class CodeRunner::Gene

This is a customised subclass of the CodeRunner::Run class which allows CodeRunner to run and analyse the GENE gyrokinetic code (see www2.ipp.mpg.de/~fsj/gene/)

Public Class Methods

defaults_file_header() click to toggle source
# File lib/genecrmod/gene.rb, line 227
    def self.defaults_file_header
      <<EOF1
############################################################################
#                                                                          #
# Automatically generated defaults file for the GENE CodeRunner module     #
#                                                                          #
# This defaults file specifies a set of defaults for GENE which are        #
# used by CodeRunner to set up and run GENE simulations.                   #
#                                                                          #
############################################################################

# Created: #{Time.now.to_s}

@defaults_file_description = ""
EOF1
    end
parse_input_file(input_file, strict=true) click to toggle source
Calls superclass method
# File lib/genecrmod/gene.rb, line 92
def self.parse_input_file(input_file, strict=true)
  if FileTest.file? input_file
    text = File.read(input_file)
  else
    text = input_file
  end
  i = 0
  text.gsub!(/^(&species)/i){p $~; "#{$1}_#{i+=1}"}
  super(text)
end

Public Instance Methods

check_parameters() click to toggle source
# File lib/genecrmod/check_parameters.rb, line 22
def check_parameters
  rcp.namelists.each do |namelist, hash|
    next if hash[:should_include].kind_of? String and not eval(hash[:should_include])
    if en = hash[:enumerator]
      next unless send(en[:name])
      send(en[:name]).times do |i|
        run_namelist_tests(namelist, hash, i+1)
      end
    else
      run_namelist_tests(namelist, hash)
    end
  end

  # Now look at namelist specific flags, catch any obvious mistakes/conflicts
  
  ###################
  # in_out namelist #
  ###################
  
  if not (@write_h5 and @write_h5.fortran_true?) 
    warning("Very little analysis will be possible without write_h5 = '.true.'") 
  end

  if not (@write_checkpoint and @write_checkpoint.fortran_true?) and 
    not (@chpt_h5 and @chpt_h5.fortran_true?)
    p @write_checkpoint, @write_checkpoint.fortran_true?
    warning("This simulation will not write out a checkpoint file.")
  end

  if (@write_std and @write_std.fortran_true?) and (@write_h5 and @write_h5.fortran_true?)
    warning("Both write_std and write_h5 are specified - will produce lots of output!")
  end
end
generate_component_runs() click to toggle source
# File lib/genecrmod/gene.rb, line 151
def generate_component_runs
  #puts "HERE"
end
generate_input_file() click to toggle source

This is a hook which gets called just before submitting a simulation. It sets up the folder and generates any necessary input files.

# File lib/genecrmod/gene.rb, line 79
def generate_input_file
    check_parameters
    if @restart_id
      @runner.run_list[@restart_id].restart(self)
    end
    @diagdir = "."
    @n_procs_sim = actual_number_of_processors
    # Simulation time limit is set to ~ 90% of wall mins to allow GENE to
    # exit gracefully
    @timelim = @wall_mins * 55 if @wall_mins
    write_input_file
end
get_completed_timesteps() click to toggle source
# File lib/genecrmod/gene.rb, line 195
      def get_completed_timesteps
              Dir.chdir(@directory) do
@completed_timesteps = %x[grep '^\\s\\+\\S\\+\\s*$' nrg.dat 2>/dev/null].split("\n").size
              end
      end
get_growth_rates() click to toggle source
# File lib/genecrmod/gene.rb, line 249
def get_growth_rates
  Dir.chdir(@directory) do
    if FileTest.exist?(ofile = 'omega.dat.h5')
      @kyvals = get_h5_narray_all(ofile, '/ky').to_gslv
      @growth_rates = get_h5_narray_all(ofile, '/gamma').to_gslv
      @frequencies = get_h5_narray_all(ofile, '/omega').to_gslv
    elsif FileTest.exist?('omega.dat')
      @kyvals, @growth_rates, @frequencies = GSL::Vector.filescan('omega.dat')
    else
      @kyvals, @growth_rates, @frequencies = [nil] * 3
    end
  end
end
get_h5_narray_all(file, dataset) click to toggle source
# File lib/genecrmod/hdf5.rb, line 3
def get_h5_narray_all(file, dataset)
  Dir.chdir(@directory) do
    file = Hdf5::H5File.new(file)
    narray =  file.dataset(dataset).narray_all
                      file.close
                      return narray
  end
end
get_status() click to toggle source
# File lib/genecrmod/gene.rb, line 172
def get_status
                    if @running
    if @status != :Queueing
      get_completed_timesteps
      if completed_timesteps == 0
        @status = :NotStarted
      else
        @status = :Incomplete
      end
    end
                    else
                            get_completed_timesteps
                            if @completed_timesteps == @ntimesteps
                                    @status = :Complete
                            else
                                    if FileTest.exist?('GENE.finished')
                                            @status = :Complete
                                    else
                                            @status = :Failed
                                    end
                            end
                    end
end
graphkit(name, options={}) click to toggle source

This is a temporary hack… we should do this properly!!!

# File lib/genecrmod/gene.rb, line 263
def graphkit(name, options={})
  case name
  when /growth_rates_vs_ky/
    return GraphKit.quick_create([@kyvals, @growth_rates])
  when /ion_n2_vs_time/
    return GraphKit.quick_create([get_h5_narray_all('nrg.dat.h5', '/nrgIons/time').to_gslv, get_h5_narray_all('nrg.dat.h5', '/nrgIons/n2').to_gslv])

  end
end
input_file_extension() click to toggle source
# File lib/genecrmod/gene.rb, line 245
def input_file_extension
  ''
end
input_file_header() click to toggle source
# File lib/genecrmod/gene.rb, line 205
    def input_file_header
      <<EOF
!==============================================================================
!     GENE input file automatically generated by CodeRunner
!==============================================================================
!
!  GENE is a code for solving the nonlinear gyrokinetic equation.
!
!    See http://www2.ipp.mpg.de/~fsj/gene/
!
!  CodeRunner is a framework for the automated running and analysis
!  of large simulations.
!
!   See http://coderunner.sourceforge.net
!
!  Created #{Time.now.to_s}
!      by CodeRunner version #{CodeRunner::CODE_RUNNER_VERSION.to_s}
!
!==============================================================================

EOF
    end
namelist_test_failed(namelist, tst) click to toggle source
# File lib/genecrmod/check_parameters.rb, line 76
  def namelist_test_failed(namelist, tst)
        return  <<EOF

---------------------------
        Test Failed
---------------------------

Namelist: #{namelist}   
Test: #{tst[:test]}
Explanation: #{tst[:explanation]}

---------------------------
EOF

  end
namelist_text(namelist, enum = nil) click to toggle source
# File lib/genecrmod/gene.rb, line 102
def namelist_text(namelist, enum = nil)
  hash = rcp.namelists[namelist]
  text = ""
  ext = enum ? "_#{enum}" : ""
  text << "!#{'='*30}\n!#{hash[:description]} #{enum} \n!#{'='*30}\n" if hash[:description]
  text << "&#{namelist}\n"
  hash[:variables].each do |var, var_hash|
    code_var = (var_hash[:code_name] or var)
    cr_var = var+ext.to_sym
    value = send(cr_var)
    if send(cr_var) and (not var_hash[:should_include] or  eval(var_hash[:should_include]))
      if value.kind_of? Array
        value.each_with_index do |v, i|
          output = formatted_variable_output(v)
          text << " #{code_var}(#{i+1}) = #{output} #{var_hash[:description] ? "! #{var_hash[:description]}": ""}\n"
        end
      else
        output = formatted_variable_output(value)
        text << " #{code_var} = #{output} #{var_hash[:description] ? "! #{var_hash[:description]}": ""}\n"
      end
    elsif rcp.namelists_to_print_not_specified? and rcp.namelists_to_print_not_specified.include?(namelist)
      text << "  ! #{code_var} not specified --- #{var_hash[:description]}\n"
    end
  end
  text << "/\n\n"
  text
end
parameter_string() click to toggle source

Parameters which follow the Trinity executable, in this case just the input file.

# File lib/genecrmod/gene.rb, line 144
def parameter_string
  ""
end
parameter_transition() click to toggle source
# File lib/genecrmod/gene.rb, line 148
def parameter_transition
end
print_out_line() click to toggle source

A hook which gets called when printing the standard run information to the screen using the status command.

process_directory_code_specific() click to toggle source

This method, as its name suggests, is called whenever CodeRunner is asked to analyse a run directory. This happens if the run status is not :Complete, or if the user has specified recalc_all(-A on the command line) or reprocess_all (-a on the command line).

# File lib/genecrmod/gene.rb, line 161
def process_directory_code_specific
  get_status
  if ctd
    #get_global_results
    if !nonlinear or nonlinear.fortran_false?
      get_growth_rates
    end
  end
  @percent_complete = completed_timesteps.to_f  * (istep_nrg||10) / ntimesteps.to_f * 100.0
end
restart(new_run) click to toggle source

Modify new_run so that it becomes a restart of self. Adjusts all the parameters of the new run to be equal to the parameters of the run that calls this function, and sets up its run name correctly

# File lib/genecrmod/gene.rb, line 57
def restart(new_run)
  (rcp.variables).each{|v| new_run.set(v, send(v)) if send(v)}
  new_run.is_a_restart = true
  new_run.restart_id = @id
  new_run.restart_run_name = @run_name
  new_run.run_name = nil
  new_run.naming_pars = @naming_pars
  new_run.update_submission_parameters(new_run.parameter_hash.inspect, false) if new_run.parameter_hash
  new_run.naming_pars.delete(:restart_id)
  new_run.generate_run_name

  eputs 'Copying GENE restart file'
  if (@chpt_h5 and @chpt_h5.fortran_true?)
    new_run.chpt_read_h5 = ".true."
    FileUtils.cp("#@directory/checkpoint.h5", "#{new_run.directory}/checkpoint.h5")
  else
    new_run.read_checkpoint = ".true."
    FileUtils.cp("#@directory/checkpoint", "#{new_run.directory}/checkpoint")
  end
end
run_namelist_tests(namelist, hash, enum = nil) click to toggle source
# File lib/genecrmod/check_parameters.rb, line 3
def run_namelist_tests(namelist, hash, enum = nil)
  ext = enum ? "_#{enum}" : ""
  hash[:must_pass].each do |tst|
    error(namelist_test_failed(namelist, tst)) unless instance_eval(tst[:test])
  end if hash[:must_pass]
  hash[:should_pass].each do |tst|
    warning(namelist_test_failed(namelist, tst)) unless instance_eval(tst[:test])
  end if hash[:should_pass]
  hash[:variables].each do |var, var_hash|
    cr_var = var+ext.to_sym 
    value = send(cr_var)
    if value.kind_of? Array
      value.each{|v| test_variable(namelist, var, var_hash, ext, v)}
    else
      test_variable(namelist, var, var_hash, ext, value)
    end
  end
end
test_failed(namelist, var, gene_var, tst) click to toggle source
# File lib/genecrmod/check_parameters.rb, line 56
  def test_failed(namelist, var, gene_var, tst)
        return  <<EOF

---------------------------
        Test Failed
---------------------------

Namelist: #{namelist}   
Variable: #{var}
GENE Name: #{gene_var}
Value: #{send(var)}
Test: #{tst[:test]}
Explanation: #{tst[:explanation]}

---------------------------
EOF

  end
test_variable(namelist, var, var_hash, ext, value) click to toggle source
# File lib/genecrmod/check_parameters.rb, line 92
def test_variable(namelist, var, var_hash, ext, value)
  gene_var = (var_hash[:gene_name] or var)
  cr_var = var+ext.to_sym 
  if value and (not var_hash[:should_include] or  eval(var_hash[:should_include]))
      var_hash[:must_pass].each do |tst|
          error(test_failed(namelist, cr_var, gene_var, tst)) unless value.instance_eval(tst[:test])
      end if var_hash[:must_pass]
      var_hash[:should_pass].each do |tst|
          warning(test_failed(namelist, cr_var, gene_var, tst)) unless value.instance_eval(tst[:test])
      end if var_hash[:should_pass]
      if (var_hash[:allowed_values] or var_hash[:text_options])
          tst = {test: "#{(var_hash[:allowed_values] or var_hash[:text_options]).inspect}.include? self", explanation: "The variable must have one of these values"}
          error(test_failed(namelist, cr_var, gene_var, tst)) unless value.instance_eval(tst[:test])
      end
  end
end
vim_output() click to toggle source
# File lib/genecrmod/gene.rb, line 133
def vim_output
  system "vim -Ro #{output_file} #{error_file}"
end
Also aliased as: vo
vo()
Alias for: vim_output
write_input_file() click to toggle source

This command uses the infrastructure provided by Run::FortranNamelist, provided by CodeRunner itself.

# File lib/genecrmod/gene.rb, line 139
def write_input_file
  File.open("parameters", 'w'){|file| file.puts input_file_text}
end