class Step STREAM_CACHE = {} STREAM_CACHE_MUTEX = Mutex.new def self.purge_stream_cache Log.debug "Purging dup. stream cache" STREAM_CACHE_MUTEX.synchronize do STREAM_CACHE.clear end end def self.dup_stream(stream) case stream when IO, File, Step return stream if stream.respond_to?(:closed?) and stream.closed? return stream if stream.respond_to?(:done?) and stream.done? STREAM_CACHE_MUTEX.synchronize do stream_key = Misc.fingerprint(stream) current = STREAM_CACHE[stream_key] case current when nil, Step Log.medium "Not duplicating stream #{stream_key}" STREAM_CACHE[stream_key] = stream when File if Open.exists? current.path Log.medium "Reopening file #{stream_key}" Open.open(current.path) else new = Misc.dup_stream(current) Log.medium "Duplicating file #{stream_key} #{current.inspect} => #{Misc.fingerprint(new)}" new end else new = Misc.dup_stream(current) Log.medium "Duplicating stream #{stream_key} #{ Misc.fingerprint(stream) } => #{Misc.fingerprint(new)}" new end end when TSV::Dumper, TSV::Parser orig_stream = stream stream = stream.stream return stream if stream.closed? STREAM_CACHE_MUTEX.synchronize do if STREAM_CACHE[stream].nil? Log.high "Not duplicating #{Misc.fingerprint orig_stream} #{ stream.inspect }" STREAM_CACHE[stream] = stream else new = Misc.dup_stream(STREAM_CACHE[stream]) Log.high "Duplicating #{Misc.fingerprint orig_stream} #{ stream.inspect } into #{new.inspect}" new end end else stream end end def dup_inputs return if @dupped or ENV["RBBT_NO_STREAM"] == 'true' return if ComputeDependency === self and self.compute == :produce Log.low "Dupping inputs for #{path}" dupped_inputs = @inputs.collect do |input| Step.dup_stream input end @inputs.replace dupped_inputs @dupped = true end def self.prepare_for_execution(job) return if job.done? && ! job.dirty? status = job.status.to_s if defined?(WorkflowRESTClient) && WorkflowRESTClient::RemoteStep === job return unless (status == 'done' or status == 'error' or status == 'aborted') else return if status == 'streaming' and job.running? end canfail = nil job.status_lock.synchronize do status = job.status.to_s if (status == 'error' && (job.recoverable_error? || job.dirty?)) || (job.noinfo? && Open.exists?(job.pid_file)) || job.aborted? || (job.done? && ! job.updated?) || (job.error? && ! job.updated?) || (job.done? && job.dirty?) || (job.error? && job.dirty?) || (!(job.noinfo? || job.done? || job.error? || job.aborted? || job.running?)) job.clean end job.dup_inputs unless status == 'done' or job.started? job.init_info unless status == 'noinfo' or status == 'done' or job.started? canfail = ComputeDependency === job && job.canfail? end raise DependencyError, job if job.error? and not canfail end def log_dependency_exec(dependency, action) task_name = self.task_name str = Log.color(:reset, "") str << Log.color(:yellow, task_name.to_s || "") str << " " str << Log.color(:magenta, action.to_s) str << " " str << Log.color(:yellow, dependency.task_name.to_s || "") str << " -- " str << "#{Log.color :blue, dependency.path}" Log.info str end def execute_dependency(dependency, log = true) task_name = self.task_name canfail_paths = self.canfail_paths already_failed = [] begin dependency.resolve_input_steps if dependency.done? dependency.inputs.each do |v| Misc.consume_stream(v) if IO === v Misc.consume_stream(TSV.get_stream v) if Step === v and not v.done? and v.streaming? end log_dependency_exec(dependency, :done) if log return end dependency.status_lock.synchronize do if dependency.aborted? || (dependency.error? && dependency.recoverable_error? && ! canfail_paths.include?(dependency.path) && ! already_failed.include?(dependency.path)) || (!Open.remote?(dependency.path) && dependency.missing?) Log.warn "Cleaning dep. on exec #{Log.color :blue, dependency.path} (missing: #{dependency.missing?}; error #{dependency.error?})" dependency.clean already_failed << dependency.path raise TryAgain end end if ! (dependency.started? || dependency.error?) log_dependency_exec(dependency, :starting) dependency.run(true) raise TryAgain end dependency.grace if dependency.error? log_dependency_exec(dependency, :error) raise DependencyError, [dependency.path, dependency.messages.last] * ": " if dependency.error? end if dependency.streaming? log_dependency_exec(dependency, :streaming) if log return end begin log_dependency_exec(dependency, :joining) dependency.join raise TryAgain unless dependency.done? rescue Aborted raise TryAgain end rescue TryAgain Log.low "Retrying dep. #{Log.color :yellow, dependency.task_name.to_s} -- [#{dependency.status}] #{(dependency.messages || ["No message"]).last}" retry rescue Aborted, Interrupt Log.error "Aborted dep. #{Log.color :red, dependency.task_name.to_s}" raise $! rescue Interrupt Log.error "Interrupted while in dep. #{Log.color :red, dependency.task_name.to_s}" raise $! rescue Exception Log.error "Exception in dep. #{ Log.color :red, dependency.task_name.to_s } -- #{$!.message}" raise $! unless canfail_paths.include? dependency.path end end def execute_and_dup(step, dep_step, log = true) dup = step.result.nil? execute_dependency(step, log) if dup and step.streaming? and not step.result.nil? if dep_step[step.path] and dep_step[step.path].length > 1 stream = step.result other_steps = dep_step[step.path] return unless other_steps.length > 1 log_dependency_exec(step, "duplicating #{other_steps.length}") copies = Misc.tee_stream_thread_multiple(stream, other_steps.length) copies.extend StreamArray step.instance_variable_set("@result", copies) end end end def run_compute_dependencies(type, list, dep_step = {}) if Array === type type, *rest = type end canfail = rest && rest.include?(:canfail) case type when :canfail list.each do |dep| begin dep.produce rescue RbbtException Log.warn "Allowing failing of #{dep.path}: #{dep.messages.last}" end nil end when :produce, :no_dup list.each do |step| Misc.insist do begin step.produce rescue RbbtException raise $! unless canfail || step.canfail? rescue Exception step.exception $! if step.recoverable_error? raise $! else raise StopInsist.new($!) end end end end nil when :bootstrap cpus = rest.nil? ? nil : rest.first cpus = config('dep_cpus', 'bootstrap', :default => [5, list.length / 2].min) if cpus.nil? || cpus.to_i == 0 respawn = rest && rest.include?(:respawn) respawn = false if rest && rest.include?(:norespawn) respawn = rest && rest.include?(:always_respawn) respawn = :always if respawn.nil? Misc.bootstrap(list, cpus, :bar => "Bootstrapping dependencies for #{path} [#{cpus}]", :respawn => respawn) do |dep| begin Signal.trap(:INT) do dep.abort raise Aborted end Misc.insist do begin dep.produce Log.warn "Error in bootstrap dependency #{dep.path}: #{dep.messages.last}" if dep.error? or dep.aborted? rescue Aborted ex = $! begin dep.abort Log.warn "Aborted bootstrap dependency #{dep.path}: #{dep.messages.last}" if dep.error? or dep.aborted? rescue end raise StopInsist.new(ex) rescue RbbtException if canfail || dep.canfail? Log.warn "Allowing failing of #{dep.path}: #{dep.messages.last}" else Log.warn "NOT Allowing failing of #{dep.path}: #{dep.messages.last}" dep.exception $! if dep.recoverable_error? begin dep.abort rescue end raise $! else raise StopInsist.new($!) end end end end rescue dep.abort raise $! end nil end else list.each do |step| execute_and_dup(step, dep_step, false) end end end def canfail_paths return Set.new if done? && ! Open.exists?(info_file) @canfail_paths ||= begin if info[:canfail] paths = info[:canfail].uniq paths = Workflow.relocate_array self.path, paths if relocated Set.new(paths) else canfail_paths = Set.new all_deps = dependencies || [] all_deps.each do |dep| next if canfail_paths.include? dep.path canfail_paths += dep.canfail_paths next unless ComputeDependency === dep && dep.canfail? canfail_paths << dep.path canfail_paths += dep.rec_dependencies.collect{|d| d.path } end canfail_paths begin set_info :canfail, canfail_paths.to_a rescue Errno::EROFS end canfail_paths end end end def run_dependencies dep_step = {} rec_dependencies = self.rec_dependencies(true) return if rec_dependencies.empty? all_deps = rec_dependencies + [self] compute_deps = rec_dependencies.collect do |dep| next unless ComputeDependency === dep dep.rec_dependencies end.compact.flatten.uniq canfail_paths = self.canfail_paths seen_paths = Set.new all_deps.uniq.each do |step| next if seen_paths.include? step.path seen_paths << step.path begin Step.prepare_for_execution(step) unless step == self rescue DependencyError raise $! unless canfail_paths.include? step.path end next unless step.dependencies and step.dependencies.any? step.dependencies.each do |step_dep| next if step_dep.done? or step_dep.running? or (ComputeDependency === step_dep and (step_dep.compute == :nodup or step_dep.compute == :ignore)) dep_step[step_dep.path] ||= [] dep_step[step_dep.path] << step_dep end step.inputs.each do |inputs| inputs = [inputs] unless Array === inputs inputs.each do |step_dep| next unless Step === step_dep next if step_dep.done? or step_dep.running? or (ComputeDependency === step_dep and (step_dep.compute == :nodup or step_dep.compute == :ignore)) dep_step[step_dep.path] ||= [] dep_step[step_dep.path] << step_dep end end end produced = [] dependencies.each do |dep| next unless ComputeDependency === dep if dep.compute == :produce dep.produce produced << dep.path end end self.dup_inputs required_dep_paths = [] dep_step.each do |path,list| required_dep_paths << path if list.length > 1 end required_dep_paths.concat dependencies.collect{|dep| dep.path } log :dependencies, "Dependencies for step #{Log.color :yellow, task.name.to_s || ""}" pre_deps = [] compute_pre_deps = {} last_deps = [] compute_last_deps = {} seen_paths = Set.new rec_dependencies.uniq.each do |step| next if seen_paths.include? step.path seen_paths << step.path next unless required_dep_paths.include? step.path if dependencies.include?(step) and step.inputs.flatten.select{|i| Step === i}.any? if ComputeDependency === step next if produced.include? step.path compute_last_deps[step.compute] ||= [] compute_last_deps[step.compute] << step else last_deps << step end else if ComputeDependency === step next if produced.include? step.path compute_pre_deps[step.compute] ||= [] compute_pre_deps[step.compute] << step else pre_deps << step #if dependencies.include?(step) end end end Log.medium "Processing pre dependencies: #{Misc.fingerprint(pre_deps)} - #{Log.color :blue, self.path}" if pre_deps.any? pre_deps.each do |step| next if compute_deps.include? step begin execute_and_dup(step, dep_step, false) rescue Exception raise $! unless canfail_paths.include?(step.path) end end Log.medium "Computing pre dependencies: #{Misc.fingerprint(compute_pre_deps)} - #{Log.color :blue, self.path}" if compute_pre_deps.any? compute_pre_deps.each do |type,list| run_compute_dependencies(type, list, dep_step) end Log.medium "Processing last dependencies: #{Misc.fingerprint(last_deps)} - #{Log.color :blue, self.path}" if last_deps.any? last_deps.each do |step| next if compute_deps.include? step begin Exception execute_and_dup(step, dep_step) rescue raise $! unless canfail_paths.include? step.path end end Log.medium "Computing last dependencies: #{Misc.fingerprint(compute_last_deps)} - #{Log.color :blue, self.path}" if compute_last_deps.any? compute_last_deps.each do |type,list| run_compute_dependencies(type, list, dep_step) end dangling_deps = all_deps.reject{|dep| dep.done? || canfail_paths.include?(dep.path) }. select{|dep| dep.waiting? } Log.medium "Aborting (actually not) waiting dangling dependencies #{Misc.fingerprint dangling_deps}" if dangling_deps.any? #dangling_deps.each{|dep| dep.abort } end def stop_dependencies return if dependencies.nil? dependencies.each do |dep| if dep.nil? Log.warn "Dependency is nil #{Misc.fingerprint step} -- #{Misc.fingerprint dependencies}" next end next if dep.done? or dep.aborted? dep.abort if dep.running? end kill_children end end