7 %w{TERM INT}.each do |sig|
10 $stderr.puts "Received #{signame} signal"
15 if ENV["CRUNCH_DISPATCH_LOCKFILE"]
16 lockfilename = ENV.delete "CRUNCH_DISPATCH_LOCKFILE"
17 lockfile = File.open(lockfilename, File::RDWR|File::CREAT, 0644)
18 unless lockfile.flock File::LOCK_EX|File::LOCK_NB
19 abort "Lock unavailable on #{lockfilename} - exit"
23 ENV["RAILS_ENV"] = ARGV[0] || ENV["RAILS_ENV"] || "development"
25 require File.dirname(__FILE__) + '/../config/boot'
26 require File.dirname(__FILE__) + '/../config/environment'
30 LOG_BUFFER_SIZE = 2**20
33 $previous_tmp_log_at = Time.now
34 TMP_LOG_BUFFER_SIZE = 4096
37 include ApplicationHelper
40 return act_as_system_user
44 @todo = Job.queue.select do |j| j.repository end
45 @todo_pipelines = PipelineInstance.queue
49 @@slurm_version ||= Gem::Version.new(`sinfo --version`.match(/\b[\d\.]+\b/)[0])
50 if Gem::Version.new('2.3') <= @@slurm_version
51 `sinfo --noheader -o '%n:%t'`.strip
53 # Expand rows with hostname ranges (like "foo[1-3,5,9-12]:idle")
54 # into multiple rows with one hostname each.
55 `sinfo --noheader -o '%N:%t'`.split("\n").collect do |line|
56 tokens = line.split ":"
57 if (re = tokens[0].match /^(.*?)\[([-,\d]+)\]$/)
58 re[2].split(",").collect do |range|
59 range = range.split("-").collect(&:to_i)
60 (range[0]..range[-1]).collect do |n|
61 [re[1] + n.to_s, tokens[1..-1]].join ":"
71 def update_node_status
72 if Server::Application.config.crunch_job_wrapper.to_s.match /^slurm/
73 @nodes_in_state = {idle: 0, alloc: 0, down: 0}
79 re = line.match /(\S+?):+(idle|alloc|down)/
82 # sinfo tells us about a node N times if it is shared by N partitions
83 next if node_seen[re[1]]
84 node_seen[re[1]] = true
86 # count nodes in each state
87 @nodes_in_state[re[2].to_sym] += 1
89 # update our database (and cache) when a node's state changes
90 if @node_state[re[1]] != re[2]
91 @node_state[re[1]] = re[2]
92 node = Node.where('hostname=?', re[1]).first
94 $stderr.puts "dispatch: update #{re[1]} state to #{re[2]}"
95 node.info[:slurm_state] = re[2]
98 $stderr.puts "dispatch: sinfo reports '#{re[1]}' is not down, but no node has that name"
112 if job.runtime_constraints['min_nodes']
113 min_nodes = begin job.runtime_constraints['min_nodes'].to_i rescue 1 end
118 next if @nodes_in_state[:idle] < min_nodes
122 next if @running[job.uuid]
126 case Server::Application.config.crunch_job_wrapper
129 when :slurm_immediate
130 cmd_args = ["salloc",
135 "--job-name=#{job.uuid}",
136 "--nodes=#{min_nodes}"]
138 raise "Unknown crunch_job_wrapper: #{Server::Application.config.crunch_job_wrapper}"
141 if Server::Application.config.crunch_job_user
142 cmd_args.unshift("sudo", "-E", "-u",
143 Server::Application.config.crunch_job_user,
144 "PERLLIB=#{ENV['PERLLIB']}")
147 job_auth = ApiClientAuthorization.
148 new(user: User.where('uuid=?', job.modified_by_user_uuid).first,
152 crunch_job_bin = (ENV['CRUNCH_JOB_BIN'] || `which arv-crunch-job`.strip)
153 if crunch_job_bin == ''
154 raise "No CRUNCH_JOB_BIN env var, and crunch-job not in path."
159 arvados_internal = Rails.configuration.git_internal_dir
160 if not File.exists? arvados_internal
161 $stderr.puts `mkdir -p #{arvados_internal.shellescape} && cd #{arvados_internal.shellescape} && git init --bare`
164 src_repo = File.join(Rails.configuration.git_repositories_dir, job.repository + '.git')
165 src_repo = File.join(Rails.configuration.git_repositories_dir, job.repository, '.git') unless File.exists? src_repo
168 $stderr.puts "dispatch: #{File.join Rails.configuration.git_repositories_dir, job.repository} doesn't exist"
174 $stderr.puts `cd #{arvados_internal.shellescape} && git fetch --no-tags #{src_repo.shellescape} && git tag #{job.uuid.shellescape} #{job.script_version.shellescape}`
176 cmd_args << crunch_job_bin
177 cmd_args << '--job-api-token'
178 cmd_args << job_auth.api_token
181 cmd_args << '--git-dir'
182 cmd_args << arvados_internal
184 $stderr.puts "dispatch: #{cmd_args.join ' '}"
187 i, o, e, t = Open3.popen3(*cmd_args)
189 $stderr.puts "dispatch: popen3: #{$!}"
195 $stderr.puts "dispatch: job #{job.uuid}"
196 start_banner = "dispatch: child #{t.pid} start #{Time.now.ctime.to_s}"
197 $stderr.puts start_banner
198 $redis.set job.uuid, start_banner + "\n"
199 $redis.publish job.uuid, start_banner
200 $redis.publish job.owner_uuid, start_banner
202 @running[job.uuid] = {
218 # no-op -- let crunch-job take care of locking.
223 # no-op -- let crunch-job take care of locking.
228 @running.each do |job_uuid, j|
231 # Throw away child stdout
233 j[:stdout].read_nonblock(2**20)
234 rescue Errno::EAGAIN, EOFError
237 # Read whatever is available from child stderr
240 stderr_buf = j[:stderr].read_nonblock(2**20)
241 rescue Errno::EAGAIN, EOFError
245 j[:stderr_buf] << stderr_buf
246 if j[:stderr_buf].index "\n"
247 lines = j[:stderr_buf].lines("\n").to_a
248 if j[:stderr_buf][-1] == "\n"
251 j[:stderr_buf] = lines.pop
254 $stderr.print "#{job_uuid} ! " unless line.index(job_uuid)
256 pub_msg = "#{Time.now.ctime.to_s} #{line.strip}"
257 $redis.publish job.owner_uuid, pub_msg
258 $redis.publish job_uuid, pub_msg
259 $redis.append job_uuid, pub_msg + "\n"
260 if LOG_BUFFER_SIZE < $redis.strlen(job_uuid)
263 .getrange(job_uuid, (LOG_BUFFER_SIZE >> 1), -1)
267 if (TMP_LOG_BUFFER_SIZE < $tmp_log_buffer.size) || ($previous_tmp_log_at+1 < Time.now)
268 $tmp_log_buffer += (pub_msg + "\n")
271 $tmp_log_buffer += (pub_msg + "\n")
280 return if 0 == @running.size
286 pid_done = waitpid(-1, Process::WNOHANG | Process::WUNTRACED)
288 j_done = @running.values.
289 select { |j| j[:wait_thr].pid == pid_done }.
292 rescue SystemCallError
293 # I have @running processes but system reports I have no
294 # children. This is likely to happen repeatedly if it happens at
295 # all; I will log this no more than once per child process I
297 if 0 < @running.select { |uuid,j| j[:warned_waitpid_error].nil? }.size
298 children = @running.values.collect { |j| j[:wait_thr].pid }.join ' '
299 $stderr.puts "dispatch: IPC bug: waitpid() error (#{$!}), but I have children #{children}"
301 @running.each do |uuid,j| j[:warned_waitpid_error] = true end
304 @running.each do |uuid, j|
305 if j[:wait_thr].status == false
306 pid_done = j[:wait_thr].pid
314 job_done = j_done[:job]
315 $stderr.puts "dispatch: child #{pid_done} exit"
316 $stderr.puts "dispatch: job #{job_done.uuid} end"
318 # Ensure every last drop of stdout and stderr is consumed
320 write_log job_done.uuid # write any remaining logs
322 if j_done[:stderr_buf] and j_done[:stderr_buf] != ''
323 $stderr.puts j_done[:stderr_buf] + "\n"
327 j_done[:wait_thr].value
329 jobrecord = Job.find_by_uuid(job_done.uuid)
330 if jobrecord.started_at
331 # Clean up state fields in case crunch-job exited without
332 # putting the job in a suitable "finished" state.
333 jobrecord.running = false
334 jobrecord.finished_at ||= Time.now
335 if jobrecord.success.nil?
336 jobrecord.success = false
340 # Don't fail the job if crunch-job didn't even get as far as
341 # starting it. If the job failed to run due to an infrastructure
342 # issue with crunch-job or slurm, we want the job to stay in the
346 # Invalidate the per-job auth token
347 j_done[:job_auth].update_attributes expires_at: Time.now
349 $redis.publish job_done.uuid, "end"
351 @running.delete job_done.uuid
355 expire_tokens = @pipe_auth_tokens.dup
356 @todo_pipelines.each do |p|
357 pipe_auth = (@pipe_auth_tokens[p.uuid] ||= ApiClientAuthorization.
358 create(user: User.where('uuid=?', p.modified_by_user_uuid).first,
360 puts `export ARVADOS_API_TOKEN=#{pipe_auth.api_token} && arv-run-pipeline-instance --run-here --no-wait --instance #{p.uuid}`
361 expire_tokens.delete p.uuid
364 expire_tokens.each do |k, v|
365 v.update_attributes expires_at: Time.now
366 @pipe_auth_tokens.delete k
373 @pipe_auth_tokens ||= { }
374 $stderr.puts "dispatch: ready"
375 while !$signal[:term] or @running.size > 0
378 @running.each do |uuid, j|
379 if !j[:started] and j[:sent_int] < 2
381 Process.kill 'INT', j[:wait_thr].pid
383 # No such pid = race condition + desired result is
390 refresh_todo unless did_recently(:refresh_todo, 1.0)
392 unless @todo.empty? or did_recently(:start_jobs, 1.0) or $signal[:term]
395 unless (@todo_pipelines.empty? and @pipe_auth_tokens.empty?) or did_recently(:update_pipelines, 5.0)
400 select(@running.values.collect { |j| [j[:stdout], j[:stderr]] }.flatten,
407 def did_recently(thing, min_interval)
409 if !@did_recently[thing] or @did_recently[thing] < Time.now - min_interval
410 @did_recently[thing] = Time.now
417 # send message to log table. we want these records to be transient
418 def write_log job_uuid
419 if $tmp_log_buffer == ''
422 log = Log.new(object_uuid: job_uuid,
423 event_type:'transient-log-entry',
424 summary: $tmp_log_buffer)
427 $previous_tmp_log_at = Time.now
431 # This is how crunch-job child procs know where the "refresh" trigger file is
432 ENV["CRUNCH_REFRESH_TRIGGER"] = Rails.configuration.crunch_refresh_trigger