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Garbage Collector Threads #526

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DarioS opened this issue Sep 7, 2021 · 0 comments
Closed

Garbage Collector Threads #526

DarioS opened this issue Sep 7, 2021 · 0 comments

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@DarioS
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DarioS commented Sep 7, 2021

gridss.sh has the following default

jvm_args="$jvm_args \
	-Dreference_fasta=$reference \
	-Dsamjdk.use_async_io_read_samtools=true \
	-Dsamjdk.use_async_io_write_samtools=true \
	-Dsamjdk.use_async_io_write_tribble=true \
	-Dsamjdk.buffer_size=4194304"

I saw the Sydney core facility is using -XX:ParallelGCThreads=${NCPUS} for GATK commands. It was found that garbage collection would be spawning 70 threads which slowed down processing quite a bit. Would such a limit be useful to GRIDSS, too?

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