Tools for Computation on Batch Systems


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Documentation for package ‘batchtools’ version 0.9.15

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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