humann2 thread efficiency

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Billy Taj

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Nov 5, 2019, 11:50:55 AM11/5/19
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Hi, I'm running HUMAnN2 on a machine with many cores (40).
How are the threads used in HUMAnN2?  Is there internal job scheduling?
Will I see a dramatic increase in runtimes if I use all 40 cores, with the thread argument?

Eric Franzosa

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Nov 5, 2019, 12:02:07 PM11/5/19
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The major speed-up from --threads N is that it's passed to the analogous bowtie2/diamond flags internally to tell those tools to use N threads. I have observed ~linear speed-ups during the rate-limiting diamond alignment stage when scaling from 1-24 threads.

Thanks,
Eric



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Billy Taj

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Nov 5, 2019, 12:10:52 PM11/5/19
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Ahh, ok.  So the thread argument is passed to those tools, but it's not like HUMAnN2 will run multiple instances of them and do process management.  
Is this accurate?

Eric Franzosa

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Nov 5, 2019, 12:15:38 PM11/5/19
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Correct - HUMAnN2 will not launch multiple instances of the alignment binaries.

Thanks,
Eric



On Tue, Nov 5, 2019 at 12:10 PM Billy Taj <bill...@gmail.com> wrote:
Ahh, ok.  So the thread argument is passed to those tools, but it's not like HUMAnN2 will run multiple instances of them and do process management.  
Is this accurate?

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