Class: CodeRunner::Gene
- Inherits:
-
Run::FortranNamelist
- Object
- Run::FortranNamelist
- CodeRunner::Gene
- 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/)
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Class Method Summary collapse
Instance Method Summary collapse
- #check_parameters ⇒ Object
- #generate_component_runs ⇒ Object
-
#generate_input_file ⇒ Object
This is a hook which gets called just before submitting a simulation.
- #get_completed_timesteps ⇒ Object
- #get_growth_rates ⇒ Object
- #get_h5_narray_all(file, dataset) ⇒ Object
- #get_status ⇒ Object
- #graphkit(name, options = {}) ⇒ Object
- #input_file_extension ⇒ Object
- #input_file_header ⇒ Object
- #namelist_test_failed(namelist, tst) ⇒ Object
- #namelist_text(namelist, enum = nil) ⇒ Object
-
#parameter_string ⇒ Object
Parameters which follow the Trinity executable, in this case just the input file.
- #parameter_transition ⇒ Object
-
#print_out_line ⇒ Object
A hook which gets called when printing the standard run information to the screen using the status command.
-
#process_directory_code_specific ⇒ Object
This method, as its name suggests, is called whenever CodeRunner is asked to analyse a run directory.
-
#restart(new_run) ⇒ Object
Modify new_run so that it becomes a restart of self.
- #run_namelist_tests(namelist, hash, enum = nil) ⇒ Object
- #test_failed(namelist, var, gs2_var, tst) ⇒ Object
- #test_variable(namelist, var, var_hash, ext, value) ⇒ Object
- #vim_output ⇒ Object (also: #vo)
-
#write_input_file ⇒ Object
This command uses the infrastructure provided by Run::FortranNamelist, provided by CodeRunner itself.
Class Method Details
.defaults_file_header ⇒ Object
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# File 'lib/genecrmod/gene.rb', line 266 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 123 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 $~; "#{$1}_#{i+=1}"} super(text) end |
Instance Method Details
#check_parameters ⇒ Object
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# File 'lib/genecrmod/check_parameters.rb', line 22 def check_parameters rcp.namelists.each do |namelist, hash| next if hash[:should_include].kind_of? String and not eval(hash[:should_include]) if en = hash[:enumerator] #ep 'en', en, namelist next unless send(en[:name]) send(en[:name]).times do |i| run_namelist_tests(namelist, hash, i+1) end else run_namelist_tests(namelist, hash) end end warning("Very little analysis will be possible without write_h5 = '.true.'") if not (@write_h5 and @write_h5.fortran_true?) end |
#generate_component_runs ⇒ Object
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# File 'lib/genecrmod/gene.rb', line 184 def generate_component_runs #puts "HERE" end |
#generate_input_file ⇒ Object
This is a hook which gets called just before submitting a simulation. It sets up the folder and generates any necessary input files.
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# File 'lib/genecrmod/gene.rb', line 113 def generate_input_file check_parameters if @restart_id @runner.run_list[@restart_id].restart(self) end @diagdir = "." @n_procs_sim = actual_number_of_processors write_input_file end |
#get_completed_timesteps ⇒ Object
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# File 'lib/genecrmod/gene.rb', line 230 def get_completed_timesteps Dir.chdir(@directory) do if FileTest.exist?('nrg.dat.h5') @completed_timesteps = get_h5_narray_all('nrg.dat.h5', '/nrgIons/time').shape[0] else @completed_timesteps = %x[grep '^\\s\\+\\S\\+\\s*$' 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 288 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 = [[]] * 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) return file.dataset(dataset).narray_all end end |
#get_status ⇒ Object
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# File 'lib/genecrmod/gene.rb', line 207 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
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# File 'lib/genecrmod/gene.rb', line 301 def graphkit(name, ={}) case name when /growth_rates_vs_ky/ return GraphKit.quick_create([@kyvals, @growth_rates]) end end |
#input_file_extension ⇒ Object
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# File 'lib/genecrmod/gene.rb', line 284 def input_file_extension '' end |
#input_file_header ⇒ Object
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# File 'lib/genecrmod/gene.rb', line 244 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 133 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 177 def parameter_string "" end |
#parameter_transition ⇒ Object
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# File 'lib/genecrmod/gene.rb', line 181 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 46 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 194 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 / 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 66 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 165 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 171 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 |