Add support for setting environment variables in the built-in job script templates [#99]

Author: HenrikBengtsson

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: future.batchtools
-Version: 0.20.0-9020
+Version: 0.20.0-9021
 Depends:
     R (>= 3.2.0),
     parallelly,

NEWS.md

@@ -10,6 +10,9 @@
    script templates. This can be done via fields 'rscript' and
    'rscript_args' of the 'resources' argument.
 
+ * Add support for setting environment variables in the built-in job
+   script templates. This can be done via field 'envs'.
+ 
  * The built-in job script templates assert that the `Rscript`
    launcher is found, and if not, they give an informative error
    message suggesting to declare environment modules, via the

R/BatchtoolsFutureBackend-class.R

@@ -30,18 +30,27 @@
 #' job-script template as variable `resources`. This is based on how
 #' [batchtools::submitJobs()] works, with the exception for specially
 #' reserved names defined by the \pkg{future.batchtools} package;
+#'
 #' * `resources[["modules"]]` is character vector of Linux environment
 #'   modules to be loaded.
+#'
 #' * `resources[["startup"]]` and `resources[["shutdown"]]` are character
 #'   vectors of shell code to be injected to the job script as-is.
+#'
 #' * `resources[["details"]]`, if TRUE, results in the job script outputting
 #'   job details and job summaries at the beginning and at the end.
+#'
 #' * `resources[["rscript"]]` is an optional character vector specifying
 #'   how the 'Rscript' is launched. The `resources[["rscript_args"]]` field
 #'   is an optional character vector specifying the 'Rscript' command-line
 #'   arguments.
+#'
+#' * `resources[["envs"]]`, is an optional names character vector specifying
+#'   environment variables to be set.
+#'
 #' * `resources[["asis"]]` is a character vector that are passed as-is to
 #'   the job script and are injected as job resource declarations.
+#'
 #' * All remaining `resources` named elements are injected as named resource
 #'   specification for the scheduler.
 #'

inst/templates/lsf.tmpl

@@ -42,6 +42,13 @@
   resources[["rscript_args"]] <- NULL
   rscript_call <- paste(c(rscript, rscript_args), collapse = " ")
 
+  ## Environment variables to be set
+  envs <- resources[["envs"]]
+  if (length(envs) > 0) {
+    stopifnot(is.character(envs), !is.null(names(envs)))
+  }
+  resources[["envs"]] <- NULL
+    
   ## As-is resource specifications
   job_declarations <- resources[["asis"]]
   resources[["asis"]] <- NULL
@@ -79,6 +86,14 @@ fi
   writeLines(startup)
 } %>
 
+<% if (length(envs) > 0) {
+  writeLines(c(
+    sprintf("echo 'Setting environment variables: [n=%d]'", length(envs)),
+    sprintf("echo ' - %s=%s'", names(envs), shQuote(envs)),
+    sprintf("export %s=%s", names(envs), shQuote(envs))
+  ))
+} %>
+
 <% if (length(modules) > 0) {
   writeLines(c(
     "echo 'Load environment modules:'",

inst/templates/openlava.tmpl

@@ -42,6 +42,13 @@
   resources[["rscript_args"]] <- NULL
   rscript_call <- paste(c(rscript, rscript_args), collapse = " ")
 
+  ## Environment variables to be set
+  envs <- resources[["envs"]]
+  if (length(envs) > 0) {
+    stopifnot(is.character(envs), !is.null(names(envs)))
+  }
+  resources[["envs"]] <- NULL
+    
   ## As-is resource specifications
   job_declarations <- resources[["asis"]]
   resources[["asis"]] <- NULL
@@ -79,6 +86,14 @@ fi
   writeLines(startup)
 } %>
 
+<% if (length(envs) > 0) {
+  writeLines(c(
+    sprintf("echo 'Setting environment variables: [n=%d]'", length(envs)),
+    sprintf("echo ' - %s=%s'", names(envs), shQuote(envs)),
+    sprintf("export %s=%s", names(envs), shQuote(envs))
+  ))
+} %>
+
 <% if (length(modules) > 0) {
   writeLines(c(
     "echo 'Load environment modules:'",

inst/templates/sge.tmpl

@@ -51,6 +51,13 @@
   resources[["rscript_args"]] <- NULL
   rscript_call <- paste(c(rscript, rscript_args), collapse = " ")
 
+  ## Environment variables to be set
+  envs <- resources[["envs"]]
+  if (length(envs) > 0) {
+    stopifnot(is.character(envs), !is.null(names(envs)))
+  }
+  resources[["envs"]] <- NULL
+    
   ## As-is resource specifications
   job_declarations <- resources[["asis"]]
   resources[["asis"]] <- NULL
@@ -88,6 +95,14 @@ fi
   writeLines(startup)
 } %>
 
+<% if (length(envs) > 0) {
+  writeLines(c(
+    sprintf("echo 'Setting environment variables: [n=%d]'", length(envs)),
+    sprintf("echo ' - %s=%s'", names(envs), shQuote(envs)),
+    sprintf("export %s=%s", names(envs), shQuote(envs))
+  ))
+} %>
+
 <% if (length(modules) > 0) {
   writeLines(c(
     "echo 'Load environment modules:'",

inst/templates/slurm.tmpl

@@ -40,7 +40,14 @@
   rscript_args <- resources[["rscript_args"]]
   resources[["rscript_args"]] <- NULL
   rscript_call <- paste(c(rscript, rscript_args), collapse = " ")
-     
+  
+  ## Environment variables to be set
+  envs <- resources[["envs"]]
+  if (length(envs) > 0) {
+    stopifnot(is.character(envs), !is.null(names(envs)))
+  }
+  resources[["envs"]] <- NULL
+    
   ## As-is resource specifications
   job_declarations <- resources[["asis"]]
   resources[["asis"]] <- NULL
@@ -78,6 +85,14 @@ fi
   writeLines(startup)
 } %>
 
+<% if (length(envs) > 0) {
+  writeLines(c(
+    sprintf("echo 'Setting environment variables: [n=%d]'", length(envs)),
+    sprintf("echo ' - %s=%s'", names(envs), shQuote(envs)),
+    sprintf("export %s=%s", names(envs), shQuote(envs))
+  ))
+} %>
+
 <% if (length(modules) > 0) {
   writeLines(c(
     "echo 'Load environment modules:'",

inst/templates/torque.tmpl

@@ -45,6 +45,13 @@
   resources[["rscript_args"]] <- NULL
   rscript_call <- paste(c(rscript, rscript_args), collapse = " ")
 
+  ## Environment variables to be set
+  envs <- resources[["envs"]]
+  if (length(envs) > 0) {
+    stopifnot(is.character(envs), !is.null(names(envs)))
+  }
+  resources[["envs"]] <- NULL
+    
   ## As-is resource specifications
   job_declarations <- resources[["asis"]]
   resources[["asis"]] <- NULL
@@ -82,6 +89,14 @@ fi
   writeLines(startup)
 } %>
 
+<% if (length(envs) > 0) {
+  writeLines(c(
+    sprintf("echo 'Setting environment variables: [n=%d]'", length(envs)),
+    sprintf("echo ' - %s=%s'", names(envs), shQuote(envs)),
+    sprintf("export %s=%s", names(envs), shQuote(envs))
+  ))
+} %>
+
 <% if (length(modules) > 0) {
   writeLines(c(
     "echo 'Load environment modules:'",