R/run_on_cluster.R

In Avi-Kenny/SimEngine: A Modular Framework for Statistical Simulations in R

#' Framework for running simulations on a cluster computing system
#'
#' @description This function allows for simulations to be run in parallel on a
#'     cluster computing system (CCS). It acts as a wrapper for the code in your
#'     simulation script, organizing the code into three sections, labeled
#'     "first" (code that is run once at the start of the simulation, e.g.
#'     setting simulation levels), "main" (running the simulation script via
#'     \code{\link{run}})), and "last" (usually code to process or summarize
#'     simulation results). This function interacts with cluster job scheduler
#'     software (e.g. Slurm or Oracle Grid Engine) to divide parallel tasks over
#'     cluster nodes. See
#'     \url{https://avi-kenny.github.io/SimEngine/parallelization/} for a
#'     detailed overview of how CCS parallelization works in \pkg{SimEngine}.
#' @param first Code to run at the start of a simulation. This should be a block
#'     of code enclosed by curly braces {} that creates a simulation object. Put
#'     everything you need in the simulation object, since global variables
#'     declared in this block will not be available when the 'main' and 'last'
#'     code blocks run.
#' @param main Code that will run for every simulation replicate. This should be
#'     a block of code enclosed by curly braces {}, and will almost always
#'     contain only a single call to the \code{\link{run}}) function. This code
#'     block will have access to the simulation object you created in the
#'     'first' code block, but any changes made here to the simulation object
#'     will not be saved.
#' @param last Code that will run after all simulation replicates have been run.
#'     This should be a block of code enclosed by curly braces {} that takes
#'     your simulation object (which at this point will contain your results)
#'     and do something with it, such as display your results on a graph.
#' @param cluster_config A list of configuration options. You must specify
#'     either \code{js} (the job scheduler you are using) or \code{tid_var} (the
#'     name of the environment variable that your task ID is stored in). Run
#'     \code{js_support()} to see a list of job schedulers that are currently
#'     supported. You can optionally also specify \code{dir}, which is a
#'     character string representing a path to a directory; this directory will
#'     serve as your working directory and hold your simulation object,
#'     temporary \pkg{SimEngine} objects, and simulation results (this defaults
#'     to the working directory of the R script that contains your simulation
#'     code).
#' @examples
#' \dontrun{
#' # The following is a toy simulation that could be run on a cluster computing
#' # environment. It runs 10 replicates of 2 simulation levels as 20 separate
#' # cluster jobs, and then summarizes the results. This function is designed to
#' # be used in conjunction with cluster job scheduler software (e.g. Slurm or
#' # Oracle Grid Engine). We include both the R code as well as sample BASH code
#' # for running the simulation using Oracle Grid Engine.
#'
#' # This code is saved in a file called my_simulation.R
#' library(SimEngine)
#' run_on_cluster(
#'
#'   first = {
#'     sim <- new_sim()
#'     create_data <- function(n) { rnorm(n) }
#'     sim %<>% set_script(function() {
#'       data <- create_data(L$n)
#'       return(list("x"=mean(data)))
#'     })
#'     sim %<>% set_levels(n=c(100,1000))
#'     sim %<>% set_config(num_sim=10)
#'   },
#'
#'   main = {
#'     sim %<>% run()
#'   },
#'
#'   last = {
#'     sim %>% summarize()
#'   },
#'
#'   cluster_config = list(js="ge")
#'
#' )
#'
#' # This code is saved in a file called run_sim.sh
#' # #!/bin/bash
#' # Rscript my_simulation.R
#'
#' # The following lines of code are run on the cluster head node.
#' # qsub -v sim_run='first' run_sim.sh
#' # qsub -v sim_run='main' -t 1-20 -hold_jid 101 run_sim.sh
#' # qsub -v sim_run='last' -hold_jid 102 run_sim.sh
#' }
#' @export
run_on_cluster <- function(first, main, last, cluster_config) {

  cluster_execute(
    substitute(first),
    substitute(main),
    substitute(last),
    cluster_config
  )

}