sge_submit: Submit expression to SGE grid
In egenn/rtemis: Machine Learning and Visualization

sge_submit

R Documentation

Submit expression to SGE grid

Description

Submit expression to SGE grid

Usage

sge_submit(
  expr,
  obj_names = NULL,
  packages = NULL,
  queue = NULL,
  n_threads = 4,
  sge_out = file.path(getwd(), "./sge_out"),
  sge_error = sge_out,
  sge_env = "#! /usr/bin/env bash",
  sge_opts = "#$ -cwd",
  R_command = NULL,
  system_command = NULL,
  h_rt = "00:25:00",
  mem_free = NULL,
  temp_dir = file.path(getwd(), ".sge_tempdir"),
  verbose = TRUE,
  trace = 1
)

Arguments

`expr`	R expression
`obj_names`	Character vector: Names of objects to copy to cluster R session
`packages`	Character vector: Names of packages to load in cluster R session
`queue`	Character: Name of SGE queue to submit to
`n_threads`	Integer: Number of threads to request from scheduler
`sge_out`	Character: Path to directory to write standard out message files
`sge_error`	Character: Path to directory to write error message files
`sge_env`	Character: Shell environment for script to be submitted to SGE
`sge_opts`	Character: SGE options that will be written in shell script. Default = "#$ -cwd"
`R_command`	Character: Optional R command(s) to run at the beginning of the R script
`system_command`	Character: system command to be run by shell script before executing R code. For example a command that export the R executable to use
`h_rt`	Character: Max time to request. Default = "00:25:00", i.e. 25 minutes
`mem_free`	Character: Amount of memory to request from the scheduler
`temp_dir`	Character: Temporary directory that is accessible to all execution nodes. Default = `file.path(getwd(), ".sge_tempdir")` You can use `tempdir()` if all execution nodes have access to the same filesystem as the submit node.
`verbose`	Logical: If TRUE, print messages to console. Default = TRUE
`trace`	Integer: If > 0 print diagnostic messages to console.