Class: CodeRunner::Gryfx

Inherits:
Gs2
  • Object
show all
Defined in:
lib/gryfxcrmod/gryfx.rb,
lib/gryfxcrmod/namelist_tools.rb

Class Method Summary collapse

Instance Method Summary collapse

Class Method Details

.defaults_file_header ⇒ Object 



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# File 'lib/gryfxcrmod/gryfx.rb', line 213

def self.defaults_file_header
  "######################################################################\n# Automatically generated defaults file for GRYFX CodeRunner module  #\n#                                                                    #\n# This defaults file specifies a set of defaults for GRYFX which are #\n# used by CodeRunner to set up and run GRYFX simulations.            #\n#                                                                    #\n# Created \#{Time.now.to_s}                                           #\n#                                                                    #\n######################################################################\n\n@defaults_file_description = \"\"\n"
end

.get_namelists_and_variables_from_source_code(source) ⇒ Object

Find all input namelists and variables by scanning the source code



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# File 'lib/gryfxcrmod/namelist_tools.rb', line 9

def self.get_namelists_and_variables_from_source_code(source)
  nms = {}
  all_variables_in_source = {}
  namelist_declarations = {}
  #source.scan(/^\s*namelist\s*\/(?<namelist>\w+)\/(?<variables>(?:(?:&\s*[\n\r]+)|[^!\n\r])*)/) do 
  #source.scan(Regexp.new("#{/^\s*namelist\s*\/\s*(?<namelist>\w+)\s*\//}(?<variables>#{FORTRAN_SINGLE_LINE})")) do 
  source.scan(rcp.fortran_namelist_variable_match_regex) do
    namelist = $~[:namelist].to_s.downcase.to_sym
    #variables = $~[:variables].gsub(/!.*/, '')
    #eputs namelist, variables
    #namelist_declarations[namelist] = variables
    #gets # if namelist == :collisions_knobs

    #next if [:stuff, :ingen_knobs].include? namelist
    nms[namelist] ||= []
    all_variables_in_source[namelist] ||= []
#     puts variables
    #variables.scan(/\w+/) do 
      var =  $~[:variable].to_sym
#       (p variables, namelist; exit) if var == :following or var == :sou
      all_variables_in_source[namelist].push var
      next if known_code_variable?(namelist, var)
      nms[namelist].push var
    #end
    nms[namelist].uniq!
    all_variables_in_source[namelist].uniq!
  end
  return [nms, all_variables_in_source, namelist_declarations]
end

.get_sample_value(source, var) ⇒ Object 



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# File 'lib/gryfxcrmod/namelist_tools.rb', line 38

def self.get_sample_value(source, var)
  sample_val = nil
  source.scan(rcp.fortran_namelist_variable_match_regex) do
    #p $~
    
    next unless var == $~[:variable].to_sym
    sample_val = eval($~[:default].sub(/(\d\.)$/, '\10').sub(/^(\.\d)/, '0\1').sub(/(\d\.)[eE]/, '\10e'))
  end
  raise "Couldn't get a sample value for #{var.inspect}" unless sample_val
  return sample_val
end

.update_defaults_from_source_code(source_code_folder = ) ⇒ Object 



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# File 'lib/gryfxcrmod/namelist_tools.rb', line 49

def self.update_defaults_from_source_code(source_code_folder = ARGV[-1])
  source = get_aggregated_source_code_text(source_code_folder)
  rcp.namelists.each do |nml, nmlhash|
    nmlhash[:variables].each do |var, varhash|
      varhash[:autoscanned_defaults] = [get_sample_value(source, varhash[:code_name]||var)] rescue []
      save_namelists
    end
  end
end

Instance Method Details

#calculate_frequencies ⇒ Object

def calculate_results end



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# File 'lib/gryfxcrmod/gryfx.rb', line 137

def calculate_frequencies
  @real_frequencies = FloatHash.new
end

#code_run_environment ⇒ Object 



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# File 'lib/gryfxcrmod/gryfx.rb', line 145

def code_run_environment
  case @sys
  when /stampede/
    "module load cuda\n module load hdf5\n module load netcdf"
  when /generic_linux/, /macosx/
    "# No configuration necessary"
  end
end

#generate_input_file ⇒ Object

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



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# File 'lib/gryfxcrmod/gryfx.rb', line 69

def generate_input_file
    write_input_file
end

#geometric_factors_gsl_tensor(options) ⇒ Object 



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# File 'lib/gryfxcrmod/gryfx.rb', line 155

def geometric_factors_gsl_tensor(options)
    theta_vec = gsl_vector(:theta, options)
    factors = GSL::Tensor.alloc(6,theta_vec.size)
    values = [:Rplot, :Zplot, :aplot, :Rprime, :Zprime, :aprime].map do |name|
      arr = netcdf_file.var(name).get.to_a
      if options[:periodic]
        arr += [arr[0]]
      end
      arr
    end
    #ep values
    shape = factors.shape
    for i in 0...shape[0]
        unless options[:interpolate_theta]
          for j in 0...shape[1]
            factors[i,j] = values[i][j]
          end
        else
          opts = options.dup
          opts[:interpolate_theta] = nil
          opts[:thetamax] = opts[:thetamin] = nil
          theta_vec_short = gsl_vector(:theta, opts)
          #p 'sizes', [theta_vec_short.size, values[i].to_gslv.size]
          interp = GSL::ScatterInterp.alloc(:cubic, [theta_vec_short, values[i].to_gslv], true, [3.0].to_gslv)
          for j in 0...theta_vec.size
            factors[i,j] = interp.eval(theta_vec[j])
          end
        end
    end
    #ep factors
    return factors
end

#get_completed_timesteps ⇒ Object 



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# File 'lib/gryfxcrmod/gryfx.rb', line 122

def get_completed_timesteps
  if FileTest.exist?(@run_name  + '.cdf')
    @completed_timesteps = gsl_vector('t').size
  else
    @completed_timesteps = 0
  end
end

#get_status ⇒ Object 



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# File 'lib/gryfxcrmod/gryfx.rb', line 102

def get_status
  if @running
    unless @status==:Queueing
      @status = :Incomplete
      get_completed_timesteps
      if @completed_timesteps.to_f/(nstep/nwrite) == 1.0
        @status=:Complete
      end

    end
  else
    get_completed_timesteps
    if (@percent_complete = 100.0*@completed_timesteps.to_f/(nstep/nwrite))  > 5.0
      @status = :Complete
    else
      @status = :Failed
    end
  end
end

#gryfx? ⇒ Boolean 



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# File 'lib/gryfxcrmod/gryfx.rb', line 141

def gryfx?
  true
end

#input_file_header ⇒ Object 



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# File 'lib/gryfxcrmod/gryfx.rb', line 189

def input_file_header
  "!==============================================================================\n!     GRYFX INPUT FILE automatically generated by CodeRunner \n!==============================================================================\n!\n!  GRYFX is a gyrofluid GPU flux tube initial value turbulence code \n!  which can be used for fusion or astrophysical plasmas.\n!  \n!   See http://gyrokinetics.sourceforge.net\n!\n!  CodeRunner is a framework for the automated running and analysis \n!  of large simulations. \n!\n!   See http://coderunner.sourceforge.net\n!\n!  Created on \#{Time.now.to_s}\n!      by CodeRunner version \#{CodeRunner::CODE_RUNNER_VERSION.to_s}\n!\n!==============================================================================\n\n"
end

#netcdf_filename ⇒ Object 



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# File 'lib/gryfxcrmod/gryfx.rb', line 130

def netcdf_filename
  @directory + '/' +  @run_name + '.cdf'
end

#parameter_string ⇒ Object

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



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# File 'lib/gryfxcrmod/gryfx.rb', line 79

def parameter_string
  @run_name + ".in"
end

#parameter_transition ⇒ Object 



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# File 'lib/gryfxcrmod/gryfx.rb', line 83

def parameter_transition
end

#print_out_line ⇒ Object

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



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# File 'lib/gryfxcrmod/gryfx.rb', line 40

def print_out_line
  #p ['id', id, 'ctd', ctd]
  #p rcp.results.zip(rcp.results.map{|r| send(r)})
  name = @run_name
  name += " (res: #@restart_id)" if @restart_id
  name += " real_id: #@real_id" if @real_id
  beginning = sprintf("%2d:%d %-60s %1s:%2.1f(%s) %3s%1s ",  @id, @job_no, name, @status.to_s[0,1],  @run_time.to_f / 60.0, @nprocs.to_s, percent_complete, "%")
  if ctd
    #beginning += sprintf("Q:%f, Pfusion:%f MW, Ti0:%f keV, Te0:%f keV, n0:%f x10^20", fusionQ, pfus, ti0, te0, ne0)
     if @nonlinear_mode == "off"
        beginning += sprintf("%3.2e %3.2e %4s", 
         @fastest_growing_mode, @max_growth_rate, 
         @freq_of_max_growth_rate||0.0)  rescue ""
     elsif @nonlinear_mode == "on"
  #     p @hflux_tot_stav
       beginning += "       sat:#{saturated.to_s[0]}"  if not @saturated.nil?
       beginning += sprintf(" hflux:%1.2e", @hflux_tot_stav) if  @hflux_tot_stav 
       beginning += sprintf("+/-%1.2e", @hflux_tot_stav_error) if  @hflux_tot_stav_error
       beginning += sprintf(" momflux:%1.2e", @es_mom_flux_stav.values.sum) if @es_mom_flux_stav and @es_mom_flux_stav.values[0]
       beginning += '  SC:' + @spectrum_check.map{|c| c.to_s}.join(',') if @spectrum_check 
       beginning += '  VC:' + @vspace_check.map{|c| sprintf("%d", ((c*10.0).to_i rescue -1))}.join(',') if @vspace_check 
     end
  end
  beginning += "  ---#{@comment}" if @comment
  beginning
end

#process_directory_code_specific ⇒ Object

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).



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# File 'lib/gryfxcrmod/gryfx.rb', line 91

def process_directory_code_specific
  @grid_option = "box" # For compatibility with the GS2 routines
  @write_phi_over_time  = "true" # For compatibility with the GS2 routines
  get_status
  #p ['id is', id, 'ctd is ', ctd]
  if ctd
    calculate_results 
  end
  #p ['fusionQ is ', fusionQ]
end

#write_input_file ⇒ Object

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



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# File 'lib/gryfxcrmod/gryfx.rb', line 74

def write_input_file
  File.open(@run_name + ".in", 'w'){|file| file.puts input_file_text}
end