trinitycrdriver 0.1.0 → 0.1.1
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- checksums.yaml +4 -4
- data/VERSION +1 -1
- data/ext/trinitycrdriver/extconf.rb +18 -14
- data/ext/trinitycrdriver/trinitycrdriver.c +7 -3
- data/lib/trinitycrdriver/optimisation.rb +98 -89
- data/lib/trinitycrdriver.rb +15 -1
- data/trinitycrdriver.gemspec +3 -3
- metadata +2 -2
checksums.yaml
CHANGED
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---
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SHA1:
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metadata.gz:
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data.tar.gz:
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metadata.gz: 99d128788dbcf852da53d869d20f874b57cdb6b4
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data.tar.gz: eca654dc62344fc0f941784cb60c3c65b6779ea5
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SHA512:
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metadata.gz:
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data.tar.gz:
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metadata.gz: 9098ed22b3dd3371c01c81728d3d83d8c6b11b3f51d0058c4dab0bc2926e2a8e0e9f4e1135b5f6e71fb9d5408cf86f8c2d5b63a37a06a891a4a9e70dce5c0523
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7
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data.tar.gz: 1a726053cdedf417eefa3b2634536592bdd5089c7781b5cbd125bb88af2e093aee0ef16582e4498cd8945c6bf0e550d0e56a895d31fe45f4573044432a44f0b0
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data/VERSION
CHANGED
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@@ -1 +1 @@
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1
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-
0.1.
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1
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0.1.1
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@@ -11,27 +11,31 @@ require 'mkmf'
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#$objs = srcs.collect { |f| f.sub(".c", ".o") }
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RbConfig::CONFIG['CC'] = CONFIG['CC'] = ENV['CC'] || "mpicc"
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RbConfig::CONFIG['CPP'] = CONFIG['CPP'] = ENV['CPP'] || "mpicc -E"
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#RbConfig::CONFIG['CPP'] = CONFIG['CPP'] = ENV['CPP'] || "mpicc -E"
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p 'CONFIG[CC]', CONFIG['CC']
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crgemspec=Gem::Specification.find_by_name('coderunner')
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crconfig = crgemspec.full_gem_path
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$CPPFLAGS = " -I#{File.join(crconfig, 'include')} "+$CPPFLAGS
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p ['CPPFLAGS', $CPPFLAGS]
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raise "Please set the environment variable TRINITY_DIR" unless ENV['TRINITY_DIR']
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have_library("
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have_library("
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have_library("
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have_library("
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have_library("
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have_library("
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#raise "Please set the environment variable TRINITY_DIR" unless ENV['TRINITY_DIR']
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#$LOCAL_LIBS = " -L#{ENV['TRINITY_DIR']} " + $LOCAL_LIBS
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#$LOCAL_LIBS = " -L#{ENV['GS2']} " + $LOCAL_LIBS
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#case ENV['GK_SYSTEM']
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#when 'debian'
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#have_library("gfortran")
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#have_library("netcdf")
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#have_library("netcdff")
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#have_library("fftw3")
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#have_library("fftw3f")
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#have_library("fftw3_mpi")
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#have_library("fftw3f_mpi")
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#have_library("simpledataio")
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#when 'stampede'
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#end
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#have_library("gs2", "__gs2_main_MOD_gs2spec_from_trin")
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have_library("gs2")
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have_library("trinity")
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#have_library("gs2")
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#have_library("trinity")
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dir_config('mpi')
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have_header("mpi.h")
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@@ -10,15 +10,19 @@ struct _Comm {
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bool free;
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};
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-
static VALUE trinitycrdriver_run_trinity(VALUE
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static VALUE trinitycrdriver_run_trinity(VALUE self, VALUE input_file_name, VALUE mpi_comm){
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printf("RUNNING TRINITY!!!\n\n");
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struct _Comm *comm;
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char * input_file_name_c;
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Data_Get_Struct(mpi_comm, struct _Comm, comm);
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/*RFCALL_12("run_trin_actual", input_file_name, INT2FIX(comm->Comm));*/
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rb_funcall(self, rb_intern("run_trin_actual2"), 2, input_file_name, INT2FIX(comm->Comm));
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/*input_file_name_c = StringValueCStr(input_file_name);*/
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/*run_trinity_c(input_file_name_c, comm->Comm);*/
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/*printf("input file name was %s\n", input_file_name_c);*/
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/**/
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@@ -1,100 +1,109 @@
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class CodeRunner::Trinity::Optimisation
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include GSL::MultiMin
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# optimisation_spec is a hash of {:code_name => {:variable => [initial_guess, dimension_scale_factor]}}
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# dimension_scale_factor is just some estimate of the length scale in which the result
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# varies significantly
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# code_name is either trinity or chease (both can be used simultaneously)
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attr_reader :optimisation_spec
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attr_reader :optimisation_variables
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attr_accessor :trinity_runner
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attr_accessor :chease_runner
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def initialize(optimised_quantity, optimisation_spec)
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#@folder = folder
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@optimised_quantity = optimised_quantity
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@optimisation_spec = optimisation_spec
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@optimisation_variables = optimisation_spec.map{|code, hash| hash.map{|var, pars| [code, var]}}.flatten(1)
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@optimisation_starts = optimisation_spec.map{|code, hash| hash.map{|var, pars| pars[0]}}.flatten(1)
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@optimisation_steps = optimisation_spec.map{|code, hash| hash.map{|var, pars| pars[1]}}.flatten(1)
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#@runner = CodeRunner.fetch_runner(
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#p ['optimisation_variables', @optimisation_variables]
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end
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def dimension
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@optimisation_variables.size
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end
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def serial_optimise(optimisation_method, parameters_obj)
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optimisation_meth = case optimisation_method
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when :simplex
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FMinimizer::NMSIMPLEX
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else
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raise "Unknown optimisation_method"
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end
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opt = FMinimizer.alloc(optimisation_meth, @optimisation_variables.size)
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func = Proc.new{|v, optimiser| optimiser.func(v)}
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gsl_func = Function.alloc(func, dimension)
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gsl_func.set_params(self)
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opt.set(gsl_func, @optimisation_starts.to_gslv, @optimisation_steps.to_gslv)
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parameters_obj.nit.times do |i|
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opt.iterate
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p ['status', opt.x, opt.minimum, i, parameters_obj.nit]
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end
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p 'heellllllo'
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MPI.Finalize
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end
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def func(v)
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pars = {}
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pars[:chease] = {}
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pars[:trinity] = {}
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for i in 0...v.size
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code, varname = @optimisation_variables[i]
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val = v[i]
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pars[code][varname] = val
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end
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if not @first_run_done
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pars[:trinity][:ntstep] = 300
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else
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#pars[:trinity].delete(:ntstep)
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pars[:trinity][:ntstep] = 100
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end
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pars[:chease][:ap] = [0.3,0.5,0.4,0.0,0.4,0.0,0.0]
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pars[:chease][:at] = [0.16,1.0,1.0,-1.1,-1.1]
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trinity_runner.run_class.instance_variable_set(:@mpi_communicator, MPI::Comm::WORLD)
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if false and trinity_runner.run_list.size > 0
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else
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crun = chease_runner.run_class.new(chease_runner)
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crun.update_submission_parameters(pars[:chease].inspect)
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if @first_run_done
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#crun.nppfun=4
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#crun.neqdsk=0
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#crun.expeq_file = trinity_runner.run_list[@id]
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end
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if chease_runner.run_list.size > 0
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crun.restart_id = @cid
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end
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chease_runner.submit(crun)
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crun = chease_runner.run_list[@cid = chease_runner.max_id]
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crun.recheck
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chease_runner.update
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#chease_runner.print_out(0)
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#FileUtils.cp(crun.directory + '/ogyropsi.dat', trinity_runner.root_folder + '/.')
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-
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run.update_submission_parameters(pars[:trinity].inspect)
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#trinity_runner.run_class.instance_variable_set(:@delay_execution, true)
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if trinity_runner.run_list.size > 0
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#run.restart_id = @id
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end
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87
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trinity_runner.submit(run)
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run = trinity_runner.run_list[@id = trinity_runner.max_id]
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run.recheck
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90
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trinity_runner.update
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#trinity_runner.print_out(0)
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result = run.send(@optimised_quantity)
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93
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p ['result is ', result]
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-
return -result
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-
end
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86
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run = trinity_runner.run_class.new(trinity_runner)
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96
87
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88
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run.update_submission_parameters(pars[:trinity].inspect)
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run.gs_folder = crun.directory
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run.evolve_geometry = ".true."
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#trinity_runner.run_class.instance_variable_set(:@delay_execution, true)
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if trinity_runner.run_list.size > 0
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run.restart_id = @id
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end
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95
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trinity_runner.submit(run)
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run = trinity_runner.run_list[@id = trinity_runner.max_id]
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run.recheck
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98
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trinity_runner.update
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#trinity_runner.print_out(0)
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100
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result = run.send(@optimised_quantity)
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101
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p ['result is ', result]
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102
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@first_run_done = true
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103
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return -result
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end
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105
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-
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99
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-
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106
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+
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107
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#v.square.sum
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end
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100
109
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end
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data/lib/trinitycrdriver.rb
CHANGED
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@@ -1,4 +1,18 @@
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1
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-
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1
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require 'ffi'
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2
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class CodeRunner
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3
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class Trinity
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module TrinityDriver
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5
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extend FFI::Library
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6
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ffi_lib ENV['TRINITY'] + '/libtrin.so'
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7
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attach_function :runtr, :run_trinity_c, [:string, :int], :void
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8
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end
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9
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def run_trin_actual2(input_file, mpicomm_int)
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10
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puts 'calling TrinityDriver.runtr'
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TrinityDriver.runtr(input_file, mpicomm_int)
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end
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private :run_trin_actual2
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end
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end
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2
16
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require 'trinitycrdriver/trinitycrdriver'
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3
17
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require 'mpi'
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4
18
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data/trinitycrdriver.gemspec
CHANGED
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@@ -2,17 +2,17 @@
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2
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# DO NOT EDIT THIS FILE DIRECTLY
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3
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# Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
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4
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# -*- encoding: utf-8 -*-
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# stub: trinitycrdriver 0.1.
|
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# stub: trinitycrdriver 0.1.1 ruby lib
|
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6
|
# stub: ext/trinitycrdriver/extconf.rb
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7
7
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Gem::Specification.new do |s|
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9
9
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s.name = "trinitycrdriver"
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10
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-
s.version = "0.1.
|
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s.version = "0.1.1"
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11
11
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12
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s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
|
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13
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s.require_paths = ["lib"]
|
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14
14
|
s.authors = ["Edmund Highcock"]
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15
|
-
s.date = "2015-07-
|
|
15
|
+
s.date = "2015-07-28"
|
|
16
16
|
s.description = "A gem to allow coderunner to run the trinity code directly."
|
|
17
17
|
s.email = "edmundhighcock@users.sourceforge.net"
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|
18
18
|
s.extensions = ["ext/trinitycrdriver/extconf.rb"]
|
metadata
CHANGED
|
@@ -1,14 +1,14 @@
|
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
|
2
2
|
name: trinitycrdriver
|
|
3
3
|
version: !ruby/object:Gem::Version
|
|
4
|
-
version: 0.1.
|
|
4
|
+
version: 0.1.1
|
|
5
5
|
platform: ruby
|
|
6
6
|
authors:
|
|
7
7
|
- Edmund Highcock
|
|
8
8
|
autorequire:
|
|
9
9
|
bindir: bin
|
|
10
10
|
cert_chain: []
|
|
11
|
-
date: 2015-07-
|
|
11
|
+
date: 2015-07-28 00:00:00.000000000 Z
|
|
12
12
|
dependencies:
|
|
13
13
|
- !ruby/object:Gem::Dependency
|
|
14
14
|
name: coderunner
|