# A batchtools SGE backend resolves futures in parallel via a Sun/Son of/Oracle/Univa/Altair Grid Engine job scheduler ```r 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 '=' 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 "- 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) ## Examples ```r 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) ``` ## References * [https://en.wikipedia.org/wiki/Oracle_Grid_Engine](https://en.wikipedia.org/wiki/Oracle_Grid_Engine)

batchtools_sge function