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#!/usr/bin/env bash
## Job name:
#$ -N fbt-<%= job.hash %>
## Merge standard error and output:
#$ -j y
## Direct streams to logfile:
#$ -o <%= log.file %>
## Email on abort (a) and termination (e), but not when starting (b)
#PBS -m ae
## Tell the queue system to use the current directory
## as the working directory
## -cwd
## Mirror environment variables
#$ -V
## Resources needed:
<% if (exists("resources", mode = "list") && length(resources) > 0) {
if (isTRUE(getOption("future.debug"))) {
R.utils::mcat("resources:")
R.utils::mstr(resources)
}
cat(sprintf("#$ %s\n", resources[["custom"]]))
} %>
## UCSF HPC Pilot specific
#$ -S /bin/bash # Required
#$ -l mem_free=1G # Memory usage, required. Note that this is per slot
#$ -R yes # SGE host reservation, highly recommended
## SPECIAL: For R CMD check package testing on HPC environments, which
## typically uses a temporary working directory that is local, we force
## it to use HPC-wide working directory
#$ -wd ~/tmp
## SPECIAL: Since we change working directory, the 'startup.Rs' file used
## by R CMD check is no longer found
export R_TESTS=
# For troubleshooting if there are errors
date
hostname
which Rscript
Rscript --version
Rscript -e ".libPaths()"
echo "Command: Rscript -e 'batchtools::doJobCollection("<%= uri %>")' ..."
Rscript -e 'batchtools::doJobCollection("<%= uri %>")'
echo "Command: Rscript -e 'batchtools::doJobCollection("<%= uri %>")' ... done"
## For troubleshooting if there are errors
## https://github.com/UCSF-HPC/pilot-testing/issues/1
qstat -j $JOB_ID
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