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 141

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 310

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

#cleanup_environment(options = {}) ⇒ Object 



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# File 'lib/rbbt/hpc/batch.rb', line 445

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

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

  if options[:sync]
    if options[:wipe_container] == 'force'
      cleanup_environment +=<<-EOF
batch_erase_contain_dir
      EOF
    elsif options[:wipe_container] == 'post' || options[:wipe_container] == 'both'
      cleanup_environment +=<<-EOF
if [ $sync_es == '0' -a $empty_contain_dir == 'true' ]; then 
  batch_erase_contain_dir
fi
      EOF
    end
  end
  cleanup_environment
end

#coda(options) ⇒ Object 



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# File 'lib/rbbt/hpc/batch.rb', line 470

def coda(options)
  coda =<<-EOF
echo $exit_status > '#{options[:fexit]}'
  EOF

  if options[:sync]
    coda +=<<-EOF
if [ $sync_es == '0' ]; then
  exit $exit_status
else
  exit $sync_es
fi
    EOF
  else
    coda +=<<-EOF
exit $exit_status
    EOF
  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 412

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

  script=<<-EOF
step_path=$( 
  #{exec_cmd} #{job_cmd} --printpath
)
exit_status=$?

[[ -z $BATCH_JOB_ID ]] || #{exec_cmd} workflow write_info --recursive --force=false --check_pid "$step_path" batch_job $BATCH_JOB_ID
[[ -z $BATCH_SYSTEM ]] || #{exec_cmd} workflow write_info --recursive --force=false --check_pid "$step_path" batch_system $BATCH_SYSTEM
#{exec_cmd} workflow write_info --recursive --force=false --check_pid "$step_path" batch_cpus #{task_cpus}
  EOF

  script
end

#follow_job(batch_dir, tail = true) ⇒ Object 



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# File 'lib/rbbt/hpc/batch.rb', line 602

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_status(job).include? job.to_s
    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 133

def header(options)
  header =<<-EOF
#!/bin/bash
  EOF

  header
end

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



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# File 'lib/rbbt/hpc/batch.rb', line 492

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)

  <<-EOF
#{header}

# #{Log.color :green, "0. Meta-data"}
#{meta_data}

# #{Log.color :green, "1. Prepare environment"}
#{prepare_environment}
env > #{batch_options[:fenv]}

# #{Log.color :green, "2. Execute"}
#{execute} 

# #{Log.color :green, "3. Sync and cleanup environment"}
#{sync_environment}
#{cleanup_environment}

# #{Log.color :green, "4. Exit"}
#{coda}
  EOF
end

#load_conda(env = nil) ⇒ Object 



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# File 'lib/rbbt/hpc/batch.rb', line 296

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

  <<-EOF
if ! type conda | grep function &> /dev/null; then
if [ ! -z $CONDA_EXE ]; then
        source "$(dirname $(dirname $CONDA_EXE))/etc/profile.d/conda.sh" &> /dev/null
fi
fi
conda activate #{ env }
  EOF
end

#load_modules(modules = []) ⇒ Object 



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# File 'lib/rbbt/hpc/batch.rb', line 285

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 272

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

  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 316

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

  prepare_environment = ""

  functions = ""

  if contain = options[:contain]
    contain = File.expand_path(contain)
    functions +=<<-EOF
function batch_erase_contain_dir(){
rm -Rfv '#{contain}' 2>1 >> '#{options[:fsync]}'
}
    EOF

    prepare_environment +=<<-EOF
if ls -A '#{contain}' &> /dev/null ; then
  empty_contain_dir="false"
else
  empty_contain_dir="true"
fi
    EOF

    prepare_environment +=<<-EOF if options[:wipe_container] == 'force'
batch_erase_contain_dir()
    EOF
  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 +=<<-EOF
function batch_sync_contain_dir(){
  mkdir -p "$(dirname '#{sync}')"
  rsync -avztAXHP --copy-unsafe-links "#{source}/" "#{sync}/" 2>1 >> '#{options[:fsync]}'
  sync_es="$?" 
  echo $sync_es > '#{options[:fsexit]}'
  find '#{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
}
    EOF
  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 +=<<-EOF
# Load singularity modules
module load intel/2018.1
module load singularity
mkdir -p "#{singularity_opt_dir}"
    EOF

    if contain && options[:hardened]

      prepare_environment +=<<-EOF
# Prepare container for singularity
mkdir -p "#{contain}/.rbbt/etc/"

for dir in .ruby_inline git home; do
mkdir -p "#{contain}/$dir"
done

for tmpd in persist_locks  produce_locks  R_sockets  sensiblewrite  sensiblewrite_locks  step_info_locks  tsv_open_locks; do
mkdir -p "#{contain}/.rbbt/tmp/$tmpd"
done

# Copy environment 
cp ~/.rbbt/etc/environment #{contain}/.rbbt/etc/

# Set search_paths
echo "singularity: /singularity_opt/{PKGDIR}/{TOPLEVEL}/{SUBPATH}" > #{contain}/.rbbt/etc/search_paths
echo "rbbt_user: /home/rbbt/.rbbt/{TOPLEVEL}/{SUBPATH}" >> #{contain}/.rbbt/etc/search_paths
echo "outside_home: #{contain}/home/{TOPLEVEL}/{SUBPATH}" >> #{contain}/.rbbt/etc/search_paths
echo "group_projects: #{projects_group_dir}/{PKGDIR}/{TOPLEVEL}/{SUBPATH}" >> #{contain}/.rbbt/etc/search_paths
echo "group_scratch: #{scratch_group_dir}/{PKGDIR}/{TOPLEVEL}/{SUBPATH}" >> #{contain}/.rbbt/etc/search_paths
echo "user_projects: #{projects_group_dir}/#{user}/{PKGDIR}/{TOPLEVEL}/{SUBPATH}" >> #{contain}/.rbbt/etc/search_paths
echo "user_scratch: #{scratch_group_dir}/#{user}/{PKGDIR}/{TOPLEVEL}/{SUBPATH}" >> #{contain}/.rbbt/etc/search_paths
      EOF
    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 531

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

  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)

  <<-EOF.strip
workflow task #{workflow} #{task} #{cmds}
EOF
end

#run_job(job, options = {}) ⇒ Object 



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# File 'lib/rbbt/hpc/batch.rb', line 556

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

  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.uniq * ","

    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)

    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 429

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

  if options[:sync]
    sync_environment +=<<-EOF
if [ $exit_status == '0' ]; then 
  batch_sync_contain_dir
else
  sync_es=$exit_status
fi
    EOF
  end

  sync_environment
end

#wait_for_job(batch_dir, time = 1) ⇒ Object 



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# File 'lib/rbbt/hpc/batch.rb', line 691

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