Overview

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