Tools for Computation on Batch Systems

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Documentation for package ‘batchtools’ version 0.9.17

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

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