Issue 733 in beast-mcmc: Error random local clock

[beast...@googlecode.com]

Status: New
Owner: ----
Labels: Type-Defect Priority-Medium

New issue 733 by fdigiall...@gmail.com: Error random local clock
http://code.google.com/p/beast-mcmc/issues/detail?id=733

Hi

I'm using BEAST 1.8 and it works fine when I use a strickt clock or
lognormal relaxed clock. However, when I want to use the random local clock
I get an error (see below)

Does anyone now why this happens and how to fix the problem?

Thanks

May 27, 2014 10:19:09 AM dr.inference.markovchain.MarkovChain runChain
SEVERE: State was not correctly calculated after an operator move.
Likelihood evaluation: -47803.09839741052
Full Likelihood evaluation: -47368.10911721017
Operator: scaleOperator(localClock.relativeRates [0.75, 1.3333333333333333]
scale(localClock.relativeRates)
May 27, 2014 10:19:09 AM dr.inference.markovchain.MarkovChain runChain
SEVERE: State was not correctly calculated after an operator move.
Likelihood evaluation: -47737.04515278441
Full Likelihood evaluation: -47301.47682139139
Operator: scaleOperator(localClock.relativeRates [0.75, 1.3333333333333333]
scale(localClock.relativeRates)
1.0426166666666667 minutes
Exception in thread "Thread-6" java.lang.RuntimeException: One or more
evaluation errors occurred during the test phase of this
run. These errors imply critical errors which may produce incorrect
results.
at dr.inference.markovchain.MarkovChain.runChain(Unknown Source)
at dr.inference.mcmc.MCMC.chain(Unknown Source)
at dr.inference.mcmc.MCMC.run(Unknown Source)
at java.lang.Thread.run(Thread.java:695)


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[beast...@googlecode.com]

Comment #1 on issue 733 by msuch...@gmail.com: Error random local clock
http://code.google.com/p/beast-mcmc/issues/detail?id=733

Unable to reproduce error and fix unless a (minimal) XML and seed are
provided.

[beast...@googlecode.com]

Updates:
Status: Duplicate
Mergedinto: 756

Comment #2 on issue 733 by ramb...@gmail.com: Error random local clock
https://code.google.com/p/beast-mcmc/issues/detail?id=733

I think this is the same as Issue 756. It is a problem with multi-threading
when using certain clock models on multiple partitions (including codon
partitioning). Interim solution is to use '-threads 1' on the command line
but this will be less efficient on multi-core machines.