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Beast2 fails with EigenDecompositionCube #1182

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aaron-wes opened this issue Feb 27, 2025 · 0 comments
Open

Beast2 fails with EigenDecompositionCube #1182

aaron-wes opened this issue Feb 27, 2025 · 0 comments

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@aaron-wes
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Hi

I'm currently running into an issue with Beast 2.7.5 on a linux cluster. When run, it fails quickly with a java runtime error, ID'ing this as the problematic frame:

C [libhmsbeagle-cpu-sse.so.31.0.0+0x21dc1] beagle::cpu::EigenDecompositionCube<double, 2>::updateTransitionMatrices(int, int const*, int const*, int const*, double const*, double const*, double**, int)+0x231

This seems to be related to the beagle library but I am not sure how to go about troubleshooting, as I'm not sure if its just a versioning issue (I built the xml with BEAUti 2.7.7 but am running Beast 2.7.5, as it is already installed on the cluster), an issue with priors (see warning below), an issue with the beagle install. Here is what returns when I call -beagle_info:

0 : CPU
    Flags: PRECISION_SINGLE PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL EIGEN_COMPLEX SCALING_MANUAL SCALING_AUTO SCALING_ALWAYS SCALERS_RAW SCALERS_LOG VECTOR_SSE VECTOR_NONE THREADING_CPP THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU

I have also been getting a warning in stderr:

WARNING: the dimension of the parameter is -1 at the start of the run.
         The operator groupSizesDelta.t:nextclade_1 has no effect (if this does not change).

From what I can tell, the warning seems to be related to the Bayesian Coalescent Skyline element of the model (I've kept default parameters for both Pop and GroupSize, as well as defaults for dimensions). Once again, I'm not sure if this is related to the beagle issue or something independent just because I built the XML using a slightly newer version of BEAUti. For background, I'm running a GTR + I + g substitution model, an ORC with tip dates, and largely default priors.

Any guidance greatly appreciated and happy to provide any other information that may be useful!

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