scout-gear 7.3.0 → 8.1.0
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- checksums.yaml +4 -4
- data/.vimproject +44 -16
- data/Rakefile +6 -1
- data/VERSION +1 -1
- data/bin/scout +21 -7
- data/doc/lib/scout/path.md +35 -0
- data/doc/lib/scout/workflow/task.md +13 -0
- data/lib/rbbt-scout.rb +1 -0
- data/lib/scout/cmd.rb +24 -25
- data/lib/scout/concurrent_stream.rb +59 -39
- data/lib/scout/config.rb +1 -1
- data/lib/scout/exceptions.rb +10 -0
- data/lib/scout/log/color.rb +15 -12
- data/lib/scout/log/progress/report.rb +8 -6
- data/lib/scout/log/progress/util.rb +61 -54
- data/lib/scout/log/progress.rb +1 -1
- data/lib/scout/log/trap.rb +107 -0
- data/lib/scout/log.rb +115 -52
- data/lib/scout/meta_extension.rb +47 -6
- data/lib/scout/misc/digest.rb +12 -3
- data/lib/scout/misc/format.rb +24 -7
- data/lib/scout/misc/insist.rb +1 -1
- data/lib/scout/misc/monitor.rb +22 -0
- data/lib/scout/misc/system.rb +58 -0
- data/lib/scout/named_array.rb +73 -3
- data/lib/scout/offsite/ssh.rb +171 -0
- data/lib/scout/offsite/step.rb +83 -0
- data/lib/scout/offsite/sync.rb +55 -0
- data/lib/scout/offsite.rb +3 -0
- data/lib/scout/open/lock/lockfile.rb +587 -0
- data/lib/scout/open/lock.rb +9 -2
- data/lib/scout/open/remote.rb +16 -1
- data/lib/scout/open/stream.rb +146 -83
- data/lib/scout/open/util.rb +22 -3
- data/lib/scout/open.rb +5 -4
- data/lib/scout/path/find.rb +24 -11
- data/lib/scout/path/util.rb +40 -0
- data/lib/scout/persist/serialize.rb +19 -6
- data/lib/scout/persist.rb +29 -13
- data/lib/scout/resource/path.rb +57 -0
- data/lib/scout/resource/produce.rb +0 -8
- data/lib/scout/resource/util.rb +12 -5
- data/lib/scout/tmpfile.rb +7 -8
- data/lib/scout/tsv/attach.rb +177 -0
- data/lib/scout/tsv/change_id.rb +40 -0
- data/lib/scout/tsv/dumper.rb +74 -46
- data/lib/scout/tsv/index.rb +85 -87
- data/lib/scout/tsv/open.rb +160 -85
- data/lib/scout/tsv/parser.rb +142 -80
- data/lib/scout/tsv/path.rb +1 -2
- data/lib/scout/tsv/persist/adapter.rb +15 -45
- data/lib/scout/tsv/persist/fix_width_table.rb +3 -0
- data/lib/scout/tsv/persist/tokyocabinet.rb +6 -1
- data/lib/scout/tsv/persist.rb +4 -0
- data/lib/scout/tsv/stream.rb +204 -0
- data/lib/scout/tsv/transformer.rb +152 -0
- data/lib/scout/tsv/traverse.rb +96 -92
- data/lib/scout/tsv/util/filter.rb +9 -0
- data/lib/scout/tsv/util/reorder.rb +81 -0
- data/lib/scout/tsv/util/select.rb +78 -33
- data/lib/scout/tsv/util/unzip.rb +86 -0
- data/lib/scout/tsv/util.rb +60 -11
- data/lib/scout/tsv.rb +34 -4
- data/lib/scout/work_queue/socket.rb +6 -1
- data/lib/scout/work_queue/worker.rb +5 -2
- data/lib/scout/work_queue.rb +51 -20
- data/lib/scout/workflow/definition.rb +23 -3
- data/lib/scout/workflow/deployment/orchestrator.rb +245 -0
- data/lib/scout/workflow/deployment.rb +1 -0
- data/lib/scout/workflow/step/dependencies.rb +56 -10
- data/lib/scout/workflow/step/file.rb +5 -0
- data/lib/scout/workflow/step/info.rb +40 -7
- data/lib/scout/workflow/step/load.rb +1 -1
- data/lib/scout/workflow/step/provenance.rb +9 -7
- data/lib/scout/workflow/step/status.rb +43 -0
- data/lib/scout/workflow/step.rb +160 -49
- data/lib/scout/workflow/task/dependencies.rb +114 -0
- data/lib/scout/workflow/task/inputs.rb +40 -32
- data/lib/scout/workflow/task.rb +38 -102
- data/lib/scout/workflow/usage.rb +48 -18
- data/lib/scout/workflow.rb +4 -2
- data/lib/scout-gear.rb +2 -0
- data/lib/scout.rb +6 -0
- data/scout-gear.gemspec +52 -23
- data/scout_commands/doc +37 -0
- data/scout_commands/find +1 -0
- data/scout_commands/offsite +30 -0
- data/scout_commands/update +29 -0
- data/scout_commands/workflow/info +15 -3
- data/scout_commands/workflow/install +102 -0
- data/scout_commands/workflow/task +57 -9
- data/test/scout/offsite/test_ssh.rb +15 -0
- data/test/scout/offsite/test_step.rb +33 -0
- data/test/scout/offsite/test_sync.rb +36 -0
- data/test/scout/offsite/test_task.rb +0 -0
- data/test/scout/open/test_stream.rb +60 -58
- data/test/scout/path/test_find.rb +10 -1
- data/test/scout/resource/test_path.rb +6 -0
- data/test/scout/resource/test_produce.rb +15 -0
- data/test/scout/test_meta_extension.rb +25 -0
- data/test/scout/test_named_array.rb +24 -0
- data/test/scout/test_persist.rb +9 -2
- data/test/scout/test_tsv.rb +229 -2
- data/test/scout/test_work_queue.rb +65 -41
- data/test/scout/tsv/persist/test_tokyocabinet.rb +29 -1
- data/test/scout/tsv/test_attach.rb +227 -0
- data/test/scout/tsv/test_change_id.rb +98 -0
- data/test/scout/tsv/test_dumper.rb +1 -1
- data/test/scout/tsv/test_index.rb +49 -3
- data/test/scout/tsv/test_open.rb +160 -2
- data/test/scout/tsv/test_parser.rb +33 -2
- data/test/scout/tsv/test_persist.rb +2 -0
- data/test/scout/tsv/test_stream.rb +200 -0
- data/test/scout/tsv/test_transformer.rb +120 -0
- data/test/scout/tsv/test_traverse.rb +88 -3
- data/test/scout/tsv/test_util.rb +1 -0
- data/test/scout/tsv/util/test_reorder.rb +94 -0
- data/test/scout/tsv/util/test_select.rb +25 -11
- data/test/scout/tsv/util/test_unzip.rb +112 -0
- data/test/scout/work_queue/test_socket.rb +0 -1
- data/test/scout/workflow/deployment/test_orchestrator.rb +272 -0
- data/test/scout/workflow/step/test_dependencies.rb +68 -0
- data/test/scout/workflow/step/test_info.rb +18 -0
- data/test/scout/workflow/step/test_status.rb +30 -0
- data/test/scout/workflow/task/test_dependencies.rb +355 -0
- data/test/scout/workflow/task/test_inputs.rb +67 -14
- data/test/scout/workflow/test_definition.rb +18 -0
- data/test/scout/workflow/test_documentation.rb +24 -0
- data/test/scout/workflow/test_step.rb +112 -3
- data/test/scout/workflow/test_task.rb +0 -151
- data/test/scout/workflow/test_usage.rb +33 -6
- data/test/test_scout.rb +9 -0
- metadata +100 -8
- data/scout_commands/workflow/task_old +0 -706
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require File.expand_path(__FILE__).sub(%r(/test/.*), '/test/test_helper.rb')
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require File.expand_path(__FILE__).sub(%r(.*/test/), '').sub(/test_(.*)\.rb/,'\1')
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class TestOrchestrator < Test::Unit::TestCase
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setup do
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module TestWF
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extend Workflow
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MULT = 0.01
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task :a => :text do
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sleep(TestWF::MULT * (rand(10) + 2))
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end
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dep :a
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task :b => :text do
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sleep(TestWF::MULT * (rand(10) + 2))
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end
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dep :a
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dep :b
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task :c => :text do
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sleep(TestWF::MULT * (rand(10) + 2))
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end
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dep :c
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task :d => :text do
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sleep(TestWF::MULT * (rand(10) + 2))
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end
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dep :c
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task :e => :text do
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sleep(TestWF::MULT * (rand(10) + 2))
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end
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end
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end
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def TODO_test_orchestrate_resources
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jobs =[]
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num = 10
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num.times do |i|
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jobs.concat %w(TEST1 TEST2).collect{|name| TestWF.job(:d, name + " #{i}") }
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end
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jobs.each do |j| j.recursive_clean end
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rules = YAML.load <<-EOF
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defaults:
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log: 4
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default_resources:
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IO: 1
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TestWF:
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a:
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resources:
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cpus: 7
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b:
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resources:
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cpus: 2
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c:
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resources:
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cpus: 10
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d:
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resources:
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cpus: 15
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EOF
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orchestrator = Workflow::Orchestrator.new(TestWF::MULT, "cpus" => 30, "IO" => 4, "size" => 10 )
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Log.with_severity 0 do
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orchestrator.process(rules, jobs)
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end
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data = Workflow.trace jobs, :plot_data => true
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eend = data.column("End.second").values.collect{|v| v.to_f}.max
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second_cpus = TSV.setup({}, "Second~CPUS#:type=:single#:cast=:to_f")
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(0..eend.to_i).each do |second|
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tasks = data.select("Start.second"){|s| s <= second}.select("End.second"){|s| s > second}
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cpus = 0
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tasks.through :key, ["Workflow", "Task"] do |k, values|
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workflow, task = values
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cpus += rules[workflow][task.to_s]["resources"]["cpus"]
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end
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second_cpus[second] = cpus
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end
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assert Misc.mean(second_cpus.values) > 15
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assert Misc.mean(second_cpus.values) < 30
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end
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def TODO_test_orchestrate_erase
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jobs =[]
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num = 10
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num.times do |i|
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jobs.concat %w(TEST1 TEST2).collect{|name| TestWF.job(:d, name + " #{i}") }
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end
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jobs.each do |j| j.recursive_clean end
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rules = YAML.load <<-EOF
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defaults:
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log: 4
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default_resources:
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IO: 1
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TestWF:
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a:
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erase: true
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resources:
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cpus: 7
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b:
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erase: true
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resources:
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cpus: 2
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c:
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resources:
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cpus: 10
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d:
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resources:
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cpus: 15
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EOF
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orchestrator = Workflow::Orchestrator.new(TestWF::MULT, "cpus" => 30, "IO" => 4, "size" => 10 )
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Log.with_severity 3 do
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orchestrator.process(rules, jobs)
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end
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jobs.each do |job|
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assert job.step(:c).dependencies.empty?
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assert job.step(:c).info[:archived_info].keys.select{|k| k.include?("TestWF/a/")}.any?
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assert job.step(:c).info[:archived_info].keys.select{|k| k.include?("TestWF/b/")}.any?
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end
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end
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def TODO_test_orchestrate_default
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jobs =[]
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num = 3
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num.times do |i|
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jobs.concat %w(TEST1 TEST2).collect{|name| TestWF.job(:d, name + " #{i}") }
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end
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jobs.each do |j| j.recursive_clean end
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rules = YAML.load <<-EOF
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defaults:
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erase: true
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log: 4
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default_resources:
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IO: 1
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TestWF:
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a:
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erase: true
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resources:
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cpus: 7
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b:
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erase: true
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resources:
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cpus: 2
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c:
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erase: false
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resources:
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cpus: 10
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d:
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resources:
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cpus: 15
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EOF
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orchestrator = Workflow::Orchestrator.new(TestWF::MULT, "cpus" => 30, "IO" => 4, "size" => 10 )
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Log.with_severity 3 do
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orchestrator.process(rules, jobs)
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end
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jobs.each do |job|
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assert job.step(:c).dependencies.empty?
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assert job.step(:c).info[:archived_info].keys.select{|k| k.include?("TestWF/a/")}.any?
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assert job.step(:c).info[:archived_info].keys.select{|k| k.include?("TestWF/b/")}.any?
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end
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end
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def TODO_test_orchestrate_top_level
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jobs =[]
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num = 3
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num.times do |i|
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jobs.concat %w(TEST1 TEST2).collect{|name| TestWF.job(:d, name + " #{i}") }
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jobs.concat %w(TEST1 TEST2).collect{|name| TestWF.job(:c, name + " #{i}") }
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end
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jobs.each do |j| j.recursive_clean end
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rules = YAML.load <<-EOF
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defaults:
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erase: true
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log: 4
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default_resources:
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IO: 1
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TestWF:
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a:
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resources:
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cpus: 7
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b:
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resources:
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cpus: 2
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c:
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resources:
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cpus: 10
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d:
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resources:
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cpus: 15
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EOF
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orchestrator = Workflow::Orchestrator.new(TestWF::MULT, "cpus" => 30, "IO" => 4, "size" => 10 )
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Log.with_severity 3 do
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orchestrator.process(rules, jobs)
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end
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jobs.each do |job|
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next unless job.task_name.to_s == 'd'
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assert job.step(:c).dependencies.empty?
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assert job.step(:c).info[:archived_info].keys.select{|k| k.include?("TestWF/a/")}.any?
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assert job.step(:c).info[:archived_info].keys.select{|k| k.include?("TestWF/b/")}.any?
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end
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end
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def TODO_test_orchestrate_top_level_double_dep
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jobs =[]
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num = 10
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num.times do |i|
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jobs.concat %w(TEST1 TEST2).collect{|name| TestWF.job(:e, name + " #{i}") }
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jobs.concat %w(TEST1 TEST2).collect{|name| TestWF.job(:d, name + " #{i}") }
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end
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jobs.each do |j| j.recursive_clean end
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rules = YAML.load <<-EOF
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defaults:
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erase: true
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log: 4
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default_resources:
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IO: 1
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TestWF:
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a:
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resources:
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cpus: 7
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b:
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resources:
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cpus: 2
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c:
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resources:
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cpus: 10
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d:
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resources:
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cpus: 15
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EOF
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orchestrator = Workflow::Orchestrator.new(TestWF::MULT, "cpus" => 30, "IO" => 4, "size" => 10 )
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Log.with_severity 3 do
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orchestrator.process(rules, jobs)
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end
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jobs.each do |job|
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next unless job.task_name.to_s == 'd' || job.task_name.to_s == 'e'
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+
assert job.info[:archived_info].keys.select{|k| k.include?("TestWF/c/")}.any?
|
267
|
+
assert job.info[:archived_info].keys.select{|k| k.include?("TestWF/c/")}.any?
|
268
|
+
end
|
269
|
+
|
270
|
+
end
|
271
|
+
end
|
272
|
+
|
@@ -21,5 +21,73 @@ class TestStepDependencies < Test::Unit::TestCase
|
|
21
21
|
assert_equal 2, step2.inputs[:input2]
|
22
22
|
assert_equal "12", step2.recursive_inputs[:input1]
|
23
23
|
end
|
24
|
+
|
25
|
+
def test_can_fail
|
26
|
+
tmpfile = tmpdir.test_step
|
27
|
+
step1 = Step.new tmpfile.step1, NamedArray.setup(["12"], %w(input1)) do |s|
|
28
|
+
raise ScoutException
|
29
|
+
end
|
30
|
+
|
31
|
+
step2 = Step.new tmpfile.step2, NamedArray.setup([2], %w(input2)) do |times|
|
32
|
+
step1 = dependencies.first
|
33
|
+
if step1.error?
|
34
|
+
(step1.inputs.first + " has unknown characters") * times
|
35
|
+
else
|
36
|
+
(step1.inputs.first + " has " + step1.load.to_s + " characters") * times
|
37
|
+
end
|
38
|
+
end
|
39
|
+
|
40
|
+
step2.dependencies = [step1]
|
41
|
+
step2.compute = {step1.path => [:canfail] }
|
42
|
+
|
43
|
+
assert_include step2.run, "unknown"
|
44
|
+
end
|
45
|
+
|
46
|
+
def test_can_stream
|
47
|
+
tmpfile = tmpdir.test_step
|
48
|
+
|
49
|
+
Misc.with_env "SCOUT_EXPLICIT_STREAMING", "true" do
|
50
|
+
times = 10_000
|
51
|
+
sleep = 1 / times
|
52
|
+
|
53
|
+
step1 = Step.new tmpfile.step1, [times, sleep] do |times,sleep|
|
54
|
+
Open.open_pipe do |sin|
|
55
|
+
times.times do |i|
|
56
|
+
sin.puts "line-#{i}"
|
57
|
+
sleep sleep
|
58
|
+
end
|
59
|
+
end
|
60
|
+
end
|
61
|
+
step1.type = :array
|
62
|
+
|
63
|
+
step2 = Step.new tmpfile.step2 do
|
64
|
+
step1 = dependencies.first
|
65
|
+
raise ScoutException unless step1.streaming?
|
66
|
+
stream = step1.stream
|
67
|
+
|
68
|
+
Open.open_pipe do |sin|
|
69
|
+
while line = stream.gets
|
70
|
+
num = line.split("-").last
|
71
|
+
next if num.to_i % 2 == 1
|
72
|
+
sin.puts line
|
73
|
+
end
|
74
|
+
end
|
75
|
+
end
|
76
|
+
step2.type = :array
|
77
|
+
step2.dependencies = [step1]
|
78
|
+
|
79
|
+
assert_raise ScoutException do
|
80
|
+
step2.run
|
81
|
+
end
|
82
|
+
|
83
|
+
step2.recursive_clean
|
84
|
+
|
85
|
+
step2.compute = {step1.path => [:stream]}
|
86
|
+
|
87
|
+
assert_nothing_raised do
|
88
|
+
step2.run
|
89
|
+
end
|
90
|
+
end
|
91
|
+
end
|
24
92
|
end
|
25
93
|
|
@@ -25,4 +25,22 @@ class TestStepInfo < Test::Unit::TestCase
|
|
25
25
|
assert_equal "12 has 2 characters", step2.run
|
26
26
|
end
|
27
27
|
end
|
28
|
+
|
29
|
+
def test_inputs_marshal
|
30
|
+
TmpFile.with_file do |tmpdir|
|
31
|
+
Path.setup(tmpdir)
|
32
|
+
tmpfile = tmpdir.test_step
|
33
|
+
|
34
|
+
path = tmpfile.foo
|
35
|
+
step1 = Step.new tmpfile.step1, [path] do |s|
|
36
|
+
s.length
|
37
|
+
end
|
38
|
+
|
39
|
+
step1.run
|
40
|
+
|
41
|
+
refute Path === step1.info[:inputs][0]
|
42
|
+
|
43
|
+
end
|
44
|
+
|
45
|
+
end
|
28
46
|
end
|
@@ -0,0 +1,30 @@
|
|
1
|
+
require File.expand_path(__FILE__).sub(%r(/test/.*), '/test/test_helper.rb')
|
2
|
+
require File.expand_path(__FILE__).sub(%r(.*/test/), '').sub(/test_(.*)\.rb/,'\1')
|
3
|
+
|
4
|
+
class TestStepStatus < Test::Unit::TestCase
|
5
|
+
def test_dependency
|
6
|
+
tmpfile = tmpdir.test_step
|
7
|
+
step1 = Step.new tmpfile.step1, ["12"] do |s|
|
8
|
+
s.length
|
9
|
+
end
|
10
|
+
|
11
|
+
step2 = Step.new tmpfile.step2 do
|
12
|
+
step1 = dependencies.first
|
13
|
+
step1.inputs.first + " has " + step1.load.to_s + " characters"
|
14
|
+
end
|
15
|
+
|
16
|
+
step2.dependencies = [step1]
|
17
|
+
|
18
|
+
Misc.with_env "SCOUT_UPDATE", "true" do
|
19
|
+
step2.run
|
20
|
+
assert step2.updated?
|
21
|
+
|
22
|
+
sleep 0.1
|
23
|
+
step1.clean
|
24
|
+
step1.run
|
25
|
+
refute step2.updated?
|
26
|
+
end
|
27
|
+
end
|
28
|
+
|
29
|
+
end
|
30
|
+
|