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From "Andrew Davidson (JIRA)" <j...@apache.org>
Subject [jira] [Commented] (SPARK-17143) pyspark unable to create UDF: java.lang.RuntimeException: org.apache.hadoop.fs.FileAlreadyExistsException: Parent path is not a directory: /tmp tmp
Date Fri, 19 Aug 2016 00:15:21 GMT

    [ https://issues.apache.org/jira/browse/SPARK-17143?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=15427394#comment-15427394
] 

Andrew Davidson commented on SPARK-17143:
-----------------------------------------

See email from user's group. I was able to find a work around. Not sure how hdfs:///tmp/ got
created or how the permissions got messed up

##############################

NICE CATCH!!! Many thanks. 

I spent all day on this bug

The error msg report /tmp. I did not think to look on hdfs.

[ec2-user@ip-172-31-22-140 notebooks]$ hadoop fs -ls hdfs:///tmp/
Found 1 items
-rw-r--r--   3 ec2-user supergroup        418 2016-04-13 22:49 hdfs:///tmp
[ec2-user@ip-172-31-22-140 notebooks]$ 


I have no idea how hdfs:///tmp got created. I deleted it. 

This causes a bunch of exceptions. These exceptions has useful message. I was able to fix
the problem as follows

$ hadoop fs -rmr hdfs:///tmp

Now I run the notebook. It creates hdfs:///tmp/hive but the permission are wrong

$ hadoop fs -chmod 777 hdfs:///tmp/hive


From: Felix Cheung <felixcheung_m@hotmail.com>
Date: Thursday, August 18, 2016 at 3:37 PM
To: Andrew Davidson <Andy@SantaCruzIntegration.com>, "user @spark" <user@spark.apache.org>
Subject: Re: pyspark unable to create UDF: java.lang.RuntimeException: org.apache.hadoop.fs.FileAlreadyExistsException:
Parent path is not a directory: /tmp tmp

Do you have a file called tmp at / on HDFS?




> pyspark unable to create UDF: java.lang.RuntimeException: org.apache.hadoop.fs.FileAlreadyExistsException:
Parent path is not a directory: /tmp tmp
> ---------------------------------------------------------------------------------------------------------------------------------------------------
>
>                 Key: SPARK-17143
>                 URL: https://issues.apache.org/jira/browse/SPARK-17143
>             Project: Spark
>          Issue Type: Bug
>          Components: PySpark
>    Affects Versions: 1.6.1
>         Environment: spark version: 1.6.1
> python version: 3.4.3 (default, Apr  1 2015, 18:10:40) 
> [GCC 4.8.2 20140120 (Red Hat 4.8.2-16)]
>            Reporter: Andrew Davidson
>         Attachments: udfBug.html, udfBug.ipynb
>
>
> For unknown reason I can not create UDF when I run the attached notebook on my cluster.
I get the following error
> Py4JJavaError: An error occurred while calling None.org.apache.spark.sql.hive.HiveContext.
> : java.lang.RuntimeException: org.apache.hadoop.fs.FileAlreadyExistsException: Parent
path is not a directory: /tmp tmp
> The notebook runs fine on my Mac
> In general I am able to run non UDF spark code with out any trouble
> I start the notebook server as the user “ec2-user" and uses master URL 
> 	spark://ec2-51-215-120-63.us-west-1.compute.amazonaws.com:6066
> I found the following message in the notebook server log file. I have log level set to
warn
> 16/08/18 21:38:45 WARN ObjectStore: Version information not found in metastore. hive.metastore.schema.verification
is not enabled so recording the schema version 1.2.0
> 16/08/18 21:38:45 WARN ObjectStore: Failed to get database default, returning NoSuchObjectException
> The cluster was originally created using spark-1.6.1-bin-hadoop2.6/ec2/spark-ec2
> #from pyspark.sql import SQLContext, HiveContext
> #sqlContext = SQLContext(sc)
> ​
> #from pyspark.sql import DataFrame
> #from pyspark.sql import functions
> ​
> from pyspark.sql.types import StringType
> from pyspark.sql.functions import udf
> ​
> print("spark version: {}".format(sc.version))
> ​
> import sys
> print("python version: {}".format(sys.version))
> spark version: 1.6.1
> python version: 3.4.3 (default, Apr  1 2015, 18:10:40)
> [GCC 4.8.2 20140120 (Red Hat 4.8.2-16)]
> # functions.lower() raises 
> # py4j.Py4JException: Method lower([class java.lang.String]) does not exist
> # work around define a UDF
> toLowerUDFRetType = StringType()
> #toLowerUDF = udf(lambda s : s.lower(), toLowerUDFRetType)
> toLowerUDF = udf(lambda s : s.lower(), StringType())
> You must build Spark with Hive. Export 'SPARK_HIVE=true' and run build/sbt assembly
> Py4JJavaErrorTraceback (most recent call last)
> <ipython-input-2-2e0f7c0bb4f9> in <module>()
>       4 toLowerUDFRetType = StringType()
>       5 #toLowerUDF = udf(lambda s : s.lower(), toLowerUDFRetType)
> ----> 6 toLowerUDF = udf(lambda s : s.lower(), StringType())
> /root/spark/python/pyspark/sql/functions.py in udf(f, returnType)
>    1595     [Row(slen=5), Row(slen=3)]
>    1596     """
> -> 1597     return UserDefinedFunction(f, returnType)
>    1598
>    1599 blacklist = ['map', 'since', 'ignore_unicode_prefix']
> /root/spark/python/pyspark/sql/functions.py in __init__(self, func, returnType, name)
>    1556         self.returnType = returnType
>    1557         self._broadcast = None
> -> 1558         self._judf = self._create_judf(name)
>    1559
>    1560     def _create_judf(self, name):
> /root/spark/python/pyspark/sql/functions.py in _create_judf(self, name)
>    1567         pickled_command, broadcast_vars, env, includes = _prepare_for_python_RDD(sc,
command, self)
>    1568         ctx = SQLContext.getOrCreate(sc)
> -> 1569         jdt = ctx._ssql_ctx.parseDataType(self.returnType.json())
>    1570         if name is None:
>    1571             name = f.__name__ if hasattr(f, '__name__') else f.__class__.__name__
> /root/spark/python/pyspark/sql/context.py in _ssql_ctx(self)
>     681         try:
>     682             if not hasattr(self, '_scala_HiveContext'):
> --> 683                 self._scala_HiveContext = self._get_hive_ctx()
>     684             return self._scala_HiveContext
>     685         except Py4JError as e:
> /root/spark/python/pyspark/sql/context.py in _get_hive_ctx(self)
>     690
>     691     def _get_hive_ctx(self):
> --> 692         return self._jvm.HiveContext(self._jsc.sc())
>     693
>     694     def refreshTable(self, tableName):
> /root/spark/python/lib/py4j-0.9-src.zip/py4j/java_gateway.py in __call__(self, *args)
>    1062         answer = self._gateway_client.send_command(command)
>    1063         return_value = get_return_value(
> -> 1064             answer, self._gateway_client, None, self._fqn)
>    1065
>    1066         for temp_arg in temp_args:
> /root/spark/python/pyspark/sql/utils.py in deco(*a, **kw)
>      43     def deco(*a, **kw):
>      44         try:
> ---> 45             return f(*a, **kw)
>      46         except py4j.protocol.Py4JJavaError as e:
>      47             s = e.java_exception.toString()
> /root/spark/python/lib/py4j-0.9-src.zip/py4j/protocol.py in get_return_value(answer,
gateway_client, target_id, name)
>     306                 raise Py4JJavaError(
>     307                     "An error occurred while calling {0}{1}{2}.\n".
> --> 308                     format(target_id, ".", name), value)
>     309             else:
>     310                 raise Py4JError(
> Py4JJavaError: An error occurred while calling None.org.apache.spark.sql.hive.HiveContext.
> : java.lang.RuntimeException: org.apache.hadoop.fs.FileAlreadyExistsException: Parent
path is not a directory: /tmp tmp
> 	at org.apache.hadoop.hdfs.server.namenode.FSDirectory.mkdirs(FSDirectory.java:1489)
> 	at org.apache.hadoop.hdfs.server.namenode.FSNamesystem.mkdirsInternal(FSNamesystem.java:2979)
> 	at org.apache.hadoop.hdfs.server.namenode.FSNamesystem.mkdirsInt(FSNamesystem.java:2932)
> 	at org.apache.hadoop.hdfs.server.namenode.FSNamesystem.mkdirs(FSNamesystem.java:2911)
> 	at org.apache.hadoop.hdfs.server.namenode.NameNodeRpcServer.mkdirs(NameNodeRpcServer.java:649)
> 	at org.apache.hadoop.hdfs.protocolPB.ClientNamenodeProtocolServerSideTranslatorPB.mkdirs(ClientNamenodeProtocolServerSideTranslatorPB.java:417)
> 	at org.apache.hadoop.hdfs.protocol.proto.ClientNamenodeProtocolProtos$ClientNamenodeProtocol$2.callBlockingMethod(ClientNamenodeProtocolProtos.java:44096)
> 	at org.apache.hadoop.ipc.ProtobufRpcEngine$Server$ProtoBufRpcInvoker.call(ProtobufRpcEngine.java:453)
> 	at org.apache.hadoop.ipc.RPC$Server.call(RPC.java:1002)
> 	at org.apache.hadoop.ipc.Server$Handler$1.run(Server.java:1695)
> 	at org.apache.hadoop.ipc.Server$Handler$1.run(Server.java:1691)
> 	at java.security.AccessController.doPrivileged(Native Method)
> 	at javax.security.auth.Subject.doAs(Subject.java:415)
> 	at org.apache.hadoop.security.UserGroupInformation.doAs(UserGroupInformation.java:1408)
> 	at org.apache.hadoop.ipc.Server$Handler.run(Server.java:1689)
> 	at org.apache.hadoop.hive.ql.session.SessionState.start(SessionState.java:522)
> 	at org.apache.spark.sql.hive.client.ClientWrapper.<init>(ClientWrapper.scala:204)
> 	at org.apache.spark.sql.hive.client.IsolatedClientLoader.createClient(IsolatedClientLoader.scala:238)
> 	at org.apache.spark.sql.hive.HiveContext.executionHive$lzycompute(HiveContext.scala:218)
> 	at org.apache.spark.sql.hive.HiveContext.executionHive(HiveContext.scala:208)
> 	at org.apache.spark.sql.hive.HiveContext.functionRegistry$lzycompute(HiveContext.scala:462)
> 	at org.apache.spark.sql.hive.HiveContext.functionRegistry(HiveContext.scala:461)
> 	at org.apache.spark.sql.UDFRegistration.<init>(UDFRegistration.scala:40)
> 	at org.apache.spark.sql.SQLContext.<init>(SQLContext.scala:330)
> 	at org.apache.spark.sql.hive.HiveContext.<init>(HiveContext.scala:90)
> 	at org.apache.spark.sql.hive.HiveContext.<init>(HiveContext.scala:101)
> 	at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
> 	at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
> 	at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
> 	at java.lang.reflect.Constructor.newInstance(Constructor.java:423)
> 	at py4j.reflection.MethodInvoker.invoke(MethodInvoker.java:234)
> 	at py4j.reflection.ReflectionEngine.invoke(ReflectionEngine.java:381)
> 	at py4j.Gateway.invoke(Gateway.java:214)
> 	at py4j.commands.ConstructorCommand.invokeConstructor(ConstructorCommand.java:79)
> 	at py4j.commands.ConstructorCommand.execute(ConstructorCommand.java:68)
> 	at py4j.GatewayConnection.run(GatewayConnection.java:209)
> 	at java.lang.Thread.run(Thread.java:745)
> Caused by: org.apache.hadoop.fs.FileAlreadyExistsException: Parent path is not a directory:
/tmp tmp
> 	at org.apache.hadoop.hdfs.server.namenode.FSDirectory.mkdirs(FSDirectory.java:1489)
> 	at org.apache.hadoop.hdfs.server.namenode.FSNamesystem.mkdirsInternal(FSNamesystem.java:2979)
> 	at org.apache.hadoop.hdfs.server.namenode.FSNamesystem.mkdirsInt(FSNamesystem.java:2932)
> 	at org.apache.hadoop.hdfs.server.namenode.FSNamesystem.mkdirs(FSNamesystem.java:2911)
> 	at org.apache.hadoop.hdfs.server.namenode.NameNodeRpcServer.mkdirs(NameNodeRpcServer.java:649)
> 	at org.apache.hadoop.hdfs.protocolPB.ClientNamenodeProtocolServerSideTranslatorPB.mkdirs(ClientNamenodeProtocolServerSideTranslatorPB.java:417)
> 	at org.apache.hadoop.hdfs.protocol.proto.ClientNamenodeProtocolProtos$ClientNamenodeProtocol$2.callBlockingMethod(ClientNamenodeProtocolProtos.java:44096)
> 	at org.apache.hadoop.ipc.ProtobufRpcEngine$Server$ProtoBufRpcInvoker.call(ProtobufRpcEngine.java:453)
> 	at org.apache.hadoop.ipc.RPC$Server.call(RPC.java:1002)
> 	at org.apache.hadoop.ipc.Server$Handler$1.run(Server.java:1695)
> 	at org.apache.hadoop.ipc.Server$Handler$1.run(Server.java:1691)
> 	at java.security.AccessController.doPrivileged(Native Method)
> 	at javax.security.auth.Subject.doAs(Subject.java:415)
> 	at org.apache.hadoop.security.UserGroupInformation.doAs(UserGroupInformation.java:1408)
> 	at org.apache.hadoop.ipc.Server$Handler.run(Server.java:1689)
> 	at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
> 	at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
> 	at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
> 	at java.lang.reflect.Constructor.newInstance(Constructor.java:423)
> 	at org.apache.hadoop.ipc.RemoteException.instantiateException(RemoteException.java:90)
> 	at org.apache.hadoop.ipc.RemoteException.unwrapRemoteException(RemoteException.java:57)
> 	at org.apache.hadoop.hdfs.DFSClient.primitiveMkdir(DFSClient.java:2110)
> 	at org.apache.hadoop.hdfs.DFSClient.mkdirs(DFSClient.java:2079)
> 	at org.apache.hadoop.hdfs.DistributedFileSystem.mkdirs(DistributedFileSystem.java:543)
> 	at org.apache.hadoop.hive.ql.exec.Utilities.createDirsWithPermission(Utilities.java:3679)
> 	at org.apache.hadoop.hive.ql.session.SessionState.createRootHDFSDir(SessionState.java:597)
> 	at org.apache.hadoop.hive.ql.session.SessionState.createSessionDirs(SessionState.java:554)
> 	at org.apache.hadoop.hive.ql.session.SessionState.start(SessionState.java:508)
> 	... 21 more
> Caused by: org.apache.hadoop.ipc.RemoteException(org.apache.hadoop.fs.FileAlreadyExistsException):
Parent path is not a directory: /tmp tmp
> 	at org.apache.hadoop.hdfs.server.namenode.FSDirectory.mkdirs(FSDirectory.java:1489)
> 	at org.apache.hadoop.hdfs.server.namenode.FSNamesystem.mkdirsInternal(FSNamesystem.java:2979)
> 	at org.apache.hadoop.hdfs.server.namenode.FSNamesystem.mkdirsInt(FSNamesystem.java:2932)
> 	at org.apache.hadoop.hdfs.server.namenode.FSNamesystem.mkdirs(FSNamesystem.java:2911)
> 	at org.apache.hadoop.hdfs.server.namenode.NameNodeRpcServer.mkdirs(NameNodeRpcServer.java:649)
> 	at org.apache.hadoop.hdfs.protocolPB.ClientNamenodeProtocolServerSideTranslatorPB.mkdirs(ClientNamenodeProtocolServerSideTranslatorPB.java:417)
> 	at org.apache.hadoop.hdfs.protocol.proto.ClientNamenodeProtocolProtos$ClientNamenodeProtocol$2.callBlockingMethod(ClientNamenodeProtocolProtos.java:44096)
> 	at org.apache.hadoop.ipc.ProtobufRpcEngine$Server$ProtoBufRpcInvoker.call(ProtobufRpcEngine.java:453)
> 	at org.apache.hadoop.ipc.RPC$Server.call(RPC.java:1002)
> 	at org.apache.hadoop.ipc.Server$Handler$1.run(Server.java:1695)
> 	at org.apache.hadoop.ipc.Server$Handler$1.run(Server.java:1691)
> 	at java.security.AccessController.doPrivileged(Native Method)
> 	at javax.security.auth.Subject.doAs(Subject.java:415)
> 	at org.apache.hadoop.security.UserGroupInformation.doAs(UserGroupInformation.java:1408)
> 	at org.apache.hadoop.ipc.Server$Handler.run(Server.java:1689)
> 	at org.apache.hadoop.ipc.Client.call(Client.java:1225)
> 	at org.apache.hadoop.ipc.ProtobufRpcEngine$Invoker.invoke(ProtobufRpcEngine.java:202)
> 	at com.sun.proxy.$Proxy21.mkdirs(Unknown Source)
> 	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
> 	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
> 	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
> 	at java.lang.reflect.Method.invoke(Method.java:498)
> 	at org.apache.hadoop.io.retry.RetryInvocationHandler.invokeMethod(RetryInvocationHandler.java:164)
> 	at org.apache.hadoop.io.retry.RetryInvocationHandler.invoke(RetryInvocationHandler.java:83)
> 	at com.sun.proxy.$Proxy21.mkdirs(Unknown Source)
> 	at org.apache.hadoop.hdfs.protocolPB.ClientNamenodeProtocolTranslatorPB.mkdirs(ClientNamenodeProtocolTranslatorPB.java:425)
> 	at org.apache.hadoop.hdfs.DFSClient.primitiveMkdir(DFSClient.java:2108)
> 	... 27 more



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