Class: CodeRunner::Gryfx

Inherits:
Gs2
  • Object
show all
Defined in:
lib/gryfxcrmod/gryfx.rb,
lib/gryfxcrmod/namelist_tools.rb

Class Method Summary collapse

Instance Method Summary collapse

Class Method Details

.defaults_file_header ⇒ Object 



217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
 
# File 'lib/gryfxcrmod/gryfx.rb', line 217

def self.defaults_file_header
	<<EOF1
######################################################################
# Automatically generated defaults file for GRYFX CodeRunner module  #
#                                                                    #
# This defaults file specifies a set of defaults for GRYFX which are #
# used by CodeRunner to set up and run GRYFX simulations.            #
#                                                                    #
# Created #{Time.now.to_s}                                           #
#                                                                    #
######################################################################

@defaults_file_description = ""
EOF1
end

.get_namelists_and_variables_from_source_code(source) ⇒ Object

Find all input namelists and variables by scanning the source code



9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
 
# File 'lib/gryfxcrmod/namelist_tools.rb', line 9

def self.get_namelists_and_variables_from_source_code(source)
	nms = {}
	all_variables_in_source = {}
	namelist_declarations = {}
	#source.scan(/^\s*namelist\s*\/(?<namelist>\w+)\/(?<variables>(?:(?:&\s*[\n\r]+)|[^!\n\r])*)/) do 
	#source.scan(Regexp.new("#{/^\s*namelist\s*\/\s*(?<namelist>\w+)\s*\//}(?<variables>#{FORTRAN_SINGLE_LINE})")) do 
	source.scan(rcp.fortran_namelist_variable_match_regex) do
		namelist = $~[:namelist].to_s.downcase.to_sym
		#variables = $~[:variables].gsub(/!.*/, '')
		#eputs namelist, variables
		#namelist_declarations[namelist] = variables
		#gets # if namelist == :collisions_knobs

		#next if [:stuff, :ingen_knobs].include? namelist
		nms[namelist] ||= []
		all_variables_in_source[namelist] ||= []
# 		puts variables
		#variables.scan(/\w+/) do 
			var =  $~[:variable].to_sym
# 			(p variables, namelist; exit) if var == :following or var == :sou
			all_variables_in_source[namelist].push var
			next if known_code_variable?(namelist, var)
			nms[namelist].push var
		#end
		nms[namelist].uniq!
		all_variables_in_source[namelist].uniq!
	end
	return [nms, all_variables_in_source, namelist_declarations]
end

.get_sample_value(source, var) ⇒ Object 



38
39
40
41
42
43
44
45
46
47
48
 
# File 'lib/gryfxcrmod/namelist_tools.rb', line 38

def self.get_sample_value(source, var)
	sample_val = nil
	source.scan(rcp.fortran_namelist_variable_match_regex) do
		#p $~
		
		next unless var == $~[:variable].to_sym
		sample_val = eval($~[:default].sub(/(\d\.)$/, '\10').sub(/^(\.\d)/, '0\1').sub(/(\d\.)[eE]/, '\10e'))
	end
	raise "Couldn't get a sample value for #{var.inspect}" unless sample_val
	return sample_val
end

.update_defaults_from_source_code(source_code_folder = ) ⇒ Object 



49
50
51
52
53
54
55
56
57
 
# File 'lib/gryfxcrmod/namelist_tools.rb', line 49

def self.update_defaults_from_source_code(source_code_folder = ARGV[-1])
	source = get_aggregated_source_code_text(source_code_folder)
	rcp.namelists.each do |nml, nmlhash|
		nmlhash[:variables].each do |var, varhash|
			varhash[:autoscanned_defaults] = [get_sample_value(source, varhash[:code_name]||var)] rescue []
			save_namelists
		end
	end
end

Instance Method Details

#calculate_frequencies ⇒ Object

def calculate_results end



141
142
143
 
# File 'lib/gryfxcrmod/gryfx.rb', line 141

def calculate_frequencies
	@real_frequencies = FloatHash.new
end

#code_run_environment ⇒ Object 



149
150
151
152
153
154
155
156
 
# File 'lib/gryfxcrmod/gryfx.rb', line 149

def code_run_environment
	case @sys
	when /stampede/
		"module load cuda\n module load hdf5\n module load netcdf"
	when /generic_linux/, /macosx/
		"# No configuration necessary"
	end
end

#generate_component_runs ⇒ Object 



136
137
 
# File 'lib/gryfxcrmod/gryfx.rb', line 136

def generate_component_runs
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.



69
70
71
 
# File 'lib/gryfxcrmod/gryfx.rb', line 69

def generate_input_file
		write_input_file
end

#geometric_factors_gsl_tensor(options) ⇒ Object 



159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
 
# File 'lib/gryfxcrmod/gryfx.rb', line 159

def geometric_factors_gsl_tensor(options)
		theta_vec = gsl_vector(:theta, options)
		factors = GSL::Tensor.alloc(6,theta_vec.size)
		values = [:Rplot, :Zplot, :aplot, :Rprime, :Zprime, :aprime].map do |name|
			arr = netcdf_file.var(name).get.to_a
			if options[:periodic]
				arr += [arr[0]]
			end
			arr
		end
		#ep values
		shape = factors.shape
		for i in 0...shape[0]
				unless options[:interpolate_theta]
					for j in 0...shape[1]
						factors[i,j] = values[i][j]
					end
				else
					opts = options.dup
					opts[:interpolate_theta] = nil
					opts[:thetamax] = opts[:thetamin] = nil
					theta_vec_short = gsl_vector(:theta, opts)
					#p 'sizes', [theta_vec_short.size, values[i].to_gslv.size]
					interp = GSL::ScatterInterp.alloc(:cubic, [theta_vec_short, values[i].to_gslv], true, [3.0].to_gslv)
					for j in 0...theta_vec.size
						factors[i,j] = interp.eval(theta_vec[j])
					end
				end
		end
		#ep factors
		return factors
end

#get_completed_timesteps ⇒ Object 



124
125
126
127
128
129
130
 
# File 'lib/gryfxcrmod/gryfx.rb', line 124

def get_completed_timesteps
	if FileTest.exist?(@run_name  + '.cdf')
		@completed_timesteps = netcdf_file.var('t').get.size #gsl_vector('t').size
	else
		@completed_timesteps = 0
	end
end

#get_status ⇒ Object 



103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
 
# File 'lib/gryfxcrmod/gryfx.rb', line 103

def get_status
	if @running
		unless @status==:Queueing
			@status = :Incomplete
			get_completed_timesteps
			@percent_complete = 100.0*@completed_timesteps.to_f/(nstep/nwrite) 
			if @completed_timesteps.to_f/(nstep/nwrite) == 1.0
				@status=:Complete
			end

		end
	else
		get_completed_timesteps
		if (@percent_complete = 100.0*@completed_timesteps.to_f/(nstep/nwrite))  > 5.0
			@status = :Complete
		else
			@status = :Failed
		end
	end
end

#gryfx? ⇒ Boolean

Returns:

  • (Boolean) 


145
146
147
 
# File 'lib/gryfxcrmod/gryfx.rb', line 145

def gryfx?
	true
end

#input_file_header ⇒ Object 



193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
 
# File 'lib/gryfxcrmod/gryfx.rb', line 193

def input_file_header
	<<EOF
!==============================================================================
!  		GRYFX INPUT FILE automatically generated by CodeRunner 
!==============================================================================
!
!  GRYFX is a gyrofluid GPU flux tube initial value turbulence code 
!  which can be used for fusion or astrophysical plasmas.
!  
!  	See http://gyrokinetics.sourceforge.net
!
!  CodeRunner is a framework for the automated running and analysis 
!  of large simulations. 
!
!  	See http://coderunner.sourceforge.net
!
!  Created on #{Time.now.to_s}
!      by CodeRunner version #{CodeRunner::CODE_RUNNER_VERSION.to_s}
!
!==============================================================================

EOF
end

#netcdf_filename ⇒ Object 



132
133
134
 
# File 'lib/gryfxcrmod/gryfx.rb', line 132

def netcdf_filename
	@directory + '/' +  @run_name + '.cdf'
end

#parameter_string ⇒ Object

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



79
80
81
 
# File 'lib/gryfxcrmod/gryfx.rb', line 79

def parameter_string
	@run_name + ".in"
end

#parameter_transition ⇒ Object 



83
84
 
# File 'lib/gryfxcrmod/gryfx.rb', line 83

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.



40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
 
# File 'lib/gryfxcrmod/gryfx.rb', line 40

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)
		 if @nonlinear_mode == "off"
				beginning += sprintf("%3.2e %3.2e %4s", 
				 @fastest_growing_mode, @max_growth_rate, 
				 @freq_of_max_growth_rate||0.0)  rescue ""
		 elsif @nonlinear_mode == "on"
	# 		 p @hflux_tot_stav
			 beginning += "       sat:#{saturated.to_s[0]}"  if not @saturated.nil?
			 beginning += sprintf(" hflux:%1.2e", @hflux_tot_stav) if  @hflux_tot_stav 
			 beginning += sprintf("+/-%1.2e", @hflux_tot_stav_error) if  @hflux_tot_stav_error
			 beginning += sprintf(" momflux:%1.2e", @es_mom_flux_stav.values.sum) if @es_mom_flux_stav and @es_mom_flux_stav.values[0]
			 beginning += '  SC:' + @spectrum_check.map{|c| c.to_s}.join(',') if @spectrum_check 
			 beginning += '  VC:' + @vspace_check.map{|c| sprintf("%d", ((c*10.0).to_i rescue -1))}.join(',') if @vspace_check 
		 end
	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).



91
92
93
94
95
96
97
98
99
100
 
# File 'lib/gryfxcrmod/gryfx.rb', line 91

def process_directory_code_specific
	@grid_option = "box" # For compatibility with the GS2 routines
	@write_phi_over_time  = "true" # For compatibility with the GS2 routines
	get_status
	#p ['id is', id, 'ctd is ', ctd]
	if ctd
		#calculate_results 
	end
	#p ['fusionQ is ', fusionQ]
end

#write_input_file ⇒ Object

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



74
75
76
 
# File 'lib/gryfxcrmod/gryfx.rb', line 74

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