Module: HPC::LSF

Extended by:
Orchestration, TemplateGeneration
Defined in:
lib/rbbt/hpc/lsf.rb

Class Method Summary collapse

Methods included from TemplateGeneration

batch_options, batch_system_variables, cleanup_environment, coda, exec_cmd, execute, follow_job, header, job_template, load_conda, load_modules, meta_data, prepare_environment, prepare_submision, rbbt_job_exec_cmd, run_job, sync_environment, wait_for_job

Methods included from Orchestration

accumulate_rules, add_batch_deps, add_config_keys, add_rules_and_consolidate, chain_batches, check_chains, get_chains, get_job_dependencies, get_recursive_job_dependencies, job_batches, job_chains, job_dependencies, job_rules, job_workload, merge_rules, orchestrate_job, parse_chains, pb, piggyback, prepare_for_execution, task_specific_rules, workflow_rules, workload

Class Method Details

.batch_system_variables ⇒ Object 



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# File 'lib/rbbt/hpc/lsf.rb', line 8

def self.batch_system_variables
  <<-EOF
let TOTAL_PROCESORS="$(cat /proc/cpuinfo|grep ^processor |wc -l)"
let MAX_MEMORY_DEFAULT="$(grep MemTotal /proc/meminfo|grep -o "[[:digit:]]*") / ( (1024 * $TOTAL_PROCESORS) / $LSB_MAX_NUM_PROCESSORS )"
[ ! -z $LSB_MAX_MEM_RUSAGE ] && let MAX_MEMORY="$LSB_MAX_MEM_RUSAGE" || MAX_MEMORY="$MAX_MEMORY_DEFAULT"
export MAX_MEMORY_DEFAULT
export MAX_MEMORY
export BATCH_JOB_ID=$LSF_JOBID
export BATCH_SYSTEM=LSF
  EOF
end

.header(options = {}) ⇒ Object 



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# File 'lib/rbbt/hpc/lsf.rb', line 20

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

  queue          = Misc.process_options options, :queue
  task_cpus      = Misc.process_options options, :task_cpus
  time           = Misc.process_options options, :time
  nodes          = Misc.process_options options, :nodes
  workdir        = Misc.process_options options, :workdir
  exclusive      = Misc.process_options options, :exclusive

  batch_dir  = Misc.process_options options, :batch_dir
  batch_name = Misc.process_options options, :batch_name
  batch_name ||= File.basename(batch_dir)

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

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

  time = time.split(":").values_at(0, 1) * ":"

  header =<<-EOF
#!/bin/bash
#BSUB -J "#{batch_name}"
#BSUB -cwd "#{workdir}"
#BSUB -oo "#{fout}"
#BSUB -eo "#{ferr}"
#BSUB -q "#{queue}"
#BSUB -n "#{task_cpus}"
#BSUB -W "#{time}"
  EOF

  header << "#BSUB -x" << "\n" if exclusive

  header
end

.job_status(job = nil) ⇒ Object 



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# File 'lib/rbbt/hpc/lsf.rb', line 114

def self.job_status(job = nil)
  if job.nil?
    CMD.cmd("bjobs -w").read
  else
    CMD.cmd("bjobs -w #{job}").read
  end
end

.run_template(batch_dir, dry_run) ⇒ Object 



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# File 'lib/rbbt/hpc/lsf.rb', line 57

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)

  STDERR.puts Log.color(:magenta, "Issuing LSF file: #{fcmd}")
  STDERR.puts 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_list = dependencies && dependencies.any? ? dependencies.collect{|d| "post_done(#{d})"} : []
    canfail_dep_list = canfail_dependencies && canfail_dependencies.any? ? canfail_dependencies.collect{|d| "done(#{d})"} : []

    dep_list = normal_dep_list + canfail_dep_list

    if dep_list.any?
      dep_str = '-w "' + dep_list * " && " + '"'
    else
      dep_str = ""
    end

    cmd = "bsub #{dep_str} < '#{fcmd}'"

    if File.exist?(fout)
      return
    elsif dry_run
      STDERR.puts Log.color(:magenta, "To execute run: ") + Log.color(:blue, cmd)
      STDERR.puts Log.color(:magenta, "To monitor progress run (needs local rbbt): ") + Log.color(:blue, "rbbt lsf tail '#{batch_dir}'")
      raise HPC::SBATCH, 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 "BSUB job id: #{job}"
      Open.write(fjob, job.to_s)
      job
    end
  end
end