BiocParallel v1.4.0

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

DONE

  • encapsulate arguments as ParallelParam()
  • Standardize signatures
  • Make functions generics
  • parLapply-like function
  • Short vignette
  • elaborate SnowParam for SnowSocketParam, SnowForkParam, SnowMpiParam, ...
  • MulticoreParam on Windows

github notes

  • commit one-liners with names

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

TO FIX

  • DoparParam does not pass foreach args (specifically access to .options.nws for chunking)

Functions in BiocParallel

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