batchtools.slurm.tmpl

#!/bin/bash

## Via https://github.com/mllg/batchtools/blob/master/inst/templates/
## Job Resource Interface Definition
##
## ntasks [integer(1)]:       Number of required tasks,
##                            Set larger than 1 if you want to further parallelize
##                            with MPI within your job.
## ncpus [integer(1)]:        Number of required cpus per task,
##                            Set larger than 1 if you want to further parallelize
##                            with multicore/parallel within each task.
## walltime [integer(1)]:     Walltime for this job, in minutes.
##                            Must be at least 1 minute.
## memory   [integer(1)]:     Memory in megabytes for each cpu.
##                            Must be at least 100 (when I tried lower values my
##                            jobs did not start at all).
##
## Default resources can be set in your .batchtools.conf.R by defining the variable
## 'default.resources' as a named list.

<%
# relative paths are not handled well by Slurm
log.file = normalizePath(log.file, winslash = "/", mustWork = FALSE)

#########################
# Set defaults if needed.

if (!"ncpus" %in% names(resources)) {
  resources$ncpus = 1
}

if (!"walltime" %in% names(resources)) {
  # Default time format is minutes but we later divide by 60 so set time in secs.
  # Set 48 hours by default.
  resources$walltime = 48 * 3600
}

if (!"partition" %in% names(resources)) {
  resources$partition = "savio2"
}


if (!"qos" %in% names(resources)) {
  resources$qos = "biostat_savio2_normal"
}


if (!"account" %in% names(resources)) {
  resources$account = "co_biostat"
}
-%>


#SBATCH --job-name=<%= job.name %>
#SBATCH --output=<%= log.file %>
#SBATCH --error=<%= log.file %>
#SBATCH --time=<%= ceiling(resources$walltime / 60) %>
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=<%= resources$ncpus %>
#SBATCH --mem-per-cpu=<%= resources$memory %>
#SBATCH --qos=<%= resources$qos %>
#SBATCH --account=<%= resources$account %>
<%= if (!is.null(resources$partition)) sprintf(paste0("#SBATCH --partition='", resources$partition, "'")) %>
<%= if (array.jobs) sprintf("#SBATCH --array=1-%i", nrow(jobs)) else "" %>

## Initialize work environment like
## source /etc/profile
source /etc/profile

## module add ...

# Load R if we are using the built-in R module.
# Comment out if using a custom compiled version of R.
# module load r

# Load a newer version of gcc than the default. Needed for C++11.
module load gcc/4.8.5

# Load Java if any R packages need RJava (bartMachine, h2o, etc.)
module load java

## Export value of DEBUGME environemnt var to slave
export DEBUGME=<%= Sys.getenv("DEBUGME") %>

## Run R:
## we merge R output with stdout from SLURM, which gets then logged via --output option
Rscript -e 'batchtools::doJobCollection("<%= uri %>")'