Force xopen to use the main thread when cores==1 #572
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marcelm
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Oct 5, 2021
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Oh by the way. Using xopen with threads=0 might incur a hefty performance penalty due to reasons which I highlight (and solve) in this PR: pycompression/xopen#78 |
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I saw the PR, thanks, will look at it later. Not sure if I have time today, though |
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Thanks! |
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Ah thanks, for letting me know you saw it. Take your time! |
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Currently cutadapt opens external programs on the default setting, thus using more than 1 core by default. Even if cores is explicitly set to 1.
Cores ==0 does not help the situation.
EDIT: As shown in many many benchmarks. There is overhead to using multithreading. The best way to utilize a cluster is to open a multitude of single threaded processes. Cutadapt is fast enough to do this in reasonable time.
EDIT2: A hidden flag that explicitly sets the xopen threads could be an alternative.