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BatchJobs

Batch Computing with R

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.

Functions (85)

BatchJobs

The BatchJobs package

addRegistryPackages

Add packages to registry.

addRegistrySourceDirs

Add source dirs to registry.

addRegistrySourceFiles

Add source files to registry.

applyJobFunction

applyJobFunction ONLY FOR INTERNAL USAGE.

batchExpandGrid

Map function over all combinations.

batchExport

Export R object to be available on the slaves.

batchMap

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

batchMapQuick

Combination of makeRegistry, batchMap and submitJobs.

batchMapResults

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

batchQuery

Manually query the BatchJobs database

batchReduce

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

batchReduceResults

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

batchUnexport

Unload exported R objects.

callFunctionOnSSHWorkers

Call an arbitrary function on specified SSH workers.

cfBrewTemplate

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

cfHandleUnknownSubmitError

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

cfKillBatchJob

Cluster functions helper: Kill a batch job via OS command

cfReadBrewTemplate

Cluster functions helper: Read in your brew template file.

checkIds

Check job ids.

configuration

BatchJobs configuration.

copyRequiredJobFiles

ONLY FOR INTERNAL USAGE.

dbCreateJobDefTable

ONLY FOR INTERNAL USAGE.

dbGetJobs

ONLY FOR INTERNAL USAGE.

debugMulticore

Helper function to debug multicore mode.

debugSSH

Helper function to debug SSH mode.

filterResults

Find all results where a specific condition is true.

findJobs

Finds ids of jobs that match a query.

findState

Find jobs depending on computional state.

getConfig

Returns a list of BatchJobs configuration settings

getErrorMessages

Get error messages of jobs.

getJob

Get job from registry by id.

getJobIds

Get ids of jobs in registry.

getJobInfo

Get computational information of jobs.

getJobLocation

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

getJobNr

Get number of jobs in registry.

getJobParamDf

Retrieve Job Parameters.

getJobResources

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

getJobs

Get jobs from registry by id.

getLogFiles

Get log file paths for jobs.

getResources

Function to get job resources in job function.

getSSHWorkersInfo

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

grepLogs

Grep log files for a pattern.

installPackagesOnSSHWorkers

Install packages on SSH workers.

killJobs

Kill some jobs on the batch system.

loadConfig

Load a specific configuration file.

loadExports

Load exported R data objects.

loadRegistry

Load a previously saved registry.

loadResult

Loads a specific result file.

loadResults

Loads result files for id vector.

makeClusterFunctions

Create a ClusterFuntions object.

makeClusterFunctionsInteractive

Create cluster functions for sequential execution in same session.

makeClusterFunctionsLSF

Create cluster functions for LSF systems.

makeClusterFunctionsLocal

Create cluster functions for sequential execution on local host.

makeClusterFunctionsMulticore

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

makeClusterFunctionsOpenLava

Create cluster functions for OpenLava systems.

makeClusterFunctionsSGE

Create cluster functions for Sun Grid Engine systems.

makeClusterFunctionsSLURM

Create cluster functions for SLURM-based systems.

makeClusterFunctionsSSH

Create an SSH cluster to execute jobs.

makeClusterFunctionsTorque

Create cluster functions for torque-based systems.

makeJob

Creates a job description.

makeRegistry

Construct a registry object.

makeSSHWorker

Create SSH worker for SSH cluster functions.

makeSubmitJobResult

Create a SubmitJobResult object.

reduceResults

Reduce results from result directory.

removeRegistry

Remove a registry object.

removeRegistryPackages

Remove packages from registry.

removeRegistrySourceDirs

Remove packages from registry.

removeRegistrySourceFiles

Remove source files from registry.

resetJobs

Reset computational state of jobs.

sanitizePath

Sanitize a path

setConfig

Set and overwrite configuration settings

setJobFunction

Sets the job function for already existing jobs.

setJobNames

Set job names.

setRegistryPackages

Set packages for a registry.

showClusterStatus

Show information about available computational resources on cluster.

showLog

Display the contents of a log file.

showStatus

Retrieve or show status information about jobs.

sourceRegistryFiles

Source registry files

submitJobs

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

sweepRegistry

Sweep obsolete files from the file system.

syncRegistry

Syncronize staged queries into the registry.

testJob

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

updateRegistry

ONLY FOR INTERNAL USAGE.

waitForJobs

Wait for termination of jobs on the batch system.

BatchJobs

Batch Computing with R

v1.8

BSD_2_clause + file LICENSE

Authors

Bernd Bischl <bernd_bischl@gmx.net>, Michel Lang <michellang@gmail.com>, Henrik Bengtsson <henrikb@braju.com>

Initial release

BatchJobs

Functions (85)

BatchJobs

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