R: Batch Computing with R

# Batch Computing with R

## Documentation for package ‘BatchJobs’ version 1.6

- DESCRIPTION file.
- Package NEWS.

## Help Pages

A B C D F G I J K L M R S T W misc

BatchJobs-package | The BatchJobs package

## -- A --

addRegistryPackages | Add packages to registry.
addRegistrySourceDirs | Add source dirs to registry.
addRegistrySourceFiles | Add source files to registry.

## -- B --

batchExpandGrid | Map function over all combinations.
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.
batchMapResults | Maps a function over the results of a registry by using batchMap.
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.

## -- C --

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.
ClusterFunctions | Create a ClusterFuntions object.
configuration | BatchJobs configuration.

## -- D --

debugMulticore | Helper function to debug multicore mode.
debugSSH | Helper function to debug SSH mode.

## -- F --

filterResults | Find all results where a specific condition is true.
findDisappeared | Find jobs depending on computional state.
findDone | Find jobs depending on computional state.
findErrors | Find jobs depending on computional state.
findExpired | Find jobs depending on computional state.
findJobs | Finds ids of jobs that match a query.
findMissingResults | Find jobs depending on computional state.
findNotDone | Find jobs depending on computional state.
findNotErrors | Find jobs depending on computional state.
findNotOnSystem | Find jobs depending on computional state.
findNotRunning | Find jobs depending on computional state.
findNotStarted | Find jobs depending on computional state.
findNotSubmitted | Find jobs depending on computional state.
findNotTerminated | Find jobs depending on computional state.
findOnSystem | Find jobs depending on computional state.
findRunning | Find jobs depending on computional state.
findStarted | Find jobs depending on computional state.
findSubmitted | Find jobs depending on computional state.
findTerminated | Find jobs depending on computional state.

## -- G --

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.
getJobNr | Get number of jobs in registry.
getJobParamDf | Returns parameters for all jobs as the rows of a data.frame.
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.
getStatus | Retrieve or show status information about jobs.
grepLogs | Grep log files for a pattern.

## -- I --

installPackagesOnSSHWorkers | Install packages on SSH workers.

## -- J --

Job | Creates a job description.

## -- K --

killJobs | Kill some jobs on the batch system.

## -- L --

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.

## -- M --

makeClusterFunctions | Create a ClusterFuntions object.
makeClusterFunctionsInteractive | Create cluster functions for sequential execution in same session.
makeClusterFunctionsLocal | Create cluster functions for sequential execution on local host.
makeClusterFunctionsLSF | Create cluster functions for LSF systems.
makeClusterFunctionsMulticore | Use multiple cores on local Linux machine to spawn parallel jobs.
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.

## -- R --

reduceResults | Reduce results from result directory.
reduceResultsDataFrame | Reduce results from result directory.
reduceResultsList | Reduce results from result directory.
reduceResultsMatrix | Reduce results from result directory.
reduceResultsVector | Reduce results from result directory.
Registry | Construct a registry object.
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.

## -- S --

sanitizePath | Sanitize a path
setConfig | Set and overwrite configuration settings
setJobFunction | Sets the job function for already existing jobs.
setJobNames | Set job names.
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
SSHWorker | Create SSH worker for SSH cluster functions.
SubmitJobResult | Create a SubmitJobResult object.
submitJobs | Submit jobs or chunks of jobs to batch system via cluster function.
sweepRegistry | Sweep obsolete files from the file system.

## -- T --

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

## -- W --

waitForJobs | Wait for termination of jobs on the batch system.

## -- misc --

.BatchJobs.R | BatchJobs configuration.