R: Tools for Computation on Batch Systems

# Tools for Computation on Batch Systems

## Documentation for package ‘batchtools’ version 0.9.11

- 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 | batchtools: Tools for Computation on Batch Systems

## -- A --

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

## -- B --

batchExport | Export Objects to the Slaves
batchMap | Map Operation for Batch Systems
batchMapResults | Map Over Results to Create New Jobs
batchReduce | Reduce Operation for Batch Systems
batchtools | batchtools: Tools for Computation on Batch Systems
binpack | Chunk Jobs for Sequential Execution
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
chunk | Chunk Jobs for Sequential Execution
clearRegistry | Remove All Jobs
ClusterFunctions | ClusterFunctions Constructor

## -- D --

doJobCollection | Execute Jobs of a JobCollection

## -- E --

estimateRuntimes | Estimate Remaining Runtimes
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
flatten | Unwrap Nested Data Frames

## -- G --

getDefaultRegistry | Get and Set the Default Registry
getErrorMessages | Retrieve Error Messages
getJobNames | Set and Retrieve Job Names
getJobPars | Query Job Information
getJobResources | Query Job Information
getJobStatus | Query Job Information
getJobTable | Query Job Information
getJobTags | Query Job Information
getLog | Inspect Log Files
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
JobNames | Set and Retrieve Job Names
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 | Load a Registry from the File System
loadResult | Load the Result of a Single Job
lpt | Chunk Jobs for Sequential Execution

## -- 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 --

print.RuntimeEstimate | Estimate Remaining Runtimes
Problem | Define Problems for Experiments

## -- R --

reduceResults | Reduce Results
reduceResultsDataTable | Apply Functions on Results
reduceResultsList | Apply Functions on Results
Registry | Registry Constructor
removeAlgorithms | Define Algorithms for Experiments
removeExperiments | Remove Experiments
removeJobTags | Add or Remove Job Tags
removeProblems | Define Problems for Experiments
removeRegistry | Remove a Registry from the File System
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 | Store the Registy to the File System
setDefaultRegistry | Get and Set the Default Registry
setJobNames | Set and Retrieve Job Names
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 | Check Consistency and Remove Obsolete Information
syncRegistry | Synchronize the Registry

## -- T --

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

## -- U --

ujoin | Inner, Left, Right, Outer, Semi and Anti Join for Data Tables
unwrap | Unwrap Nested Data Frames

## -- W --

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