Module: HPC::SLURM

Extended by:
Orchestration, TemplateGeneration
Defined in:
lib/rbbt/hpc/slurm.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_modules, meta_data, prepare_environment, prepare_submision, rbbt_job_exec_cmd, run_job, sync_environment, wait_for_job

Methods included from Orchestration

get_chains, get_job_dependencies, get_recursive_job_dependencies, job_rules, orchestrate_job, piggyback, workload

Class Method Details

.batch_system_variables ⇒ Object 



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# File 'lib/rbbt/hpc/slurm.rb', line 9

def self.batch_system_variables
  <<-EOF
let "MAX_MEMORY=$SLURM_MEM_PER_CPU * $SLURM_CPUS_PER_TASK" || let MAX_MEMORY="$(grep MemTotal /proc/meminfo|grep -o "[[:digit:]]*") / 1024"
BATCH_JOB_ID=$SLURM_JOB_ID
BATCH_SYSTEM=SLURM
  EOF
end

.header(options = {}) ⇒ Object 



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# File 'lib/rbbt/hpc/slurm.rb', line 17

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

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

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

  header =<<-EOF
#!/bin/bash
#SBATCH --job-name="#{batch_name}"
#SBATCH --workdir="#{workdir}"
#SBATCH --output="#{fout}"
#SBATCH --error="#{ferr}"
#SBATCH --qos="#{queue}"
#SBATCH --cpus-per-task="#{task_cpus}"
#SBATCH --time="#{time}"
#SBATCH --nodes="#{nodes}"
  EOF

  header << "#SBATCH --exclusive" << "\n" if exclusive

  header
end

.job_status(job = nil) ⇒ Object 



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# File 'lib/rbbt/hpc/slurm.rb', line 106

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

.run_template(batch_dir, dry_run) ⇒ Object 



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# File 'lib/rbbt/hpc/slurm.rb', line 52

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 SLURM file: #{fcmd}")
  STDERR.puts Open.read(fcmd)

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

    dependencies = Open.read(fdep).split("\n") if File.exists? fdep
    canfail_dependencies = Open.read(fcfdep).split("\n") if File.exists? 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 = '--dependency=' + [normal_dep_str, canfail_dep_str].compact * ","
    end

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

    if File.exists?(fout)
      return
    elsif dry_run
      STDERR.puts Log.color(:magenta, "To execute run: ") + Log.color(:blue, "sbatch '#{fcmd}'")
      STDERR.puts Log.color(:magenta, "To monitor progress run (needs local rbbt): ") + Log.color(:blue, "rbbt slurm 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 "SBATCH job id: #{job}"
      Open.write(fjob, job.to_s)
      job
    end
  end
end