I am trying to import a table from my oracle database using spark and here I am using Scala to import the table.
My jdbc driver is ojdbc7.jar and it's added in both the parameter spark.driver.extraClassPath and spark.executor.extraClassPath in configuration file
spark.driver.extraClassPath :/usr/lib/hadoop-lzo/lib/*:/usr/lib/hadoop/hadoop-aws.jar:/usr/share/aws/aws-java-sdk/*:/usr/share/aws/emr/emrfs/conf:/usr/s
hare/aws/emr/emrfs/lib/*:/usr/share/aws/emr/emrfs/auxlib/*:/usr/share/aws/emr/security/conf:/usr/share/aws/emr/security/lib/*:/home/hadoop/ojdbc7.jar
spark.driver.extraLibraryPath /usr/lib/hadoop/lib/native:/usr/lib/hadoop-lzo/lib/native
spark.executor.extraClassPath :/usr/lib/hadoop-lzo/lib/*:/usr/lib/hadoop/hadoop-aws.jar:/usr/share/aws/aws-java-sdk/*:/usr/share/aws/emr/emrfs/conf:/usr/s
hare/aws/emr/emrfs/lib/*:/usr/share/aws/emr/emrfs/auxlib/*:/usr/share/aws/emr/security/conf:/usr/share/aws/emr/security/lib/*:/home/hadoop/ojdbc7.jar
spark.executor.extraLibraryPath /usr/lib/hadoop/lib/native:/usr/lib/hadoop-lzo/lib/native
I can successfully import the table. I can print the schema of the table. But while performing any operations like Count,show() it throws below error
`
Caused by: java.lang.ClassNotFoundException: oracle.jdbc.OracleDriver
at java.lang.ClassLoader.findClass(ClassLoader.java:530) at
org.apache.spark.util.ParentClassLoader.findClass(ParentClassLoader.scala:26)
at java.lang.ClassLoader.loadClass(ClassLoader.java:424) at
org.apache.spark.util.ParentClassLoader.loadClass(ParentClassLoader.scala:34)
at java.lang.ClassLoader.loadClass(ClassLoader.java:357) at
org.apache.spark.util.ParentClassLoader.loadClass(ParentClassLoader.scala:30)
at
org.apache.spark.repl.ExecutorClassLoader.findClass(ExecutorClassLoader.scala:77)
... 21 more
`
This error was because Spark was not able to locate the ojdbc7.jar from every core node. So placing this jar in a shared location like /usr/lib/spark/jars will resolve this issue.
You can also do few other things including adding jar file full location as a dependency under spark section in the interpreter as an artifact
If you just want %jdbc to work, update the jdbc section under interpreter, add the jar file full location as a artifact under the dependencies and also update the default.driver, default.url, default.user, default.password accordingly
Related
Connection to databricks works fine, working with DataFrames goes smoothly (operations like join, filter, etc).
The problem appears when I call cache on a dataframe.
py4j.protocol.Py4JJavaError: An error occurred while calling o342.cache.
: java.io.InvalidClassException: failed to read class descriptor
...
Caused by: java.lang.ClassNotFoundException: org.apache.spark.rdd.RDD$client53442a94a3$$anonfun$mapPartitions$1$$anonfun$apply$23
at java.lang.ClassLoader.findClass(ClassLoader.java:523)
at org.apache.spark.util.ParentClassLoader.findClass(ParentClassLoader.java:35)
at java.lang.ClassLoader.loadClass(ClassLoader.java:418)
at org.apache.spark.util.ParentClassLoader.loadClass(ParentClassLoader.java:40)
at org.apache.spark.util.ChildFirstURLClassLoader.loadClass(ChildFirstURLClassLoader.java:48)
at java.lang.ClassLoader.loadClass(ClassLoader.java:351)
at java.lang.Class.forName0(Native Method)
at java.lang.Class.forName(Class.java:348)
at org.apache.spark.util.Utils$.classForName(Utils.scala:257)
at org.apache.spark.sql.util.ProtoSerializer.org$apache$spark$sql$util$ProtoSerializer$$readResolveClassDescriptor(ProtoSerializer.scala:4316)
at org.apache.spark.sql.util.ProtoSerializer$$anon$4.readClassDescriptor(ProtoSerializer.scala:4304)
at java.io.ObjectInputStream.readNonProxyDesc(ObjectInputStream.java:1857)
... 71 more
I work with java8 as required, clearing pycache doesn't help.
The same code submitted as a job to databricks works fine.
It looks like a local problem on a bridge python-jvm level but java version (8) and python (3.7) is as required. Switching to java13 produces quite the same message.
Versions databricks-connect==6.2.0, openjdk version "1.8.0_242", Python 3.7.6
EDIT:
Behavior depends on how DF is created, if the source of DF is external then it works fine, if DF is created locally then such error appears.
# works fine
df = spark.read.csv("dbfs:/some.csv")
df.cache()
# ERROR in 'cache' line
df = spark.createDataFrame([("a",), ("b",)])
df.cache()
This is a known issue and I think a recent patch fixed it. This was seen for Azure, I am not sure whether you are using which Azure or AWS but it's solved. Please check the issue - https://github.com/MicrosoftDocs/azure-docs/issues/52431
I am new to Apache Spark. I have a use case where I have to save data frame data in MySQL. I got the below code to do the same:
data_frame.write.format('jdbc').options(
url='URI',
driver='com.mysql.jdbc.Driver',
dbtable=table_name,
user=user_name,
password='your_password').mode('append').save()
But when I ran the code, I got the below error:
File "/usr/local/Cellar/apache-spark/2.3.1/libexec/python/lib/py4j-0.10.7-src.zip/py4j/protocol.py", line 328, in get_return_value
py4j.protocol.Py4JJavaError: An error occurred while calling o207.save.
: java.lang.ClassNotFoundException: com.mysql.jdbc.Driver
I might be missing out on very minute detail. How can I fix this?
The error description is clearly indicating that it's not able to locate the JDBC driver class. You will have to include the JAR file for com.mysql.jdbc.Driver using
pyspark --jars <jar-file-location>
See this question - How to add third-party Java JAR files for use in PySpark.
Can you tell me the exact location where jar file need to be copied. A jar will be required for the below issue.
Connection failure. You must change the Database Settings.
org.talend.utils.exceptions.MissingDriverException: can not find class :oracle.jdbc.OracleDriver
missing JDBC driver :
ojdbc7.jar
at org.talend.core.model.metadata.builder.database.ExtractMetaDataUtils.connect(ExtractMetaDataUtils.java:1128)
at org.talend.core.model.metadata.builder.database.ExtractMetaDataFromDataBase.testConnection(ExtractMetaDataFromDataBase.java:315)
at org.talend.metadata.managment.repository.ManagerConnection.check(ManagerConnection.java:289)
at org.talend.repository.ui.wizards.metadata.connection.database.DatabaseForm$59.runWithCancel(DatabaseForm.java:3812)
at org.talend.repository.ui.wizards.metadata.connection.database.DatabaseForm$59.runWithCancel(DatabaseForm.java:1)
at org.talend.repository.ui.dialog.AProgressMonitorDialogWithCancel$1.runnableWithCancel(AProgressMonitorDialogWithCancel.java:77)
at org.talend.repository.ui.dialog.AProgressMonitorDialogWithCancel$ARunnableWithProgressCancel$1.call(AProgressMonitorDialogWithCancel.java:161)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.lang.Thread.run(Thread.java:745)
In Talend, try to go to Windows>Show View..>Modules. There you can import or download external jar files for your components.
I am trying to connect from a Hive Database to a collection in MongoDB using a driver (jars) provided on the wiki site. Here are the steps I did: -
I created a collection in MongoDB called "Diamond" under a database called "Moe" and it has got 20 documents:
I wanted to connect from Hive via the Hadoop MongoDB Driver and view these documents via Hive.
I have both MongoDB and Hive installed on the same server and configured. However I don't see any variable called the HIVE_CLASPATH I wonder where that is.
So I installed 3 divers on the server: -
mongo-hadoop-core-1.5.2.jar;
mongo-hadoop-hive-1.5.2.jar;
mongo-java-driver-3.0.0.jar;
Now, I connect to Hive, and then add these 2 jar's to my classpath by the following commands: - (they get added successfully)
add jar /hadoopgdc/hadoop-2.6.0/share/hadoop/common/lib/mongo-hadoop-hive-1.5.2.jar;
add jar /hadoopgdc/hadoop-2.6.0/share/hadoop/common/lib/mongo-hadoop-core-1.5.2.jar;
add jar /hadoopgdc/hadoop-2.6.0/share/hadoop/common/lib/mongo-java-driver-3.0.0.jar;
Now I create a table in HIVE: -
CREATE TABLE Diamond
(
carat DOUBLE,
cut STRING,
color STRING,
clarity STRING,
depth DOUBLE,
table DOUBLE,
price DOUBLE,
xcord DOUBLE,
ycord DOUBLE,
zcord DOUBLE
)
STORED BY 'com.mongodb.hadoop.hive.MongoStorageHandler'
WITH SERDEPROPERTIES('mongo.columns.mapping'='{"carat":"carat","cut":"cut",
"color":"color", "clarity":"clarity", "depth":"depth", "table":"table",
"price":"price", "xcord":"x", "ycord":"y", "zcord":"z"}')
TBLPROPERTIES('mongo.uri'='mongodb://localhost:27017/Moe.Diamond');
However when I execute the above command in Hive I get the error below: -
java.lang.NoClassDefFoundError: com/mongodb/util/JSON
at com.mongodb.hadoop.hive.BSONSerDe.initialize(BSONSerDe.java:110)
at org.apache.hadoop.hive.metastore.MetaStoreUtils.getDeserializer(MetaStoreUtils.java:210)
at org.apache.hadoop.hive.ql.metadata.Table.getDeserializerFromMetaStore(Table.java:268)
at org.apache.hadoop.hive.ql.metadata.Table.getDeserializer(Table.java:261)
at org.apache.hadoop.hive.ql.metadata.Table.getCols(Table.java:587)
at org.apache.hadoop.hive.ql.metadata.Hive.createTable(Hive.java:573)
at org.apache.hadoop.hive.ql.exec.DDLTask.createTable(DDLTask.java:3784)
at org.apache.hadoop.hive.ql.exec.DDLTask.execute(DDLTask.java:256)
at org.apache.hadoop.hive.ql.exec.Task.executeTask(Task.java:155)
at org.apache.hadoop.hive.ql.exec.TaskRunner.runSequential(TaskRunner.java:57)
at org.apache.hadoop.hive.ql.Driver.launchTask(Driver.java:1355)
at org.apache.hadoop.hive.ql.Driver.execute(Driver.java:1139)
at org.apache.hadoop.hive.ql.Driver.run(Driver.java:945)
at org.apache.hadoop.hive.cli.CliDriver.processLocalCmd(CliDriver.java:259)
at org.apache.hadoop.hive.cli.CliDriver.processCmd(CliDriver.java:216)
at org.apache.hadoop.hive.cli.CliDriver.processLine(CliDriver.java:413)
at org.apache.hadoop.hive.cli.CliDriver.run(CliDriver.java:756)
at org.apache.hadoop.hive.cli.CliDriver.main(CliDriver.java:614)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
at org.apache.hadoop.util.RunJar.main(RunJar.java:212)
Caused by: java.lang.ClassNotFoundException: com.mongodb.util.JSON
at java.net.URLClassLoader$1.run(URLClassLoader.java:366)
at java.net.URLClassLoader$1.run(URLClassLoader.java:355)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:354)
at java.lang.ClassLoader.loadClass(ClassLoader.java:425)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:308)
at java.lang.ClassLoader.loadClass(ClassLoader.java:358)
... 23 more
FAILED: Execution Error, return code -101 from
org.apache.hadoop.hive.ql.exec.DDLTask
I have tried the following: -
- placing the jars in every possible directory with no effect
- The class that is supposed to be missing, is pretty much present in the jar file.
- oh yes and the MongoStorageHandler class is very much in the jar.
I am done breaking my head with this !! If anyone can shed some light on what I could do to alleviate my anxiety, it would be great.
Thanks again.
Mario
I identified what the issue was. To connect from HIVE to MongoDB, the MongoDb Driver uses invokes a java class in a hive jar library
**
java.lang.ClassNotFoundException:
org.apache.hadoop.hive.ql.hooks.PreExecutePrinter
**
Now this class is supposed to be found in the jar file - hive-exec-0.11.0.1.3.2.0-111.jar. However it is available only in more recent versions of HIVE and not older ones.
It is not available in 0.11.0.1.3.2.0-111 but is visibly detectable in 0.13.0.2.1.7.0-784.
The solution here was to connect to a version of HIVE that is supported by the driver. MongoDB does state that its driver supports a certain version of Hadoop, but doesn't drill down to the individual Application (HIVE / SQOOP).
I am using MongoDB hadoop connector to query mongoDB using hive table in hadoop.
I am able to execute
select * from mongoDBTestHiveTable;
But when I try to execute following query
select id from mongoDBTestHiveTable;
it throws following exception.
Following class exist in hive lib folder.
Exception stacktrace:
Diagnostic Messages for this Task:
Error: java.io.IOException: Cannot create an instance of InputSplit class = com.mongodb.hadoop.hive.input.HiveMongoInputFormat$MongoHiveInputSplit:Class com.mongodb.hadoop.hive.input.HiveMongoInputFormat$MongoHiveInputSplit not found
at org.apache.hadoop.hive.ql.io.HiveInputFormat$HiveInputSplit.readFields(HiveInputFormat.java:147)
at org.apache.hadoop.io.serializer.WritableSerialization$WritableDeserializer.deserialize(WritableSerialization.java:71)
at org.apache.hadoop.io.serializer.WritableSerialization$WritableDeserializer.deserialize(WritableSerialization.java:42)
at org.apache.hadoop.mapred.MapTask.getSplitDetails(MapTask.java:370)
at org.apache.hadoop.mapred.MapTask.runOldMapper(MapTask.java:402)
at org.apache.hadoop.mapred.MapTask.run(MapTask.java:341)
at org.apache.hadoop.mapred.YarnChild$2.run(YarnChild.java:162)
at java.security.AccessController.doPrivileged(Native Method)
at javax.security.auth.Subject.doAs(Subject.java:415)
at org.apache.hadoop.security.UserGroupInformation.doAs(UserGroupInformation.java:1491)
at org.apache.hadoop.mapred.YarnChild.main(YarnChild.java:157)
Caused by: java.lang.ClassNotFoundException: Class com.mongodb.hadoop.hive.input.HiveMongoInputFormat$MongoHiveInputSplit not found
at org.apache.hadoop.conf.Configuration.getClassByName(Configuration.java:1626)
at org.apache.hadoop.hive.ql.io.HiveInputFormat$HiveInputSplit.readFields(HiveInputFormat.java:144)
... 10 more
Container killed by the ApplicationMaster.
Please advice.
You also need to add mongo-hadoop-* and well as mongo driver jars to MR1/MR2 classpath on all workers