Man pages for BatchJobs
Batch Computing with R
| addRegistryPackages | Add packages to registry. |
| addRegistrySourceDirs | Add source dirs to registry. |
| addRegistrySourceFiles | Add source files to registry. |
| applyJobFunction | applyJobFunction ONLY FOR INTERNAL USAGE. |
| 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... |
| batchMapQuick | Combination of makeRegistry, batchMap and submitJobs. |
| batchMapResults | Maps a function over the results of a registry by using... |
| batchQuery | Manually query the BatchJobs database |
| batchReduce | Reduces via a binary function over a list adding jobs to a... |
| batchReduceResults | Reduces results via a binary function and adds jobs for this... |
| batchUnexport | Unload exported R objects. |
| callFunctionOnSSHWorkers | Call an arbitrary function on specified SSH workers. |
| cfBrewTemplate | Cluster functions helper: Brew your template into a job... |
| cfHandleUnknownSubmitError | Cluster functions helper: Handle an unknown error during job... |
| 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. |
| configuration | BatchJobs configuration. |
| copyRequiredJobFiles | ONLY FOR INTERNAL USAGE. |
| dbCreateJobDefTable | ONLY FOR INTERNAL USAGE. |
| dbGetJobs | ONLY FOR INTERNAL USAGE. |
| debugMulticore | Helper function to debug multicore mode. |
| debugSSH | Helper function to debug SSH mode. |
| filterResults | Find all results where a specific condition is true. |
| findJobs | Finds ids of jobs that match a query. |
| findState | Find jobs depending on computional state. |
| 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... |
| 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... |
| grepLogs | Grep log files for a pattern. |
| installPackagesOnSSHWorkers | Install packages on SSH workers. |
| killJobs | Kill some jobs on the batch system. |
| 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. |
| makeClusterFunctions | Create a ClusterFuntions object. |
| makeClusterFunctionsInteractive | Create cluster functions for sequential execution in same... |
| makeClusterFunctionsLocal | Create cluster functions for sequential execution on local... |
| makeClusterFunctionsLSF | Create cluster functions for LSF systems. |
| makeClusterFunctionsMulticore | Use multiple cores on local Linux machine to spawn parallel... |
| 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. |
| reduceResults | Reduce results from result directory. |
| 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. |
| 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... |
| showLog | Display the contents of a log file. |
| showStatus | Retrieve or show status information about jobs. |
| sourceRegistryFiles | Source registry files |
| submitJobs | Submit jobs or chunks of jobs to batch system via cluster... |
| sweepRegistry | Sweep obsolete files from the file system. |
| syncRegistry | Syncronize staged queries into the registry. |
| testJob | Tests a job by running it with Rscript in a new process. |
| updateRegistry | ONLY FOR INTERNAL USAGE. |
| waitForJobs | Wait for termination of jobs on the batch system. |
