X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/a7f12322bab34a27863d90de9ddb95f69697bf29..4d56f9b913fcf41fbf89bf5016463b5353fa3a9f:/services/api/script/crunch-dispatch.rb diff --git a/services/api/script/crunch-dispatch.rb b/services/api/script/crunch-dispatch.rb deleted file mode 100755 index 00144d3da4..0000000000 --- a/services/api/script/crunch-dispatch.rb +++ /dev/null @@ -1,586 +0,0 @@ -#!/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, - stderr_buf: '', - started: false, - sent_int: 0, - job_auth: job_auth, - stderr_buf_to_flush: '', - stderr_flushed_at: 0, - bytes_logged: 0, - events_logged: 0, - log_truncated: false - } - i.close - update_node_status - end - end - - def read_pipes - @running.each do |job_uuid, j| - job = j[:job] - - # Throw away child stdout - begin - j[:stdout].read_nonblock(2**20) - rescue Errno::EAGAIN, EOFError - end - - # Read whatever is available from child stderr - stderr_buf = false - begin - stderr_buf = j[:stderr].read_nonblock(2**20) - rescue Errno::EAGAIN, EOFError - end - - if stderr_buf - j[:stderr_buf] << stderr_buf - if j[:stderr_buf].index "\n" - lines = j[:stderr_buf].lines("\n").to_a - if j[:stderr_buf][-1] == "\n" - j[:stderr_buf] = '' - else - j[:stderr_buf] = lines.pop - end - lines.each do |line| - $stderr.print "#{job_uuid} ! " unless line.index(job_uuid) - $stderr.puts line - pub_msg = "#{Time.now.ctime.to_s} #{line.strip} \n" - if not j[:log_truncated] - j[:stderr_buf_to_flush] << pub_msg - end - end - - if not j[:log_truncated] - if (Rails.configuration.crunch_log_bytes_per_event < j[:stderr_buf_to_flush].size or - (j[:stderr_flushed_at] + Rails.configuration.crunch_log_seconds_between_events < Time.now.to_i)) - 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 - write_log j_done # write any remaining logs - - if j_done[:stderr_buf] and j_done[:stderr_buf] != '' - $stderr.puts j_done[:stderr_buf] + "\n" - end - - # Wait the thread (returns a Process::Status) - exit_status = j_done[:wait_thr].value - - jobrecord = Job.find_by_uuid(job_done.uuid) - if exit_status.to_i != 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" - jobrecord.save! - 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 too_many_bytes_logged_for_job(j) - return (j[:bytes_logged] + j[:stderr_buf_to_flush].size > - Rails.configuration.crunch_limit_log_event_bytes_per_job) - end - - def too_many_events_logged_for_job(j) - return (j[:events_logged] >= Rails.configuration.crunch_limit_log_events_per_job) - end - - 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[:log_truncated] - return if running_job[:stderr_buf_to_flush] == '' - begin - # Truncate logs if they exceed crunch_limit_log_event_bytes_per_job - # or crunch_limit_log_events_per_job. - if (too_many_bytes_logged_for_job(running_job)) - running_job[:log_truncated] = true - running_job[:stderr_buf_to_flush] = - "Server configured limit reached (crunch_limit_log_event_bytes_per_job: #{Rails.configuration.crunch_limit_log_event_bytes_per_job}). Subsequent logs truncated" - elsif (too_many_events_logged_for_job(running_job)) - running_job[:log_truncated] = true - running_job[:stderr_buf_to_flush] = - "Server configured limit reached (crunch_limit_log_events_per_job: #{Rails.configuration.crunch_limit_log_events_per_job}). Subsequent logs 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[:bytes_logged] += running_job[:stderr_buf_to_flush].size - running_job[:events_logged] += 1 - rescue - running_job[:stderr_buf] = "Failed to write logs\n" + running_job[:stderr_buf] - end - running_job[:stderr_buf_to_flush] = '' - running_job[:stderr_flushed_at] = Time.now.to_i - 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