Built-in templates: Add support 'shutdown' job-script code

Author: HenrikBengtsson

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: future.batchtools
-Version: 0.12.2-9977
+Version: 0.12.2-9978
 Depends:
     R (>= 3.2.0),
     parallelly,

NEWS.md

@@ -40,10 +40,11 @@
      specified, corresponding `module load <name>` entries are
      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 support "startup" and
+     "shutdown" code resource specifications via
+     `resources[["startup"]]` and `resources[["shutdown"]]`. When
+     specified, corresponding lines are injected in the generated job
+     script and the beginning and end, respectively.
 
    - 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

@@ -20,6 +20,10 @@ trap 'echo "ERROR: future.batchtools job script failed on line $LINENO" >&2; exi
   startup <- resources[["startup"]]
   resources[["startup"]] <- NULL
 
+  ## Shell "shutdown" code to evaluate
+  shutdown <- resources[["shutdown"]]
+  resources[["shutdown"]] <- NULL
+     
   ## Environment modules specifications
   modules <- resources[["modules"]]
   resources[["modules"]] <- NULL
@@ -36,4 +40,16 @@ echo "Load environment modules:"
 } %>
 
 # Launch R and evaluate the batchtools R job
+echo "Command: Rscript -e 'batchtools::doJobCollection("<%= uri %>")' ..."
 <%= timeout %> Rscript -e 'batchtools::doJobCollection("<%= uri %>", output = "<%= log.file %>")'
+res=$?
+echo " - exit code: ${res}"
+echo "Command: Rscript -e 'batchtools::doJobCollection("<%= uri %>")' ... done"
+
+<% if (length(shutdown) > 0) {
+  ## Inject optional shell code
+  writeLines(shutdown)
+} %>
+
+## Relay the exit code from Rscript
+exit "${res}"

inst/templates/lsf.tmpl

@@ -21,6 +21,10 @@
   startup <- resources[["startup"]]
   resources[["startup"]] <- NULL
 
+  ## Shell "shutdown" code to evaluate
+  shutdown <- resources[["shutdown"]]
+  resources[["shutdown"]] <- NULL
+     
   ## Environment modules specifications
   modules <- resources[["modules"]]
   resources[["modules"]] <- NULL
@@ -80,5 +84,10 @@ echo "Command: Rscript -e 'batchtools::doJobCollection("<%= uri %>")' ... done"
 ## End-of-job summary
 bjobs -l "${LSB_JOBID}"
 
+<% if (length(shutdown) > 0) {
+  ## Inject optional shell code
+  writeLines(shutdown)
+} %>
+
 ## Relay the exit code from Rscript
 exit "${res}"

inst/templates/openlava.tmpl

@@ -21,6 +21,10 @@
   startup <- resources[["startup"]]
   resources[["startup"]] <- NULL
 
+  ## Shell "shutdown" code to evaluate
+  shutdown <- resources[["shutdown"]]
+  resources[["shutdown"]] <- NULL
+     
   ## Environment modules specifications
   modules <- resources[["modules"]]
   resources[["modules"]] <- NULL
@@ -80,5 +84,10 @@ echo "Command: Rscript -e 'batchtools::doJobCollection("<%= uri %>")' ... done"
 ## End-of-job summary
 bjobs -l "${LSB_JOBID}"
 
+<% if (length(shutdown) > 0) {
+  ## Inject optional shell code
+  writeLines(shutdown)
+} %>
+
 ## Relay the exit code from Rscript
 exit "${res}"

inst/templates/sge.tmpl

@@ -30,6 +30,10 @@
   startup <- resources[["startup"]]
   resources[["startup"]] <- NULL
 
+  ## Shell "shutdown" code to evaluate
+  shutdown <- resources[["shutdown"]]
+  resources[["shutdown"]] <- NULL
+     
   ## Environment modules specifications
   modules <- resources[["modules"]]
   resources[["modules"]] <- NULL
@@ -89,5 +93,10 @@ echo "Command: Rscript -e 'batchtools::doJobCollection("<%= uri %>")' ... done"
 ## End-of-job summary
 qstat -j "${JOB_ID}"
 
+<% if (length(shutdown) > 0) {
+  ## Inject optional shell code
+  writeLines(shutdown)
+} %>
+
 ## Relay the exit code from Rscript
 exit "${res}"

inst/templates/slurm.tmpl

@@ -20,6 +20,10 @@
   startup <- resources[["startup"]]
   resources[["startup"]] <- NULL
 
+  ## Shell "shutdown" code to evaluate
+  shutdown <- resources[["shutdown"]]
+  resources[["shutdown"]] <- NULL
+     
   ## Environment modules specifications
   modules <- resources[["modules"]]
   resources[["modules"]] <- NULL
@@ -79,5 +83,10 @@ echo "Command: Rscript -e 'batchtools::doJobCollection("<%= uri %>")' ... done"
 ## End-of-job summary
 sstat --format="JobID,AveCPU,MaxRSS,MaxPages,MaxDiskRead,MaxDiskWrite" --allsteps --jobs="${SLURM_JOB_ID}"
 
+<% if (length(shutdown) > 0) {
+  ## Inject optional shell code
+  writeLines(shutdown)
+} %>
+
 ## Relay the exit code from Rscript
 exit "${res}"

inst/templates/torque.tmpl

@@ -24,6 +24,10 @@
   startup <- resources[["startup"]]
   resources[["startup"]] <- NULL
 
+  ## Shell "shutdown" code to evaluate
+  shutdown <- resources[["shutdown"]]
+  resources[["shutdown"]] <- NULL
+     
   ## Environment modules specifications
   modules <- resources[["modules"]]
   resources[["modules"]] <- NULL
@@ -83,5 +87,10 @@ echo "Command: Rscript -e 'batchtools::doJobCollection("<%= uri %>")' ... done"
 ## End-of-job summary
 qstat -f "${PBS_JOBID}"
 
+<% if (length(shutdown) > 0) {
+  ## Inject optional shell code
+  writeLines(shutdown)
+} %>
+
 ## Relay the exit code from Rscript
 exit "${res}"