comana 0.1.0 → 0.1.1

data/bin/machinestatus

@@ -1,192 +0,0 @@
-#! /usr/bin/env ruby
-# coding: utf-8
-
-
-puts "machinestatus is obsoleted. use 'hostinfo'"
-exit
-
-USAGE = <<HERE
-machinestatus HostA HostB
-machinestatus -g GroupA GroupB #-g option interprets as group name
-HERE
-
-require "pp"
-require "optparse"
-require "rubygems"
-require "comana"
-require "highline"
-require "tefil"
-
-HIGHLINE = HighLine.new
-
-##Analyze options
-OPTIONS = {}
-op = OptionParser.new
-op.on("-a", "--ping-alive", "Check only alive using ping"){OPTIONS[:ping] = true}
-#op.on("-t", "--top"       , "Info from top.     "){OPTIONS[:top     ] = true}
-#op.on("-p", "--ps"        , "Info from ps.      "){OPTIONS[:ps      ] = true}
-op.on("-n", "--pbsnodes"  , "Info from pbsnodes."){OPTIONS[:pbsnodes] = true}
-op.on("-l", "--load"      , "Pbsnodes; state, loadave."){
-  OPTIONS[:pbsnodes] = true
-  OPTIONS[:load] = true
-}
-#op.on("-d", "--dmesg"     , "Info from dmesg.   "){OPTIONS[:dmesg   ] = true}
-
-op.on("-g", "--group"  , "Indicate group of hosts"    ){OPTIONS[:group] = true}
-op.on("-q", "--quiet"  , "No output 'Wainting for...'"){OPTIONS[:quiet] = true}
-op.parse!(ARGV)
-
-
-##Select hosts
-cs = Comana::ClusterSetting.load_file
-groups = {}
-cs.groups.each do |key, val|
-  cluster = key
-  groups[key] = val["members"]
-end
-
-hs = Comana::HostSelector.new groups
-if OPTIONS[:group]
-  hosts = []
-  ARGV.each do |group|
-    begin
-      hosts << hs.select_group(group)
-    rescue Comana::HostSelector::NoEntryError
-      $stderr.puts "Unknown group: #{group}"
-    end
-  end
-  hosts.flatten!
-else
-  hosts = ARGV
-end
-hosts = hs.select_all if ARGV.empty?
-
-##Collect information
-Thread.abort_on_exception = true
-results = {}
-threads = {}
-hosts.each do |host|
-  threads[host] = Thread.start do
-    results[host] = {}
-    if OPTIONS[:ping]
-      results[host][:ping] = Comana::HostInspector::Ping.new host
-    end
-    if OPTIONS[:pbsnodes]
-      begin
-        results[host][:pbsnodes] = Comana::HostInspector::Pbsnodes.new(host, cs.pbs_server)
-      rescue Comana::HostInspector::Pbsnodes::UnknownNodeError
-        #results[host][:pbsnodes] = Comana::HostInspector::Pbsnodes.new(host, cs.pbs_server)
-        results[host][:pbsnodes] = nil
-        #results[host][:pbsnodes]["status"] = {}
-      end
-    end
-  end
-end
-
-threads.each do |host, thread|
-  print "Waiting for #{host}...\n" unless OPTIONS[:quiet]
-  thread.join              # wait until all processes are completed
-end
-
-##Titles
-titles = []
-titles << "host"
-if OPTIONS[:ping]
-  titles << "ping"
-end
-if OPTIONS[:pbsnodes]
-  titles << "state"
-  titles << "np"          unless OPTIONS[:load]
-  titles << "properties"  unless OPTIONS[:load]
-  titles << "ntype"       unless OPTIONS[:load]
-  titles << "gpus"        unless OPTIONS[:load]
-  titles << "rectime"     unless OPTIONS[:load]
-  titles << "varattr"     unless OPTIONS[:load]
-  titles << "jobs"
-  titles << "state"       unless OPTIONS[:load]
-  titles << "netload"     unless OPTIONS[:load]
-  titles << "gres"        unless OPTIONS[:load]
-  titles << "loadave"
-  titles << "ncpus"       unless OPTIONS[:load]
-  titles << "physmem"     unless OPTIONS[:load]
-  titles << "availmem"    unless OPTIONS[:load]
-  titles << "totmem"      unless OPTIONS[:load]
-  titles << "idletime"    unless OPTIONS[:load]
-  titles << "nusers"      unless OPTIONS[:load]
-  titles << "nsessions"   unless OPTIONS[:load]
-  titles << "sessions"    unless OPTIONS[:load]
-  titles << "uname"       unless OPTIONS[:load]
-  titles << "opsys"       unless OPTIONS[:load]
-end
-
-##Data
-data = []
-results.keys.sort.each do |host|
-  items = [host]
-  #printf("%9s: ", )
-  #
-  if OPTIONS[:ping]
-    #state = HIGHLINE.color("dead", :red)
-    state = "dead"
-    state = "alive" if results[host][:ping].alive?
-    items << state
-    #sprintf("%5s", state)
-  end
-
-  if OPTIONS[:pbsnodes]
-    if results[host][:pbsnodes]
-      items << results[host][:pbsnodes].state
-      items << results[host][:pbsnodes].np                  unless OPTIONS[:load] 
-      items << results[host][:pbsnodes].properties          unless OPTIONS[:load] 
-      items << results[host][:pbsnodes].ntype               unless OPTIONS[:load] 
-      items << results[host][:pbsnodes].gpus                unless OPTIONS[:load] 
-      items << results[host][:pbsnodes].status["rectime"  ] unless OPTIONS[:load] 
-      items << results[host][:pbsnodes].status["varattr"  ] unless OPTIONS[:load] 
-      items << results[host][:pbsnodes].status["jobs"     ]                       
-      items << results[host][:pbsnodes].status["state"    ] unless OPTIONS[:load] 
-      items << results[host][:pbsnodes].status["netload"  ] unless OPTIONS[:load] 
-      items << results[host][:pbsnodes].status["gres"     ] unless OPTIONS[:load] 
-      items << results[host][:pbsnodes].status["loadave"  ]                       
-      items << results[host][:pbsnodes].status["ncpus"    ] unless OPTIONS[:load] 
-      items << results[host][:pbsnodes].status["physmem"  ] unless OPTIONS[:load] 
-      items << results[host][:pbsnodes].status["availmem" ] unless OPTIONS[:load] 
-      items << results[host][:pbsnodes].status["totmem"   ] unless OPTIONS[:load] 
-      items << results[host][:pbsnodes].status["idletime" ] unless OPTIONS[:load] 
-      items << results[host][:pbsnodes].status["nusers"   ] unless OPTIONS[:load] 
-      items << results[host][:pbsnodes].status["nsessions"] unless OPTIONS[:load] 
-      items << results[host][:pbsnodes].status["sessions" ] unless OPTIONS[:load] 
-      items << results[host][:pbsnodes].status["uname"    ] unless OPTIONS[:load] 
-      items << results[host][:pbsnodes].status["opsys"    ] unless OPTIONS[:load] 
-    else
-      items << "pbs_unknown_host"
-      items << "" unless OPTIONS[:load] 
-      items << "" unless OPTIONS[:load] 
-      items << "" unless OPTIONS[:load] 
-      items << "" unless OPTIONS[:load] 
-      items << "" unless OPTIONS[:load] 
-      items << "" unless OPTIONS[:load] 
-      items << ""                       
-      items << "" unless OPTIONS[:load] 
-      items << "" unless OPTIONS[:load] 
-      items << "" unless OPTIONS[:load] 
-      items << ""                       
-      items << "" unless OPTIONS[:load] 
-      items << "" unless OPTIONS[:load] 
-      items << "" unless OPTIONS[:load] 
-      items << "" unless OPTIONS[:load] 
-      items << "" unless OPTIONS[:load] 
-      items << "" unless OPTIONS[:load] 
-      items << "" unless OPTIONS[:load] 
-      items << "" unless OPTIONS[:load] 
-      items << "" unless OPTIONS[:load] 
-      items << "" unless OPTIONS[:load] 
-
-    end
-  end
-  data << items
-end
-
-data = data.unshift(titles)
-#pp data
-t = Tefil::ColumnFormer.new
-t.form(data, $stdout, "|")

data/bin/queueinfo

@@ -1,28 +0,0 @@
-#! /usr/bin/env ruby
-
-
-require 'thor'
-require 'comana'
-require 'pp'
-
-### Command template
-class Queueinfo < Thor
-  desc "light", "Detect the lightest queue."
-
-  def lightqueue
-    qinfo = Comana::QueueManager.new
-    qinfo.light_queue
-  end
-
-  #def job
-  #end
-
-  def show
-
-  end
-
-end
-
-Queueinfo.start(ARGV)
-
-

data/lib/comana/gridenginescript.rb

@@ -1,68 +0,0 @@
-#! /usr/bin/env ruby
-# coding: utf-8
-
-#
-#
-#
-class GridEngineScript
-  #DEFAULT_QSUB_FILE = 'qsub.sh'
-  QSUB_PATH = '/usr/bin/qsub'
-
-  #
-  def initialize()
-  end
-
-  # series: name of computers' series
-  # ppn:    number of using cores
-  def self.generate(io, series, ppn, command)
-    io.puts self.string(series, ppn, command)
-  end
-
-  def self.string(series, ppn, command)
-    string = <<HERE
-\#! /bin/sh
-\#$ -S /bin/sh
-\#$ -cwd
-\#$ -o stdout
-\#$ -e stderr
-\#$ -q #{series}.q
-\#$ -pe #{series}.openmpi #{ppn}
-
-MACHINE_FILE="machines"
-ENV_FILE="printenv.log"
-
-LD_LIBRARY_PATH=/usr/lib:/usr/local/lib:/opt/intel/mkl/lib/intel64:/opt/intel/lib/intel64:/opt/intel/lib:/opt/openmpi-intel/lib
-export LD_LIBRARY_PATH
-
-cd $SGE_O_WORKDIR
-if [ -e $ENV_FILE ]; then
-    echo "$ENV_FILE already exist. Exit."
-    exit
-fi
-printenv | sort > printenv.log
-cut -d " " -f 1,2 $PE_HOSTFILE | sed 's/ / cpu=/' > $MACHINE_FILE
-
-#{command}
-HERE
-    string
-  end
-
-  def self.write(series, ppn, command, io)
-    io.puts self.string(series, ppn, command)
-  end
-
-  def self.write_submit(series, ppn, command, filename)
-    #qsub_file = DEFAULT_QSUB_FILE
-    io = File.open(filename, 'w')
-    self.write(series, ppn, command, io)
-    io.close
-
-    logfile  = filename.sub(/#{File.extname filename}$/, '.log')
-    command = "#{QSUB_PATH} #{filename} > #{logfile}"
-    #command = "qsub #{filename}"
-    puts command
-    system command
-  end
-
-end
-

data/lib/comana/queuemanager.rb

@@ -1,34 +0,0 @@
-#! /usr/bin/env ruby
-# coding: utf-8
-
-#
-#
-#
-class Comana::QueueManager
-  #
-  def initialize()
-  end
-
-  #
-  def queues
-    `qconf -sql`.split("\n")
-  end
-
-  # return a queue name with less tasks.
-  def light_queue
-    queues.each do |queue|
-      hostlist(queue)
-    end
-
-  end
-
-  def qhost
-    
-  end
-
-  private
-
-
-
-end
-

data/lib/comana/queuesubmitter.rb

@@ -1,156 +0,0 @@
-#! /usr/bin/env ruby
-# coding: utf-8
-
-require "fileutils"
-#require "comana/computationmanager.rb"
-#require "comana/clustersetting.rb"
-#
-#For Torque. This class will be obsoleted.
-
-#
-#
-#
-class Comana::QueueSubmitter < Comana::ComputationManager
-  SCRIPT = "script.sh"
-  PROLOGUE = "prologue_script.sh"
-  EPILOGUE = "epilogue_script.sh"
-  WALLTIME = "7:00:00:00" # day:hour:minute:second
-
-  class PrepareNextError < Exception; end
-  class InitializeError < Exception; end
-  class InvalidArgumentError < Exception; end
-
-  # opts is a hash includes data belows:
-  #   :command => executable command line written in script.
-  #   :cluster => name of cluster.
-  #   :target => calculation as ComputationManager subclass.
-  #     Note that this is not target name, to check calculatable.
-  def initialize(opts)
-    [:target, :command].each do |symbol|
-      raise InitializeError, "No '#{symbol}' in argument 'opts'"  unless opts.has_key?(symbol)
-      #raise InitializeError unless opts.has_key?(symbol)
-    end
-
-    super(opts[:target].dir)
-
-    @command    = opts[:command]
-    @cluster    = opts[:cluster]
-    @num_nodes  = opts[:num_nodes]
-    @priority   = opts[:priority]
-    @lockdir    = "lock_queuesubmitter"
-  end
-
-  def calculate
-    # prologue
-    prologue_path = "#{@dir}/#{PROLOGUE}"
-    File.open(prologue_path, "w") { |io| dump_prologue(io) }
-    FileUtils.chmod(0700, prologue_path)
-
-    # epilogue
-    epilogue_path = "#{@dir}/#{EPILOGUE}"
-    File.open(epilogue_path, "w") { |io| dump_epilogue(io) }
-    FileUtils.chmod(0700, epilogue_path)
-
-    # script
-    script_path = "#{@dir}/#{SCRIPT}"
-    File.open(script_path, "w") { |io| dump_script(io) }
-
-    # exec
-    system("cd #{@dir}; qsub -l prologue=#{prologue_path} -l epilogue=#{epilogue_path} #{script_path} > jobid.log")
-  end
-
-  # Raise QueueSubmitter::PrepareNextError when called.
-  def prepare_next
-    raise PrepareNextError
-  end
-
-  # Return true after qsub executed.
-  def finished?
-    Dir.exist? @dir + "/" +@lockdir
-  end
-
-  private
-
-  def dump_prologue(io = nil)
-    str = [
-      '#! /bin/sh',
-      'LOGFILE="${PBS_O_WORKDIR}/prologue_script.log"',
-      'echo "hostname                         : `hostname`" >> $LOGFILE',
-      'echo "job id                           : $1" >> $LOGFILE',
-      'echo "job execution user name          : $2" >> $LOGFILE',
-      'echo "job execution group name         : $3" >> $LOGFILE',
-      'echo "job name                         : $4" >> $LOGFILE',
-      'echo "list of requested resource limits: $5" >> $LOGFILE',
-      'echo "job execution queue              : $6" >> $LOGFILE',
-      'echo "job account                      : $7" >> $LOGFILE',
-      'echo "PBS_O_WORKDIR                    : ${PBS_O_WORKDIR}" >> $LOGFILE',
-      'echo "nodes in pbs_nodefile            : " >> $LOGFILE',
-      'cat ${PBS_NODEFILE} >> $LOGFILE',
-      'exit 0',
-    ].join("\n")
-
-    if io
-      io.puts str
-    else
-      return str
-    end
-  end
-
-  def dump_script(io = nil)
-    lines = []
-    lines << "#! /bin/sh"
-    lines << "#PBS -N #{@dir}"
-
-    if @num_nodes || @cluster
-      tmp = []
-      @num_nodes ||= 1
-      tmp << "nodes=#{@num_nodes}"
-      tmp << "ppn=1"
-      #pp @cluster
-      tmp << @cluster if @cluster
-      lines << "#PBS -l #{tmp.join(":")},walltime=#{WALLTIME}"
-    else
-      lines << "#PBS -l walltime=#{WALLTIME}"
-    end
-
-    lines << "#PBS -p #{@priority}" if @priority
-
-    lines << "#PBS -j oe"
-    lines << ""
-    lines << "cd ${PBS_O_WORKDIR} && \\"
-    lines << "#{@command}"
-
-    str = lines.join("\n")
-
-    if io
-      io.puts str
-    else
-      return str
-    end
-  end
-
-  def dump_epilogue(io = nil)
-    str = [
-      '#! /bin/sh',
-      'LOGFILE="${PBS_O_WORKDIR}/epilogue_script.log"',
-      'echo "job id                           : $1" >> $LOGFILE',
-      'echo "job execution user name          : $2" >> $LOGFILE',
-      'echo "job execution group name         : $3" >> $LOGFILE',
-      'echo "job name                         : $4" >> $LOGFILE',
-      'echo "session id                       : $5" >> $LOGFILE',
-      'echo "list of requested resource limits: $6" >> $LOGFILE',
-      'echo "list of resources used by job    : $7" >> $LOGFILE',
-      'echo "job execution queue              : $8" >> $LOGFILE',
-      'echo "job account                      : $9" >> $LOGFILE',
-      'echo "job exit code                    : $10" >> $LOGFILE',
-      'exit 0',
-    ].join("\n")
-
-    if io
-      io.puts str
-    else
-      return str
-    end
-  end
-end
-

data/memo.txt

@@ -1,34 +0,0 @@
-# Comana: COmputation MANAger
-
-Comana don't have information of output files.
-Because it is difficult to define final output and to deal systematically.
-e.g., repeated calculation till convergence.
-
-0.0.10
-
-0.0.9 release
-  Change opts specification in QueueSubmitter; symbol to string
-
-0.0.8 release
-  Changed queuesubmitter option. (long name symbol)
-  Add prologue and epilogue to QueueSubmitter.
-
-0.0.7 release
-  Bugfix of danger to rsync large directory:
-    - bin/submitqueue is removed.
-    - lib/queuesubmitter.rb is modified.
-  lib/queuesubmitter.rb is modified.
-    - finished? returns bool.
-    - content of qsub script to use "rsync" and "mv dir ~/.trash".
-
-0.0.6 release
-  bin/submitqueue is add.
-  lib/queuesubmitter.rb is add.
-
-0.0.5 release
-  Directory structure and file names are changed.
-  Method names are hanged.
-  MachineInfo is added.
-
-0.0.4 release
-

data/test/test_gridenginescript.rb

@@ -1,16 +0,0 @@
-#! /usr/bin/env ruby
-# coding: utf-8
-
-require "pp"
-require "helper"
-#require "test/unit"
-#require "pkg/klass.rb"
-
-
-class TC_GridEngineScript < Test::Unit::TestCase
-  def setup
-    @g00 = GridEngineScript.new
-  end
-
-end
-

data/test/test_queuemanager.rb

@@ -1,19 +0,0 @@
-#! /usr/bin/env ruby
-# coding: utf-8
-
-require "helper"
-#require "test/unit"
-#require "pkg/klass.rb"
-
-class TC_QueueManager < Test::Unit::TestCase
-  def setup
-    @qm00 = Comana::QueueManager.new
-  end
-
-  def test_qhost
-    @qm00.qhost
-
-  end
-
-end
-