qtools 0.1.0

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data/.gitignore

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+/.bundle/
+/.yardoc
+/Gemfile.lock
+/_yardoc/
+/coverage/
+/doc/
+/pkg/
+/spec/reports/
+/tmp/

data/.travis.yml

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+language: ruby
+rvm:
+  - 2.0.0
+before_install: gem install bundler -v 1.10.6

data/Gemfile

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+source 'https://rubygems.org'
+
+# Specify your gem's dependencies in qtools.gemspec
+gemspec
+

data/LICENSE.txt

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+The MIT License (MIT)
+
+Copyright (c) 2016 Daniel
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.

data/README.md

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+# qtools
+
+`qtools` offers the shortcuts for some common procedures when working with the Open Grid Scheduler.
+
+
+## Installation
+
+Install `qtools` using `gem`:
+
+    $ gem install qtools
+
+## Usage
+
+- `qqsub`  to submit a script or a compiled executable
+- `qwatch` to see the running jobs for the current user
+- `qcount` to see the number of running jobs for the current user
+- `qclean` to remove `.e[0-9]*` and `.o[0-9]*` files in the current directory
+
+### qqsub
+
+Usage:
+
+    $ qqsub 'python3 my_script.py -i input.txt -v' -n my_name -m 8gb
+
+The command above will create a shell script file with the corresponding content and submit a job which will feature the name `my_name` and require `8gb` of memory.
+
+### qwatch
+
+Usage:
+
+    $ qwatch
+
+The command above is equivalent to running `watch -n1 -d "qstat -u $USER"`.
+
+Flags:
+
+  - `-n`, `--nodes` to show information on nodes too (`qstat -n1 -u $USER`)
+
+### qclean
+
+Usage:
+
+    $ qclean
+
+The command above will run `rm *.[eo][0-9]*` in the current directory (if such files exist).
+
+### qcount
+
+Usage:
+
+    $ qcount
+
+Count the number of jobs for the `$USER`. Running `qcount -a` will output the number of jobs for all the users.
+
+## Contributing
+
+Bug reports and pull requests are welcome on [GitHub](https://github.com/kerkomen/qtools).
+
+## License
+
+The gem is available as open source under the terms of the [MIT License](http://opensource.org/licenses/MIT).
+

data/Rakefile

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+require "bundler/gem_tasks"

data/bin/console

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+#!/usr/bin/env ruby
+
+require "bundler/setup"
+require "qtools"
+
+# You can add fixtures and/or initialization code here to make experimenting
+# with your gem easier. You can also use a different console, if you like.
+
+# (If you use this, don't forget to add pry to your Gemfile!)
+# require "pry"
+# Pry.start
+
+require "irb"
+IRB.start

data/bin/qclean

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+#!/usr/bin/env ruby
+
+require 'qtools'
+
+files = `ls *.[eo][0-9]* 2> /dev/null`
+
+unless files.empty?
+  puts "-- The following files will be removed:"
+  puts files
+  puts "-- Continue? [y/n]"
+
+  answer = gets.strip.downcase
+  if answer == 'y' or answer == 'yes'
+    system("rm *.[eo][0-9]*")
+    puts "-- Ok, master. The files are removed!"
+  else
+    puts "-- Ok, master. No means no."
+  end
+else
+  puts "-- It's pretty clean in this folder... No files to be removed."
+end

data/bin/qcount

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+#!/usr/bin/env ruby
+
+require 'qtools'
+require 'optparse'
+
+options = {}
+OptionParser.new do |opts|
+  opts.banner = "Usage: qwatch [options]"
+
+  opts.on("-a", "--all", "Count jobs for all users") do |n|
+    options[:all] = n
+  end
+end.parse!
+
+flags = []
+flags << '-u $USER' unless options[:all]
+flags_str = flags.join(' ')
+ 
+puts `qstat #{flags_str} | grep -c ^[0-9]`

data/bin/qqsub

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+#!/usr/bin/env ruby
+
+require 'qtools'
+require 'optparse'
+
+Options = Struct.new(:name, :mem)
+
+args = Options.new(:name, :mem)
+OptionParser.new do |opts|
+  opts.banner = "Usage: qtools 'python3 my_script.py ...' [options]"
+
+  opts.on("-n", "--name NAME", "Name for the job") do |n|
+    args.name = n
+  end
+  opts.on("-m", "--memory MEMORY", "Memory for the job (e.g., 80gb)") do |m|
+    args.mem = m
+  end
+end.parse!
+
+command = ARGV
+
+if command.empty?
+  fail "Usage: qtools 'python3 my_script.py ...' [options]"
+end
+
+header_sge = <<-HEADER
+#!/bin/bash
+
+#$ -V
+#$ -cwd
+HEADER
+
+header_shell = "#!/bin/bash\n"
+
+header_pbs_tree = {}
+header_pbs_tree[:l] = ['walltime=24:00:00']
+header_pbs_tree[:d] = ['.']
+
+unless args.name.is_a? Symbol
+  header_pbs_tree[:N] = [args.name]
+end
+
+unless args.mem.is_a? Symbol
+  header_pbs_tree[:l] << "mem=#{args.mem}"
+end
+
+header_pbs = header_pbs_tree.map { |k, v| "#PBS -#{k} #{v.join(',')}" }.join("\n")
+
+sh_name = command[0].split[1].match(/(.*)\.(.*?)/)[1] + '.sh'
+
+File.write(sh_name, [header_shell, header_pbs, "", command[0]].join("\n"))
+
+puts "-- Submit #{sh_name} for execution? [y/n]"
+answer = STDIN.gets.strip.downcase
+if answer == 'y' or answer == 'yes'
+  system("qsub #{sh_name}")
+  puts "-- Ok, master, #{sh_name} is submitted."
+else
+  puts "-- Ok, master. No means no."
+end

data/bin/qwatch

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+#!/usr/bin/env ruby
+
+require 'qtools'
+require 'optparse'
+
+options = {}
+OptionParser.new do |opts|
+  opts.banner = "Usage: qwatch [options]"
+
+  opts.on("-n", "--nodes", "Show nodes") do |n|
+    options[:nodes] = n
+  end
+end.parse!
+
+flags = []
+flags << '-n1' if options[:nodes]
+flags_str = flags.join(' ')
+ 
+system("watch -n1 -d \"qstat #{flags_str} -u $USER\"")

data/bin/setup

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+#!/bin/bash
+set -euo pipefail
+IFS=$'\n\t'
+
+bundle install
+
+# Do any other automated setup that you need to do here

data/lib/qtools.rb

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+#!/usr/bin/env ruby
+
+help_string = <<-HELP
+
+-- qtools:
+- qqsub  to submit a script or a compiled executable
+- qwatch to see the running jobs for the current user
+- qclean to remove .e* and .o* run files in the current directory
+
+HELP
+
+
+def help
+  puts help_string
+end

data/lib/qtools/version.rb

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+module Qtools
+  VERSION = "0.1.0"
+end

data/qtools.gemspec

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+# coding: utf-8
+lib = File.expand_path('../lib', __FILE__)
+$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
+require 'qtools/version'
+
+Gem::Specification.new do |spec|
+  spec.name          = "qtools"
+  spec.version       = Qtools::VERSION
+  spec.authors       = ["Daniel"]
+  spec.email         = ["@"]
+
+  spec.summary       = %q{ Shortcuts for the Open Grid Scheduler }
+  spec.description   = %q{ Make the most common Sun Grid Engine programs more effective.  }
+  spec.homepage      = "https://github.com/kerkomen/qtools"
+  spec.license       = "MIT"
+
+  # Prevent pushing this gem to RubyGems.org by setting 'allowed_push_host', or
+  # delete this section to allow pushing this gem to any host.
+  if spec.respond_to?(:metadata)
+    spec.metadata['allowed_push_host'] = "https://rubygems.org"
+  else
+    raise "RubyGems 2.0 or newer is required to protect against public gem pushes."
+  end
+
+  # spec.files         = `git ls-files -z`.split("\x0").reject { |f| f.match(%r{^(test|spec|features)/}) }
+  spec.files         = %w{ .gitignore .travis.yml Gemfile LICENSE.txt README.md Rakefile bin/console bin/qclean bin/qqsub bin/qwatch bin/qcount bin/setup lib/qtools.rb lib/qtools/version.rb qtools.gemspec}
+  spec.bindir        = "bin"
+  spec.executables   = ["qwatch", "qclean", "qqsub", "qcount"]
+  spec.require_paths = ["lib"]
+
+  spec.add_development_dependency "bundler", "~> 1.10"
+  spec.add_development_dependency "rake", "~> 10.0"
+end

metadata

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+--- !ruby/object:Gem::Specification
+name: qtools
+version: !ruby/object:Gem::Version
+  version: 0.1.0
+platform: ruby
+authors:
+- Daniel
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2016-05-09 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.10'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.10'
+- !ruby/object:Gem::Dependency
+  name: rake
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '10.0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '10.0'
+description: " Make the most common Sun Grid Engine programs more effective.  "
+email:
+- "@"
+executables:
+- qwatch
+- qclean
+- qqsub
+- qcount
+extensions: []
+extra_rdoc_files: []
+files:
+- ".gitignore"
+- ".travis.yml"
+- Gemfile
+- LICENSE.txt
+- README.md
+- Rakefile
+- bin/console
+- bin/qclean
+- bin/qcount
+- bin/qqsub
+- bin/qwatch
+- bin/setup
+- lib/qtools.rb
+- lib/qtools/version.rb
+- qtools.gemspec
+homepage: https://github.com/kerkomen/qtools
+licenses:
+- MIT
+metadata:
+  allowed_push_host: https://rubygems.org
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: 
+rubygems_version: 2.5.1
+signing_key: 
+specification_version: 4
+summary: Shortcuts for the Open Grid Scheduler
+test_files: []