Module: HPC::Orchestration

Included in:
LSF, SLURM
Defined in:
lib/rbbt/hpc/orchestrate.rb

Instance Method Summary collapse

Instance Method Details

#get_chains(job, rules, chains = {}) ⇒ Object 



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# File 'lib/rbbt/hpc/orchestrate.rb', line 75

def get_chains(job, rules, chains = {})
  job_rules = self.job_rules(rules, job)
  job_deps = get_job_dependencies(job)

  input_deps = []
  job.rec_dependencies.each do |dep|
    input_deps.concat dep.input_dependencies
  end

  job_deps.each do |dep|
    input_deps.concat dep.input_dependencies
    get_chains(dep, rules, chains)
  end

  job_deps.select do |dep|
    chained = job_rules["chain_tasks"] &&
      job_rules["chain_tasks"][job.workflow.to_s] && job_rules["chain_tasks"][job.workflow.to_s].include?(job.task_name.to_s)  &&
      job_rules["chain_tasks"][dep.workflow.to_s] && job_rules["chain_tasks"][dep.workflow.to_s].include?(dep.task_name.to_s) 

    dep_skip = dep.done? && ! input_deps.include?(dep) && self.job_rules(rules, dep)["skip"] 
    chained || dep_skip
  end.each do |dep|
    chains[job] ||= [] 
    chains[job] << dep 
    chains[job].concat chains[dep] if chains[dep]
  end

  chains
end

#get_job_dependencies(job, job_rules = nil) ⇒ Object 



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# File 'lib/rbbt/hpc/orchestrate.rb', line 56

def get_job_dependencies(job, job_rules = nil)
  deps = job.dependencies || []
  deps += job.input_dependencies || []
  deps
end

#get_recursive_job_dependencies(job) ⇒ Object 



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# File 'lib/rbbt/hpc/orchestrate.rb', line 62

def get_recursive_job_dependencies(job)
  deps = get_job_dependencies(job) 
  (deps + deps.collect{|dep| get_recursive_job_dependencies(dep) }).flatten
end

#job_rules(rules, job) ⇒ Object 



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# File 'lib/rbbt/hpc/orchestrate.rb', line 5

def job_rules(rules, job)
  workflow = job.workflow.to_s
  task_name = job.task_name.to_s
  task_name = job.overriden.to_s if Symbol === job.overriden

  defaults = rules["defaults"] || {}
  defaults = defaults.merge(rules[workflow]["defaults"] || {}) if rules[workflow]

  job_rules = IndiferentHash.setup(defaults.dup)

  rules["chains"].each do |name,info|
    IndiferentHash.setup(info)
    chain_tasks = info[:tasks].split(/,\s*/)

    chain_tasks.each do |task|
      task_workflow, chain_task = task.split("#")
      chain_task, task_workflow = task_workflow, info[:workflow] if chain_task.nil? or chain_tasks.empty?
      job_rules["chain_tasks"] ||= {}
      job_rules["chain_tasks"][task_workflow] ||= []
      job_rules["chain_tasks"][task_workflow]  << chain_task
      next unless task_name == chain_task.to_s && workflow == task_workflow.to_s
      config_keys = job_rules.delete :config_keys
      job_rules = IndiferentHash.setup(job_rules.merge(info)) 
      if config_keys
        config_keys.gsub!(/,\s+/,',') 
        job_rules[:config_keys] = job_rules[:config_keys] ? config_keys + "," + job_rules[:config_keys] : config_keys
      end
    end

    if job_rules["chain_tasks"][workflow] && job_rules["chain_tasks"][workflow].include?(task_name)
      break
    else
      job_rules.delete "chain_tasks" 
    end
  end if rules["chains"]

  config_keys = job_rules.delete :config_keys
  job_rules = IndiferentHash.setup(job_rules.merge(rules[workflow][task_name])) if rules[workflow] && rules[workflow][task_name]

  if config_keys
    config_keys.gsub!(/,\s+/,',') 
    job_rules[:config_keys] = job_rules[:config_keys] ? config_keys + "," + job_rules[:config_keys] : config_keys
  end

  if rules["skip"] && rules["skip"][workflow]
    job_rules["skip"] = true if rules["skip"][workflow].split(/,\s*/).include? task_name
  end

  job_rules
end

#orchestrate_job(job, options) ⇒ Object 



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# File 'lib/rbbt/hpc/orchestrate.rb', line 193

def orchestrate_job(job, options)
  options.delete "recursive_clean"
  options.delete "clean_task"
  options.delete "clean"
  options.delete "tail"
  options.delete "printpath"
  options.delete "detach"
  options.delete "jobname"

  rules = YAML.load(Open.read(options[:orchestration_rules])) if options[:orchestration_rules]
  rules ||= {}
  IndiferentHash.setup(rules)

  chains = get_chains(job, rules)

  workload(job, rules, chains, options)
end

#piggyback(job, job_rules, job_deps) ⇒ Object 



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# File 'lib/rbbt/hpc/orchestrate.rb', line 67

def piggyback(job, job_rules, job_deps)
  return false unless job_rules["skip"]
  final_deps = job_deps - job_deps.collect{|dep| get_recursive_job_dependencies(dep)}.flatten.uniq
  final_deps = final_deps.reject{|dep| dep.done? }
  return final_deps.first if final_deps.length == 1
  return false
end

#workload(job, rules, chains, options, seen = nil) ⇒ Object 



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# File 'lib/rbbt/hpc/orchestrate.rb', line 105

def workload(job, rules, chains, options, seen = nil)
  return [] if job.done?
  if seen.nil?
    seen = {}
    target_job = true
  end

  job_rules = self.job_rules(rules, job)
  job_deps = get_job_dependencies(job)

  chain = chains[job]
  chain = chain.reject{|j| seen.include? j.path} if chain
  chain = chain.reject{|dep| dep.done? } if chain
  piggyback = piggyback(job, job_rules, job_deps)
  dep_ids = job_deps.collect do |dep|
    seen[dep.path] ||= nil if chain && chain.include?(dep) #&& ! job.input_dependencies.include?(dep) 
    next_options = IndiferentHash.setup(options.dup)
    if piggyback and piggyback == dep
      next_options[:piggyback] ||= []
      next_options[:piggyback].push job
      ids = workload(dep, rules, chains, next_options, seen)
    else
      next_options.delete :piggyback
      ids = workload(dep, rules, chains, next_options, seen)
    end

    ids = [ids].flatten.compact.collect{|id| ['canfail', id] * ":"} if job.canfail_paths.include? dep.path

    seen[dep.path] = ids
    ids
  end.compact.flatten.uniq

  return seen[job.path] || dep_ids if seen.include?(job.path)

  if piggyback and seen[piggyback.path]
    return seen[job.path] = seen[piggyback.path] 
  end

  job_rules.delete :chain_tasks
  job_rules.delete :tasks
  job_rules.delete :workflow
  

  job_options = IndiferentHash.setup(options.merge(job_rules).merge(:batch_dependencies => dep_ids))
  job_options.delete :orchestration_rules

  config_keys = job_rules.delete(:config_keys)
  if config_keys
    config_keys.gsub!(/,\s+/,',') 
    job_options[:config_keys] = job_options[:config_keys] ? config_keys + "," + job_options[:config_keys] : config_keys
  end

  if options[:piggyback]
    manifest = options[:piggyback].uniq
    manifest += [job]
    manifest.concat chain if chain

    job = options[:piggyback].first

    job_rules = self.job_rules(rules, job)
    new_config_keys = self.job_rules(rules, job)[:config_keys]
    if new_config_keys
      new_config_keys = new_config_keys.gsub(/,\s+/,',') 
      job_options[:config_keys] = job_options[:config_keys] ? new_config_keys + "," + job_options[:config_keys] : new_config_keys
    end

    job_options.delete :piggyback
  else
    manifest = [job]
    manifest.concat chain if chain
  end

  manifest.uniq!

  job_options[:manifest] = manifest.collect{|j| j.task_signature }

  job_options[:config_keys] = job_options[:config_keys].split(",").uniq * "," if job_options[:config_keys]

  if options[:dry_run]
    puts Log.color(:magenta, "Manifest: ") + Log.color(:blue, job_options[:manifest] * ", ") + " - tasks: #{job_options[:task_cpus] || 1} - time: #{job_options[:time]} - config: #{job_options[:config_keys]}"
    puts Log.color(:yellow, "Deps: ") + Log.color(:blue, job_options[:batch_dependencies]*", ")
    job_options[:manifest].first
  else
    run_job(job, job_options)
  end
end