comana 0.0.4 → 0.0.5

data/Rakefile

@@ -18,7 +18,8 @@ Jeweler::Tasks.new do |gem|
   gem.homepage = "http://github.com/ippei94da/comana"
   gem.license = "MIT"
   gem.summary = %Q{Manager for scientific computing}
-  gem.description = %Q{An aim of this gem is to provide a framework of
+  gem.description = %Q{Comana, COmputation MANAger,
+    is a software to provide a framework of
     managing scientific computing.
     Researchers on computing have to check calculation and
     generate new calculation and execute, repeatedly.

data/VERSION

@@ -1 +1 @@
-0.0.4
+0.0.5

data/comana.gemspec

@@ -5,12 +5,12 @@
 
 Gem::Specification.new do |s|
   s.name = "comana"
-  s.version = "0.0.4"
+  s.version = "0.0.5"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["ippei94da"]
-  s.date = "2012-04-23"
-  s.description = "An aim of this gem is to provide a framework of\n    managing scientific computing.\n    Researchers on computing have to check calculation and\n    generate new calculation and execute, repeatedly.\n    The abstract class that this gem provide would help the work.\n  "
+  s.date = "2012-05-07"
+  s.description = "Comana, COmputation MANAger,\n    is a software to provide a framework of\n    managing scientific computing.\n    Researchers on computing have to check calculation and\n    generate new calculation and execute, repeatedly.\n    The abstract class that this gem provide would help the work.\n  "
   s.email = "ippei94da@gmail.com"
   s.extra_rdoc_files = [
     "LICENSE.txt",
@@ -25,15 +25,23 @@ Gem::Specification.new do |s|
     "Rakefile",
     "VERSION",
     "comana.gemspec",
+    "dot.machineinfo",
     "lib/comana.rb",
-    "spec/comana_spec.rb",
+    "lib/comana/computationmanager.rb",
+    "lib/comana/machineinfo.rb",
+    "memo.txt",
+    "spec/computationmanager_spec.rb",
+    "spec/locked/comana_lock/dummy",
     "spec/locked/input_a",
     "spec/locked/input_b",
+    "spec/locked_outputted/comana_lock/dummy",
     "spec/locked_outputted/input_a",
     "spec/locked_outputted/input_b",
     "spec/locked_outputted/output",
-    "spec/not_calculated/input_a",
-    "spec/not_calculated/input_b",
+    "spec/machineinfo",
+    "spec/machineinfo_spec.rb",
+    "spec/not_started/input_a",
+    "spec/not_started/input_b",
     "spec/outputted/input_a",
     "spec/outputted/input_b",
     "spec/outputted/output",

data/dot.machineinfo

@@ -0,0 +1,3 @@
+--- # vim:syntax=yaml
+"Host1":
+  "vasp": "/usr/local/calc/vasp/vasp4631serial"

data/lib/comana/computationmanager.rb

@@ -0,0 +1,86 @@
+#! /usr/bin/env ruby
+# coding: utf-8
+
+#
+# Comana: COmputation MANAger
+#
+# This profides a framework of scientific computation.
+# Users have to redefine some methods in subclasses for various computation.
+# 
+class Comana
+  class NotImplementedError < Exception; end
+  class AlreadyStartedError < Exception; end
+
+  attr_reader :dir
+
+  # You can redefine in subclass to modify from default values.
+  def initialize(dir)
+    @dir = dir # redefine in subclass. 
+    @lockdir    = "comana_lock"
+    @alive_time = 3600
+  end
+
+  # Return a symbol which indicate state of calculation.
+  #   :yet           not started
+  #   :started       started, but not ended, including short time from last output
+  #   :terminated    started, but long time no output
+  #   :finished      started, normal ended and not need next calculation
+  def state
+    return :finished   if finished?
+    return :yet        unless started?
+    return :terminated if (Time.now - latest_modified_time > @alive_time)
+    return :started    
+  end
+
+  # Execute calculation.
+  # If log of Comana exist, raise Comana::AlreadyStartedError,
+  # because the calculation has been done by other process already.
+  def start
+    begin
+      Dir.mkdir "#{@dir}/#{@lockdir}"
+    rescue Errno::EEXIST
+      raise AlreadyStartedError, "Exist #{@dir}/#{@lockdir}"
+    end
+
+    while true
+      calculate
+      if finished?
+        break
+      else
+        prepare_next
+      end
+    end
+    puts "Done."
+  end
+
+  private
+
+  def calculate
+    raise NotImplementedError, "#{self.class}::calculate need to be redefined"
+  end
+
+  def prepare_next
+    raise NotImplementedError, "#{self.class}::prepare_next need to be redefined"
+  end
+
+  # Return latest modified time of files in calc dir recursively.
+  # require "find"
+  def latest_modified_time
+    tmp = Dir.glob("#{@dir}/**/*").max_by do |file|
+      File.mtime(file)
+    end
+    File.mtime(tmp)
+  end
+
+  def started?
+    return true if File.exist?( "#{@dir}/#{@lockdir}" )
+    return false
+  end
+
+  # Return true if the condition is satisfied.
+  def finished?
+    raise NotImplementedError, "#{self.class}::finished? need to be redefined"
+  end
+
+end
+

data/lib/comana/machineinfo.rb

@@ -0,0 +1,33 @@
+#! /usr/bin/env ruby
+# coding: utf-8
+
+require "yaml"
+
+#
+#
+#
+class MachineInfo
+
+  class NoEntryError < Exception; end
+
+  #
+  def initialize(data)
+    @data = data
+  end
+
+  def self.load_file(data_file)
+    #pp data_file
+    #pp ENV["PWD"]
+    #pp File.open(DATA_FILE, "r").readlines
+    data = YAML.load_file(data_file)
+    MachineInfo.new data
+    #pp @data
+  end
+
+  def get_host(host)
+    raise NoEntryError unless @data.has_key?(host)
+    @data[host]
+  end
+
+end
+

data/lib/comana.rb

@@ -1,86 +1,2 @@
-#! /usr/bin/env ruby
-# coding: utf-8
-
-#
-# Comana: COmputation MANAger
-#
-# This profides a framework of scientific computation.
-# Users have to redefine some methods in subclasses for various computation.
-# 
-class Comana
-  class NotImplementedError < Exception; end
-  class AlreadyStartedError < Exception; end
-
-  attr_reader :dir
-
-  #
-  def initialize(dir)
-    @dir = dir
-    set_parameters
-  end
-
-  # Return a symbol which indicate state of calculation.
-  #   :yet           not started
-  #   :started       started, but not ended, including short time from last output
-  #   :terminated    started, but long time no output
-  #   :finished      started, normal ended and not need next calculation
-  def state
-    return :finished   if finished?
-    return :yet        unless started?
-    return :terminated if (Time.now - latest_modified_time > @alive_time)
-    return :started    
-  end
-
-  # Execute calculation.
-  # If log of Comana exist, raise Comana::AlreadyStartedError,
-  # because the calculation has been done by other process already.
-  def calculate
-    begin
-      Dir.mkdir @lockdir
-    rescue Errno::EEXIST
-      raise AlreadyStartedError
-    end
-    send_command
-  end
-
-  private
-
-  def send_command
-    raise NotImplementedError, "#{self.class}::send_command need to be redefined"
-  end
-
-  def set_parameters
-    raise NotImplementedError, "#{self.class}::set_parameters need to be redefined"
-
-    # e.g.,
-    #@lockdir    = "comana_lock"
-    #@alive_time = 3600
-    #@outfiles   = ["output_a", "ouput_b"] # Files only to output should be indicated.
-  end
-
-  # Return latest modified time of files in calc dir recursively.
-  # require "find"
-  # Not only @outfiles, to catch an irregular state at the beginning before output.
-  def latest_modified_time
-    tmp = Dir.glob("#{@dir}/**/*").max_by do |file|
-      File.mtime(file)
-    end
-    File.mtime(tmp)
-  end
-
-  def started?
-    return true if File.exist?( "#{@dir}/#{@lockdir}" )
-    #@outfiles.each do |file|
-    #  return true if File.exist?( "#{@dir}/#{file}" )
-    #end
-    return false
-  end
-
-  # Return true if the condition is satisfied.
-  # E.g., when calculation output contains orthodox ending sequences.
-  def finished?
-    raise NotImplementedError, "#{self.class}::finished? need to be redefined"
-  end
-
-end
-
+require "comana/computationmanager.rb"
+require "comana/machineinfo.rb"

data/memo.txt

@@ -0,0 +1,11 @@
+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.
+
+0.0.5 release
+  Changed directory structure and file name.
+  Changed method name.
+  Added MachineInfo.
+
+0.0.4 release
+

data/spec/{comana_spec.rb → computationmanager_spec.rb}

@@ -7,22 +7,17 @@ class Comana
   public :latest_modified_time, :started?
 end
 
-describe Comana, "not calculated" do
+describe Comana, "not started" do
   class CalcYet < Comana
     def finished?         ; false     ; end
-    def set_parameters
-      @lockdir   = "lock"
-      @alive_time = 3600
-      @outfiles   = ["output"]
-    end
   end
   before do
-    calc_dir = "spec/not_calculated"
+    calc_dir = "spec/not_started"
     @calc = CalcYet.new(calc_dir)
 
     File.utime(NOW - 1000 ,NOW - 1000, "#{calc_dir}/input_a")
     File.utime(NOW - 2000 ,NOW - 2000, "#{calc_dir}/input_b")
-    @lockdir = "#{calc_dir}/lockdir"
+    @lockdir = "#{calc_dir}/comana_lock"
     FileUtils.rm(@lockdir) if File.exist?(@lockdir)
   end
 
@@ -51,11 +46,6 @@ end
 describe Comana, "with lock" do
   class CalcStarted < Comana
     def finished?         ; false     ; end
-    def set_parameters
-      @lockdir   = "lock"
-      @alive_time = 5000
-      @outfiles   = ["output"]
-    end
   end
 
   before do
@@ -73,11 +63,6 @@ end
 describe Comana, "with output, without lock" do
   class CalcStarted < Comana
     def finished?         ; false     ; end
-    def set_parameters
-      @lockdir   = "lock"
-      @alive_time = 5000
-      @outfiles   = ["output"]
-    end
   end
 
   before do
@@ -99,10 +84,10 @@ end
 describe Comana, "terminated" do
   class CalcTerminated < Comana
     def finished?         ; false     ; end
-    def set_parameters
-      @lockdir   = "lock"
+    def initialize(dir)
+      @dir = dir
+      @lockdir   = "comana_lock"
       @alive_time = 500
-      @outfiles   = ["output"]
     end
   end
 
@@ -113,7 +98,7 @@ describe Comana, "terminated" do
     File.utime(NOW - 1000 ,NOW - 1000, "#{calc_dir}/input_a")
     File.utime(NOW - 2000 ,NOW - 2000, "#{calc_dir}/input_b")
     File.utime(NOW - 9000 ,NOW - 9000, "#{calc_dir}/output")
-    File.utime(NOW - 9000 ,NOW - 9000, "#{calc_dir}/lock")
+    File.utime(NOW - 9000 ,NOW - 9000, "#{calc_dir}/comana_lock")
   end
 
   it "should return the state" do
@@ -124,11 +109,6 @@ end
 describe Comana, "finished" do
   class CalcFinished    < Comana
     def finished?         ; true      ; end
-    def set_parameters
-      @lockdir    = "lock"
-      @alive_time =  500
-      @outfiles   = ["output"]
-    end
   end
 
   before do

data/spec/machineinfo

@@ -0,0 +1,7 @@
+--- # vim:syntax=yaml
+"Host1":
+  "data1": "1-1"
+  "data2": "1-2"
+"Host2":
+  "data1": "2-1"
+  "data2": "2-2"

data/spec/machineinfo_spec.rb

@@ -0,0 +1,56 @@
+#! /usr/bin/env ruby
+# coding: utf-8
+
+require "fileutils"
+
+require File.expand_path(File.dirname(__FILE__) + "/spec_helper")
+require "comana/machineinfo.rb"
+
+describe MachineInfo do
+  describe "#load_file" do
+    context "not exist machineinfo file" do
+      DATA_FILE = "spec/machineinfo"
+      #DATA_FILE = "spec/dummy.yaml"
+      #data = {
+      #  "Host1" => { "data1" => "1-1", "data2" => "1-2" },
+      #  "Host2" => { "data1" => "2-1", "data2" => "2-2" },
+      #}
+      #io = File.open(DATA_FILE, "w")
+      #YAML.dump(data, io)
+      #io.close
+
+      #pp File.open(DATA_FILE, "r").readlines
+
+      it { lambda{MachineInfo.load_file(DATA_FILE)}.should_not raise_error}
+
+      mi00 = MachineInfo.load_file(DATA_FILE)
+      it {mi00.get_host("Host1").should == { "data1" => "1-1", "data2" => "1-2" } }
+
+      #FileUtils.rm DATA_FILE
+    end
+
+    context "not exist machineinfo file" do
+      it { lambda{ MachineInfo.load_file("") }.should raise_error(Errno::ENOENT) }
+    end
+  end
+
+  describe "#get_host" do
+    before do
+      @mi00 = MachineInfo.new({
+        "Host1" => { "data1" => "1-1", "data2" => "1-2" },
+        "Host2" => { "data1" => "2-1", "data2" => "2-2" },
+      })
+    end
+
+    context "exist in data" do
+      subject { @mi00.get_host("Host1") }
+      it {should == { "data1" => "1-1", "data2" => "1-2" } }
+    end
+
+    context "no entry" do
+      it {lambda{@mi00.get_host("")}.should raise_error(MachineInfo::NoEntryError)}
+    end
+  end
+
+end
+

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: comana
 version: !ruby/object:Gem::Version
-  version: 0.0.4
+  version: 0.0.5
   prerelease: 
 platform: ruby
 authors:
@@ -9,11 +9,11 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-04-23 00:00:00.000000000 Z
+date: 2012-05-07 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rspec
-  requirement: &84974590 !ruby/object:Gem::Requirement
+  requirement: &75511580 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -21,10 +21,10 @@ dependencies:
         version: 2.9.0
   type: :development
   prerelease: false
-  version_requirements: *84974590
+  version_requirements: *75511580
 - !ruby/object:Gem::Dependency
   name: rdoc
-  requirement: &84974230 !ruby/object:Gem::Requirement
+  requirement: &75526670 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -32,10 +32,10 @@ dependencies:
         version: '3.12'
   type: :development
   prerelease: false
-  version_requirements: *84974230
+  version_requirements: *75526670
 - !ruby/object:Gem::Dependency
   name: bundler
-  requirement: &84973850 !ruby/object:Gem::Requirement
+  requirement: &75525340 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -43,10 +43,10 @@ dependencies:
         version: 1.1.3
   type: :development
   prerelease: false
-  version_requirements: *84973850
+  version_requirements: *75525340
 - !ruby/object:Gem::Dependency
   name: jeweler
-  requirement: &84973550 !ruby/object:Gem::Requirement
+  requirement: &75524370 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -54,10 +54,10 @@ dependencies:
         version: 1.8.3
   type: :development
   prerelease: false
-  version_requirements: *84973550
+  version_requirements: *75524370
 - !ruby/object:Gem::Dependency
   name: simplecov
-  requirement: &84973190 !ruby/object:Gem::Requirement
+  requirement: &75523390 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -65,11 +65,11 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *84973190
-description: ! "An aim of this gem is to provide a framework of\n    managing scientific
-  computing.\n    Researchers on computing have to check calculation and\n    generate
-  new calculation and execute, repeatedly.\n    The abstract class that this gem provide
-  would help the work.\n  "
+  version_requirements: *75523390
+description: ! "Comana, COmputation MANAger,\n    is a software to provide a framework
+  of\n    managing scientific computing.\n    Researchers on computing have to check
+  calculation and\n    generate new calculation and execute, repeatedly.\n    The
+  abstract class that this gem provide would help the work.\n  "
 email: ippei94da@gmail.com
 executables: []
 extensions: []
@@ -85,15 +85,23 @@ files:
 - Rakefile
 - VERSION
 - comana.gemspec
+- dot.machineinfo
 - lib/comana.rb
-- spec/comana_spec.rb
+- lib/comana/computationmanager.rb
+- lib/comana/machineinfo.rb
+- memo.txt
+- spec/computationmanager_spec.rb
+- spec/locked/comana_lock/dummy
 - spec/locked/input_a
 - spec/locked/input_b
+- spec/locked_outputted/comana_lock/dummy
 - spec/locked_outputted/input_a
 - spec/locked_outputted/input_b
 - spec/locked_outputted/output
-- spec/not_calculated/input_a
-- spec/not_calculated/input_b
+- spec/machineinfo
+- spec/machineinfo_spec.rb
+- spec/not_started/input_a
+- spec/not_started/input_b
 - spec/outputted/input_a
 - spec/outputted/input_b
 - spec/outputted/output
@@ -113,7 +121,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
       segments:
       - 0
-      hash: -295869967
+      hash: 196413437
 required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
   requirements: