There could be many reasons for it. Could you post the stacktrace for the 
JDOFatal?

Some reasons could be
That mysql client libs are in the classpath.
That there is a database called 'hive' in mysql
That there is schema already created in that database (otherwise set 
autoCreateSchema to true) etc...

Check documentation for the many jpox options
________________________________
From: Josh Ferguson <[email protected]>
Reply-To: <[email protected]>
Date: Sat, 24 Jan 2009 12:48:27 -0800
To: <[email protected]>
Subject: Still can't get metastore working with mysql

Ok I still can't manage to get the metastore working with mysql after
all this time trying. The error is:

FAILED: Error in metadata: MetaException(message:Got exception:
javax.jdo.JDOFatalInternalException Error creating transactional
connection factory)
FAILED: Execution Error, return code 1 from
org.apache.hadoop.hive.ql.exec.DDLTask

The relevant config is:

<!-- Hadoop Setup -->
<property>
   <name>hadoop.bin.path</name>
   <value>/usr/local/hadoop/bin/hadoop</value>
   <description>Path to hadoop binary. Assumes that by default we are
executing from hive</description>
</property>

<property>
   <name>hadoop.config.dir</name>
   <value>/usr/local/hadoop/conf</value>
   <description>Path to hadoop configuration. Again assumes that by
default we are executing from hive/</description>
</property>

<!-- Hive Execution Parameters -->
<property>
   <name>hive.exec.scratchdir</name>
   <value>/tmp/hive-${user.name}</value>
   <description>Scratch space for Hive jobs</description>
</property>

<property>
   <name>javax.jdo.option.ConnectionURL</name>
   <value>jdbc:mysql://localhost/hive</value>
</property>

<property>
   <name>javax.jdo.option.ConnectionDriverName</name>
   <value>com.mysql.jdbc.Driver</value>
</property>

<property>
   <name>javax.jdo.option.ConnectionUserName</name>
   <value>******</value>
</property>

<property>
   <name>javax.jdo.option.ConnectionPassword</name>
   <value>******</value>
</property>

<property>
   <name>org.jpox.autoCreateSchema</name>
   <value>false</value>
</property>

<property>
   <name>org.jpox.fixedDatastore</name>
   <value>true</value>
</property>

<property>
   <name>hive.metastore.usefilestore</name>
   <value>false</value>
</property>

<property>
   <name>hive.metastore.checkForDefaultDb</name>
   <value>false</value>
</property>

<property>
   <name>hive.metastore.rawstore.impl</name>
   <value>org.apache.hadoop.hive.metastore.ObjectStore</value>
   <description>Name of the class that implements
org.apache.hadoop.hive.metastore.rawstore interface. This class is
used to store and retrieval of raw metadata objects such as table,
database</description>
</property>

<property>
   <name>hive.metastore.local</name>
   <value>true</value>
   <description>controls whether to connect to remove metastore server
or open a new metastore server in Hive Client JVM</description>
</property>


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