BiocParallel v1.0.3

Bioconductor facilities for parallel evaluation

This package provides modified versions and novel implementation of functions for parallel evaluation, tailored to use with Bioconductor objects.

Readme

BiocParallel

Bioconductor facilities for parallel evaluation (experimental)

Possible TODO

  • map/reduce-like function
  • bpforeach?
  • Abstract scheduler
  • lazy DoparParam
  • SnowParam support for setSeed, recursive, cleanup
  • subset SnowParam
  • elaborate SnowParam for SnowSocketParam, SnowForkParam, SnowMpiParam, ...
  • MulticoreParam on Windows
  • Short vignette

DONE

  • encapsulate arguments as ParallelParam()
  • Standardize signatures
  • Make functions generics
  • parLapply-like function

github notes

  • commit one-liners with names

    git log --pretty=format:"- %h %an: %s"

Functions in BiocParallel

Name Description
bpschedule Schedule back-end Params
bpvec Parallel, vectorized evaluation
BatchJobsParam-class Enable parallelization on batch systems
BiocParallelParam-class Virtual classes (for developer reference)
bpaggregate Apply a function on subsets of data frames
bpcontrols Control (start, stop, query) back-end Params
bpiterate Parallel iteration over an indeterminate number of data chunks
bplapply Parallel lapply-like functionality
bpmapply Parallel mapply-like functionality
bpresume Resume computation with partial results
SnowParam-class Enable simple network of workstations (SNOW)-style parallel evaluation
SerialParam-class Enable serial evaluation
MulticoreParam-class Enable multi-core parallel evaluation
register Maintain a global registry of available back-end Params
bpvectorize Transform vectorized functions into parallelized, vectorized function
DoparParam-class Enable parallel evaluation using registered dopar backend
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Details

Type Package
biocViews Infrastructure
License GPL-2 | GPL-3
Collate.unix AllGenerics.R BiocParallelParam-class.R ErrorHandling.R bpbackend-methods.R bpisup-methods.R bplapply-methods.R bpmapply-methods.R bpiterate-methods.R bpschedule-methods.R bpstart-methods.R bpstop-methods.R bpvec-methods.R bpvectorize-methods.R bpworkers-methods.R bpaggregate-methods.R DoparParam-class.R MulticoreParam-class.R register.R SerialParam-class.R SnowParam-class.R BatchJobsParam-class.R utilities.R unix/mclapply.R unix/pvec.R unix/bpiterate.R unix/zzz.R
Collate.windows AllGenerics.R BiocParallelParam-class.R ErrorHandling.R bpbackend-methods.R bpisup-methods.R bplapply-methods.R bpmapply-methods.R bpiterate-methods.R bpschedule-methods.R bpstart-methods.R bpstop-methods.R bpvec-methods.R bpvectorize-methods.R bpworkers-methods.R bpaggregate-methods.R DoparParam-class.R MulticoreParam-class.R register.R SerialParam-class.R SnowParam-class.R BatchJobsParam-class.R utilities.R windows/zzz.R
VignetteBuilder knitr

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