BatchJobs v1.7

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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 in BatchJobs

Name Description
applyJobFunction applyJobFunction ONLY FOR INTERNAL USAGE.
BatchJobs The BatchJobs package
batchMapQuick Combination of makeRegistry, batchMap and submitJobs.
addRegistryPackages Add packages to registry.
batchMapResults Maps a function over the results of a registry by using batchMap.
batchExport Export R object to be available on the slaves.
batchQuery Manually query the BatchJobs database
batchMap Maps a function over lists or vectors, adding jobs to a registry.
batchReduce Reduces via a binary function over a list adding jobs to a registry.
checkIds Check job ids.
addRegistrySourceDirs Add source dirs to registry.
batchUnexport 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.
cfKillBatchJob Cluster functions helper: Kill a batch job via OS command
configuration BatchJobs configuration.
batchReduceResults Reduces results via a binary function and adds jobs for this to a registry.
copyRequiredJobFiles ONLY FOR INTERNAL USAGE.
cfBrewTemplate Cluster functions helper: Brew your template into a job description file.
findDone Find jobs depending on computional state.
cfReadBrewTemplate Cluster functions helper: Read in your brew template file.
getConfig Returns a list of BatchJobs configuration settings
dbCreateJobDefTable ONLY FOR INTERNAL USAGE.
getJobLocation Get the physical location of job files on the hard disk.
dbGetJobs ONLY FOR INTERNAL USAGE.
getJobNr Get number of jobs in registry.
getJobs Get jobs from registry by id.
loadResult Loads a specific result file.
debugMulticore Helper function to debug multicore mode.
loadResults Loads result files for id vector.
debugSSH Helper function to debug SSH mode.
makeClusterFunctionsSSH Create an SSH cluster to execute jobs.
makeClusterFunctionsTorque Create cluster functions for torque-based systems.
getJobIds Get ids of jobs in registry.
getLogFiles Get log file paths for jobs.
getJobInfo Get computational information of jobs.
grepLogs Grep log files for a pattern.
installPackagesOnSSHWorkers Install packages on SSH workers.
makeClusterFunctions Create a ClusterFuntions object.
killJobs Kill some jobs on the batch system.
makeClusterFunctionsSLURM Create cluster functions for SLURM-based systems.
loadConfig Load a specific configuration file.
removeRegistryPackages Remove packages from registry.
removeRegistrySourceDirs Remove packages from registry.
makeClusterFunctionsSGE Create cluster functions for Sun Grid Engine systems.
reduceResults Reduce results from result directory.
sourceRegistryFiles Source registry files
removeRegistry Remove a registry object.
submitJobs Submit jobs or chunks of jobs to batch system via cluster function.
sanitizePath Sanitize a path
getErrorMessages Get error messages of jobs.
waitForJobs Wait for termination of jobs on the batch system.
getJob Get job from registry by id.
filterResults Find all results where a specific condition is true.
loadExports Load exported R data objects.
loadRegistry Load a previously saved registry.
findJobs Finds ids of jobs that match a query.
setConfig Set and overwrite configuration settings
getJobParamDf Retrieve Job Parameters.
makeClusterFunctionsInteractive Create cluster functions for sequential execution in same session.
makeSSHWorker Create SSH worker for SSH cluster functions.
getJobResources Function to get the resources that were submitted for some jobs.
makeSubmitJobResult Create a SubmitJobResult object.
getResources 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.
sweepRegistry Sweep obsolete files from the file system.
makeJob Creates a job description.
syncRegistry Syncronize staged queries into the registry.
makeRegistry Construct a registry object.
showLog Display the contents of a log file.
makeClusterFunctionsOpenLava Create cluster functions for OpenLava systems.
showStatus Retrieve or show status information about jobs.
removeRegistrySourceFiles Remove source files from registry.
testJob Tests a job by running it with Rscript in a new process.
resetJobs Reset computational state of jobs.
updateRegistry ONLY FOR INTERNAL USAGE.
setJobFunction Sets the job function for already existing jobs.
setJobNames Set job names.
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URL https://github.com/tudo-r/BatchJobs
BugReports https://github.com/tudo-r/BatchJobs/issues
MailingList batchjobs@googlegroups.com
License BSD_2_clause + file LICENSE
LazyData yes
ByteCompile yes
RoxygenNote 6.0.1
NeedsCompilation no
Packaged 2017-11-28 15:42:44 UTC; bischl
Repository CRAN
Date/Publication 2017-11-28 17:41:32 UTC

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