Class: CodeRunner::Gene

Inherits:
Run::FortranNamelist
  • Object
show all
Defined in:
lib/genecrmod/gene.rb,
lib/genecrmod/hdf5.rb,
lib/genecrmod/check_parameters.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 267

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 124

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/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]
      #ep 'en', en, namelist
      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
  warning("Very little analysis will be possible without write_h5 = '.true.'") if not (@write_h5 and @write_h5.fortran_true?)
end

#generate_component_runs ⇒ Object 



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# File 'lib/genecrmod/gene.rb', line 185

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 114

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 231

def get_completed_timesteps
	Dir.chdir(@directory) do
      #if FileTest.exist?('nrg.dat.h5')
        #@completed_timesteps = get_h5_narray_all('nrg.dat.h5', '/nrgIons/time').shape[0]
      #else
        @completed_timesteps = %x[grep '^\\s\\+\\S\\+\\s*$' nrg.dat 2>/dev/null].split("\n").size
      #end
	end
end

#get_growth_rates ⇒ Object 



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# File 'lib/genecrmod/gene.rb', line 289

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) ⇒ Object 



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# 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 ⇒ Object 



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# File 'lib/genecrmod/gene.rb', line 208

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 = {}) ⇒ Object

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



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# File 'lib/genecrmod/gene.rb', line 303

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 ⇒ Object 



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# File 'lib/genecrmod/gene.rb', line 285

def input_file_extension
  ''
end

#input_file_header ⇒ Object 



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# File 'lib/genecrmod/gene.rb', line 245

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) ⇒ Object 



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# File 'lib/genecrmod/check_parameters.rb', line 57

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) ⇒ Object 



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# File 'lib/genecrmod/gene.rb', line 134

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 178

def parameter_string
  ""
end

#parameter_transition ⇒ Object 



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# File 'lib/genecrmod/gene.rb', line 182

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 47

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 195

def process_directory_code_specific
  get_status
  #p ['id is', id, 'ctd is ', ctd]
  if ctd
    #get_global_results
    if !nonlinear or nonlinear.fortran_false?
      get_growth_rates
    end
  end
  #p ['fusionQ is ', fusionQ]
  @percent_complete = completed_timesteps.to_f  * (istep_nrg||10) / 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 67

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

#run_namelist_tests(namelist, hash, enum = nil) ⇒ Object 



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# 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|
    #gs2_var = (var_hash[:gs2_name] or var)
    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, gs2_var, tst) ⇒ Object 



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# File 'lib/genecrmod/check_parameters.rb', line 37

def test_failed(namelist, var, gs2_var, tst)
	return  <<EOF

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

Namelist: #{namelist}	
Variable: #{var}
GS2 Name: #{gs2_var}
Value: #{send(var)}
Test: #{tst[:test]}
Explanation: #{tst[:explanation]}

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

end

#test_variable(namelist, var, var_hash, ext, value) ⇒ Object 



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# File 'lib/genecrmod/check_parameters.rb', line 72

def test_variable(namelist, var, var_hash, ext, value)
		gs2_var = (var_hash[:gs2_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, gs2_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, gs2_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, gs2_var, tst)) unless value.instance_eval(tst[:test])
			end

		end
end

#vim_output ⇒ Object Also known as: vo 



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# File 'lib/genecrmod/gene.rb', line 166

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 172

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