Batch Computing with R

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Documentation for package ‘BatchJobs’ version 1.6

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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.