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Bowtie2 performance suffers when using many threads in some conditions #21

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bede opened this issue Jul 14, 2023 · 3 comments
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Bowtie2 performance suffers when using many threads in some conditions #21

bede opened this issue Jul 14, 2023 · 3 comments
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bede commented Jul 14, 2023

For some datasets, Bowtie2's CPU utilisation decreases with increasing numbers of threads. Workaround is not to use more than 8-16 threads. Raised upstream BenLangmead/bowtie2#437
@bede bede added the upstream label Jul 14, 2023
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bede commented Jul 25, 2023

Considering pinning bowtie2=2.4.4 in next release as per BenLangmead/bowtie2#437 (comment)

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bede commented Jul 26, 2023 •
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bowtie2=2.4.5 also works BenLangmead/bowtie2#437 (comment)

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bede commented Oct 23, 2023

Fixed upstream BenLangmead/bowtie2#437

@bede bede closed this as completed Oct 23, 2023
bede added a commit that referenced this issue Oct 23, 2023
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Fix test and pin bowtie2=2.5.2, addressing issue #21
3568169
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