Skip to contents

A batchtools SGE backend resolves futures in parallel via a Sun/Son of/Oracle/Univa/Altair Grid Engine job scheduler

Source: R/batchtools_sge.R
batchtools_sge.Rd

A batchtools SGE backend resolves futures in parallel via a Sun/Son of/Oracle/Univa/Altair Grid Engine job scheduler

Usage

batchtools_sge(
  ...,
  template = "sge",
  scheduler.latency = 1,
  fs.latency = 65,
  resources = list(),
  delete = getOption("future.batchtools.delete", "on-success"),
  workers = getOption("future.batchtools.workers", default = 100L)
)

Arguments

template

(optional) Name of job-script template to be searched for by batchtools::findTemplateFile(). If not found, it defaults to the templates/sge.tmpl part of this package (see below).

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.

resources

(optional) A named list passed to the batchtools job-script template as variable resources. This is based on how batchtools::submitJobs() works, with the exception for specially reserved names defined by the future.batchtools package;

  • resources[["details"]], if TRUE, results in the job script outputting job details and job summaries at the beginning and at the end.

  • resources[["startup"]] and resources[["shutdown"]] are character vectors of shell code to be injected to the job script as-is.

  • resources[["modules"]] is character vector of Linux environment modules to be loaded.

  • resources[["envs"]], is an optional names character vector specifying environment variables to be set.

  • resources[["rscript"]] is an optional character vector specifying how the 'Rscript' is launched. The resources[["rscript_args"]] field is an optional character vector specifying the 'Rscript' command-line arguments.

  • resources[["asis"]] is a character vector that are passed as-is to the job script and are injected as job resource declarations.

  • All remaining resources named elements are injected as named resource specification for the scheduler.

delete

Controls if and when the batchtools job registry folder is deleted. If "on-success" (default), it is deleted if the future was resolved successfully and the expression did not produce an error. If "never", then it is never deleted. If "always", then it is always deleted.

workers

The maximum number of workers the batchtools backend may use at any time, which for HPC schedulers corresponds to the maximum number of queued jobs. The default is getOption("future.batchtools.workers", 100).

...

Not used.

Details

Batchtools SGE futures use batchtools cluster functions created by batchtools::makeClusterFunctionsSGE(), which are used to interact with the SGE job scheduler. This requires that SGE commands qsub, qstat, and qdel are available on the current machine.

The default template script templates/sge.tmpl can be found in:

system.file("templates", "sge.tmpl", package = "future.batchtools")

and comprise:

#!/bin/bash
######################################################################
# A batchtools launch script template for SGE
#
# Author: Henrik Bengtsson
######################################################################
## Shell
#$ -S /bin/bash

## Job name
#$ -N <%= job.name %>

## Direct streams to logfile
#$ -o <%= log.file %>

## Merge standard error and output
#$ -j y

## Tell the queue system to use the current directory
## as the working directory
#$ -cwd

## Resources needed
<%
  ## Should scheduler "details" be seen?
  details <- isTRUE(resources[["details"]])
  resources[["details"]] <- NULL

  ## Shell "startup" code to evaluate
  startup <- resources[["startup"]]
  resources[["startup"]] <- NULL

  ## Shell "shutdown" code to evaluate
  shutdown <- resources[["shutdown"]]
  resources[["shutdown"]] <- NULL

  ## Environment modules specifications
  modules <- resources[["modules"]]
  resources[["modules"]] <- NULL

  ## Environment variables to be set
  envs <- resources[["envs"]]
  if (length(envs) > 0) {
    stopifnot(is.character(envs), !is.null(names(envs)))
  }
  resources[["envs"]] <- NULL

  ## Custom "Rscript" command and Rscript arguments
  rscript <- resources[["rscript"]]
  if (is.null(rscript)) {
    rscript <- "Rscript"
  } else if (length(rscript) == 0 || !nzchar(rscript)[1]) {
    stop("Argument 'resources' specifies an empty 'rscript' field")
  }
  resources[["rscript"]] <- NULL
  rscript_args <- resources[["rscript_args"]]
  resources[["rscript_args"]] <- NULL
  rscript_call <- paste(c(rscript, rscript_args), collapse = " ")

  ## As-is resource specifications
  job_declarations <- resources[["asis"]]
  resources[["asis"]] <- NULL

  ## Remaining resources are assumed to be of type '<key>=<value>'
  opts <- unlist(resources, use.names = TRUE)
  opts <- sprintf("%s=%s", names(opts), opts)
  job_declarations <- sprintf("#$ %s", c(job_declarations, sprintf("-l %s", opts)))
  writeLines(job_declarations)
%>

## Bash settings
set -e          # exit on error
set -u          # error on unset variables
set -o pipefail # fail a pipeline if any command fails
trap 'echo "ERROR: future.batchtools job script failed on line $LINENO" >&2; exit 1' ERR

<% if (length(job_declarations) > 0) {
  writeLines(c(
    "echo 'Job submission declarations:'",
    sprintf("echo '%s'", job_declarations),
    "echo"
  ))
} %>

<% if (details) { %>
if command -v qstat > /dev/null; then
  echo "Job information:"
  qstat -j "${JOB_ID}"
  echo
fi
<% } %>

<% if (length(startup) > 0) {
  writeLines(startup)
} %>

<% if (length(modules) > 0) {
  writeLines(c(
    "echo 'Load environment modules:'",
    sprintf("echo '- modules: %s'", paste(modules, collapse = ", ")),
    sprintf("module load %s", paste(modules, collapse = " ")),
    "module list"
  ))
} %>

<% if (length(envs) > 0) {
  writeLines(c(
    sprintf("echo 'Setting environment variables: [n=%d]'", length(envs)),
    sprintf("echo ' - %s=%s'", names(envs), shQuote(envs)),
    sprintf("export %s=%s", names(envs), shQuote(envs))
  ))
} %>

echo "Session information:"
echo "- timestamp: $(date +"%Y-%m-%d %H:%M:%S%z")"
echo "- hostname: $(hostname)"
echo "- Rscript call: <%= rscript_call %>"
if ! command -v <%= rscript[1] %> &> /dev/null; then
    >&2 echo "ERROR: Argument 'resources' specifies a non-existing 'Rscript' launch command: <%= rscript[1] %>. Maybe you need to specify which environment modules to load in the 'resources' argument, e.g. 'plan(future.batchtools::batchtools_slurm, resources = list(modules = c(\"r\")))'. The search PATH for '%<= rscript[1] %>' was ${PATH}"
    exit 1
fi
echo "- Rscript version: $(<%= paste(rscript, collapse = " ") %> --version)"
echo "- R_LIBS_USER=${R_LIBS_USER:-<not set>}"
echo "- R_LIBS_SITE=${R_LIBS_SITE:-<not set>}"
echo "- R_LIBS=${R_LIBS:-<not set>}"
echo "- Rscript library paths: $(<%= rscript_call %> -e "cat(shQuote(.libPaths()), sep = ' ')")"
echo


## Launch R and evaluate the batchtools R job
echo "Calling 'batchtools::doJobCollection()' ..."
echo "- job name: '<%= job.name %>'"
echo "- job log file: '<%= log.file %>'"
echo "- job uri: '<%= uri %>'"
<%= rscript_call %> -e 'batchtools::doJobCollection("<%= uri %>")'
res=$?
echo " - exit code: ${res}"
echo "Calling 'batchtools::doJobCollection()' ... done"
echo

<% if (details) { %>
if command -v qstat > /dev/null; then
  echo "Job summary:"
  qstat -j "${JOB_ID}"
fi
<% } %>

<% if (length(shutdown) > 0) {
  writeLines(shutdown)
} %>

echo "End time: $(date +"%Y-%m-%d %H:%M:%S%z")"

## Relay the exit code from Rscript
exit "${res}"

This template and the built-in batchtools::makeClusterFunctionsSGE() have been verified to work on a few different Grid Engine HPC clusters;

  1. SGE 8.1.9 (Son of Grid Engine), Rocky 8 Linux, BeeGFS global filesystem (August 2025)

  2. AGE 2024.1.0 (8.9.0), Rocky 9 Linux, NSF global filesystem (August 2025)

References

Examples

if (FALSE) { # interactive()
library(future)

# Limit runtime to 10 minutes and memory to 400 MiB per future,
# request a parallel environment with four slots on a single host.
# Submit to the 'freecycle' queue. Load environment modules 'r' and
# 'jags'. Report on job details at startup and at the end of the job.
plan(future.batchtools::batchtools_sge, resources = list(
  h_rt = "00:10:00", mem_free = "100M",  ## memory is per process
  asis = c("-pe smp 4", "-q freecycle.q"),
  modules = c("r", "jags"),
  details = TRUE
))

f <- future({
  data.frame(
     hostname = Sys.info()[["nodename"]],
           os = Sys.info()[["sysname"]],
    osVersion = utils::osVersion,
        cores = unname(parallelly::availableCores()),
      modules = Sys.getenv("LOADEDMODULES")
  )
})
info <- value(f)
print(info)
}