Submit expression to SGE grid

Submit expression to SGE grid

Usage

sge_submit(
  expr,
  obj_names = NULL,
  packages = NULL,
  queue = NULL,
  n_workers = 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"),
  verbosity = 1L
)

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_workers

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.

verbosity

Integer: Verbosity level.

Author

EDG