osc-machete 1.1.4 → 1.2.0
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- checksums.yaml +4 -4
- data/.gitignore +1 -0
- data/CHANGELOG.md +51 -1
- data/lib/osc/machete/job.rb +1 -1
- data/lib/osc/machete/process.rb +3 -0
- data/lib/osc/machete/status.rb +50 -29
- data/lib/osc/machete/torque_helper.rb +48 -59
- data/lib/osc/machete/user.rb +3 -0
- data/lib/osc/machete/version.rb +1 -1
- data/osc-machete.gemspec +2 -1
- data/test/test_job_dir.rb +1 -1
- data/test/test_location.rb +19 -19
- data/test/test_torque_helper.rb +74 -29
- data/test/test_torque_helper_live.rb +12 -11
- metadata +7 -8
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:
|
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: 02bb808f1fcf915c8b6c5cbe38b00e692e021b03
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4
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+
data.tar.gz: dbed1c7b521247a391709633bb67a8e87dd37d93
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5
5
|
SHA512:
|
6
|
-
metadata.gz:
|
7
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-
data.tar.gz:
|
6
|
+
metadata.gz: 84d14aa284eeac069213601ccd58ef5e8ebbdcc533c20cc1b2c646f339bbcf25815c77093099f3e06ea44755f27b10808b14f8beda4d80a4585cb5a6795e6e7e
|
7
|
+
data.tar.gz: 67295194bd75c9cf59a6cdc077025e199051bb7144b8de17650cdb002ec095e9a2a199fb1786328a266ad584370ad1a0daa5825197db68cd9e34683c49fe714e
|
data/.gitignore
CHANGED
data/CHANGELOG.md
CHANGED
@@ -5,6 +5,52 @@ This project adheres to [Semantic Versioning](http://semver.org/).
|
|
5
5
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|
6
6
|
## [Unreleased]
|
7
7
|
|
8
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+
## [1.2.0] - 2016-09-06
|
9
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+
|
10
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+
### Added
|
11
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+
|
12
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+
- TorqueHelper.default= so we can specify a different TorqueHelper
|
13
|
+
- TorqueHelper#pbs to get the PBS::Batch object for the given id, script, or host.
|
14
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+
This lets us change the TorqueHelper instance used as a default with a
|
15
|
+
different TorqueHelper class or instance that has a different implementation
|
16
|
+
of TorqueHelper#pbs.
|
17
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+
- (OSC specific) Owens cluster support
|
18
|
+
- (OSC specific) LIB and BIN for specifying torque lib locations
|
19
|
+
|
20
|
+
### Changed
|
21
|
+
|
22
|
+
- Depends on latest version of pbs ruby gem 2.0
|
23
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+
- TorqueHelper.default returns the same instance every time (which is now
|
24
|
+
memoized) instead of creating a new instance
|
25
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+
|
26
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+
### Deprecated
|
27
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+
|
28
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+
- `OSC::Machete::User` - use `OodSupport::User` instead
|
29
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+
- `OSC::Machete::Process` - use `OodSupport::Process` instead
|
30
|
+
|
31
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+
### Fixed
|
32
|
+
|
33
|
+
- yardoc documentation for OSC::Machete::Status class methods
|
34
|
+
- deprecation warnings by using File.exist? instead of File.exists?
|
35
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+
|
36
|
+
## [1.1.4] - 2016-08-17
|
37
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+
|
38
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+
### Added
|
39
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+
|
40
|
+
- `Job#host` getter (which should have been there but was accidentally omitted)
|
41
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+
|
42
|
+
## [1.1.3] - 2016-06-07
|
43
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+
|
44
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+
### Fixed
|
45
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+
|
46
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+
- README and gemspec docs update for rubygems.org release
|
47
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+
|
48
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+
## [1.1.2] - 2016-06-07
|
49
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+
|
50
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+
### Fixed
|
51
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+
|
52
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+
- Copyright in LICENSE.txt
|
53
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+
|
8
54
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## [1.1.1] - 2016-02-24
|
9
55
|
|
10
56
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### Fixed
|
@@ -79,7 +125,11 @@ lib/osc/machete/torque_helper.rb _(still an internal class right now, not meant
|
|
79
125
|
|
80
126
|
Previous release of osc-machete
|
81
127
|
|
82
|
-
[Unreleased]: https://github.com/AweSim-OSC/osc-machete/compare/v1.
|
128
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+
[Unreleased]: https://github.com/AweSim-OSC/osc-machete/compare/v1.2.0...master
|
129
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+
[1.2.0]: https://github.com/AweSim-OSC/osc-machete/compare/v1.1.4...v1.2.0
|
130
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+
[1.1.4]: https://github.com/AweSim-OSC/osc-machete/compare/v1.1.3...v1.1.4
|
131
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+
[1.1.3]: https://github.com/AweSim-OSC/osc-machete/compare/v1.1.2...v1.1.3
|
132
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+
[1.1.2]: https://github.com/AweSim-OSC/osc-machete/compare/v1.1.1...v1.1.2
|
83
133
|
[1.1.1]: https://github.com/AweSim-OSC/osc-machete/compare/v1.1.0...v1.1.1
|
84
134
|
[1.1.0]: https://github.com/AweSim-OSC/osc-machete/compare/v1.0.1...v1.1.0
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85
135
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[1.0.1]: https://github.com/AweSim-OSC/osc-machete/compare/v1.0.0...v1.0.1
|
data/lib/osc/machete/job.rb
CHANGED
@@ -205,7 +205,7 @@ class OSC::Machete::Job
|
|
205
205
|
# something if the script name is munged
|
206
206
|
|
207
207
|
# recursively delete the directory after killing the job
|
208
|
-
Pathname.new(path).rmtree if path && rmdir && File.
|
208
|
+
Pathname.new(path).rmtree if path && rmdir && File.exist?(path)
|
209
209
|
end
|
210
210
|
end
|
211
211
|
|
data/lib/osc/machete/process.rb
CHANGED
@@ -1,10 +1,13 @@
|
|
1
1
|
# Class that maintains the User and additional methods for the process.
|
2
2
|
# Helper methods provided use the Process module underneath.
|
3
3
|
#
|
4
|
+
# @deprecated Please use {http://www.rubydoc.info/gems/ood_support/OodSupport/Process OodSupport::Process} instead.
|
4
5
|
class OSC::Machete::Process
|
5
6
|
|
6
7
|
def initialize
|
7
8
|
@user = OSC::Machete::User.from_uid(Process.uid)
|
9
|
+
|
10
|
+
warn "[DEPRECATION] `OSC::Machete::Process` is deprecated. Please use `OodSupport::Process` instead (see ood_support gem)."
|
8
11
|
end
|
9
12
|
|
10
13
|
# The system name of the process user
|
data/lib/osc/machete/status.rb
CHANGED
@@ -55,27 +55,42 @@ class OSC::Machete::Status
|
|
55
55
|
end
|
56
56
|
|
57
57
|
|
58
|
-
#
|
59
|
-
#
|
60
|
-
|
61
|
-
#
|
62
|
-
|
63
|
-
#
|
64
|
-
|
65
|
-
#
|
66
|
-
|
67
|
-
#
|
68
|
-
|
69
|
-
# @return [Status]
|
70
|
-
def self.running() end
|
71
|
-
# @return [Status]
|
72
|
-
def self.queued() end
|
73
|
-
# @return [Status]
|
74
|
-
def self.held() end
|
75
|
-
# @return [Status]
|
76
|
-
def self.suspended() end
|
77
|
-
|
58
|
+
# NOTE: on yard documentation: to do something like what I do below,
|
59
|
+
# documenting a set of class methods, you must have the documentation block be
|
60
|
+
# inside the `class << self` block or else the last documented method will be
|
61
|
+
# ignored or hidden if newlines exist between each @!method block. If no
|
62
|
+
# newlines exist, like below, the entire block would have been ignored.
|
63
|
+
# Also, indenting the tags for the rest of the methods is required when
|
64
|
+
# omitting newlines, otherwise, each method includes all of the returns below
|
65
|
+
# it - so yard displays 6 return Status lines for the method.
|
66
|
+
#
|
67
|
+
# Why do we have no newlines here? So that "View source" on each of these
|
68
|
+
# class methods points to the block itself.
|
78
69
|
class << self
|
70
|
+
# @!method undetermined
|
71
|
+
# A 'null' special case for Status
|
72
|
+
# @return [Status]
|
73
|
+
#
|
74
|
+
# @!method not_submitted
|
75
|
+
# @return [Status]
|
76
|
+
#
|
77
|
+
# @!method passed
|
78
|
+
# @return [Status]
|
79
|
+
#
|
80
|
+
# @!method failed
|
81
|
+
# @return [Status]
|
82
|
+
#
|
83
|
+
# @!method running
|
84
|
+
# @return [Status]
|
85
|
+
#
|
86
|
+
# @!method queued
|
87
|
+
# @return [Status]
|
88
|
+
#
|
89
|
+
# @!method held
|
90
|
+
# @return [Status]
|
91
|
+
#
|
92
|
+
# @!method suspended
|
93
|
+
# @return [Status]
|
79
94
|
VALUES_HASH.each do |char, name|
|
80
95
|
define_method(name) do
|
81
96
|
OSC::Machete::Status.new(char)
|
@@ -84,22 +99,28 @@ class OSC::Machete::Status
|
|
84
99
|
end
|
85
100
|
|
86
101
|
# @!method undetermined?
|
87
|
-
#
|
88
|
-
|
102
|
+
# @return [Boolean] true if undetermined
|
103
|
+
|
89
104
|
# @!method not_submitted?
|
90
|
-
#
|
105
|
+
# @return [Boolean] true if not_submitted
|
106
|
+
|
91
107
|
# @!method failed?
|
92
|
-
#
|
108
|
+
# @return [Boolean] true if failed
|
109
|
+
|
93
110
|
# @!method passed?
|
94
|
-
#
|
111
|
+
# @return [Boolean] true if passed
|
112
|
+
|
95
113
|
# @!method held?
|
96
|
-
#
|
114
|
+
# @return [Boolean] true if held
|
115
|
+
|
97
116
|
# @!method queued?
|
98
|
-
#
|
117
|
+
# @return [Boolean] true if queued
|
118
|
+
|
99
119
|
# @!method running?
|
100
|
-
#
|
120
|
+
# @return [Boolean] true if running
|
121
|
+
|
101
122
|
# @!method suspended?
|
102
|
-
#
|
123
|
+
# @return [Boolean] true if suspended
|
103
124
|
VALUES_HASH.each do |char, name|
|
104
125
|
define_method("#{name}?") do
|
105
126
|
self == OSC::Machete::Status.new(char)
|
@@ -7,18 +7,32 @@ require 'pbs'
|
|
7
7
|
#
|
8
8
|
# == FIXME: This contains no state whatsoever. It should probably be changed into a module.
|
9
9
|
class OSC::Machete::TorqueHelper
|
10
|
-
|
11
|
-
|
12
|
-
|
13
|
-
|
10
|
+
# FIXME: Use ood_cluster gem
|
11
|
+
LIB = ENV['TORQUE_LIB'] || '/opt/torque/lib64'
|
12
|
+
BIN = ENV['TORQUE_BIN'] || '/opt/torque/bin'
|
13
|
+
HOSTS = {
|
14
|
+
'oakley' => 'oak-batch.osc.edu',
|
15
|
+
'ruby' => 'ruby-batch.osc.edu',
|
16
|
+
'quick' => 'quick-batch.osc.edu',
|
17
|
+
'owens' => 'owens-batch.ten.osc.edu',
|
18
|
+
:default => 'oak-batch.osc.edu'
|
19
|
+
}
|
20
|
+
|
21
|
+
class << self
|
22
|
+
#@!attribute default
|
23
|
+
# @return [TorqueHelper] default TorqueHelper instance to use
|
24
|
+
attr_writer :default
|
25
|
+
def default
|
26
|
+
@default ||= self::new()
|
27
|
+
end
|
14
28
|
end
|
15
29
|
|
16
30
|
# Returns an OSC::Machete::Status ValueObject for a char
|
17
31
|
#
|
18
32
|
# @param [String] char The Torque status char
|
19
33
|
#
|
20
|
-
# @example
|
21
|
-
# status_for_char("C") #=> OSC::Machete::Status.
|
34
|
+
# @example Passed
|
35
|
+
# status_for_char("C") #=> OSC::Machete::Status.passed
|
22
36
|
# @example Queued
|
23
37
|
# status_for_char("W") #=> OSC::Machete::Status.queued
|
24
38
|
#
|
@@ -51,12 +65,6 @@ class OSC::Machete::TorqueHelper
|
|
51
65
|
#
|
52
66
|
# Bills against the project specified by the primary group of the user.
|
53
67
|
def qsub(script, host: nil, depends_on: {}, account_string: nil)
|
54
|
-
# if the script is set to run on Oakley in PBS headers
|
55
|
-
# this is to obviate current torque filter defect in which
|
56
|
-
# a script with PBS header set to specify oak-batch ends
|
57
|
-
# isn't properly handled and the job gets limited to 4GB
|
58
|
-
pbs_job = get_pbs_job( host.nil? ? get_pbs_conn(script: script) : get_pbs_conn(host: host) )
|
59
|
-
|
60
68
|
headers = { depend: qsub_dependencies_header(depends_on) }
|
61
69
|
headers.clear if headers[:depend].empty?
|
62
70
|
|
@@ -70,7 +78,7 @@ class OSC::Machete::TorqueHelper
|
|
70
78
|
headers[PBS::ATTR[:A]] = default_account_string
|
71
79
|
end
|
72
80
|
|
73
|
-
|
81
|
+
pbs(host: host, script: script).submit_script(script, headers: headers, qsub: true)
|
74
82
|
end
|
75
83
|
|
76
84
|
# convert dependencies hash to a PBS header string
|
@@ -103,16 +111,10 @@ class OSC::Machete::TorqueHelper
|
|
103
111
|
#
|
104
112
|
# @return [Status] The job state
|
105
113
|
def qstat(pbsid, host: nil)
|
106
|
-
|
107
|
-
|
108
|
-
|
109
|
-
|
110
|
-
|
111
|
-
job_status = pbs_job.status
|
112
|
-
# Get the status char value from the job.
|
113
|
-
status_for_char job_status[:attribs][:job_state][0]
|
114
|
-
|
115
|
-
rescue PBS::UnkjobidError => err
|
114
|
+
id = pbsid.to_s
|
115
|
+
status = pbs(host: host, id: id).get_job(id, filters: [:job_state])
|
116
|
+
status_for_char status[id][:job_state][0] # get status from status char value
|
117
|
+
rescue PBS::UnkjobidError
|
116
118
|
OSC::Machete::Status.passed
|
117
119
|
end
|
118
120
|
|
@@ -122,54 +124,43 @@ class OSC::Machete::TorqueHelper
|
|
122
124
|
#
|
123
125
|
# @return [nil]
|
124
126
|
def qdel(pbsid, host: nil)
|
125
|
-
|
126
|
-
|
127
|
-
|
128
|
-
|
129
|
-
pbs_job.delete
|
130
|
-
|
131
|
-
rescue PBS::UnkjobidError => err
|
127
|
+
id = pbsid.to_s
|
128
|
+
pbs(host: host, id: id).delete_job(id)
|
129
|
+
rescue PBS::UnkjobidError
|
132
130
|
# Common use case where trying to delete a job that is no longer in the system.
|
133
131
|
end
|
134
132
|
|
135
|
-
|
133
|
+
def pbs(host: nil, id: nil, script: nil)
|
134
|
+
if host
|
135
|
+
# actually check if host is "oakley" i.e. a cluster key
|
136
|
+
host = HOSTS.fetch(host.to_s, host.to_s)
|
137
|
+
else
|
138
|
+
# try to determine host
|
139
|
+
key = host_from_pbsid(id) if id
|
140
|
+
key = host_from_script_pbs_header(script) if script && key.nil?
|
136
141
|
|
137
|
-
|
138
|
-
def get_pbs_job(conn, pbsid=nil)
|
139
|
-
pbsid.nil? ? PBS::Job.new(conn: conn) : PBS::Job.new(conn: conn, id: pbsid.to_s)
|
142
|
+
host = HOSTS.fetch(key, HOSTS.fetch(:default))
|
140
143
|
end
|
141
144
|
|
142
|
-
|
143
|
-
|
144
|
-
|
145
|
-
|
146
|
-
|
147
|
-
|
148
|
-
def get_pbs_conn(options={})
|
149
|
-
if options[:script]
|
150
|
-
PBS::Conn.batch(host_from_script_pbs_header(options[:script]))
|
151
|
-
elsif options[:pbsid]
|
152
|
-
PBS::Conn.batch(host_from_pbsid(options[:pbsid]))
|
153
|
-
elsif options[:host]
|
154
|
-
PBS::Conn.batch(options[:host])
|
155
|
-
else
|
156
|
-
PBS::Conn.batch("oakley")
|
157
|
-
end
|
158
|
-
end
|
145
|
+
PBS::Batch.new(
|
146
|
+
host: host,
|
147
|
+
lib: LIB,
|
148
|
+
bin: BIN
|
149
|
+
)
|
150
|
+
end
|
159
151
|
|
152
|
+
private
|
160
153
|
# return the name of the host to use based on the pbs header
|
161
154
|
# TODO: Think of a more efficient way to do this.
|
162
155
|
def host_from_script_pbs_header(script)
|
163
156
|
if (File.open(script) { |f| f.read =~ /#PBS -q @oak-batch/ })
|
164
157
|
"oakley"
|
165
|
-
elsif (File.open(script) { |f| f.read =~ /#PBS -q @opt-batch/ })
|
166
|
-
"glenn"
|
167
158
|
elsif (File.open(script) { |f| f.read =~ /#PBS -q @ruby-batch/ })
|
168
159
|
"ruby"
|
169
160
|
elsif (File.open(script) { |f| f.read =~ /#PBS -q @quick-batch/ })
|
170
161
|
"quick"
|
171
|
-
|
172
|
-
"
|
162
|
+
elsif (File.open(script) { |f| f.read =~ /#PBS -q @owens-batch/ })
|
163
|
+
"owens"
|
173
164
|
end
|
174
165
|
end
|
175
166
|
|
@@ -177,14 +168,12 @@ class OSC::Machete::TorqueHelper
|
|
177
168
|
def host_from_pbsid(pbsid)
|
178
169
|
if (pbsid =~ /oak-batch/ )
|
179
170
|
"oakley"
|
180
|
-
elsif (pbsid =~ /opt-batch/ )
|
181
|
-
"glenn"
|
182
171
|
elsif (pbsid.to_s =~ /^\d+$/ )
|
183
172
|
"ruby"
|
184
173
|
elsif (pbsid =~ /quick/ )
|
185
174
|
"quick"
|
186
|
-
|
187
|
-
"
|
175
|
+
elsif (pbsid =~ /owens/ )
|
176
|
+
"owens"
|
188
177
|
end
|
189
178
|
end
|
190
179
|
end
|
data/lib/osc/machete/user.rb
CHANGED
@@ -1,6 +1,7 @@
|
|
1
1
|
# Class that maintains the name and home identifiers of a User.
|
2
2
|
# Helper methods provided use the Etc module underneath.
|
3
3
|
#
|
4
|
+
# @deprecated Please use {http://www.rubydoc.info/gems/ood_support/OodSupport/User OodSupport::User} instead.
|
4
5
|
class OSC::Machete::User
|
5
6
|
|
6
7
|
attr_reader :name
|
@@ -19,6 +20,8 @@ class OSC::Machete::User
|
|
19
20
|
#
|
20
21
|
def initialize(username = Etc.getpwuid.name)
|
21
22
|
@name = username
|
23
|
+
|
24
|
+
warn "[DEPRECATION] `OSC::Machete::User` is deprecated. Please use `OodSupport::User` instead (see ood_support gem)."
|
22
25
|
end
|
23
26
|
|
24
27
|
# factory method to produce a User from specified uid
|
data/lib/osc/machete/version.rb
CHANGED
data/osc-machete.gemspec
CHANGED
@@ -18,6 +18,7 @@ Gem::Specification.new do |spec|
|
|
18
18
|
spec.executables = spec.files.grep(%r{^bin/}) { |f| File.basename(f) }
|
19
19
|
spec.test_files = spec.files.grep(%r{^(test|spec|features)/})
|
20
20
|
spec.require_paths = ["lib"]
|
21
|
+
spec.required_ruby_version = '~> 2.2'
|
21
22
|
|
22
23
|
spec.add_development_dependency "bundler", "~> 1.3"
|
23
24
|
spec.add_development_dependency "rake"
|
@@ -25,6 +26,6 @@ Gem::Specification.new do |spec|
|
|
25
26
|
spec.add_development_dependency "minitest", ">= 5.0"
|
26
27
|
|
27
28
|
spec.add_runtime_dependency "mustache"
|
28
|
-
spec.add_runtime_dependency "pbs", "~>
|
29
|
+
spec.add_runtime_dependency "pbs", "~> 2.0"
|
29
30
|
end
|
30
31
|
|
data/test/test_job_dir.rb
CHANGED
@@ -34,6 +34,6 @@ class TestJobDir < Minitest::Test
|
|
34
34
|
# Create unique directory
|
35
35
|
new_jobdir = OSC::Machete::JobDir.new(@parent).new_jobdir
|
36
36
|
Dir.mkdir(new_jobdir)
|
37
|
-
assert Dir.
|
37
|
+
assert Dir.exist?("#{@parent}/9"), "Directory was not created: #{@parent}/9"
|
38
38
|
end
|
39
39
|
end
|
data/test/test_location.rb
CHANGED
@@ -24,41 +24,41 @@ class TestLocation < Minitest::Test
|
|
24
24
|
def test_render_default_replace_template
|
25
25
|
setup_render
|
26
26
|
@location1.render("")
|
27
|
-
assert_equal true, File.
|
28
|
-
assert_equal false, File.
|
27
|
+
assert_equal true, File.exist?("#{@dir1}/file.txt")
|
28
|
+
assert_equal false, File.exist?("#{@dir1}/file.txt.mustache")
|
29
29
|
end
|
30
30
|
|
31
31
|
def test_render_user_replace_template
|
32
32
|
setup_render
|
33
33
|
@location1.render("", {replace: true})
|
34
|
-
assert_equal true, File.
|
35
|
-
assert_equal false, File.
|
34
|
+
assert_equal true, File.exist?("#{@dir1}/file.txt")
|
35
|
+
assert_equal false, File.exist?("#{@dir1}/file.txt.mustache")
|
36
36
|
end
|
37
37
|
|
38
38
|
def test_render_user_doesnt_replace_template
|
39
39
|
setup_render
|
40
40
|
@location1.render("", {replace: false})
|
41
|
-
assert_equal true, File.
|
42
|
-
assert_equal true, File.
|
41
|
+
assert_equal true, File.exist?("#{@dir1}/file.txt")
|
42
|
+
assert_equal true, File.exist?("#{@dir1}/file.txt.mustache")
|
43
43
|
end
|
44
44
|
|
45
45
|
def test_copy_to_shouldnt_copy_developer_files
|
46
46
|
setup_copy_to
|
47
47
|
|
48
48
|
@location1.copy_to(@dir2)
|
49
|
-
assert_equal true, Dir.
|
50
|
-
assert_equal false, Dir.
|
51
|
-
assert_equal false, Dir.
|
52
|
-
assert_equal false, Dir.
|
53
|
-
assert_equal true, Dir.
|
54
|
-
assert_equal true, File.
|
55
|
-
assert_equal false, File.
|
56
|
-
assert_equal true, File.
|
57
|
-
assert_equal false, File.
|
58
|
-
assert_equal false, File.
|
59
|
-
assert_equal false, File.
|
60
|
-
assert_equal true, File.
|
61
|
-
assert_equal false, File.
|
49
|
+
assert_equal true, Dir.exist?("#{@dir2}")
|
50
|
+
assert_equal false, Dir.exist?("#{@dir2}/.git")
|
51
|
+
assert_equal false, Dir.exist?("#{@dir2}/.svn")
|
52
|
+
assert_equal false, Dir.exist?("#{@dir2}/test.dir.1")
|
53
|
+
assert_equal true, Dir.exist?("#{@dir2}/test.dir.2")
|
54
|
+
assert_equal true, File.exist?("#{@dir2}/test.1")
|
55
|
+
assert_equal false, File.exist?("#{@dir2}/test.2")
|
56
|
+
assert_equal true, File.exist?("#{@dir2}/test.3")
|
57
|
+
assert_equal false, File.exist?("#{@dir2}/test.4")
|
58
|
+
assert_equal false, File.exist?("#{@dir2}/test.dir.2/test.1")
|
59
|
+
assert_equal false, File.exist?("#{@dir2}/test.dir.2/test.2")
|
60
|
+
assert_equal true, File.exist?("#{@dir2}/test.dir.2/test.4")
|
61
|
+
assert_equal false, File.exist?("#{@dir2}/.gitignore")
|
62
62
|
end
|
63
63
|
|
64
64
|
|
data/test/test_torque_helper.rb
CHANGED
@@ -58,81 +58,81 @@ class TestTorqueHelper < Minitest::Test
|
|
58
58
|
# end
|
59
59
|
|
60
60
|
def test_qstat_state_no_job
|
61
|
-
PBS::
|
61
|
+
PBS::Batch.any_instance.stubs(:get_job).raises(PBS::UnkjobidError, "Unknown Job Id")
|
62
62
|
assert_equal @job_state_completed, @shell.qstat("")
|
63
63
|
assert_equal @job_state_completed, @shell.qstat(nil)
|
64
|
-
PBS::
|
64
|
+
PBS::Batch.any_instance.unstub(:get_job)
|
65
65
|
end
|
66
66
|
|
67
67
|
# Test that qstat returns Running job StatusValue
|
68
68
|
def test_qstat_state_running_oakley
|
69
|
-
PBS::
|
69
|
+
PBS::Batch.any_instance.stubs(:get_job).returns({ "123.oak-batch.osc.edu" => { :job_state => "R" }})
|
70
70
|
assert_equal @job_state_running, @shell.qstat("123.oak-batch.osc.edu")
|
71
|
-
PBS::
|
71
|
+
PBS::Batch.any_instance.unstub(:get_job)
|
72
72
|
end
|
73
73
|
|
74
74
|
# Test that qstat returns Queued job StatusValue
|
75
75
|
def test_qstat_state_queued_oakley
|
76
|
-
PBS::
|
76
|
+
PBS::Batch.any_instance.stubs(:get_job).returns({ "123.oak-batch.osc.edu" => { :job_state => "Q" }})
|
77
77
|
assert_equal @job_state_queued, @shell.qstat("123.oak-batch.osc.edu")
|
78
|
-
PBS::
|
78
|
+
PBS::Batch.any_instance.unstub(:get_job)
|
79
79
|
end
|
80
80
|
|
81
81
|
# Test that qstat returns Queued job StatusValue
|
82
82
|
def test_qstat_state_running_ruby
|
83
|
-
PBS::
|
83
|
+
PBS::Batch.any_instance.stubs(:get_job).returns({ "12398765" => { :job_state => "Q" }})
|
84
84
|
assert_equal @job_state_queued, @shell.qstat("12398765")
|
85
|
-
PBS::
|
85
|
+
PBS::Batch.any_instance.unstub(:get_job)
|
86
86
|
end
|
87
87
|
|
88
88
|
# Test that qstat returns Completed job StatusValue when state is nil.
|
89
89
|
def test_qstat_state_completed_oakley
|
90
|
-
PBS::
|
90
|
+
PBS::Batch.any_instance.stubs(:get_job).raises(PBS::UnkjobidError, "Unknown Job Id Error")
|
91
91
|
assert_equal @job_state_completed, @shell.qstat("123.oak-batch.osc.edu")
|
92
|
-
PBS::
|
92
|
+
PBS::Batch.any_instance.unstub(:get_job)
|
93
93
|
|
94
|
-
PBS::
|
94
|
+
PBS::Batch.any_instance.stubs(:get_job).raises(PBS::UnkjobidError, "Unknown Job Id")
|
95
95
|
assert_equal @job_state_completed, @shell.qstat("123.oak-batch.osc.edu")
|
96
|
-
PBS::
|
96
|
+
PBS::Batch.any_instance.unstub(:get_job)
|
97
97
|
end
|
98
98
|
|
99
99
|
# Test that qdel works for oakley
|
100
100
|
def test_qdel_oakley_ok
|
101
|
-
PBS::
|
101
|
+
PBS::Batch.any_instance.stubs(:delete_job).returns(true)
|
102
102
|
assert_equal true, @shell.qdel("123.oak-batch.osc.edu")
|
103
|
-
PBS::
|
103
|
+
PBS::Batch.any_instance.unstub(:delete_job)
|
104
104
|
end
|
105
105
|
|
106
106
|
# Test that qdel works for quick batch
|
107
107
|
def test_qdel_quick
|
108
|
-
PBS::
|
108
|
+
PBS::Batch.any_instance.stubs(:delete_job).returns(true)
|
109
109
|
assert_equal true, @shell.qdel("123.quick-batch.osc.edu")
|
110
|
-
PBS::
|
110
|
+
PBS::Batch.any_instance.unstub(:delete_job)
|
111
111
|
end
|
112
112
|
|
113
113
|
# Test that qdel works for Ruby cluster
|
114
114
|
def test_qdel_ruby
|
115
|
-
PBS::
|
115
|
+
PBS::Batch.any_instance.stubs(:delete_job).returns(true)
|
116
116
|
assert_equal true, @shell.qdel("12365478")
|
117
|
-
PBS::
|
117
|
+
PBS::Batch.any_instance.unstub(:delete_job)
|
118
118
|
end
|
119
119
|
|
120
120
|
# Test that qdel throws exception on PBS exception
|
121
121
|
def test_qdel_throws_exception
|
122
|
-
PBS::
|
122
|
+
PBS::Batch.any_instance.stubs(:delete_job).raises(PBS::Error)
|
123
123
|
assert_raises(PBS::Error) { @shell.qdel("123.quick-batch.osc.edu") }
|
124
|
-
PBS::
|
124
|
+
PBS::Batch.any_instance.unstub(:delete_job)
|
125
125
|
|
126
|
-
PBS::
|
126
|
+
PBS::Batch.any_instance.stubs(:delete_job).raises(PBS::SystemError)
|
127
127
|
assert_raises(PBS::SystemError) { @shell.qdel("123.quick-batch.osc.edu") }
|
128
|
-
PBS::
|
128
|
+
PBS::Batch.any_instance.unstub(:delete_job)
|
129
129
|
end
|
130
130
|
|
131
131
|
# Test that qdel doesn't throw exception if Unknown Job Id exception
|
132
132
|
def test_qdel_doesnt_throw_exception_on_unknown_job_id
|
133
|
-
PBS::
|
133
|
+
PBS::Batch.any_instance.stubs(:delete_job).raises(PBS::UnkjobidError)
|
134
134
|
@shell.qdel("123.quick-batch.osc.edu")
|
135
|
-
PBS::
|
135
|
+
PBS::Batch.any_instance.unstub(:delete_job)
|
136
136
|
end
|
137
137
|
|
138
138
|
def assert_qsub_dependency_list(dependency_list, dependencies, host=nil)
|
@@ -188,22 +188,67 @@ class TestTorqueHelper < Minitest::Test
|
|
188
188
|
end
|
189
189
|
|
190
190
|
def test_account_string_passed_into_qsub_used_during_submit_call
|
191
|
-
PBS::
|
191
|
+
PBS::Batch.any_instance.expects(:submit_script).with(@script_oakley, has_entry(headers: {Account_Name: "XXX"})).returns('1234598.oak-batch.osc.edu')
|
192
192
|
@shell.qsub(@script_oakley, account_string: "XXX")
|
193
|
-
PBS::
|
193
|
+
PBS::Batch.any_instance.unstub(:submit_script)
|
194
194
|
end
|
195
195
|
|
196
196
|
def test_default_account_string_used_in_qsub_during_submit_call
|
197
197
|
@shell.stubs(:default_account_string).returns("PZS3000")
|
198
198
|
|
199
|
-
PBS::
|
199
|
+
PBS::Batch.any_instance.expects(:submit_script).with(@script_oakley, has_entry(headers: {Account_Name: @shell.default_account_string})).returns('1234598.oak-batch.osc.edu')
|
200
200
|
@shell.qsub(@script_oakley)
|
201
201
|
|
202
202
|
@shell.stubs(:default_account_string).returns("appl")
|
203
|
-
PBS::
|
203
|
+
PBS::Batch.any_instance.expects(:submit_script).with(@script_oakley, has_entry(headers: {})).returns('1234598.oak-batch.osc.edu')
|
204
204
|
@shell.qsub(@script_oakley)
|
205
205
|
|
206
|
-
PBS::
|
206
|
+
PBS::Batch.any_instance.unstub(:submit_script)
|
207
207
|
@shell.unstub(:default_account_string)
|
208
208
|
end
|
209
|
+
|
210
|
+
def test_pbs_default_host
|
211
|
+
s = @shell.pbs
|
212
|
+
assert_equal 'oak-batch.osc.edu', s.host
|
213
|
+
assert_equal OSC::Machete::TorqueHelper::LIB, s.lib.to_s
|
214
|
+
assert_equal OSC::Machete::TorqueHelper::BIN, s.bin.to_s
|
215
|
+
end
|
216
|
+
|
217
|
+
def test_pbs_host_variations
|
218
|
+
# you can use the cluster ids
|
219
|
+
assert_equal 'ruby-batch.osc.edu', @shell.pbs(host: 'ruby').host
|
220
|
+
|
221
|
+
# or you can use the host itself
|
222
|
+
assert_equal 'ruby-batch.osc.edu', @shell.pbs(host: 'ruby-batch.osc.edu').host
|
223
|
+
assert_equal '@ruby-batch', @shell.pbs(host: '@ruby-batch').host
|
224
|
+
|
225
|
+
assert_equal 'ruby-batch.osc.edu', @shell.pbs(id: '4567').host
|
226
|
+
assert_equal 'ruby-batch.osc.edu', @shell.pbs(script: @script_ruby).host
|
227
|
+
assert_equal 'oak-batch.osc.edu', @shell.pbs(script: @script_oakley).host
|
228
|
+
end
|
229
|
+
|
230
|
+
def test_setting_default_torque_helper
|
231
|
+
d = OSC::Machete::TorqueHelper.default
|
232
|
+
|
233
|
+
assert_equal 'oak-batch.osc.edu', OSC::Machete::TorqueHelper.default.pbs.host
|
234
|
+
|
235
|
+
# this is an example of how you can quickly modify the default behavior of
|
236
|
+
# a TorqueHelper instance to provide a new host, id, and script
|
237
|
+
d2 = OSC::Machete::TorqueHelper.new
|
238
|
+
class << d2
|
239
|
+
def pbs(host: nil, id: nil, script: nil)
|
240
|
+
PBS::Batch.new(
|
241
|
+
host: "ruby-batch.osc.edu",
|
242
|
+
lib: LIB,
|
243
|
+
bin: BIN
|
244
|
+
)
|
245
|
+
end
|
246
|
+
end
|
247
|
+
|
248
|
+
OSC::Machete::TorqueHelper.default = d2
|
249
|
+
|
250
|
+
assert_equal 'ruby-batch.osc.edu', OSC::Machete::TorqueHelper.default.pbs.host
|
251
|
+
|
252
|
+
OSC::Machete::TorqueHelper.default = d
|
253
|
+
end
|
209
254
|
end
|
@@ -2,6 +2,7 @@ require 'minitest/autorun'
|
|
2
2
|
require 'osc/machete'
|
3
3
|
require 'pbs'
|
4
4
|
require 'mocha/setup'
|
5
|
+
require 'socket'
|
5
6
|
|
6
7
|
# test helper class
|
7
8
|
class TestTorqueHelperLive < Minitest::Test
|
@@ -29,7 +30,7 @@ class TestTorqueHelperLive < Minitest::Test
|
|
29
30
|
# This raises an issue mentioning that it is not being submitted on the
|
30
31
|
# correct host, comment out the raise to skip the live tests.
|
31
32
|
# Maybe this would be better accomplished with a separate rake task.
|
32
|
-
@submit_host = "
|
33
|
+
@submit_host = "webdev02.hpc.osc.edu"
|
33
34
|
|
34
35
|
@job_state_queued = OSC::Machete::Status.queued
|
35
36
|
@job_state_completed = OSC::Machete::Status.passed
|
@@ -70,11 +71,11 @@ class TestTorqueHelperLive < Minitest::Test
|
|
70
71
|
|
71
72
|
# Qstat it to make sure it's queued.
|
72
73
|
live_status = torque.qstat(live_job)
|
73
|
-
|
74
|
+
assert_includes OSC::Machete::Status.active_values, live_status
|
74
75
|
|
75
76
|
# Delete it and assert true returned.
|
76
77
|
live_delete_status = torque.qdel(live_job)
|
77
|
-
assert_equal
|
78
|
+
assert_equal 0, live_delete_status
|
78
79
|
else
|
79
80
|
puts "Run test 'test_qsub_oakley' on the batch system from #{@submit_host}."
|
80
81
|
end
|
@@ -101,11 +102,11 @@ class TestTorqueHelperLive < Minitest::Test
|
|
101
102
|
|
102
103
|
# Qstat it to make sure it's queued.
|
103
104
|
live_status = torque.qstat(live_job)
|
104
|
-
|
105
|
+
assert_includes OSC::Machete::Status.active_values, live_status
|
105
106
|
|
106
107
|
# Delete it and assert true returned.
|
107
108
|
live_delete_status = torque.qdel(live_job)
|
108
|
-
assert_equal
|
109
|
+
assert_equal 0, live_delete_status
|
109
110
|
else
|
110
111
|
puts "Run test 'test_qsub_ruby_with_oakley_script' on the batch system from #{@submit_host}."
|
111
112
|
end
|
@@ -127,15 +128,15 @@ class TestTorqueHelperLive < Minitest::Test
|
|
127
128
|
if Socket.gethostname == @submit_host
|
128
129
|
# Submit a small job.
|
129
130
|
live_job = torque.qsub(@script_ruby)
|
130
|
-
assert_match
|
131
|
+
assert_match(/^\d+$/, live_job)
|
131
132
|
|
132
133
|
# Qstat it to make sure it's queued.
|
133
134
|
live_status = torque.qstat(live_job)
|
134
|
-
|
135
|
+
assert_includes OSC::Machete::Status.active_values, live_status
|
135
136
|
|
136
137
|
# Delete it and assert true returned.
|
137
138
|
live_delete_status = torque.qdel(live_job)
|
138
|
-
assert_equal
|
139
|
+
assert_equal 0, live_delete_status
|
139
140
|
else
|
140
141
|
puts "Run test 'test_qsub_ruby' on the batch system from #{@submit_host}."
|
141
142
|
end
|
@@ -156,15 +157,15 @@ class TestTorqueHelperLive < Minitest::Test
|
|
156
157
|
if Socket.gethostname == @submit_host
|
157
158
|
# Submit a small job.
|
158
159
|
live_job = torque.qsub(@script_quick, host: 'quick')
|
159
|
-
assert_match
|
160
|
+
assert_match(/\d+.quick-batch.osc.edu/, live_job)
|
160
161
|
|
161
162
|
# Qstat it to make sure it's queued.
|
162
163
|
live_status = torque.qstat(live_job)
|
163
|
-
|
164
|
+
assert_includes OSC::Machete::Status.active_values, live_status
|
164
165
|
|
165
166
|
# Delete it and assert true returned.
|
166
167
|
live_delete_status = torque.qdel(live_job)
|
167
|
-
assert_equal
|
168
|
+
assert_equal 0, live_delete_status
|
168
169
|
else
|
169
170
|
puts "Run test 'test_qsub_quick' on the batch system from #{@submit_host}."
|
170
171
|
end
|
metadata
CHANGED
@@ -1,14 +1,14 @@
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
2
2
|
name: osc-machete
|
3
3
|
version: !ruby/object:Gem::Version
|
4
|
-
version: 1.
|
4
|
+
version: 1.2.0
|
5
5
|
platform: ruby
|
6
6
|
authors:
|
7
7
|
- Eric Franz
|
8
8
|
autorequire:
|
9
9
|
bindir: bin
|
10
10
|
cert_chain: []
|
11
|
-
date: 2016-
|
11
|
+
date: 2016-09-06 00:00:00.000000000 Z
|
12
12
|
dependencies:
|
13
13
|
- !ruby/object:Gem::Dependency
|
14
14
|
name: bundler
|
@@ -86,14 +86,14 @@ dependencies:
|
|
86
86
|
requirements:
|
87
87
|
- - "~>"
|
88
88
|
- !ruby/object:Gem::Version
|
89
|
-
version: '
|
89
|
+
version: '2.0'
|
90
90
|
type: :runtime
|
91
91
|
prerelease: false
|
92
92
|
version_requirements: !ruby/object:Gem::Requirement
|
93
93
|
requirements:
|
94
94
|
- - "~>"
|
95
95
|
- !ruby/object:Gem::Version
|
96
|
-
version: '
|
96
|
+
version: '2.0'
|
97
97
|
description: Common interface for PBS (and eventually other resource managers and
|
98
98
|
batch schedulers - currently OSC specific)
|
99
99
|
email:
|
@@ -144,9 +144,9 @@ require_paths:
|
|
144
144
|
- lib
|
145
145
|
required_ruby_version: !ruby/object:Gem::Requirement
|
146
146
|
requirements:
|
147
|
-
- - "
|
147
|
+
- - "~>"
|
148
148
|
- !ruby/object:Gem::Version
|
149
|
-
version: '
|
149
|
+
version: '2.2'
|
150
150
|
required_rubygems_version: !ruby/object:Gem::Requirement
|
151
151
|
requirements:
|
152
152
|
- - ">="
|
@@ -154,7 +154,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
|
|
154
154
|
version: '0'
|
155
155
|
requirements: []
|
156
156
|
rubyforge_project:
|
157
|
-
rubygems_version: 2.4.
|
157
|
+
rubygems_version: 2.4.8
|
158
158
|
signing_key:
|
159
159
|
specification_version: 4
|
160
160
|
summary: Common interface for working with HPC batch jobs (currently OSC specific)
|
@@ -175,4 +175,3 @@ test_files:
|
|
175
175
|
- test/test_status.rb
|
176
176
|
- test/test_torque_helper.rb
|
177
177
|
- test/test_torque_helper_live.rb
|
178
|
-
has_rdoc:
|