Updates after actually runing something

drivers/linux/R/manager.R

@@ -21,7 +21,13 @@ do_linux_cancel <- function(scheduler_id, config) {
 
 
 do_linux_submit_pbs <- function(path_batch, id, config, path_root) {
-  withr::with_dir(path_root, system3("qsub", path_batch, stdout = TRUE))
+  res <- withr::with_dir(path_root, system3("qsub", path_batch, stdout = TRUE))
+  if (!res$success) {
+    output <- paste(res$output, collapse = "\n")
+    cli::cli_abort(
+      "Job submission failed with code {res$code} and error: {output}")
+  }
+  sub(".pbs$", "", res$output)
 }
 
 

drivers/linux/R/util.R

@@ -35,3 +35,13 @@ read_lines <- function(...) {
 normalize_path <- function(path) {
   normalizePath(path, winslash = "/", mustWork = TRUE)
 }
+
+
+system3 <- function(command, args) {
+  res <- suppressWarnings(system2(command, args, stdout = TRUE, stderr = TRUE))
+  code <- attr(res, "status") %||% 0
+  attr(res, "status") <- NULL
+  list(success = code == 0,
+       code = code,
+       output = res)
+}

drivers/linux/inst/templates/pbs/task_run.sh

@@ -1,7 +1,8 @@
 #!/bin/bash
 
-#PBS -lwalltime={{walltime}}
-#PBS -lselect=1:ncpus={{cores}}:mem={{memory}}gb
+#PBS -l walltime={{walltime}}
+#PBS -l select=1:ncpus={{cores}}:mem={{memory}}gb
+#PBS -N {{task_id}}
 
 ### This technically makes this driver dependent on easybuild or
 ### this module system, and other ways would be possible.  However, we