Module: OffsiteStep

Extended by:
Annotation
Defined in:
lib/scout/offsite/step.rb

Instance Method Summary collapse

Methods included from Annotation

list_tsv_values, load_info, load_tsv, load_tsv_values, obj_tsv_values, resolve_tsv_array, tsv

Instance Method Details

#done? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/scout/offsite/step.rb', line 67

def done?
  status == :done
end

#exec ⇒ Object 



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# File 'lib/scout/offsite/step.rb', line 84

def exec
  bundle_files = offsite_job_ssh <<~EOF
  job.run
  job.bundle_files
  EOF
  SSHLine.sync(bundle_files, source: server)
  self.load
end

#info ⇒ Object 



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# File 'lib/scout/offsite/step.rb', line 55

def info
  info = @info ||= offsite_job_ssh <<~EOF
  info = Open.exists?(job.info_file) ? job.info : {}
  info[:running] = true if job.running?
  info
  EOF

  @info = nil unless %w(done aborted error).include?(info[:status].to_s)

  info
end

#inputs_directory ⇒ Object 



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# File 'lib/scout/offsite/step.rb', line 10

def inputs_directory
  @inputs_directory ||= begin
                          if provided_inputs && provided_inputs.any?
                            file = ".scout/tmp/step_inputs/#{workflow}/#{task_name}/#{name}"
                            TmpFile.with_path do |inputs_dir|
                              save_inputs(inputs_dir)
                              SSHLine.rsync(inputs_dir, file, target: server, directory: true)
                            end
                            file
                          end
                        end
end

#offsite_job_ssh(script) ⇒ Object 



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# File 'lib/scout/offsite/step.rb', line 27

def offsite_job_ssh(script)
  parts = []
  parts << <<~EOF.strip
wf = Workflow.require_workflow "#{workflow_name}";
  EOF

  if inputs_directory
    parts << <<~EOF.strip
job = wf.job(:#{task_name}, "#{clean_name}", :load_inputs => "#{inputs_directory}");
    EOF
  else
    parts << <<~EOF.strip
job = wf.job(:#{task_name}, "#{clean_name}");
    EOF
  end

  parts << script


  SSHLine.scout server, parts * "\n"
end

#offsite_path ⇒ Object 



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# File 'lib/scout/offsite/step.rb', line 49

def offsite_path
  @path = offsite_job_ssh <<~EOF
    job.path.identify
  EOF
end

#orchestrate_slurm ⇒ Object 



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# File 'lib/scout/offsite/step.rb', line 71

def orchestrate_slurm
  bundle_files = offsite_job_ssh <<~EOF
  require 'rbbt/hpc'
  HPC::BATCH_MODULE = HPC.batch_system "SLURM"
  HPC::BATCH_MODULE.orchestrate_job(job, {})
  job.join
  job.bundle_files
  EOF
  SSHLine.sync(bundle_files, source: server)
  self.load
end

#run ⇒ Object 



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# File 'lib/scout/offsite/step.rb', line 93

def run
  if slurm
    orchestrate_slurm
  else
    exec
  end
end

#workflow_name ⇒ Object 



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# File 'lib/scout/offsite/step.rb', line 23

def workflow_name
  @workflow_name || workflow.to_s
end