Learn R Programming
⚠️There's a newer version (0.9.17) of this package.Take me there.

batchtools

As a successor of the packages BatchJobs and BatchExperiments, batchtools provides a parallel implementation of Map for high performance computing systems managed by schedulers like Slurm, Torque, or SGE. Moreover, the package provides an abstraction mechanism to define large-scale computer experiments in a well-organized and reproducible way.

Installation

Install the development version via devtools:

devtools::install_github("mllg/batchtools")

Resources

Copy Link

Version

Install

install.packages('batchtools')

Monthly Downloads

2,095

Version

0.9.0

License

LGPL-3

Issues

85

Pull Requests

7

Stars

183

Forks

52

Maintainer

Michel Lang

Last Published

April 20th, 2023

Functions in batchtools (0.9.0)

cfBrewTemplate

Cluster Functions Helper to Write Job Description Files
batchtools-package

Tools for Computation on Batch Systems
cfKillJob

Cluster Functions Helper to Kill Batch Jobs
batchMap

Map Operation for Batch Systems
batchExport

Export Objects to the Slaves
addExperiments

Add Experiments to the Registry
btlapply

Synchronous Apply Functions
batchMapResults

Map Over Results to Create New Jobs
cfHandleUnknownSubmitError

Cluster Functions Helper to Handle Unknown Errors
cfReadBrewTemplate

Cluster Functions Helper to Parse a Brew Template
execJob

Execute a Single Jobs
ExperimentRegistry

ExperimentRegistry Constructor
getJobTable

Query Job Information
grepLogs

Grep Log Files for a Pattern
getStatus

Summarize the Computational Status
makeJobCollection

JobCollection Constructor
findJobs

Find and Filter Jobs
getErrorMessages

Retrieve Error Messages
chunkIds

Chunk Jobs for Sequential Execution
doJobCollection

Execute Jobs of a JobCollection
makeClusterFunctionsLSF

ClusterFunctions for LSF Systems
killJobs

Kill Jobs
makeJob

Jobs and Experiments
makeClusterFunctionsInteractive

ClusterFunctions for Sequential Execution in the Running R Session
JoinTables

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

ClusterFunctions Constructor
loadResult

Load the Result of a Single Job
makeClusterFunctionsMulticore

ClusterFunctions for Parallel Multicore Execution
makeClusterFunctionsOpenLava

ClusterFunctions for OpenLava
makeClusterFunctionsDocker

ClusterFunctions for Docker
ProblemAlgorithm

Define Problems and Algorithms for Experiments
Registry

Registry Constructor
makeClusterFunctionsSSH

ClusterFunctions for Remote SSH Execution
makeClusterFunctionsSlurm

ClusterFunctions for Slurm Systems
makeClusterFunctionsSocket

ClusterFunctions for Parallel Socket Execution
reduceResultsList

Apply Functions on Results
makeClusterFunctionsTorque

ClusterFunctions for OpenPBS/Torque Systems
makeSubmitJobResult

Create a SubmitJobResult
makeClusterFunctionsSGE

ClusterFunctions for SGE Systems
reduceResults

Reduce Results
runOSCommand

Run OS Commands on Local or Remote Machines
testJob

Run Jobs Interactively
submitJobs

Submit Jobs to the Batch Systems
showLog

Inspect Log Files
waitForJobs

Wait for Termination of Jobs
removeExperiments

Remove Experiments
resetJobs

Reset the Computational State of Jobs
summarizeExperiments

Quick Summary over Experiments
Tags

Add or Remove Job Tags
runHook

Trigger Evaluation of Custom Function
Worker

Create a Linux-Worker