Module: SchedulerJob

Extended by:
SchedulerJob
Included in:
LSF, PBS, SLURM, SchedulerJob
Defined in:
lib/scout/workflow/deployment/scheduler/job.rb

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Attribute Details

#batch_base_dir ⇒ Object

Returns the value of attribute batch_base_dir.



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# File 'lib/scout/workflow/deployment/scheduler/job.rb', line 3

def batch_base_dir
  @batch_base_dir
end

Class Method Details

.batch_dir_for_id(batch_base_dir, id) ⇒ Object 



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# File 'lib/scout/workflow/deployment/scheduler/job.rb', line 550

def batch_dir_for_id(batch_base_dir, id)
  job_id_file = Dir.glob(File.join(batch_base_dir, '*/job.id')).select{|f| Open.read(f).strip == id.to_s }.first
  job_id_file ? File.dirname(job_id_file) : nil
end

.batch_options(job, options) ⇒ Object 



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# File 'lib/scout/workflow/deployment/scheduler/job.rb', line 123

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,
    :constraints,
    :licenses,
    :batch_dir,
    :batch_name,
    :contain,
    :sync,
    :contain_and_sync,
    :copy_image,
    :launcher,
    :development,
    :env_cmd,
    :env,
    :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] = IndiferentHash.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,
    :launcher,
    :development,
    :env_cmd,
    :env,
    :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 = Scout::Config.get(key, "batch_#{key}", "batch")
    next if default_value.nil? 
    IndiferentHash.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 = Scout::Config.get(:contain_base_dir, :batch_contain, :batch, :default => "/scratch/tmp/scout-[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] ||= "~/.scout/var/jobs" 
    batch_options[:wipe_container] ||= 'post'
  end

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

  IndiferentHash.add_defaults batch_options, 
    :batch_name => batch_name,
    :inputs_dir => inputs_dir, 
    :nodes => 1, 
    :step_path => job.path,
    :task_cpus => 1,
    :time => '2min', 
    :env => {'JDK_JAVA_OPTIONS' => "-Xms1g -Xmx${MAX_MEMORY}m"},
    :singularity_img => ENV["SINGULARITY_IMG"] || "~/scout.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)
  scout_cmd = scout_job_exec_cmd(job, options)

  IndiferentHash.add_defaults batch_options, 
    :exec_cmd => exec_cmd,
    :scout_cmd => scout_cmd

  batch_dir = batch_options[:batch_dir]

  IndiferentHash.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/scout/workflow/deployment/scheduler/job.rb', line 297

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

.cleanup_environment(options = {}) ⇒ Object 



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# File 'lib/scout/workflow/deployment/scheduler/job.rb', line 440

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

.coda(options) ⇒ Object 



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# File 'lib/scout/workflow/deployment/scheduler/job.rb', line 465

def coda(options)
  coda ="echo $exit_status > '\#{options[:fexit]}'\n  EOF\n\n  if options[:sync]\n    coda +=<<-EOF\nif [ $sync_es == '0' ]; then\nexit $exit_status\nelse\nexit $sync_es\nfi\n    EOF\n  else\n    coda +=<<-EOF\nexit $exit_status\n    EOF\n  end\n\n  coda\nend\n"

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



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# File 'lib/scout/workflow/deployment/scheduler/job.rb', line 13

def exec_cmd(job, options = {})
  options = IndiferentHash.add_defaults options, :launcher => :srun if self.system == :slurm

  launcher, env_cmd, development = IndiferentHash.process_options options, :launcher, :env_cmd, :development

  if contain = options[:contain]
    contain = File.expand_path(contain)
    env_cmd ||= ""
    env_cmd << " TMPDIR='#{contain}/.scout/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?('~/.scout/software/opt/')? '-B ~/.scout/software/opt/:"/opt/":ro' : '' } \
-B ~/.scout:"#{contain}/home/":ro)
    end

    singularity_cmd << " #{singularity_img} "
  end

  base_cmd = if launcher
               %(#{launcher} scout)
             else
               %(scout)
             end

  if env_cmd
    exec_cmd = %(env #{env_cmd} #{ base_cmd })
  else
    exec_cmd = base_cmd
  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/scout/workflow/deployment/scheduler/job.rb', line 405

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

  script="step_path=$( \n    \#{exec_cmd} \#{job_cmd} --printpath\n)\nexit_status=$?\n\nif [ $exit_status -eq 0 ]; then\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}\nfi\n  EOF\n\n  script\nend\n"

.follow_job(batch_dir, tail = true) ⇒ Object 



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# File 'lib/scout/workflow/deployment/scheduler/job.rb', line 632

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 + 1).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)

      tout = Thread.new do
        while c = out.getc
          STDOUT << c
        end
      end

      terr = Thread.new do
        while c = err.getc
          STDERR << c
        end
      end

      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/scout/workflow/deployment/scheduler/job.rb', line 115

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

.hold_dependencies(job, batch_job) ⇒ Object 



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# File 'lib/scout/workflow/deployment/scheduler/job.rb', line 620

def hold_dependencies(job, batch_job)
  job.init_info
  job.set_info :batch_job, batch_job
  job.set_info :batch_system, self.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/scout/workflow/deployment/scheduler/job.rb', line 730

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/scout/workflow/deployment/scheduler/job.rb', line 487

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(batch_options)}\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  EOF\nend\n"

.jobs ⇒ Object 



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# File 'lib/scout/workflow/deployment/scheduler/job.rb', line 734

def jobs
  job_status.split("\n").collect{|l| l.scan(/\d{5,}/).first}.compact.flatten.uniq
end

.load_conda(env = nil) ⇒ Object 



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# File 'lib/scout/workflow/deployment/scheduler/job.rb', line 283

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

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

.load_modules(modules = []) ⇒ Object 



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# File 'lib/scout/workflow/deployment/scheduler/job.rb', line 272

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/scout/workflow/deployment/scheduler/job.rb', line 259

def meta_data(options)
  meta ="#MANIFEST: \#{(options[:manifest] || []) * \", \"}\n#DEPENDENCIES: \#{(options[:dependencies] || []) * \", \"}\n#EXEC_CMD: \#{options[:exec_cmd]}\n#CMD: \#{options[:scout_cmd]}\n#STEP_PATH: \#{options[:step_path]}\n  EOF\n\n  meta = meta.split(\"\\n\").reject{|line| line =~ /: $/} * \"\\n\"\n  meta\nend\n"

.prepare_environment(options = {}) ⇒ Object 



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# File 'lib/scout/workflow/deployment/scheduler/job.rb', line 303

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(){\n  rm -Rfv '\#{contain}' 2>1 >> '\#{options[:fsync]}'\n}\n    EOF\n\n    prepare_environment +=<<-EOF\nif ls -A '\#{contain}' &> /dev/null ; then\nempty_contain_dir=\"false\"\nelse\nempty_contain_dir=\"true\"\nfi\n    EOF\n\n    prepare_environment +=<<-EOF if options[:wipe_container] == 'force'\nbatch_erase_contain_dir()\n    EOF\n  end\n\n  if sync = options[:sync]\n    source = if options[:singularity]\n               File.join(options[:contain], '.scout/var/jobs')\n             elsif options[:contain]\n               File.join(options[:contain], 'var/jobs')\n             else\n               '~/.scout/var/jobs/'\n             end\n\n    source = File.expand_path(source)\n    sync = File.expand_path(sync)\n    functions +=<<-EOF\nfunction 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 $A; done\n}\n    EOF\n  end\n\n  if options[:env]\n    prepare_environment +=<<-EOF\n# Set ENV variables \n\#{options[:env].collect{|n,v| \"export \#{n}=\\\"\#{v}\\\"\" } * \"\\n\"}\n    EOF\n  end\n\n  if options[:singularity]\n\n    group, user, user_group, scratch_group_dir, projects_group_dir = options.values_at :group, :user, :user_group, :scratch_group_dir, :projects_group_dir\n\n    singularity_img, singularity_opt_dir, singularity_ruby_inline = options.values_at :singularity_img, :singularity_opt_dir, :singularity_ruby_inline\n\n    prepare_environment +=<<-EOF\n# Load singularity modules\ncommand -v singularity &> /dev/null || module load singularity\nmkdir -p \"\#{File.expand_path singularity_opt_dir}\"\n    EOF\n\n    if contain && options[:hardened]\n\n      prepare_environment +=<<-EOF\n# Prepare container for singularity\nmkdir -p \"\#{contain}\"/.scout/etc/\n\nfor dir in .ruby_inline git home; do\n  mkdir -p \"\#{contain}\"/$dir\ndone\n\nfor tmpd in persist_locks  produce_locks  R_sockets  sensiblewrite  sensiblewrite_locks  step_info_locks  tsv_open_locks; do\n  mkdir -p \"\#{contain}/.scout/tmp/$tmpd\"\ndone\n\n# Copy environment \ncp ~/.scout/etc/environment \#{contain}/.scout/etc/\n\n# Set search_paths\necho \"singularity: /singularity_opt/{PKGDIR}/{TOPLEVEL}/{SUBPATH}\" > \#{contain}/.scout/etc/search_paths\necho \"scout_user: /home/scout/.scout/{TOPLEVEL}/{SUBPATH}\" >> \#{contain}/.scout/etc/search_paths\necho \"outside_home: \#{contain}/home/{TOPLEVEL}/{SUBPATH}\" >> \#{contain}/.scout/etc/search_paths\necho \"group_projects: \#{projects_group_dir}/{PKGDIR}/{TOPLEVEL}/{SUBPATH}\" >> \#{contain}/.scout/etc/search_paths\necho \"group_scratch: \#{scratch_group_dir}/{PKGDIR}/{TOPLEVEL}/{SUBPATH}\" >> \#{contain}/.scout/etc/search_paths\necho \"user_projects: \#{projects_group_dir}/\#{user}/{PKGDIR}/{TOPLEVEL}/{SUBPATH}\" >> \#{contain}/.scout/etc/search_paths\necho \"user_scratch: \#{scratch_group_dir}/\#{user}/{PKGDIR}/{TOPLEVEL}/{SUBPATH}\" >> \#{contain}/.scout/etc/search_paths\n      EOF\n    end\n  end\n\n  [batch_system_variables, load_modules(modules), load_conda(conda), functions, prepare_environment].reject{|s| s.empty? } * \"\\n\"\nend\n"

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



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# File 'lib/scout/workflow/deployment/scheduler/job.rb', line 526

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

.run_job(job, options = {}) ⇒ Object 



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# File 'lib/scout/workflow/deployment/scheduler/job.rb', line 555

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, orchestration_rules_file = IndiferentHash.process_options options, 
    :batch_base_dir, :clean_batch_job, :remove_batch_dir, :batch_procpath, :tail, :batch_dependencies, :dry_run, :orchestration_rules,
    :batch_base_dir => SchedulerJob.batch_base_dir

  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, batch_dir_for_id(batch_base_dir, batch_job) 
  end

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

    if job.info[:batch_job]
      return job.info[:batch_job], batch_dir_for_id(batch_base_dir, batch_job)
    else
      return 
    end
  end

  workflow = job.workflow
  task_name = job.task_name

  options = IndiferentHash.setup(Workflow::Orchestrator.job_rules(Batch::Orchestration.orchestration_rules(orchestration_rules_file), job, true)).merge(options) if orchestration_rules_file

  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}_scout_job-#{workflow.to_s}-#{task_name}-") do |batch_dir|
    IndiferentHash.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

.scout_job_exec_cmd(job, options) ⇒ Object 



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# File 'lib/scout/workflow/deployment/scheduler/job.rb', line 74

def scout_job_exec_cmd(job, options)

  jobname  = job.clean_name
  workflow = job.workflow
  task     = job.task_name

  IndiferentHash.add_defaults options, :jobname => jobname

  task = job.task_name

  if job.recursive_overriden_deps.any?
    override_deps = job.recursive_overriden_deps.
      select do |dep| Symbol === dep.overriden end.
      collect do |dep| 
        o_workflow = dep.overriden_workflow || dep.workflow
        o_workflow = o_workflow.name if o_workflow.respond_to?(:name)
        o_task_name = dep.overriden_task || dep.task.name
        name = [o_workflow, o_task_name] * "#"
        [name, dep.path] * "="  
      end.uniq * ","
      options[:override_deps] = override_deps unless override_deps.empty?
  end

  # Save inputs into inputs_dir (only if provided)
  inputs_dir = IndiferentHash.process_options options, :inputs_dir
  if inputs_dir
    saved = job.save_inputs(inputs_dir)
    options[:load_inputs] = inputs_dir if saved && !saved.nil? && !saved.empty?

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

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

  "workflow task \#{workflow} \#{task} \#{cmds}\n  EOF\nend\n".strip

.sync_environment(options = {}) ⇒ Object 



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# File 'lib/scout/workflow/deployment/scheduler/job.rb', line 424

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    EOF\n  end\n\n  sync_environment\nend\n"

.system ⇒ Object 



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# File 'lib/scout/workflow/deployment/scheduler/job.rb', line 9

def system
  :batch
end

.wait_for_job(batch_dir, time = 1) ⇒ Object 



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# File 'lib/scout/workflow/deployment/scheduler/job.rb', line 738

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