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CompEvol / beast2

Bayesian Evolutionary Analysis by Sampling Trees
www.beast2.org
GNU Lesser General Public License v2.1
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BEAST2: fatal error has been detected by the Java Runtime Environment #1132

Open Rutaiwan opened 1 year ago

Rutaiwan commented 1 year ago

Hello,

Anyone have this kind of error before when running BEAST2? Do you know how to fix this issue? I'm using BEAST2 version 2.6.7, not sure if it's something about software version or java.

A fatal error has been detected by the Java Runtime Environment: #

SIGILL (0x4) at pc=0x00007ffb0800bc4b, pid=1613621, tid=0x00007ffba7dff640

#

JRE version: OpenJDK Runtime Environment (8.0_121-b15) (build 1.8.0_121-b15)

Java VM: OpenJDK 64-Bit Server VM (25.121-b15 mixed mode linux-amd64 compressed oops)

Problematic frame:

C [libhmsbeagle.so.1+0x5c4b] beagleLoadPlugins()+0x1db

#

Failed to write core dump. Core dumps have been disabled. To enable core dumping, try "ulimit -c unlimited" before starting Java again

Thanks a lot in advance,

rbouckaert commented 1 year ago

@Rutaiwan The error message suggest something is going wrong with loading the BEAGLE library. This can happen when BEAGLE is installed with CUDA support while CUDA is not installed. What can help is uninstalling BEAGLE, then installing it again, but make sure that CUDA support for BEAGLE is not installed.

Hope this helps.

Remco

PS you might want to consider upgrading to BEAST v2.7.

sbrobeson commented 6 months ago

I am having this issue in BEAST 2.6.x and 2.7.x alike. I installed BEAST 2.6.7 via the Bioconda package, and BEAST 2.7.6 manually, but the error is the exact same in both cases.

rbouckaert commented 6 months ago

@sbrobeson Do you have beagle installed? It might be the source of this problem if it is installed with CUDA support while the hardware does not support it.