Alternative to adding Beagle library to PATH - not compatible with Condor

[Mary O'Neill]

I am trying to run beast on a cluster and get the following error when I submit a BEAST run through Condor:

Failed to load BEAGLE library: no hmsbeagle-jni in java.library.path

Failed to load BEAGLE library: no hmsbeagle-jni in java.library.path

Failed to load parser: dr.inferencexml.trace.GeneralizedHarmonicMeanAnalysisParser

line = dr.inferencexml.trace.GeneralizedHarmonicMeanAnalysisParser

Failed to load BEAGLE library: no hmsbeagle-jni in java.library.path

Fatal exception: No acceptable BEAGLE library plugins found. Make sure that BEAGLE is properly installed or try changing resource requirements.

java.lang.RuntimeException: No acceptable BEAGLE library plugins found. Make sure that BEAGLE is properly installed or try changing resource requirements.

    at beagle.BeagleFactory.loadBeagleInstance(Unknown Source)

    at dr.app.beagle.evomodel.treelikelihood.BeagleTreeLikelihood.<init>(Unknown Source)

    at dr.app.beagle.evomodel.parsers.BeagleTreeLikelihoodParser.createTreeLikelihood(Unknown Source)

    at dr.app.beagle.evomodel.parsers.BeagleTreeLikelihoodParser.parseXMLObject(Unknown Source)

    at dr.xml.AbstractXMLObjectParser.parseXMLObject(Unknown Source)

    at dr.xml.XMLParser.convert(Unknown Source)

    at dr.xml.XMLParser.convert(Unknown Source)

    at dr.xml.XMLParser.parse(Unknown Source)

    at dr.app.beast.BeastMain.<init>(Unknown Source)

    at dr.app.beast.BeastMain.main(Unknown Source)

java.lang.RuntimeException: Terminate

    at dr.app.beast.BeastMain.<init>(Unknown Source)

    at dr.app.beast.BeastMain.main(Unknown Source)

On our server the command works just fine, as the Beagle library has been added to the PATH. Unfortunately the other servers in the cluster to do not share this - is there a way to specify the path to the beagle library in the command or some other solution?

Thank you,

Mary

[Andrew Rambaut]

Dear Mary,

If you can control the environment of the cluster nodes, you can add the location of BEAGLE to LD_LIBRARY_PATH. 

Alternatively, you can edit the shell script that runs BEAST (./bin/beast) and add the location to the java.library.path

in the command line at the end.

Andrew

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