R: ClusterFunctions for LSF Systems

makeClusterFunctionsLSF {batchtools} | R Documentation

## ClusterFunctions for LSF Systems

### Description

Cluster functions for LSF (https://www.ibm.com/us-en/marketplace/hpc-workload-management).

Job files are created based on the brew template `template.file`. This file is processed with brew and then submitted to the queue using the `bsub` command. Jobs are killed using the `bkill` command and the list of running jobs is retrieved using `bjobs -u $USER -w`. The user must have the appropriate privileges to submit, delete and list jobs on the cluster (this is usually the case).

The template file can access all resources passed to `submitJobs` as well as all variables stored in the `JobCollection`. It is the template file's job to choose a queue for the job and handle the desired resource allocations.

### Usage

    makeClusterFunctionsLSF(template = "lsf", scheduler.latency = 1,
      fs.latency = 65)

### Arguments

`template` | [`character(1)`] Either a path to a brew template file (with extension “tmpl”), or a short descriptive name enabling the following heuristic for the file lookup: “batchtools.[template].tmpl” in the path specified by the environment variable “R_BATCHTOOLS_SEARCH_PATH”. “batchtools.[template].tmpl” in the current working directory. “[template].tmpl” in the user config directory (see `user_config_dir`); on linux this is usually “~/.config/batchtools/[template].tmpl”. “.batchtools.[template].tmpl” in the home directory. “[template].tmpl” in the package installation directory in the subfolder “templates”.
`scheduler.latency` | [`numeric(1)`] Time to sleep after important interactions with the scheduler to ensure a sane state. Currently only triggered after calling `submitJobs`.
`fs.latency` | [`numeric(1)`] Expected maximum latency of the file system, in seconds. Set to a positive number for network file systems like NFS which enables more robust (but also more expensive) mechanisms to access files and directories. Usually safe to set to `0` to disable the heuristic, e.g. if you are working on a local file system.

### Value

[`ClusterFunctions`].

### Note

Array jobs are currently not supported.

### See Also

Other ClusterFunctions: `makeClusterFunctionsDocker`, `makeClusterFunctionsInteractive`, `makeClusterFunctionsMulticore`, `makeClusterFunctionsOpenLava`, `makeClusterFunctionsSGE`, `makeClusterFunctionsSSH`, `makeClusterFunctionsSlurm`, `makeClusterFunctionsSocket`, `makeClusterFunctionsTORQUE`, `makeClusterFunctions`

[Package batchtools version 0.9.11 Index]