Batch Computing with R

Documentation for package ‘BatchJobs’ version 1.9

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-- A --

-- 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.
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.

-- 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.
checkIds	Check job ids.
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.
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.
getStatus	Retrieve or show status information about jobs.
grepLogs	Grep log files for a pattern.

-- I --

Install packages on SSH workers.

-- J --

Job	Creates a job description.

-- K --

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.
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.

-- R --

reduceResults	Reduce results from result directory.
reduceResultsDataFrame	Reduce results from result directory.
reduceResultsDataTable	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.
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
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.
syncRegistry	Syncronize staged queries into the registry.

-- T --

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

-- W --

Wait for termination of jobs on the batch system.

-- misc --

BatchJobs configuration.