server_scripts 0.0.1

checksums.yaml

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+SHA1:
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+  data.tar.gz: 8d9d49ee51086a521c8144f935348302bf13cfb7
+SHA512:
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data/Gemfile

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+source 'https://rubygems.org'
+gemspec

data/README.md

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+# server-scripts
+
+A gem providing easily usable server scripts for various supercomputers and servers.
+The following functionality is provided:
+
+* Generate job scripts and run batch jobs on TSUBAME 3.0, ABCI and reedbush machines.
+* Parse various kinds of profiling files and generate meaningful output.
+
+# Usage
+
+## ENV variables
+
+Make sure the `SYSTEM` variable is set on your machine so that the gem will automatically
+select the appropriate commands to run.
+
+## Writing job scripts
+
+### Simple openMPI job script
+
+Use the `ServerScripts::BatchJob` class in your Ruby for outputting and submitting
+job files. A simple MPI job can be generated and submitted as follows:
+
+``` ruby
+require 'server_scripts'
+
+include ServerScripts
+
+task = BatchJob.new do |t|
+  t.nodes = 4
+  t.npernode = 4
+  t.wall_time = "1:30:00"
+  t.out_file = "out.log"
+  t.err_file = "err.log"
+  t.node_type = NodeType::FULL
+  t.mpi = OPENMPI
+  t.set_env "STARPU_SCHED", "dmda"
+  t.set_env "MKL_NUM_THREADS", "1"
+  t.executable = "a.out"
+  t.options = "3 32768 2048 2 2"
+end
+
+task.submit!
+```
+This will generate a unique file name and submit it using the system's batch
+job submission command.
+
+### Intel MPI profiling job script
+
+If you want to generate traces using intel MPI, you can use additional options
+like setting the ITAC and VTUNE output file/folder names.
+
+## Parse intel ITAC output
+
+The intel ITAC tool can be helpful for generating traces of parallel MPI programs.
+This class can be used for converting an ITAC file to an ideal trace and then generating
+the function profile for obtaining things like the MPI wait time.
+
+For extracting the MPI wait time from an ITAC trace, do the following:
+``` ruby
+require 'server_scripts'
+
+itac = ServerScripts::Parser::ITAC.new("itac_file.stf")
+itac.generate_ideal_trace!
+
+# All times are reported in seconds.
+
+puts itac.mpi_time(kind: :ideal)
+puts itac.mpi_time(kind: :real)
+puts itac.event_time("getrf_start", how: :total, kind: :real)
+puts itac.event_time("getrf_start", how: :per_proc, kind: :real)
+```
+
+## Parse starpu worker info
+
+

data/Rakefile

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+require 'rake'
+require 'rake/testtask'
+require 'fileutils'
+require 'server_scripts/version.rb'
+
+gemspec = eval(IO.read("server_scripts.gemspec"))
+
+Rake::TestTask.new(:test) do |t|
+  t.libs << "test"
+  t.libs << "lib"
+  t.test_files = FileList['test/**/test_*.rb']
+end

data/lib/server_scripts/computer/abci.rb

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+module ServerScripts
+  module Computer
+    class ABCI < Base
+      FULL_NODE = "rt_F"
+      
+      def header(node_type: FULL_NODE)
+        h = %q{
+#!/bin/bash
+
+#$ -cwd
+#$ -l %{node_type}=%{nodes}
+#$ -l h_rt=%{walltime}
+#$ -N %{job_name}
+#$ -o %{out_file}.log
+#$ -e %{err_file}.log
+        }
+      end
+    end    
+  end
+end
+

data/lib/server_scripts/computer/base.rb

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+module ServerScripts
+  module Computer
+    class Base
+      def initialize(node_type, nodes, job_name, wall_time, out_file,
+        err_file, env)
+        @node_type = node_type
+        @nodes = nodes
+        @job_name = job_name
+        @wall_time = wall_time
+        @out_file = out_file
+        @err_file = err_file
+        @env = env
+      end
+
+      def node_type
+        if @node_type == NodeType::FULL
+          self.class::FULL_NODE
+        end
+      end
+
+      def env_setter
+        raise NotImplementedError
+      end
+
+      def job_submit_cmd
+        raise NotImplementedError
+      end
+    end    
+  end
+end

data/lib/server_scripts/computer/sameer_pc.rb

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+module ServerScripts
+  module Computer
+    class SameerPC < Base
+      def initialize
+        
+      end
+
+      def full_node
+        ""
+      end
+    end    
+  end
+end

data/lib/server_scripts/computer/tsubame.rb

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+module ServerScripts
+  module Computer
+    class TSUBAME < Base
+      HEADER = %q{#!/bin/bash
+
+#$ -cwd
+#$ -l %{node_type}=%{nodes}
+#$ -l h_rt=%{wall_time}
+#$ -N %{job_name}
+#$ -o %{out_file}.log
+#$ -e %{err_file}.log
+      }
+
+      FULL_NODE = "f_node"
+      
+      def header
+        HEADER % {node_type: node_type, nodes: @nodes, wall_time: @wall_time,
+          job_name: @job_name, out_file: @out_file, err_file: @err_file}
+      end
+
+      def env_setter
+        str = "\n"
+        @env.each do |var, value|
+          str += "export #{var}=#{value}\n"
+        end
+
+        str
+      end
+
+      def job_submit_cmd res_id: nil, batch_script:
+        res = res_id ? " -ar #{res_id} " : ""
+        "qsub -g #{ServeScripts.group_name} #{res} #{batch_script}"
+      end
+    end    
+  end
+end

data/lib/server_scripts/computer.rb

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+require 'server_scripts/computer/base'
+require 'server_scripts/computer/tsubame'
+require 'server_scripts/computer/abci'
+require 'server_scripts/computer/sameer_pc'
+

data/lib/server_scripts/executor/base.rb

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+module ServerScripts
+  module Executor
+    class Base
+      def run_cmd
+        raise NotImplementedError
+      end
+    end
+  end  
+end
+

data/lib/server_scripts/executor/mpi_program.rb

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+# coding: utf-8
+module ServerScripts
+  module Executor
+    class MPIProgram < Base
+      attr_reader :npernode
+      attr_reader :nprocs
+      attr_reader :env
+      
+      def initialize(npernode: , nprocs:, env: {})
+        @npernode = npernode
+        @nprocs = nprocs
+        @env = env
+      end
+    end
+    
+    class OpenMPI < MPIProgram
+      def run_cmd
+        "mpirun --mca mpi_cuda_support 0 #{env_variables} -N #{@npernode} -np #{@nprocs}"
+      end
+
+      private
+
+      def env_variables
+        str = ""
+        @env.each_key do |k|
+          str += " -x #{k} "
+        end
+        
+        str
+      end
+    end
+
+    class IntelMPI < MPIProgram
+      attr_accessor :enable_itac
+      attr_accessor :vtune_fname
+
+      def initialize(*args)
+        super
+        @vtune_fname = "DEFAULT_VTUNE"
+      end
+      
+      def run_cmd
+        hydra = @enable_itac ? "mpiexec.hydra -trace" : "mpiexec.hydra"
+        cmd = "#{hydra} -ppn #{@npernode} -np #{@nprocs} "
+        if @enable_itac
+          cmd += "amplxe-cl -trace-mpi –collect hpc-performance –r #{@vtune_fname} "
+        end
+
+        cmd
+      end
+    end
+    
+  end
+end

data/lib/server_scripts/executor/valgrind.rb

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+module ServerScripts
+  module Executor
+    class Valgrind < Base
+      
+    end
+  end
+end

data/lib/server_scripts/executor/vanilla.rb

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+module ServerScripts
+  module Executor
+    class Vanilla < Base
+      
+    end
+  end
+end

data/lib/server_scripts/executor.rb

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+require 'server_scripts/executor/base'
+require 'server_scripts/executor/mpi_program'
+require 'server_scripts/executor/valgrind'
+require 'server_scripts/executor/vanilla'

data/lib/server_scripts/node_type.rb

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+module ServerScripts
+  module NodeType
+    FULL = :full
+    HALF = :half
+  end
+end # moduel ServerScripts

data/lib/server_scripts/version.rb

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+module ServerScripts
+  VERSION = "0.0.1"
+end

data/lib/server_scripts.rb

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+# -*- coding: utf-8 -*-
+require 'server_scripts/node_type'
+require 'server_scripts/executor'
+require 'server_scripts/computer'
+require 'server_scripts/version'
+
+module ServerScripts
+  class << self
+    def system
+      sys = ENV["SYSTEM"]
+
+      if sys == "SAMEER-PC"
+        ServerScripts::Computer::SameerPC
+      elsif sys == "TSUBAME"
+        ServerScripts::Computer::TSUBAME
+      elsif sys == "ABCI"
+        ServerScripts::Computer::ABCI
+      elsif sys == "REEDBUSH"
+        ServerScripts::Computer::REEDBUSH
+      end
+    end
+
+    def group_name
+      ENV["GROUP_NAME"]
+    end
+  end
+
+  class BatchJob
+    attr_accessor :job_name
+    attr_accessor :out_file
+    attr_accessor :err_file
+    attr_accessor :wall_time
+    attr_accessor :node_type
+    attr_accessor :options
+    attr_accessor :nodes
+    attr_accessor :npernode
+    attr_accessor :nprocs
+    attr_accessor :run_cmd, :executor, :executable
+    attr_accessor :additional_commands
+    attr_accessor :enable_intel_itac
+    attr_accessor :intel_vtune_fname
+
+    attr_reader :env
+    attr_reader :job_fname
+    attr_reader :system
+      
+    def initialize job_fname
+      @job_fname = "sample_job_script.sh"
+      @job_name = "sample"
+      @out_file = "sample_out"
+      @err_file = "sample_err"
+      @wall_time = "1:00:00"
+      @node_type = NodeType::FULL
+      @nodes = 1
+      @npernode = 1
+      @nprocs = nil
+      @run_cmd = nil
+      @executor = :vanilla
+      @env = {}
+      @executable = "./a.out"
+      @job_script = ""
+      @enable_intel_itac = false
+      @additional_commands = []
+
+      yield self
+    end
+
+    def set_env var, value
+      raise ArgumentError, "Env #{var} is already set to #{value}." if @env[var]
+      @env[var] = value
+    end
+
+    def generate_job_script!
+      @system = ServerScripts.system.new(@node_type, @nodes, @job_name,
+        @wall_time, @out_file, @err_file, @env)
+      configure_executor!
+
+      @job_script += @system.header
+      @job_script += @system.env_setter
+      @additional_commands.each do |c|
+        @job_script += c + "\n"
+      end
+      @job_script += "#{@executor.run_cmd} #{@executable} #{@options}"
+    end
+
+    def submit!
+      generate_job_script! unless @job_script
+      File.write(@job_fname, @job_script)
+#      system(@system.job_submit_cmd(batch_script: @job_fname))
+    end
+
+    private
+
+    def configure_executor!
+      check_process_counts
+      @nprocs = @npernode * @nodes
+
+      if @executor == :openmpi
+        @executor = Executor::OpenMPI.new(npernode: @npernode, nprocs: @nprocs, env: @env)
+      elsif @executor == :intel
+        @executor = Executor::IntelMPI.new(npernode: @npernode, nprocs: @nprocs, env: @env)
+        @executor.enable_itac = !!@enable_intel_itac
+        @executor.vtune_fname = @intel_vtune_fname
+      elsif @executor == :vanilla
+        @executor = Executor::Vanilla.new
+      else
+        raise ArgumentError, "Cannot find MPI implementation #{@executor}."
+      end
+    end
+
+    def check_process_counts
+      if @nprocs && @nprocs != @npernode * @nodes
+        raise ArgumentError, "Number of processes should be #{@npernode * @nodes} not #{@nprocs}"
+      end
+    end
+  end
+
+  class Parser
+    class ITAC
+      attr_reader :ideal_trace_file, :real_trace_file
+      
+      def initialize itac_file
+        @itac_file = itac_file
+        @ideal_trace_file = nil
+        @real_trace_file = nil
+      end
+
+      def generate_ideal_trace!
+        
+      end
+    end # class ITAC
+  end # module Parser
+end # module ServerScripts
+
+
+

data/server_scripts.gemspec

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+#coding: utf-8
+$:.unshift File.expand_path("../lib", __FILE__)
+
+require 'server_scripts/version.rb'
+
+def self.get_files
+  files = []
+  ['ext', 'lib', 'spec'].each do |folder|
+    files.concat Dir.glob "#{folder}/**/*"
+  end
+
+  files.concat(
+    ["Gemfile", "server_scripts.gemspec", "README.md", "Rakefile"])
+  
+  files
+end
+files = get_files
+
+ServerScripts::DESCRIPTION = <<MSG
+Easily write scripts for submitted jobs to various machines.
+MSG
+
+Gem::Specification.new do |spec|
+  spec.name          = 'server_scripts'
+  spec.version       = ServerScripts::VERSION
+  spec.authors       = ['Sameer Deshmukh']
+  spec.email         = ['sameer.deshmukh93@gmail.com']
+  spec.summary       = %q{Easily write scripts for submitted jobs to various machines.}
+  spec.description   = ServerScripts::DESCRIPTION
+  spec.homepage      = "https://github.com/v0dro/server-scripts"
+  spec.license       = 'BSD-3 Clause'
+
+  spec.files         = files
+  spec.executables   = spec.files.grep(%r{^bin/}) { |f| File.basename(f) }
+  spec.test_files    = spec.files.grep(%r{^(test|spec|features)/})
+  spec.require_paths = ["lib"]
+
+  spec.add_development_dependency 'minitest', '~> 5.11'
+  spec.add_development_dependency 'minitest-hooks'
+  spec.add_development_dependency 'minitest-fail-fast'
+end

metadata

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+--- !ruby/object:Gem::Specification
+name: server_scripts
+version: !ruby/object:Gem::Version
+  version: 0.0.1
+platform: ruby
+authors:
+- Sameer Deshmukh
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2020-01-22 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: minitest
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '5.11'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '5.11'
+- !ruby/object:Gem::Dependency
+  name: minitest-hooks
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: minitest-fail-fast
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+description: 'Easily write scripts for submitted jobs to various machines.
+
+'
+email:
+- sameer.deshmukh93@gmail.com
+executables: []
+extensions: []
+extra_rdoc_files: []
+files:
+- Gemfile
+- README.md
+- Rakefile
+- lib/server_scripts.rb
+- lib/server_scripts/computer.rb
+- lib/server_scripts/computer/abci.rb
+- lib/server_scripts/computer/base.rb
+- lib/server_scripts/computer/sameer_pc.rb
+- lib/server_scripts/computer/tsubame.rb
+- lib/server_scripts/executor.rb
+- lib/server_scripts/executor/base.rb
+- lib/server_scripts/executor/mpi_program.rb
+- lib/server_scripts/executor/valgrind.rb
+- lib/server_scripts/executor/vanilla.rb
+- lib/server_scripts/node_type.rb
+- lib/server_scripts/version.rb
+- server_scripts.gemspec
+homepage: https://github.com/v0dro/server-scripts
+licenses:
+- BSD-3 Clause
+metadata: {}
+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: 2.6.14
+signing_key: 
+specification_version: 4
+summary: Easily write scripts for submitted jobs to various machines.
+test_files: []