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Contents
#!/usr/bin/env ruby
require 'rbbt/util/simpleopt'
require 'rbbt/workflow'
require 'rbbt/workflow/usage'
require 'rbbt/hpc'
require 'time'
$slurm_options = SOPT.get <<EOF
-dr--dry_run Print only the template
-cj--clean_job Clean job
--drbbt* Use development version of rbbt
-sing--singularity Use Singularity
-si--singularity_img* Singularity image to use
-ug--user_group* Use alternative user group for group project directory
-c--contain* Contain in directory (using Singularity)
-s--sync* Contain in directory and sync jobs
-e--exclusive Make exclusive use of the node
-hm--highmem Make use of highmem cores
-wc--wipe_container* Wipe the jobs from the contain directory
-CS--contain_and_sync Contain and sync to default locations
-ci--copy_image When using a container directory, copy image there
-t--tail Tail the logs
-BPP--batch_procpath* Save Procpath performance for batch job; specify only options
-q--queue* Queue
-t--task_cpus* Tasks
-W--workflows* Additional workflows
-tm--time* Time
-rmb--remove_batch_dir Remove the batch working directory (command, STDIN, exit status, ...)
-bs--batch_system* Batch system to use: auto, lsf, slurm (default is auto-detect)
EOF
batch_system = $slurm_options.delete :batch_system
batch_system ||= 'auto'
HPC::BATCH_MODULE = HPC.batch_system batch_system
raise ParameterException.new("Could not detect batch_system: #{Misc.fingerprint batch_system}") if HPC::BATCH_MODULE.nil?
class Step
def run(*args)
if done?
self.load
else
begin
Log.debug "Issuing SLURM job for #{self.path}"
HPC::BATCH_MODULE.run_job(self, SOPT::GOT_OPTIONS.merge($slurm_options))
rescue HPC::SBATCH
end
end
end
end
ARGV.concat ["-W", $slurm_options[:workflows]] if $slurm_options[:workflows]
load Rbbt.share.rbbt_commands.workflow.task.find
Version data entries
11 entries across 9 versions & 1 rubygems