How big is your cpd file? Can you please post the whole thread dump?

The cpd file is 38MB. Below is the complete dump.
INFO: Code_Duplicity #1 main build action completed: SUCCESS
Exception in thread "Ping thread for channel hudson.remoting.Channel@6f4dbda2:tools" Exception in thread "Channel reader thread: vagrant_buildserver" Exception in thread "Ping thread for channel hudson.remoting.Channel@1d1c75d:vagrant_buildserver" Exception in thread "Thread-5" Exception in thread "Ping thread for channel hudson.remoting.Channel@16e7ae76:vagrant_tibi" Exception in thread "Ping thread for channel hudson.remoting.Channel@5d6577bf:InV_CI" java.lang.OutOfMemoryError: GC overhead limit exceeded
at java.lang.AbstractStringBuilder.<init>(AbstractStringBuilder.java:68)
at java.lang.StringBuffer.<init>(StringBuffer.java:116)
java.lang.OutOfMemoryError: GC overhead limit exceeded
java.lang.OutOfMemoryError: GC overhead limit exceeded
at java.util.Arrays.copyOf(Arrays.java:3332)
at java.lang.AbstractStringBuilder.expandCapacity(AbstractStringBuilder.java:137)
at java.lang.AbstractStringBuilder.ensureCapacityInternal(AbstractStringBuilder.java:121)
at java.lang.AbstractStringBuilder.append(AbstractStringBuilder.java:421)
at java.lang.StringBuilder.append(StringBuilder.java:136)
at com.trilead.ssh2.transport.TransportConnection.receiveMessage(TransportConnection.java:278)
at com.trilead.ssh2.transport.TransportManager.receiveLoop(TransportManager.java:693)
at com.trilead.ssh2.transport.TransportManager$1.run(TransportManager.java:489)
at java.lang.Thread.run(Thread.java:745)

Exception: java.lang.OutOfMemoryError thrown from the UncaughtExceptionHandler in thread "Ping thread for channel hudson.remoting.Channel@5d6577bf:InV_CI"
java.lang.OutOfMemoryError: GC overhead limit exceeded
java.lang.OutOfMemoryError: GC overhead limit exceeded
at java.io.ObjectOutputStream$BlockDataOutputStream.<init>(ObjectOutputStream.java:1754)
at java.io.ObjectOutputStream.<init>(ObjectOutputStream.java:242)
at hudson.remoting.MultiClassLoaderSerializer$Output.<init>(MultiClassLoaderSerializer.java:38)
at hudson.remoting.UserRequest._serialize(UserRequest.java:154)
at hudson.remoting.UserRequest.serialize(UserRequest.java:167)
at hudson.remoting.UserRequest.<init>(UserRequest.java:63)
at hudson.remoting.Channel.callAsync(Channel.java:779)
at hudson.remoting.PingThread.ping(PingThread.java:104)
at hudson.remoting.PingThread.run(PingThread.java:85)
java.lang.OutOfMemoryError: GC overhead limit exceeded
May 27, 2015 6:52:34 PM org.eclipse.jetty.util.log.JavaUtilLog warn
WARNING:
java.lang.OutOfMemoryError: GC overhead limit exceeded

May 27, 2015 6:47:59 PM hudson.triggers.Trigger$Cron doRun

This is what I got in Jenkins.

</pmd-cpd>
[DRY] Collecting duplicate code analysis files...
[DRY] Finding all files that match the pattern cpd_report.xml
[DRY] Parsing 1 file in /home/dprusty/jenkins/workspace/RAA_Code_Duplicity
[DRY] Successfully parsed file /home/dprusty/jenkins/workspace/RAA_Code_Duplicity/cpd_report.xml with 41062 unique warnings and 0 duplicates.
FATAL: GC overhead limit exceeded
java.lang.OutOfMemoryError: GC overhead limit exceeded
at com.thoughtworks.xstream.io.path.PathTracker.getPath(PathTracker.java:166)
at com.thoughtworks.xstream.core.AbstractReferenceMarshaller.convert(AbstractReferenceMarshaller.java:53)
at com.thoughtworks.xstream.core.TreeMarshaller.convertAnother(TreeMarshaller.java:58)
at com.thoughtworks.xstream.core.TreeMarshaller.convertAnother(TreeMarshaller.java:43)
at com.thoughtworks.xstream.core.AbstractReferenceMarshaller$1.convertAnother(AbstractReferenceMarshaller.java:88)
at com.thoughtworks.xstream.converters.collections.AbstractCollectionConverter.writeItem(AbstractCollectionConverter.java:64)
at com.thoughtworks.xstream.converters.collections.CollectionConverter.marshal(CollectionConverter.java:74)
at com.thoughtworks.xstream.core.AbstractReferenceMarshaller.convert(AbstractReferenceMarshaller.java:69)
at com.thoughtworks.xstream.core.TreeMarshaller.convertAnother(TreeMarshaller.java:58)
at com.thoughtworks.xstream.core.AbstractReferenceMarshaller$1.convertAnother(AbstractReferenceMarshaller.java:84)
at hudson.util.RobustReflectionConverter.marshallField(RobustReflectionConverter.java:223)
at hudson.util.RobustReflectionConverter$2.writeField(RobustReflectionConverter.java:210)
at hudson.util.RobustReflectionConverter$2.visit(RobustReflectionConverter.java:182)
at com.thoughtworks.xstream.converters.reflection.PureJavaReflectionProvider.visitSerializableFields(PureJavaReflectionProvider.java:138)
at hudson.util.RobustReflectionConverter.doMarshal(RobustReflectionConverter.java:167)
at hudson.util.RobustReflectionConverter.marshal(RobustReflectionConverter.java:108)
at com.thoughtworks.xstream.core.AbstractReferenceMarshaller.convert(AbstractReferenceMarshaller.java:69)
at com.thoughtworks.xstream.core.TreeMarshaller.convertAnother(TreeMarshaller.java:58)
at com.thoughtworks.xstream.core.TreeMarshaller.convertAnother(TreeMarshaller.java:43)
at com.thoughtworks.xstream.core.AbstractReferenceMarshaller$1.convertAnother(AbstractReferenceMarshaller.java:88)
at com.thoughtworks.xstream.converters.collections.AbstractCollectionConverter.writeItem(AbstractCollectionConverter.java:64)
at com.thoughtworks.xstream.converters.collections.CollectionConverter.marshal(CollectionConverter.java:74)
at com.thoughtworks.xstream.core.AbstractReferenceMarshaller.convert(AbstractReferenceMarshaller.java:69)
at com.thoughtworks.xstream.core.TreeMarshaller.convertAnother(TreeMarshaller.java:58)
at com.thoughtworks.xstream.core.AbstractReferenceMarshaller$1.convertAnother(AbstractReferenceMarshaller.java:84)
at hudson.util.RobustReflectionConverter.marshallField(RobustReflectionConverter.java:223)
at hudson.util.RobustReflectionConverter$2.writeField(RobustReflectionConverter.java:210)
at hudson.util.RobustReflectionConverter$2.visit(RobustReflectionConverter.java:182)
at com.thoughtworks.xstream.converters.reflection.PureJavaReflectionProvider.visitSerializableFields(PureJavaReflectionProvider.java:138)
at hudson.util.RobustReflectionConverter.doMarshal(RobustReflectionConverter.java:167)
at hudson.util.RobustReflectionConverter.marshal(RobustReflectionConverter.java:108)
at com.thoughtworks.xstream.core.AbstractReferenceMarshaller.convert(AbstractReferenceMarshaller.java:69)
Finished: FAILURE

Hmm, still no dry plugin class in stack trace visible.

However, this looks like JENKINS-1960. The plug-in is not made for such large amount of warnigs...

Yes. I think you are right. When I run it for Java (about 1200 warnings), it's working fine. But failing for cpp may be due to huge number of warnings. I tried even with -Xmx2048M still it failed.

So I left it for cpp now and publishing for Java only. Hope the enhancement will come someday.