class WorkflowManager::HydraCluster
Public Instance Methods
cluster_nodes()
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# File lib/workflow_manager/cluster.rb, line 346 def cluster_nodes # TODO nodes = { 'cluster/largemem' => 'cluster/largemem', } end
copy_commands(org_dir, dest_parent_dir, now=nil)
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# File lib/workflow_manager/cluster.rb, line 336 def copy_commands(org_dir, dest_parent_dir, now=nil) # TODO end
delete_command(target)
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# File lib/workflow_manager/cluster.rb, line 343 def delete_command(target) # TODO end
job_ends?(log_file)
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# File lib/workflow_manager/cluster.rb, line 330 def job_ends?(log_file) # TODO end
job_pending?(job_id)
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# File lib/workflow_manager/cluster.rb, line 333 def job_pending?(job_id) # TODO end
job_running?(job_id)
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# File lib/workflow_manager/cluster.rb, line 327 def job_running?(job_id) # TODO end
kill_command(job_id)
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# File lib/workflow_manager/cluster.rb, line 339 def kill_command(job_id) # TODO command = "ssh hydra; scancel #{job_id}" end
submit_job(script_file, script_content, option='')
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# File lib/workflow_manager/cluster.rb, line 313 def submit_job(script_file, script_content, option='') # TODO if script_name = File.basename(script_file) and script_name =~ /\.sh$/ new_job_script = generate_new_job_script(script_name, script_content) new_job_script_base = File.basename(new_job_script) log_file = File.join(@log_dir, new_job_script_base + "_o.log") err_file = File.join(@log_dir, new_job_script_base + "_e.log") #command = "g-sub -o #{log_file} -e #{err_file} #{option} #{new_job_script}" command = "cat #{new_job_script} |ssh hydra 'cat > #{new_job_script_base}; source /etc/profile; module load cluster/largemem; sbatch #{new_job_script_base};'" job_id = `#{command}` job_id = job_id.match(/Submitted batch job (\d+)/)[1] [job_id, log_file, command] end end