Package: BiocParallel 1.41.0

Martin Morgan

BiocParallel: Bioconductor facilities for parallel evaluation

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

Authors:Martin Morgan [aut, cre], Jiefei Wang [aut], Valerie Obenchain [aut], Michel Lang [aut], Ryan Thompson [aut], Nitesh Turaga [aut], Aaron Lun [ctb], Henrik Bengtsson [ctb], Madelyn Carlson [ctb], Phylis Atieno [ctb], Sergio Oller [ctb]

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BiocParallel.pdf |BiocParallel.html✨
BiocParallel/json (API)
NEWS

# Install 'BiocParallel' in R:
install.packages('BiocParallel', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/bioconductor/biocparallel/issues

Uses libs:
  • c++– GNU Standard C++ Library v3

On BioConductor:BiocParallel-1.39.0(bioc 3.20)BiocParallel-1.38.0(bioc 3.19)

infrastructurebioconductor-packagecore-package

16.13 score 67 stars 1.1k packages 6.4k scripts 86k downloads 104 exports 8 dependencies

Last updated 23 days agofrom:0f688b6a07. Checks:OK: 1 NOTE: 6 ERROR: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 30 2024
R-4.5-win-x86_64NOTEOct 30 2024
R-4.5-linux-x86_64NOTEOct 30 2024
R-4.4-win-x86_64NOTEOct 30 2024
R-4.4-mac-x86_64NOTEOct 30 2024
R-4.4-mac-aarch64ERROROct 30 2024
R-4.3-win-x86_64NOTEOct 30 2024
R-4.3-mac-x86_64NOTEOct 30 2024
R-4.3-mac-aarch64ERROROct 23 2024

Exports:.BiocParallelParam_prototype.bpiterate_impl.bplapply_impl.bpstart_impl.bpstop_impl.bpworker_impl.close.error_worker_comm.manager.manager_capacity.manager_cleanup.manager_flush.manager_recv.manager_recv_all.manager_send.manager_send_all.prettyPath.prototype_update.recv.recv_all.recv_any.registerOption.send.send_all.send_to.task_const.task_dynamic.task_remakebatchtoolsClusterBatchtoolsParambatchtoolsRegistryargsbatchtoolsTemplatebatchtoolsWorkersbpaggregatebpbackendbpbackend<-bperrorTypesbpexportglobalsbpexportglobals<-bpexportvariablesbpexportvariables<-bpfallbackbpfallback<-bpforceGCbpforceGC<-bpisupbpiteratebpiterateAlongbpjobnamebpjobname<-bplapplybplogbplog<-bplogdirbplogdir<-bploopbpmapplybpnworkersbpokbpoptionsbpparambpprogressbarbpprogressbar<-bpresultbpresultdirbpresultdir<-bpRNGseedbpRNGseed<-bprunMPIworkerbpschedulebpstartbpstopbpstopOnErrorbpstopOnError<-bptasksbptasks<-bpthresholdbpthreshold<-bptimeoutbptimeout<-bptrybpvalidatebpvecbpvectorizebpworkersbpworkers<-DoparParamipcidipclockipclockedipcremoveipcresetipctrylockipcunlockipcvalueipcyieldMulticoreParammulticoreWorkersregisterregisteredSerialParamshowSnowParamsnowWorkers

Dependencies:BHcodetoolscpp11formatRfutile.loggerfutile.optionslambda.rsnow

Introduction to BiocParallel

Valerie Obenchain, Vincent Carey, Michael Lawrence, Phylis Atieno, Martin Morgan

Rendered fromIntroduction_To_BiocParallel.Rmdusingknitr::rmarkdownon Oct 30 2024.

Last update: 2023-08-16
Started: 2022-10-24

Introduction to BatchtoolsParam

Rendered fromBiocParallel_BatchtoolsParam.Rnwusingknitr::knitron Oct 30 2024.

Last update: 2022-11-01
Started: 2018-03-20

Errors, Logs and Debugging

Rendered fromErrors_Logs_And_Debugging.Rnwusingknitr::knitron Oct 30 2024.

Last update: 2023-03-23
Started: 2015-05-13

Random Numbers in BiocParallel

Martin Morgan

Rendered fromRandom_Numbers.Rmdusingknitr::rmarkdownon Oct 30 2024.

Last update: 2022-08-01
Started: 2022-08-01

Readme and manuals

Help Manual

Help pageTopics
Bioconductor facilities for parallel evaluationBiocParallel-package BiocParallel
Enable parallelization on batch systemsbatchtoolsCluster BatchtoolsParam BatchtoolsParam-class batchtoolsRegistryargs batchtoolsTemplate batchtoolsWorkers bpbackend,BatchtoolsParam-method bpisup,BatchtoolsParam-method bplapply,ANY,BatchtoolsParam-method bplogdir,BatchtoolsParam-method bplogdir<-,BatchtoolsParam,character-method bpRNGseed,BatchtoolsParam-method bpRNGseed<-,BatchtoolsParam,numeric-method bpschedule,BatchtoolsParam-method bpstart,BatchtoolsParam-method bpstop,BatchtoolsParam-method bpworkers,BatchtoolsParam-method show,BatchtoolsParam-method
Defunct Objects in Package 'BiocParallel'BatchJobsParam bprunMPIslave
Deprecated Functions in Package 'BiocParallel'BiocParallel-deprecated
BiocParallelParam objectsBiocParallelParam BiocParallelParam-class bpbackend bpbackend,missing-method bpbackend<- bpbackend<-,missing,ANY-method bpexportglobals bpexportglobals,BiocParallelParam-method bpexportglobals<- bpexportglobals<-,BiocParallelParam,logical-method bpexportvariables bpexportvariables,BiocParallelParam-method bpexportvariables<- bpexportvariables<-,BiocParallelParam,logical-method bpfallback bpfallback,BiocParallelParam-method bpfallback<- bpfallback<-,BiocParallelParam,logical-method bpforceGC bpforceGC,BiocParallelParam-method bpforceGC<- bpforceGC<-,BiocParallelParam,numeric-method bpisup bpisup,ANY-method bpisup,missing-method bpjobname bpjobname,BiocParallelParam-method bpjobname<- bpjobname<-,BiocParallelParam,character-method bplog bplog,BiocParallelParam-method bplog<- bplogdir bplogdir,BiocParallelParam-method bplogdir<- bplogdir<-,BiocParallelParam,character-method bpnworkers bpprogressbar bpprogressbar,BiocParallelParam-method bpprogressbar<- bpprogressbar<-,BiocParallelParam,logical-method bpresultdir bpresultdir,BiocParallelParam-method bpresultdir<- bpresultdir<-,BiocParallelParam,character-method bpRNGseed bpRNGseed,BiocParallelParam-method bpRNGseed<- bpRNGseed<-,BiocParallelParam,NULL-method bpRNGseed<-,BiocParallelParam,numeric-method bpstart bpstart,ANY-method bpstart,BiocParallelParam-method bpstart,missing-method bpstop bpstop,ANY-method bpstop,BiocParallelParam-method bpstop,missing-method bpstopOnError bpstopOnError,BiocParallelParam-method bpstopOnError<- bpstopOnError<-,BiocParallelParam,logical-method bpstopOnError<-,DoparParam,logical-method bptasks bptasks,BiocParallelParam-method bptasks<- bptasks<-,BiocParallelParam,ANY-method bptasks<-,BiocParallelParam-method bpthreshold bpthreshold,BiocParallelParam-method bpthreshold<- bptimeout bptimeout,BiocParallelParam-method bptimeout<- bptimeout<-,BiocParallelParam,numeric-method bpworkers bpworkers,BiocParallelParam-method bpworkers,missing-method bpworkers<- print.remote_error show,BiocParallel-method
Apply a function on subsets of data framesbpaggregate bpaggregate,ANY,missing-method bpaggregate,data.frame,BiocParallelParam-method bpaggregate,formula,BiocParallelParam-method bpaggregate,matrix,BiocParallelParam-method
Parallel iteration over an indeterminate number of data chunksbpiterate bpiterate,ANY,ANY,BatchtoolsParam-method bpiterate,ANY,ANY,BiocParallelParam-method bpiterate,ANY,ANY,DoparParam-method bpiterate,ANY,ANY,missing-method bpiterate,ANY,ANY,SerialParam-method bpiterate,ANY,ANY,SnowParam-method bpiterateAlong
Parallel lapply-like functionalitybplapply bplapply,ANY,BiocParallelParam-method bplapply,ANY,DoparParam-method bplapply,ANY,list-method bplapply,ANY,missing-method bplapply,ANY,SerialParam-method bplapply,ANY,SnowParam-method
Internal Functions for SNOW-style Parallel Evaluationbploop bploop.iterate bploop.lapply bprunMPIworker
Parallel mapply-like functionalitybpmapply bpmapply,ANY,BiocParallelParam-method bpmapply,ANY,list-method bpmapply,ANY,missing-method
Resume computation with partial resultsbperrorTypes bpok bpresult
Additional options to parallel evaluationbpoptions
Schedule back-end Paramsbpschedule bpschedule,ANY-method bpschedule,missing-method
Try expression evaluation, recovering from bperror signalsbptry
Tools for developing functions for parallel execution in distributed memorybpvalidate BPValidate-class show,BPValidate-method
Parallel, vectorized evaluationbpvec bpvec,ANY,BiocParallelParam-method bpvec,ANY,list-method bpvec,ANY,missing-method
Transform vectorized functions into parallelized, vectorized functionbpvectorize bpvectorize,ANY,ANY-method bpvectorize,ANY,missing-method
Developer interface.BiocParallelParam_prototype .bpiterate_impl .bplapply_impl .bpstart_impl .bpstop_impl .bpworker_impl .close .close,ANY-method .manager .manager,ANY-method .manager,DoparParam-method .manager,SnowParam-method .manager,TransientMulticoreParam-method .manager_capacity .manager_capacity,ANY-method .manager_capacity,DoparParamManager-method .manager_capacity,TaskManager-method .manager_cleanup .manager_cleanup,ANY-method .manager_cleanup,SOCKmanager-method .manager_cleanup,TaskManager-method .manager_flush .manager_flush,ANY-method .manager_flush,TaskManager-method .manager_recv .manager_recv,ANY-method .manager_recv,DoparParamManager-method .manager_recv,TaskManager-method .manager_recv_all .manager_recv_all,ANY-method .manager_recv_all,DoparParamManager-method .manager_recv_all,TaskManager-method .manager_send .manager_send,ANY-method .manager_send,DoparParamManager-method .manager_send,SOCKmanager-method .manager_send,TaskManager-method .manager_send_all .manager_send_all,ANY-method .manager_send_all,DoparParamManager-method .manager_send_all,TaskManager-method .prototype_update .recv .recv,ANY-method .recv,SOCKnode-method .recv_all .recv_all,ANY-method .recv_any .recv_any,ANY-method .recv_any,SerialBackend-method .registerOption .send .send,ANY-method .send_all .send_all,ANY-method .send_to .send_to,ANY-method .send_to,SerialBackend-method .task_const .task_dynamic .task_remake
Enable parallel evaluation using registered dopar backendbpbackend,DoparParam-method bpbackend<-,DoparParam,SOCKcluster-method bpisup,DoparParam-method bpstart,DoparParam-method bpstop,DoparParam-method bpworkers,DoparParam-method coerce,SOCKcluster,DoparParam-method DoparParam DoparParam-class show,DoparParam-method
Inter-process locks and countersipcid ipclock ipclocked ipcremove ipcreset ipctrylock ipcunlock ipcvalue ipcyield
Enable multi-core parallel evaluation.close,TransientMulticoreParam-method .recv,TransientMulticoreParam-method .recv_all,TransientMulticoreParam-method .recv_any,TransientMulticoreParam-method .send,TransientMulticoreParam-method .send_to,TransientMulticoreParam-method bpbackend,TransientMulticoreParam-method bpisup,MulticoreParam-method bpschedule,MulticoreParam-method bpstart,TransientMulticoreParam-method bpstop,TransientMulticoreParam-method bpworkers<-,MulticoreParam,numeric-method length,TransientMulticoreParam-method MulticoreParam MulticoreParam-class multicoreWorkers show,MulticoreParam-method
Maintain a global registry of available back-end Paramsbpparam register registered
Enable serial evaluationbpbackend,SerialParam-method bpisup,SerialParam-method bplog,SerialParam-method bplog<-,SerialParam,logical-method bplogdir,SerialParam-method bplogdir<-,SerialParam,character-method bpstart,SerialParam-method bpstop,SerialParam-method bpthreshold<-,SerialParam,character-method bpworkers,SerialParam-method length,SerialBackend-method SerialParam SerialParam-class
Enable simple network of workstations (SNOW)-style parallel evaluationbpbackend,SnowParam-method bpbackend<-,SnowParam,cluster-method bpisup,SnowParam-method bplog,SnowParam-method bplog<-,SnowParam,logical-method bpstart,SnowParam-method bpstop,SnowParam-method bpthreshold,SnowParam-method bpthreshold<-,SnowParam,character-method bpworkers,SnowParam-method bpworkers<-,SnowParam,character-method bpworkers<-,SnowParam,numeric-method coerce,SOCKcluster,SnowParam-method coerce,spawnedMPIcluster,SnowParam-method show,SnowParam-method SnowParam SnowParam-class snowWorkers
Environment control of worker numberBIOCPARALLEL_WORKER_MAX BIOCPARALLEL_WORKER_NUMBER R_PARALLELLY_AVAILABLECORES_FALLBACK