Module: PBS

Extended by:
SchedulerJob
Defined in:
lib/scout/workflow/deployment/scheduler/pbs.rb

Instance Attribute Summary

Attributes included from SchedulerJob

#batch_base_dir

Class Method Summary collapse

Methods included from SchedulerJob

batch_dir_for_id, batch_options, cleanup_environment, coda, exec_cmd, execute, follow_job, hold_dependencies, job_queued, job_template, jobs, load_conda, load_modules, meta_data, prepare_environment, prepare_submision, run_job, scout_job_exec_cmd, sync_environment, wait_for_job

Class Method Details

.batch_system_variables ⇒ Object 



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# File 'lib/scout/workflow/deployment/scheduler/pbs.rb', line 11

def self.batch_system_variables
  "let TOTAL_PROCESORS=\"$(cat /proc/cpuinfo|grep ^processor |wc -l)\"\nlet MAX_MEMORY_DEFAULT=\"$(grep MemTotal /proc/meminfo|grep -o \"[[:digit:]]*\") / ( (1024 * $TOTAL_PROCESORS) / $PBS_CPUS_PER_TASK )\"\nMAX_MEMORY=\"$MAX_MEMORY_DEFAULT\"\n[ ! -z $PBS_MEM_PER_CPU ] && let MAX_MEMORY=\"$PBS_MEM_PER_CPU * $PBS_CPUS_PER_TASK\" \n[ ! -z $PBS_MEM_PER_NODE ] && MAX_MEMORY=\"$PBS_MEM_PER_NODE\"\nexport MAX_MEMORY_DEFAULT\nexport MAX_MEMORY\nexport BATCH_JOB_ID=$PBS_JOBID\nexport BATCH_SYSTEM=\#{system}\n\ncd ${PBS_O_WORKDIR}\n  EOF\nend\n"

.header(options = {}) ⇒ Object 



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# File 'lib/scout/workflow/deployment/scheduler/pbs.rb', line 27

def self.header(options = {})
  options = options.dup

  workdir    = IndiferentHash.process_options options, :workdir
  batch_dir  = IndiferentHash.process_options options, :batch_dir
  batch_name = IndiferentHash.process_options options, :batch_name

  queue      = IndiferentHash.process_options options, :queue
      = IndiferentHash.process_options options, :account
  time       = IndiferentHash.process_options options, :time
  nodes      = IndiferentHash.process_options options, :nodes

  # PBS 
  place      = IndiferentHash.process_options options, :place, :place => 'scatter'
  system     = IndiferentHash.process_options options, :partition
  filesystems = IndiferentHash.process_options options, :filesystems

  filesystems = "home" if filesystems.nil?

  filesystems = filesystems * "," if Array === filesystems

  # NOT USED 
  partition  = IndiferentHash.process_options options, :partition
  task_cpus  = IndiferentHash.process_options options, :task_cpus
  exclusive  = IndiferentHash.process_options options, :exclusive
  highmem    = IndiferentHash.process_options options, :highmem
  licenses   = IndiferentHash.process_options options, :licenses
  constraint = IndiferentHash.process_options options, :constraint
  gres       = IndiferentHash.process_options options, :gres

  constraint     = [constraint, "highmem"].compact * "&" if highmem

  mem            = IndiferentHash.process_options options, :mem
  mem_per_cpu    = IndiferentHash.process_options options, :mem_per_cpu

  fout       = File.join(batch_dir, 'std.out')
  ferr       = File.join(batch_dir, 'std.err')

  time = Misc.format_seconds Misc.timespan(time) unless time.include? ":"

  qsub_params = {  "-l filesystems=" => filesystems,
                   "-l system=" => system,
                   "-l select=" => nodes,
                   "-l place=" => place,
                   "-l walltime=" => time,
                   "-q " => queue,
                   "-A " => ,
                   "-o " => fout,
                   "-e " => ferr,
                   "-k doe" => true,
                   # "cpus-per-task" => task_cpus,
                   # "nodes" => nodes,
                   # "time" => time,
                   # "constraint" => constraint,
                   # "exclusive" => exclusive,
                   # "licenses" => licenses,
                   # "gres" => gres,
                   # "mem" => mem,
                   # "mem-per-cpu" => mem_per_cpu,
  }


  header ="#!/bin/bash\n  EOF\n\n  qsub_params.each do |name,value|\n    next if value.nil? || value == \"\"\n    if TrueClass === value\n      header << \"#PBS \#{name}\" << \"\\n\"\n    elsif Array === value\n      value.each do |v|\n        header << \"#PBS \#{name}\\\"\#{v}\\\"\" << \"\\n\"\n      end\n    else\n      header << \"#PBS \#{name}\\\"\#{value}\\\"\" << \"\\n\"\n    end\n  end\n\n  header\nend\n"

.job_status(job = nil) ⇒ Object 



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# File 'lib/scout/workflow/deployment/scheduler/pbs.rb', line 163

def self.job_status(job = nil)
  if job.nil?
    CMD.cmd("qstat").read
  else
    begin
      CMD.cmd("qstat #{job}").read
    rescue
      ""
    end
  end
end

.run_template(batch_dir, dry_run) ⇒ Object 



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# File 'lib/scout/workflow/deployment/scheduler/pbs.rb', line 109

def self.run_template(batch_dir, dry_run)

  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')
  fcmd   = File.join(batch_dir, 'command.batch')

  return if Open.exists?(fexit)

  Log.info "Issuing PBS file: #{fcmd}"
  Log.debug Open.read(fcmd)

  if File.exist?(fjob)
    job = Open.read(fjob).to_i
  else

    dependencies = Open.read(fdep).split("\n") if File.exist? fdep
    canfail_dependencies = Open.read(fcfdep).split("\n") if File.exist? fcfdep

    normal_dep_str = dependencies && dependencies.any? ? "afterok:" + dependencies * ":" : nil
    canfail_dep_str = canfail_dependencies && canfail_dependencies.any? ? "afterany:" + canfail_dependencies * ":" : nil

    if normal_dep_str.nil? && canfail_dep_str.nil?
      dep_str = ""
    else
      dep_str = '-W depend=' + [normal_dep_str, canfail_dep_str].compact * ","
    end

    cmd = "qsub #{dep_str} '#{fcmd}'"

    if File.exist?(fout)
      return
    elsif dry_run
      STDERR.puts Log.color(:magenta, "To execute run: ") + Log.color(:blue, "squb '#{fcmd}'")
      STDERR.puts Log.color(:magenta, "To monitor progress run (needs local rbbt): ") + Log.color(:blue, "rbbt pbs tail '#{batch_dir}'")
      raise DryRun, batch_dir
    else
      Open.rm fsync
      Open.rm fexit
      Open.rm fout
      Open.rm ferr

      job = CMD.cmd(cmd).read.scan(/\d+/).first.to_i
      Log.debug "SBATCH job id: #{job}"
      Open.write(fjob, job.to_s)
      job
    end
  end
end

.system ⇒ Object 



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# File 'lib/scout/workflow/deployment/scheduler/pbs.rb', line 7

def self.system
  "PBS"
end