ripe 0.0.2 → 0.0.3
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- checksums.yaml +4 -4
- data/Guardfile +5 -0
- data/bin/ripe +1 -1
- data/lib/ripe/controller.rb +2 -1
- data/lib/ripe/version.rb +1 -1
- data/lib/ripe/worker.rb +1 -119
- data/lib/ripe/worker_controller.rb +130 -0
- data/lib/ripe.rb +2 -2
- data/ripe.gemspec +2 -1
- data/spec/block_spec.rb +7 -0
- data/spec/spec_helper.rb +5 -3
- metadata +20 -2
checksums.yaml
CHANGED
@@ -1,7 +1,7 @@
|
|
1
1
|
---
|
2
2
|
SHA1:
|
3
|
-
metadata.gz:
|
4
|
-
data.tar.gz:
|
3
|
+
metadata.gz: f8c9495954bce6425a4043a52c79d40e8ea3945f
|
4
|
+
data.tar.gz: e8e3ab0a02addf1ac505aa8193e238d4eefd3020
|
5
5
|
SHA512:
|
6
|
-
metadata.gz:
|
7
|
-
data.tar.gz:
|
6
|
+
metadata.gz: c494c400af63cf21c2c55a8d87cb6688e9175a0b029a7c6c91a8f4cb6cecc906a1c72509268b97c30f9d291036a24ef558565387ff688419f5203b6b8022ce67
|
7
|
+
data.tar.gz: 2e2ae3f075bd43b9a9e575a509c1276a549c0283d7453575aaf99ea2365ddb25411ebb8cbf0a8affdb365a55e9f10913b6c36ea315b1e67c5bfa98a9cb4d18fb
|
data/Guardfile
ADDED
data/bin/ripe
CHANGED
data/lib/ripe/controller.rb
CHANGED
@@ -2,6 +2,7 @@ require 'active_record'
|
|
2
2
|
require 'fileutils'
|
3
3
|
require_relative 'block'
|
4
4
|
require_relative 'worker'
|
5
|
+
require_relative 'worker_controller'
|
5
6
|
require_relative 'worker_migration'
|
6
7
|
require_relative 'working_block'
|
7
8
|
require_relative 'liquid_block'
|
@@ -45,7 +46,7 @@ module Ripe
|
|
45
46
|
end
|
46
47
|
|
47
48
|
def prepare(samples, callback, vars = {})
|
48
|
-
|
49
|
+
WorkerController.instance.prepare(samples, callback, vars)
|
49
50
|
end
|
50
51
|
end
|
51
52
|
end
|
data/lib/ripe/version.rb
CHANGED
data/lib/ripe/worker.rb
CHANGED
@@ -30,126 +30,8 @@ module Ripe
|
|
30
30
|
FileUtils.rm_r dir if Dir.exists? dir
|
31
31
|
end
|
32
32
|
|
33
|
-
def self.prepare(samples, callback, vars = {})
|
34
|
-
vars = {
|
35
|
-
wd: Dir.pwd,
|
36
|
-
mode: :patch,
|
37
|
-
group_num: 1,
|
38
|
-
}.merge(vars)
|
39
|
-
|
40
|
-
return if ![:patch, :force, :depend].include? vars[:mode].to_sym
|
41
|
-
|
42
|
-
samples = samples.map do |sample|
|
43
|
-
block = callback.call(sample, vars).prune(vars[:mode].to_sym == :force,
|
44
|
-
vars[:mode].to_sym == :depend)
|
45
|
-
if block != nil
|
46
|
-
puts "Preparing sample #{sample}"
|
47
|
-
[sample, block]
|
48
|
-
else
|
49
|
-
puts "Nothing to do for sample #{sample}"
|
50
|
-
nil
|
51
|
-
end
|
52
|
-
end
|
53
|
-
samples = samples.compact
|
54
|
-
|
55
|
-
samples.each_slice(vars[:group_num].to_i).map do |worker_samples|
|
56
|
-
worker = Worker.create(handle: vars[:handle])
|
57
|
-
|
58
|
-
blocks = worker_samples.map do |sample, block|
|
59
|
-
# Preorder traversal of blocks -- assign incremental numbers starting from
|
60
|
-
# 1 to each node as it is being traversed.
|
61
|
-
post_var_assign = lambda do |subblock|
|
62
|
-
if subblock.blocks.length == 0
|
63
|
-
task = worker.tasks.create({
|
64
|
-
sample: sample,
|
65
|
-
block: subblock.id,
|
66
|
-
})
|
67
|
-
subblock.vars.merge!(log: task.log)
|
68
|
-
else
|
69
|
-
subblock.blocks.each(&post_var_assign)
|
70
|
-
end
|
71
|
-
end
|
72
|
-
|
73
|
-
post_var_assign.call(block)
|
74
|
-
block
|
75
|
-
end
|
76
|
-
|
77
|
-
vars = vars.merge({
|
78
|
-
name: worker.id,
|
79
|
-
stdout: worker.stdout,
|
80
|
-
stderr: worker.stderr,
|
81
|
-
command: SerialBlock.new(*blocks).command,
|
82
|
-
})
|
83
|
-
|
84
|
-
file = File.new(worker.sh, 'w')
|
85
|
-
file.puts LiquidBlock.new("#{PATH}/share/moab.sh", vars).command
|
86
|
-
file.close
|
87
|
-
|
88
|
-
worker.update({
|
89
|
-
status: :prepared,
|
90
|
-
ppn: vars[:ppn],
|
91
|
-
queue: vars[:queue],
|
92
|
-
walltime: vars[:walltime],
|
93
|
-
})
|
94
|
-
worker
|
95
|
-
end
|
96
|
-
end
|
97
|
-
|
98
33
|
def self.sync
|
99
|
-
|
100
|
-
lists = lists.map do |status, op|
|
101
|
-
showq = `showq -u $(whoami) #{op} | grep $(whoami)`.split("\n")
|
102
|
-
showq.map do |job|
|
103
|
-
{
|
104
|
-
moab_id: job[/^([0-9]+) /, 1],
|
105
|
-
time: job[/ ([0-9]{1,2}(\:[0-9]{2})+) /, 1],
|
106
|
-
status: status,
|
107
|
-
}
|
108
|
-
end
|
109
|
-
end
|
110
|
-
|
111
|
-
# Update status
|
112
|
-
lists = lists.inject(&:+).each do |job|
|
113
|
-
moab_id = job[:moab_id]
|
114
|
-
time = job[:time]
|
115
|
-
status = job[:status]
|
116
|
-
worker = Worker.find_by(moab_id: moab_id)
|
117
|
-
|
118
|
-
if worker
|
119
|
-
worker.update(time: time)
|
120
|
-
unless ['cancelled', status].include? worker.status
|
121
|
-
checkjob = `checkjob #{moab_id}`
|
122
|
-
worker.update({
|
123
|
-
host: checkjob[/Allocated Nodes:\n\[(.*):[0-9]+\]\n/, 1],
|
124
|
-
status: status, # Queued jobs that appear become either idle, blocked or active
|
125
|
-
})
|
126
|
-
end
|
127
|
-
end
|
128
|
-
end
|
129
|
-
|
130
|
-
# Mark workers that were previously in active, blocked or idle as completed
|
131
|
-
# if they cannot be found anymore.
|
132
|
-
jobs = lists.map { |job| job[:moab_id] }
|
133
|
-
Worker.where('status in (:statuses)',
|
134
|
-
:statuses => ['active', 'idle', 'blocked']).each do |worker|
|
135
|
-
if jobs.include? worker.moab_id
|
136
|
-
jobs.delete(worker.moab_id) # Remove from list
|
137
|
-
elsif (worker.status != 'cancelled')
|
138
|
-
if File.exists? worker.stdout
|
139
|
-
stdout = File.new(worker.stdout).readlines.join
|
140
|
-
else
|
141
|
-
stdout = ""
|
142
|
-
end
|
143
|
-
worker.update({
|
144
|
-
cpu_used: stdout[/Resources:[ \t]*cput=([0-9]{1,2}(\:[0-9]{2})+),/, 1],
|
145
|
-
exit_code: stdout[/Exit code:[ \t]*(.*)$/, 1],
|
146
|
-
host: stdout[/Nodes:[ \t]*(.*)$/, 1],
|
147
|
-
memory_used: stdout[/Resources:.*,mem=([0-9]*[a-zA-Z]*),/, 1],
|
148
|
-
time: stdout[/Resources:.*,walltime=([0-9]{1,2}(\:[0-9]{2})+)$/, 1],
|
149
|
-
status: :completed,
|
150
|
-
})
|
151
|
-
end
|
152
|
-
end
|
34
|
+
WorkerController.instance.sync
|
153
35
|
end
|
154
36
|
|
155
37
|
def start!
|
@@ -0,0 +1,130 @@
|
|
1
|
+
require 'singleton'
|
2
|
+
require_relative 'worker'
|
3
|
+
|
4
|
+
module Ripe
|
5
|
+
class WorkerController
|
6
|
+
include Singleton
|
7
|
+
|
8
|
+
def prepare(samples, callback, vars = {})
|
9
|
+
vars = {
|
10
|
+
wd: Dir.pwd,
|
11
|
+
mode: :patch,
|
12
|
+
group_num: 1,
|
13
|
+
}.merge(vars)
|
14
|
+
|
15
|
+
return if ![:patch, :force, :depend].include? vars[:mode].to_sym
|
16
|
+
|
17
|
+
samples = samples.map do |sample|
|
18
|
+
block = callback.call(sample, vars).prune(vars[:mode].to_sym == :force,
|
19
|
+
vars[:mode].to_sym == :depend)
|
20
|
+
if block != nil
|
21
|
+
puts "Preparing sample #{sample}"
|
22
|
+
[sample, block]
|
23
|
+
else
|
24
|
+
puts "Nothing to do for sample #{sample}"
|
25
|
+
nil
|
26
|
+
end
|
27
|
+
end
|
28
|
+
samples = samples.compact
|
29
|
+
|
30
|
+
samples.each_slice(vars[:group_num].to_i).map do |worker_samples|
|
31
|
+
worker = Worker.create(handle: vars[:handle])
|
32
|
+
|
33
|
+
blocks = worker_samples.map do |sample, block|
|
34
|
+
# Preorder traversal of blocks -- assign incremental numbers starting from
|
35
|
+
# 1 to each node as it is being traversed.
|
36
|
+
post_var_assign = lambda do |subblock|
|
37
|
+
if subblock.blocks.length == 0
|
38
|
+
task = worker.tasks.create({
|
39
|
+
sample: sample,
|
40
|
+
block: subblock.id,
|
41
|
+
})
|
42
|
+
subblock.vars.merge!(log: task.log)
|
43
|
+
else
|
44
|
+
subblock.blocks.each(&post_var_assign)
|
45
|
+
end
|
46
|
+
end
|
47
|
+
|
48
|
+
post_var_assign.call(block)
|
49
|
+
block
|
50
|
+
end
|
51
|
+
|
52
|
+
vars = vars.merge({
|
53
|
+
name: worker.id,
|
54
|
+
stdout: worker.stdout,
|
55
|
+
stderr: worker.stderr,
|
56
|
+
command: SerialBlock.new(*blocks).command,
|
57
|
+
})
|
58
|
+
|
59
|
+
file = File.new(worker.sh, 'w')
|
60
|
+
file.puts LiquidBlock.new("#{PATH}/share/moab.sh", vars).command
|
61
|
+
file.close
|
62
|
+
|
63
|
+
worker.update({
|
64
|
+
status: :prepared,
|
65
|
+
ppn: vars[:ppn],
|
66
|
+
queue: vars[:queue],
|
67
|
+
walltime: vars[:walltime],
|
68
|
+
})
|
69
|
+
worker
|
70
|
+
end
|
71
|
+
end
|
72
|
+
|
73
|
+
def sync
|
74
|
+
lists = {idle: '-i', blocked: '-b', active: '-r'}
|
75
|
+
lists = lists.map do |status, op|
|
76
|
+
showq = `showq -u $(whoami) #{op} | grep $(whoami)`.split("\n")
|
77
|
+
showq.map do |job|
|
78
|
+
{
|
79
|
+
moab_id: job[/^([0-9]+) /, 1],
|
80
|
+
time: job[/ ([0-9]{1,2}(\:[0-9]{2})+) /, 1],
|
81
|
+
status: status,
|
82
|
+
}
|
83
|
+
end
|
84
|
+
end
|
85
|
+
|
86
|
+
# Update status
|
87
|
+
lists = lists.inject(&:+).each do |job|
|
88
|
+
moab_id = job[:moab_id]
|
89
|
+
time = job[:time]
|
90
|
+
status = job[:status]
|
91
|
+
worker = Worker.find_by(moab_id: moab_id)
|
92
|
+
|
93
|
+
if worker
|
94
|
+
worker.update(time: time)
|
95
|
+
unless ['cancelled', status].include? worker.status
|
96
|
+
checkjob = `checkjob #{moab_id}`
|
97
|
+
worker.update({
|
98
|
+
host: checkjob[/Allocated Nodes:\n\[(.*):[0-9]+\]\n/, 1],
|
99
|
+
status: status, # Queued jobs that appear become either idle, blocked or active
|
100
|
+
})
|
101
|
+
end
|
102
|
+
end
|
103
|
+
end
|
104
|
+
|
105
|
+
# Mark workers that were previously in active, blocked or idle as completed
|
106
|
+
# if they cannot be found anymore.
|
107
|
+
jobs = lists.map { |job| job[:moab_id] }
|
108
|
+
Worker.where('status in (:statuses)',
|
109
|
+
:statuses => ['active', 'idle', 'blocked']).each do |worker|
|
110
|
+
if jobs.include? worker.moab_id
|
111
|
+
jobs.delete(worker.moab_id) # Remove from list
|
112
|
+
elsif (worker.status != 'cancelled')
|
113
|
+
if File.exists? worker.stdout
|
114
|
+
stdout = File.new(worker.stdout).readlines.join
|
115
|
+
else
|
116
|
+
stdout = ""
|
117
|
+
end
|
118
|
+
worker.update({
|
119
|
+
cpu_used: stdout[/Resources:[ \t]*cput=([0-9]{1,2}(\:[0-9]{2})+),/, 1],
|
120
|
+
exit_code: stdout[/Exit code:[ \t]*(.*)$/, 1],
|
121
|
+
host: stdout[/Nodes:[ \t]*(.*)$/, 1],
|
122
|
+
memory_used: stdout[/Resources:.*,mem=([0-9]*[a-zA-Z]*),/, 1],
|
123
|
+
time: stdout[/Resources:.*,walltime=([0-9]{1,2}(\:[0-9]{2})+)$/, 1],
|
124
|
+
status: :completed,
|
125
|
+
})
|
126
|
+
end
|
127
|
+
end
|
128
|
+
end
|
129
|
+
end
|
130
|
+
end
|
data/lib/ripe.rb
CHANGED
data/ripe.gemspec
CHANGED
@@ -1,7 +1,7 @@
|
|
1
1
|
# coding: utf-8
|
2
2
|
lib = File.expand_path('../lib', __FILE__)
|
3
3
|
$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
|
4
|
-
|
4
|
+
require_relative 'lib/ripe/version'
|
5
5
|
|
6
6
|
Gem::Specification.new do |spec|
|
7
7
|
spec.name = "ripe"
|
@@ -22,6 +22,7 @@ Gem::Specification.new do |spec|
|
|
22
22
|
spec.add_development_dependency "rake", "~> 10.0"
|
23
23
|
spec.add_development_dependency "rspec", "~> 3.2"
|
24
24
|
spec.add_development_dependency "rspec-nc", "~> 0.2"
|
25
|
+
spec.add_development_dependency "guard-rspec", "~> 4.5"
|
25
26
|
|
26
27
|
spec.add_runtime_dependency "activerecord", "~> 4.2"
|
27
28
|
spec.add_runtime_dependency "fileutils", "~> 0.7"
|
data/spec/block_spec.rb
ADDED
data/spec/spec_helper.rb
CHANGED
metadata
CHANGED
@@ -1,14 +1,14 @@
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
2
2
|
name: ripe
|
3
3
|
version: !ruby/object:Gem::Version
|
4
|
-
version: 0.0.
|
4
|
+
version: 0.0.3
|
5
5
|
platform: ruby
|
6
6
|
authors:
|
7
7
|
- Nicolas De Jay
|
8
8
|
autorequire:
|
9
9
|
bindir: bin
|
10
10
|
cert_chain: []
|
11
|
-
date: 2015-04-
|
11
|
+
date: 2015-04-30 00:00:00.000000000 Z
|
12
12
|
dependencies:
|
13
13
|
- !ruby/object:Gem::Dependency
|
14
14
|
name: bundler
|
@@ -66,6 +66,20 @@ dependencies:
|
|
66
66
|
- - "~>"
|
67
67
|
- !ruby/object:Gem::Version
|
68
68
|
version: '0.2'
|
69
|
+
- !ruby/object:Gem::Dependency
|
70
|
+
name: guard-rspec
|
71
|
+
requirement: !ruby/object:Gem::Requirement
|
72
|
+
requirements:
|
73
|
+
- - "~>"
|
74
|
+
- !ruby/object:Gem::Version
|
75
|
+
version: '4.5'
|
76
|
+
type: :development
|
77
|
+
prerelease: false
|
78
|
+
version_requirements: !ruby/object:Gem::Requirement
|
79
|
+
requirements:
|
80
|
+
- - "~>"
|
81
|
+
- !ruby/object:Gem::Version
|
82
|
+
version: '4.5'
|
69
83
|
- !ruby/object:Gem::Dependency
|
70
84
|
name: activerecord
|
71
85
|
requirement: !ruby/object:Gem::Requirement
|
@@ -190,6 +204,7 @@ files:
|
|
190
204
|
- ".ruby-version"
|
191
205
|
- ".travis.yml"
|
192
206
|
- Gemfile
|
207
|
+
- Guardfile
|
193
208
|
- LICENSE.txt
|
194
209
|
- README.md
|
195
210
|
- Rakefile
|
@@ -205,10 +220,12 @@ files:
|
|
205
220
|
- lib/ripe/task_migration.rb
|
206
221
|
- lib/ripe/version.rb
|
207
222
|
- lib/ripe/worker.rb
|
223
|
+
- lib/ripe/worker_controller.rb
|
208
224
|
- lib/ripe/worker_migration.rb
|
209
225
|
- lib/ripe/working_block.rb
|
210
226
|
- ripe.gemspec
|
211
227
|
- share/moab.sh
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228
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+
- spec/block_spec.rb
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212
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- spec/ripe_spec.rb
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- spec/spec_helper.rb
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homepage: https://github.com/ndejay/ripe
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@@ -236,5 +253,6 @@ signing_key:
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specification_version: 4
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summary: Abstraction layer between the MOAB/Torque stack and your pipeline.
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test_files:
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256
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+
- spec/block_spec.rb
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239
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- spec/ripe_spec.rb
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240
258
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- spec/spec_helper.rb
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