Class: CodeRunner::Gene

Inherits:
Run::FortranNamelist
  • Object
show all
Defined in:
lib/genecrmod/gene.rb

Overview

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/)

p ‘hellllllooooo!!!’

Class Method Summary collapse

Instance Method Summary collapse

Class Method Details

.defaults_file_header ⇒ Object 



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# File 'lib/genecrmod/gene.rb', line 256

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) ⇒ Object 



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# File 'lib/genecrmod/gene.rb', line 120

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

Instance Method Details

#check_parameters ⇒ Object 



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# File 'lib/genecrmod/gene.rb', line 159

def check_parameters
end

#generate_component_runs ⇒ Object 



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# File 'lib/genecrmod/gene.rb', line 183

def generate_component_runs
  #puts "HERE"
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/genecrmod/gene.rb', line 110

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
    write_input_file
end

#get_completed_timesteps ⇒ Object 



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# File 'lib/genecrmod/gene.rb', line 224

def get_completed_timesteps
	Dir.chdir(@directory) do
      @completed_timesteps = %x[grep '^\\s\\+\\S\\+\\s*$' nrg.dat].split("\n").size
	end
end

#get_status ⇒ Object 



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# File 'lib/genecrmod/gene.rb', line 203

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 == @ntimesteps
	@status = :Complete
else
	if FileTest.exist?('GENE.finished')
		@status = :Complete
	else
		@status = :Failed
	end
end
			end
end

#input_file_extension ⇒ Object 



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# File 'lib/genecrmod/gene.rb', line 274

def input_file_extension
  ''
end

#input_file_header ⇒ Object 



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# File 'lib/genecrmod/gene.rb', line 234

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_text(namelist, enum = nil) ⇒ Object 



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# File 'lib/genecrmod/gene.rb', line 130

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}#{ext}\n"
  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 ⇒ Object

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



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# File 'lib/genecrmod/gene.rb', line 176

def parameter_string
  ""
end

#parameter_transition ⇒ Object 



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# File 'lib/genecrmod/gene.rb', line 180

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/genecrmod/gene.rb', line 43

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).



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# File 'lib/genecrmod/gene.rb', line 193

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 / ntimesteps.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



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# File 'lib/genecrmod/gene.rb', line 63

def restart(new_run)
  raise "Restart not tested yet"
  #new_run = self.dup
  (rcp.variables).each{|v| new_run.set(v, send(v)) if send(v)}
  #if @flux_option == "gs2"
    #gs2_runs.each_with_index do |run, i|
      #CodeRunner::Gs2.rcp.variables.each{|v| new_run.gs2_runs[i].set(v, run.send(v)) if run.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.nopt = -1
  #new_run.init_option = "restart"
  #new_run.iternt_file = @run_name + ".iternt"
  #new_run.iterflx_file = @run_name + ".iterflx"
  #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
  #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 !new_run.nprocs or new_run.nprocs != @nprocs
###   @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 GENE Restart file'
  ##system "ls #@directory"
  FileUtils.cp("#@directory/NOUT", "#{new_run.directory}/NIN")
  ##########if new_run.flux_option == "gs2" and @flux_option == "gs2"
    ##########for i in 0...n_flux_tubes
      ##########new_run.gs2_runs[i].directory = new_run.directory + "/flux_tube_#{i+1}"
      ##########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

#vim_output ⇒ Object Also known as: vo 



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# File 'lib/genecrmod/gene.rb', line 164

def vim_output
  system "vim -Ro #{output_file} #{error_file}"
end

#write_input_file ⇒ Object

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



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# File 'lib/genecrmod/gene.rb', line 170

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