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| .BatchJobs.R | BatchJobs configuration. |
| applyJobFunction | ONLY FOR INTERNAL USAGE. |
| batchExpandGrid | Map function over all combinations. |
| 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. |
| callFunctionOnSSHWorkers | Call an arbitrary function on specified SSH workers. |
| cfBrewTemplate | Cluster functions helper: Brew your template into a job description file. |
| cfHandleUnkownSubmitError | 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. |
| 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. |
| 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. |
| 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. |
| findSubmitted | Find jobs depending on computional state. |
| findTerminated | Find jobs depending on computional state. |
| getErrors | 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. |
| 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. |
| grepLogs | Grep log files for a pattern. |
| installPackagesOnSSHWorkers | Install packages on SSH workers. |
| Job | Creates a job description. |
| killJobs | Kill a job on the batch system. |
| loadConfig | Load a specific configuration file. |
| 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 synchronous execution in same session. |
| makeClusterFunctionsLocal | Create cluster functions for synchronous 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. |
| 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. |
| 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. |
| resetJobs | Reset computational state of jobs. |
| setJobFunction | Sets the job function for already existing jobs. |
| showClusterStatus | Show information about available computational resources on cluster. |
| showConf | Display BatchJobs configuration. |
| showLog | Display the contents of a log file. |
| showStatus | Show status information about jobs. |
| 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. |
| 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. |