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#' @title ClusterFunctions for Slurm Systems
#'
#' @description
#' Cluster functions for Slurm (\url{https://slurm.schedmd.com/}).
#'
#' Job files are created based on the brew template \code{template.file}. This
#' file is processed with brew and then submitted to the queue using the
#' \code{sbatch} command. Jobs are killed using the \code{scancel} command and
#' the list of running jobs is retrieved using \code{squeue}. The user must
#' have the appropriate privileges to submit, delete and list jobs on the
#' cluster (this is usually the case).
#'
#' The template file can access all resources passed to \code{\link{submitJobs}}
#' as well as all variables stored in the \code{\link{JobCollection}}.
#' It is the template file's job to choose a queue for the job and handle the desired resource
#' allocations.
#'
#' Note that you might have to specify the cluster name here if you do not want to use the default,
#' otherwise the commands for listing and killing jobs will not work.
#'
#' @template template
#' @param array.jobs [\code{logical(1)}]\cr
#' If array jobs are disabled on the computing site, set to \code{FALSE}.
#' @template nodename
#' @inheritParams makeClusterFunctions
#' @return [\code{\link{ClusterFunctions}}].
#' @family ClusterFunctions
#' @export
makeClusterFunctionsSlurm = function(template = "slurm", array.jobs = TRUE, nodename = "localhost", scheduler.latency = 1, fs.latency = 65) { # nocov start
assertFlag(array.jobs)
assertString(nodename)
template = findTemplateFile(template)
if (testScalarNA(template))
stopf("Argument 'template' (=\"%s\") must point to a readable template file", template)
template = cfReadBrewTemplate(template, "##")
quote = if (isLocalHost(nodename)) identity else shQuote
getClusters = function(reg) {
clusters = filterNull(lapply(reg$resources$resources, "[[", "cluster"))
if (length(clusters))
return(stri_flatten(unique(as.character(clusters)), ","))
return(character(0L))
}
submitJob = function(reg, jc) {
assertRegistry(reg, writeable = TRUE)
assertClass(jc, "JobCollection")
if (jc$array.jobs) {
logs = sprintf("%s_%i", fs::path_file(jc$log.file), seq_row(jc$jobs))
jc$log.file = stri_join(jc$log.file, "_%a")
}
outfile = cfBrewTemplate(reg, template, jc)
res = runOSCommand("sbatch", shQuote(outfile), nodename = nodename)
output = stri_flatten(stri_trim_both(res$output), "\n")
if (res$exit.code > 0L) {
temp.errors = c(
"Batch job submission failed: Job violates accounting policy (job submit limit, user's size and/or time limits)",
"Socket timed out on send/recv operation",
"Submission rate too high, suggest using job arrays"
)
i = wf(stri_detect_fixed(output, temp.errors))
if (length(i) == 1L)
return(makeSubmitJobResult(status = i, batch.id = NA_character_, msg = temp.errors[i]))
return(cfHandleUnknownSubmitError("sbatch", res$exit.code, res$output))
}
id = stri_split_fixed(output[1L], " ")[[1L]][4L]
if (jc$array.jobs) {
if (!array.jobs)
stop("Array jobs not supported by cluster function")
makeSubmitJobResult(status = 0L, batch.id = sprintf("%s_%i", id, seq_row(jc$jobs)), log.file = logs)
} else {
makeSubmitJobResult(status = 0L, batch.id = id)
}
}
listJobs = function(reg, args) {
assertRegistry(reg, writeable = FALSE)
args = c(args, "--noheader", "--format=%i")
if (array.jobs)
args = c(args, "-r")
clusters = getClusters(reg)
if (length(clusters))
args = c(args, sprintf("--clusters=%s", clusters))
res = runOSCommand("squeue", args, nodename = nodename)
if (res$exit.code > 0L)
OSError("Listing of jobs failed", res)
if (length(clusters)) tail(res$output, -1L) else res$output
}
listJobsQueued = function(reg) {
args = c(quote("--user=$USER"), "--states=PD")
listJobs(reg, args)
}
listJobsRunning = function(reg) {
args = c(quote("--user=$USER"), "--states=R,S,CG")
listJobs(reg, args)
}
killJob = function(reg, batch.id) {
assertRegistry(reg, writeable = TRUE)
assertString(batch.id)
cfKillJob(reg, "scancel", c(sprintf("--clusters=%s", getClusters(reg)), batch.id), nodename = nodename)
}
makeClusterFunctions(name = "Slurm", submitJob = submitJob, killJob = killJob, listJobsRunning = listJobsRunning,
listJobsQueued = listJobsQueued, array.var = "SLURM_ARRAY_TASK_ID", store.job.collection = TRUE,
store.job.files = !isLocalHost(nodename), scheduler.latency = scheduler.latency, fs.latency = fs.latency)
} # nocov end
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