Module: HPC::TemplateGeneration

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

Instance Method Summary collapse

Instance Method Details

#batch_options(job, options) ⇒ Object 



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# File 'lib/rbbt/hpc/batch.rb', line 146

def batch_options(job, options)
  IndiferentHash.setup(options)

  batch_options = IndiferentHash.setup({})

  keys = [
    :queue,
    :account,
    :partition,
    :exclusive,
    :highmem,
    :time,
    :nodes,
    :task_cpus,
    :mem,
    :mem_per_cpu,
    :gres,
    :lua_modules,
    :conda,
    :contraints,
    :licenses,
    :batch_dir,
    :batch_name,
    :contain,
    :sync,
    :contain_and_sync,
    :copy_image,
    :drbbt,
    :env_cmd,
    :manifest,
    :user_group,
    :wipe_container,
    :workdir,
    :purge_deps,
    :singularity,
    :singularity_img,
    :singularity_mounts,
    :singularity_opt_dir,
    :singularity_ruby_inline
  ]

  keys.each do |key|
    next if options[key].nil?
    batch_options[key] = Misc.process_options options, key
  end

  batch_dir = batch_options[:batch_dir]

  batch_name = File.basename(batch_dir)
  inputs_dir = File.join(batch_dir, 'inputs_dir')

  keys_from_config = [
    :queue,
    :highmem,
    :exclusive,
    :env_cmd,
    :user_group,
    :singularity_img,
    :singularity_mounts,
    :singularity_opt_dir,
    :singularity_ruby_inline,
    :singularity
  ]

  keys_from_config.each do |key|
    next unless batch_options.include? key
    default_value = Rbbt::Config.get(key, "batch_#{key}", "batch")
    next if default_value.nil? 
    Misc.add_defaults batch_options, default_value
  end

  user = batch_options[:user] ||= ENV['USER'] || `whoami`.strip
  group = batch_options[:group] ||= File.basename(File.dirname(ENV['HOME']))
  batch_options[:scratch_group_dir] = File.join('/gpfs/scratch/', group)
  batch_options[:projects_group_dir] = File.join('/gpfs/projects/', group)

  batch_options[:singularity] = true if batch_options[:singularity_img]

  if batch_options[:contain_and_sync]
    if batch_options[:contain].nil?
      contain_base = Rbbt::Config.get(:contain_base_dir, :batch_contain, :batch, :default => "/scratch/tmp/rbbt-[USER]")
      contain_base = contain_base.sub('[USER]', user)
      random_file = TmpFile.random_name
      batch_options[:contain] = File.join(contain_base, random_file)
    end

    batch_options[:sync] ||= "~/.rbbt/var/jobs" 
    batch_options[:wipe_container] ||= 'post'
  end

  if batch_options[:contain] && ! batch_options[:hardened]
    options[:workdir_all] = batch_options[:contain]
  end

  Misc.add_defaults batch_options, 
    :batch_name => batch_name,
    :inputs_dir => inputs_dir, 
    :nodes => 1, 
    :step_path => job.path,
    :task_cpus => 1,
    :time => '2min', 
    :env_cmd => '_JAVA_OPTIONS="-Xms1g -Xmx${MAX_MEMORY}m"',
    :singularity_img => ENV["SINGULARITY_IMG"] || "~/rbbt.singularity.img",
    :singularity_ruby_inline => ENV["SINGULARITY_RUBY_INLINE"] || "~/.singularity_ruby_inline",
    :singularity_opt_dir => ENV["SINGULARITY_OPT_DIR"] || "~/singularity_opt",
    :workdir => Dir.pwd 

  exec_cmd = exec_cmd(job, batch_options)
  rbbt_cmd = rbbt_job_exec_cmd(job, options)

  Misc.add_defaults batch_options, 
    :exec_cmd => exec_cmd,
    :rbbt_cmd => rbbt_cmd

  batch_dir = batch_options[:batch_dir]

  Misc.add_defaults batch_options,
    :fout   => File.join(batch_dir, 'std.out'),
    :ferr   => File.join(batch_dir, 'std.err'),
    :fjob   => File.join(batch_dir, 'job.id'),
    :fdep   => File.join(batch_dir, 'dependencies.list'),
    :fcfdep => File.join(batch_dir, 'canfail_dependencies.list'),
    :fexit  => File.join(batch_dir, 'exit.status'),
    :fsync  => File.join(batch_dir, 'sync.log'),
    :fsexit  => File.join(batch_dir, 'sync.status'),
    :fenv  => File.join(batch_dir, 'env.vars'),
    :fcmd   => File.join(batch_dir, 'command.batch')

  batch_options
end

#batch_system_variables ⇒ Object 



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# File 'lib/rbbt/hpc/batch.rb', line 315

def batch_system_variables
  "let MAX_MEMORY=\"$(grep MemTotal /proc/meminfo|grep -o \"[[:digit:]]*\") / 1024\"\n"
end

#cleanup_environment(options = {}) ⇒ Object 



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# File 'lib/rbbt/hpc/batch.rb', line 449

def cleanup_environment(options = {})
  cleanup_environment = ""

  cleanup_environment +="if [ $exit_status == '0' ]; then\n\#{options[:exec_cmd]} workflow forget_deps --purge --recursive_purge \"$step_path\" 2>1 >> '\#{options[:fsync]}'\nfi\n" if options[:purge_deps]

  if options[:sync]
    if options[:wipe_container] == 'force'
      cleanup_environment +="batch_erase_contain_dir\n"
    elsif options[:wipe_container] == 'post' || options[:wipe_container] == 'both'
      cleanup_environment +="if [ $sync_es == '0' -a $empty_contain_dir == 'true' ]; then\nbatch_erase_contain_dir\nfi\n"
    end
  end
  cleanup_environment
end

#coda(options) ⇒ Object 



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# File 'lib/rbbt/hpc/batch.rb', line 474

def coda(options)
  coda ="echo $exit_status > '\#{options[:fexit]}'\n"

  if options[:sync]
    coda +="if [ $sync_es == '0' ]; then\nexit $exit_status\nelse\nexit $sync_es\nfi\n"
  else
    coda +="exit $exit_status\n"
  end

  coda
end

#exec_cmd(job, options = {}) ⇒ Object 



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# File 'lib/rbbt/hpc/batch.rb', line 40

def exec_cmd(job, options = {})
  env_cmd     = Misc.process_options options, :env_cmd
  development = Misc.process_options options, :development

  if contain = options[:contain]
    contain = File.expand_path(contain)
    env_cmd ||= ""
    env_cmd << " TMPDIR='#{contain}/.rbbt/tmp' "
  end

  if options[:singularity]

    group, user, user_group, scratch_group_dir, projects_group_dir = options.values_at :group, :user, :user_group, :scratch_group_dir, :projects_group_dir

    singularity_img, singularity_opt_dir, singularity_ruby_inline, singularity_mounts = options.values_at :singularity_img, :singularity_opt_dir, :singularity_ruby_inline, :singularity_mounts

    singularity_cmd = %(singularity exec -e -B "#{File.expand_path singularity_opt_dir}":/singularity_opt/ -B "#{File.expand_path singularity_ruby_inline}":"/.singularity_ruby_inline":rw ) 

    if singularity_mounts
      singularity_mounts.split(",").each do |mount|
        singularity_cmd += "-B #{ mount } "
      end
    end

    if contain && options[:hardened]
      singularity_cmd << %( -C -H "#{contain}" \
-B "/.singularity_ruby_inline":"#{contain}/.singularity_ruby_inline":rw 
-B "#{options[:batch_dir]}" \
-B /scratch/tmp \
      #{ group != user_group ? "-B /gpfs/projects/#{user_group}" : "" } \
-B #{scratch_group_dir} \
-B #{projects_group_dir} \
-B /apps/ \
-B ~/git:"#{contain}/git":ro \
      #{Open.exists?('~/.rbbt/software/opt/')? '-B ~/.rbbt/software/opt/:"/opt/":ro' : '' } \
-B ~/.rbbt:"#{contain}/home/":ro)
    end

    singularity_cmd << " #{singularity_img} "
  end

  if env_cmd
    exec_cmd = %(env #{env_cmd} rbbt)
  else
    exec_cmd = %(rbbt)
  end

  exec_cmd << "--dev '#{development}'" if development

  exec_cmd = singularity_cmd  + exec_cmd if singularity_cmd

  exec_cmd
end

#execute(options) ⇒ Object 



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# File 'lib/rbbt/hpc/batch.rb', line 416

def execute(options)
  exec_cmd, job_cmd, task_cpus = options.values_at :exec_cmd, :rbbt_cmd, :task_cpus

  script="step_path=$(\n\#{exec_cmd} \#{job_cmd} --printpath\n)\nexit_status=$?\n\n[[ -z $BATCH_JOB_ID ]] || \#{exec_cmd} workflow write_info --recursive --force=false --check_pid \"$step_path\" batch_job $BATCH_JOB_ID\n[[ -z $BATCH_SYSTEM ]] || \#{exec_cmd} workflow write_info --recursive --force=false --check_pid \"$step_path\" batch_system $BATCH_SYSTEM\n\#{exec_cmd} workflow write_info --recursive --force=false --check_pid \"$step_path\" batch_cpus \#{task_cpus}\n"

  script
end

#follow_job(batch_dir, tail = true) ⇒ Object 



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# File 'lib/rbbt/hpc/batch.rb', line 629

def follow_job(batch_dir, tail = true)
  fjob = File.join(batch_dir, 'job.id')
  fout = File.join(batch_dir, 'std.out')
  ferr = File.join(batch_dir, 'std.err')
  fexit = File.join(batch_dir, 'exit.status')
  fstatus = File.join(batch_dir, 'job.status')

  job = Open.read(fjob).strip if Open.exists?(fjob)

  if job && ! File.exist?(fexit)
    begin
      status_txt = job_status(job)
      STDERR.puts Log.color(:magenta, "Status [#{job.to_i}]:")
      STDERR.puts status_txt
      lines = status_txt.split("\n").length
    rescue
      if ! File.exist?(fexit)
        STDERR.puts Log.color(:magenta, "Job #{job.to_i} not done and not running. STDERR:")
        STDERR.puts Open.read(ferr)
      end
      return
    end
  end

  if File.exist?(fexit)
    exit_status = Open.read(fexit)
    if exit_status.to_i == 0
      STDERR.puts Log.color(:magenta, "Job #{job} done with exit_status 0. STDOUT:")
      STDERR.puts Open.read(fout)
    else
      STDERR.puts Log.color(:magenta, "Job #{job.to_i} done with exit_status #{exit_status}. STDERR:")
      STDERR.puts Open.read(ferr)
    end
    return
  end

  if tail
    Log.severity = 10
    while ! File.exist? fout
      if job
        STDERR.puts
        Log.clear_line(STDERR)
        STDERR.write Log.color(:magenta, "Waiting for Output")
        3.times do
          STDERR.write Log.color(:magenta, ".")
          sleep 1
        end
        status_txt = job_status(job)
        lines.times do
          Log.clear_line(STDERR)
        end
        Log.clear_line(STDERR)
        STDERR.puts Log.color(:magenta, "Status [#{job.to_i}]:")
        STDERR.puts status_txt
        lines = status_txt.split("\n").length
      end
    end
    STDERR.puts
    Log.clear_line(STDERR)
    STDERR.puts Log.color(:magenta, "Output:")
    begin
      status_txt = job_status(job)
      Open.write(fstatus, status_txt) unless status_txt.nil? || status_txt.empty?
      out = CMD.cmd("tail -f '#{fout}'", :pipe => true) if File.exist?(fout) and not tail == :STDERR
      err = CMD.cmd("tail -f '#{ferr}'", :pipe => true) if File.exist?(ferr)

      terr = Misc.consume_stream(err, true, STDERR) if err
      tout = Misc.consume_stream(out, true, STDOUT) if out

      sleep 3 while job_queued(job)
    rescue Aborted
    ensure
      begin
        terr.exit if terr
        tout.exit if tout
        err.close if err
        err.join if err
      rescue Exception
      end

      begin
        out.close if out
        out.join if out
      rescue Exception
      end
    end
  end
end

#header(options) ⇒ Object 



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# File 'lib/rbbt/hpc/batch.rb', line 138

def header(options)
  header ="#!/bin/bash\n"

  header
end

#hold_dependencies(job, batch_job) ⇒ Object 



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# File 'lib/rbbt/hpc/batch.rb', line 618

def hold_dependencies(job, batch_job)
  job.set_info :batch_job, batch_job
  job.set_info :batch_system, self.batch_system
  job.dependencies.each do |dep|
    next unless dep.waiting?
    next if (dep_batch_job = dep.info[:batch_job]) && job_queued(dep_batch_job)

    hold_dependencies(dep, batch_job)
  end
end

#job_queued(job) ⇒ Object 



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# File 'lib/rbbt/hpc/batch.rb', line 718

def job_queued(job)
  job_status(job).split(/\s+/).include?(job.to_s)
end

#job_template(job, options = {}) ⇒ Object 



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# File 'lib/rbbt/hpc/batch.rb', line 496

def job_template(job, options = {})
  batch_options = batch_options job, options

  header              = self.header(batch_options)

  meta_data           = self.meta_data(batch_options)

  prepare_environment = self.prepare_environment(batch_options)

  execute             = self.execute(batch_options)

  sync_environment    = self.sync_environment(batch_options)

  cleanup_environment = self.cleanup_environment(batch_options)

  coda                = self.coda(batch_options)

  "\#{header}\n\n# \#{Log.color :green, \"0. Meta-data\"}\n\#{meta_data}\n\n# \#{Log.color :green, \"1. Prepare environment\"}\n\#{prepare_environment}\nenv > \#{batch_options[:fenv]}\n\n# \#{Log.color :green, \"2. Execute\"}\n\#{execute}\n\n# \#{Log.color :green, \"3. Sync and cleanup environment\"}\n\#{sync_environment}\n\#{cleanup_environment}\n\n# \#{Log.color :green, \"4. Exit\"}\n\#{coda}\n"
end

#load_conda(env = nil) ⇒ Object 



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# File 'lib/rbbt/hpc/batch.rb', line 301

def load_conda(env = nil)
  return "" if env.nil? || env.empty?

  "if ! type conda | grep function &> /dev/null; then\nif [ ! -z $CONDA_EXE ]; then\nsource \"$(dirname $(dirname $CONDA_EXE))/etc/profile.d/conda.sh\" &> /dev/null\nfi\nfi\nconda activate \#{ env }\n"
end

#load_modules(modules = []) ⇒ Object 



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# File 'lib/rbbt/hpc/batch.rb', line 290

def load_modules(modules = [])
  modules = modules.split(/,\s*/) if String === modules

  str = ""
  modules.each do |mod|
    str << "module load #{ mod }" << "\n"
  end if modules

  str
end

#meta_data(options) ⇒ Object 



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# File 'lib/rbbt/hpc/batch.rb', line 277

def meta_data(options)
  meta ="#MANIFEST: \#{(options[:manifest] || []) * \", \"}\n#DEPENDENCIES: \#{(options[:dependencies] || []) * \", \"}\n#EXEC_CMD: \#{options[:exec_cmd]}\n#CMD: \#{options[:rbbt_cmd]}\n#STEP_PATH: \#{options[:step_path]}\n"

  meta = meta.split("\n").reject{|line| line =~ /: $/} * "\n"
  meta
end

#prepare_environment(options = {}) ⇒ Object 



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# File 'lib/rbbt/hpc/batch.rb', line 321

def prepare_environment(options = {})
  modules = options[:lua_modules]
  conda = options[:conda]

  prepare_environment = ""

  functions = ""

  if contain = options[:contain]
    contain = File.expand_path(contain)
    functions +="function batch_erase_contain_dir(){\nrm -Rfv '\#{contain}' 2>1 >> '\#{options[:fsync]}'\n}\n"

    prepare_environment +="if ls -A '\#{contain}' &> /dev/null ; then\nempty_contain_dir=\"false\"\nelse\nempty_contain_dir=\"true\"\nfi\n"

    prepare_environment +="batch_erase_contain_dir()\n" if options[:wipe_container] == 'force'
  end

  if sync = options[:sync]
    source = if options[:singularity]
               File.join(options[:contain], '.rbbt/var/jobs')
             elsif options[:contain]
               File.join(options[:contain], 'var/jobs')
             else
               '~/.rbbt/var/jobs/'
             end

    source = File.expand_path(source)
    sync = File.expand_path(sync)
    functions +="function batch_sync_contain_dir(){\nmkdir -p \"$(dirname '\#{sync}')\"\nrsync -avztAXHP --copy-unsafe-links \"\#{source}/\" \"\#{sync}/\" 2>1 >> '\#{options[:fsync]}'\nsync_es=\"$?\"\necho $sync_es > '\#{options[:fsexit]}'\nfind '\#{sync}' -type l -ls | awk '$13 ~ /^\#{sync.gsub('/','\\/')}/ { sub(\"\#{source}\", \"\#{sync}\", $13); print $11, $13 }' | while read A B; do rm $A; ln -s $B $A; done\n}\n"
  end

  if options[:singularity]

    group, user, user_group, scratch_group_dir, projects_group_dir = options.values_at :group, :user, :user_group, :scratch_group_dir, :projects_group_dir

    singularity_img, singularity_opt_dir, singularity_ruby_inline = options.values_at :singularity_img, :singularity_opt_dir, :singularity_ruby_inline

    prepare_environment +="# Load singularity modules\ncommand -v singularity &> /dev/null || module load singularity\nmkdir -p \"\#{File.expand_path singularity_opt_dir}\"\n"

    if contain && options[:hardened]

      prepare_environment +="# Prepare container for singularity\nmkdir -p \"\#{contain}\"/.rbbt/etc/\n\nfor dir in .ruby_inline git home; do\nmkdir -p \"\#{contain}\"/$dir\ndone\n\nfor tmpd in persist_locks  produce_locks  R_sockets  sensiblewrite  sensiblewrite_locks  step_info_locks  tsv_open_locks; do\nmkdir -p \"\#{contain}/.rbbt/tmp/$tmpd\"\ndone\n\n# Copy environment\ncp ~/.rbbt/etc/environment \#{contain}/.rbbt/etc/\n\n# Set search_paths\necho \"singularity: /singularity_opt/{PKGDIR}/{TOPLEVEL}/{SUBPATH}\" > \#{contain}/.rbbt/etc/search_paths\necho \"rbbt_user: /home/rbbt/.rbbt/{TOPLEVEL}/{SUBPATH}\" >> \#{contain}/.rbbt/etc/search_paths\necho \"outside_home: \#{contain}/home/{TOPLEVEL}/{SUBPATH}\" >> \#{contain}/.rbbt/etc/search_paths\necho \"group_projects: \#{projects_group_dir}/{PKGDIR}/{TOPLEVEL}/{SUBPATH}\" >> \#{contain}/.rbbt/etc/search_paths\necho \"group_scratch: \#{scratch_group_dir}/{PKGDIR}/{TOPLEVEL}/{SUBPATH}\" >> \#{contain}/.rbbt/etc/search_paths\necho \"user_projects: \#{projects_group_dir}/\#{user}/{PKGDIR}/{TOPLEVEL}/{SUBPATH}\" >> \#{contain}/.rbbt/etc/search_paths\necho \"user_scratch: \#{scratch_group_dir}/\#{user}/{PKGDIR}/{TOPLEVEL}/{SUBPATH}\" >> \#{contain}/.rbbt/etc/search_paths\n"
    end
  end

  batch_system_variables + load_modules(modules) + "\n" + load_conda(conda) + "\n"  + functions + "\n" + prepare_environment
end

#prepare_submision(template, batch_dir, clean_batch_job = false, batch_dependencies = []) ⇒ Object 



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# File 'lib/rbbt/hpc/batch.rb', line 535

def prepare_submision(template, batch_dir, clean_batch_job = false, batch_dependencies = [])
  Open.mkdir batch_dir
  fcmd   = File.join(batch_dir, 'command.batch')
  fdep   = File.join(batch_dir, 'dependencies.list')
  fcfdep = File.join(batch_dir, 'canfail_dependencies.list')

  Open.write(fcmd, template)

  %w(std.out std.err job.id job.status dependencies.list canfail_dependencies.list exit.status sync.log inputs_dir).each do |filename|
    path = File.join(batch_dir, filename)
    Open.rm_rf path if File.exist? path
  end if clean_batch_job

  batch_dependencies = [] if batch_dependencies.nil?

  canfail_dependencies = batch_dependencies.select{|dep| dep =~ /^canfail:(\d+)/ }.collect{|dep| dep.partition(":").last}
  dependencies = batch_dependencies.reject{|dep| dep =~ /^canfail:(\d+)/ }

  Open.write(fdep, dependencies * "\n") if dependencies.any?
  Open.write(fcfdep, canfail_dependencies * "\n") if canfail_dependencies.any?

  fcmd
end

#rbbt_job_exec_cmd(job, options) ⇒ Object 



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# File 'lib/rbbt/hpc/batch.rb', line 94

def rbbt_job_exec_cmd(job, options)

  jobname  = job.clean_name
  workflow = job.original_workflow || job.workflow
  task     = job.original_task_name || job.task_name

  Misc.add_defaults options, :jobname => jobname

  task = Symbol === job.overriden ? job.overriden : job.task_name

  #override_deps = job.overriden_deps.collect do |dep| 
  #  name = [dep.workflow.to_s, dep.task_name] * "#"
  #  [name, dep.path] * "="  
  #end.uniq * ","

  if job.overriden?
    #override_deps = job.rec_dependencies.
    #  select{|dep| Symbol === dep.overriden }.
    
    override_deps = job.overriden_deps.
      collect do |dep| 
      name = [dep.workflow.to_s, dep.task_name] * "#"
      [name, dep.path] * "="  
    end.uniq * ","

    options[:override_deps] = override_deps unless override_deps.empty?
  end

  # Save inputs into inputs_dir
  inputs_dir = Misc.process_options options, :inputs_dir
  saved = Step.save_job_inputs(job, inputs_dir) if inputs_dir
  options[:load_inputs] = inputs_dir if saved && saved.any?

  saved.each do |input|
    options.delete input
  end if saved

  cmds = CMD.process_cmd_options options.merge(:add_option_dashes => true)

  "workflow task \#{workflow} \#{task} \#{cmds}\n".strip
end

#run_job(job, options = {}) ⇒ Object 



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# File 'lib/rbbt/hpc/batch.rb', line 560

def run_job(job, options = {})
  system = self.to_s.split("::").last

  if (batch_job = job.info[:batch_job]) && job_queued(batch_job)
    Log.info "Job #{job.short_path} already queued in #{batch_job}"
    return batch_job 
  end

  if job.running?
    Log.info "Job #{job.short_path} already running in #{job.info[:pid]}"
    return job.info[:batch_job]
  end

  batch_base_dir, clean_batch_job, remove_batch_dir, procpath, tail, batch_dependencies, dry_run = Misc.process_options options, 
    :batch_base_dir, :clean_batch_job, :remove_batch_dir, :batch_procpath, :tail, :batch_dependencies, :dry_run,
    :batch_base_dir => File.expand_path(File.join('~/rbbt-batch')) 

  workflow = job.original_workflow ||job.workflow
  task_name = job.original_task_name || job.task_name

  workflows_to_load = job.rec_dependencies.select{|d| Step === d}.collect{|d| d.workflow }.compact.collect(&:to_s) - [workflow.to_s]

  TmpFile.with_file(nil, remove_batch_dir, :tmpdir => batch_base_dir, :prefix => "#{system}_rbbt_job-#{workflow.to_s}-#{task_name}-") do |batch_dir|
    Misc.add_defaults options, 
      :batch_dir => batch_dir, 
      :inputs_dir => File.join(batch_dir, "inputs_dir"),
      :workflows => workflows_to_load.any? ? workflows_to_load.uniq * "," : nil

    options[:procpath_performance] ||= File.join(batch_dir, "procpath##{procpath.gsub(',', '#')}") if procpath

    template = self.job_template(job, options.dup)

    fcmd = prepare_submision(template, options[:batch_dir], clean_batch_job, batch_dependencies)

    batch_job = run_template(batch_dir, dry_run)

    hold_dependencies(job, batch_job) unless dry_run

    return [batch_job, batch_dir] unless tail

    t_monitor = Thread.new do
      self.follow_job(batch_dir, :STDERR)
    end
    self.wait_for_job(batch_dir)
    t_monitor.raise Aborted
    return unless Open.read(File.join(batch_dir, 'exit.status')).strip == '0'
    path = Open.read(File.join(batch_dir, 'std.out')).strip
    if Open.exists?(path) && job.path != path
      Log.info "Path of BATCH job #{path} is different from original job #{job.path}. Stablishing link."
      Open.ln path, job.path
      Open.ln path + '.info', job.path + '.info'  if Open.exists?(path + '.info')
      Open.ln path + '.files', job.path + '.files' if Open.exists?(path + '.files')
    end

    [batch_job, batch_dir]
  end
end

#sync_environment(options = {}) ⇒ Object 



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# File 'lib/rbbt/hpc/batch.rb', line 433

def sync_environment(options = {})
  sync_environment = ""

  if options[:sync]
    sync_environment +="if [ $exit_status == '0' ]; then\nbatch_sync_contain_dir\nelse\nsync_es=$exit_status\nfi\n"
  end

  sync_environment
end

#wait_for_job(batch_dir, time = 1) ⇒ Object 



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# File 'lib/rbbt/hpc/batch.rb', line 722

def wait_for_job(batch_dir, time = 1)
  fexit = File.join(batch_dir, 'exit.status')
  fjob = File.join(batch_dir, 'job.id')
  job = Open.read(fjob) if Open.exists?(fjob)

  while ! Open.exists?(fexit)
    sleep time
  end
end