batchtools: makeClusterFunctionsSGE – R documentation

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batchtools

makeClusterFunctionsSGE

ClusterFunctions for SGE Systems

Description

Cluster functions for Univa Grid Engine / Oracle Grid Engine / Sun Grid Engine (https://www.univa.com/).

Job files are created based on the brew template template. This file is processed with brew and then submitted to the queue using the qsub command. Jobs are killed using the qdel command and the list of running jobs is retrieved using qselect. 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

makeClusterFunctionsSGE(
  template = "sge",
  nodename = "localhost",
  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”.
`nodename`	[`character(1)`] Nodename of the master host. All commands are send via SSH to this host. Only works iff Passwordless authentication (e.g., via SSH public key authentication) is set up. The file directory is shared across machines, e.g. mounted via SSHFS. Either the absolute path to the `file.dir` is identical on the machines, or paths are provided relative to the home directory. Symbolic links should work.
`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.