Additional parameters for SLURM to work correctly on LRZ cluster

R/clusterFunctionsSLURM.R

@@ -19,10 +19,23 @@
 #' @template arg_template
 #' @template arg_list_jobs_cmd
 #' @template ret_cf
+#' @param list.job.line.skip [\code{integer(1)}]\cr
+#'    Change how many lines of the job list should be skipped. Can be useful if \code{squeue} is giving
+#'    additional output.
+#' @param cluster.name [\code{character(1)}]\cr
+#'    If an additional cluster name has to be specified for listing or deleting jobs it can be 
+#'    supplied with this argument. it will be added as \code{--clusters=cluster.name} for SLURM.
 #' @family clusterFunctions
 #' @export
-makeClusterFunctionsSLURM = function(template.file, list.jobs.cmd = c("squeue", "-h", "-o %i", "-u $USER")) {
+makeClusterFunctionsSLURM = function(template.file, list.jobs.cmd = c("squeue", "-h", "-o %i", "-u $USER"),
+                                     list.job.line.skip = 0L, cluster.name = NULL) {
+
+  if (!is.null(cluster.name)) {
+    assertString(cluster.name)
+    list.jobs.cmd = append(list.jobs.cmd, paste0("--clusters=", cluster.name))
+  }
   assertCharacter(list.jobs.cmd, min.len = 1L, any.missing = FALSE)
+  assertCount(list.job.line.skip)
   template = cfReadBrewTemplate(template.file)
 
   submitJob = function(conf, reg, job.name, rscript, log.file, job.dir, resources, arrayjobs) {
@@ -45,12 +58,22 @@ makeClusterFunctionsSLURM = function(template.file, list.jobs.cmd = c("squeue",
   }
 
   killJob = function(conf, reg, batch.job.id) {
+
+
+    if (!is.null(cluster.name)) {
+      cfKillBatchJob("scancel",paste0("--clusters=", cluster.name, " ", batch.job.id))
+    }
     cfKillBatchJob("scancel", batch.job.id)
   }
 
   listJobs = function(conf, reg) {
     # Result is lines of fully quantified batch.job.ids
     jids = runOSCommandLinux(list.jobs.cmd[1L], list.jobs.cmd[-1L])$output
+    # if squeue returns additional information (like cluster name), one or more
+    # lines can be omitted
+    if (list.job.line.skip > 0L) {
+      jids = jids[-seq_len(list.job.line.skip)]
+    }
     stri_extract_first_regex(jids, "[0-9]+")
   }