Class: CodeRunner::Trinity

Inherits:
Run::FortranNamelist
  • Object
show all
Includes:
ActualParameterValues, OutputFiles, TrinityGraphKits
Defined in:
lib/trinitycrmod/trinity.rb,
lib/trinitycrmod/trinity_gs2.rb,
lib/trinitycrmod/output_files.rb,
lib/trinitycrmod/check_parameters.rb,
lib/trinitycrmod/actual_parameter_values.rb,
lib/trinitycrmod/graphs.rb,
lib/trinitycrmod/chease.rb

Overview

This is a customised subclass of the CodeRunner::Run class which allows CodeRunner to run and analyse the multiscale gyrokinetic turbulent transport solver Trinity.

It  generates the Trinity input file, and both analyses the results and allows easy plotting of them. It also interfaces with the GS2 CodeRunner  module to allow analysis of the individual GS2 results if GS2 is being used as the flux code.

Defined Under Namespace

Modules: ActualParameterValues, OutputFiles, TrinityGraphKits Classes: FluxOptionError

Class Method Summary collapse

Instance Method Summary collapse

Methods included from TrinityGraphKits

#ang_mom_prof_graphkit, #dens_prof_graphkit, #eln_hflux_gb_prof_graphkit, #eln_hflux_prof_graphkit, #eln_pwr_prof_graphkit, #eln_temp_prof_graphkit, #fluxes_prof_graphkit, #ion_hflux_gb_prof_graphkit, #ion_hflux_prof_graphkit, #ion_pwr_prof_graphkit, #ion_temp_prof_graphkit, #lflux_gb_prof_graphkit, #nt_prof_graphkit, #pbalance_prof_graphkit, #prof_graphkit, #pwr_prof_graphkit, #torque_prof_graphkit

Methods included from ActualParameterValues

#dflx_stencil_actual, #evolve_grads_only_actual, #fork_flag_actual

Methods included from OutputFiles

#fluxes_outfile, #info_outfile, #nt_outfile, #pbalance_outfile, #pwr_outfile, #time_outfile, #view_outfiles

Class Method Details

.defaults_file_header ⇒ Object 



534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
 
# File 'lib/trinitycrmod/trinity.rb', line 534

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

.get_input_help_from_source_code(source_folder) ⇒ Object 



482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
 
# File 'lib/trinitycrmod/trinity.rb', line 482

def self.get_input_help_from_source_code(source_folder)
  source = get_aggregated_source_code_text(source_folder)
  rcp.namelists.each do |nmlst, hash|
    hash[:variables].each do |var, var_hash|

#       next unless var == :w_antenna
      var = var_hash[:code_name] || var
      values_text = source.scan(Regexp.new("\\W#{var}\\s*=\\s*.+")).join("\n") 
      ep values_text
      values = scan_text_for_variables(values_text).map{|(v,val)| val} 
      values.uniq!
#       ep values if var == :nbeta
      values.delete_if{|val| val.kind_of? String} if values.find{|val| val.kind_of? Numeric}
      values.delete_if{|val| val.kind_of? String and not String::FORTRAN_BOOLS.include? val} if values.find{|val| val.kind_of? String and String::FORTRAN_BOOLS.include? val}
#       values.sort!
#       ep var
#       ep values
      sample_val = values[0]
      p sample_val
      help = values_text.scan(/ !(.*)/).flatten[0]
      p help
      #gets
      var_hash[:help] = help
      var_hash[:description] = help
      save_namelists

    end
  end
end

.use_new_defaults_file_with_gs2(name = ARGV[-3], trinity_input_file = ARGV[-2], gs2_input_file = ARGV[-1]) ⇒ Object

This function creates a new Trinity defaults file, with Trinity parameters taken from trinity_input_file, and GS2 parameters taken from gs2_input_file. The file is then moved to the CodeRunner central defaults location, the current folder is configured to use the defaults file.



50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
 
# File 'lib/trinitycrmod/trinity_gs2.rb', line 50

def self.use_new_defaults_file_with_gs2(name = ARGV[-3], trinity_input_file = ARGV[-2], gs2_input_file = ARGV[-1])
   raise "Please specify a name, a trinity input file and a gs2 input file" if name == "use_new_gs2_defaults_file"
   defaults_filename = "#{name}_defaults.rb"
  tmp_filename = "#{name}_gs2tmp_defaults.rb"
  central_defaults_filename = rcp.user_defaults_location + "/" + defaults_filename
  FileUtils.rm(name + '_defaults.rb') if FileTest.exist?(name + '_defaults.rb')
  FileUtils.rm(central_defaults_filename) if FileTest.exist?(central_defaults_filename)
  FileUtils.rm(tmp_filename) if FileTest.exist?(tmp_filename)
  raise "Defaults file: #{central_defaults_filename} already exists" if FileTest.exist? central_defaults_filename


  make_new_defaults_file(name, trinity_input_file)
  CodeRunner::Gs2.make_new_defaults_file(name + '_gs2tmp', gs2_input_file)

  File.open(defaults_filename, 'a'){|file| file.puts "gs2_runs.each do |run|\nrun.instance_eval do\n\#{File.read(tmp_filename).gsub(/\\A|\\n/, \"\\n  \")}\nend\nend\n\n\n"
  
    }
  FileUtils.mv(defaults_filename, central_defaults_filename)
  FileUtils.rm(tmp_filename)
  CodeRunner.fetch_runner(C: rcp.code, m: (rcp.modlet? ? rcp.modlet : nil), D: name)

end

Instance Method Details

#check_flux_option ⇒ Object 



21
22
23
24
25
 
# File 'lib/trinitycrmod/check_parameters.rb', line 21

def check_flux_option
  if @flux_option == "gs2"
   error("subfolders must be .true. ") unless @subfolders and @subfolders.fortran_true?
  end
end

#check_geometery ⇒ Object 



11
12
13
 
# File 'lib/trinitycrmod/check_parameters.rb', line 11

def check_geometery
  error( "Can't find geo_file #@geo_file (the path of geo file should be either absolute or set relative to the run folder #@directory). If you are not using a geometry file for this run please unset the parameter geo_file.") if @geo_file and not FileTest.exist? @geo_file
end

#check_parallelisation ⇒ Object 



15
16
17
18
19
 
# File 'lib/trinitycrmod/check_parameters.rb', line 15

def check_parallelisation
  error("nrad must be explicitly specified") unless @nrad
  error("Number of jobs: #{n_flux_tubes_jac} must evenly divide the number of processors: #{actual_number_of_processors} when fork_flag is .true.") if fork_flag_actual.fortran_true? and not actual_number_of_processors%n_flux_tubes_jac == 0

end

#check_parameters ⇒ Object 



3
4
5
6
7
8
9
 
# File 'lib/trinitycrmod/check_parameters.rb', line 3

def check_parameters

  check_geometery
  check_parallelisation
  check_flux_option

end

#evaluate_defaults_file(filename) ⇒ Object

Override standard CodeRunner method to allow for Gs2 variables



101
102
103
104
105
106
107
108
109
110
111
 
# File 'lib/trinitycrmod/trinity_gs2.rb', line 101

def evaluate_defaults_file(filename)
  text = File.read(filename)
  instance_eval(text)
  text.scan(/^\s*@(\w+)/) do
    var_name = $~[1].to_sym
    next if var_name == :defaults_file_description
    unless rcp.variables.include? var_name or (flux_gs2? and Gs2.rcp.variables.include? var_name)
      warning("---#{var_name}---, specified in #{File.expand_path(filename)}, is not a variable. This could be an error")
    end
  end
end

#flux_gs2? ⇒ Boolean

Is the flux tube code being used gs2?

Returns:

  • (Boolean) 


125
126
127
 
# File 'lib/trinitycrmod/trinity_gs2.rb', line 125

def flux_gs2?
  @flux_option == "gs2"
end

#generate_component_runs ⇒ Object 



343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
 
# File 'lib/trinitycrmod/trinity.rb', line 343

def generate_component_runs
  #puts "HERE"
  @component_runs ||= []
  if @flux_option == "gs2"
  #puts "HERE"
    #puts "generate_component_runs", @component_runs.size, @runner.run_list.size, caller.to_a.slice(0..9)
    #puts @component_runs[1].ginit_option if @component_runs.size > 0
    #STDIN.gets
  
    for i in 0...n_flux_tubes
      component = @component_runs[i] 
        #p [i, '9,', component, '4', !@component_runs[i]]; STDIN.gets
      if not component
        #p "HEELO"
        #p [i, '3,', component, '4', @component_runs.size]
        component = @component_runs[i] =  Gs2::TrinityComponent.new(@runner, self).create_component
        #component.instance_variable_set(:@output_file, output_file)
        #p [i, '3,', component, '4', @component_runs.size]
        if i > 0 and @component_runs[i-1]
          component.rcp.variables.each do |var|
            val = @component_runs[i-1].send(var)
            component.set(var, val) if val
          end 
        end
      end 
      #p [i,'1', component, '2', @component_runs.size]; STDIN.gets
      component = @component_runs[i] 
      #p [i,'1', component, '2']; STDIN.gets


      component.component_runs = []
      #component.runner = nil
      #pp component; STDIN.gets
      #component.instance_variables.each{|var| puts var; pp var;  puts Marshal.dump(component.instance_variable_get(var)); STDIN.gets}
      #puts Marshal.dump(component); STDIN.gets
      #pp component; STDIN.gets
      #p component.class
      component.job_no = @job_no 
      #component.status = @status
  #p ["HERE2", @component_runs.size, @component_runs[i]]
      #Dir.chdir(@directory) {
        compdir = gs2_folder_name(i) #  "flux_tube_#{i+1}"
        Dir.chdir(compdir){component.process_directory} if FileTest.exist? compdir
      #}
      component.component_runs = []
      component.trinity_run = self
      #@component_runs.push component
      component.real_id = @id
      #@gs2_run_list[i] = component
      #pp component; STDIN.gets
      #component.runner = nil
      #puts Marshal.dump(component); STDIN.gets
      #pp component; STDIN.gets
      #component.component_runs = []
    end
  end
end

#generate_gs2_input_files ⇒ Object

Writes the gs2 input files, creating separate subfolders for them if @subfolders is .true.



269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
 
# File 'lib/trinitycrmod/trinity.rb', line 269

def generate_gs2_input_files
  # At the moment we must use subfolders
  for i in 0...n_flux_tubes
    #gs2run = gs2_run(:base).dup
    #gs2_run(i).instance_variables.each do |var|
      #gs2run.instance_variable_set(var, gs2_run(i).instance_variable_get(var))
    #end
    gs2run = gs2_runs[i]
    #ep ['gs2_runs[i] in generate', gs2_runs[i].nwrite]
    #p ['i',i]
      #if i >= n_flux_tubes_jac
        #jn = i - n_flux_tubes_jac + 1
        #run_name = "calibrate_" + @run_name + (jn).to_s
        #folder = "calibrate_#{jn}"
      #else
        #jn = i + 1
        #run_name = @run_name + (jn).to_s
        #folder = "flux_tube_#{jn}"
      #end 

      folder = gs2_folder_name(i)
      run_name = gs2_run_name(i)
      
    if @subfolders and @subfolders.fortran_true?
      gs2run.directory = @directory + "/" + folder
      FileUtils.makedirs(gs2run.directory)
      gs2run.relative_directory = @relative_directory + "/" + folder
      gs2run.restart_dir = gs2run.directory + "/nc"
    else
      gs2run.directory = @directory
      gs2run.relative_directory = @relative_directory
    end
    gs2run.run_name = run_name
    gs2run.nprocs = @nprocs
    if i==0
      block = Proc.new{check_parameters}
    else
      block = Proc.new{}
    end
    #if @restart_id
      #gs2run.restart_id = 
    Dir.chdir(gs2run.directory) do 
      gs2run.generate_input_file(&block)
      gs2run.write_info
    end

    ### Hack the input file so that gs2 gets the location of 
    # the restart dir correctly within trinity
    if @subfolders and @subfolders.fortran_true?
      infile = gs2run.directory + "/" + gs2run.run_name + ".in"
      text = File.read(infile)
      File.open(infile, 'w'){|f| f.puts text.sub(/restart_dir\s*=\s*"nc"/, "restart_dir = \"#{folder}/nc\"")}
    end
  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.



162
163
164
165
166
167
168
169
170
171
 
# File 'lib/trinitycrmod/trinity.rb', line 162

def generate_input_file
    @run_name += "_t"
    if @restart_id
      @runner.run_list[@restart_id].restart(self)
    end
    setup_chease if uses_chease?
    check_parameters
    write_input_file
    generate_gs2_input_files if @flux_option == "gs2"
end

#generate_run_name ⇒ Object

Override CodeRunner::Run method to deal with flux_pars properly when generating run_name



223
224
225
226
227
228
229
230
231
232
233
 
# File 'lib/trinitycrmod/trinity.rb', line 223

def generate_run_name
    @run_name = %[v#@version] + @naming_pars.inject("") do |str, par|
      case par
      when :flux_pars
        str+="_flx_#{send(par).map{|k,v| "#{k}_#{v.to_s[0..8]}"}.join("_")}}"
      else
        str+="_#{par}_#{send(par).to_s[0...8]}"
      end
    end
    @run_name = @run_name.gsub(/\s+/, "_").gsub(/[\/{}"><:=]/, '') + "_id_#@id"
end

#get_2d_array_float(outfile, column_header, index_header) ⇒ Object

Return a two-dimensional array of floatingpoint numbers from the file ending in outfile,

from the column whose header matches column_header,  indexed by index_header. See
TextDataTools::Column::DataFile for more information. Outfile is a symbol, use e.g. :nt 
for data from 'run_name.nt'.



48
49
50
51
52
 
# File 'lib/trinitycrmod/output_files.rb', line 48

def get_2d_array_float(outfile, column_header, index_header)
  cache[:array_2d] = {} unless [:Complete, :Failed].include? @status
  cache[:array_2d] ||= {}
  cache[:array_2d][[outfile, column_header, index_header]] ||= send(outfile + :_outfile).get_2d_array_float(column_header, index_header)
end

#get_completed_timesteps ⇒ Object 



459
460
461
462
463
464
465
 
# File 'lib/trinitycrmod/trinity.rb', line 459

def get_completed_timesteps
  Dir.chdir(@directory) do
    @completed_timesteps = time_outfile.exists? ? 
      time_outfile.get_1d_array_integer(/itstep/).max :
      0
  end
end

#get_global_results ⇒ Object 



468
469
470
471
472
473
474
475
476
477
478
479
480
 
# File 'lib/trinitycrmod/trinity.rb', line 468

def get_global_results
  @fusionQ = info_outfile.get_variable_value('Q').to_f
  @pfus = info_outfile.get_variable_value(/fusion\s+power/i).to_f
  @pnet = info_outfile.get_variable_value(/net\s+power/i).to_f
  @aux_power = info_outfile.get_variable_value(/aux.*\s+power/i).to_f
  @alpha_power = info_outfile.get_variable_value(/alpha\s+power/i).to_f
  @rad_power = info_outfile.get_variable_value(/radiated\s+power/i).to_f
  @ne0 = info_outfile.get_variable_value(/core\s+density/i).to_f
  @ti0 = info_outfile.get_variable_value(/core\s+T_i/i).to_f
  @te0 = info_outfile.get_variable_value(/core\s+T_e/i).to_f
  @omega0 = info_outfile.get_variable_value(/core\s+omega/i).to_f rescue 0.0 # Old info files don't have omega
  #p 'send(fusionQ)', send(:fusionQ)
end

#get_status ⇒ Object 



437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
 
# File 'lib/trinitycrmod/trinity.rb', line 437

def get_status
  if @running
    get_completed_timesteps
    if completed_timesteps == 0
      @status = :NotStarted
    else
      @status = :Incomplete
    end
  else
    get_completed_timesteps
    if @completed_timesteps == @ntstep
      @status = :Complete
    else
      if FileTest.exist?(output_file) and File.read(output_file) =~/trinity\s+finished/i
        @status = :Complete
      else
        @status = :Failed
      end
    end
  end
end

#graphkit(name, options) ⇒ Object

This is the hook that is called by CodeRunner, providing the graphkit with the given name and functions to the CodeRunner framework



101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
 
# File 'lib/trinitycrmod/graphs.rb', line 101

def graphkit(name, options)
  [:t].each do |var|
    #ep 'index', var
    if options[var].class == Symbol and options[var] == :all
      options[var] = list(var).values
    elsif options[var+:_index].class == Symbol and options[var+:_index] == :all
      #ep 'Symbol'
      options[var+:_index] = list(var).keys
    end
    if options[var].class == Array
      return options[var].map{|value| graphkit(name, options.dup.absorb({var =>  value}))}.sum
    elsif options[var+:_index].class == Array
      #ep 'Array'
      return options[var+:_index].map{|value| graphkit(name, options.dup.absorb({var+:_index =>  value}))}.sum
    end
    if options[var].class == Symbol and options[var] == :max
      options[var] = list(var).values.max
    elsif options[var+:_index].class == Symbol and options[var+:_index] == :max
      ep 'Symbol'
      options[var+:_index] = list(var).keys.max
    end
  end
  if meth = TrinityGraphKits.instance_methods.find{|m| m.to_s == name + '_graphkit'}
    return send(meth, options)
  else
    raise "GraphKit not found: #{name}"
  end  
end

#gs2_folder_name(i) ⇒ Object 



139
140
141
142
143
144
145
146
147
148
 
# File 'lib/trinitycrmod/trinity_gs2.rb', line 139

def gs2_folder_name(i)
  if i >= n_flux_tubes_jac
    jn = i - n_flux_tubes_jac + 1
    folder = "calibrate_#{jn}"
  else
    jn = i + 1
    folder = "flux_tube_#{jn}"
  end 
  folder
end

#gs2_run_name(i) ⇒ Object 



129
130
131
132
133
134
135
136
137
138
 
# File 'lib/trinitycrmod/trinity_gs2.rb', line 129

def gs2_run_name(i)
  if i >= n_flux_tubes_jac
    jn = i - n_flux_tubes_jac + 1
    run_name = "calibrate_" + @run_name + (jn).to_s
  else
    jn = i + 1
    run_name = @run_name + (jn).to_s
  end 
  run_name
end

#gs2_run_times ⇒ Object

An array of arrays containing the GS2 run times for each iteration. Produced unscientifically by scanning the stdout.

Raises:



115
116
117
118
119
120
121
122
 
# File 'lib/trinitycrmod/trinity_gs2.rb', line 115

def gs2_run_times
  raise FluxOptionError.new("gs2_run_times called and flux_option != gs2") if not flux_gs2?
  run_times = []
  File.open(@directory + '/' + output_file, "r").each_line{|l| l.scan(/Job.*timer.*(\b\d+\.\d+\b)/){run_times.push $~[1].to_f}}
  sz = run_times.size.to_f
  return run_times.pieces((sz / n_flux_tubes.to_f).ceil)

end

#gs2_runs ⇒ Object

Generates the component runs for GS2 and returns the hash Raises an error if flux_option != “gs2”

Raises:



83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
 
# File 'lib/trinitycrmod/trinity_gs2.rb', line 83

def gs2_runs
  raise FluxOptionError.new("gs2_runs called and flux_option != gs2") if not flux_gs2?

  #puts "2@COMMMMMMMMMMMMMPOOOOOOOOOOOOOONNNETN", @component_runs
  generate_component_runs if not (@component_runs and @component_runs.size == n_flux_tubes)
  #p ["@COMMMMMMMMMMMMMPOOOOOOOOOOOOOONNNETN", @component_runs]
  @component_runs
  #@gs2_run_list ||= {}
  #raise TypeError.new("@runner is nil") if @runner.nil?
  #@gs2_run_list[key] ||= Gs2.new(@runner)
  ##if key != :base
    ##raise "key in gs2_run must be either :base or an integer" unless key.kind_of? Integer
    ##@gs2_run_list[key] ||= @gs2_run_list[:base].dup
  ##end
  #@gs2_run_list[key]
end

#input_file_extension ⇒ Object 



564
565
566
 
# File 'lib/trinitycrmod/trinity.rb', line 564

def input_file_extension
  '.trin'
end

#input_file_header ⇒ Object 



512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
 
# File 'lib/trinitycrmod/trinity.rb', line 512

def input_file_header
  "!==============================================================================\n!     Trinity INPUT FILE automatically generated by CodeRunner \n!==============================================================================\n!\n!  Trinity is a multiscale turbulent transport code for fusion 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 \#{Time.now.to_s}\n!      by CodeRunner version \#{CodeRunner::CODE_RUNNER_VERSION.to_s}\n!\n!==============================================================================\n\n"
end

#list(var) ⇒ Object

Returns a hash of the specified dimension in the form value where index is 1-based Dimension can be: :t :rho :rho_cc



59
60
61
62
63
64
65
66
 
# File 'lib/trinitycrmod/output_files.rb', line 59

def list(var)
  case var
  when :t
    hash  = {}
    get_2d_array_float(:nt, /1:\s+time/, /1:\s+time/).map{|arr| arr[0]}.each_with_index{|t,i| hash[i+1] = t}
    hash
  end
end

#n_flux_tubes ⇒ Object 



258
259
260
261
262
263
264
265
 
# File 'lib/trinitycrmod/trinity.rb', line 258

def n_flux_tubes
  if @neval_calibrate and @neval_calibrate > 0
    raise "neval_calibrate set but ncc_calibrate not set" unless @ncc_calibrate
    n_flux_tubes_jac + @ncc_calibrate
  else
    n_flux_tubes_jac
  end
end

#n_flux_tubes_jac ⇒ Object

The number of separate flux tube results needed for the jacobian



236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
 
# File 'lib/trinitycrmod/trinity.rb', line 236

def n_flux_tubes_jac
  d1 = dflx_stencil_actual - 1
  ngrads =d1 * case @grad_option
                when "tigrad", "ngrad", "lgrad"
                  1
                when "tgrads"
                  2
                when "ltgrads", "ntgrads"
                  3
                when "all"
                  4
                else
                  raise "unknown grad_option: #@grad_option"
                end
  if evolve_grads_only_actual.fortran_true?
    njac = ngrads + 1
  else
    njac = 2*ngrads+1
  end
  #p 'nraaad', @nrad
  (@nrad-1) * njac
end

#parameter_string ⇒ Object

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



336
337
338
 
# File 'lib/trinitycrmod/trinity.rb', line 336

def parameter_string
  @run_name + ".trin"
end

#parameter_transition ⇒ Object 



340
341
 
# File 'lib/trinitycrmod/trinity.rb', line 340

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.



69
70
71
72
73
74
75
76
77
78
79
80
81
 
# File 'lib/trinitycrmod/trinity.rb', line 69

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)
  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).



427
428
429
430
431
432
433
434
435
 
# File 'lib/trinitycrmod/trinity.rb', line 427

def process_directory_code_specific
  get_status
  #p ['id is', id, 'ctd is ', ctd]
  if ctd
    get_global_results 
  end
  #p ['fusionQ is ', fusionQ]
  @percent_complete = completed_timesteps.to_f / ntstep.to_f * 100.0
end

#restart(new_run) ⇒ Object

Modify new_run so that it becomes a restart of self. Adusts 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



95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
 
# File 'lib/trinitycrmod/trinity.rb', line 95

def restart(new_run)
  #new_run = self.dup
  (rcp.variables).each{|v| new_run.set(v, send(v)) if send(v) or new_run.send(v)}
  if @flux_option == "gs2"
    gs2_runs.each_with_index do |run, i|
      CodeRunner::Gs2.rcp.variables.each{|v| 
          next if [:ginit_option, :delt_option].include? v and new_run.no_restart_gs2
          new_run.gs2_runs[i].set(v, run.send(v)) if run.send(v) or new_run.gs2_runs[i].send(v)
        }
    end
  end
  @naming_pars.delete(:preamble)
  SUBMIT_OPTIONS.each{|v| new_run.set(v, self.send(v)) unless new_run.send(v)}
  #(rcp.results + rcp.gs2_run_info).each{|result| new_run.set(result, nil)}
  new_run.is_a_restart = true
  new_run.restart_id = @id
  new_run.restart_run_name = @run_name
  new_run.init_option = "restart"
  new_run.iternt_file = @run_name + ".iternt"
  new_run.iterflx_file = @run_name + ".iterflx"
  new_run.itercalib_file = @run_name + ".itercalib"
  new_run.init_file = @run_name + ".tmp"
  @runner.nprocs = @nprocs if @runner.nprocs == "1" # 1 is the default so this means the user probably didn't specify nprocs 
    # This is unnecessary for single restart file.
  raise "Restart must be on the same number of processors as the previous run: new is #{new_run.nprocs.inspect} and old is #{@nprocs.inspect}" if not new_run.no_restart_gs2 and (!new_run.nprocs or new_run.nprocs != @nprocs)
    raise "Restart cannot have a different sized jacobian: new is #{new_run.n_flux_tubes_jac} and old is #{n_flux_tubes_jac}" unless new_run.n_flux_tubes_jac == n_flux_tubes_jac
#   @runner.parameters.each{|var, value| new_run.set(var,value)} if @runner.parameters
#   ep @runner.parameters
  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
  new_run.run_name += '_t'
  eputs 'Copying Trinity Restart files', ''
  #system "ls #@directory"
  ['iternt', 'iterflx', 'tmp', 'itercalib'].each do |ext|
      next if ext=='itercalib' and not FileTest.exist?("#@directory/#@run_name.#{ext}")
    FileUtils.cp("#@directory/#@run_name.#{ext}", "#{new_run.directory}/.")
  end
  if new_run.flux_option == "gs2" and @flux_option == "gs2" and not new_run.no_restart_gs2
    for i in 0...n_flux_tubes
        break if i >= new_run.n_flux_tubes
        #if i >= n_flux_tubes_jac
          #jn = i - n_flux_tubes_jac + 1
          ##run_name = "calibrate_" + @run_name + (jn).to_s
          #folder = "calibrate_#{jn}"
        #else
          #jn = i + 1
          ##run_name = @run_name + (jn).to_s
          #folder = "flux_tube_#{jn}"
        #end 
        #
        folder = gs2_folder_name(i)

      new_run.gs2_runs[i].directory = new_run.directory + "/#{folder}"
      FileUtils.makedirs(new_run.gs2_runs[i].directory)
      #ep ['gs2_runs[i] before', gs2_runs[i].nwrite, new_run.gs2_runs[i].nwrite, new_run.gs2_runs[i].parameter_hash]
      gs2_runs[i].restart(new_run.gs2_runs[i])
      #ep ['gs2_runs[i] after', gs2_runs[i].nwrite, new_run.gs2_runs[i].nwrite, new_run.gs2_runs[i].parameter_hash]
      #new_run.gs2_runs[i].run_name = new_run.run_name + (i+1).to_s
    end
  end
  #@runner.submit(new_run)
  new_run
end

#run_heuristic_analysis ⇒ Object

Raises:

  • (CRMild) 


551
552
553
554
555
556
557
558
559
560
561
562
 
# File 'lib/trinitycrmod/trinity.rb', line 551

def run_heuristic_analysis
  ep 'run_heuristic_analysis', Dir.pwd
  infiles = Dir.entries.grep(/^[^\.].*\.trin$/)
  ep infiles
  raise CRMild.new('No input file') unless infiles[0]
  raise CRError.new("More than one input file in this directory: \n\t#{infiles}") if infiles.size > 1
  input_file = infiles[0]
  #ep 'asdf'
  @nprocs ||= "1"
  @executable ||= "/dev/null"
  make_info_file(input_file, false)
end

#save ⇒ Object 



402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
 
# File 'lib/trinitycrmod/trinity.rb', line 402

def save
  #@gs2_run_list.values.each{|r| r.runner = nil; r.component_runs = []} if @gs2_run_list.kind_of? Hash
  super
  #@gs2_run_list.values.each{|r| r.runner = @runner} if @gs2_run_list.kind_of? Hash

  #logf(:save)
  #raise CRFatal.new("Something has gone horribly wrong: runner.class is #{@runner.class} instead of CodeRunner") unless @runner.class.to_s == "CodeRunner"
  #runner, @runner = @runner, nil
  #@system_triers, old_triers = nil, @system_triers
  #@component_runs.each{|run| run.runner = nil; run.component_runs = []} if @component_runs
  ##@component_runs.each{|run| run.runner = nil} if @component_runs
##   logi(self)
  ##pp self
  ##@component_runs.each{|ph| ph.instance_variables.each{|var| puts var; pp ph.instance_variable_get(var); STDIN.gets;  puts ph.Marshal.dump(instance_variable_get(var))}} if @component_runs
  ##instance_variables.each{|var| puts var;  instance_variable_get(var);  puts Marshal.dump(instance_variable_get(var)); STDIN.gets}
  #Dir.chdir(@directory){File.open(".code_runner_run_data", 'w'){|file| file.puts Marshal.dump(self)}}
  #@runner = runner
  #@component_runs.each{|run| run.runner = runner} if @component_runs
  #@system_triers = old_triers
end

#setup_chease ⇒ Object 



5
6
7
8
9
10
 
# File 'lib/trinitycrmod/chease.rb', line 5

def setup_chease
  ep "Setting up chease files..."
  FileUtils.mkdir('chease') unless FileTest.exist? 'chease'
  origfile = @runner.root_folder + '/ogyropsi.dat'
  FileUtils.cp(origfile, 'chease/ogyropsi.dat') if FileTest.exist? origfile
end

#update_submission_parameters(parameters, start_from_defaults = true) ⇒ Object

Update submission parameters in the normal way then deal with parameters for the flux code. Each flux code will behave differently.

  • Gs2 flux_pars: 43, delt: {1=> 0.01, 2=>0.05}

will set nx for all runs to be 43, and delt for run 1 to 0.01, delt
for run 2 to be 0.05



181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
 
# File 'lib/trinitycrmod/trinity.rb', line 181

def update_submission_parameters(parameters, start_from_defaults=true)
  super(parameters, start_from_defaults)
  if @flux_pars
    gs2_parameter_hashes = {}
    @flux_pars.each do |par, val|
      if @flux_option == "gs2"
        if val.kind_of? Hash
          #val.each{|n,v| gs2_runs[n].set(par, v)}
          val.each do |n,v| 
              if n == :jac
                range =  0...n_flux_tubes_jac
              elsif n == :calib
                range =  n_flux_tubes_jac...n_flux_tubes
              else
                range = n..n
              end
              for i in range
                gs2_parameter_hashes[i] ||= {}
                gs2_parameter_hashes[i][par] = v
              end
            #gs2_parameter_hashes[n] ||= {}
            #gs2_parameter_hashes[n][par] = v
          end
        else
          for i in 0...n_flux_tubes
            #gs2_runs.each{|r| r.set(par, val)}
            gs2_parameter_hashes[i] ||= {}
            gs2_parameter_hashes[i][par] = val
          end
        end
        for i in 0...n_flux_tubes
          gs2_runs[i].parameter_hash = (gs2_parameter_hashes[i] || {}).inspect 
          gs2_runs[i].update_submission_parameters(gs2_runs[i].parameter_hash, false) 
        end
      end
    end
  end
  self
end

#uses_chease? ⇒ Boolean

Returns:

  • (Boolean) 


2
3
4
 
# File 'lib/trinitycrmod/chease.rb', line 2

def uses_chease?
  @geo_option == "chease" or @init_option == "chease" or @species_option == "chease"
end

#vim_output ⇒ Object Also known as: vo 



325
326
327
 
# File 'lib/trinitycrmod/trinity.rb', line 325

def vim_output
  system "vim -Ro #{output_file} #{error_file} #@directory/#@run_name.error #@directory/#@run_name.out "
end

#write_input_file ⇒ Object

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



331
332
333
 
# File 'lib/trinitycrmod/trinity.rb', line 331

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