Why is `k2mask` set to use only half the number of available cores?

Lines 485 to 487 in 4cbdc5f

    
           argv = masking_binary + " -outfmt fasta -threads {} -r x".format( 
        
               multiprocessing.cpu_count() // 2 
        
           )

For kraken2 I observed that performance is best at 1/2 to 3/4 of available cores. After that performance decreases.

Not sure about if it is the same case with k2mask. Need to run verify it.

https://avilpage.com/2024/07/mastering-kraken2-performance-optimisation.html

For kraken2 I observed that performance is best at 1/2 to 3/4 of available cores. After that performance decreases.

Not sure about if it is the same case with k2mask. Need to run verify it.

https://avilpage.com/2024/07/mastering-kraken2-performance-optimisation.html

The downside to it being hardcoded like that is when you run Kraken2 in a cluster environment you don't want the script looking at all the cores available on a node because you typically request a certain number of cores to use for the job and the job could be assigned to a node with a lot more cores than what you requested (that other jobs are using).

I agree that it shouldn't be hardcoded. I am trying to understand why it could be hardcoded to multiprocessing.cpu_count() // 2 in the initial stage.

I agree that this change should be configurable via the command line. I will address this in my next commit to k2.

Raised PR for that #866

	argv = masking_binary + " -outfmt fasta -threads {} -r x".format(
	multiprocessing.cpu_count() // 2
	)