4062: update python testing to handle the multiple fixture object creation, similar...

[arvados.git] / services / api / script / crunch-dispatch.rb

#!/usr/bin/env ruby

include Process

$options = {}
(ARGV.any? ? ARGV : ['--jobs', '--pipelines']).each do |arg|
  case arg
  when '--jobs'
    $options[:jobs] = true
  when '--pipelines'
    $options[:pipelines] = true
  else
    abort "Unrecognized command line option '#{arg}'"
  end
end
if not ($options[:jobs] or $options[:pipelines])
  abort "Nothing to do. Please specify at least one of: --jobs, --pipelines."
end

ARGV.reject! { |a| a =~ /--jobs|--pipelines/ }

$warned = {}
$signal = {}
%w{TERM INT}.each do |sig|
  signame = sig
  Signal.trap(sig) do
    $stderr.puts "Received #{signame} signal"
    $signal[:term] = true
  end
end

if ENV["CRUNCH_DISPATCH_LOCKFILE"]
  lockfilename = ENV.delete "CRUNCH_DISPATCH_LOCKFILE"
  lockfile = File.open(lockfilename, File::RDWR|File::CREAT, 0644)
  unless lockfile.flock File::LOCK_EX|File::LOCK_NB
    abort "Lock unavailable on #{lockfilename} - exit"
  end
end

ENV["RAILS_ENV"] = ARGV[0] || ENV["RAILS_ENV"] || "development"

require File.dirname(__FILE__) + '/../config/boot'
require File.dirname(__FILE__) + '/../config/environment'
require 'open3'

class Dispatcher
  include ApplicationHelper

  def sysuser
    return act_as_system_user
  end

  def refresh_todo
    @todo = []
    if $options[:jobs]
      @todo = Job.queue.select(&:repository)
    end
    @todo_pipelines = []
    if $options[:pipelines]
      @todo_pipelines = PipelineInstance.queue
    end
  end

  def each_slurm_line(cmd, outfmt, max_fields=nil)
    max_fields ||= outfmt.split(":").size
    max_fields += 1  # To accommodate the node field we add
    @@slurm_version ||= Gem::Version.new(`sinfo --version`.match(/\b[\d\.]+\b/)[0])
    if Gem::Version.new('2.3') <= @@slurm_version
      `#{cmd} --noheader -o '%n:#{outfmt}'`.each_line do |line|
        yield line.chomp.split(":", max_fields)
      end
    else
      # Expand rows with hostname ranges (like "foo[1-3,5,9-12]:idle")
      # into multiple rows with one hostname each.
      `#{cmd} --noheader -o '%N:#{outfmt}'`.each_line do |line|
        tokens = line.chomp.split(":", max_fields)
        if (re = tokens[0].match /^(.*?)\[([-,\d]+)\]$/)
          tokens.shift
          re[2].split(",").each do |range|
            range = range.split("-").collect(&:to_i)
            (range[0]..range[-1]).each do |n|
              yield [re[1] + n.to_s] + tokens
            end
          end
        else
          yield tokens
        end
      end
    end
  end

  def slurm_status
    slurm_nodes = {}
    each_slurm_line("sinfo", "%t") do |hostname, state|
      state.sub!(/\W+$/, "")
      state = "down" unless %w(idle alloc down).include?(state)
      slurm_nodes[hostname] = {state: state, job: nil}
    end
    each_slurm_line("squeue", "%j") do |hostname, job_uuid|
      slurm_nodes[hostname][:job] = job_uuid if slurm_nodes[hostname]
    end
    slurm_nodes
  end

  def update_node_status
    return unless Server::Application.config.crunch_job_wrapper.to_s.match /^slurm/
    @node_state ||= {}
    slurm_status.each_pair do |hostname, slurmdata|
      next if @node_state[hostname] == slurmdata
      begin
        node = Node.where('hostname=?', hostname).order(:last_ping_at).last
        if node
          $stderr.puts "dispatch: update #{hostname} state to #{slurmdata}"
          node.info["slurm_state"] = slurmdata[:state]
          node.job_uuid = slurmdata[:job]
          if node.save
            @node_state[hostname] = slurmdata
          else
            $stderr.puts "dispatch: failed to update #{node.uuid}: #{node.errors.messages}"
          end
        elsif slurmdata[:state] != 'down'
          $stderr.puts "dispatch: SLURM reports '#{hostname}' is not down, but no node has that name"
        end
      rescue => error
        $stderr.puts "dispatch: error updating #{hostname} node status: #{error}"
      end
    end
  end

  def positive_int(raw_value, default=nil)
    value = begin raw_value.to_i rescue 0 end
    if value > 0
      value
    else
      default
    end
  end

  NODE_CONSTRAINT_MAP = {
    # Map Job runtime_constraints keys to the corresponding Node info key.
    'min_ram_mb_per_node' => 'total_ram_mb',
    'min_scratch_mb_per_node' => 'total_scratch_mb',
    'min_cores_per_node' => 'total_cpu_cores',
  }

  def nodes_available_for_job_now(job)
    # Find Nodes that satisfy a Job's runtime constraints (by building
    # a list of Procs and using them to test each Node).  If there
    # enough to run the Job, return an array of their names.
    # Otherwise, return nil.
    need_procs = NODE_CONSTRAINT_MAP.each_pair.map do |job_key, node_key|
      Proc.new do |node|
        positive_int(node.info[node_key], 0) >=
          positive_int(job.runtime_constraints[job_key], 0)
      end
    end
    min_node_count = positive_int(job.runtime_constraints['min_nodes'], 1)
    usable_nodes = []
    Node.find_each do |node|
      good_node = (node.info['slurm_state'] == 'idle')
      need_procs.each { |node_test| good_node &&= node_test.call(node) }
      if good_node
        usable_nodes << node
        if usable_nodes.count >= min_node_count
          return usable_nodes.map { |node| node.hostname }
        end
      end
    end
    nil
  end

  def nodes_available_for_job(job)
    # Check if there are enough idle nodes with the Job's minimum
    # hardware requirements to run it.  If so, return an array of
    # their names.  If not, up to once per hour, signal start_jobs to
    # hold off launching Jobs.  This delay is meant to give the Node
    # Manager an opportunity to make new resources available for new
    # Jobs.
    #
    # The exact timing parameters here might need to be adjusted for
    # the best balance between helping the longest-waiting Jobs run,
    # and making efficient use of immediately available resources.
    # These are all just first efforts until we have more data to work
    # with.
    nodelist = nodes_available_for_job_now(job)
    if nodelist.nil? and not did_recently(:wait_for_available_nodes, 3600)
      $stderr.puts "dispatch: waiting for nodes for #{job.uuid}"
      @node_wait_deadline = Time.now + 5.minutes
    end
    nodelist
  end

  def start_jobs
    @todo.each do |job|
      next if @running[job.uuid]

      cmd_args = nil
      case Server::Application.config.crunch_job_wrapper
      when :none
        if @running.size > 0
            # Don't run more than one at a time.
            return
        end
        cmd_args = []
      when :slurm_immediate
        nodelist = nodes_available_for_job(job)
        if nodelist.nil?
          if Time.now < @node_wait_deadline
            break
          else
            next
          end
        end
        cmd_args = ["salloc",
                    "--chdir=/",
                    "--immediate",
                    "--exclusive",
                    "--no-kill",
                    "--job-name=#{job.uuid}",
                    "--nodelist=#{nodelist.join(',')}"]
      else
        raise "Unknown crunch_job_wrapper: #{Server::Application.config.crunch_job_wrapper}"
      end

      if Server::Application.config.crunch_job_user
        cmd_args.unshift("sudo", "-E", "-u",
                         Server::Application.config.crunch_job_user,
                         "PATH=#{ENV['PATH']}",
                         "PERLLIB=#{ENV['PERLLIB']}",
                         "PYTHONPATH=#{ENV['PYTHONPATH']}",
                         "RUBYLIB=#{ENV['RUBYLIB']}",
                         "GEM_PATH=#{ENV['GEM_PATH']}")
      end

      job_auth = ApiClientAuthorization.
        new(user: User.where('uuid=?', job.modified_by_user_uuid).first,
            api_client_id: 0)
      if not job_auth.save
        $stderr.puts "dispatch: job_auth.save failed"
        next
      end

      crunch_job_bin = (ENV['CRUNCH_JOB_BIN'] || `which arv-crunch-job`.strip)
      if crunch_job_bin == ''
        raise "No CRUNCH_JOB_BIN env var, and crunch-job not in path."
      end

      require 'shellwords'

      arvados_internal = Rails.configuration.git_internal_dir
      if not File.exists? arvados_internal
        $stderr.puts `mkdir -p #{arvados_internal.shellescape} && cd #{arvados_internal.shellescape} && git init --bare`
      end

      repo_root = Rails.configuration.git_repositories_dir
      src_repo = File.join(repo_root, job.repository + '.git')
      if not File.exists? src_repo
        src_repo = File.join(repo_root, job.repository, '.git')
        if not File.exists? src_repo
          $stderr.puts "dispatch: No #{job.repository}.git or #{job.repository}/.git at #{repo_root}"
          sleep 1
          next
        end
      end

      git = "git --git-dir=#{arvados_internal.shellescape}"

      # check if the commit needs to be fetched or not
      commit_rev = `#{git} rev-list -n1 #{job.script_version.shellescape} 2>/dev/null`.chomp
      unless $? == 0 and commit_rev == job.script_version
        # commit does not exist in internal repository, so import the source repository using git fetch-pack
        cmd = "#{git} fetch-pack --no-progress --all #{src_repo.shellescape}"
        $stderr.puts cmd
        $stderr.puts `#{cmd}`
        unless $? == 0
          $stderr.puts "dispatch: git fetch-pack failed"
          sleep 1
          next
        end
      end

      # check if the commit needs to be tagged with this job uuid
      tag_rev = `#{git} rev-list -n1 #{job.uuid.shellescape} 2>/dev/null`.chomp
      if $? != 0
        # no job tag found, so create one
        cmd = "#{git} tag #{job.uuid.shellescape} #{job.script_version.shellescape}"
        $stderr.puts cmd
        $stderr.puts `#{cmd}`
        unless $? == 0
          $stderr.puts "dispatch: git tag failed"
          sleep 1
          next
        end
      else
        # job tag found, check that it has the expected revision
        unless tag_rev == job.script_version
          # Uh oh, the tag doesn't point to the revision we were expecting.
          # Someone has been monkeying with the job record and/or git.
          $stderr.puts "dispatch: Already a tag #{job.script_version} pointing to commit #{tag_rev} but expected commit #{job.script_version}"
          job.state = "Failed"
          if not job.save
            $stderr.puts "dispatch: job.save failed"
            next
          end
          next
        end
      end

      cmd_args << crunch_job_bin
      cmd_args << '--job-api-token'
      cmd_args << job_auth.api_token
      cmd_args << '--job'
      cmd_args << job.uuid
      cmd_args << '--git-dir'
      cmd_args << arvados_internal

      $stderr.puts "dispatch: #{cmd_args.join ' '}"

      begin
        i, o, e, t = Open3.popen3(*cmd_args)
      rescue
        $stderr.puts "dispatch: popen3: #{$!}"
        sleep 1
        next
      end

      $stderr.puts "dispatch: job #{job.uuid}"
      start_banner = "dispatch: child #{t.pid} start #{Time.now.ctime.to_s}"
      $stderr.puts start_banner

      @running[job.uuid] = {
        stdin: i,
        stdout: o,
        stderr: e,
        wait_thr: t,
        job: job,
        buf: {stderr: '', stdout: ''},
        started: false,
        sent_int: 0,
        job_auth: job_auth,
        stderr_buf_to_flush: '',
        stderr_flushed_at: Time.new(0),
        bytes_logged: 0,
        events_logged: 0,
        log_throttle_timestamp: Time.new(0),
        log_throttle_bytes_so_far: 0,
        log_throttle_lines_so_far: 0,
        log_throttle_bytes_skipped: 0,
      }
      i.close
      update_node_status
    end
  end

  # Test for hard cap on total output and for log throttling.  Returns whether
  # the log line should go to output or not.  Modifies "line" in place to
  # replace it with an error if a logging limit is tripped.
  def rate_limit running_job, line
    if running_job[:bytes_logged] > Rails.configuration.crunch_limit_log_bytes_per_job
      # Don't log anything if the hard cap has already been exceeded
      return false
    end

    now = Time.now
    throttle_period = Rails.configuration.crunch_log_throttle_period

    if running_job[:log_throttle_bytes_skipped] > 0
      # We've skipped some log in the current time period already, so continue to
      # skip the log
      running_job[:log_throttle_bytes_skipped] += line.size
      return false
    end

    # Count lines and bytes logged in this period, and total bytes logged for the job
    running_job[:log_throttle_lines_so_far] += 1
    running_job[:log_throttle_bytes_so_far] += line.size
    running_job[:bytes_logged] += line.size

    if running_job[:log_throttle_bytes_so_far] > Rails.configuration.crunch_log_throttle_bytes or
        running_job[:log_throttle_lines_so_far] > Rails.configuration.crunch_log_throttle_lines
      # We've exceeded the per-period throttle, so start skipping
      running_job[:log_throttle_bytes_skipped] += line.size

      # Replace log line with a message about skipping the log
      remaining_time = throttle_period - (now - running_job[:log_throttle_timestamp])
      if running_job[:log_throttle_bytes_so_far] > Rails.configuration.crunch_log_throttle_bytes
        line.replace "Exceeded rate #{Rails.configuration.crunch_log_throttle_bytes} bytes per #{throttle_period} seconds (crunch_log_throttle_bytes), logging will be silenced for the next #{remaining_time.round} seconds\n"
      else
        line.replace "Exceeded rate #{Rails.configuration.crunch_log_throttle_lines} lines per #{throttle_period} seconds (crunch_log_throttle_lines), logging will be silenced for the next #{remaining_time.round} seconds\n"
      end
    end

    if running_job[:bytes_logged] > Rails.configuration.crunch_limit_log_bytes_per_job
      # Replace log line with a message about truncating the log
      line.replace "Exceeded log limit #{Rails.configuration.crunch_limit_log_bytes_per_job} bytes (crunch_limit_log_bytes_per_job).  Log will be truncated."
    end

    true
  end

  def read_pipes
    @running.each do |job_uuid, j|
      job = j[:job]

      now = Time.now
      if (now - j[:log_throttle_timestamp]) > Rails.configuration.crunch_log_throttle_period
        # It has been more than throttle_period seconds since the last checkpoint so reset the
        # throttle
        if j[:log_throttle_bytes_skipped] > 0
          j[:stderr_buf_to_flush] << "Skipped #{j[:log_throttle_bytes_skipped]} bytes of log"
        end

        j[:log_throttle_timestamp] = now
        j[:log_throttle_bytes_so_far] = 0
        j[:log_throttle_lines_so_far] = 0
        j[:log_throttle_bytes_skipped] = 0
      end

      j[:buf].each do |stream, streambuf|
        # Read some data from the child stream
        buf = false
        begin
          buf = j[stream].read_nonblock(2**16)
        rescue Errno::EAGAIN, EOFError
        end

        if buf
          # Add to the stream buffer
          streambuf << buf

          # Check for at least one complete line
          if streambuf.index "\n"
            lines = streambuf.lines("\n").to_a

            # check if the last line is partial or not
            streambuf.replace(if streambuf[-1] == "\n"
                                ''        # ends on a newline
                              else
                                lines.pop # Put the partial line back into the buffer
                              end)

            # Now spool the lines to the log output buffer
            lines.each do |line|
              # rate_limit returns true or false as to whether to actually log
              # the line or not.  It also modifies "line" in place to replace
              # it with an error if a logging limit is tripped.
              if rate_limit j, line
                $stderr.print "#{job_uuid} ! " unless line.index(job_uuid)
                $stderr.puts line
                pub_msg = "#{Time.now.ctime.to_s} #{line.strip} \n"
                j[:stderr_buf_to_flush] << pub_msg
              end
              # Send log output to the logs table
              write_log j
            end
          end
        end
      end
    end
  end

  def reap_children
    return if 0 == @running.size
    pid_done = nil
    j_done = nil

    if false
      begin
        pid_done = waitpid(-1, Process::WNOHANG | Process::WUNTRACED)
        if pid_done
          j_done = @running.values.
            select { |j| j[:wait_thr].pid == pid_done }.
            first
        end
      rescue SystemCallError
        # I have @running processes but system reports I have no
        # children. This is likely to happen repeatedly if it happens at
        # all; I will log this no more than once per child process I
        # start.
        if 0 < @running.select { |uuid,j| j[:warned_waitpid_error].nil? }.size
          children = @running.values.collect { |j| j[:wait_thr].pid }.join ' '
          $stderr.puts "dispatch: IPC bug: waitpid() error (#{$!}), but I have children #{children}"
        end
        @running.each do |uuid,j| j[:warned_waitpid_error] = true end
      end
    else
      @running.each do |uuid, j|
        if j[:wait_thr].status == false
          pid_done = j[:wait_thr].pid
          j_done = j
        end
      end
    end

    return if !pid_done

    job_done = j_done[:job]
    $stderr.puts "dispatch: child #{pid_done} exit"
    $stderr.puts "dispatch: job #{job_done.uuid} end"

    # Ensure every last drop of stdout and stderr is consumed
    read_pipes
    j_done[:stderr_flushed_at] = Time.new(0) # reset flush timestamp to make sure log gets written
    write_log j_done # write any remaining logs

    j_done[:buf].each do |stream, streambuf|
      if streambuf != ''
        $stderr.puts streambuf + "\n"
      end
    end

    # Wait the thread (returns a Process::Status)
    exit_status = j_done[:wait_thr].value.exitstatus

    jobrecord = Job.find_by_uuid(job_done.uuid)
    if exit_status != 75 and jobrecord.state == "Running"
      # crunch-job did not return exit code 75 (see below) and left the job in
      # the "Running" state, which means there was an unhandled error.  Fail
      # the job.
      jobrecord.state = "Failed"
      if not jobrecord.save
        $stderr.puts "dispatch: jobrecord.save failed"
      end
    else
      # Don't fail the job if crunch-job didn't even get as far as
      # starting it. If the job failed to run due to an infrastructure
      # issue with crunch-job or slurm, we want the job to stay in the
      # queue. If crunch-job exited after losing a race to another
      # crunch-job process, it exits 75 and we should leave the job
      # record alone so the winner of the race do its thing.
      #
      # There is still an unhandled race condition: If our crunch-job
      # process is about to lose a race with another crunch-job
      # process, but crashes before getting to its "exit 75" (for
      # example, "cannot fork" or "cannot reach API server") then we
      # will assume incorrectly that it's our process's fault
      # jobrecord.started_at is non-nil, and mark the job as failed
      # even though the winner of the race is probably still doing
      # fine.
    end

    # Invalidate the per-job auth token
    j_done[:job_auth].update_attributes expires_at: Time.now

    @running.delete job_done.uuid
  end

  def update_pipelines
    expire_tokens = @pipe_auth_tokens.dup
    @todo_pipelines.each do |p|
      pipe_auth = (@pipe_auth_tokens[p.uuid] ||= ApiClientAuthorization.
                   create(user: User.where('uuid=?', p.modified_by_user_uuid).first,
                          api_client_id: 0))
      puts `export ARVADOS_API_TOKEN=#{pipe_auth.api_token} && arv-run-pipeline-instance --run-pipeline-here --no-wait --instance #{p.uuid}`
      expire_tokens.delete p.uuid
    end

    expire_tokens.each do |k, v|
      v.update_attributes expires_at: Time.now
      @pipe_auth_tokens.delete k
    end
  end

  def run
    act_as_system_user
    @running ||= {}
    @pipe_auth_tokens ||= { }
    $stderr.puts "dispatch: ready"
    while !$signal[:term] or @running.size > 0
      read_pipes
      if $signal[:term]
        @running.each do |uuid, j|
          if !j[:started] and j[:sent_int] < 2
            begin
              Process.kill 'INT', j[:wait_thr].pid
            rescue Errno::ESRCH
              # No such pid = race condition + desired result is
              # already achieved
            end
            j[:sent_int] += 1
          end
        end
      else
        refresh_todo unless did_recently(:refresh_todo, 1.0)
        update_node_status
        unless @todo.empty? or did_recently(:start_jobs, 1.0) or $signal[:term]
          start_jobs
        end
        unless (@todo_pipelines.empty? and @pipe_auth_tokens.empty?) or did_recently(:update_pipelines, 5.0)
          update_pipelines
        end
      end
      reap_children
      select(@running.values.collect { |j| [j[:stdout], j[:stderr]] }.flatten,
             [], [], 1)
    end
  end

  protected

  def did_recently(thing, min_interval)
    @did_recently ||= {}
    if !@did_recently[thing] or @did_recently[thing] < Time.now - min_interval
      @did_recently[thing] = Time.now
      false
    else
      true
    end
  end

  # send message to log table. we want these records to be transient
  def write_log running_job
    return if running_job[:stderr_buf_to_flush] == ''
    return if running_job[:events_logged] > Rails.configuration.crunch_limit_log_events_per_job

    # Send out to log event if buffer size exceeds the bytes per event or if
    # it has been at least crunch_log_seconds_between_events seconds since
    # the last flush.
    if running_job[:stderr_buf_to_flush].size > Rails.configuration.crunch_log_bytes_per_event or
        (Time.now - running_job[:stderr_flushed_at]) >= Rails.configuration.crunch_log_seconds_between_events
      begin
        # Just reached crunch_limit_log_events_per_job so replace log with notification.
        if running_job[:events_logged] == Rails.configuration.crunch_limit_log_events_per_job
          running_job[:stderr_buf_to_flush] =
            "Exceeded live log limit #{Rails.configuration.crunch_limit_log_events_per_job} events (crunch_limit_log_events_per_job).  Live log will be truncated."
        end
        log = Log.new(object_uuid: running_job[:job].uuid,
                      event_type: 'stderr',
                      owner_uuid: running_job[:job].owner_uuid,
                      properties: {"text" => running_job[:stderr_buf_to_flush]})
        log.save!
        running_job[:events_logged] += 1
      rescue => exception
        $stderr.puts "Failed to write logs"
        $stderr.puts exception.backtrace
      end
      running_job[:stderr_buf_to_flush] = ''
      running_job[:stderr_flushed_at] = Time.now
    end
  end
end

# This is how crunch-job child procs know where the "refresh" trigger file is
ENV["CRUNCH_REFRESH_TRIGGER"] = Rails.configuration.crunch_refresh_trigger

Dispatcher.new.run