Now all built-in template job scripts supports as-is resource specifications via resources[["asis"]]

Author: HenrikBengtsson

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: future.batchtools
-Version: 0.12.2-9945
+Version: 0.12.2-9946
 Depends:
     R (>= 3.2.0),
     parallelly,

NEWS.md

@@ -17,7 +17,10 @@
  * Tidy up built-in template job script for Bash, SGE, Slurm and
    Torque/PBS.
 
- * Add built-in template job script for LSF and OpenLava.
+ * Add built-in template job scripts for LSF and OpenLava.
+
+ * Now all built-in template job scripts supports as-is resource
+   specifications via `resources[["asis"]]`.
 
 ## Documentation
 

inst/templates/lsf.tmpl

@@ -13,9 +13,18 @@
 
 ## Resources needed:
 <% if (length(resources) > 0) {
+  prefix <- "#BSUB "
+    
+  ## As-is resource specifications
+  if ("asis" %in% names(resources)) {
+    writeLines(sprintf("%s%s", prefix, resources[["asis"]]))
+    resources <- resources[names(resources) != "asis"]
+  }
+     
+  ## Remaining resources are assumed to be of type '-<key>=<value>'
   opts <- unlist(resources, use.names = TRUE)
   opts <- sprintf("-%s=%s", names(opts), opts)
-  writeLines(sprintf("#BSUB %s", opts))
+  writeLines(sprintf("%s%s", prefix, opts))
 } %>
 
 echo "Batchtools information:"

inst/templates/openlava.tmpl

@@ -13,9 +13,18 @@
 
 ## Resources needed:
 <% if (length(resources) > 0) {
+  prefix <- "#BSUB "
+    
+  ## As-is resource specifications
+  if ("asis" %in% names(resources)) {
+    writeLines(sprintf("%s%s", prefix, resources[["asis"]]))
+    resources <- resources[names(resources) != "asis"]
+  }
+     
+  ## Remaining resources are assumed to be of type '-<key>=<value>'
   opts <- unlist(resources, use.names = TRUE)
   opts <- sprintf("-%s=%s", names(opts), opts)
-  writeLines(sprintf("#BSUB %s", opts))
+  writeLines(sprintf("%s%s", prefix, opts))
 } %>
 
 echo "Batchtools information:"

inst/templates/sge.tmpl

@@ -25,19 +25,21 @@
 
 ## Resources needed:
 <% if (length(resources) > 0) {
+  prefix <- "#$ "
+    
   ## As-is resource specifications, e.g.
   ## sge_options <- c("-pe smp 2", "-R yes")
   ## plan(batchtools_sge, resources = list(asis = sge_options))
   if ("asis" %in% names(resources)) {
-    cat(sprintf("#$ %s\n", resources[["asis"]]))
+    writeLines(sprintf("%s%s", prefix, resources[["asis"]]))
     resources <- resources[names(resources) != "asis"]
   }
 
-  ## Remaining resources are assumed to be of type '-l', e.g.
+  ## Remaining resources are assumed to be of type '-l <key>=<value>', e.g.
   ## plan(batchtools_sge, resources = list(mem_free = "1G", h_rt="00:20:00"))
   opts <- unlist(resources, use.names = TRUE)
   opts <- sprintf("-l %s=%s", names(opts), opts)
-  writeLines(sprintf("#$ %s", opts))
+  writeLines(sprintf("%s%s", prefix, opts))
 } %>
 
 echo "Batchtools information:"

inst/templates/slurm.tmpl

@@ -8,17 +8,22 @@
 
 #SBATCH --job-name=<%= job.name %>
 #SBATCH --output=<%= log.file %>
-<%
-defaults <- list(
-  nodes = 1,         # single-host processing
-  time = "00:05:00", # 5-min runtime
-  mem  = "100M"      # 100 MiB memory
-)
-resources <- c(resources, defaults[setdiff(names(defaults), names(resources))])
-opts <- unlist(resources, use.names = TRUE)
-opts <- sprintf("--%s=%s", names(opts), opts)
-writeLines(sprintf("#SBATCH %s", opts))
-%>
+
+## Resources needed:
+<% if (length(resources) > 0) {
+  prefix <- "#SBATCH "
+    
+  ## As-is resource specifications
+  if ("asis" %in% names(resources)) {
+    writeLines(sprintf("%s%s", prefix, resources[["asis"]]))
+    resources <- resources[names(resources) != "asis"]
+  }
+
+  ## Remaining resources are assumed to be of type '--<key>=<value>'
+  opts <- unlist(resources, use.names = TRUE)
+  opts <- sprintf("--%s=%s", names(opts), opts)
+  writeLines(sprintf("%s%s", prefix, opts))
+} %>
 
 echo "Batchtools information:"
 echo "- job name: '<%= job.name %>'"

inst/templates/torque.tmpl

@@ -19,9 +19,18 @@
 
 ## Resources needed:
 <% if (length(resources) > 0) {
+  prefix <- "#PBS "
+    
+  ## As-is resource specifications
+  if ("asis" %in% names(resources)) {
+    writeLines(sprintf("%s%s", prefix, resources[["asis"]]))
+    resources <- resources[names(resources) != "asis"]
+  }
+     
+  ## Remaining resources are assumed to be of type '-l <key>=<value>'
   opts <- unlist(resources, use.names = TRUE)
-  opts <- sprintf("%s=%s", names(opts), opts)
-  writeLines(sprintf("#PBS -l %s", opts))
+  opts <- sprintf("-l %s=%s", names(opts), opts)
+  writeLines(sprintf("%s%s", prefix, opts))
 } %>
 
 echo "Batchtools information:"