Package: BiocParallel 1.39.0
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:
BiocParallel_1.39.0.tar.gz
BiocParallel_1.39.0.zip(r-4.5)BiocParallel_1.39.0.zip(r-4.4)BiocParallel_1.39.0.zip(r-4.3)
BiocParallel_1.39.0.tgz(r-4.4-arm64)BiocParallel_1.39.0.tgz(r-4.4-x86_64)BiocParallel_1.39.0.tgz(r-4.3-arm64)BiocParallel_1.39.0.tgz(r-4.3-x86_64)
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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')) |
Bug tracker:https://github.com/bioconductor/biocparallel/issues
On BioConductor:BiocParallel-1.39.0(bioc 3.20)BiocParallel-1.38.0(bioc 3.19)
Last updated 2 months agofrom:aa329b3a29
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
Rendered fromIntroduction_To_BiocParallel.Rmdusingknitr::rmarkdownon Jun 25 2024.Last update: 2023-08-16
Started: 2022-10-24
Introduction to BatchtoolsParam
Rendered fromBiocParallel_BatchtoolsParam.Rnwusingknitr::knitron Jun 25 2024.Last update: 2022-11-01
Started: 2018-03-20
Errors, Logs and Debugging
Rendered fromErrors_Logs_And_Debugging.Rnwusingknitr::knitron Jun 25 2024.Last update: 2023-03-23
Started: 2015-05-13
Random Numbers in BiocParallel
Rendered fromRandom_Numbers.Rmdusingknitr::rmarkdownon Jun 25 2024.Last update: 2022-08-01
Started: 2022-08-01
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Bioconductor facilities for parallel evaluation | BiocParallel-package BiocParallel |
| Enable parallelization on batch systems | batchtoolsCluster 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 objects | BiocParallelParam 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 frames | bpaggregate 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 chunks | bpiterate 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 functionality | bplapply 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 Evaluation | bploop bploop.iterate bploop.lapply bprunMPIworker |
| Parallel mapply-like functionality | bpmapply bpmapply,ANY,BiocParallelParam-method bpmapply,ANY,list-method bpmapply,ANY,missing-method |
| Resume computation with partial results | bperrorTypes bpok bpresult |
| Additional options to parallel evaluation | bpoptions |
| Schedule back-end Params | bpschedule bpschedule,ANY-method bpschedule,missing-method |
| Try expression evaluation, recovering from bperror signals | bptry |
| Tools for developing functions for parallel execution in distributed memory | bpvalidate BPValidate-class show,BPValidate-method |
| Parallel, vectorized evaluation | bpvec bpvec,ANY,BiocParallelParam-method bpvec,ANY,list-method bpvec,ANY,missing-method |
| Transform vectorized functions into parallelized, vectorized function | bpvectorize 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 backend | bpbackend,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 counters | ipcid 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 Params | bpparam register registered |
| Enable serial evaluation | bpbackend,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 evaluation | bpbackend,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 number | BIOCPARALLEL_WORKER_MAX BIOCPARALLEL_WORKER_NUMBER R_PARALLELLY_AVAILABLECORES_FALLBACK |
