rbiom: rbiom: Read/Write, Transform, and Summarize BIOM Data

Description Multithreading

Description

A toolkit for working with Biological Observation Matrix (BIOM) files. Features include reading/writing all BIOM formats, rarefaction, alpha diversity, beta diversity (including UniFrac), summarizing counts by taxonomic level, and sample subsetting. Standalone functions for reading, writing, and subsetting phylogenetic trees are also provided. All CPU intensive operations are encoded in C with multi-thread support.

Multithreading

Many rbiom functions support multithreading:

The default behavior of these function is to run on as many cores as are available in the local compute environment. If you wish to limit the number of simultaneous threads, set the rbiom.max.threads option. For instance:

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    options('rbiom.max.threads' = 6)

Alternatively, you can register a custom parallel backend, which will be detected and used for multithreaded functions. Please note that only the doSNOW backend currently supports progress tracking. With other backends, you will only be notified of the beginning and ending of computations.

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    cl <- parallel::makeCluster(ncores)
    doSNOW::registerDoSNOW(cl)

cmmr/rbiom documentation built on Nov. 21, 2018, 10:04 a.m.