rbbt-util 5.44.0 → 6.0.3
Sign up to get free protection for your applications and to get access to all the features.
- checksums.yaml +4 -4
- data/bin/rbbt +67 -90
- data/etc/app.d/base.rb +3 -3
- data/etc/app.d/semaphores.rb +3 -3
- data/lib/rbbt/annotations/annotated_array.rb +207 -207
- data/lib/rbbt/annotations/refactor.rb +27 -0
- data/lib/rbbt/annotations/util.rb +282 -282
- data/lib/rbbt/annotations.rb +343 -320
- data/lib/rbbt/association/database.rb +200 -225
- data/lib/rbbt/association/index.rb +294 -291
- data/lib/rbbt/association/item.rb +227 -227
- data/lib/rbbt/association/open.rb +35 -34
- data/lib/rbbt/association/util.rb +0 -169
- data/lib/rbbt/association.rb +2 -4
- data/lib/rbbt/entity/identifiers.rb +119 -118
- data/lib/rbbt/entity/refactor.rb +12 -0
- data/lib/rbbt/entity.rb +319 -315
- data/lib/rbbt/hpc/batch.rb +72 -53
- data/lib/rbbt/hpc/lsf.rb +2 -2
- data/lib/rbbt/hpc/orchestrate/batches.rb +2 -2
- data/lib/rbbt/hpc/orchestrate/chains.rb +25 -5
- data/lib/rbbt/hpc/orchestrate/rules.rb +2 -2
- data/lib/rbbt/hpc/orchestrate.rb +19 -13
- data/lib/rbbt/hpc/slurm.rb +18 -18
- data/lib/rbbt/knowledge_base/entity.rb +13 -5
- data/lib/rbbt/knowledge_base/query.rb +2 -2
- data/lib/rbbt/knowledge_base/registry.rb +32 -31
- data/lib/rbbt/knowledge_base/traverse.rb +1 -1
- data/lib/rbbt/knowledge_base.rb +1 -1
- data/lib/rbbt/monitor.rb +36 -25
- data/lib/rbbt/persist/refactor.rb +166 -0
- data/lib/rbbt/persist/tsv/sharder.rb +1 -1
- data/lib/rbbt/persist/tsv/tokyocabinet.rb +105 -105
- data/lib/rbbt/persist/tsv.rb +187 -185
- data/lib/rbbt/persist.rb +556 -551
- data/lib/rbbt/refactor.rb +20 -0
- data/lib/rbbt/resource/path/refactor.rb +178 -0
- data/lib/rbbt/resource/path.rb +317 -497
- data/lib/rbbt/resource/util.rb +0 -48
- data/lib/rbbt/resource.rb +3 -390
- data/lib/rbbt/tsv/accessor.rb +2 -838
- data/lib/rbbt/tsv/attach.rb +303 -299
- data/lib/rbbt/tsv/change_id.rb +244 -245
- data/lib/rbbt/tsv/csv.rb +87 -85
- data/lib/rbbt/tsv/dumper.rb +2 -100
- data/lib/rbbt/tsv/excel.rb +26 -24
- data/lib/rbbt/tsv/field_index.rb +4 -1
- data/lib/rbbt/tsv/filter.rb +3 -2
- data/lib/rbbt/tsv/index.rb +2 -284
- data/lib/rbbt/tsv/manipulate.rb +750 -747
- data/lib/rbbt/tsv/marshal.rb +3 -3
- data/lib/rbbt/tsv/matrix.rb +2 -2
- data/lib/rbbt/tsv/parallel/through.rb +2 -1
- data/lib/rbbt/tsv/parallel/traverse.rb +783 -781
- data/lib/rbbt/tsv/parser.rb +678 -678
- data/lib/rbbt/tsv/refactor.rb +195 -0
- data/lib/rbbt/tsv/stream.rb +253 -251
- data/lib/rbbt/tsv/util.rb +420 -420
- data/lib/rbbt/tsv.rb +210 -208
- data/lib/rbbt/util/R/eval.rb +4 -4
- data/lib/rbbt/util/R/plot.rb +62 -166
- data/lib/rbbt/util/R.rb +21 -18
- data/lib/rbbt/util/cmd.rb +2 -318
- data/lib/rbbt/util/color.rb +269 -269
- data/lib/rbbt/util/colorize.rb +89 -89
- data/lib/rbbt/util/concurrency/processes/refactor.rb +22 -0
- data/lib/rbbt/util/concurrency/processes/worker.rb +2 -2
- data/lib/rbbt/util/concurrency/processes.rb +389 -386
- data/lib/rbbt/util/config.rb +169 -167
- data/lib/rbbt/util/iruby.rb +20 -0
- data/lib/rbbt/util/log/progress/report.rb +241 -241
- data/lib/rbbt/util/log/progress/util.rb +99 -99
- data/lib/rbbt/util/log/progress.rb +102 -102
- data/lib/rbbt/util/log/refactor.rb +49 -0
- data/lib/rbbt/util/log.rb +486 -532
- data/lib/rbbt/util/migrate.rb +1 -1
- data/lib/rbbt/util/misc/concurrent_stream.rb +248 -246
- data/lib/rbbt/util/misc/development.rb +12 -11
- data/lib/rbbt/util/misc/exceptions.rb +117 -112
- data/lib/rbbt/util/misc/format.rb +2 -230
- data/lib/rbbt/util/misc/indiferent_hash.rb +2 -107
- data/lib/rbbt/util/misc/inspect.rb +2 -476
- data/lib/rbbt/util/misc/lock.rb +109 -106
- data/lib/rbbt/util/misc/omics.rb +10 -1
- data/lib/rbbt/util/misc/pipes.rb +765 -793
- data/lib/rbbt/util/misc/refactor.rb +20 -0
- data/lib/rbbt/util/misc/ssw.rb +308 -0
- data/lib/rbbt/util/misc/system.rb +0 -15
- data/lib/rbbt/util/misc.rb +39 -20
- data/lib/rbbt/util/named_array/refactor.rb +4 -0
- data/lib/rbbt/util/named_array.rb +3 -220
- data/lib/rbbt/util/open/refactor.rb +7 -0
- data/lib/rbbt/util/open.rb +3 -857
- data/lib/rbbt/util/procpath.rb +6 -6
- data/lib/rbbt/util/python/paths.rb +27 -0
- data/lib/rbbt/util/python/run.rb +115 -0
- data/lib/rbbt/util/python/script.rb +110 -0
- data/lib/rbbt/util/python/util.rb +3 -3
- data/lib/rbbt/util/python.rb +22 -81
- data/lib/rbbt/util/semaphore.rb +152 -148
- data/lib/rbbt/util/simpleopt.rb +9 -8
- data/lib/rbbt/util/ssh/refactor.rb +19 -0
- data/lib/rbbt/util/ssh.rb +122 -118
- data/lib/rbbt/util/tar.rb +117 -115
- data/lib/rbbt/util/tmpfile.rb +69 -67
- data/lib/rbbt/util/version.rb +2 -0
- data/lib/rbbt/workflow/refactor/entity.rb +11 -0
- data/lib/rbbt/workflow/refactor/export.rb +66 -0
- data/lib/rbbt/workflow/refactor/inputs.rb +24 -0
- data/lib/rbbt/workflow/refactor/recursive.rb +64 -0
- data/lib/rbbt/workflow/refactor/task_info.rb +65 -0
- data/lib/rbbt/workflow/refactor.rb +153 -0
- data/lib/rbbt/workflow/remote_workflow/driver/ssh.rb +55 -32
- data/lib/rbbt/workflow/remote_workflow/remote_step/rest.rb +3 -1
- data/lib/rbbt/workflow/remote_workflow/remote_step/ssh.rb +14 -5
- data/lib/rbbt/workflow/remote_workflow/remote_step.rb +19 -7
- data/lib/rbbt/workflow/remote_workflow.rb +6 -1
- data/lib/rbbt/workflow/step/info.rb +2 -2
- data/lib/rbbt/workflow/step/run.rb +766 -766
- data/lib/rbbt/workflow/step/save_load_inputs.rb +254 -254
- data/lib/rbbt/workflow/step.rb +2 -362
- data/lib/rbbt/workflow/task.rb +118 -118
- data/lib/rbbt/workflow/usage.rb +289 -287
- data/lib/rbbt/workflow/util/archive.rb +6 -5
- data/lib/rbbt/workflow/util/data.rb +1 -1
- data/lib/rbbt/workflow/util/orchestrator.rb +249 -246
- data/lib/rbbt/workflow/util/trace.rb +79 -44
- data/lib/rbbt/workflow.rb +4 -882
- data/lib/rbbt-util.rb +21 -13
- data/lib/rbbt.rb +16 -3
- data/python/rbbt/__init__.py +19 -1
- data/share/Rlib/plot.R +37 -37
- data/share/Rlib/svg.R +22 -5
- data/share/install/software/lib/install_helpers +1 -1
- data/share/rbbt_commands/hpc/list +2 -3
- data/share/rbbt_commands/hpc/orchestrate +4 -4
- data/share/rbbt_commands/hpc/tail +2 -0
- data/share/rbbt_commands/hpc/task +10 -7
- data/share/rbbt_commands/lsf/list +2 -3
- data/share/rbbt_commands/lsf/orchestrate +4 -4
- data/share/rbbt_commands/lsf/tail +2 -0
- data/share/rbbt_commands/lsf/task +10 -7
- data/share/rbbt_commands/migrate +1 -1
- data/share/rbbt_commands/pbs/list +2 -3
- data/share/rbbt_commands/pbs/orchestrate +4 -4
- data/share/rbbt_commands/pbs/tail +2 -0
- data/share/rbbt_commands/pbs/task +10 -7
- data/share/rbbt_commands/resource/produce +8 -1
- data/share/rbbt_commands/slurm/list +2 -3
- data/share/rbbt_commands/slurm/orchestrate +4 -4
- data/share/rbbt_commands/slurm/tail +2 -0
- data/share/rbbt_commands/slurm/task +10 -7
- data/share/rbbt_commands/system/clean +5 -5
- data/share/rbbt_commands/system/status +5 -5
- data/share/rbbt_commands/tsv/get +2 -3
- data/share/rbbt_commands/tsv/info +10 -13
- data/share/rbbt_commands/tsv/keys +18 -14
- data/share/rbbt_commands/tsv/slice +2 -2
- data/share/rbbt_commands/tsv/transpose +6 -2
- data/share/rbbt_commands/workflow/info +20 -24
- data/share/rbbt_commands/workflow/list +1 -1
- data/share/rbbt_commands/workflow/prov +20 -13
- data/share/rbbt_commands/workflow/server +16 -1
- data/share/rbbt_commands/workflow/task +76 -71
- data/share/rbbt_commands/workflow/write_info +26 -9
- data/share/software/opt/ssw/ssw.c +861 -0
- data/share/software/opt/ssw/ssw.h +130 -0
- data/share/workflow_config.ru +3 -3
- metadata +42 -3
@@ -1,246 +1,249 @@
|
|
1
|
-
|
2
|
-
|
3
|
-
|
4
|
-
|
5
|
-
|
6
|
-
|
7
|
-
|
8
|
-
|
9
|
-
|
10
|
-
job.
|
11
|
-
|
12
|
-
|
13
|
-
|
14
|
-
workload
|
15
|
-
workload[job]
|
16
|
-
|
17
|
-
|
18
|
-
|
19
|
-
|
20
|
-
|
21
|
-
|
22
|
-
workload
|
23
|
-
workload[job]
|
24
|
-
|
25
|
-
|
26
|
-
|
27
|
-
|
28
|
-
|
29
|
-
|
30
|
-
|
31
|
-
|
32
|
-
|
33
|
-
|
34
|
-
|
35
|
-
|
36
|
-
|
37
|
-
|
38
|
-
|
39
|
-
|
40
|
-
|
41
|
-
|
42
|
-
|
43
|
-
|
44
|
-
|
45
|
-
|
46
|
-
|
47
|
-
|
48
|
-
job_rules
|
49
|
-
|
50
|
-
|
51
|
-
|
52
|
-
|
53
|
-
|
54
|
-
|
55
|
-
|
56
|
-
|
57
|
-
|
58
|
-
|
59
|
-
|
60
|
-
|
61
|
-
|
62
|
-
|
63
|
-
|
64
|
-
|
65
|
-
|
66
|
-
|
67
|
-
|
68
|
-
|
69
|
-
|
70
|
-
default_resources
|
71
|
-
|
72
|
-
default_resources
|
73
|
-
|
74
|
-
resources
|
75
|
-
|
76
|
-
|
77
|
-
|
78
|
-
|
79
|
-
|
80
|
-
|
81
|
-
|
82
|
-
|
83
|
-
|
84
|
-
|
85
|
-
|
86
|
-
|
87
|
-
|
88
|
-
|
89
|
-
|
90
|
-
|
91
|
-
|
92
|
-
|
93
|
-
|
94
|
-
|
95
|
-
|
96
|
-
|
97
|
-
|
98
|
-
|
99
|
-
|
100
|
-
|
101
|
-
|
102
|
-
|
103
|
-
candidates
|
104
|
-
|
105
|
-
|
106
|
-
|
107
|
-
|
108
|
-
|
109
|
-
|
110
|
-
|
111
|
-
|
112
|
-
|
113
|
-
|
114
|
-
|
115
|
-
|
116
|
-
@
|
117
|
-
@
|
118
|
-
|
119
|
-
|
120
|
-
|
121
|
-
|
122
|
-
|
123
|
-
|
124
|
-
|
125
|
-
|
126
|
-
|
127
|
-
|
128
|
-
|
129
|
-
|
130
|
-
|
131
|
-
|
132
|
-
|
133
|
-
|
134
|
-
|
135
|
-
|
136
|
-
|
137
|
-
|
138
|
-
|
139
|
-
|
140
|
-
|
141
|
-
|
142
|
-
|
143
|
-
|
144
|
-
|
145
|
-
|
146
|
-
|
147
|
-
|
148
|
-
|
149
|
-
|
150
|
-
|
151
|
-
|
152
|
-
|
153
|
-
|
154
|
-
|
155
|
-
|
156
|
-
|
157
|
-
|
158
|
-
|
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
|
-
|
191
|
-
|
192
|
-
|
193
|
-
|
194
|
-
|
195
|
-
|
196
|
-
|
197
|
-
|
198
|
-
|
199
|
-
|
200
|
-
|
201
|
-
|
202
|
-
|
203
|
-
candidates.
|
204
|
-
|
205
|
-
|
206
|
-
|
207
|
-
|
208
|
-
|
209
|
-
|
210
|
-
|
211
|
-
|
212
|
-
|
213
|
-
|
214
|
-
|
215
|
-
|
216
|
-
|
217
|
-
|
218
|
-
|
219
|
-
|
220
|
-
|
221
|
-
|
222
|
-
|
223
|
-
|
224
|
-
|
225
|
-
|
226
|
-
|
227
|
-
|
228
|
-
|
229
|
-
|
230
|
-
|
231
|
-
|
232
|
-
|
233
|
-
|
234
|
-
|
235
|
-
|
236
|
-
|
237
|
-
|
238
|
-
|
239
|
-
|
240
|
-
|
241
|
-
|
242
|
-
|
243
|
-
|
244
|
-
|
245
|
-
|
246
|
-
end
|
1
|
+
require_relative '../../refactor'
|
2
|
+
Rbbt.require_instead 'scout/workflow/deployment/orchestrator'
|
3
|
+
#require 'rbbt/workflow'
|
4
|
+
#
|
5
|
+
#module Workflow
|
6
|
+
# class Orchestrator
|
7
|
+
#
|
8
|
+
# def self.job_workload(job)
|
9
|
+
# workload = {job => []}
|
10
|
+
# return workload if job.done? && job.updated?
|
11
|
+
#
|
12
|
+
# job.dependencies.each do |dep|
|
13
|
+
# next if dep.done? && job.updated?
|
14
|
+
# workload.merge!(job_workload(dep))
|
15
|
+
# workload[job] += workload[dep]
|
16
|
+
# workload[job] << dep
|
17
|
+
# workload[job].uniq!
|
18
|
+
# end
|
19
|
+
#
|
20
|
+
# job.input_dependencies.each do |dep|
|
21
|
+
# next if dep.done? && job.updated?
|
22
|
+
# workload.merge!(job_workload(dep))
|
23
|
+
# workload[job] += workload[dep]
|
24
|
+
# workload[job] << dep
|
25
|
+
# workload[job].uniq!
|
26
|
+
# end
|
27
|
+
#
|
28
|
+
# workload
|
29
|
+
# end
|
30
|
+
#
|
31
|
+
# def self.workload(jobs)
|
32
|
+
# jobs.inject({}) do |acc,job|
|
33
|
+
# Orchestrator.job_workload(job).each do |j,d|
|
34
|
+
# acc[j] = d unless acc.keys.collect{|k| k.path }.include? j.path
|
35
|
+
# end
|
36
|
+
# acc
|
37
|
+
# end
|
38
|
+
# end
|
39
|
+
#
|
40
|
+
# def self.job_rules(rules, job)
|
41
|
+
# workflow = job.workflow.to_s
|
42
|
+
# task_name = job.task_name.to_s
|
43
|
+
# defaults = rules["defaults"] || {}
|
44
|
+
#
|
45
|
+
# return IndiferentHash.setup(defaults) unless rules[workflow]
|
46
|
+
# return IndiferentHash.setup(defaults) unless rules[workflow][task_name]
|
47
|
+
#
|
48
|
+
# job_rules = IndiferentHash.setup(rules[workflow][task_name])
|
49
|
+
# defaults.each{|k,v| job_rules[k] = v if job_rules[k].nil? } if defaults
|
50
|
+
# job_rules
|
51
|
+
# end
|
52
|
+
#
|
53
|
+
# def self.purge_duplicates(candidates)
|
54
|
+
# seen = Set.new
|
55
|
+
# candidates.select do |job|
|
56
|
+
# if seen.include? job.path
|
57
|
+
# false
|
58
|
+
# else
|
59
|
+
# seen << job.path
|
60
|
+
# true
|
61
|
+
# end
|
62
|
+
# end
|
63
|
+
# end
|
64
|
+
#
|
65
|
+
# def self.job_resources(rules, job)
|
66
|
+
# resources = (job_rules(rules, job) || {})["resources"] || {}
|
67
|
+
#
|
68
|
+
# IndiferentHash.setup(resources)
|
69
|
+
#
|
70
|
+
# default_resources = rules["default_resources"]
|
71
|
+
# default_resources ||= rules["defaults"]["resources"] if rules["defaults"]
|
72
|
+
# default_resources ||= {}
|
73
|
+
#
|
74
|
+
# default_resources.each{|k,v| resources[k] ||= v } if default_resources
|
75
|
+
#
|
76
|
+
# resources = {:cpus => 1} if resources.empty?
|
77
|
+
# resources
|
78
|
+
# end
|
79
|
+
#
|
80
|
+
# def self.sort_candidates(candidates, rules)
|
81
|
+
# seen = Set.new
|
82
|
+
# candidates.sort_by do |job|
|
83
|
+
# - job_resources(rules, job).values.inject(0){|acc,e| acc += e}
|
84
|
+
# end
|
85
|
+
# end
|
86
|
+
#
|
87
|
+
# def self.candidates(workload, rules)
|
88
|
+
# if rules.empty?
|
89
|
+
# candidates = workload.
|
90
|
+
# select{|k,v| v.empty? }.
|
91
|
+
# collect{|k,v| k }.
|
92
|
+
# reject{|k| k.done? }
|
93
|
+
# else
|
94
|
+
# candidates = workload. #select{|k,v| Orchestrator.job_rules(rules, k) }.
|
95
|
+
# select{|k,v| v.empty? }.
|
96
|
+
# collect{|k,v| k }.
|
97
|
+
# reject{|k| k.done? }
|
98
|
+
# end
|
99
|
+
#
|
100
|
+
# top_level = workload.keys - workload.values.flatten
|
101
|
+
#
|
102
|
+
# candidates = purge_duplicates candidates
|
103
|
+
# candidates = sort_candidates candidates, rules
|
104
|
+
#
|
105
|
+
# candidates
|
106
|
+
# end
|
107
|
+
#
|
108
|
+
# def self.process(*args)
|
109
|
+
# self.new.process(*args)
|
110
|
+
# end
|
111
|
+
#
|
112
|
+
# attr_accessor :available_resources, :resources_requested, :resources_used, :timer
|
113
|
+
#
|
114
|
+
# def initialize(timer = 5, available_resources = nil)
|
115
|
+
# available_resources = {:cpus => Etc.nprocessors } if available_resources.nil?
|
116
|
+
# @timer = timer
|
117
|
+
# @available_resources = IndiferentHash.setup(available_resources)
|
118
|
+
# @resources_requested = IndiferentHash.setup({})
|
119
|
+
# @resources_used = IndiferentHash.setup({})
|
120
|
+
# end
|
121
|
+
#
|
122
|
+
# def release_resources(job)
|
123
|
+
# if resources_used[job]
|
124
|
+
# Log.debug "Orchestrator releasing resouces from #{job.path}"
|
125
|
+
# resources_used[job].each do |resource,value|
|
126
|
+
# next if resource == 'size'
|
127
|
+
# resources_requested[resource] -= value.to_i
|
128
|
+
# end
|
129
|
+
# resources_used.delete job
|
130
|
+
# end
|
131
|
+
# end
|
132
|
+
#
|
133
|
+
# def check_resources(rules, job)
|
134
|
+
# resources = Orchestrator.job_resources(rules, job)
|
135
|
+
#
|
136
|
+
# limit_resources = resources.select{|resource,value| available_resources[resource] && ((resources_requested[resource] || 0) + value) > available_resources[resource] }.collect{|resource,v| resource }
|
137
|
+
# if limit_resources.any?
|
138
|
+
# Log.debug "Orchestrator waiting on #{job.path} due to #{limit_resources * ", "}"
|
139
|
+
# else
|
140
|
+
#
|
141
|
+
# resources_used[job] = resources
|
142
|
+
# resources.each do |resource,value|
|
143
|
+
# resources_requested[resource] ||= 0
|
144
|
+
# resources_requested[resource] += value.to_i
|
145
|
+
# end
|
146
|
+
# Log.low "Orchestrator producing #{job.path} with resources #{resources}"
|
147
|
+
#
|
148
|
+
# return yield
|
149
|
+
# end
|
150
|
+
# end
|
151
|
+
#
|
152
|
+
# def run_with_rules(rules, job)
|
153
|
+
# job_rules = Orchestrator.job_rules(rules, job)
|
154
|
+
#
|
155
|
+
# Rbbt::Config.with_config do
|
156
|
+
# job_rules[:config_keys].each do |config|
|
157
|
+
# Rbbt::Config.process_config config
|
158
|
+
# end if job_rules && job_rules[:config_keys]
|
159
|
+
#
|
160
|
+
# log = job_rules[:log] if job_rules
|
161
|
+
# log = Log.severity if log.nil?
|
162
|
+
# Log.with_severity log do
|
163
|
+
# #job.produce(false, :nowait)
|
164
|
+
# job.produce(with_fork: true)
|
165
|
+
# end
|
166
|
+
# end
|
167
|
+
# end
|
168
|
+
#
|
169
|
+
# def erase_job_dependencies(job, rules, all_jobs, top_level_jobs)
|
170
|
+
# job.dependencies.each do |dep|
|
171
|
+
# next if top_level_jobs.include? dep.path
|
172
|
+
# next unless Orchestrator.job_rules(rules, dep)["erase"].to_s == 'true'
|
173
|
+
#
|
174
|
+
# dep_path = dep.path
|
175
|
+
# parents = all_jobs.select do |parent|
|
176
|
+
# paths = parent.info[:dependencies].nil? ? parent.dependencies.collect{|d| d.path } : parent.info[:dependencies].collect{|d| d.last }
|
177
|
+
# paths.include? dep_path
|
178
|
+
# end
|
179
|
+
#
|
180
|
+
# next unless parents.reject{|parent| parent.done? }.empty?
|
181
|
+
#
|
182
|
+
# parents.each do |parent|
|
183
|
+
# Log.high "Erasing #{dep.path} from #{parent.path}"
|
184
|
+
# parent.archive_deps
|
185
|
+
# parent.copy_files_dir
|
186
|
+
# parent.dependencies = parent.dependencies - [dep]
|
187
|
+
# end
|
188
|
+
# dep.clean
|
189
|
+
# end
|
190
|
+
# end
|
191
|
+
#
|
192
|
+
# def process(rules, jobs = nil)
|
193
|
+
# jobs, rules = rules, {} if jobs.nil?
|
194
|
+
# jobs = [jobs] if Step === jobs
|
195
|
+
# begin
|
196
|
+
#
|
197
|
+
# workload = Orchestrator.workload(jobs)
|
198
|
+
# all_jobs = workload.keys
|
199
|
+
#
|
200
|
+
# top_level_jobs = jobs.collect{|job| job.path }
|
201
|
+
# while workload.any?
|
202
|
+
#
|
203
|
+
# candidates = resources_used.keys + Orchestrator.candidates(workload, rules)
|
204
|
+
# raise "No candidates and no running jobs" if candidates.empty?
|
205
|
+
#
|
206
|
+
# candidates.each do |job|
|
207
|
+
# case
|
208
|
+
# when (job.error? || job.aborted?)
|
209
|
+
# begin
|
210
|
+
# if job.recoverable_error?
|
211
|
+
# job.clean
|
212
|
+
# raise TryAgain
|
213
|
+
# else
|
214
|
+
# next
|
215
|
+
# end
|
216
|
+
# ensure
|
217
|
+
# Log.warn "Releases resources from failed job: #{job.path}"
|
218
|
+
# release_resources(job)
|
219
|
+
# end
|
220
|
+
# when job.done?
|
221
|
+
# Log.debug "Orchestrator done #{job.path}"
|
222
|
+
# release_resources(job)
|
223
|
+
# erase_job_dependencies(job, rules, all_jobs, top_level_jobs)
|
224
|
+
#
|
225
|
+
# when job.running?
|
226
|
+
# next
|
227
|
+
#
|
228
|
+
# else
|
229
|
+
# check_resources(rules, job) do
|
230
|
+
# run_with_rules(rules, job)
|
231
|
+
# end
|
232
|
+
# end
|
233
|
+
# end
|
234
|
+
#
|
235
|
+
# new_workload = {}
|
236
|
+
# workload.each do |k,v|
|
237
|
+
# next if k.done? || k.error? || k.aborted?
|
238
|
+
# #new_workload[k] = v.reject{|d| d.done? || ((d.error? || d.aborted?) && ! d.recoverable_error?)}
|
239
|
+
# new_workload[k] = v.reject{|d| d.done? || d.error? || d.aborted?}
|
240
|
+
# end
|
241
|
+
# workload = new_workload
|
242
|
+
# sleep timer
|
243
|
+
# end
|
244
|
+
# rescue TryAgain
|
245
|
+
# retry
|
246
|
+
# end
|
247
|
+
# end
|
248
|
+
# end
|
249
|
+
#end
|