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BatchJobs (version 1.7)

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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Install

install.packages('BatchJobs')

Monthly Downloads

985

Version

1.7

License

BSD_2_clause + file LICENSE

Issues

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Repository

https://github.com/tudo-r/BatchJobs

Maintainer

Bernd Bischl

Last Published

November 28th, 2017

Functions in BatchJobs (1.7)

applyJobFunction

applyJobFunction ONLY FOR INTERNAL USAGE.

The BatchJobs package

Combination of makeRegistry, batchMap and submitJobs.

addRegistryPackages

Add packages to registry.

batchMapResults

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

Export R object to be available on the slaves.

Manually query the BatchJobs database

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

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

addRegistrySourceDirs

Add source dirs to registry.

Unload exported R objects.

addRegistrySourceFiles

Add source files to registry.

cfHandleUnknownSubmitError

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

batchExpandGrid

Map function over all combinations.

callFunctionOnSSHWorkers

Call an arbitrary function on specified SSH workers.

Cluster functions helper: Kill a batch job via OS command

BatchJobs configuration.

batchReduceResults

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

copyRequiredJobFiles

ONLY FOR INTERNAL USAGE.

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

Find jobs depending on computional state.

cfReadBrewTemplate

Cluster functions helper: Read in your brew template file.

Returns a list of BatchJobs configuration settings

dbCreateJobDefTable

ONLY FOR INTERNAL USAGE.

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

ONLY FOR INTERNAL USAGE.

Get number of jobs in registry.

Get jobs from registry by id.

Loads a specific result file.

Helper function to debug multicore mode.

Loads result files for id vector.

Helper function to debug SSH mode.

makeClusterFunctionsSSH

Create an SSH cluster to execute jobs.

makeClusterFunctionsTorque

Create cluster functions for torque-based systems.

Get ids of jobs in registry.

Get log file paths for jobs.

Get computational information of jobs.

Grep log files for a pattern.

installPackagesOnSSHWorkers

Install packages on SSH workers.

makeClusterFunctions

Create a ClusterFuntions object.

Kill some jobs on the batch system.

makeClusterFunctionsSLURM

Create cluster functions for SLURM-based systems.

Load a specific configuration file.

removeRegistryPackages

Remove packages from registry.

removeRegistrySourceDirs

Remove packages from registry.

makeClusterFunctionsSGE

Create cluster functions for Sun Grid Engine systems.

Reduce results from result directory.

sourceRegistryFiles

Source registry files

Remove a registry object.

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

Sanitize a path

getErrorMessages

Get error messages of jobs.

Wait for termination of jobs on the batch system.

Get job from registry by id.

Find all results where a specific condition is true.

Load exported R data objects.

Load a previously saved registry.

Finds ids of jobs that match a query.

Set and overwrite configuration settings

Retrieve Job Parameters.

makeClusterFunctionsInteractive

Create cluster functions for sequential execution in same session.

Create SSH worker for SSH cluster functions.

getJobResources

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

makeSubmitJobResult

Create a SubmitJobResult object.

Function to get job resources in job function.

setRegistryPackages

Set packages for a registry.

getSSHWorkersInfo

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

showClusterStatus

Show information about available computational resources on cluster.

makeClusterFunctionsMulticore

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

makeClusterFunctionsLSF

Create cluster functions for LSF systems.

makeClusterFunctionsLocal

Create cluster functions for sequential execution on local host.

Sweep obsolete files from the file system.

Creates a job description.

Syncronize staged queries into the registry.

Construct a registry object.

Display the contents of a log file.

makeClusterFunctionsOpenLava

Create cluster functions for OpenLava systems.

Retrieve or show status information about jobs.

removeRegistrySourceFiles

Remove source files from registry.

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

Reset computational state of jobs.

ONLY FOR INTERNAL USAGE.

Sets the job function for already existing jobs.