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BatchJobs (version 1.8)

Batch Computing with R

Description

Provides Map, Reduce and Filter variants to generate jobs on batch computing systems like PBS/Torque, LSF, SLURM and Sun Grid Engine. Multicore and SSH systems are also supported. For further details see the project web page.

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Version

Install

install.packages('BatchJobs')

Monthly Downloads

985

Version

1.8

License

BSD_2_clause + file LICENSE

Issues

41

Pull Requests

7

Stars

85

Forks

20

Maintainer

Bernd Bischl

Last Published

May 14th, 2019

Functions in BatchJobs (1.8)

batchExpandGrid

Map function over all combinations.
cfReadBrewTemplate

Cluster functions helper: Read in your brew template file.
callFunctionOnSSHWorkers

Call an arbitrary function on specified SSH workers.
makeClusterFunctionsSSH

Create an SSH cluster to execute jobs.
getResources

Function to get job resources in job function.
makeRegistry

Construct a registry object.
makeJob

Creates a job description.
getSSHWorkersInfo

Print and return R installation and other information for SSH workers.
showLog

Display the contents of a log file.
makeClusterFunctionsTorque

Create cluster functions for torque-based systems.
cfBrewTemplate

Cluster functions helper: Brew your template into a job description file.
debugMulticore

Helper function to debug multicore mode.
showStatus

Retrieve or show status information about jobs.
addRegistrySourceDirs

Add source dirs to registry.
cfHandleUnknownSubmitError

Cluster functions helper: Handle an unknown error during job submission.
sweepRegistry

Sweep obsolete files from the file system.
filterResults

Find all results where a specific condition is true.
batchQuery

Manually query the BatchJobs database
batchReduce

Reduces via a binary function over a list adding jobs to a registry.
addRegistrySourceFiles

Add source files to registry.
findJobs

Finds ids of jobs that match a query.
debugSSH

Helper function to debug SSH mode.
cfKillBatchJob

Cluster functions helper: Kill a batch job via OS command
batchUnexport

Unload exported R objects.
findDone

Find jobs depending on computional state.
getErrorMessages

Get error messages of jobs.
checkIds

Check job ids.
configuration

BatchJobs configuration.
getConfig

Returns a list of BatchJobs configuration settings
syncRegistry

Syncronize staged queries into the registry.
getJobLocation

Get the physical location of job files on the hard disk.
copyRequiredJobFiles

ONLY FOR INTERNAL USAGE.
getJobIds

Get ids of jobs in registry.
getJobParamDf

Retrieve Job Parameters.
getJobNr

Get number of jobs in registry.
getJobInfo

Get computational information of jobs.
makeClusterFunctionsSLURM

Create cluster functions for SLURM-based systems.
makeClusterFunctionsSGE

Create cluster functions for Sun Grid Engine systems.
reduceResults

Reduce results from result directory.
getJobResources

Function to get the resources that were submitted for some jobs.
removeRegistry

Remove a registry object.
loadExports

Load exported R data objects.
sanitizePath

Sanitize a path
killJobs

Kill some jobs on the batch system.
loadConfig

Load a specific configuration file.
getJobs

Get jobs from registry by id.
getLogFiles

Get log file paths for jobs.
dbGetJobs

ONLY FOR INTERNAL USAGE.
dbCreateJobDefTable

ONLY FOR INTERNAL USAGE.
loadRegistry

Load a previously saved registry.
removeRegistrySourceFiles

Remove source files from registry.
loadResult

Loads a specific result file.
setRegistryPackages

Set packages for a registry.
resetJobs

Reset computational state of jobs.
showClusterStatus

Show information about available computational resources on cluster.
makeClusterFunctionsLSF

Create cluster functions for LSF systems.
testJob

Tests a job by running it with Rscript in a new process.
loadResults

Loads result files for id vector.
makeClusterFunctions

Create a ClusterFuntions object.
setConfig

Set and overwrite configuration settings
makeClusterFunctionsLocal

Create cluster functions for sequential execution on local host.
setJobFunction

Sets the job function for already existing jobs.
updateRegistry

ONLY FOR INTERNAL USAGE.
waitForJobs

Wait for termination of jobs on the batch system.
setJobNames

Set job names.
getJob

Get job from registry by id.
makeClusterFunctionsInteractive

Create cluster functions for sequential execution in same session.
grepLogs

Grep log files for a pattern.
installPackagesOnSSHWorkers

Install packages on SSH workers.
removeRegistryPackages

Remove packages from registry.
makeClusterFunctionsMulticore

Use multiple cores on local Linux machine to spawn parallel jobs.
removeRegistrySourceDirs

Remove packages from registry.
makeClusterFunctionsOpenLava

Create cluster functions for OpenLava systems.
makeSSHWorker

Create SSH worker for SSH cluster functions.
makeSubmitJobResult

Create a SubmitJobResult object.
submitJobs

Submit jobs or chunks of jobs to batch system via cluster function.
sourceRegistryFiles

Source registry files
batchMapResults

Maps a function over the results of a registry by using batchMap.
batchExport

Export R object to be available on the slaves.
BatchJobs

The BatchJobs package
batchMap

Maps a function over lists or vectors, adding jobs to a registry.
batchMapQuick

Combination of makeRegistry, batchMap and submitJobs.
addRegistryPackages

Add packages to registry.
applyJobFunction

applyJobFunction ONLY FOR INTERNAL USAGE.
batchReduceResults

Reduces results via a binary function and adds jobs for this to a registry.