corfucrmod 1.0.0

checksums.yaml

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+---
+SHA1:
+  metadata.gz: 560d6ee96bf999ecb52a78212c96a8ff0b2ca3ee
+  data.tar.gz: c1a07d5e1c42eeef2e9b726cd75fa1cd95d02b1d
+SHA512:
+  metadata.gz: 0a9bef5ea41425fe687d0a37afbe7e542a51fc537adb4fe30c986c92b2eec587543b83d1a59c45d1e5895a7c71cfd6dfeb792068fea60cda60dbeaabcf9cf469
+  data.tar.gz: 3f8e1dbea324c8072e74c62d923989a780929c7033b0780e49fa820c0384ad45cb1916a482f3107870568e38efc21cee475ebddb02e5421e52fc20a66023aae0

data/.document

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+lib/**/*.rb
+bin/*
+- 
+features/**/*.feature
+LICENSE.txt

data/Gemfile

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+source "http://rubygems.org"
+# Add dependencies required to use your gem here.
+# Example:
+   gem "coderunner", ">= 0.14.2"
+   gem "text-data-tools", ">= 1.1.3"
+	 gem "gs2crmod", ">=0.11.33"
+	 gem "trinitycrmod", ">= 0.7.11"
+	 gem "ruby-mpi", ">=0.2.0"
+	 gem "cheasecrmod", ">=0.1.0"
+   gem "tokfile", ">=0.0.3"
+
+# Add dependencies to develop your gem here.
+# Include everything needed to run rake, tests, features, etc.
+group :development do
+  gem "shoulda", " 3.0.1"
+  gem "rdoc", "~> 3.12"
+  gem "bundler", "> 1.0.0"
+  gem "jeweler", ">= 2.0.1"
+	gem "simplecov", ">=0" 
+	gem "minitest", "~> 4"
+	gem "rake-compiler"
+end

data/LICENSE.txt

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+Copyright (c) 2014 Edmund Highcock
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+"Software"), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
+the following conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
+LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
+WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

data/README.rdoc

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+= corfucrmod
+
+Description goes here.
+
+== Contributing to corfucrmod
+ 
+* Check out the latest master to make sure the feature hasn't been implemented or the bug hasn't been fixed yet.
+* Check out the issue tracker to make sure someone already hasn't requested it and/or contributed it.
+* Fork the project.
+* Start a feature/bugfix branch.
+* Commit and push until you are happy with your contribution.
+* Make sure to add tests for it. This is important so I don't break it in a future version unintentionally.
+* Please try not to mess with the Rakefile, version, or history. If you want to have your own version, or is otherwise necessary, that is fine, but please isolate to its own commit so I can cherry-pick around it.
+
+== Copyright
+
+Copyright (c) 2014 Edmund Highcock. See LICENSE.txt for
+further details.
+

data/README.rdoc.orig

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+= trinitycrdriver
+
+Description goes here.
+
+== Contributing to trinitycrdriver
+ 
+* Check out the latest master to make sure the feature hasn't been implemented or the bug hasn't been fixed yet.
+* Check out the issue tracker to make sure someone already hasn't requested it and/or contributed it.
+* Fork the project.
+* Start a feature/bugfix branch.
+* Commit and push until you are happy with your contribution.
+* Make sure to add tests for it. This is important so I don't break it in a future version unintentionally.
+* Please try not to mess with the Rakefile, version, or history. If you want to have your own version, or is otherwise necessary, that is fine, but please isolate to its own commit so I can cherry-pick around it.
+
+== Copyright
+
+Copyright (c) 2014 Edmund Highcock. See LICENSE.txt for
+further details.
+

data/Rakefile

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+# encoding: utf-8
+
+require 'rubygems'
+require 'bundler'
+begin
+  Bundler.setup(:default, :development)
+rescue Bundler::BundlerError => e
+  $stderr.puts e.message
+  $stderr.puts "Run `bundle install` to install missing gems"
+  exit e.status_code
+end
+require 'rake'
+
+require 'jeweler'
+Jeweler::Tasks.new do |gem|
+  # gem is a Gem::Specification... see http://guides.rubygems.org/specification-reference/ for more options
+  gem.name = "corfucrmod"
+  gem.homepage = "http://github.com/edmundhighcock/corfucrmod"
+  gem.license = "GPLv3.0"
+  gem.summary = %Q{A gem which implements the CorFu Optimisation Framework.}
+  gem.description = %Q{CorFu, the Coderunner/Trinity Fusion Optimisation Framework
+    allows the optimisation of fusion performance using first principles
+    flux calculations via Trinity.}
+  gem.email = "edmundhighcock@users.sourceforge.net"
+  gem.authors = ["Edmund Highcock"]
+	gem.files.exclude 'test/**/*'
+	gem.extensions = %w[ext/corfucrmod/extconf.rb]
+  # dependencies defined in Gemfile
+end
+Jeweler::RubygemsDotOrgTasks.new
+
+require 'rake/testtask'
+Rake::TestTask.new(:test) do |test|
+  test.libs << 'lib' << 'test'
+  test.pattern = 'test/**/test_*.rb'
+  test.verbose = true
+end
+
+desc "Code coverage detail"
+task :simplecov do
+  ENV['COVERAGE'] = "true"
+  Rake::Task['test'].execute
+end
+
+task :default => :test
+
+require 'rdoc/task'
+Rake::RDocTask.new do |rdoc|
+  version = File.exist?('VERSION') ? File.read('VERSION') : ""
+
+  rdoc.rdoc_dir = 'rdoc'
+  rdoc.title = "corfucrmod #{version}"
+  rdoc.rdoc_files.include('README*')
+  rdoc.rdoc_files.include('lib/**/*.rb')
+end
+
+NAME = 'corfucrmod'
+
+require "rake/extensiontask"
+
+Rake::ExtensionTask.new "corfucrmod" do |ext|
+	  ext.lib_dir = "lib/corfucrmod"
+end

data/VERSION

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+1.0.0

data/clean.sh

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+rm -rf lib/trinitycrdriver/trinitycrdriver.so
+rm -rf rake_test_opt_chease_defaults.rb
+rm -rf rake_test_opt_defaults.rb
+rm -rf test/chease_opt/.CODE_RUNNER_TEMP_RUN_LIST_CACHE
+rm -rf test/chease_opt/ogyropsi.dat
+rm -rf test/chease_opt/v/
+rm -rf test/chease_opt_chease/.CODE_RUNNER_TEMP_RUN_LIST_CACHE
+rm -rf test/chease_opt_chease/v/
+rm -rf test/trinopt/

data/corfucrmod.gemspec

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+# Generated by jeweler
+# DO NOT EDIT THIS FILE DIRECTLY
+# Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
+# -*- encoding: utf-8 -*-
+# stub: corfucrmod 1.0.0 ruby lib
+# stub: ext/corfucrmod/extconf.rb
+
+Gem::Specification.new do |s|
+  s.name = "corfucrmod".freeze
+  s.version = "1.0.0"
+
+  s.required_rubygems_version = Gem::Requirement.new(">= 0".freeze) if s.respond_to? :required_rubygems_version=
+  s.require_paths = ["lib".freeze]
+  s.authors = ["Edmund Highcock".freeze]
+  s.date = "2019-07-28"
+  s.description = "CorFu, the Coderunner/Trinity Fusion Optimisation Framework\n    allows the optimisation of fusion performance using first principles\n    flux calculations via Trinity.".freeze
+  s.email = "edmundhighcock@users.sourceforge.net".freeze
+  s.extensions = ["ext/corfucrmod/extconf.rb".freeze]
+  s.extra_rdoc_files = [
+    "LICENSE.txt",
+    "README.rdoc",
+    "README.rdoc.orig"
+  ]
+  s.files = [
+    ".document",
+    "Gemfile",
+    "LICENSE.txt",
+    "README.rdoc",
+    "Rakefile",
+    "VERSION",
+    "clean.sh",
+    "corfucrmod.gemspec",
+    "ext/corfucrmod/extconf.rb",
+    "ext/corfucrmod/trinitycrdriver_ext.c",
+    "lib/corfucrmod.rb",
+    "lib/corfucrmod/corfu.rb",
+    "lib/corfucrmod/optimisation.rb",
+    "lib/corfucrmod/trinitycrdriver.rb"
+  ]
+  s.homepage = "http://github.com/edmundhighcock/corfucrmod".freeze
+  s.licenses = ["GPLv3.0".freeze]
+  s.rubygems_version = "2.6.8".freeze
+  s.summary = "A gem which implements the CorFu Optimisation Framework.".freeze
+
+  if s.respond_to? :specification_version then
+    s.specification_version = 4
+
+    if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
+      s.add_runtime_dependency(%q<coderunner>.freeze, [">= 0.14.2"])
+      s.add_runtime_dependency(%q<text-data-tools>.freeze, [">= 1.1.3"])
+      s.add_runtime_dependency(%q<gs2crmod>.freeze, [">= 0.11.33"])
+      s.add_runtime_dependency(%q<trinitycrmod>.freeze, [">= 0.7.11"])
+      s.add_runtime_dependency(%q<ruby-mpi>.freeze, [">= 0.2.0"])
+      s.add_runtime_dependency(%q<cheasecrmod>.freeze, [">= 0.1.0"])
+      s.add_runtime_dependency(%q<tokfile>.freeze, [">= 0.0.3"])
+      s.add_development_dependency(%q<shoulda>.freeze, ["= 3.0.1"])
+      s.add_development_dependency(%q<rdoc>.freeze, ["~> 3.12"])
+      s.add_development_dependency(%q<bundler>.freeze, ["> 1.0.0"])
+      s.add_development_dependency(%q<jeweler>.freeze, [">= 2.0.1"])
+      s.add_development_dependency(%q<simplecov>.freeze, [">= 0"])
+      s.add_development_dependency(%q<minitest>.freeze, ["~> 4"])
+      s.add_development_dependency(%q<rake-compiler>.freeze, [">= 0"])
+    else
+      s.add_dependency(%q<coderunner>.freeze, [">= 0.14.2"])
+      s.add_dependency(%q<text-data-tools>.freeze, [">= 1.1.3"])
+      s.add_dependency(%q<gs2crmod>.freeze, [">= 0.11.33"])
+      s.add_dependency(%q<trinitycrmod>.freeze, [">= 0.7.11"])
+      s.add_dependency(%q<ruby-mpi>.freeze, [">= 0.2.0"])
+      s.add_dependency(%q<cheasecrmod>.freeze, [">= 0.1.0"])
+      s.add_dependency(%q<tokfile>.freeze, [">= 0.0.3"])
+      s.add_dependency(%q<shoulda>.freeze, ["= 3.0.1"])
+      s.add_dependency(%q<rdoc>.freeze, ["~> 3.12"])
+      s.add_dependency(%q<bundler>.freeze, ["> 1.0.0"])
+      s.add_dependency(%q<jeweler>.freeze, [">= 2.0.1"])
+      s.add_dependency(%q<simplecov>.freeze, [">= 0"])
+      s.add_dependency(%q<minitest>.freeze, ["~> 4"])
+      s.add_dependency(%q<rake-compiler>.freeze, [">= 0"])
+    end
+  else
+    s.add_dependency(%q<coderunner>.freeze, [">= 0.14.2"])
+    s.add_dependency(%q<text-data-tools>.freeze, [">= 1.1.3"])
+    s.add_dependency(%q<gs2crmod>.freeze, [">= 0.11.33"])
+    s.add_dependency(%q<trinitycrmod>.freeze, [">= 0.7.11"])
+    s.add_dependency(%q<ruby-mpi>.freeze, [">= 0.2.0"])
+    s.add_dependency(%q<cheasecrmod>.freeze, [">= 0.1.0"])
+    s.add_dependency(%q<tokfile>.freeze, [">= 0.0.3"])
+    s.add_dependency(%q<shoulda>.freeze, ["= 3.0.1"])
+    s.add_dependency(%q<rdoc>.freeze, ["~> 3.12"])
+    s.add_dependency(%q<bundler>.freeze, ["> 1.0.0"])
+    s.add_dependency(%q<jeweler>.freeze, [">= 2.0.1"])
+    s.add_dependency(%q<simplecov>.freeze, [">= 0"])
+    s.add_dependency(%q<minitest>.freeze, ["~> 4"])
+    s.add_dependency(%q<rake-compiler>.freeze, [">= 0"])
+  end
+end
+

data/ext/corfucrmod/extconf.rb

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+require 'mkmf'
+
+#Need to link with C GSL libraries to use in C extensions
+#gsl_inc = `gsl-config --cflags`
+
+#$CFLAGS = " -Wall -I../include #{gsl_inc}"
+
+#srcs = Dir.glob("*.c")
+
+#p ['srcs', srcs]
+                                                                                                         
+#$objs = srcs.collect { |f| f.sub(".c", ".o") }                                                           
+RbConfig::CONFIG['CC'] = CONFIG['CC'] = ENV['CC'] || "mpicc"
+#RbConfig::CONFIG['CPP'] = CONFIG['CPP'] = ENV['CPP'] || "mpicc -E"
+p 'CONFIG[CC]', CONFIG['CC']
+crgemspec=Gem::Specification.find_by_name('coderunner')
+crconfig = crgemspec.full_gem_path
+$CPPFLAGS = " -I#{File.join(crconfig, 'include')} "+$CPPFLAGS
+p ['CPPFLAGS', $CPPFLAGS]
+#raise "Please set the environment variable TRINITY_DIR" unless ENV['TRINITY_DIR']
+#$LOCAL_LIBS = " -L#{ENV['TRINITY_DIR']} " + $LOCAL_LIBS
+#$LOCAL_LIBS = " -L#{ENV['GS2']} " + $LOCAL_LIBS
+#case ENV['GK_SYSTEM']
+#when 'debian'
+  #have_library("gfortran")
+  #have_library("netcdf")
+  #have_library("netcdff")
+  #have_library("fftw3")
+  #have_library("fftw3f")
+  #have_library("fftw3_mpi")
+  #have_library("fftw3f_mpi")
+  #have_library("simpledataio")
+#when 'stampede'
+#end
+
+#have_library("gs2", "__gs2_main_MOD_gs2spec_from_trin")
+#have_library("gs2")
+#have_library("trinity")
+
+dir_config('mpi')
+have_header("mpi.h")
+have_library("mpi")
+have_library("mpi_f90")
+have_library("mpi_f77")
+
+create_makefile("corfucrmod/trinitycrdriver_ext")  

data/ext/corfucrmod/trinitycrdriver_ext.c

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+#include <math.h>
+#include <string.h>
+#include "code_runner_ext.h"
+#include <mpi.h>
+#include <stdbool.h>
+
+/* Taken from the ruby-mpi gem*/
+struct _Comm {
+	  MPI_Comm Comm;
+		bool free;
+};
+
+static VALUE corfucrmod_run_trinity(VALUE self, VALUE input_file_name, VALUE mpi_comm){
+	printf("RUNNING TRINITY!!!\n\n");
+
+	struct _Comm *comm;
+	char * input_file_name_c;
+
+	Data_Get_Struct(mpi_comm, struct _Comm, comm);
+
+  /*RFCALL_12("run_trin_actual", input_file_name, INT2FIX(comm->Comm));*/
+  rb_funcall(self, rb_intern("run_trin_actual2"), 2, input_file_name, INT2FIX(comm->Comm));
+  
+  /*input_file_name_c = StringValueCStr(input_file_name);*/
+  /*run_trinity_c(input_file_name_c, comm->Comm);*/
+
+	/*printf("input file name was %s\n", input_file_name_c);*/
+	/**/
+	/*free(input_file_name_c);*/
+
+	
+
+	return Qnil;
+
+}
+
+void Init_corfucrmod()
+{
+	
+	VALUE ctrinity;
+
+	cgraph_kit = Qnil;
+	ccode_runner_gs2 = Qnil;
+	ccode_runner_ext = Qnil;
+	printf("HERE!!!\n\n");
+	ccode_runner =  RGET_CLASS_TOP("CodeRunner");
+	/*VALUE ctrinity =  RGET_CLASS_TOP("CodeRunner");*/
+  ctrinity	= RGET_CLASS(ccode_runner, "Trinity");
+	rb_define_method(ctrinity, "run_trinity", corfucrmod_run_trinity, 2);
+		/*rb_define_class_under(ccode_runner, "Trinity",*/
+		/*RGET_CLASS(*/
+		/*RGET_CLASS(ccode_runner, "Run"), */
+		/*"FortranNamelist"*/
+		/*)*/
+		/*);*/
+
+	/*ccode_runner_gs2_gsl_tensor_complexes = rb_define_module_under(ccode_runner_gs2, "GSLComplexTensors");*/
+	/*rb_include_module(ccode_runner_gs2, ccode_runner_gs2_gsl_tensor_complexes);*/
+
+	/*ccode_runner_gs2_gsl_tensors = rb_define_module_under(ccode_runner_gs2, "GSLTensors"); */
+	/*rb_include_module(ccode_runner_gs2, ccode_runner_gs2_gsl_tensors);*/
+
+	/*cgsl = RGET_CLASS_TOP("GSL");*/
+	/*cgsl_vector = RGET_CLASS(cgsl, "Vector");*/
+	/*cgsl_vector_complex = RGET_CLASS(cgsl_vector, "Complex");*/
+
+	/*rb_define_method(ccode_runner_gs2_gsl_tensor_complexes, "field_gsl_tensor_complex_2", gs2crmod_tensor_complexes_field_gsl_tensor_complex_2, 1);*/
+	/*rb_define_method(ccode_runner_gs2_gsl_tensors, "field_real_space_gsl_tensor", gs2crmod_tensor_field_gsl_tensor, 1);*/
+	/*rb_define_method(ccode_runner_gs2_gsl_tensors, "field_correlation_gsl_tensor", gs2crmod_tensor_field_correlation_gsl_tensor, 1);*/
+
+	/*rb_define_method(ccode_runner_ext, "hello_world", code_runner_ext_hello_world, 0);*/
+}
+

data/lib/corfucrmod.rb

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+require 'corfucrmod/corfu'

data/lib/corfucrmod/corfu.rb

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+require 'mpi'
+class CodeRunner
+	#  This is a customised subclass of the CodeRunner::Run  class  which is designed to run the CodeRunner/Trinity optimisation framework
+	#
+  CodeRunner.setup_run_class('trinity')
+  CodeRunner.setup_run_class('chease')
+	class Corfu < Run
+
+
+		# Where this file is
+		@code_module_folder = File.dirname(File.expand_path(__FILE__)) # i.e. the directory this file is in
+
+
+		################################################
+		# Quantities that are read or determined by CodeRunner
+		# after the simulation has ended
+		###################################################
+
+		@results = [
+		]
+
+		@code_long="CodeRunner/Trinity Optimisation Framework"
+
+		@run_info=[:time, :is_a_restart, :restart_id, :restart_run_name, :completed_steps, :percent_complete, :start_time]
+
+    @variables = [
+      :chease_exec,
+      :ecom_exec,
+      :output,
+      :search,
+      :trinity_defaults,
+      :trinity_defaults_strings,
+      :gs_defaults,
+      :chease_defaults_strings,
+      :ecom_defaults_strings,
+      :nit,
+      :ntstep_first,
+      :ntstep,
+      :delete_final_run, 
+      :trinity_pars,
+      :chease_pars,
+      :ecom_pars,
+      :gs_code,
+      :convergence,
+      :max_func_evals,
+      :use_previous_pressure,
+      :use_ifspppl_first,
+      :wall_mins_margin
+    ]
+    def gs_defaults_strings
+      case @gs_code
+      when 'chease'
+        @chease_defaults_strings ||= @gs_defaults_strings # For backwards compatibility
+      else
+        @ecom_defaults_strings
+      end
+    end
+    def gs_defaults_strings=(strs)
+      @chease_defaults_strings = strs
+    end
+    def gs_pars
+      case @gs_code
+      when 'chease'
+        @chease_pars ||= @gs_pars
+      when 'ecom'
+        @gs_pars
+      end
+    end
+
+    # For backwards compatibility
+    def gs_pars=(pars)
+      @chease_pars = pars
+    end
+
+		@uses_mpi = true
+
+		@modlet_required = false
+		
+		@naming_pars = []
+
+		#  Any folders which are a number will contain the results from flux simulations.
+		@excluded_sub_folders = ['trinity_runs', 'gs_runs']
+
+    def initialize(*args)
+      @trinity_defaults_strings = []
+      @chease_defaults_strings = []
+      @ecom_defaults_strings = []
+      @convergence = 0.05
+      @max_func_evals = 4
+      @wall_mins_margin = 5.0
+      @wall_mins = 1.0e10
+      super(*args)
+    end
+		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
+				next if var_name == :code_run_environment
+				unless rcp.variables.include? var_name or (CodeRunner::Trinity.rcp.variables.include? var_name) or (CodeRunner::Chease.rcp.variables.include? var_name or CodeRunner::Gryfx.rcp.variables.include? var_name or CodeRunner::Gs2.rcp.variables.include? var_name or CodeRunner::Ecom.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
+      eputs '@nstep_is', @nstep
+      eputs '@nstep_first', @nstep_first
+		end
+
+		#  A hook which gets called when printing the standard run information to the screen using the status command.
+		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
+			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
+
+
+
+		# 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
+		def restart(new_run)
+			#new_run = self.dup
+			(rcp.variables).each{|v| new_run.set(v, send(v)) if send(v)}
+			new_run.is_a_restart = true
+			new_run.restart_id = @id
+			new_run.restart_run_name = @run_name
+			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.trinity_pars = @trinity_pars.absorb(new_run.trinity_pars) if @trinity_pars and new_run.trinity_pars
+			new_run.naming_pars.delete(:restart_id)
+			new_run.generate_run_name
+      raise "trinity_runs directory already exists" if FileTest.exist? new_run.directory + '/trinity_runs'
+      FileUtils.ln_s(@directory + '/trinity_runs', new_run.directory + '/trinity_runs')
+      FileUtils.ln_s(@directory + '/gs_runs', new_run.directory + '/gs_runs')
+		end	
+		#  This is a hook which gets called just before submitting a simulation. It sets up the folder and generates any necessary input files.
+		def generate_input_file
+				check_parameters
+				if @restart_id
+					@runner.run_list[@restart_id].restart(self)
+        else
+          FileUtils.makedirs('trinity_runs')
+          FileUtils.makedirs('gs_runs')
+				end
+        File.open("driver_script.rb", "w"){|f| f.puts optimisation_script}
+        #FileUtils.ln_s("../../#{@trinity_defaults}_defaults.rb", "trinity_runs")
+        #FileUtils.ln_s("../../#{@gs_defaults}_defaults.rb", "gs_runs")
+        save
+		end
+
+    def optimisation_script
+      return <<EOF
+      require 'mpi'
+      class MPI::Comm
+        def Bcast_string(str)
+          @arr = NArray.int(1)
+          if rank==0
+            @arr[0] = str.length
+            Bcast(@arr, 0)
+            Bcast(str, 0)
+          else
+            Bcast(@arr,0)
+            str << " " while str.length < @arr[0]
+            Bcast(str,0)
+          end
+        end
+      end
+      puts 'Initializing mpi'
+		  MPI.Init
+      comm = MPI::Comm::WORLD
+      rank = comm.rank
+      puts ['Rank is: ', rank]
+      if rank==0
+        begin
+          require 'coderunner'
+          CodeRunner.setup_run_class('trinity')
+          CodeRunner.setup_run_class('corfu')
+          #require 'corfucrmod'
+          require 'corfucrmod/trinitycrdriver'
+          CodeRunner::Corfu.run_optimisation(#@id)
+        rescue =>err
+          arr = NArray.int(1)
+          arr[0] = 0
+          comm.Bcast(arr,0)
+          raise err
+        end
+        arr = NArray.int(1)
+        arr[0] = 0
+        comm.Bcast(arr,0)
+      else
+        require 'corfucrmod/trinitycrdriver'
+        arr = NArray.int(1)
+        puts "Proc \#{comm.rank} waiting for message"
+        loop do
+          comm.Bcast(arr, 0)
+          puts "Proc \#{comm.rank} received instructions: \#{arr[0]}"
+          dir = ""
+          run_name  = ""
+          if arr[0] == 1
+            comm.Bcast_string(dir)
+            comm.Bcast_string(run_name)
+            puts "Proc \#{comm.rank} calling Trinity with run_name: \#{run_name}"
+            Dir.chdir(dir){CodeRunner::Trinity.new.run_trinity(run_name+'.trin', comm)}
+          else
+            break
+          end
+        end
+      end
+      MPI.Finalize
+EOF
+    end
+
+		def check_parameters
+      if delete_final_run
+        raise CRFatal.new("Cancelled submission") unless Feedback.get_boolean("You have set delete_final_run which will cause the final run to be deleted. Is this correct?")
+      end
+		end
+
+
+    def self.run_optimisation(id = ARGV[-1])
+        eputs 'Fetching runner'
+        runner = CodeRunner.fetch_runner(Y: '../../', U: true)
+        eputs 'Got runner'
+        #@run = @runner.run_list[id.to_i]
+        #run = self.load(Dir.pwd, runner)
+        run = self.new(runner)
+        run.read_info
+        run.start_time = Time.now.to_i
+        eputs 'Loaded run'
+        #ep @run
+        #raise "Can't find run with id #{id}; #{@runner.run_list.keys}" unless @run
+        opt = CodeRunner::Corfu::Optimisation.new(
+          run.output, run.search
+        )
+        eputs 'Created opt'
+        trinity_runner = CodeRunner.fetch_runner(Y: 'trinity_runs', X: '/dev/null', C: 'trinity')
+        trinity_runner.nprocs = MPI::Comm::WORLD.size
+        eputs 'Got trinity runner'
+        case run.gs_code
+        when 'chease'
+          gs_runner = CodeRunner.fetch_runner(Y: 'gs_runs', X: run.chease_exec, C: 'chease')
+          gs_runner.nprocs = '1'
+        when 'ecom'
+          gs_runner = CodeRunner.fetch_runner(Y: 'gs_runs', X: run.ecom_exec, C: 'ecom')
+          gs_runner.nprocs = '1'
+        else
+          raise "Unknown gs_code #{run.gs_code.inspect}"
+        end
+        eputs 'Got gs runner'
+        opt.trinity_runner = trinity_runner
+        opt.gs_runner = gs_runner
+        opt.serial_optimise(:simplex, run)
+    end
+
+
+
+    def vim_output
+      system "vim -Ro #{output_file} #{error_file}"
+    end
+    alias :vo :vim_output
+
+
+		# Parameters which follow the Trinity executable, in this case just the input file.
+		def parameter_string
+			" driver_script.rb #@id"
+		end
+
+		def parameter_transition
+		end
+
+		def generate_component_runs
+			#puts "HERE"
+		end
+
+		
+
+		@source_code_subfolders = []
+
+		# 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).
+		#
+		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
+      @percent_complete = 0.0
+		end
+
+		def get_status
+			return :Unknown
+		end
+
+
+		def input_file_extension
+			''
+		end
+
+    def graphkit(name, options)
+      results = eval(File.read(@directory + '/results'))
+      case name
+      when 'evolution'
+        data = {}
+        pars_already_listed = []
+        results[:func_calls].reverse.each do |pars, res|
+          next if pars_already_listed.include? pars
+          pars_already_listed.push pars
+          pars.each do |code,cpars|
+            cpars.each do |vname, val|
+              label = "#{code}_#{vname}"
+              data[label] ||= []
+              data[label].push val
+            end
+          end
+          data['results']||=[]
+          data['results'].push res
+        end
+        kit = GraphKit.quick_create(data.values)
+        data.keys.zip(GraphKit::AXES).each{|lbl,ax| kit.set(ax + :label, lbl)}
+        kit
+      when 'iteration'
+        require 'tokfile/ogyropsi'
+        step = options[:step_index]
+        raise "Please specify step_index" unless step
+        iter, _trinstep = trinrunstep(step)[0]
+          kit = TokFile::Ogyropsi.new("#@directory/trinity_runs/v/id_#{iter}/chease/ogyropsi#{sprintf("%05d", step)}.dat").summary_graphkit
+          kit.gp.multiplot = " layout 3,3 title 'Iteration: #{iter}; Step: #{step}; Pars: #{results[:func_calls][iter-1][0]}; Result: #{results[:func_calls][iter-1][1].inspect}'"
+          kit[-1].gp.size = "ratio 1"
+          #pp 'kit', kit
+        return kit
+      end
+    end
+
+    def trinstep_mappings
+      @trinstep_mappings = (
+        trinity_runner = CodeRunner.fetch_runner(Y: @directory + '/trinity_runs')
+        sizes = trinity_runner.run_list.values.sort_by{|r| r.id}.map{|r| r.get_completed_timesteps; r.completed_timesteps}
+        i = 0; cs = 0
+        sizes.inject({}){|h,sz| cs+=sz; h[i+=1]=cs; h}
+      )
+    end
+
+    def trinrunstep(overall_step)
+      p 'trinstep_mappings', trinstep_mappings
+      trinrun, cusum = trinstep_mappings.to_a.find{|t, c| c>=overall_step}
+      [trinrun, cusum-overall_step + 1]
+    end
+
+    def max_step
+      trinstep_mappings[-1][1]
+    end
+
+	end
+end
+require 'corfucrmod/optimisation'
+