All built-in template job scripts support "startup code" resource specifications via resources[["startup"]]

Author: HenrikBengtsson

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: future.batchtools
-Version: 0.12.2-9976
+Version: 0.12.2-9977
 Depends:
     R (>= 3.2.0),
     parallelly,

NEWS.md

@@ -38,7 +38,12 @@
    - All built-in template job scripts support "environment module"
      resource specifications via `resources[["modules"]]`. When
      specified, corresponding `module load <name>` entries are
-     injected to the job script.
+     injected to the generated job script.
+     
+   - All built-in template job scripts support "startup code" resource
+     specifications via `resources[["startup"]]`. When specified,
+     corresponding lines are injected early in the generated job
+     script.
 
    - All built-in template job scripts, which are written in Bash,
      error and exit early, but setting more strict Bash options. This

inst/templates/bash.tmpl

@@ -11,17 +11,25 @@ set -u          # error on unset variables
 set -o pipefail # fail a pipeline if any command fails
 trap 'echo "ERROR: future.batchtools job script failed on line $LINENO" >&2; exit 1' ERR
 
-
 <%
   ## Maximum runtime?
   runtime <- resources[["timeout"]]
   timeout <- if (is.null(runtime)) "" else sprintf("timeout %s", runtime)
-  
+    
+  ## Shell "startup" code to evaluate
+  startup <- resources[["startup"]]
+  resources[["startup"]] <- NULL
+
   ## Environment modules specifications
   modules <- resources[["modules"]]
   resources[["modules"]] <- NULL
 %>
 
+<% if (length(startup) > 0) {
+  ## Inject optional shell code
+  writeLines(startup)
+} %>
+
 echo "Load environment modules:"
 <% if (length(modules) > 0) {
   writeLines(c(sprintf("module load %s", modules), "module list"))

inst/templates/lsf.tmpl

@@ -16,6 +16,10 @@
   ## As-is resource specifications
   job_declarations <- resources[["asis"]]
   resources[["asis"]] <- NULL
+    
+  ## Shell "startup" code to evaluate
+  startup <- resources[["startup"]]
+  resources[["startup"]] <- NULL
 
   ## Environment modules specifications
   modules <- resources[["modules"]]
@@ -39,6 +43,11 @@ echo "- job name: '<%= job.name %>'"
 echo "- job log file: '<%= log.file %>'"
 echo
 
+<% if (length(startup) > 0) {
+  ## Inject optional shell code
+  writeLines(startup)
+} %>
+
 echo "Load environment modules:"
 <% if (length(modules) > 0) {
   writeLines(c(sprintf("module load %s", modules), "module list"))

inst/templates/openlava.tmpl

@@ -16,6 +16,10 @@
   ## As-is resource specifications
   job_declarations <- resources[["asis"]]
   resources[["asis"]] <- NULL
+    
+  ## Shell "startup" code to evaluate
+  startup <- resources[["startup"]]
+  resources[["startup"]] <- NULL
 
   ## Environment modules specifications
   modules <- resources[["modules"]]
@@ -39,6 +43,11 @@ echo "- job name: '<%= job.name %>'"
 echo "- job log file: '<%= log.file %>'"
 echo
 
+<% if (length(startup) > 0) {
+  ## Inject optional shell code
+  writeLines(startup)
+} %>
+
 echo "Load environment modules:"
 <% if (length(modules) > 0) {
   writeLines(c(sprintf("module load %s", modules), "module list"))

inst/templates/sge.tmpl

@@ -25,6 +25,10 @@
   ## As-is resource specifications
   job_declarations <- resources[["asis"]]
   resources[["asis"]] <- NULL
+    
+  ## Shell "startup" code to evaluate
+  startup <- resources[["startup"]]
+  resources[["startup"]] <- NULL
 
   ## Environment modules specifications
   modules <- resources[["modules"]]
@@ -48,6 +52,11 @@ echo "- job name: '<%= job.name %>'"
 echo "- job log file: '<%= log.file %>'"
 echo
 
+<% if (length(startup) > 0) {
+  ## Inject optional shell code
+  writeLines(startup)
+} %>
+
 echo "Load environment modules:"
 <% if (length(modules) > 0) {
   writeLines(c(sprintf("module load %s", modules), "module list"))

inst/templates/slurm.tmpl

@@ -15,6 +15,10 @@
   ## As-is resource specifications
   job_declarations <- resources[["asis"]]
   resources[["asis"]] <- NULL
+    
+  ## Shell "startup" code to evaluate
+  startup <- resources[["startup"]]
+  resources[["startup"]] <- NULL
 
   ## Environment modules specifications
   modules <- resources[["modules"]]
@@ -38,6 +42,11 @@ echo "- job name: '<%= job.name %>'"
 echo "- job log file: '<%= log.file %>'"
 echo
 
+<% if (length(startup) > 0) {
+  ## Inject optional shell code
+  writeLines(startup)
+} %>
+
 echo "Load environment modules:"
 <% if (length(modules) > 0) {
   writeLines(c(sprintf("module load %s", modules), "module list"))

inst/templates/torque.tmpl

@@ -2,7 +2,7 @@
 ######################################################################
 # A batchtools launch script template for TORQUE/PBS
 #
-# Author: Henrik Bengtsson 
+# Author: Henrik Bengtsson
 ######################################################################
 
 ## Job name
@@ -19,6 +19,10 @@
   ## As-is resource specifications
   job_declarations <- resources[["asis"]]
   resources[["asis"]] <- NULL
+    
+  ## Shell "startup" code to evaluate
+  startup <- resources[["startup"]]
+  resources[["startup"]] <- NULL
 
   ## Environment modules specifications
   modules <- resources[["modules"]]
@@ -42,6 +46,11 @@ echo "- job name: '<%= job.name %>'"
 echo "- job log file: '<%= log.file %>'"
 echo
 
+<% if (length(startup) > 0) {
+  ## Inject optional shell code
+  writeLines(startup)
+} %>
+
 echo "Load environment modules:"
 <%
   writeLines(sprintf("module load %s", modules))