allow LSF commands via ssh

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: batchtools
 Title: Tools for Computation on Batch Systems
-Version: 0.9.16
+Version: 0.9.15.9006
 Authors@R: c(
     person("Michel", "Lang", NULL, "[email protected]",
       role = c("cre", "aut"), comment = c(ORCID = "0000-0001-9754-0393")),
@@ -63,4 +63,4 @@ Suggests:
     tibble
 VignetteBuilder: knitr
 Roxygen: list(r6 = FALSE)
-RoxygenNote: 7.1.1
+RoxygenNote: 7.1.2

R/clusterFunctionsLSF.R

@@ -15,19 +15,22 @@
 #' It is the template file's job to choose a queue for the job and handle the desired resource
 #' allocations.
 #'
-#' @note
-#' Array jobs are currently not supported.
-#'
 #' @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
-makeClusterFunctionsLSF = function(template = "lsf", scheduler.latency = 1, fs.latency = 65) { # nocov start
+makeClusterFunctionsLSF = function(template = "lsf", 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 or contain the template itself as string (containing at least one newline)", template)
-  template = cfReadBrewTemplate(template)
+  template = cfReadBrewTemplate(template, '##')
+  quote = if (isLocalHost(nodename)) identity else shQuote
 
   # When LSB_BJOBS_CONSISTENT_EXIT_CODE = Y, the bjobs command exits with 0 only
   # when unfinished jobs are found, and 255 when no jobs are found,
@@ -37,20 +40,31 @@ makeClusterFunctionsLSF = function(template = "lsf", scheduler.latency = 1, fs.l
   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$log.file, "_%I")
+    }
     outfile = cfBrewTemplate(reg, template, jc)
-    res = runOSCommand("bsub", stdin = outfile)
+    res = runOSCommand("bsub", stdin = outfile, nodename = nodename)
+    output = stri_flatten(stri_trim_both(res$output), "\n")
 
     if (res$exit.code > 0L) {
       cfHandleUnknownSubmitError("bsub", res$exit.code, res$output)
     } else {
       batch.id = stri_extract_first_regex(stri_flatten(res$output, " "), "\\d+")
-      makeSubmitJobResult(status = 0L, batch.id = batch.id)
+      if (jc$array.jobs) {
+        if (!array.jobs)
+          stop("Array jobs not supported by cluster function")
+        makeSubmitJobResult(status = 0L, batch.id = sprintf("%s_%i", batch.id, seq_row(jc$jobs)), log.file = logs)
+      } else {
+        makeSubmitJobResult(status = 0L, batch.id = batch.id)
+      }
     }
   }
 
   listJobs = function(reg, args) {
     assertRegistry(reg, writeable = FALSE)
-    res = runOSCommand("bjobs", args)
+    res = runOSCommand("bjobs", args, nodename = nodename)
     if (res$exit.code > 0L) {
       if (res$exit.code == 255L || any(stri_detect_regex(res$output, "No (unfinished|pending|running) job found")))
         return(character(0L))
@@ -70,9 +84,9 @@ makeClusterFunctionsLSF = function(template = "lsf", scheduler.latency = 1, fs.l
   killJob = function(reg, batch.id) {
     assertRegistry(reg, writeable = TRUE)
     assertString(batch.id)
-    cfKillJob(reg, "bkill", batch.id)
+    cfKillJob(reg, "bkill", batch.id, nodename = nodename)
   }
 
-  makeClusterFunctions(name = "LSF", submitJob = submitJob, killJob = killJob, listJobsQueued = listJobsQueued,
+  makeClusterFunctions(name = "LSF", submitJob = submitJob, killJob = killJob, listJobsQueued = listJobsQueued, array.var = "LSB_JOBINDEX",
     listJobsRunning = listJobsRunning, store.job.collection = TRUE, scheduler.latency = scheduler.latency, fs.latency = fs.latency)
 } # nocov end

tests/testthat/test_ClusterFunctions.R

@@ -18,7 +18,7 @@ test_that("clusterFunctions constructor", {
   check(makeClusterFunctionsTORQUE("torque-lido"))
   check(makeClusterFunctionsSlurm("slurm-dortmund"))
   check(makeClusterFunctionsDocker("image"))
-  expect_error(makeClusterFunctionsLSF(), "point to a readable template file")
+  expect_error(makeClusterFunctionsLSF(template = "doesnotexist"), "point to a readable template file")
 
   skip_on_os(c("windows", "solaris")) # system2 is broken on solaris
     check(makeClusterFunctionsSSH(workers = list(Worker$new(nodename = "localhost", ncpus = 1L))))