Overview

batchtools-package

batchtools: Tools for Computation on Batch Systems

Registry

makeRegistry

Registry Constructor

makeExperimentRegistry

ExperimentRegistry Constructor

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 getProblemIds

Define Problems for Experiments

addAlgorithm removeAlgorithms getAlgorithmIds

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

chunkIds

Chunk Jobs for Sequential Execution

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

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

makeClusterFunctionsSlurm

ClusterFunctions for Slurm Systems

makeClusterFunctionsSocket

ClusterFunctions for Parallel Socket Execution

makeClusterFunctionsSSH

ClusterFunctions for Remote SSH 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

Estimate Remaining Runtimes