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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