Package index • batchtools

Overview

batchtools batchtools-package: batchtools: Tools for Computation on Batch Systems

Registry

makeRegistry(): Registry Constructor

makeExperimentRegistry(): ExperimentRegistry Constructor

assertRegistry(): assertRegistry

loadRegistry(): Load a Registry from the File System

saveRegistry(): Store the Registy to the File System

syncRegistry(): Synchronize the Registry

sweepRegistry(): Check Consistency and Remove Obsolete Information

removeRegistry(): Remove a Registry from the File System

getDefaultRegistry() setDefaultRegistry(): Get and Set the Default Registry

Define Jobs

batchMap(): Map Operation for Batch Systems

batchReduce(): Reduce Operation for Batch Systems

batchMapResults(): Map Over Results to Create New Jobs

addProblem() removeProblems(): Define Problems for Experiments

addAlgorithm() removeAlgorithms(): Define Algorithms for Experiments

addExperiments(): Add Experiments to the Registry

Submit Jobs

submitJobs(): Submit Jobs to the Batch Systems

batchExport(): Export Objects to the Slaves

waitForJobs(): Wait for Termination of Jobs

chunk() lpt() binpack(): Chunk Jobs for Sequential Execution

setJobNames() getJobNames(): Set and Retrieve Job Names

Query Job Information

getStatus(): Summarize the Computational Status

findJobs() findExperiments() findSubmitted() findNotSubmitted() findStarted() findNotStarted() findDone() findNotDone() findErrors() findOnSystem() findRunning() findQueued() findExpired() findTagged(): Find and Filter Jobs

getJobTable() getJobStatus() getJobResources() getJobPars() getJobTags(): Query Job Information

summarizeExperiments(): Quick Summary over Experiments

Retrieve Results

reduceResults(): Reduce Results

reduceResultsList() reduceResultsDataTable(): Apply Functions on Results

loadResult(): Load the Result of a Single Job

unwrap() flatten(): Unwrap Nested Data Frames

Debugging

resetJobs(): Reset the Computational State of Jobs

testJob(): Run Jobs Interactively

showLog() getLog(): Inspect Log Files

getErrorMessages(): Retrieve Error Messages

grepLogs(): Grep Log Files for a Pattern

Remove Jobs

killJobs(): Kill Jobs

clearRegistry(): Remove All Jobs

removeExperiments(): Remove Experiments

Additional objects

makeJob(): Jobs and Experiments

makeJobCollection(): JobCollection Constructor

Cluster Functions

cfKillJob(): Cluster Functions Helper to Kill Batch Jobs

cfBrewTemplate(): Cluster Functions Helper to Write Job Description Files

cfReadBrewTemplate(): Cluster Functions Helper to Parse a Brew Template

cfHandleUnknownSubmitError(): Cluster Functions Helper to Handle Unknown Errors

makeClusterFunctions(): ClusterFunctions Constructor

makeClusterFunctionsDocker(): ClusterFunctions for Docker

makeClusterFunctionsInteractive(): ClusterFunctions for Sequential Execution in the Running R Session

makeClusterFunctionsLSF(): ClusterFunctions for LSF Systems

makeClusterFunctionsMulticore(): ClusterFunctions for Parallel Multicore Execution

makeClusterFunctionsOpenLava(): ClusterFunctions for OpenLava

makeClusterFunctionsSGE(): ClusterFunctions for SGE Systems

makeClusterFunctionsSSH(): ClusterFunctions for Remote SSH Execution

makeClusterFunctionsSlurm(): ClusterFunctions for Slurm Systems

makeClusterFunctionsSocket(): ClusterFunctions for Parallel Socket Execution

makeClusterFunctionsTORQUE(): ClusterFunctions for OpenPBS/TORQUE Systems

makeSubmitJobResult(): Create a SubmitJobResult

runHook(): Trigger Evaluation of Custom Function

Worker: Create a Linux-Worker

Miscellaneous

addJobTags() removeJobTags() getUsedJobTags(): Add or Remove Job Tags

btlapply() btmapply(): Synchronous Apply Functions

ijoin() ljoin() rjoin() ojoin() sjoin() ajoin() ujoin(): Inner, Left, Right, Outer, Semi and Anti Join for Data Tables

runOSCommand(): Run OS Commands on Local or Remote Machines

execJob(): Execute a Single Jobs

doJobCollection(): Execute Jobs of a JobCollection

estimateRuntimes() print(<RuntimeEstimate>): Estimate Remaining Runtimes