comana 0.0.6 → 0.0.7

data/VERSION

@@ -1 +1 @@
-0.0.6
+0.0.7

data/comana.gemspec

@@ -5,14 +5,13 @@
 
 Gem::Specification.new do |s|
   s.name = "comana"
-  s.version = "0.0.6"
+  s.version = "0.0.7"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["ippei94da"]
-  s.date = "2012-05-08"
+  s.date = "2012-05-10"
   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.executables = ["submitqueue"]
   s.extra_rdoc_files = [
     "LICENSE.txt",
     "README.rdoc"
@@ -25,7 +24,6 @@ Gem::Specification.new do |s|
     "README.rdoc",
     "Rakefile",
     "VERSION",
-    "bin/submitqueue",
     "comana.gemspec",
     "dot.machineinfo",
     "lib/comana.rb",
@@ -48,6 +46,8 @@ Gem::Specification.new do |s|
     "spec/outputted/input_a",
     "spec/outputted/input_b",
     "spec/outputted/output",
+    "spec/queuesubmitter/locked/lock_queuesubmitter/dummy",
+    "spec/queuesubmitter/unlocked/dummy",
     "spec/queuesubmitter_spec.rb",
     "spec/spec_helper.rb"
   ]

data/dot.machineinfo

@@ -1,3 +1,14 @@
 --- # vim:syntax=yaml
-"Host1":
-  "vasp": "/usr/local/calc/vasp/vasp4631serial"
+
+fileserver: Pt
+
+SeriesA:
+  economy_nodes: 1 # num of nodes for prior efficiency mode.
+  speed_nodes: 4   # num of nodes for prior speed mode.
+  vasp: "/usr/local/calc/bin/mpiexec /usr/local/calc/bin/vasp4631-mpich2"
+
+SeriesB:
+  economy_nodes: 1
+  speed_nodes: 8
+  vasp: "/usr/local/calc/bin/mpiexec /usr/local/calc/bin/vasp4631-mpich2"
+

data/lib/comana/computationmanager.rb

@@ -1,10 +1,7 @@
 #! /usr/bin/env ruby
 # coding: utf-8
 
-#
-# Comana: COmputation MANAger
-#
-# This profides a framework of scientific computation.
+# This class profides a framework of scientific computation.
 # Users have to redefine some methods in subclasses for various computation.
 # 
 class ComputationManager
@@ -44,22 +41,17 @@ class ComputationManager
     end
 
     while true
-      end_status = calculate
-      raise ExecuteError unless end_status
-      if finished?
-        break
-      else
-        prepare_next
-      end
+      calculate
+      break if finished?
+      prepare_next
     end
-    puts "Done."
   end
 
   private
 
-  # Redefine in subclass.
-  # Return nil if cannot execute, return false if error in executing,
-  # like Kernel.system.
+  # Redefine in subclass, e.g., 
+  #   end_status = system "command"
+  #   raise ExecuteError unless end_status
   def calculate
     raise NotImplementedError, "#{self.class}::calculate need to be redefined"
   end

data/lib/comana/queuesubmitter.rb

@@ -9,24 +9,36 @@ require "comana/machineinfo.rb"
 #
 class QueueSubmitter < ComputationManager
   QSUB_SCRIPT = "script.qsub"
+  WALLTIME = "7:00:00:00" # day:hour:minute:second
 
   class PrepareNextError < Exception; end
+  class InitializeError < Exception; end
 
-  #
+  # opts is a hash includes data belows:
+  #   :d => calculation as comana subclass.
+  #   :c => command line.
+  #   :n => name of cluster.
+  #   :s => flag for speed prior mode (option).
+  #   :machineinfo => MachineInfo class instance.
+  # NOTE:
+  #   :d is a comana subclass not directory name to check to be calculatable.
   def initialize(opts)
-    super(opts[:d])
+    raise InitializeError, "No :d entry in options" unless opts.has_key?(:d)
+    raise InitializeError, "No :c entry in options" unless opts.has_key?(:c)
+    raise InitializeError, "No :n entry in options" unless opts.has_key?(:n)
+    raise InitializeError, "No :machineinfo entry in options" unless opts.has_key?(:machineinfo)
+
+    super(opts[:d].dir)
     @command = opts[:c]
     @nodes   = opts[:n]
-    @speed  = opts[:s]
+    @speed   = opts[:s]
     @machineinfo = opts[:machineinfo]
     @lockdir = "lock_queuesubmitter"
   end
 
   def calculate
     script_path = "#{@dir}/#{QSUB_SCRIPT}"
-    File.open(script_path, "w") do |io|
-      dump_qsub_str(io)
-    end
+    File.open(script_path, "w") { |io| dump_qsub_str(io) }
 
     system("cd #{@dir}; qsub #{script_path} > #{@dir}/#{@lockdir}/stdout")
   end
@@ -36,8 +48,9 @@ class QueueSubmitter < ComputationManager
     raise PrepareNextError
   end
 
+  # Return true after qsub executed.
   def finished?
-    # do nothing
+    Dir.exist? @dir + "/" +@lockdir
   end
 
   private
@@ -51,15 +64,16 @@ class QueueSubmitter < ComputationManager
     str = [
       "#! /bin/sh",
       "#PBS -N #{@dir}",
-      "#PBS -l nodes=#{num}:ppn=1:#{@nodes},walltime=168:00:00",
+      "#PBS -l nodes=#{num}:ppn=1:#{@nodes},walltime=#{WALLTIME}",
       "#PBS -j oe",
-      "mkdir -p ${PBS_O_WORKDIR}",
-      "cp ${PBS_NODEFILE} ${PBS_O_WORKDIR}/pbs_nodefile",
-      "rsync -azq --delete #{fs}:${PBS_O_WORKDIR}/ ${PBS_O_WORKDIR}",
-      "cd ${PBS_O_WORKDIR}",
-      "#{@command}",
-      "#rsync -azq --delete ${PBS_O_WORKDIR}/ #{fs}:${PBS_O_WORKDIR}",
+      "mkdir -p ${PBS_O_WORKDIR} && \\",
+      "rsync -azq --delete #{fs}:${PBS_O_WORKDIR}/ ${PBS_O_WORKDIR} && \\",
+      "cp ${PBS_NODEFILE} ${PBS_O_WORKDIR}/pbs_nodefile && \\",
+      "cd ${PBS_O_WORKDIR} && \\",
+      "#{@command} && \\",
+      "rsync -azq --delete ${PBS_O_WORKDIR}/ #{fs}:${PBS_O_WORKDIR} && \\",
       "#rm -rf ${PBS_O_WORKDIR}",
+      "mv ${PBS_O_WORKDIR} ~/.trash",
     ].join("\n")
 
     if io

data/memo.txt

@@ -1,15 +1,25 @@
+# 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.
 
+0.0.7 release [2012-05-10]
+  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
-  Add bin/submitqueue.
-  Add lib/queuesubmitter.rb.
+  bin/submitqueue is add.
+  lib/queuesubmitter.rb is add.
 
 0.0.5 release
-  Changed directory structure and file name.
-  Changed method name.
-  Added MachineInfo.
+  Directory structure and file names are changed.
+  Method names are hanged.
+  MachineInfo is added.
 
 0.0.4 release
 

data/spec/computationmanager_spec.rb

@@ -127,7 +127,8 @@ end
 describe ComputationManager, "cannot execute" do
   class CalcNotExecutable    < ComputationManager
     def calculate
-      system "" # notExistCommand
+      end_status = system "" # notExistCommand
+      raise ExecuteError unless end_status
     end
 
     def finished?

data/spec/queuesubmitter_spec.rb

@@ -11,10 +11,72 @@ end
 
 #describe QueueSubmitter, "with chars to be escaped" do
 describe QueueSubmitter do
+  describe "#initialize" do
+    context "opts not have :d" do
+      opts = {
+        #:d => "dir_name",
+        :c => "command_line",
+        :n => "Nodes",
+        :s => true,
+        :machineinfo => MachineInfo.new(
+          "fileserver" => "FS",
+          "Nodes" => { "speed_nodes" => 4, "economy_nodes" => 1, }
+        )
+      }
+      it {lambda{QueueSubmitter.new(opts)}.should raise_error(
+        QueueSubmitter::InitializeError)}
+    end
+
+    context "opts not have :c" do
+      opts = {
+        :d => "dir_name",
+        #:c => "command_line",
+        :n => "Nodes",
+        :s => true,
+        :machineinfo => MachineInfo.new(
+          "fileserver" => "FS",
+          "Nodes" => { "speed_nodes" => 4, "economy_nodes" => 1, }
+        )
+      }
+      it {lambda{QueueSubmitter.new(opts)}.should raise_error(
+        QueueSubmitter::InitializeError)}
+    end
+
+    context "opts not have :n" do
+      opts = {
+        :d => "dir_name",
+        :c => "command_line",
+        #:n => "Nodes",
+        :s => true,
+        :machineinfo => MachineInfo.new(
+          "fileserver" => "FS",
+          "Nodes" => { "speed_nodes" => 4, "economy_nodes" => 1, }
+        )
+      }
+      it {lambda{QueueSubmitter.new(opts)}.should raise_error(
+        QueueSubmitter::InitializeError)}
+    end
+
+    context "opts not have :c" do
+      opts = {
+        :d => "dir_name",
+        :c => "command_line",
+        :n => "Nodes",
+        :s => true,
+        #:machineinfo => MachineInfo.new(
+        #  "fileserver" => "FS",
+        #  "Nodes" => { "speed_nodes" => 4, "economy_nodes" => 1, }
+        #)
+      }
+      it {lambda{QueueSubmitter.new(opts)}.should raise_error(
+        QueueSubmitter::InitializeError)}
+    end
+  end
+
   describe "#dump_qsub_str" do
     before do
       opts = {
-        :d => "dir_name",
+        :d => ComputationManager.new("spec/not_started"),
         :c => "command_line",
         :n => "Nodes",
         :s => true,
@@ -27,16 +89,17 @@ describe QueueSubmitter do
 
       @correct = [
         "#! /bin/sh",
-        "#PBS -N dir_name",
-        "#PBS -l nodes=4:ppn=1:Nodes,walltime=168:00:00",
+        "#PBS -N spec/not_started",
+        "#PBS -l nodes=4:ppn=1:Nodes,walltime=7:00:00:00",
         "#PBS -j oe",
-        "mkdir -p ${PBS_O_WORKDIR}",
-        "cp ${PBS_NODEFILE} ${PBS_O_WORKDIR}/pbs_nodefile",
-        "rsync -azq --delete FS:${PBS_O_WORKDIR}/ ${PBS_O_WORKDIR}",
-        "cd ${PBS_O_WORKDIR}",
-        "command_line",
-        "#rsync -azq --delete ${PBS_O_WORKDIR}/ FS:${PBS_O_WORKDIR}",
+        "mkdir -p ${PBS_O_WORKDIR} && \\",
+        "rsync -azq --delete FS:${PBS_O_WORKDIR}/ ${PBS_O_WORKDIR} && \\",
+        "cp ${PBS_NODEFILE} ${PBS_O_WORKDIR}/pbs_nodefile && \\",
+        "cd ${PBS_O_WORKDIR} && \\",
+        "command_line && \\",
+        "rsync -azq --delete ${PBS_O_WORKDIR}/ FS:${PBS_O_WORKDIR} && \\",
         "#rm -rf ${PBS_O_WORKDIR}",
+        "mv ${PBS_O_WORKDIR} ~/.trash",
       ].join("\n")
     end
 
@@ -52,4 +115,42 @@ describe QueueSubmitter do
       end
     end
   end
+
+  describe "#finished?" do
+    context "locked" do
+      it do
+        opts = {
+          :d => ComputationManager.new("spec/queuesubmitter/locked"),
+          :c => "command_line",
+          :n => "Nodes",
+          :s => true,
+          :machineinfo => MachineInfo.new(
+            "fileserver" => "FS",
+            "Nodes" => { "speed_nodes" => 4, "economy_nodes" => 1, }
+          )
+        }
+        @qs00 = QueueSubmitter.new(opts)
+
+        @qs00.finished?.should == true
+      end
+    end
+
+    context "unlocked" do
+      it do
+        opts = {
+          :d => ComputationManager.new("spec/queuesubmitter/unlocked"),
+          :c => "command_line",
+          :n => "Nodes",
+          :s => true,
+          :machineinfo => MachineInfo.new(
+            "fileserver" => "FS",
+            "Nodes" => { "speed_nodes" => 4, "economy_nodes" => 1, }
+          )
+        }
+        @qs00 = QueueSubmitter.new(opts)
+
+        @qs00.finished?.should == false
+      end
+    end
+  end
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: comana
 version: !ruby/object:Gem::Version
-  version: 0.0.6
+  version: 0.0.7
   prerelease: 
 platform: ruby
 authors:
@@ -9,11 +9,11 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-05-08 00:00:00.000000000 Z
+date: 2012-05-10 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rspec
-  requirement: &81878250 !ruby/object:Gem::Requirement
+  requirement: &80007130 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -21,10 +21,10 @@ dependencies:
         version: 2.9.0
   type: :development
   prerelease: false
-  version_requirements: *81878250
+  version_requirements: *80007130
 - !ruby/object:Gem::Dependency
   name: rdoc
-  requirement: &81877750 !ruby/object:Gem::Requirement
+  requirement: &80006610 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -32,10 +32,10 @@ dependencies:
         version: '3.12'
   type: :development
   prerelease: false
-  version_requirements: *81877750
+  version_requirements: *80006610
 - !ruby/object:Gem::Dependency
   name: bundler
-  requirement: &81877070 !ruby/object:Gem::Requirement
+  requirement: &80005810 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -43,10 +43,10 @@ dependencies:
         version: 1.1.3
   type: :development
   prerelease: false
-  version_requirements: *81877070
+  version_requirements: *80005810
 - !ruby/object:Gem::Dependency
   name: jeweler
-  requirement: &81876620 !ruby/object:Gem::Requirement
+  requirement: &80005240 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -54,10 +54,10 @@ dependencies:
         version: 1.8.3
   type: :development
   prerelease: false
-  version_requirements: *81876620
+  version_requirements: *80005240
 - !ruby/object:Gem::Dependency
   name: simplecov
-  requirement: &81875300 !ruby/object:Gem::Requirement
+  requirement: &80004850 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -65,14 +65,13 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *81875300
+  version_requirements: *80004850
 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:
-- submitqueue
+executables: []
 extensions: []
 extra_rdoc_files:
 - LICENSE.txt
@@ -85,7 +84,6 @@ files:
 - README.rdoc
 - Rakefile
 - VERSION
-- bin/submitqueue
 - comana.gemspec
 - dot.machineinfo
 - lib/comana.rb
@@ -108,6 +106,8 @@ files:
 - spec/outputted/input_a
 - spec/outputted/input_b
 - spec/outputted/output
+- spec/queuesubmitter/locked/lock_queuesubmitter/dummy
+- spec/queuesubmitter/unlocked/dummy
 - spec/queuesubmitter_spec.rb
 - spec/spec_helper.rb
 homepage: http://github.com/ippei94da/comana
@@ -125,7 +125,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
       segments:
       - 0
-      hash: 362387791
+      hash: 244597455
 required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
   requirements:

data/bin/submitqueue

@@ -1,65 +0,0 @@
-#! /usr/bin/env ruby
-# coding: utf-8
-
-require "optparse"
-require "yaml"
-require "pp"
-require "comana/queuesubmitter.rb"
-require "comana/machineinfo.rb"
-
-## option analysis
-OPTS = {}
-op = OptionParser.new
-#op.on("-e", "--economy"  , "Prior efficiency."){OPTS[:e] = true}
-op.on("-s"        , "--speed"  , "Prior speed to efficiency."){OPTS[:s] = true}
-op.on("-n nodes"  , "--nodes"  , "Node series."              ){|v| OPTS[:n] = v}
-op.on("-c command", "--command", "Command to calculate."     ){|v| OPTS[:c] = v}
-op.on("-d dir"    , "--dir"    , "Directory to calculate."   ){|v| OPTS[:d] = v}
-op.parse!(ARGV)
-#cluster = ARGV[0]
-#cluster = ARGV
-
-OPTS[:machineinfo] = MachineInfo.load_file
-
-qs = QueueSubmitter.new(OPTS)
-begin
-  qs.start
-rescue QueueSubmitter::AlreadyStartedError
-  puts "Already started. Exit"
-  exit
-rescue QueueSubmitter::PrepareNextError
-  puts "Submitted. Exit"
-  exit
-end
-
-#yaml = YAML.load_file("#{ENV["HOME"]}/.machineinfo")
-#pp yaml
-#
-#if File.exits?(SCRIPT_FILE)
-#  puts "#{SCRIPT_FILE} already exist. Exit."
-#  exit
-#end
-#
-#File.open(SCRIPT_FILE, "w") do |io|
-#  io.puts "#PBS -N task"
-#  io.puts "#PBS -l nodes=4:ppn=1:Ga"
-#  io.puts "cd $PBS_O_WORKDIR"
-#  io.puts "runvasp"
-#  #io.puts "#/usr/local/bin/mpiexec /usr/local/bin/vasp5212mpi-ifc11-fast"
-#  #io.puts "#/home/ippei/local/mpi/mpiexec-0.84/mpiexec /usr/local/calc/bin/vasp5212-mpich2"
-#  #io.puts "#/usr/local/calc/mpiexec/bin/mpiexec /usr/local/calc/bin/vasp5212-mpich2"
-#  #io.puts "#~/tmp.rb #OK"
-#
-#  #io.puts condition
-#  #io.puts rsync
-#  #io.puts run
-#  #io.puts rsync
-#  #io.puts mv to trash？
-#end
-#
-## Record job_id in pbs. Overwrite if exists.
-#job_id = `qsub #{SCRIPT_FILE}`
-#File.open(PBS_LOG, "w") do |io|
-#  io.puts job_id
-#end
-#