OutOfMemoryError with Mallet CRF classifier

[tilak kumar]

Hi,

The classifier frequently fails with OutOfMemoryError. Heap dump shows that 42% of heap size is char[] and 15% is String.
java.lang.OutOfMemoryError: Java heap space
    at cc.mallet.types.IndexedSparseVector.setIndex2Location(IndexedSparseVector.java:109)
    at cc.mallet.types.IndexedSparseVector.dotProduct(IndexedSparseVector.java:157)
    at cc.mallet.fst.CRF$TransitionIterator.<init>(CRF.java:1856)
    at cc.mallet.fst.CRF$TransitionIterator.<init>(CRF.java:1835)
    at cc.mallet.fst.CRF$State.transitionIterator(CRF.java:1776)
    at cc.mallet.fst.MaxLatticeDefault.<init>(MaxLatticeDefault.java:252)
    at cc.mallet.fst.MaxLatticeDefault.<init>(MaxLatticeDefault.java:197)
    at cc.mallet.fst.MaxLatticeDefault$Factory.newMaxLattice(MaxLatticeDefault.java:494)
    at cc.mallet.fst.MaxLatticeFactory.newMaxLattice(MaxLatticeFactory.java:11)
    at cc.mallet.fst.Transducer.transduce(Transducer.java:124)
    at org.cleartk.ml.mallet.MalletCrfStringOutcomeClassifier.classify(MalletCrfStringOutcomeClassifier.java:90)

Model is created based on MalletCrfStringOutcomeDataWriter.
AnalysisEngineFactory.createEngineDescription(DataChunkAnnotator.class,
        CleartkSequenceAnnotator.PARAM_IS_TRAINING, true, DirectoryDataWriterFactory.PARAM_OUTPUT_DIRECTORY,
        options.getModelsDirectory(), DefaultSequenceDataWriterFactory.PARAM_DATA_WRITER_CLASS_NAME, MalletCrfStringOutcomeDataWriter.class)

The annotator code looks as follows.
 if (this.isTraining()) {
        List<DataAnnotation> namedEntityMentions = JCasUtil.selectCovered(jCas, DataAannotation.class, sentence);
        List<String> outcomes = this.chunking.createOutcomes(jCas, tokens, namedEntityMentions);
        this.dataWriter.write(Instances.toInstances(outcomes, featureLists));
      } else {
        List<String> outcomes = this.classifier.classify(featureLists);
        this.chunking.createChunks(jCas, tokens, outcomes);
      }

Please suggest.


Thanks
Tilak

[Steven Bethard]

Mallet can require a lot of memory. Consider increasing your Java heap space, e.g.,

http://stackoverflow.com/questions/1596009/java-lang-outofmemoryerror-java-heap-space

Steve

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[tilak kumar]

Thanks Steven.
We have UIMA pipeline which invokes 5 model jars(based on mallet CRF) around 30MB each. -Xms is set to 2G and -Xmx is set to 4G.
Every 4th time we invoke the pipeline it runs into OutofMemeory. Is there any guidelines/bench marking on setting the heap space.

Looks like mallet CRF has memory leak issues - https://code.google.com/p/cleartk/issues/detail?id=408
The out of memory issue is reproducible even after applying the patch.

Thanks
Tilak

[Steven Bethard]

I see. So the error is in a long-running classification process. Can you tell if your alphabet size is growing, like it was in the unpatched version?

If that doesn't seem to be the problem, you might ask on the Mallet list. We have a fairly thin wrapper over Mallet, so they might be able to suggest what other things in mallet might cause OutOfMemoryError.

Steve

[tilak kumar]

Thanks Steve. Can you please point Mallet list ?
I could not find its google group. Mail to majo...@cs.umass.edu or mal...@cs.umass.edu fails.

[Steven Bethard]

I think those are the right thing to be emailing, but they're also failing for me. In the meantime, you could try:

Adding an issue on the Mallet tracker on Github:

https://github.com/mimno/Mallet/issues

Posting a "mallet" question on StackOverflow:

http://stackoverflow.com/questions/tagged/mallet

That said, it looks like the Mallet developers are about as bad at responding to these things as we ClearTK developers are. =)

Steve

On Mon, Nov 16, 2015 at 2:51 AM tilak kumar <tilakk...@gmail.com> wrote:

Thanks Steve. Can you please point Mallet list ?
I could not find its google group. Mail to majo...@cs.umass.edu or mal...@cs.umass.edu fails.

[tilak kumar]

Thanks Steven. I have posted a question http://stackoverflow.com/questions/33811026/outofmemoryerror-with-mallet-crf-classifier.