.java:258)
        at org.apache.hadoop.util.ReflectionUtils.setConf(ReflectionUtils.java:76)
        at org.apache.hadoop.util.ReflectionUtils.newInstance(ReflectionUtils.java:136)
        at org.apache.hadoop.hive.metastore.RawStoreProxy.<init>(RawStoreProxy.java:57)
        at org.apache.hadoop.hive.metastore.RawStoreProxy.getProxy(RawStoreProxy.java:66)
        at org.apache.hadoop.hive.metastore.HiveMetaStore$HMSHandler.newRawStore(HiveMetaStore.java:593)
        at org.apache.hadoop.hive.metastore.HiveMetaStore$HMSHandler.getMS(HiveMetaStore.java:571)
        at org.apache.hadoop.hive.metastore.HiveMetaStore$HMSHandler.createDefaultDB(HiveMetaStore.java:620)
        at org.apache.hadoop.hive.metastore.HiveMetaStore$HMSHandler.init(HiveMetaStore.java:461)
        at org.apache.hadoop.hive.metastore.RetryingHMSHandler.<init>(RetryingHMSHandler.java:66)
        at org.apache.hadoop.hive.metastore.RetryingHMSHandler.getProxy(RetryingHMSHandler.java:72)
        at org.apache.hadoop.hive.metastore.HiveMetaStore.newRetryingHMSHandler(HiveMetaStore.java:5762)
        at org.apache.hadoop.hive.metastore.HiveMetaStoreClient.<init>(HiveMetaStoreClient.java:199)
        at org.apache.hadoop.hive.ql.metadata.SessionHiveMetaStoreClient.<init>(SessionHiveMetaStoreClient.java:74)
        at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
        at sun.reflect.NativeConstructorAccessorImpl.newInstance(Unknown Source)
        at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown Source)
        at java.lang.reflect.Constructor.newInstance(Unknown Source)
        at org.apache.hadoop.hive.metastore.MetaStoreUtils.newInstance(MetaStoreUtils.java:1521)
        at org.apache.hadoop.hive.metastore.RetryingMetaStoreClient.<init>(RetryingMetaStoreClient.java:86)
        at org.apache.hadoop.hive.metastore.RetryingMetaStoreClient.getProxy(RetryingMetaStoreClient.java:132)
        at org.apache.hadoop.hive.metastore.RetryingMetaStoreClient.getProxy(RetryingMetaStoreClient.java:104)
        at org.apache.hadoop.hive.ql.metadata.Hive.createMetaStoreClient(Hive.java:3005)
        at org.apache.hadoop.hive.ql.metadata.Hive.getMSC(Hive.java:3024)
        at org.apache.hadoop.hive.ql.metadata.Hive.getAllDatabases(Hive.java:1234)
        at org.apache.hadoop.hive.ql.metadata.Hive.reloadFunctions(Hive.java:174)
        at org.apache.hadoop.hive.ql.metadata.Hive.<clinit>(Hive.java:166)
        at org.apache.hadoop.hive.ql.session.SessionState.start(SessionState.java:503)
        at org.apache.spark.sql.hive.client.HiveClientImpl.<init>(HiveClientImpl.scala:191)
        at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
        at sun.reflect.NativeConstructorAccessorImpl.newInstance(Unknown Source)
        at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown Source)
        at java.lang.reflect.Constructor.newInstance(Unknown Source)
        at org.apache.spark.sql.hive.client.IsolatedClientLoader.createClient(IsolatedClientLoader.scala:264)
        at org.apache.spark.sql.hive.HiveUtils$.newClientForMetadata(HiveUtils.scala:362)
        at org.apache.spark.sql.hive.HiveUtils$.newClientForMetadata(HiveUtils.scala:266)
        at org.apache.spark.sql.hive.HiveExternalCatalog.client$lzycompute(HiveExternalCatalog.scala:66)
        at org.apache.spark.sql.hive.HiveExternalCatalog.client(HiveExternalCatalog.scala:65)
        at org.apache.spark.sql.hive.HiveExternalCatalog$$anonfun$databaseExists$1.apply$mcZ$sp(HiveExternalCatalog.scala:194)
        at org.apache.spark.sql.hive.HiveExternalCatalog$$anonfun$databaseExists$1.apply(HiveExternalCatalog.scala:194)
        at org.apache.spark.sql.hive.HiveExternalCatalog$$anonfun$databaseExists$1.apply(HiveExternalCatalog.scala:194)
        at org.apache.spark.sql.hive.HiveExternalCatalog.withClient(HiveExternalCatalog.scala:97)
        at org.apache.spark.sql.hive.HiveExternalCatalog.databaseExists(HiveExternalCatalog.scala:193)
        at org.apache.spark.sql.internal.SharedState.externalCatalog$lzycompute(SharedState.scala:105)
        at org.apache.spark.sql.internal.SharedState.externalCatalog(SharedState.scala:93)
        at org.apache.spark.sql.hive.HiveSessionStateBuilder.externalCatalog(HiveSessionStateBuilder.scala:39)
        at org.apache.spark.sql.hive.HiveSessionStateBuilder.catalog$lzycompute(HiveSessionStateBuilder.scala:54)
        at org.apache.spark.sql.hive.HiveSessionStateBuilder.catalog(HiveSessionStateBuilder.scala:52)
        at org.apache.spark.sql.hive.HiveSessionStateBuilder.catalog(HiveSessionStateBuilder.scala:35)
        at org.apache.spark.sql.internal.BaseSessionStateBuilder.build(BaseSessionStateBuilder.scala:289)
        at org.apache.spark.sql.SparkSession$.org$apache$spark$sql$SparkSession$$instantiateSessionState(SparkSession.scala:1050)
        at org.apache.spark.sql.SparkSession$$anonfun$sessionState$2.apply(SparkSession.scala:130)
        at org.apache.spark.sql.SparkSession$$anonfun$sessionState$2.apply(SparkSession.scala:130)
        at scala.Option.getOrElse(Option.scala:121)
        at org.apache.spark.sql.SparkSession.sessionState$lzycompute(SparkSession.scala:129)
        at org.apache.spark.sql.SparkSession.sessionState(SparkSession.scala:126)
        at org.apache.spark.sql.Dataset$.ofRows(Dataset.scala:65)
        at org.apache.spark.sql.SparkSession.createDataFrame(SparkSession.scala:283)
        at org.apache.spark.mllib.api.python.PythonMLLibAPI.getMatrixEntries(PythonMLLibAPI.scala:1207)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
        at java.lang.reflect.Method.invoke(Unknown Source)
        at py4j.reflection.MethodInvoker.invoke(MethodInvoker.java:244)
        at py4j.reflection.ReflectionEngine.invoke(ReflectionEngine.java:357)
        at py4j.Gateway.invoke(Gateway.java:280)
        at py4j.commands.AbstractCommand.invokeMethod(AbstractCommand.java:132)
        at py4j.commands.CallCommand.execute(CallCommand.java:79)
        at py4j.GatewayConnection.run(GatewayConnection.java:214)
        at java.lang.Thread.run(Unknown Source)
Caused by: ERROR XJ040: Failed to start database 'metastore_db' with class loader org.apache.spark.sql.hive.client.IsolatedClientLoader$$anon$1@700d488a, see the next exception for details.
        at org.apache.derby.iapi.error.StandardException.newException(Unknown Source)
        at org.apache.derby.impl.jdbc.SQLExceptionFactory.wrapArgsForTransportAcrossDRDA(Unknown Source)
        ... 113 more
Caused by: ERROR XSDB6: Another instance of Derby may have already booted the database C:\Users\USER\Desktop\ColumnSimilarities\metastore_db.
        at org.apache.derby.iapi.error.StandardException.newException(Unknown Source)
        at org.apache.derby.iapi.error.StandardException.newException(Unknown Source)
        at org.apache.derby.impl.store.raw.data.BaseDataFileFactory.privGetJBMSLockOnDB(Unknown Source)
        at org.apache.derby.impl.store.raw.data.BaseDataFileFactory.run(Unknown Source)
        at java.security.AccessController.doPrivileged(Native Method)
        at org.apache.derby.impl.store.raw.data.BaseDataFileFactory.getJBMSLockOnDB(Unknown Source)
        at org.apache.derby.impl.store.raw.data.BaseDataFileFactory.boot(Unknown Source)
        at org.apache.derby.impl.services.monitor.BaseMonitor.boot(Unknown Source)
        at org.apache.derby.impl.services.monitor.TopService.bootModule(Unknown Source)
        at org.apache.derby.impl.services.monitor.BaseMonitor.startModule(Unknown Source)
        at org.apache.derby.impl.services.monitor.FileMonitor.startModule(Unknown Source)
        at org.apache.derby.iapi.services.monitor.Monitor.bootServiceModule(Unknown Source)
        at org.apache.derby.impl.store.raw.RawStore$6.run(Unknown Source)
        at java.security.AccessController.doPrivileged(Native Method)
        at org.apache.derby.impl.store.raw.RawStore.bootServiceModule(Unknown Source)
        at org.apache.derby.impl.store.raw.RawStore.boot(Unknown Source)
        at org.apache.derby.impl.services.monitor.BaseMonitor.boot(Unknown Source)
        at org.apache.derby.impl.services.monitor.TopService.bootModule(Unknown Source)
        at org.apache.derby.impl.services.monitor.BaseMonitor.startModule(Unknown Source)
        at org.apache.derby.impl.services.monitor.FileMonitor.startModule(Unknown Source)
        at org.apache.derby.iapi.services.monitor.Monitor.bootServiceModule(Unknown Source)
        at org.apache.derby.impl.store.access.RAMAccessManager$5.run(Unknown Source)
        at java.security.AccessController.doPrivileged(Native Method)
        at org.apache.derby.impl.store.access.RAMAccessManager.bootServiceModule(Unknown Source)
        at org.apache.derby.impl.store.access.RAMAccessManager.boot(Unknown Source)
        at org.apache.derby.impl.services.monitor.BaseMonitor.boot(Unknown Source)
        at org.apache.derby.impl.services.monitor.TopService.bootModule(Unknown Source)
        at org.apache.derby.impl.services.monitor.BaseMonitor.startModule(Unknown Source)
        at org.apache.derby.impl.services.monitor.FileMonitor.startModule(Unknown Source)
        at org.apache.derby.iapi.services.monitor.Monitor.bootServiceModule(Unknown Source)
        at org.apache.derby.impl.db.BasicDatabase$5.run(Unknown Source)
        at java.security.AccessController.doPrivileged(Native Method)
        at org.apache.derby.impl.db.BasicDatabase.bootServiceModule(Unknown Source)
        at org.apache.derby.impl.db.BasicDatabase.bootStore(Unknown Source)
        at org.apache.derby.impl.db.BasicDatabase.boot(Unknown Source)
        at org.apache.derby.impl.services.monitor.BaseMonitor.boot(Unknown Source)
        at org.apache.derby.impl.services.monitor.TopService.bootModule(Unknown Source)
        at org.apache.derby.impl.services.monitor.BaseMonitor.bootService(Unknown Source)
        at org.apache.derby.impl.services.monitor.BaseMonitor.startProviderService(Unknown Source)
        at org.apache.derby.impl.services.monitor.BaseMonitor.findProviderAndStartService(Unknown Source)
        at org.apache.derby.impl.services.monitor.BaseMonitor.startPersistentService(Unknown Source)
        at org.apache.derby.iapi.services.monitor.Monitor.startPersistentService(Unknown Source)
        at org.apache.derby.impl.jdbc.EmbedConnection$4.run(Unknown Source)
        at org.apache.derby.impl.jdbc.EmbedConnection$4.run(Unknown Source)
        at java.security.AccessController.doPrivileged(Native Method)
        at org.apache.derby.impl.jdbc.EmbedConnection.startPersistentService(Unknown Source)
        ... 110 more

*Update

I used this portion of code I found in the documentations it was working.

from pyspark.mllib.linalg.distributed import  RowMatrix, IndexedRowMatrix,CoordinateMatrix, MatrixEntry

#Create an RDD of coordinate entries.
#   - This can be done explicitly with the MatrixEntry class:
# entries = sc.parallelize([MatrixEntry(0, 0, 1.2), MatrixEntry(1, 0, 2.1), MatrixEntry(6, 1, 3.7)])
#   - or using (long, long, float) tuples:
entries = sc.parallelize([(1, 2, 3), (4, 5, 6), (7, 8, 9), (10, 11, 12)])
#([(0, 0, 1.2), (1, 0, 2.1), (2, 1, 3.7)])
mat1 = RowMatrix(entries)

exact = mat1.columnSimilarities()
exact.entries.collect()

Answer 1

tl;dr Close the other instance of the Spark application in C:\\Users\\USER\\Desktop\\ColumnSimilarities\\metastore_db and start over.

The exception:

ERROR XSDB6: Another instance of Derby may have already booted the database C:\\Users\\USER\\Desktop\\ColumnSimilarities\\metastore_db

says it all. You've got two instances of a Spark application up and running in C:\\Users\\USER\\Desktop\\ColumnSimilarities . It is not possible with the default hive external catalog (aka metastore).

Spark SQL uses an external catalog (aka metastore) to manage the metadata of persistent tables and uses Derby as the underlying database that allows a single client to access it.

You can only have one Spark application in a given directory (or you'd have to change the directory where the HiveExternalCatalog stores the metadata).

Answer 2

from pyspark.mllib.linalg.distributed import  RowMatrix, IndexedRowMatrix,CoordinateMatrix, MatrixEntry

#Create an RDD of coordinate entries.
#   - This can be done explicitly with the MatrixEntry class:
# entries = sc.parallelize([MatrixEntry(0, 0, 1.2), MatrixEntry(1, 0, 2.1), MatrixEntry(6, 1, 3.7)])
#   - or using (long, long, float) tuples:
entries = sc.parallelize([(1, 2, 3), (4, 5, 6), (7, 8, 9), (10, 11, 12)])
#([(0, 0, 1.2), (1, 0, 2.1), (2, 1, 3.7)])
mat1 = RowMatrix(entries)

exact = mat1.columnSimilarities()
exact.entries.collect()

Did another try using the code found in the documentation.

Answer 3

i had same mistake on spark 2.2.0 so i checked the ports i discovered some other spark processes hold the port . so all u have to do is go to your shell and type the "JPS" command to see if other spark process does exist

user@server:~$ JPS

so you will see a list of java process which have been running on your system like :

78849 Jps
53409 RemoteInterpreterServer
78627 RemoteInterpreterServer
78515 RemoteInterpreterServer
76244 RemoteInterpreterServer
58566 SparkSubmit
77510 NameNode
74601 ZeppelinServer
17912 Master
77755 SecondaryNameNode
74684 LivyServer
77854 SparkSubmit

enter image description here

then you have to kill spark session by their Process ID use the below command :

sudo kill -9 #process id#
ex : sudo kill -9 58566

or you can use this one

 sudo killall -9 SparkSubmit

if there is no open spark session in your memory you will receive : " no process found"

now try to run your code again !

Godspeed