CUDA Out of Memory
Gavin Thomas
Using Beagle I am trying to run a fairly large data set (287 taxa,
14445 bp nucleotide alignment, 13 partitions). When allocating the job
to the GPUs (2 x GeForce 8800GT, 512mb VRAM) I get a CUDA Out of
Memory message. My guess it that this is simply a limitation of the
hardware but I wondered if there was any way to increase the memory
available through Beagle or CUDA?
The data set runs ok using Beagle if the job is allocated to the CPU
alone....
Thanks
Gavin
Marc Suchard
For example, the 8800GT has 512MB, a GTX280 has 1GB and many Teslas
have 4GB. To maximize speed, my recommendation is to try to stuff as
many of the largest partitions onto your GPUs (don't forget to use
both .. use the command-line option -Dbeagle.resource.order= to
specify how the partitions get distributed) and leave the rest on the
CPU.
best, Marc
Paolo Zanotto
I am trying o run some of my datasets and getting errors (see below).
Looks like that after the MCMC rejects a proposal it is not able to
reconstitute the current state.
Have any of you seen this error?
Best,
Paolo
BEAST v1.5.2 loads the xml sets up a tree, then:
tree height = 1713.9725552728598
Bayesian skyline plot: 10 stepwise control points
Exponential markov model on parameter skyline.popSize (jeffreys=true,
reverse=false)
Using discretized relaxed clock model.
over sampling = 1
parametric model = logNormalDistributionModel
rate categories = 934
Creating state frequencies model: Using empirical frequencies from
data = {0.40927, 0.15813, 0.20113, 0.23146}
Creating HKY substitution model. Initial kappa = 1.0
diff = 1.0E-10 freq = 1.0E-10
Creating site model:
4 category discrete gamma with initial shape = 0.5
Using BEAGLE TreeLikelihood
Branch rate model used: discretizedBranchRates
Beagle initializeInstance returnValue: 0
Using BEAGLE resource 1 : GeForce 8600M GT
Global memory (MB): 512
Clock speed (Ghz): 0.34
Number of cores: 32
Flags: SINGLE ASYNCH SYNCH COMPLEX LSCALE GPU
Ignoring ambiguities in tree likelihood.
With 390 unique site patterns.
Partials scaling scheme used: dynamicRescaling
Creating swap operator for parameter branchRates.categories
(weight=10.0)
Likelihood is using a cached thread pool.
Creating the MCMC chain:
chainLength=10000000
autoOptimize=true
autoOptimize delayed for 100000 steps
# BEAST v1.5.2, Build r2376
# Generated Thu Oct 22 11:45:53 BRT 2009 [seed=1256222751820]
state Posterior Prior Likelihood Root Height Rate
0 -208,393.2939 -30,384.8547 -178,008.4393 1713.97 2.35326E-6 -
Oct 22, 2009 11:47:14 AM dr.inference.markovchain.MarkovChain runChain
SEVERE: State was not correctly restored after reject step.
Likelihood before: -194540.80844641055 Likelihood after:
-194540.8104001316
Operator: dr.evomodel.operators.ExchangeOperator@c386d Narrow Exchange
(treeModel)
Oct 22, 2009 11:47:14 AM dr.inference.markovchain.MarkovChain runChain
SEVERE: CompoundLikelihood(compoundModel)=(OneOnX(hky.kappa)=-0.173,
DistributionLikelihood=-55.4691, DistributionLikelihood=8.857,
BayesianSkylineLikelihood(generalizedSkyLineLikelihood)=-25473.6846,
ExponentialMarkovModel(exponentialMarkovLikelihood)=-33.9151),
CompoundLikelihood(compoundModel)=(BeagleTreeLikelihood
(treeLikelihood)=-168986.4237)
Oct 22, 2009 11:47:14 AM dr.inference.markovchain.MarkovChain runChain
SEVERE: CompoundLikelihood(compoundModel)=(OneOnX(hky.kappa)=-0.173,
DistributionLikelihood=-55.4691, DistributionLikelihood=8.857,
BayesianSkylineLikelihood(generalizedSkyLineLikelihood)=-25473.6846,
ExponentialMarkovModel(exponentialMarkovLikelihood)=-33.9151),
CompoundLikelihood(compoundModel)=(BeagleTreeLikelihood
(treeLikelihood)=-168986.4237)
Oct 22, 2009 11:47:14 AM dr.inference.markovchain.MarkovChain runChain
SEVERE: CompoundLikelihood(compoundModel)=(OneOnX(hky.kappa)=-0.173,
DistributionLikelihood=-55.4691, DistributionLikelihood=8.857,
BayesianSkylineLikelihood(generalizedSkyLineLikelihood)=-25473.6846,
ExponentialMarkovModel(exponentialMarkovLikelihood)=-33.9151),
CompoundLikelihood(compoundModel)=(BeagleTreeLikelihood
(treeLikelihood)=-168986.4257)
Oct 22, 2009 11:47:14 AM dr.inference.markovchain.MarkovChain runChain
SEVERE: State was not correctly restored after reject step.
Likelihood before: -194540.80844641055 Likelihood after:
-194540.8104001316
Operator: dr.evomodel.operators.SubtreeSlideOperator@6bf551
subtreeSlide(treeModel)
Oct 22, 2009 11:47:14 AM dr.inference.markovchain.MarkovChain runChain
SEVERE: CompoundLikelihood(compoundModel)=(OneOnX(hky.kappa)=-0.173,
DistributionLikelihood=-55.4691, DistributionLikelihood=8.857,
BayesianSkylineLikelihood(generalizedSkyLineLikelihood)=-25473.6846,
ExponentialMarkovModel(exponentialMarkovLikelihood)=-33.9151),
CompoundLikelihood(compoundModel)=(BeagleTreeLikelihood
(treeLikelihood)=-168986.4257)
Oct 22, 2009 11:47:14 AM dr.inference.markovchain.MarkovChain runChain
SEVERE: CompoundLikelihood(compoundModel)=(OneOnX(hky.kappa)=-0.173,
DistributionLikelihood=-55.4691, DistributionLikelihood=8.857,
BayesianSkylineLikelihood(generalizedSkyLineLikelihood)=-25473.6846,
ExponentialMarkovModel(exponentialMarkovLikelihood)=-33.9151),
CompoundLikelihood(compoundModel)=(BeagleTreeLikelihood
(treeLikelihood)=-168986.4257)
Oct 22, 2009 11:47:14 AM dr.inference.markovchain.MarkovChain runChain
SEVERE: CompoundLikelihood(compoundModel)=(OneOnX(hky.kappa)=-0.173,
DistributionLikelihood=-55.4691, DistributionLikelihood=8.857,
BayesianSkylineLikelihood(generalizedSkyLineLikelihood)=-25473.6846,
ExponentialMarkovModel(exponentialMarkovLikelihood)=-33.9151),
CompoundLikelihood(compoundModel)=(BeagleTreeLikelihood
(treeLikelihood)=-168986.4257)
Oct 22, 2009 11:47:14 AM dr.inference.markovchain.MarkovChain runChain
SEVERE: State was not correctly restored after reject step.
Likelihood before: -194540.80844641055 Likelihood after:
-194540.8104001316
Operator: uniformOperator(nodeHeights(treeModel)) uniform(nodeHeights
(treeModel))
Oct 22, 2009 11:47:14 AM dr.inference.markovchain.MarkovChain runChain
SEVERE: CompoundLikelihood(compoundModel)=(OneOnX(hky.kappa)=-0.173,
DistributionLikelihood=-55.4691, DistributionLikelihood=8.857,
BayesianSkylineLikelihood(generalizedSkyLineLikelihood)=-25473.6846,
ExponentialMarkovModel(exponentialMarkovLikelihood)=-33.9151),
CompoundLikelihood(compoundModel)=(BeagleTreeLikelihood
(treeLikelihood)=-168986.4257)
Oct 22, 2009 11:47:14 AM dr.inference.markovchain.MarkovChain runChain
SEVERE: CompoundLikelihood(compoundModel)=(OneOnX(hky.kappa)=-0.173,
DistributionLikelihood=-55.4691, DistributionLikelihood=8.857,
BayesianSkylineLikelihood(generalizedSkyLineLikelihood)=-25473.6846,
ExponentialMarkovModel(exponentialMarkovLikelihood)=-33.9151),
CompoundLikelihood(compoundModel)=(BeagleTreeLikelihood
(treeLikelihood)=-168986.4257)
Oct 22, 2009 11:47:14 AM dr.inference.markovchain.MarkovChain runChain
SEVERE: CompoundLikelihood(compoundModel)=(OneOnX(hky.kappa)=-0.173,
DistributionLikelihood=-55.4691, DistributionLikelihood=8.857,
BayesianSkylineLikelihood(generalizedSkyLineLikelihood)=-25473.6846,
ExponentialMarkovModel(exponentialMarkovLikelihood)=-33.9151),
CompoundLikelihood(compoundModel)=(BeagleTreeLikelihood
(treeLikelihood)=-168986.4257)
Oct 22, 2009 11:47:14 AM dr.inference.markovchain.MarkovChain runChain
SEVERE: State was not correctly restored after reject step.
Likelihood before: -194540.80844641055 Likelihood after:
-194540.8104001316
Operator: uniformOperator(nodeHeights(treeModel)) uniform(nodeHeights
(treeModel))
Oct 22, 2009 11:47:14 AM dr.inference.markovchain.MarkovChain runChain
SEVERE: CompoundLikelihood(compoundModel)=(OneOnX(hky.kappa)=-0.173,
DistributionLikelihood=-55.4691, DistributionLikelihood=8.857,
BayesianSkylineLikelihood(generalizedSkyLineLikelihood)=-25473.6846,
ExponentialMarkovModel(exponentialMarkovLikelihood)=-33.9151),
CompoundLikelihood(compoundModel)=(BeagleTreeLikelihood
(treeLikelihood)=-168986.4257)
Oct 22, 2009 11:47:14 AM dr.inference.markovchain.MarkovChain runChain
SEVERE: CompoundLikelihood(compoundModel)=(OneOnX(hky.kappa)=-0.173,
DistributionLikelihood=-55.4691, DistributionLikelihood=8.857,
BayesianSkylineLikelihood(generalizedSkyLineLikelihood)=-25473.6846,
ExponentialMarkovModel(exponentialMarkovLikelihood)=-33.9151),
CompoundLikelihood(compoundModel)=(BeagleTreeLikelihood
(treeLikelihood)=-168986.4257)
Oct 22, 2009 11:47:14 AM dr.inference.markovchain.MarkovChain runChain
SEVERE: CompoundLikelihood(compoundModel)=(OneOnX(hky.kappa)=-0.173,
DistributionLikelihood=-55.4691, DistributionLikelihood=8.857,
BayesianSkylineLikelihood(generalizedSkyLineLikelihood)=-25473.6846,
ExponentialMarkovModel(exponentialMarkovLikelihood)=-33.9151),
CompoundLikelihood(compoundModel)=(BeagleTreeLikelihood
(treeLikelihood)=-168986.4257)
Oct 22, 2009 11:47:14 AM dr.inference.markovchain.MarkovChain runChain
SEVERE: State was not correctly restored after reject step.
Likelihood before: -194540.80844641055 Likelihood after:
-194540.8104001316
Operator: uniformOperator(nodeHeights(treeModel)) uniform(nodeHeights
(treeModel))
Oct 22, 2009 11:47:14 AM dr.inference.markovchain.MarkovChain runChain
SEVERE: CompoundLikelihood(compoundModel)=(OneOnX(hky.kappa)=-0.173,
DistributionLikelihood=-55.4691, DistributionLikelihood=8.857,
BayesianSkylineLikelihood(generalizedSkyLineLikelihood)=-25473.6846,
ExponentialMarkovModel(exponentialMarkovLikelihood)=-33.9151),
CompoundLikelihood(compoundModel)=(BeagleTreeLikelihood
(treeLikelihood)=-168986.4257)
Oct 22, 2009 11:47:14 AM dr.inference.markovchain.MarkovChain runChain
SEVERE: CompoundLikelihood(compoundModel)=(OneOnX(hky.kappa)=-0.173,
DistributionLikelihood=-55.4691, DistributionLikelihood=8.857,
BayesianSkylineLikelihood(generalizedSkyLineLikelihood)=-25473.6846,
ExponentialMarkovModel(exponentialMarkovLikelihood)=-33.9151),
CompoundLikelihood(compoundModel)=(BeagleTreeLikelihood
(treeLikelihood)=-168986.4257)
Oct 22, 2009 11:47:14 AM dr.inference.markovchain.MarkovChain runChain
SEVERE: CompoundLikelihood(compoundModel)=(OneOnX(hky.kappa)=-0.173,
DistributionLikelihood=-55.4691, DistributionLikelihood=8.857,
BayesianSkylineLikelihood(generalizedSkyLineLikelihood)=-25473.6846,
ExponentialMarkovModel(exponentialMarkovLikelihood)=-33.9151),
CompoundLikelihood(compoundModel)=(BeagleTreeLikelihood
(treeLikelihood)=-168986.4257)
Oct 22, 2009 11:47:14 AM dr.inference.markovchain.MarkovChain runChain
SEVERE: State was not correctly restored after reject step.
Likelihood before: -194540.80844641055 Likelihood after:
-194540.8104001316
Operator: dr.evomodel.operators.SubtreeSlideOperator@6bf551
subtreeSlide(treeModel)
Oct 22, 2009 11:47:14 AM dr.inference.markovchain.MarkovChain runChain
SEVERE: CompoundLikelihood(compoundModel)=(OneOnX(hky.kappa)=-0.173,
DistributionLikelihood=-55.4691, DistributionLikelihood=8.857,
BayesianSkylineLikelihood(generalizedSkyLineLikelihood)=-25473.6846,
ExponentialMarkovModel(exponentialMarkovLikelihood)=-33.9151),
CompoundLikelihood(compoundModel)=(BeagleTreeLikelihood
(treeLikelihood)=-168986.4257)
Oct 22, 2009 11:47:14 AM dr.inference.markovchain.MarkovChain runChain
SEVERE: CompoundLikelihood(compoundModel)=(OneOnX(hky.kappa)=-0.173,
DistributionLikelihood=-55.4691, DistributionLikelihood=8.857,
BayesianSkylineLikelihood(generalizedSkyLineLikelihood)=-25473.6846,
ExponentialMarkovModel(exponentialMarkovLikelihood)=-33.9151),
CompoundLikelihood(compoundModel)=(BeagleTreeLikelihood
(treeLikelihood)=-168986.4257)
Oct 22, 2009 11:47:14 AM dr.inference.markovchain.MarkovChain runChain
SEVERE: CompoundLikelihood(compoundModel)=(OneOnX(hky.kappa)=-0.173,
DistributionLikelihood=-55.4691, DistributionLikelihood=8.857,
BayesianSkylineLikelihood(generalizedSkyLineLikelihood)=-25473.6846,
ExponentialMarkovModel(exponentialMarkovLikelihood)=-33.9151),
CompoundLikelihood(compoundModel)=(BeagleTreeLikelihood
(treeLikelihood)=-168986.4257)
Oct 22, 2009 11:47:14 AM dr.inference.markovchain.MarkovChain runChain
SEVERE: State was not correctly restored after reject step.
Likelihood before: -194540.80844641055 Likelihood after:
-194540.8104001316
Operator: uniformOperator(nodeHeights(treeModel)) uniform(nodeHeights
(treeModel))
Oct 22, 2009 11:47:14 AM dr.inference.markovchain.MarkovChain runChain
SEVERE: CompoundLikelihood(compoundModel)=(OneOnX(hky.kappa)=-0.173,
DistributionLikelihood=-55.4691, DistributionLikelihood=8.857,
BayesianSkylineLikelihood(generalizedSkyLineLikelihood)=-25473.6846,
ExponentialMarkovModel(exponentialMarkovLikelihood)=-33.9151),
CompoundLikelihood(compoundModel)=(BeagleTreeLikelihood
(treeLikelihood)=-168986.4257)
Oct 22, 2009 11:47:14 AM dr.inference.markovchain.MarkovChain runChain
SEVERE: CompoundLikelihood(compoundModel)=(OneOnX(hky.kappa)=-0.173,
DistributionLikelihood=-55.4691, DistributionLikelihood=8.857,
BayesianSkylineLikelihood(generalizedSkyLineLikelihood)=-25473.6846,
ExponentialMarkovModel(exponentialMarkovLikelihood)=-33.9151),
CompoundLikelihood(compoundModel)=(BeagleTreeLikelihood
(treeLikelihood)=-168986.4257)
Oct 22, 2009 11:47:14 AM dr.inference.markovchain.MarkovChain runChain
SEVERE: CompoundLikelihood(compoundModel)=(OneOnX(hky.kappa)=-0.173,
DistributionLikelihood=-55.4691, DistributionLikelihood=8.857,
BayesianSkylineLikelihood(generalizedSkyLineLikelihood)=-25473.6846,
ExponentialMarkovModel(exponentialMarkovLikelihood)=-33.9151),
CompoundLikelihood(compoundModel)=(BeagleTreeLikelihood
(treeLikelihood)=-168986.4257)
Oct 22, 2009 11:47:15 AM dr.inference.markovchain.MarkovChain runChain
SEVERE: State was not correctly restored after reject step.
Likelihood before: -194540.80844641055 Likelihood after:
-194540.8104001316
Operator: dr.evomodel.operators.SubtreeSlideOperator@6bf551
subtreeSlide(treeModel)
Oct 22, 2009 11:47:15 AM dr.inference.markovchain.MarkovChain runChain
SEVERE: CompoundLikelihood(compoundModel)=(OneOnX(hky.kappa)=-0.173,
DistributionLikelihood=-55.4691, DistributionLikelihood=8.857,
BayesianSkylineLikelihood(generalizedSkyLineLikelihood)=-25473.6846,
ExponentialMarkovModel(exponentialMarkovLikelihood)=-33.9151),
CompoundLikelihood(compoundModel)=(BeagleTreeLikelihood
(treeLikelihood)=-168986.4257)
Oct 22, 2009 11:47:15 AM dr.inference.markovchain.MarkovChain runChain
SEVERE: CompoundLikelihood(compoundModel)=(OneOnX(hky.kappa)=-0.173,
DistributionLikelihood=-55.4691, DistributionLikelihood=8.857,
BayesianSkylineLikelihood(generalizedSkyLineLikelihood)=-25473.6846,
ExponentialMarkovModel(exponentialMarkovLikelihood)=-33.9151),
CompoundLikelihood(compoundModel)=(BeagleTreeLikelihood
(treeLikelihood)=-168986.4257)
Oct 22, 2009 11:47:15 AM dr.inference.markovchain.MarkovChain runChain
SEVERE: CompoundLikelihood(compoundModel)=(OneOnX(hky.kappa)=-0.173,
DistributionLikelihood=-55.4691, DistributionLikelihood=8.857,
BayesianSkylineLikelihood(generalizedSkyLineLikelihood)=-25473.6846,
ExponentialMarkovModel(exponentialMarkovLikelihood)=-33.9151),
CompoundLikelihood(compoundModel)=(BeagleTreeLikelihood
(treeLikelihood)=-168986.4257)
Oct 22, 2009 11:47:15 AM dr.inference.markovchain.MarkovChain runChain
SEVERE: State was not correctly restored after reject step.
Likelihood before: -194540.80844641055 Likelihood after:
-194540.8104001316
Operator: dr.evomodel.operators.WilsonBalding@b6a350 wilsonBalding
(treeModel)
Oct 22, 2009 11:47:15 AM dr.inference.markovchain.MarkovChain runChain
SEVERE: CompoundLikelihood(compoundModel)=(OneOnX(hky.kappa)=-0.173,
DistributionLikelihood=-55.4691, DistributionLikelihood=8.857,
BayesianSkylineLikelihood(generalizedSkyLineLikelihood)=-25473.6846,
ExponentialMarkovModel(exponentialMarkovLikelihood)=-33.9151),
CompoundLikelihood(compoundModel)=(BeagleTreeLikelihood
(treeLikelihood)=-168986.4257)
Oct 22, 2009 11:47:15 AM dr.inference.markovchain.MarkovChain runChain
SEVERE: CompoundLikelihood(compoundModel)=(OneOnX(hky.kappa)=-0.173,
DistributionLikelihood=-55.4691, DistributionLikelihood=8.857,
BayesianSkylineLikelihood(generalizedSkyLineLikelihood)=-25473.6846,
ExponentialMarkovModel(exponentialMarkovLikelihood)=-33.9151),
CompoundLikelihood(compoundModel)=(BeagleTreeLikelihood
(treeLikelihood)=-168986.4257)
Oct 22, 2009 11:47:15 AM dr.inference.markovchain.MarkovChain runChain
SEVERE: CompoundLikelihood(compoundModel)=(OneOnX(hky.kappa)=-0.173,
DistributionLikelihood=-55.4691, DistributionLikelihood=8.857,
BayesianSkylineLikelihood(generalizedSkyLineLikelihood)=-25473.6846,
ExponentialMarkovModel(exponentialMarkovLikelihood)=-33.9151),
CompoundLikelihood(compoundModel)=(BeagleTreeLikelihood
(treeLikelihood)=-168986.4257)
Oct 22, 2009 11:47:15 AM dr.inference.markovchain.MarkovChain runChain
SEVERE: State was not correctly restored after reject step.
Likelihood before: -194540.80844641055 Likelihood after:
-194540.8104001316
Operator: uniformOperator(nodeHeights(treeModel)) uniform(nodeHeights
(treeModel))
Oct 22, 2009 11:47:15 AM dr.inference.markovchain.MarkovChain runChain
SEVERE: CompoundLikelihood(compoundModel)=(OneOnX(hky.kappa)=-0.173,
DistributionLikelihood=-55.4691, DistributionLikelihood=8.857,
BayesianSkylineLikelihood(generalizedSkyLineLikelihood)=-25473.6846,
ExponentialMarkovModel(exponentialMarkovLikelihood)=-33.9151),
CompoundLikelihood(compoundModel)=(BeagleTreeLikelihood
(treeLikelihood)=-168986.4257)
Oct 22, 2009 11:47:15 AM dr.inference.markovchain.MarkovChain runChain
SEVERE: CompoundLikelihood(compoundModel)=(OneOnX(hky.kappa)=-0.173,
DistributionLikelihood=-55.4691, DistributionLikelihood=8.857,
BayesianSkylineLikelihood(generalizedSkyLineLikelihood)=-25473.6846,
ExponentialMarkovModel(exponentialMarkovLikelihood)=-33.9151),
CompoundLikelihood(compoundModel)=(BeagleTreeLikelihood
(treeLikelihood)=-168986.4257)
Oct 22, 2009 11:47:15 AM dr.inference.markovchain.MarkovChain runChain
SEVERE: CompoundLikelihood(compoundModel)=(OneOnX(hky.kappa)=-0.173,
DistributionLikelihood=-55.4691, DistributionLikelihood=8.857,
BayesianSkylineLikelihood(generalizedSkyLineLikelihood)=-25473.6846,
ExponentialMarkovModel(exponentialMarkovLikelihood)=-33.9151),
CompoundLikelihood(compoundModel)=(BeagleTreeLikelihood
(treeLikelihood)=-168986.4257)
Oct 22, 2009 11:47:15 AM dr.inference.markovchain.MarkovChain runChain
SEVERE: State was not correctly restored after reject step.
Likelihood before: -194540.80844641055 Likelihood after:
-194540.8104001316
Operator: dr.evomodel.operators.SubtreeSlideOperator@6bf551
subtreeSlide(treeModel)
Oct 22, 2009 11:47:15 AM dr.inference.markovchain.MarkovChain runChain
SEVERE: CompoundLikelihood(compoundModel)=(OneOnX(hky.kappa)=-0.173,
DistributionLikelihood=-55.4691, DistributionLikelihood=8.857,
BayesianSkylineLikelihood(generalizedSkyLineLikelihood)=-25473.6846,
ExponentialMarkovModel(exponentialMarkovLikelihood)=-33.9151),
CompoundLikelihood(compoundModel)=(BeagleTreeLikelihood
(treeLikelihood)=-168986.4257)
Oct 22, 2009 11:47:15 AM dr.inference.markovchain.MarkovChain runChain
SEVERE: CompoundLikelihood(compoundModel)=(OneOnX(hky.kappa)=-0.173,
DistributionLikelihood=-55.4691, DistributionLikelihood=8.857,
BayesianSkylineLikelihood(generalizedSkyLineLikelihood)=-25473.6846,
ExponentialMarkovModel(exponentialMarkovLikelihood)=-33.9151),
CompoundLikelihood(compoundModel)=(BeagleTreeLikelihood
(treeLikelihood)=-168986.4257)
Oct 22, 2009 11:47:15 AM dr.inference.markovchain.MarkovChain runChain
SEVERE: CompoundLikelihood(compoundModel)=(OneOnX(hky.kappa)=-0.173,
DistributionLikelihood=-55.4691, DistributionLikelihood=8.857,
BayesianSkylineLikelihood(generalizedSkyLineLikelihood)=-25473.6846,
ExponentialMarkovModel(exponentialMarkovLikelihood)=-33.9151),
CompoundLikelihood(compoundModel)=(BeagleTreeLikelihood
(treeLikelihood)=-168986.4257)
Oct 22, 2009 11:47:15 AM dr.inference.markovchain.MarkovChain runChain
SEVERE: State was not correctly restored after reject step.
Likelihood before: -194540.80844641055 Likelihood after:
-194540.8104001316
Operator: dr.evomodel.operators.SubtreeSlideOperator@6bf551
subtreeSlide(treeModel)
Oct 22, 2009 11:47:15 AM dr.inference.markovchain.MarkovChain runChain
SEVERE: CompoundLikelihood(compoundModel)=(OneOnX(hky.kappa)=-0.173,
DistributionLikelihood=-55.4691, DistributionLikelihood=8.857,
BayesianSkylineLikelihood(generalizedSkyLineLikelihood)=-25473.6846,
ExponentialMarkovModel(exponentialMarkovLikelihood)=-33.9151),
CompoundLikelihood(compoundModel)=(BeagleTreeLikelihood
(treeLikelihood)=-168986.4257)
Oct 22, 2009 11:47:15 AM dr.inference.markovchain.MarkovChain runChain
SEVERE: CompoundLikelihood(compoundModel)=(OneOnX(hky.kappa)=-0.173,
DistributionLikelihood=-55.4691, DistributionLikelihood=8.857,
BayesianSkylineLikelihood(generalizedSkyLineLikelihood)=-25473.6846,
ExponentialMarkovModel(exponentialMarkovLikelihood)=-33.9151),
CompoundLikelihood(compoundModel)=(BeagleTreeLikelihood
(treeLikelihood)=-168986.4257)
Oct 22, 2009 11:47:15 AM dr.inference.markovchain.MarkovChain runChain
SEVERE: CompoundLikelihood(compoundModel)=(OneOnX(hky.kappa)=-0.173,
DistributionLikelihood=-55.4691, DistributionLikelihood=8.857,
BayesianSkylineLikelihood(generalizedSkyLineLikelihood)=-25473.6846,
ExponentialMarkovModel(exponentialMarkovLikelihood)=-33.9151),
CompoundLikelihood(compoundModel)=(BeagleTreeLikelihood
(treeLikelihood)=-168986.4257)
Oct 22, 2009 11:47:15 AM dr.inference.markovchain.MarkovChain runChain
SEVERE: State was not correctly restored after reject step.
Likelihood before: -194540.80844641055 Likelihood after:
-194540.8104001316
Operator: uniformOperator(nodeHeights(treeModel)) uniform(nodeHeights
(treeModel))
Oct 22, 2009 11:47:15 AM dr.inference.markovchain.MarkovChain runChain
SEVERE: CompoundLikelihood(compoundModel)=(OneOnX(hky.kappa)=-0.173,
DistributionLikelihood=-55.4691, DistributionLikelihood=8.857,
BayesianSkylineLikelihood(generalizedSkyLineLikelihood)=-25473.6846,
ExponentialMarkovModel(exponentialMarkovLikelihood)=-33.9151),
CompoundLikelihood(compoundModel)=(BeagleTreeLikelihood
(treeLikelihood)=-168986.4257)
Oct 22, 2009 11:47:15 AM dr.inference.markovchain.MarkovChain runChain
SEVERE: CompoundLikelihood(compoundModel)=(OneOnX(hky.kappa)=-0.173,
DistributionLikelihood=-55.4691, DistributionLikelihood=8.857,
BayesianSkylineLikelihood(generalizedSkyLineLikelihood)=-25473.6846,
ExponentialMarkovModel(exponentialMarkovLikelihood)=-33.9151),
CompoundLikelihood(compoundModel)=(BeagleTreeLikelihood
(treeLikelihood)=-168986.4257)
Oct 22, 2009 11:47:15 AM dr.inference.markovchain.MarkovChain runChain
SEVERE: CompoundLikelihood(compoundModel)=(OneOnX(hky.kappa)=-0.173,
DistributionLikelihood=-55.4691, DistributionLikelihood=8.857,
BayesianSkylineLikelihood(generalizedSkyLineLikelihood)=-25473.6846,
ExponentialMarkovModel(exponentialMarkovLikelihood)=-33.9151),
CompoundLikelihood(compoundModel)=(BeagleTreeLikelihood
(treeLikelihood)=-168986.4257)
Exception in thread "Thread-1" java.lang.RuntimeException: One or
more evaluation errors occured 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:613)
WARNING: Element named object with idref=mcmc does not match stored
object with same id and tag name mcmc
1.9561166666666667 minutes