BiocParallel v1.2.22

Bioconductor facilities for parallel evaluation

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

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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

DONE

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

github notes

  • commit one-liners with names

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

Functions in BiocParallel

Name Description
bpvec Parallel, vectorized evaluation
DoparParam-class Enable parallel evaluation using registered dopar backend
bpvectorize Transform vectorized functions into parallelized, vectorized function
bpmapply Parallel mapply-like functionality
bpvalidate Tools for developing functions for parallel execution in distributed memory
bplapply Parallel lapply-like functionality
bpok Resume computation with partial results
bpschedule Schedule back-end Params
SerialParam-class Enable serial evaluation
BatchJobsParam-class Enable parallelization on batch systems
BiocParallelParam-class BiocParallelParam objects
register Maintain a global registry of available back-end Params
MulticoreParam-class Enable multi-core parallel evaluation
SnowParam-class Enable simple network of workstations (SNOW)-style parallel evaluation
bpaggregate Apply a function on subsets of data frames
bpiterate Parallel iteration over an indeterminate number of data chunks
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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 bpvalidate.R SnowParam-class.R MulticoreParam-class.R register.R SerialParam-class.R DoparParam-class.R SnowParam-utils.R BatchJobsParam-class.R progress.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 bpvalidate.R SnowParam-class.R MulticoreParam-class.R register.R SerialParam-class.R DoparParam-class.R SnowParam-utils.R BatchJobsParam-class.R progress.R utilities.R windows/zzz.R
VignetteBuilder knitr

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