pbs 1.1.4 → 2.0.0

data/config/websvcs02.osc.edu.yml

@@ -1,24 +0,0 @@
-oakley: &oakley
-    lib: '/usr/local/torque-4.2.8/lib/libtorque.so'
-    server: &oakley_server 'oak-batch.osc.edu'
-    qsub: 'LD_LIBRARY_PATH=/usr/local/torque-4.2.8/lib:$LD_LIBRARY_PATH /usr/local/torque-4.2.8/bin/qsub'
-*oakley_server:
-  <<: *oakley
-ruby: &ruby
-    lib: '/usr/local/torque-4.2.8/lib/libtorque.so'
-    server: &ruby_server 'ruby-batch.ten.osc.edu'
-    qsub: 'LD_LIBRARY_PATH=/usr/local/torque-4.2.8/lib:$LD_LIBRARY_PATH /usr/local/torque-4.2.8/bin/qsub'
-*ruby_server:
-  <<: *ruby
-oxymoron: &oxymoron
-    lib: '/usr/local/torque-4.2.8/lib/libtorque.so'
-    server: &oxymoron_server 'oak-batch.osc.edu:17001'
-    qsub: 'LD_LIBRARY_PATH=/usr/local/torque-4.2.8/lib:$LD_LIBRARY_PATH /usr/local/torque-4.2.8/bin/qsub'
-*oxymoron_server:
-  <<: *oxymoron
-quick: &quick
-    lib: '/usr/local/torque-4.2.8/lib/libtorque.so'
-    server: &quick_server 'quick-batch.osc.edu'
-    qsub: 'LD_LIBRARY_PATH=/usr/local/torque-4.2.8/lib:$LD_LIBRARY_PATH /usr/local/torque-4.2.8/bin/qsub'
-*quick_server:
-  <<: *quick

data/config/websvcs08.osc.edu.yml

@@ -1,18 +0,0 @@
-oakley: &oakley
-  lib: '/usr/local/torque/5.1.1-1_fba25d92/lib/libtorque.so'
-  server: &oakley_server 'oak-batch.osc.edu'
-  qsub: 'LD_LIBRARY_PATH=/usr/local/torque/5.1.1-1_fba25d92/lib:$LD_LIBRARY_PATH /usr/local/torque/5.1.1-1_fba25d92/bin/qsub'
-*oakley_server:
-  <<: *oakley
-ruby: &ruby
-  lib: '/usr/local/torque/5.1.1-1_fba25d92/lib/libtorque.so'
-  server: &ruby_server 'ruby-batch.ten.osc.edu'
-  qsub: 'LD_LIBRARY_PATH=/usr/local/torque/5.1.1-1_fba25d92/lib:$LD_LIBRARY_PATH /usr/local/torque/5.1.1-1_fba25d92/bin/qsub'
-*ruby_server:
-  <<: *ruby
-quick: &quick
-  lib: '/usr/local/torque/5.1.1-1_fba25d92/lib/libtorque.so'
-  server: &quick_server 'quick-batch.osc.edu'
-  qsub: 'LD_LIBRARY_PATH=/usr/local/torque/5.1.1-1_fba25d92/lib:$LD_LIBRARY_PATH /usr/local/torque/5.1.1-1_fba25d92/bin/qsub'
-*quick_server:
-  <<: *quick

data/examples/simplejob.rb

@@ -1,66 +0,0 @@
-require 'pbs'
-require 'yaml'
-
-# Set up connection to local server
-c = PBS::Conn.batch 'oakley'
-
-# Check info for local server
-q = PBS::Query.new(conn: c, type: :server)
-puts "# Batch server information ---"
-puts q.find.to_yaml
-puts ""
-
-# Check if I have any jobs currently running
-q = PBS::Query.new(conn: c, type: :job)
-filters = [PBS::ATTR[:state], PBS::ATTR[:owner]]
-puts "# All jobs you currently have in the batch ---"
-puts q.where.user(ENV['USER']).find(filters: filters).to_yaml
-puts ""
-
-# Setup new job
-j = PBS::Job.new(conn: c)
-
-headers = { PBS::ATTR[:N] => "SimpleJob" }
-resources = { walltime: "00:10:00" }
-envvars = { WORLD: "world" }
-script = "echo \"Hello ${WORLD}!\""
-
-
-# Submit new job
-puts "# Submitting new job ---"
-puts j.submit(string: script, headers: headers, resources: resources, envvars: envvars, qsub: true).id
-puts ""
-
-# Show details of new job
-puts "# Details of submitted job ---"
-puts j.status.to_yaml
-puts ""
-
-# Hold job
-puts "# Holding job now ---"
-j.hold
-puts j.status(filter: PBS::ATTR[:state]).to_yaml
-puts ""
-
-# Show only jobs on hold
-puts "# All running jobs on hold ---"
-puts q.where.user(ENV['USER']).where(PBS::ATTR[:state]) {|v| v == 'H'}.find(filters: filters).to_yaml
-puts ""
-puts "# All running jobs not on hold ---"
-puts q.where.user(ENV['USER']).where.not(PBS::ATTR[:state] => 'H').find(filters: filters).to_yaml
-puts ""
-puts "# All running jobs not queued ---"
-puts q.where.user(ENV['USER']).where.is(PBS::ATTR[:state] => 'H').find(filters: filters).to_yaml
-puts ""
-
-# Release job
-puts "# Releasing job now ---"
-j.release
-puts j.status(filter: PBS::ATTR[:state]).to_yaml
-puts ""
-
-# Delete submitted job
-puts "# Deleting job now ---"
-j.delete
-puts "Complete."
-puts ""

data/lib/pbs/conn.rb

@@ -1,75 +0,0 @@
-module PBS
-  class Conn
-    # @example Torque 4.2.8
-    #   "/usr/local/torque-4.2.8/lib/libtorque.so"
-    # @return [String] The torque library to use for connection.
-    attr_reader :lib
-
-    # @example Oakley
-    #   "oak-batch.osc.edu"
-    # @return [String] The batch server to connect to.
-    attr_reader :server
-
-    # @example Torque 4.2.8
-    #   "PATH=/usr/local/torque-4.2.8/bin:$PATH LD_LIBRARY_PATH=/usr/local/torque-4.2.8/lib:$LD_LIBRARY_PATH"
-    # @return [String] The qsub command to be called from the command line.
-    attr_reader :qsub
-
-    # @return [Fixnum, nil] The connection id number if connected.
-    attr_reader :conn_id
-
-    # Create a new connection object from pre-defined batch server defined in
-    # batch config yaml.
-    # @example Create Oakley connection
-    #   PBS::Conn.batch 'oakley'
-    #
-    # @param name [String] The name of the pre-defined batch server.
-    # @param opts [Hash] The options to create a connection object with.
-    # @option opts [String] :lib The torque library used to establish connection.
-    # @option opts [String] :server The batch server to connect to.
-    # @option opts [String] :qsub The qsub command to be called from the command line.
-    # @raise [Error] if pre-defined batch server doesn't exist.
-    def self.batch(name, opts = {})
-      context = PBS.batch_config[name] || raise(PBS::Error, "No pre-defined batch server (#{name})")
-      lib = opts[:lib]    || context.fetch('lib', nil)
-      svr = opts[:server] || context.fetch('server', nil)
-      qsb = opts[:qsub]   || context.fetch('qsub', nil)
-      Conn.new(lib: lib, server: svr, qsub: qsb)
-    end
-
-    # @param opts [Hash] The options to create a connection object with.
-    # @option opts [String] :lib The torque library used to establish connection.
-    # @option opts [String] :server The batch server to connect to.
-    # @option opts [String] :qsub The qsub command to be called from the command line.
-    def initialize(opts)
-      @lib    = opts[:lib] || "torque"
-      @server = opts[:server]
-      @qsub   = opts[:qsub] || "qsub"
-    end
-
-    # Creates a torque connection
-    #
-    # @return [Integer] The connection id.
-    def connect
-      Torque.init lib: lib          # reset library used in Torque
-      disconnect if connected?      # clean up any old connection
-      @conn_id = Torque.pbs_connect(server)
-      Torque.raise_error(@conn_id.abs) if @conn_id < 0  # raise error if negative conn_id
-      Torque.check_for_error        # check for any other error that slipped by
-      conn_id
-    end
-
-    # Disconnects from the connection and sets the connection id to nil.
-    def disconnect
-      Torque.pbs_disconnect(@conn_id)
-      @conn_id = nil    # reset connection id
-    end
-
-    # Returns true if the connection id is not nil and is greater than zero.
-    #
-    # @return [Boolean] Are we connected?
-    def connected?
-      !@conn_id.nil? && @conn_id > 0
-    end
-  end
-end

data/lib/pbs/job.rb

@@ -1,189 +0,0 @@
-require "socket"
-require "tempfile"
-require "open3"
-
-module PBS
-  class Job
-    HOSTNAME = Socket.gethostname
-
-    attr_accessor :id
-    attr_reader :conn
-
-    # Needs a connection object and headers
-    # Examples of headers found in 'headers.rb'
-    def initialize(args = {})
-      # Job specific args
-      @id = args[:id]
-      @conn = args[:conn] || Conn.new
-    end
-
-    # Put job on hold
-    def hold(args = {})
-      # hold_type::
-      # The parameter, hold_type, contains the type of hold to be applied. The possible values are (default is 'u'):
-      # "u" : Available to the owner of the job, the batch operator and the batch administrator.
-      # "o" : Available to the batch operator and the batch administrator.
-      # "s" : Available only to the batch administrator.
-      hold_type = args[:hold_type] || "u"
-
-      _pbs_hold(hold_type)
-      self
-    end
-
-    # Release job from hold
-    def release(args = {})
-      # hold_type::
-      # The parameter, hold_type, contains the type of hold to be applied. The possible values are (default is 'u'):
-      # "u" : Available to the owner of the job, the batch operator and the batch administrator.
-      # "o" : Available to the batch operator and the batch administrator.
-      # "s" : Available only to the batch administrator.
-      hold_type = args[:hold_type] || "u"
-
-      _pbs_release(hold_type)
-      self
-    end
-
-    # Delete job
-    def delete(args = {})
-      _pbs_delete()
-    end
-
-    # Get status of job by creating a Query object
-    def status(args = {})
-      q = Query.new(type: :job, conn: conn)
-      q.find(args.merge(id: id))[0]
-    end
-
-    # Can submit a script as a file or string
-    # @param args [Hash] The options when submitting a job.
-    # @option args [String] :string The batch script as a string.
-    # @option args [String] :file The batch script file if a string is not supplied.
-    # @option args [Boolean] :qsub (true) Whether the <tt>qsub</tt> command is used from command line.
-    # @option args [Hash] :headers ({}) PBS headers.
-    # @option args [Hash] :resources ({}) PBS resources.
-    # @option args [Hash] :envvars ({}) PBS environment variables.
-    # @raise [Error] if fail to submit batch job.
-    def submit(args)
-      string = args.fetch(:string) { File.open(args[:file]).read }
-      queue  = args.fetch(:queue, nil)
-      qsub   = args.fetch(:qsub, true)
-
-      headers   = args.fetch(:headers,   {})
-      resources = args.fetch(:resources, {})
-      envvars   = args.fetch(:envvars,   {})
-
-      # Create batch script in tmp file, submit, remove tmp file
-      script = Tempfile.new('qsub.')
-      begin
-        script.write string
-        script.close
-        if qsub
-          _qsub_submit(script.path, queue, headers, resources, envvars)
-        else
-          _pbs_submit(script.path, queue, headers, resources, envvars)
-        end
-      ensure
-        script.unlink # deletes the temp file
-      end
-
-      self
-    end
-
-    private
-      # Connect to batch server, put job on hold,
-      # disconnect, and finally check for errors
-      def _pbs_hold(hold_type)
-        conn.connect unless conn.connected?
-        Torque.pbs_holdjob(conn.conn_id, id, hold_type, nil)
-        conn.disconnect
-        Torque.check_for_error
-      end
-
-      # Connect to batch server, release job from hold,
-      # disconnect, and finally check for errors
-      def _pbs_release(hold_type)
-        conn.connect unless conn.connected?
-        Torque.pbs_rlsjob(conn.conn_id, id, hold_type, nil)
-        conn.disconnect
-        Torque.check_for_error
-      end
-
-      # Connect to batch server, delete job,
-      # disconnect, and finally check for errors
-      def _pbs_delete()
-        conn.connect unless conn.connected?
-        Torque.pbs_deljob(conn.conn_id, id, nil)
-        conn.disconnect
-        Torque.check_for_error
-      end
-
-      # Connect to server, submit job with headers,
-      # disconnect, and finally check for errors
-      def _pbs_submit(script, queue, headers, resources, envvars)
-        # Generate attribute hash for this job
-        attribs = _default_headers.merge(headers)
-        attribs[ATTR[:l]] = _default_resources.merge(resources)
-        attribs[ATTR[:v]] = _default_envvars.merge(envvars).map{|k,v| "#{k}=#{v}"}.join(",")
-
-        # Filter some of the attributes
-        attribs[ATTR[:o]].prepend("#{HOSTNAME}:")
-        attribs[ATTR[:e]].prepend("#{HOSTNAME}:")
-
-        # Submit job
-        conn.connect unless conn.connected?
-        attropl = Torque::Attropl.from_hash(attribs)
-        self.id = Torque.pbs_submit(conn.conn_id, attropl, script, queue, nil)
-        conn.disconnect
-        Torque.check_for_error
-      end
-
-      # Submit using system call `qsub`
-      # Note: Do not need to filter as OSC has personal torque filter
-      def _qsub_submit(script, queue, headers, resources, envvars)
-        params = "-q #{queue}@#{conn.server}"
-        params << resources.map{|k,v| " -l '#{k}=#{v}'"}.join("")
-        params << " -v '#{envvars.map{|k,v| "#{k}=#{v}"}.join(",")}'" unless envvars.empty?
-        params << headers.map do |k,v|
-          param = ATTR.key(k)
-          if param && param.length == 1
-            " -#{param} '#{v}'"
-          else
-            " -W '#{k}=#{v}'"
-          end
-        end.join("")
-        cmd = "#{conn.qsub} #{params} #{script}"
-        Open3.popen3(cmd) do |stdin, stdout, stderr, wait_thr|
-          exit_status = wait_thr.value
-          unless exit_status.success?
-            raise PBS::Error, "#{stderr.read}"
-          end
-
-          self.id = stdout.read.chomp   # newline char at end of job id
-        end
-      end
-
-      # Hash representing the job headers
-      def _default_headers
-        {
-          ATTR[:N] => "Jobname",
-          ATTR[:o] => "#{Dir.pwd}/",
-          ATTR[:e] => "#{Dir.pwd}/",
-          ATTR[:S] => "/bin/bash",
-        }
-      end
-
-      # Hash representing the resources used
-      def _default_resources
-        {
-          walltime: "01:00:00",
-        }
-      end
-
-      # Hash representing the PBS working directory
-      def _default_envvars
-        {
-          PBS_O_WORKDIR: "#{Dir.pwd}",
-        }
-      end
-  end
-end

data/lib/pbs/query.rb

@@ -1,103 +0,0 @@
-module PBS
-  class Query
-    attr_reader :type
-    attr_reader :conn
-    attr_accessor :where_procs
-
-    STATTYPE = {job: :pbs_statjob, queue: :pbs_statque,
-                node: :pbs_statnode, server: :pbs_statserver}
-
-    # Needs a connection object and a query type
-    # Query types: :job, :queue, :server, :node
-    def initialize(args = {})
-      @conn = args[:conn] || Conn.new
-      @type = args[:type] || :job
-      @where_procs = []
-    end
-
-    # Boolean procs used to filter out query results
-    # Examples:
-    #   where {|h| h[PBS::ATTR[:N]] == "SimpleJob"}
-    #   where(PBS::ATTR[:N]) {|v| v == "SimpleJob"}
-    #   where
-    # the last one is used with other methods
-    # i.e., where.not(PBS::ATTR[:N]) => "SimpleJob")
-    def where(arg = nil, &block)
-      relation = self.clone
-      relation.where_procs = @where_procs.clone
-      relation.where_procs << (arg ? Proc.new {|h| block.call(h[arg])} : block)
-      relation
-    end
-
-    # Used to filter where key attrib is equal to value
-    #   where.is(PBS::ATTR[:N] => "SimpleJob")
-    def is(hash)
-      key, value = hash.first
-      raise PBS::Error, "`where' method not called before" if where_procs.empty? || where_procs[-1]
-      self.where_procs[-1] = Proc.new {|h| h[key] == value}
-      self
-    end
-
-    # Used to filter where key attrib is NOT equal to value
-    #   where.not(PBS::ATTR[:N] => "SimpleJob")
-    def not(hash)
-      key, value = hash.first
-      raise PBS::Error, "`where' method not called before" if where_procs.empty? || where_procs[-1]
-      self.where_procs[-1] = Proc.new {|h| h[key] != value}
-      self
-    end
-
-    # Used to filter specific user
-    #   where.user("username")
-    def user(name)
-      raise PBS::Error, "`where' method not called before" if where_procs.empty? || where_procs[-1]
-      self.where_procs[-1] = Proc.new {|h| /^#{name}@/ =~ h[ATTR[:owner]]}
-      self
-    end
-
-    def find(args = {})
-      id = args[:id] || nil
-      filters = args[:filters]
-      filters = [args[:filter]] if args[:filter]
-
-      # Get array of batch status hashes
-      batch_list = _pbs_batchstat(id, filters)
-
-      # Further filter results and then output them
-      _filter_where_values(batch_list)
-    end
-
-    # Filter an array of hashes based on the defined where procs
-    # Comparisons are done inside the :attribs hash only
-    def _filter_where_values(array)
-      array.select do |hash|
-        pass = true
-        where_procs.each do |p|
-          pass = false unless p.call(hash[:attribs])
-        end
-        pass
-      end
-    end
-
-    # Connect, get status on batch server,
-    # disconnect, parse output, and finally check for errors
-    # Don't forget to free up memory the C-library creates
-    def _pbs_batchstat(id, filters)
-      # Generate attribute list from filter list
-      attrib_list = PBS::Torque::Attrl.from_list(filters) if filters
-
-      batch_status = nil
-      conn.connect unless conn.connected?
-      if type == :server
-        batch_status = Torque.send(STATTYPE[type], conn.conn_id, attrib_list, nil)
-      else
-        batch_status = Torque.send(STATTYPE[type], conn.conn_id, id, attrib_list, nil)
-      end
-      conn.disconnect
-      batch_list = batch_status.to_a
-      Torque.pbs_statfree(batch_status)
-      Torque.check_for_error
-      batch_list
-    end
-  end
-end