Class: WorkflowManager::Server
- Inherits:
-
Object
- Object
- WorkflowManager::Server
- Defined in:
- lib/workflow_manager/server.rb
Defined Under Namespace
Classes: Config, KyotoDB, PStoreDB, RedisDB
Constant Summary collapse
- @@config =
nil
Class Method Summary collapse
Instance Method Summary collapse
- #cluster_node_list ⇒ Object
- #cluster_nodes ⇒ Object
- #config ⇒ Object
- #copy_commands(org_dir, dest_parent_dir, now = nil) ⇒ Object
- #default_node ⇒ Object
- #delete_command(target) ⇒ Object
- #finalize_monitoring(current_status, log_file, log_dir) ⇒ Object
- #get_log(job_id, with_err = false) ⇒ Object
- #get_script(job_id) ⇒ Object
- #get_script_path(job_id) ⇒ Object
- #hello ⇒ Object
-
#initialize ⇒ Server
constructor
A new instance of Server.
- #input_dataset_exist?(file_list) ⇒ Boolean
- #input_dataset_file_list(dataset_tsv_path) ⇒ Object
- #input_dataset_tsv_path(script_content) ⇒ Object
- #job_list(with_results = false, project_number = nil, job_ids: nil) ⇒ Object
- #kill_job(job_id) ⇒ Object
- #log_puts(str) ⇒ Object
- #start_monitoring(submit_command, user = 'sushi lover', resubmit = 0, script = '', project_number = 0, sge_options = '', log_dir = '') ⇒ Object
- #start_monitoring2(script_path, script_content, user = 'sushi_lover', project_number = 0, sge_options = '', log_dir = '') ⇒ Object
- #status(job_id, new_status = nil) ⇒ Object
- #success_or_fail(job_id, log_file) ⇒ Object (also: #check_status)
- #update_time_status(job_id, current_status, script_name, user, project_number) ⇒ Object
Constructor Details
#initialize ⇒ Server
Returns a new instance of Server.
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# File 'lib/workflow_manager/server.rb', line 127 def initialize @interval = config.interval @resubmit = config.resubmit extension = case DB_MODE when "PStore" '.pstore' when "KyotoCabinet" '.kch' when "Redis" @redis_conf = config.redis_conf '.rdb' end @db_stat = File.join(config.db_dir, 'statuses'+extension) @db_logs = File.join(config.db_dir, 'logs'+extension) @log_dir = File.(config.log_dir) @db_dir = File.(config.db_dir) FileUtils.mkdir_p @log_dir unless File.exist?(@log_dir) FileUtils.mkdir_p @db_dir unless File.exist?(@db_dir) @statuses = case DB_MODE when "PStore" PStoreDB.new(@db_stat) when "KyotoCabinet" KyotoDB.new(@db_stat) when "Redis" RedisDB.new(0, @redis_conf) end @logs = case DB_MODE when "PStore" PStoreDB.new(@db_logs) when "KyotoCabinet" KyotoDB.new(@db_logs) when "Redis" RedisDB.new(1, @redis_conf) end @system_log = File.join(@log_dir, "system.log") @mutex = Mutex.new @cluster = config.cluster puts("DB = #{DB_MODE}") if DB_MODE == "Redis" puts("Redis conf = #{config.redis_conf}") puts("Redis port = #{@logs.port}") end puts("Cluster = #{@cluster.name}") log_puts("DB = #{DB_MODE}") log_puts("Cluster = #{@cluster.name}") log_puts("Server starts") end |
Class Method Details
.config ⇒ Object
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# File 'lib/workflow_manager/server.rb', line 61 def self.config @@config end |
.config=(config) ⇒ Object
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# File 'lib/workflow_manager/server.rb', line 58 def self.config=(config) @@config = config end |
.configure {|@@config| ... } ⇒ Object
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# File 'lib/workflow_manager/server.rb', line 67 def self.configure @@config = Config.new # default values @@config.log_dir = LOG_DIR @@config.db_dir = DB_DIR @@config.interval = INTERVAL # interval to check jobs, [s] @@config.resubmit = RESUBMIT # how many times at maximum to resubmit when job fails yield(@@config) if @@config.cluster @@config.cluster.log_dir = File.(@@config.log_dir) end @@config end |
Instance Method Details
#cluster_node_list ⇒ Object
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# File 'lib/workflow_manager/server.rb', line 512 def cluster_node_list @cluster.node_list end |
#cluster_nodes ⇒ Object
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# File 'lib/workflow_manager/server.rb', line 189 def cluster_nodes @cluster.cluster_nodes end |
#config ⇒ Object
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# File 'lib/workflow_manager/server.rb', line 64 def config @@config ||= WorkflowManager.configure{} end |
#copy_commands(org_dir, dest_parent_dir, now = nil) ⇒ Object
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# File 'lib/workflow_manager/server.rb', line 179 def copy_commands(org_dir, dest_parent_dir, now=nil) @cluster.copy_commands(org_dir, dest_parent_dir, now) end |
#default_node ⇒ Object
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# File 'lib/workflow_manager/server.rb', line 192 def default_node @cluster.default_node.to_s end |
#delete_command(target) ⇒ Object
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# File 'lib/workflow_manager/server.rb', line 186 def delete_command(target) @cluster.delete_command(target) end |
#finalize_monitoring(current_status, log_file, log_dir) ⇒ Object
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# File 'lib/workflow_manager/server.rb', line 259 def finalize_monitoring(current_status, log_file, log_dir) if current_status == 'success' or current_status == 'fail' unless log_dir.empty? copy_commands(log_file, log_dir).each do |command| log_puts(command) system command end err_file = log_file.gsub('_o.log','_e.log') copy_commands(err_file, log_dir).each do |command| log_puts(command) system command end end Thread.current.kill end end |
#get_log(job_id, with_err = false) ⇒ Object
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# File 'lib/workflow_manager/server.rb', line 457 def get_log(job_id, with_err=false) log_file = nil @logs.transaction do |logs| log_file = logs[job_id.to_s] end log_data = if log_file and File.exist?(log_file) "__STDOUT LOG__\n\n" + File.read(log_file) else 'no log file' end if with_err err_file = log_file.gsub(/_o\.log/,'_e.log') if err_file and File.exist?(err_file) log_data << "\n\n__STDERR LOG__\n\n" log_data << File.read(err_file) end end log_data end |
#get_script(job_id) ⇒ Object
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# File 'lib/workflow_manager/server.rb', line 476 def get_script(job_id) script_file = nil @logs.transaction do |logs| script_file = logs[job_id.to_s] end if script_file script_file = script_file.gsub(/_o\.log/,'') end script = if script_file and File.exist?(script_file) File.read(script_file) else 'no script file' end script end |
#get_script_path(job_id) ⇒ Object
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# File 'lib/workflow_manager/server.rb', line 491 def get_script_path(job_id) script_file = nil @logs.transaction do |logs| script_file = logs[job_id.to_s] end script_path = if script_file and File.exist?(script_file) script_file.gsub(/_o\.log/,'') end end |
#hello ⇒ Object
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# File 'lib/workflow_manager/server.rb', line 176 def hello 'hello test hoge, '+ @cluster.name end |
#input_dataset_exist?(file_list) ⇒ Boolean
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# File 'lib/workflow_manager/server.rb', line 227 def input_dataset_exist?(file_list) flag = true file_list.each do |file| unless File.exist?(file) flag = false break end end flag end |
#input_dataset_file_list(dataset_tsv_path) ⇒ Object
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# File 'lib/workflow_manager/server.rb', line 216 def input_dataset_file_list(dataset_tsv_path) file_list = [] CSV.foreach(dataset_tsv_path, :headers=>true, :col_sep=>"\t") do |row| row.each do |header, value| if header =~ /\[File\]/ file_list << value end end end file_list end |
#input_dataset_tsv_path(script_content) ⇒ Object
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# File 'lib/workflow_manager/server.rb', line 203 def input_dataset_tsv_path(script_content) gstore_dir = nil input_dataset_path = nil script_content.split(/\n/).each do |line| if line =~ /GSTORE_DIR=(.+)/ gstore_dir = $1.chomp elsif line =~ /INPUT_DATASET=(.+)/ input_dataset_path = $1.chomp break end end [gstore_dir, input_dataset_path] end |
#job_list(with_results = false, project_number = nil, job_ids: nil) ⇒ Object
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# File 'lib/workflow_manager/server.rb', line 436 def job_list(with_results=false, project_number=nil, job_ids:nil) s = [] job_idsh = if job_ids Hash[*(job_ids.split(',')).map{|job_id| [job_id, true]}.flatten] end @statuses.transaction do |statuses| statuses.each do |key, value| if project_number if x = value.split(/,/)[4].to_i==project_number.to_i s << [key, value] end else s << [key, value] end end end if job_ids s = s.select{|job_id, stat| job_idsh[job_id]} end s.sort_by{|key, value| value.split(',')[2]}.reverse.map{|v| v.join(',')}.join("\n") end |
#kill_job(job_id) ⇒ Object
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# File 'lib/workflow_manager/server.rb', line 182 def kill_job(job_id) status(job_id, 'fail') status = `#{@cluster.kill_command(job_id)}` end |
#log_puts(str) ⇒ Object
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# File 'lib/workflow_manager/server.rb', line 195 def log_puts(str) time = Time.now.strftime("[%Y.%m.%d %H:%M:%S]") @mutex.synchronize do open(@system_log, "a") do |out| out.print time + " " + str + "\n" end end end |
#start_monitoring(submit_command, user = 'sushi lover', resubmit = 0, script = '', project_number = 0, sge_options = '', log_dir = '') ⇒ Object
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# File 'lib/workflow_manager/server.rb', line 325 def start_monitoring(submit_command, user = 'sushi lover', resubmit = 0, script = '', project_number = 0, ='', log_dir = '') log_puts("monitoring: script=" + submit_command + " user=" + user + " resubmit=" + resubmit.to_s + " project=" + project_number.to_s + " sge option=" + + " log dir=" + log_dir.to_s) #warn submit_command # # TODO: analyze arguments # job_id, log_file, command = @cluster.submit_job(submit_command, script, ) log_puts("submit: " + job_id + " " + command) # # monitor worker # if job_id and log_file monitor_worker = Thread.new(job_id, log_file, submit_command, user, resubmit, script, project_number, , log_dir) do |t_job_id, t_log_file, t_submit_command, t_user, t_resubmit, t_script, t_project_number, , t_log_dir| loop do status = success_or_fail(t_job_id, t_log_file) script_name = File.basename(submit_command).split(/-/).first #@statuses.open(@db_stat) @statuses.transaction do |statuses| #start_time = if stat = @statuses[t_job_id] and stat = stat.split(/,/) and time = stat[2] start_time = if stat = statuses[t_job_id] and stat = stat.split(/,/) and time = stat[2] time end time = if start_time if status == 'success' or status == 'fail' start_time + '/' + Time.now.strftime("%Y-%m-%d %H:%M:%S") else start_time end else Time.now.strftime("%Y-%m-%d %H:%M:%S") end #@statuses[t_job_id] = [status, script_name, time, user, project_number].join(',') statuses[t_job_id] = [status, script_name, time, user, project_number].join(',') #@statuses.close end @logs.transaction do |logs| logs[t_job_id] = t_log_file end #warn t_job_id + " " + status if status == 'success' log_puts(status + ": " + t_job_id) unless t_log_dir.empty? copy_commands(t_log_file, t_log_dir).each do |command| log_puts(command) system command end err_file = t_log_file.gsub('_o.log','_e.log') copy_commands(err_file, t_log_dir).each do |command| log_puts(command) system command end end Thread.current.kill elsif status == 'fail' log_puts(status + ": " + t_job_id) # # TODO: re-submit # if t_resubmit < RESUBMIT log_puts("resubmit: " + t_job_id) resubmit_job_id = start_monitoring(t_submit_command, t_user, t_resubmit + 1, t_script, t_project_number, ) script_name = File.basename(submit_command).split(/-/).first #@statuses.open(@db_stat) @statuses.transaction do |statuses| statuses[t_job_id] = ["resubmit: " + resubmit_job_id.to_s, script_name, Time.now.strftime("%Y-%m-%d %H:%M:%S"), t_user, t_project_number].join(',') #@statuses.close end else log_puts("fail: " + t_job_id) end unless t_log_dir.empty? copy_commands(t_log_file, t_log_dir).each do |command| log_puts(command) system command end err_file = t_log_file.gsub('_o.log','_e.log') copy_commands(err_file, t_log_dir).each do |command| log_puts(command) system command end end Thread.current.kill end sleep @interval end end job_id.to_i end end |
#start_monitoring2(script_path, script_content, user = 'sushi_lover', project_number = 0, sge_options = '', log_dir = '') ⇒ Object
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# File 'lib/workflow_manager/server.rb', line 275 def start_monitoring2(script_path, script_content, user='sushi_lover', project_number=0, ='', log_dir='') # script_path is only used to generate a log file name # It is not used to read the script contents go_submit = false waiting_time = 0 gstore_dir, input_dataset_path = input_dataset_tsv_path(script_content) if gstore_dir and input_dataset_path waiting_max = 60*60*8 # 8h # wait until the files come until waiting_time > waiting_max or File.exist?(input_dataset_path) and file_list = input_dataset_file_list(input_dataset_path) and file_list.map!{|file| File.join(gstore_dir, file)} and go_submit = input_dataset_exist?(file_list) sleep @interval waiting_time += @interval end end job_id, log_file, command = if go_submit @cluster.submit_job(script_path, script_content, ) else raise "stop submitting #{File.basename(script_path)}, since waiting_time #{waiting_time} > #{waiting_max}" end if job_id and log_file # save log_file in logs @logs.transaction do |logs| logs[job_id] = log_file end # job status check until it finishes with success or fail worker = Thread.new(log_dir, script_path, script_content, ) do |log_dir, script_path, script_content, | loop do # check status current_status = check_status(job_id, log_file) # save time and status update_time_status(job_id, current_status, script_path, user, project_number) # finalize (kill current thred) in case of success or fail finalize_monitoring(current_status, log_file, log_dir) # wait sleep @interval end # loop end job_id end end |
#status(job_id, new_status = nil) ⇒ Object
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# File 'lib/workflow_manager/server.rb', line 416 def status(job_id, new_status=nil) stat = nil #@statuses.open(@db_stat) @statuses.transaction do |statuses| if new_status and stat = statuses[job_id.to_s] status_list = ['success', 'running', 'pending', 'fail'] if status_list.include?(new_status) items = stat.split(/,/) items.shift items.unshift(new_status) stat = items.join(',') statuses[job_id.to_s] = stat end else stat = statuses[job_id.to_s] end end #@statuses.close stat end |
#success_or_fail(job_id, log_file) ⇒ Object Also known as: check_status
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# File 'lib/workflow_manager/server.rb', line 500 def success_or_fail(job_id, log_file) msg = if @cluster.job_running?(job_id) 'running' elsif @cluster.job_ends?(log_file) 'success' elsif @cluster.job_pending?(job_id) 'pending' else 'fail' end end |
#update_time_status(job_id, current_status, script_name, user, project_number) ⇒ Object
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# File 'lib/workflow_manager/server.rb', line 237 def update_time_status(job_id, current_status, script_name, user, project_number) # if the current status changed from last time, then save, otherwise do nothing # once status changes into success or fail, then the thread is expected to be killed in later process @statuses.transaction do |statuses| start_time = nil if stat = statuses[job_id] last_status, script_name, start_time, user, project_number = stat.split(/,/) end time = if start_time if current_status == 'success' or current_status == 'fail' start_time + '/' + Time.now.strftime("%Y-%m-%d %H:%M:%S") elsif current_status != last_status Time.now.strftime("%Y-%m-%d %H:%M:%S") end else Time.now.strftime("%Y-%m-%d %H:%M:%S") end if time statuses[job_id] = [current_status, script_name, time, user, project_number].join(',') end end end |