batchtools_openlava(): help + add template script

Author: HenrikBengtsson

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: future.batchtools
-Version: 0.12.2-9922
+Version: 0.12.2-9923
 Depends:
     R (>= 3.2.0),
     parallelly,

NEWS.md

@@ -14,7 +14,7 @@
  * Canceling batchtools futures will now interrupt them by default,
    if the backend supports it.
 
- * Add built-in template job script for LSF.
+ * Add built-in template job script for LSF and OpenLava.
 
 ## Documentation
 

R/batchtools_template.R R/BatchtoolsTemplateFutureBackend-class.RR/batchtools_template.R renamed to R/BatchtoolsTemplateFutureBackend-class.R

@@ -32,7 +32,6 @@
 #'    [TORQUE](https://en.wikipedia.org/wiki/TORQUE) / PBS
 #'
 #' @aliases BatchtoolsLsfFutureBackend BatchtoolsOpenLavaFutureBackend BatchtoolsSGEFutureBackend BatchtoolsSlurmFutureBackend BatchtoolsTorqueFutureBackend
-#' @aliases batchtools_openlava
 #'     
 #' @importFrom batchtools makeClusterFunctionsLSF
 #' @importFrom batchtools makeClusterFunctionsOpenLava
@@ -84,30 +83,3 @@ BatchtoolsTemplateFutureBackend <- function(..., template = NULL, type = c("lsf"
   core <- structure(core, class = c("BatchtoolsTemplateFutureBackend", class(core)))
   core
 }
-
-
-#' @export
-BatchtoolsOpenLavaFutureBackend <- function(...) {
-  core <- BatchtoolsTemplateFutureBackend(..., type = "openlava")
-  core[["futureClasses"]] <- c("BatchtoolsOpenLavaFuture", core[["futureClasses"]])
-  core <- structure(core, class = c("BatchtoolsOpenLavaFutureBackend", class(core)))
-  core
-}
-
-#' @export
-batchtools_openlava <- function(...) {
- stop("INTERNAL ERROR: The future.batchtools::batchtools_openlava() must never be called directly")
-}
-class(batchtools_openlava) <- c(
-  "batchtools_openlava", "batchtools_template",
-  "batchtools_multiprocess", "batchtools",
-  "multiprocess", "future", "function"
-)
-attr(batchtools_openlava, "tweakable") <- c(
-  "workers",
-  "finalize",
-  ## Arguments to batchtools::makeClusterFunctionsOpenLava()
-  "scheduler.latency", "fs.latency"
-)
-attr(batchtools_openlava, "init") <- TRUE
-attr(batchtools_openlava, "factory") <- BatchtoolsOpenLavaFutureBackend

R/batchtools_openlava.R

@@ -0,0 +1,63 @@
+#' @export
+BatchtoolsOpenLavaFutureBackend <- function(...) {
+  core <- BatchtoolsTemplateFutureBackend(..., type = "openlava")
+  core[["futureClasses"]] <- c("BatchtoolsOpenLavaFuture", core[["futureClasses"]])
+  core <- structure(core, class = c("BatchtoolsOpenLavaFutureBackend", class(core)))
+  core
+}
+
+
+#' A batchtools openlava backend resolves futures in parallel via a OpenLava 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/openlava.tmpl` part of this package (see below).
+#'
+#' @param \ldots Not used.
+#'
+#' @details
+#' Batchtools openlava futures use \pkg{batchtools} cluster functions
+#' created by [batchtools::makeClusterFunctionsOpenLava()], which requires
+#' that OpenLava commands `sbatch`, `squeue`, and `scancel` are installed on
+#' the current machine.
+#'
+#' The default template script `templates/openlava.tmpl` can be found in:
+#'
+#' ```r
+#' system.file("templates", "openlava.tmpl", package = "future.batchtools")
+#' ```
+#'
+#' and comprise:
+#'
+#' `r paste(c("\x60\x60\x60bash", readLines("inst/templates/openlava.tmpl"), "\x60\x60\x60"), collapse = "\n")`
+#'
+#' @examplesIf interactive()
+#' # Limit runtime to 3 minutes and memory to 200 MiB per future
+#' plan(batchtools_openlava, resources = list(time = "00:03:00", mem = "200M"))
+#'
+#' message("Main process ID: ", Sys.getpid())
+#'
+#' f <- future(Sys.getpid())
+#' pid <- value(f)
+#' message("Worker process ID: ", pid)
+#' 
+#' @export
+batchtools_openlava <- function(..., template = "openlava") {
+ stop("INTERNAL ERROR: The future.batchtools::batchtools_openlava() must never be called directly")
+}
+class(batchtools_openlava) <- c(
+  "batchtools_openlava", "batchtools_template",
+  "batchtools_multiprocess", "batchtools",
+  "multiprocess", "future", "function"
+)
+attr(batchtools_openlava, "tweakable") <- c(
+  "workers",
+  "finalize",
+  ## Arguments to batchtools::makeClusterFunctionsOpenLava()
+  "scheduler.latency", "fs.latency"
+)
+attr(batchtools_openlava, "init") <- TRUE
+attr(batchtools_openlava, "factory") <- BatchtoolsOpenLavaFutureBackend

inst/templates/openlava.tmpl

@@ -0,0 +1,41 @@
+#!/bin/bash
+######################################################################
+# A batchtools launch script template for OpenLava
+#
+# Author: Henrik Bengtsson 
+######################################################################
+
+## Job name:
+#BSUB -J <%= job.name %>
+
+## Direct streams to logfile:
+#BSUB -o <%= log.file %>
+
+## Resources needed:
+<% if (length(resources) > 0) {
+  opts <- unlist(resources, use.names = TRUE)
+  opts <- sprintf("-%s=%s", names(opts), opts)
+  cat(sprintf("#BSUB %s\n", opts))
+<% } %>
+
+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: ${res}"
+echo "Command: Rscript -e 'batchtools::doJobCollection("<%= uri %>")' ... done"
+
+## End-of-job summary
+bjobs -l "${LSB_JOBID}"
+
+## Relay the exit code from Rscript
+exit "${res}"