# Tools for Computation on Batch Systems

## Documentation for package ‘batchtools’ version 0.9.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

A B C D E F G H I J K L M O P R S T U W

batchtools-package | Tools for Computation on Batch Systems

## -- A --

addAlgorithm | Define Problems and Algorithms for Experiments
addExperiments | Add Experiments to the Registry
addJobTags | Add or Remove Job Tags
addProblem | Define Problems and Algorithms for Experiments
ajoin | Inner, Left, Right, Outer, Semi and Anti Join for Data Tables
Algorithm | Define Problems and Algorithms for Experiments

## -- B --

batchExport | Export Objects to the Slaves
batchMap | Map Operation for Batch Systems
batchMapResults | Map Over Results to Create New Jobs
batchtools | Tools for Computation on Batch Systems
btlapply | Synchronous Apply Functions
btmapply | Synchronous Apply Functions

## -- C --

cfBrewTemplate | Cluster Functions Helper to Write Job Description Files
cfHandleUnknownSubmitError | Cluster Functions Helper to Handle Unknown Errors
cfKillJob | Cluster Functions Helper to Kill Batch Jobs
cfReadBrewTemplate | Cluster Functions Helper to Parse a Brew Template
chunkIds | Chunk Jobs for Sequential Execution
clearRegistry | Registry Constructor
ClusterFunctions | ClusterFunctions Constructor

## -- D --

doJobCollection | Execute Jobs of a JobCollection

## -- E --

execJob | Execute a Single Jobs
Experiment | Jobs and Experiments
ExperimentRegistry | ExperimentRegistry Constructor

## -- F --

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

## -- G --

getAlgorithmIds | Define Problems and Algorithms for Experiments
getDefaultRegistry | Registry Constructor
getErrorMessages | Retrieve Error Messages
getJobPars | Query Job Information
getJobResources | Query Job Information
getJobStatus | Query Job Information
getJobTable | Query Job Information
getJobTags | Query Job Information
getLog | Inspect Log Files
getProblemIds | Define Problems and Algorithms for Experiments
getStatus | Summarize the Computational Status
getUsedJobTags | Add or Remove Job Tags
grepLogs | Grep Log Files for a Pattern

## -- H --

Hook | Trigger Evaluation of Custom Function
Hooks | Trigger Evaluation of Custom Function

## -- I --

ijoin | Inner, Left, Right, Outer, Semi and Anti Join for Data Tables

## -- J --

Job | Jobs and Experiments
JobCollection | JobCollection Constructor
JoinTables | Inner, Left, Right, Outer, Semi and Anti Join for Data Tables

## -- K --

killJobs | Kill Jobs

## -- L --

ljoin | Inner, Left, Right, Outer, Semi and Anti Join for Data Tables
loadRegistry | Registry Constructor
loadResult | Load the Result of a Single Job

## -- M --

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
makeExperimentRegistry | ExperimentRegistry Constructor
makeJob | Jobs and Experiments
makeJobCollection | JobCollection Constructor
makeRegistry | Registry Constructor
makeSubmitJobResult | Create a SubmitJobResult

## -- O --

ojoin | Inner, Left, Right, Outer, Semi and Anti Join for Data Tables

## -- P --

Problem | Define Problems and Algorithms for Experiments
ProblemAlgorithm | Define Problems and Algorithms for Experiments

## -- R --

reduceResults | Reduce Results
reduceResultsDataTable | Apply Functions on Results
reduceResultsList | Apply Functions on Results
Registry | Registry Constructor
removeAlgorithms | Define Problems and Algorithms for Experiments
removeExperiments | Remove Experiments
removeJobTags | Add or Remove Job Tags
removeProblems | Define Problems and Algorithms for Experiments
resetJobs | Reset the Computational State of Jobs
rjoin | Inner, Left, Right, Outer, Semi and Anti Join for Data Tables
runHook | Trigger Evaluation of Custom Function
runOSCommand | Run OS Commands on Local or Remote Machines

## -- S --

saveRegistry | Registry Constructor
setDefaultRegistry | Registry Constructor
showLog | Inspect Log Files
sjoin | Inner, Left, Right, Outer, Semi and Anti Join for Data Tables
SubmitJobResult | Create a SubmitJobResult
submitJobs | Submit Jobs to the Batch Systems
summarizeExperiments | Quick Summary over Experiments
sweepRegistry | Registry Constructor
syncRegistry | Registry Constructor

## -- T --

Tags | Add or Remove Job Tags
testJob | Run Jobs Interactively

## -- U --

ujoin | Inner, Left, Right, Outer, Semi and Anti Join for Data Tables

## -- W --

waitForJobs | Wait for Termination of Jobs
Worker | Create a Linux-Worker