trinitycrmod 0.7.3 → 0.7.4
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- checksums.yaml +4 -4
- data/Gemfile +1 -0
- data/Rakefile +36 -1
- data/VERSION +1 -1
- data/lib/trinitycrmod/trinity.rb +49 -88
- data/lib/trinitycrmod/trinity_gs2.rb +40 -17
- data/trinitycrmod.gemspec +5 -2
- metadata +15 -1
checksums.yaml
CHANGED
@@ -1,7 +1,7 @@
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1
1
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---
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2
2
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SHA1:
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3
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-
metadata.gz:
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4
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-
data.tar.gz:
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3
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+
metadata.gz: b4c4064ac49be83fd3218fe6019c7c43abe85f88
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4
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+
data.tar.gz: 310f019da68adf055c8cc32a70048fdfac956ceb
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5
5
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SHA512:
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6
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-
metadata.gz:
|
7
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-
data.tar.gz:
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6
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+
metadata.gz: 1d8442ecee17f61f52c84115d1db381bfa806fd97a343ea46ae6112a744be096aa353dbb83ad5eda37a3a35c60c66ee64e7afb928b38001838dc0985883158b3
|
7
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+
data.tar.gz: 1fd338e931c0d1fd2dc94d86c8fb6c2382154f3bdea2e0ff5349b0792ece360b3e5dc1eb9ca76954c69069088d5f6494f51db6742342374f8534c564aab0c568
|
data/Gemfile
CHANGED
@@ -4,6 +4,7 @@ source "http://rubygems.org"
|
|
4
4
|
gem "coderunner", ">= 0.16.10"
|
5
5
|
gem "text-data-tools", ">= 1.1.6"
|
6
6
|
gem "gs2crmod", ">=0.11.76"
|
7
|
+
gem "gryfxcrmod", ">=0.1.9"
|
7
8
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|
8
9
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# Add dependencies to develop your gem here.
|
9
10
|
# Include everything needed to run rake, tests, features, etc.
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data/Rakefile
CHANGED
@@ -27,7 +27,7 @@ end
|
|
27
27
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Jeweler::RubygemsDotOrgTasks.new
|
28
28
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|
29
29
|
require 'rake/testtask'
|
30
|
-
Rake::TestTask.new(:test) do |test|
|
30
|
+
Rake::TestTask.new(:test => [:clean_tests]) do |test|
|
31
31
|
test.libs << 'lib' << 'test'
|
32
32
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test.pattern = 'test/**/test_*.rb'
|
33
33
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test.verbose = true
|
@@ -38,6 +38,41 @@ Rake::TestTask.new(:sync_variables) do |test|
|
|
38
38
|
test.pattern = 'sync_variables/sync_variables.rb'
|
39
39
|
test.verbose = true
|
40
40
|
end
|
41
|
+
|
42
|
+
task :clean_tests do
|
43
|
+
require 'coderunner'
|
44
|
+
require 'rubygems'
|
45
|
+
require 'bundler'
|
46
|
+
begin
|
47
|
+
Bundler.setup(:default, :development)
|
48
|
+
rescue Bundler::BundlerError => e
|
49
|
+
$stderr.puts e.message
|
50
|
+
$stderr.puts "Run `bundle install` to install missing gems"
|
51
|
+
exit e.status_code
|
52
|
+
end
|
53
|
+
$LOAD_PATH.unshift(File.join(File.dirname(__FILE__), 'lib'))
|
54
|
+
$LOAD_PATH.unshift(File.dirname(__FILE__))
|
55
|
+
@runner = CodeRunner.fetch_runner(Y: 'test/gs2_42982', C: 'trinity', X: '/dev/null')
|
56
|
+
FileUtils.rm(@runner.run_class.rcp.user_defaults_location + '/rake_test_gs2_42982_defaults.rb') rescue nil
|
57
|
+
FileUtils.rm('test/gs2_42982/rake_test_gs2_42982_defaults.rb') rescue nil
|
58
|
+
FileUtils.rm('test/gs2_42982/pr08_jet_42982_1d.dat') rescue nil
|
59
|
+
FileUtils.rm('test/gs2_42982/pr08_jet_42982_2d.dat') rescue nil
|
60
|
+
FileUtils.rm('test/gs2_42982/.CODE_RUNNER_TEMP_RUN_LIST_CACHE') rescue nil
|
61
|
+
#STDIN.gets
|
62
|
+
FileUtils.rm_r('test/gs2_42982/v/') rescue nil
|
63
|
+
FileUtils.rm_r('test/gs2_42982_results/v') rescue nil
|
64
|
+
FileUtils.rm('test/gs2_42982_results/.code_runner_script_defaults.rb') rescue nil
|
65
|
+
FileUtils.rm('test/gs2_42982_results/.CODE_RUNNER_TEMP_RUN_LIST_CACHE') rescue nil
|
66
|
+
FileUtils.rm('test/ifspppl_results/.code_runner_script_defaults.rb') rescue nil
|
67
|
+
FileUtils.rm_r('test/ifspppl_results/v/id_1/') rescue nil
|
68
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+
FileUtils.rm('test/ifspppl/.code_runner_script_defaults.rb') rescue nil
|
69
|
+
FileUtils.rm('test/ifspppl/.CODE_RUNNER_TEMP_RUN_LIST_CACHE') rescue nil
|
70
|
+
FileUtils.rm('test/gs2_42982/pr08_jet_42982_1d.dat') rescue nil
|
71
|
+
FileUtils.rm('test/gs2_42982/pr08_jet_42982_2d.dat') rescue nil
|
72
|
+
FileUtils.rm_r('test/ifspppl/v') rescue nil
|
73
|
+
end
|
74
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+
|
75
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+
|
41
76
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|
42
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43
78
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#require 'rcov/rcovtask
|
data/VERSION
CHANGED
@@ -1 +1 @@
|
|
1
|
-
0.7.
|
1
|
+
0.7.4
|
data/lib/trinitycrmod/trinity.rb
CHANGED
@@ -12,6 +12,11 @@ class CodeRunner
|
|
12
12
|
class FluxOptionError < StandardError; end
|
13
13
|
|
14
14
|
|
15
|
+
# Setup gs2 in case people are using it
|
16
|
+
CodeRunner.setup_run_class('gs2')
|
17
|
+
# Setup gryfx in case people are using it
|
18
|
+
CodeRunner.setup_run_class('gryfx')
|
19
|
+
require 'trinitycrmod/trinity_gs2'
|
15
20
|
|
16
21
|
# Where this file is
|
17
22
|
@code_module_folder = File.dirname(File.expand_path(__FILE__)) # i.e. the directory this file is in
|
@@ -28,12 +33,6 @@ class CodeRunner
|
|
28
33
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require 'trinitycrmod/flux_interpolator'
|
29
34
|
require 'trinitycrmod/read_netcdf'
|
30
35
|
|
31
|
-
# Setup gs2 in case people are using it
|
32
|
-
CodeRunner.setup_run_class('gs2')
|
33
|
-
require 'trinitycrmod/trinity_gs2'
|
34
|
-
|
35
|
-
# Setup gryfx in case people are using it
|
36
|
-
CodeRunner.setup_run_class('gryfx')
|
37
36
|
|
38
37
|
################################################
|
39
38
|
# Quantities that are read or determined by CodeRunner
|
@@ -102,10 +101,10 @@ class CodeRunner
|
|
102
101
|
#new_run = self.dup
|
103
102
|
(rcp.variables).each{|v| new_run.set(v, send(v)) if send(v) or new_run.send(v)}
|
104
103
|
if @flux_option == "gs2"
|
105
|
-
|
104
|
+
flux_runs.each_with_index do |run, i|
|
106
105
|
CodeRunner::Gs2.rcp.variables.each{|v|
|
107
106
|
next if [:ginit_option, :delt_option].include? v and new_run.no_restart_gs2
|
108
|
-
new_run.
|
107
|
+
new_run.flux_runs[i].set(v, run.send(v)) if run.send(v) or new_run.flux_runs[i].send(v)
|
109
108
|
}
|
110
109
|
end
|
111
110
|
end
|
@@ -122,7 +121,7 @@ class CodeRunner
|
|
122
121
|
new_run.init_file = @run_name + ".tmp"
|
123
122
|
@runner.nprocs = @nprocs if @runner.nprocs == "1" # 1 is the default so this means the user probably didn't specify nprocs
|
124
123
|
# This is unnecessary for single restart file.
|
125
|
-
warning( "Restart is not on the same number of processors as the previous run: new is #{new_run.nprocs.inspect} and old is #{@nprocs.inspect}... this is only OK if you are using parallel netcdf and single restart files.") if not new_run.no_restart_gs2 and (!new_run.nprocs or new_run.nprocs != @nprocs)
|
124
|
+
warning( "Restart is not on the same number of processors as the previous run: new is #{new_run.nprocs.inspect} and old is #{@nprocs.inspect}... this is only OK if you are using parallel netcdf and single restart files.") if flux_gs2? and not new_run.no_restart_gs2 and (!new_run.nprocs or new_run.nprocs != @nprocs)
|
126
125
|
raise "Restart cannot have a different sized jacobian: new is #{new_run.n_flux_tubes_jac} and old is #{n_flux_tubes_jac}" unless new_run.n_flux_tubes_jac == n_flux_tubes_jac
|
127
126
|
# @runner.parameters.each{|var, value| new_run.set(var,value)} if @runner.parameters
|
128
127
|
# ep @runner.parameters
|
@@ -141,38 +140,24 @@ class CodeRunner
|
|
141
140
|
# run.
|
142
141
|
FileUtils.cp("#@directory/#@run_name.#{ext}", "#{new_run.directory}/.")
|
143
142
|
end
|
144
|
-
if new_run.
|
143
|
+
if (new_run.flux_gs2? and flux_gs2?) and not new_run.no_restart_gs2
|
145
144
|
for i in 0...n_flux_tubes
|
146
145
|
break if i >= new_run.n_flux_tubes
|
147
|
-
|
148
|
-
|
149
|
-
|
150
|
-
|
151
|
-
|
152
|
-
#jn = i + 1
|
153
|
-
##run_name = @run_name + (jn).to_s
|
154
|
-
#folder = "flux_tube_#{jn}"
|
155
|
-
#end
|
156
|
-
#
|
157
|
-
folder = gs2_folder_name(i)
|
158
|
-
|
159
|
-
new_run.gs2_runs[i].directory = new_run.directory + "/#{folder}"
|
160
|
-
FileUtils.makedirs(new_run.gs2_runs[i].directory)
|
161
|
-
#ep ['gs2_runs[i] before', gs2_runs[i].nwrite, new_run.gs2_runs[i].nwrite, new_run.gs2_runs[i].parameter_hash]
|
162
|
-
gs2_runs[i].restart(new_run.gs2_runs[i])
|
146
|
+
folder = flux_folder_name(i)
|
147
|
+
|
148
|
+
new_run.flux_runs[i].directory = new_run.directory + "/#{folder}"
|
149
|
+
FileUtils.makedirs(new_run.flux_runs[i].directory)
|
150
|
+
flux_runs[i].restart(new_run.flux_runs[i])
|
163
151
|
if new_run.neval_calibrate and new_run.neval_calibrate > 0 and
|
164
|
-
new_run.
|
152
|
+
new_run.flux_runs[i].nonlinear_mode == "off"
|
165
153
|
|
166
|
-
new_run.
|
167
|
-
new_run.
|
168
|
-
new_run.
|
169
|
-
new_run.
|
154
|
+
new_run.flux_runs[i].ginit_option = "noise"
|
155
|
+
new_run.flux_runs[i].delt_option = "default"
|
156
|
+
new_run.flux_runs[i].is_a_restart = false
|
157
|
+
new_run.flux_runs[i].restart_id = nil
|
170
158
|
end
|
171
|
-
#ep ['gs2_runs[i] after', gs2_runs[i].nwrite, new_run.gs2_runs[i].nwrite, new_run.gs2_runs[i].parameter_hash]
|
172
|
-
#new_run.gs2_runs[i].run_name = new_run.run_name + (i+1).to_s
|
173
159
|
end
|
174
160
|
end
|
175
|
-
#@runner.submit(new_run)
|
176
161
|
new_run
|
177
162
|
end
|
178
163
|
# This is a hook which gets called just before submitting a simulation. It sets up the folder and generates any necessary input files.
|
@@ -184,7 +169,7 @@ class CodeRunner
|
|
184
169
|
setup_chease if uses_chease?
|
185
170
|
check_parameters
|
186
171
|
write_input_file
|
187
|
-
|
172
|
+
generate_flux_input_files if flux_gs2? or flux_gryfx?
|
188
173
|
end
|
189
174
|
|
190
175
|
|
@@ -198,10 +183,10 @@ class CodeRunner
|
|
198
183
|
def update_submission_parameters(parameters, start_from_defaults=true)
|
199
184
|
@set_flux_defaults_procs ||= []
|
200
185
|
super(parameters, start_from_defaults)
|
201
|
-
if
|
186
|
+
if flux_gs2? or flux_gryfx?
|
202
187
|
raise "No set_flux_defaults_procs defined" unless @set_flux_defaults_procs.size > 0
|
203
188
|
@set_flux_defaults_procs.each{|prc| prc.call}
|
204
|
-
|
189
|
+
flux_parameter_hashes = {}
|
205
190
|
if @flux_pars
|
206
191
|
@flux_pars.each do |par, val|
|
207
192
|
if val.kind_of? Hash
|
@@ -215,8 +200,8 @@ class CodeRunner
|
|
215
200
|
range = n..n
|
216
201
|
end
|
217
202
|
for i in range
|
218
|
-
|
219
|
-
|
203
|
+
flux_parameter_hashes[i] ||= {}
|
204
|
+
flux_parameter_hashes[i][par] = v
|
220
205
|
end
|
221
206
|
#gs2_parameter_hashes[n] ||= {}
|
222
207
|
#gs2_parameter_hashes[n][par] = v
|
@@ -224,15 +209,15 @@ class CodeRunner
|
|
224
209
|
else
|
225
210
|
for i in 0...n_flux_tubes
|
226
211
|
#gs2_runs.each{|r| r.set(par, val)}
|
227
|
-
|
228
|
-
|
212
|
+
flux_parameter_hashes[i] ||= {}
|
213
|
+
flux_parameter_hashes[i][par] = val
|
229
214
|
end
|
230
215
|
end
|
231
216
|
end
|
232
217
|
end
|
233
218
|
for i in 0...n_flux_tubes
|
234
|
-
|
235
|
-
|
219
|
+
flux_runs[i].parameter_hash = (flux_parameter_hashes[i] || {}).inspect
|
220
|
+
flux_runs[i].update_submission_parameters(flux_runs[i].parameter_hash, false)
|
236
221
|
end
|
237
222
|
end
|
238
223
|
self
|
@@ -286,14 +271,14 @@ class CodeRunner
|
|
286
271
|
|
287
272
|
# Writes the gs2 input files, creating separate subfolders
|
288
273
|
# for them if @subfolders is .true.
|
289
|
-
def
|
274
|
+
def generate_flux_input_files
|
290
275
|
# At the moment we must use subfolders
|
291
276
|
for i in 0...n_flux_tubes
|
292
277
|
#gs2run = gs2_run(:base).dup
|
293
278
|
#gs2_run(i).instance_variables.each do |var|
|
294
279
|
#gs2run.instance_variable_set(var, gs2_run(i).instance_variable_get(var))
|
295
280
|
#end
|
296
|
-
|
281
|
+
fluxrun = flux_runs[i]
|
297
282
|
#ep ['gs2_runs[i] in generate', gs2_runs[i].nwrite]
|
298
283
|
#p ['i',i]
|
299
284
|
#if i >= n_flux_tubes_jac
|
@@ -306,20 +291,20 @@ class CodeRunner
|
|
306
291
|
#folder = "flux_tube_#{jn}"
|
307
292
|
#end
|
308
293
|
|
309
|
-
folder =
|
310
|
-
run_name =
|
294
|
+
folder = flux_folder_name(i)
|
295
|
+
run_name = flux_run_name(i)
|
311
296
|
|
312
297
|
if @subfolders and @subfolders.fortran_true?
|
313
|
-
|
314
|
-
FileUtils.makedirs(
|
315
|
-
|
316
|
-
|
298
|
+
fluxrun.directory = @directory + "/" + folder
|
299
|
+
FileUtils.makedirs(fluxrun.directory)
|
300
|
+
fluxrun.relative_directory = @relative_directory + "/" + folder
|
301
|
+
fluxrun.restart_dir = fluxrun.directory + "/nc"
|
317
302
|
else
|
318
|
-
|
319
|
-
|
303
|
+
fluxrun.directory = @directory
|
304
|
+
fluxrun.relative_directory = @relative_directory
|
320
305
|
end
|
321
|
-
|
322
|
-
|
306
|
+
fluxrun.run_name = run_name
|
307
|
+
fluxrun.nprocs = @nprocs
|
323
308
|
if i==0
|
324
309
|
block = Proc.new{check_parameters}
|
325
310
|
else
|
@@ -327,15 +312,15 @@ class CodeRunner
|
|
327
312
|
end
|
328
313
|
#if @restart_id
|
329
314
|
#gs2run.restart_id =
|
330
|
-
Dir.chdir(
|
331
|
-
|
332
|
-
|
315
|
+
Dir.chdir(fluxrun.directory) do
|
316
|
+
fluxrun.generate_input_file(&block)
|
317
|
+
fluxrun.write_info
|
333
318
|
end
|
334
319
|
|
335
320
|
### Hack the input file so that gs2 gets the location of
|
336
321
|
# the restart dir correctly within trinity
|
337
|
-
if @subfolders and @subfolders.fortran_true?
|
338
|
-
infile =
|
322
|
+
if @subfolders and @subfolders.fortran_true?
|
323
|
+
infile = fluxrun.directory + "/" + fluxrun.run_name + ".in"
|
339
324
|
text = File.read(infile)
|
340
325
|
File.open(infile, 'w'){|f| f.puts text.sub(/restart_dir\s*=\s*"nc"/, "restart_dir = \"#{folder}/nc\"")}
|
341
326
|
end
|
@@ -377,11 +362,8 @@ class CodeRunner
|
|
377
362
|
def generate_component_runs
|
378
363
|
#puts "HERE"
|
379
364
|
@component_runs ||= []
|
380
|
-
if
|
381
|
-
|
382
|
-
#puts "generate_component_runs", @component_runs.size, @runner.run_list.size, caller.to_a.slice(0..9)
|
383
|
-
#puts @component_runs[1].ginit_option if @component_runs.size > 0
|
384
|
-
#STDIN.gets
|
365
|
+
if flux_gryfx? or flux_gs2?
|
366
|
+
fclass = flux_class
|
385
367
|
|
386
368
|
for i in 0...n_flux_tubes
|
387
369
|
component = @component_runs[i]
|
@@ -389,7 +371,7 @@ class CodeRunner
|
|
389
371
|
if not component
|
390
372
|
#p "HEELO"
|
391
373
|
#p [i, '3,', component, '4', @component_runs.size]
|
392
|
-
component = @component_runs[i] =
|
374
|
+
component = @component_runs[i] = fclass.new(@runner, self).create_component
|
393
375
|
#component.instance_variable_set(:@output_file, output_file)
|
394
376
|
#p [i, '3,', component, '4', @component_runs.size]
|
395
377
|
if false
|
@@ -417,7 +399,7 @@ class CodeRunner
|
|
417
399
|
#component.status = @status
|
418
400
|
#p ["HERE2", @component_runs.size, @component_runs[i]]
|
419
401
|
#Dir.chdir(@directory) {
|
420
|
-
compdir =
|
402
|
+
compdir = flux_folder_name(i) # "flux_tube_#{i+1}"
|
421
403
|
Dir.chdir(compdir){component.process_directory} if FileTest.exist? compdir
|
422
404
|
#}
|
423
405
|
component.component_runs = []
|
@@ -435,27 +417,6 @@ class CodeRunner
|
|
435
417
|
end
|
436
418
|
|
437
419
|
|
438
|
-
def save
|
439
|
-
#@gs2_run_list.values.each{|r| r.runner = nil; r.component_runs = []} if @gs2_run_list.kind_of? Hash
|
440
|
-
super
|
441
|
-
#@gs2_run_list.values.each{|r| r.runner = @runner} if @gs2_run_list.kind_of? Hash
|
442
|
-
|
443
|
-
#logf(:save)
|
444
|
-
#raise CRFatal.new("Something has gone horribly wrong: runner.class is #{@runner.class} instead of CodeRunner") unless @runner.class.to_s == "CodeRunner"
|
445
|
-
#runner, @runner = @runner, nil
|
446
|
-
#@system_triers, old_triers = nil, @system_triers
|
447
|
-
#@component_runs.each{|run| run.runner = nil; run.component_runs = []} if @component_runs
|
448
|
-
##@component_runs.each{|run| run.runner = nil} if @component_runs
|
449
|
-
## logi(self)
|
450
|
-
##pp self
|
451
|
-
##@component_runs.each{|ph| ph.instance_variables.each{|var| puts var; pp ph.instance_variable_get(var); STDIN.gets; puts ph.Marshal.dump(instance_variable_get(var))}} if @component_runs
|
452
|
-
##instance_variables.each{|var| puts var; instance_variable_get(var); puts Marshal.dump(instance_variable_get(var)); STDIN.gets}
|
453
|
-
#Dir.chdir(@directory){File.open(".code_runner_run_data", 'w'){|file| file.puts Marshal.dump(self)}}
|
454
|
-
#@runner = runner
|
455
|
-
#@component_runs.each{|run| run.runner = runner} if @component_runs
|
456
|
-
#@system_triers = old_triers
|
457
|
-
end
|
458
|
-
|
459
420
|
@source_code_subfolders = []
|
460
421
|
|
461
422
|
# 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).
|
@@ -7,8 +7,8 @@
|
|
7
7
|
#end
|
8
8
|
#end
|
9
9
|
class CodeRunner
|
10
|
-
class
|
11
|
-
|
10
|
+
class Trinity
|
11
|
+
module TrinityComponent
|
12
12
|
attr_accessor :trinity_run
|
13
13
|
def initialize(runner, trinity_run)
|
14
14
|
super(runner)
|
@@ -40,30 +40,37 @@ class CodeRunner
|
|
40
40
|
@trinity_run = trinrun
|
41
41
|
end
|
42
42
|
end
|
43
|
-
|
44
|
-
|
43
|
+
|
44
|
+
class TrinityComponent::Gs2 < CodeRunner::Gs2
|
45
|
+
include TrinityComponent
|
46
|
+
end
|
47
|
+
|
48
|
+
class TrinityComponent::Gryfx < CodeRunner::Gryfx
|
49
|
+
include TrinityComponent
|
50
|
+
end
|
45
51
|
|
46
52
|
# This function creates a new Trinity defaults file, with Trinity parameters taken from
|
47
53
|
# trinity_input_file, and GS2 parameters taken from gs2_input_file. The file is then moved
|
48
54
|
# to the CodeRunner central defaults location, the current folder is configured to use
|
49
55
|
# the defaults file.
|
50
|
-
def self.
|
51
|
-
raise "Please specify a name, a trinity input file and a
|
56
|
+
def self.use_new_defaults_file_with_flux(name = ARGV[-4], trinity_input_file = ARGV[-3], flux_input_file = ARGV[-2], fluxcode=ARGV[-1])
|
57
|
+
raise "Please specify a name, a trinity input file and a flux code input file" if name == "use_new_defaults_file_with_flux"
|
52
58
|
defaults_filename = "#{name}_defaults.rb"
|
53
|
-
tmp_filename = "#{name}
|
59
|
+
tmp_filename = "#{name}_flxtmp_defaults.rb"
|
54
60
|
central_defaults_filename = rcp.user_defaults_location + "/" + defaults_filename
|
55
|
-
FileUtils.rm(name + '_defaults.rb') if FileTest.exist?(name + '_defaults.rb')
|
56
|
-
FileUtils.rm(central_defaults_filename) if FileTest.exist?(central_defaults_filename)
|
61
|
+
#FileUtils.rm(name + '_defaults.rb') if FileTest.exist?(name + '_defaults.rb')
|
62
|
+
#FileUtils.rm(central_defaults_filename) if FileTest.exist?(central_defaults_filename)
|
57
63
|
FileUtils.rm(tmp_filename) if FileTest.exist?(tmp_filename)
|
58
64
|
raise "Defaults file: #{central_defaults_filename} already exists" if FileTest.exist? central_defaults_filename
|
59
65
|
|
66
|
+
flxclass = flux_class(fluxcode)
|
60
67
|
|
61
68
|
make_new_defaults_file(name, trinity_input_file)
|
62
|
-
|
69
|
+
flxclass.make_new_defaults_file(name + '_flxtmp', flux_input_file)
|
63
70
|
|
64
71
|
File.open(defaults_filename, 'a'){|file| file.puts <<EOF2
|
65
72
|
@set_flux_defaults_procs.push(Proc.new do
|
66
|
-
|
73
|
+
flux_runs.each do |run|
|
67
74
|
run.instance_eval do
|
68
75
|
#{File.read(tmp_filename).gsub(/\A|\n/, "\n ")}
|
69
76
|
end
|
@@ -82,8 +89,9 @@ EOF2
|
|
82
89
|
|
83
90
|
# Generates the component runs for GS2 and returns the hash
|
84
91
|
# Raises an error if flux_option != "gs2"
|
85
|
-
def
|
86
|
-
raise FluxOptionError.new("
|
92
|
+
def flux_runs
|
93
|
+
raise FluxOptionError.new("flux_runs called and flux_option != gs2 or gryfx") if not flux_gs2? or flux_gryfx?
|
94
|
+
|
87
95
|
|
88
96
|
#puts "2@COMMMMMMMMMMMMMPOOOOOOOOOOOOOONNNETN", @component_runs
|
89
97
|
generate_component_runs if not (@component_runs and @component_runs.size == n_flux_tubes)
|
@@ -99,14 +107,14 @@ EOF2
|
|
99
107
|
#@gs2_run_list[key]
|
100
108
|
end
|
101
109
|
|
102
|
-
# Override standard CodeRunner method to allow for
|
110
|
+
# Override standard CodeRunner method to allow for flux code variables
|
103
111
|
def evaluate_defaults_file(filename)
|
104
112
|
text = File.read(filename)
|
105
113
|
instance_eval(text)
|
106
114
|
text.scan(/^\s*@(\w+)/) do
|
107
115
|
var_name = $~[1].to_sym
|
108
116
|
next if var_name == :defaults_file_description
|
109
|
-
unless rcp.variables.include? var_name or (flux_gs2? and Gs2.rcp.variables.include? var_name)
|
117
|
+
unless rcp.variables.include? var_name or (flux_gs2? and Gs2.rcp.variables.include? var_name) or (flux_gryfx? and Gryfx.rcp.variables.include? var_name)
|
110
118
|
warning("---#{var_name}---, specified in #{File.expand_path(filename)}, is not a variable. This could be an error")
|
111
119
|
end
|
112
120
|
end
|
@@ -123,12 +131,27 @@ EOF2
|
|
123
131
|
|
124
132
|
end
|
125
133
|
|
134
|
+
def self.flux_class(code)
|
135
|
+
case code
|
136
|
+
when "gs2"
|
137
|
+
CodeRunner::Trinity::TrinityComponent::Gs2
|
138
|
+
when "gryfx"
|
139
|
+
CodeRunner::Trinity::TrinityComponent::Gryfx
|
140
|
+
end
|
141
|
+
end
|
142
|
+
def flux_class
|
143
|
+
self.class.flux_class(@flux_option)
|
144
|
+
end
|
126
145
|
# Is the flux tube code being used gs2?
|
127
146
|
def flux_gs2?
|
128
147
|
@flux_option == "gs2"
|
129
148
|
end
|
149
|
+
# Is the flux tube code being used gryfx?
|
150
|
+
def flux_gryfx?
|
151
|
+
@flux_option == "gryfx"
|
152
|
+
end
|
130
153
|
|
131
|
-
def
|
154
|
+
def flux_run_name(i)
|
132
155
|
if i >= n_flux_tubes_jac
|
133
156
|
jn = i - n_flux_tubes_jac + 1
|
134
157
|
run_name = "calibrate_" + @run_name + (jn).to_s
|
@@ -138,7 +161,7 @@ EOF2
|
|
138
161
|
end
|
139
162
|
run_name
|
140
163
|
end
|
141
|
-
def
|
164
|
+
def flux_folder_name(i)
|
142
165
|
if i >= n_flux_tubes_jac
|
143
166
|
jn = i - n_flux_tubes_jac + 1
|
144
167
|
folder = "calibrate_#{jn}"
|
data/trinitycrmod.gemspec
CHANGED
@@ -2,11 +2,11 @@
|
|
2
2
|
# DO NOT EDIT THIS FILE DIRECTLY
|
3
3
|
# Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
|
4
4
|
# -*- encoding: utf-8 -*-
|
5
|
-
# stub: trinitycrmod 0.7.
|
5
|
+
# stub: trinitycrmod 0.7.4 ruby lib
|
6
6
|
|
7
7
|
Gem::Specification.new do |s|
|
8
8
|
s.name = "trinitycrmod"
|
9
|
-
s.version = "0.7.
|
9
|
+
s.version = "0.7.4"
|
10
10
|
|
11
11
|
s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
|
12
12
|
s.require_paths = ["lib"]
|
@@ -54,6 +54,7 @@ Gem::Specification.new do |s|
|
|
54
54
|
s.add_runtime_dependency(%q<coderunner>, [">= 0.16.10"])
|
55
55
|
s.add_runtime_dependency(%q<text-data-tools>, [">= 1.1.6"])
|
56
56
|
s.add_runtime_dependency(%q<gs2crmod>, [">= 0.11.76"])
|
57
|
+
s.add_runtime_dependency(%q<gryfxcrmod>, [">= 0.1.9"])
|
57
58
|
s.add_development_dependency(%q<shoulda>, [">= 0"])
|
58
59
|
s.add_development_dependency(%q<rdoc>, ["~> 3.12"])
|
59
60
|
s.add_development_dependency(%q<bundler>, ["> 1.0.0"])
|
@@ -62,6 +63,7 @@ Gem::Specification.new do |s|
|
|
62
63
|
s.add_dependency(%q<coderunner>, [">= 0.16.10"])
|
63
64
|
s.add_dependency(%q<text-data-tools>, [">= 1.1.6"])
|
64
65
|
s.add_dependency(%q<gs2crmod>, [">= 0.11.76"])
|
66
|
+
s.add_dependency(%q<gryfxcrmod>, [">= 0.1.9"])
|
65
67
|
s.add_dependency(%q<shoulda>, [">= 0"])
|
66
68
|
s.add_dependency(%q<rdoc>, ["~> 3.12"])
|
67
69
|
s.add_dependency(%q<bundler>, ["> 1.0.0"])
|
@@ -71,6 +73,7 @@ Gem::Specification.new do |s|
|
|
71
73
|
s.add_dependency(%q<coderunner>, [">= 0.16.10"])
|
72
74
|
s.add_dependency(%q<text-data-tools>, [">= 1.1.6"])
|
73
75
|
s.add_dependency(%q<gs2crmod>, [">= 0.11.76"])
|
76
|
+
s.add_dependency(%q<gryfxcrmod>, [">= 0.1.9"])
|
74
77
|
s.add_dependency(%q<shoulda>, [">= 0"])
|
75
78
|
s.add_dependency(%q<rdoc>, ["~> 3.12"])
|
76
79
|
s.add_dependency(%q<bundler>, ["> 1.0.0"])
|
metadata
CHANGED
@@ -1,7 +1,7 @@
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
2
2
|
name: trinitycrmod
|
3
3
|
version: !ruby/object:Gem::Version
|
4
|
-
version: 0.7.
|
4
|
+
version: 0.7.4
|
5
5
|
platform: ruby
|
6
6
|
authors:
|
7
7
|
- Edmund Highcock
|
@@ -52,6 +52,20 @@ dependencies:
|
|
52
52
|
- - ">="
|
53
53
|
- !ruby/object:Gem::Version
|
54
54
|
version: 0.11.76
|
55
|
+
- !ruby/object:Gem::Dependency
|
56
|
+
name: gryfxcrmod
|
57
|
+
requirement: !ruby/object:Gem::Requirement
|
58
|
+
requirements:
|
59
|
+
- - ">="
|
60
|
+
- !ruby/object:Gem::Version
|
61
|
+
version: 0.1.9
|
62
|
+
type: :runtime
|
63
|
+
prerelease: false
|
64
|
+
version_requirements: !ruby/object:Gem::Requirement
|
65
|
+
requirements:
|
66
|
+
- - ">="
|
67
|
+
- !ruby/object:Gem::Version
|
68
|
+
version: 0.1.9
|
55
69
|
- !ruby/object:Gem::Dependency
|
56
70
|
name: shoulda
|
57
71
|
requirement: !ruby/object:Gem::Requirement
|