Class: QueueManager

Inherits:
Object
  • Object
show all
Defined in:
lib/autoflow/queue_manager.rb

Direct Known Subclasses

BashManager, SlurmManager, SlurmManager2

Class Method Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(exec_folder, options, commands, persist_variables) ⇒ QueueManager 



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# File 'lib/autoflow/queue_manager.rb', line 4

def initialize(exec_folder, options, commands, persist_variables)
  @exec_folder = exec_folder
  @commands = commands
  @persist_variables = persist_variables
  @verbose = options[:verbose]
  @show_submit = options[:show_submit_command]
  @job_identifier = options[:identifier]
  @files = {}
  @remote = options[:remote]
  @ssh = options[:ssh]
  @write_sh = options[:write_sh]
  @external_dependencies = options[:external_dependencies]
  @active_jobs = []
  @extended_logging = options[:extended_logging]
  @comment = options[:comment]
end

Class Method Details

.available? ⇒ Boolean 



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# File 'lib/autoflow/queue_manager.rb', line 328

def self.available?
  return FALSE
end

.descendants ⇒ Object

SELECT AND PREPARE MANAGER



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# File 'lib/autoflow/queue_manager.rb', line 25

def self.descendants
  ObjectSpace.each_object(Class).select { |klass| klass < self }
end

.priority ⇒ Object 



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# File 'lib/autoflow/queue_manager.rb', line 332

def self.priority
  return -1
end

.select_manager(options) ⇒ Object 



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# File 'lib/autoflow/queue_manager.rb', line 43

def self.select_manager(options)
  queue_manager = nil
  priority = 0
  descendants.each do |descendant|
    if descendant.available?(options) && priority <= descendant.priority
      queue_manager = descendant
      priority = descendant.priority
    end
  end
  return queue_manager
end

.select_queue_manager(exec_folder, options, jobs, persist_variables) ⇒ Object 



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# File 'lib/autoflow/queue_manager.rb', line 29

def self.select_queue_manager(exec_folder, options, jobs, persist_variables)
  path_managers = File.join(File.dirname(__FILE__),'queue_managers')
  Dir.glob(path_managers+'/*').each do |manager|
    require manager
  end
  if options[:batch]
    queue_manager = BashManager
  else
    queue_manager = select_manager(options)
  end
  warn("Selected queue manager: #{queue_manager}")
  return queue_manager.new(exec_folder, options, jobs, persist_variables)
end

.system_call(cmd, path = nil, remote = FALSE, ssh = nil) ⇒ Object 



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# File 'lib/autoflow/queue_manager.rb', line 260

def self.system_call(cmd, path = nil, remote = FALSE, ssh = nil)
  cmd = "cd #{path}; " + cmd if !path.nil?
  if remote
    call = ssh.exec!(cmd)
  else
    call = %x[#{cmd}] 
  end
  return call
end

Instance Method Details

#asign_queue_id(ar_jobs, id) ⇒ Object 



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# File 'lib/autoflow/queue_manager.rb', line 292

def asign_queue_id(ar_jobs, id)
  ar_jobs.each do |id_job, job|
    job.queue_id=id
  end
end

#close_file(file_name, permissions = nil) ⇒ Object

SSH



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# File 'lib/autoflow/queue_manager.rb', line 225

def close_file(file_name, permissions = nil) #SSH
  path, content = @files.delete(file_name)
  file_path = File.join(path, file_name)
  if @remote
    @ssh.exec!("echo '#{content}' > #{file_path}")
    @ssh.exec!("chmod #{permissions} #{file_path}") if !permissions.nil?
  else
    local_file = File.open(file_path,'w')
    local_file.chmod(permissions) if !permissions.nil?
    local_file.print content
    local_file.close
  end
end

#create_file(file_name, path) ⇒ Object 



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# File 'lib/autoflow/queue_manager.rb', line 217

def create_file(file_name, path) 
  @files[file_name] = [path, '']
end

#create_folder(folder_name) ⇒ Object 



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# File 'lib/autoflow/queue_manager.rb', line 209

def create_folder(folder_name)
  if @remote
    @ssh.exec!("if ! [ -d  #{folder_name} ]; then mkdir -p #{folder_name}; fi")
  else
    Dir.mkdir(folder_name) if !File.exists?(folder_name)
  end
end

#exec ⇒ Object

EXECUTING WORKFLOW WITH MANAGER



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# File 'lib/autoflow/queue_manager.rb', line 59

def exec
  create_folder(@exec_folder)
  make_environment_file if !@persist_variables.empty?
  create_file('versions', @exec_folder)
  write_file('versions',"autoflow\t#{Autoflow::VERSION}")
  close_file('versions')
  create_file('index_execution', @exec_folder)
  launch_all_jobs
  close_file('index_execution')
end

#get_all_deps(ar_dependencies) ⇒ Object 



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# File 'lib/autoflow/queue_manager.rb', line 306

def get_all_deps(ar_dependencies)
  final_dep = []
  final_dep.concat(get_queue_system_dependencies(ar_dependencies)) if !ar_dependencies.empty?
  final_dep.concat(@external_dependencies)
  return final_dep
end

#get_dependencies(job, id = nil) ⇒ Object 



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# File 'lib/autoflow/queue_manager.rb', line 285

def get_dependencies(job, id = nil)
  ar_dependencies = []
  ar_dependencies += job.dependencies
  ar_dependencies.delete(id) if !id.nil? #Delete autodependency
  return ar_dependencies
end

#get_queue_system_dependencies(ar_dependencies) ⇒ Object 



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# File 'lib/autoflow/queue_manager.rb', line 298

def get_queue_system_dependencies(ar_dependencies)
  queue_system_ids=[]
  ar_dependencies.each do |dependency|
    queue_system_ids << @commands[dependency].queue_id
  end
  return queue_system_ids
end

#get_queue_system_id(shell_output) ⇒ Object 



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# File 'lib/autoflow/queue_manager.rb', line 324

def get_queue_system_id(shell_output)

end

#get_relations_and_folders ⇒ Object 



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# File 'lib/autoflow/queue_manager.rb', line 90

def get_relations_and_folders
  relations = {}
  @commands.each do |name, job|
    relations[name] = [job.attrib[:exec_folder], job.dependencies]
  end
  return relations
end

#init_log ⇒ Object

TODO adapt to remote execution



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# File 'lib/autoflow/queue_manager.rb', line 70

def init_log #TODO adapt to remote execution
  log_path = [@exec_folder, '.wf_log'].join('/') #Join must assume linux systems so File.join canot be used for windows hosts
  log = parse_log(log_path) #TODO modify to folder
  job_relations_with_folders = get_relations_and_folders
  if @write_sh
    create_file('wf.json', @exec_folder)
    write_file('wf.json', job_relations_with_folders.to_json)
    close_file('wf.json')
  end
    @active_jobs.each do |task|
      query = log[task]
      if query.nil?
      log[task] = {'set' => [Time.now.to_i]}
      else
      log[task]['set'] << Time.now.to_i
      end
  end
  write_log(log, log_path, job_relations_with_folders)
end

#launch2queue_system(job, id, buffered_jobs) ⇒ Object 



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# File 'lib/autoflow/queue_manager.rb', line 155

def launch2queue_system(job, id, buffered_jobs)
  sh_name = job.name+'.sh'
  if @write_sh
    # Write sh file
    #--------------------------------
    create_file(sh_name, job.attrib[:exec_folder])
    write_file(sh_name, '#!/usr/bin/env bash')
    write_file(sh_name, '##JOB_GROUP_ID='+@job_identifier)
    write_header(id, job, sh_name)
  end

  #Get dependencies
  #------------------------------------
  ar_dependencies = get_dependencies(job, id)
  buffered_jobs.each do |id_buff_job, buff_job|
    ar_dependencies += get_dependencies(buff_job, id_buff_job)
    if @write_sh
      write_job(buff_job, sh_name)
      buff_job.attrib[:exec_folder] = job.attrib[:exec_folder]
    end
  end
  ar_dependencies.uniq!

  if @write_sh
    #Write sh body
    #--------------------------------
    write_file(sh_name, 'hostname')
    log_file_path = [@exec_folder, '.wf_log', File.basename(job.attrib[:exec_folder])].join('/')
    write_file(sh_name, "flow_logger -e #{log_file_path} -s #{job.name}")
    write_file(sh_name, "source #{File.join(@exec_folder, 'env_file')}") if !@persist_variables.empty?
    write_job(job, sh_name)
    write_file(sh_name, "flow_logger -e #{log_file_path} -f #{job.name}")
    write_file(sh_name, "echo 'General time'")
    write_file(sh_name, "times")
    close_file(sh_name, 0755)
  end

  #Submit node
  #-----------------------------------
  if !@verbose
    queue_id = submit_job(job, ar_dependencies)
    job.queue_id = queue_id # Returns id of running tag on queue system 
    asign_queue_id(buffered_jobs, queue_id)
  end
end

#launch_all_jobs ⇒ Object 



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# File 'lib/autoflow/queue_manager.rb', line 98

def launch_all_jobs
  buffered_jobs = []
  sorted_jobs = sort_jobs_by_dependencies
  sorted_jobs.each do |name, job|
    @active_jobs << job.name if !job.attrib[:done]
  end
  init_log
  sorted_jobs.each do |name, job|
    write_file('index_execution', "#{name}\t#{job.attrib[:exec_folder]}") 
    if job.attrib[:done]
      next
    else
      rm_done_dependencies(job)
    end 
    buffered_jobs = launch_job_in_folder(job, name, buffered_jobs)
  end
end

#launch_job_in_folder(job, id, buffered_jobs) ⇒ Object 



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# File 'lib/autoflow/queue_manager.rb', line 143

def launch_job_in_folder(job, id, buffered_jobs)
  create_folder(job.attrib[:exec_folder])
  if !job.attrib[:buffer]  # Launch with queue_system the job and all buffered jobs
    launch2queue_system(job, id, buffered_jobs)
    buffered_jobs = []#Clean buffer
  else # Buffer job
    buffered_jobs << [id, job]
  end
  return buffered_jobs 
end

#make_environment_file ⇒ Object 



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# File 'lib/autoflow/queue_manager.rb', line 201

def make_environment_file
  create_file('env_file', @exec_folder)
  @persist_variables.each do |var, value|
    write_file('env_file', "export #{var}=#{value}")
  end
  close_file('env_file')
end

#read_file(file_path) ⇒ Object 



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# File 'lib/autoflow/queue_manager.rb', line 239

def read_file(file_path)
  content = nil
  if @remote
    res = @ssh.exec!("[ ! -f #{file_path} ] && echo 'Autoflow:File Not Found' || cat #{file_path}")
    content = res if !content.include?('Autoflow:File Not Found')
  else
    content = File.open(file_path).read if File.exists?(file_path)
  end
  return content
end

#rm_done_dependencies(job) ⇒ Object 



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# File 'lib/autoflow/queue_manager.rb', line 133

def rm_done_dependencies(job)
  remove=[]
  job.dependencies.each do |dependency|      
    remove << dependency if @commands[dependency].attrib[:done]
  end
  remove.each do |rm|
    job.dependencies.delete(rm)
  end
end

#sort_jobs_by_dependencies ⇒ Object

We need job ids from queue system so we ask for each job and we give the previous queue system ids as dependencies if necessary



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# File 'lib/autoflow/queue_manager.rb', line 116

def sort_jobs_by_dependencies # We need job ids from queue system so we ask for each job and we give the previous queue system ids as dependencies if necessary
  ar_jobs = @commands.to_a
  sorted_jobs = []
  jobs_without_dep = ar_jobs.select{|job| job.last.dependencies.empty?}
  sorted_jobs.concat(jobs_without_dep)
  while ar_jobs.length != sorted_jobs.length
    ids = sorted_jobs.map{|job| job.first}
    ar_jobs.each do |job|
      if !sorted_jobs.include?(job) 
        deps = job.last.dependencies - ids
        sorted_jobs << job if deps.empty?
      end
    end
  end
  return sorted_jobs
end

#submit_job(job, ar_dependencies) ⇒ Object 



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# File 'lib/autoflow/queue_manager.rb', line 320

def submit_job(job, ar_dependencies)

end

#system_call(cmd, path = nil) ⇒ Object 



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# File 'lib/autoflow/queue_manager.rb', line 250

def system_call(cmd, path = nil)
  cmd = "cd #{path}; " + cmd if !path.nil?
  if @remote
    call = @ssh.exec!(cmd)
  else
    call = %x[#{cmd}] 
  end
  return call
end

#write_file(file_name, content) ⇒ Object 



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# File 'lib/autoflow/queue_manager.rb', line 221

def write_file(file_name, content)
  @files[file_name].last << content+"\n"
end

#write_header(id, node, sh) ⇒ Object

QUEUE DEPENDANT METHODS



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# File 'lib/autoflow/queue_manager.rb', line 316

def write_header(id, node, sh)

end

#write_job(job, sh_name) ⇒ Object 



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# File 'lib/autoflow/queue_manager.rb', line 270

def write_job(job, sh_name) 
  write_file(sh_name, job.initialization) if !job.initialization.nil?
  if @comment
    cmd = '#' + job.parameters
  else
    if @extended_logging
      log_command = '/usr/bin/time -o process_data -v '
    else
      log_command = 'time '
    end
    cmd = log_command + job.parameters
  end
  write_file(sh_name, cmd)
end