Comments (2)
macmanes
commented on August 30, 2024
Hi Karen,
This is an issue with Java, indeed. See
Exception in thread "main" java.lang.OutOfMemoryError: GC overhead limit exceeded
This is an issue we used to see in older versions of Trinity, but up until recently, we (I) have not seen it. In the last few days, using Trinity 2.8.4, this error has cropped up several times for my students. The general advice is not super, but to reduce the number of CPUs you're using. So, specifically for you, I'd start the assembly up again, using the exact same command, except for that I would change CPU=16 to CPU=8. This will prolong the assembly process a bit, but hopefully it will finish successfully. @brianjohnhaas any other suggestions?
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brianjohnhaas
commented on August 30, 2024
not sure.... I haven't had complaints about this in a long time, and I
thought it was largely solved. Dialing down the number total concurrent
java process via lowering CPU is one way to go, but it's unfortunate that
this is happening.
…On Fri, Nov 16, 2018 at 5:08 PM Matt MacManes ***@***.***> wrote:
Hi Karen,
This is an issue with Java, indeed. See
Exception in thread "main" java.lang.OutOfMemoryError: GC overhead limit exceeded
This is an issue we used to see in older versions of Trinity, but up until
recently, we (I) have not seen it. In the last few days, using Trinity
2.8.4, this error has cropped up several times for my students. The general
advice is not super, but to reduce the number of CPUs your using. So,
specifically for you, I'd start the assembly up again, using the exact same
command, except for that I would change CPU=16 to CPU=8. This will
prolong the assembly process a bit, but hopefully it will finish
successfully. @brianjohnhaas <https://github.com/brianjohnhaas> any other
suggestions?
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