batchtools_torque(): help + tweak template script

Author: HenrikBengtsson

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: future.batchtools
-Version: 0.12.2-9920
+Version: 0.12.2-9921
 Depends:
     R (>= 3.2.0),
     parallelly,

R/batchtools_template.R

@@ -32,7 +32,7 @@
 #'    [TORQUE](https://en.wikipedia.org/wiki/TORQUE) / PBS
 #'
 #' @aliases BatchtoolsLsfFutureBackend BatchtoolsOpenLavaFutureBackend BatchtoolsSGEFutureBackend BatchtoolsSlurmFutureBackend BatchtoolsTorqueFutureBackend
-#' @aliases batchtools_lsf batchtools_openlava batchtools_torque
+#' @aliases batchtools_lsf batchtools_openlava
 #'     
 #' @importFrom batchtools makeClusterFunctionsLSF
 #' @importFrom batchtools makeClusterFunctionsOpenLava
@@ -138,31 +138,3 @@ attr(batchtools_openlava, "tweakable") <- c(
 )
 attr(batchtools_openlava, "init") <- TRUE
 attr(batchtools_openlava, "factory") <- BatchtoolsOpenLavaFutureBackend
-
-
-
-#' @export
-BatchtoolsTorqueFutureBackend <- function(...) {
-  core <- BatchtoolsTemplateFutureBackend(..., type = "torque")
-  core[["futureClasses"]] <- c("BatchtoolsTorqueFuture", core[["futureClasses"]])
-  core <- structure(core, class = c("BatchtoolsTorqueFutureBackend", class(core)))
-  core
-}
-
-#' @export
-batchtools_torque <- function(...) {
- stop("INTERNAL ERROR: The future.batchtools::batchtools_torque() must never be called directly")
-}
-class(batchtools_torque) <- c(
-  "batchtools_torque", "batchtools_template",
-  "batchtools_multiprocess", "batchtools",
-  "multiprocess", "future", "function"
-)
-attr(batchtools_torque, "tweakable") <- c(
-  "workers",
-  "finalize",
-  ## Arguments to batchtools::makeClusterFunctionsTORQUE()
-  "scheduler.latency", "fs.latency"
-)
-attr(batchtools_torque, "init") <- TRUE
-attr(batchtools_torque, "factory") <- BatchtoolsTorqueFutureBackend

R/batchtools_torque.R

@@ -0,0 +1,62 @@
+#' @export
+BatchtoolsTorqueFutureBackend <- function(...) {
+  core <- BatchtoolsTemplateFutureBackend(..., type = "torque")
+  core[["futureClasses"]] <- c("BatchtoolsTorqueFuture", core[["futureClasses"]])
+  core <- structure(core, class = c("BatchtoolsTorqueFutureBackend", class(core)))
+  core
+}
+
+#' A batchtools TORQUE backend resolves futures in parallel via a TORQUE/PBS job scheduler
+#'
+#' @inheritParams BatchtoolsFutureBackend
+#' @inheritParams BatchtoolsTemplateFutureBackend
+#'
+#' @param template (optional) Name of job-script template to be searched
+#' for by [batchtools::findTemplateFile()]. If not found, it defaults to
+#' the `templates/torque.tmpl` part of this package (see below).
+#'
+#' @param \ldots Not used.
+#'
+#' @details
+#' Batchtools torque futures use \pkg{batchtools} cluster functions
+#' created by [batchtools::makeClusterFunctionsTORQUE()], which requires
+#' that TORQUE commands `qsub`, `qselect`, and `qdel` are installed on
+#' the current machine.
+#'
+#' The default template script `templates/torque.tmpl` can be found in:
+#'
+#' ```r
+#' system.file("templates", "torque.tmpl", package = "future.batchtools")
+#' ```
+#'
+#' and comprise:
+#'
+#' `r paste(c("\x60\x60\x60bash", readLines("inst/templates/torque.tmpl"), "\x60\x60\x60"), collapse = "\n")`
+#'
+#' @examplesIf interactive()
+#' # Limit runtime to 3 minutes and memory to 200 MiB per future
+#' plan(batchtools_torque, resources = list(walltime = "00:03:00", mem = "200mb"))
+#'
+#' message("Main process ID: ", Sys.getpid())
+#'
+#' f <- future(Sys.getpid())
+#' pid <- value(f)
+#' message("Worker process ID: ", pid)
+#' 
+#' @export
+batchtools_torque <- function(..., template = "torque") {
+ stop("INTERNAL ERROR: The future.batchtools::batchtools_torque() must never be called directly")
+}
+class(batchtools_torque) <- c(
+  "batchtools_torque", "batchtools_template",
+  "batchtools_multiprocess", "batchtools",
+  "multiprocess", "future", "function"
+)
+attr(batchtools_torque, "tweakable") <- c(
+  "workers",
+  "finalize",
+  ## Arguments to batchtools::makeClusterFunctionsTORQUE()
+  "scheduler.latency", "fs.latency"
+)
+attr(batchtools_torque, "init") <- TRUE
+attr(batchtools_torque, "factory") <- BatchtoolsTorqueFutureBackend

inst/templates/torque.tmpl

@@ -1,12 +1,12 @@
 #!/bin/bash
 ######################################################################
-# A batchtools launch script template for Torque/PBS
+# A batchtools launch script template for TORQUE/PBS
 #
 # Author: Henrik Bengtsson 
 ######################################################################
 
 ## Job name:
-#PBS -N <%= if (exists("job.name", mode = "character")) job.name else job.hash %>
+#PBS -N <%= job.name %>
 
 ## Direct streams to logfile:
 #PBS -o <%= log.file %>
@@ -25,5 +25,24 @@
 #PBS -l <%= opts %>
 <% } %>
 
-## Launch R and evaluated the batchtools R job
+echo "Batchtools job name: '<%= job.name %>'"
+
+echo "Session information:"
+date
+hostname
+which Rscript
+Rscript --version
+Rscript -e ".libPaths()"
+
+## Launch R and evaluate the batchtools R job
+echo "Command: Rscript -e 'batchtools::doJobCollection("<%= uri %>")' ..."
 Rscript -e 'batchtools::doJobCollection("<%= uri %>")'
+res=$?
+echo " - exit code: ${res}"
+echo "Command: Rscript -e 'batchtools::doJobCollection("<%= uri %>")' ... done"
+
+## End-of-job summary
+qstat -f "${PBS_JOBID}"
+
+## Relay the exit code from Rscript
+exit "${res}"