rbbt-util 5.26.89 → 5.26.91
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- checksums.yaml +4 -4
- data/lib/rbbt/workflow/util/archive.rb +3 -2
- data/share/rbbt_commands/workflow/slurm +38 -0
- metadata +3 -2
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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SHA256:
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3
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-
metadata.gz:
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4
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-
data.tar.gz:
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3
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+
metadata.gz: cf3015ae621537a668dd0dfc4d88629013baaa64f566e0c1367d9456f223d90d
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4
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+
data.tar.gz: 94f1605ffde34b1781b3b46bd7dd3fa6fb361a5345aae5a7f37da6f1626d3f6c
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5
5
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SHA512:
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6
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-
metadata.gz:
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7
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-
data.tar.gz:
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6
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+
metadata.gz: f020fe934da94e1f454e087cfd4baf002f5d7f6260fbc3f803a2f48e5b3d5ae21816c68ce1ac3dc4431b8ceb7e4f97557e0220b9dc57690f3591ee82adcb27f8
|
7
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+
data.tar.gz: 648f2530c6e4fa265adf7092c5abdc7d3c7b508751a0969575f2731a4d364937279d7cd7cfc3b1718f7fce6981a67398e7c63b312cca92db01a43f239901c532
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@@ -1,3 +1,4 @@
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1
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+
require 'rbbt/workflow/remote/ssh/driver'
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1
2
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class Step
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2
3
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def self.link_job(path, target_dir, task = nil, workflow = nil)
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3
4
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Path.setup(target_dir)
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@@ -124,7 +125,7 @@ class Step
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124
125
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relocate = options[:relocate]
|
125
126
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|
126
127
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paths = if options[:source]
|
127
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-
|
128
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+
SSHDriver.run(options[:source], <<-EOF).split("\n")
|
128
129
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require 'rbbt-util'
|
129
130
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require 'rbbt/workflow'
|
130
131
|
|
@@ -155,7 +156,7 @@ puts files * "\n"
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|
155
156
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end
|
156
157
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|
157
158
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target = if options[:target]
|
158
|
-
target =
|
159
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+
target = SSHDriver.run(options[:target], <<-EOF).split("\n").first
|
159
160
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require 'rbbt-util'
|
160
161
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path = "var/jobs"
|
161
162
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resource = #{resource.to_s}
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@@ -0,0 +1,38 @@
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1
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+
#!/usr/bin/env ruby
|
2
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+
|
3
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+
require 'rbbt/util/simpleopt'
|
4
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+
require 'rbbt/workflow'
|
5
|
+
require 'rbbt/workflow/usage'
|
6
|
+
require 'rbbt/hpc'
|
7
|
+
require 'time'
|
8
|
+
|
9
|
+
$slurm_options = SOPT.get <<EOF
|
10
|
+
-dr--dry_run Print only the template
|
11
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+
-cj--clean_job Clean job
|
12
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+
--drbbt Use development version of rbbt
|
13
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+
-sing--singularity Use Singularity
|
14
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+
-c--contain* Contain in directory (using Singularity)
|
15
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+
-s--sync* Contain in directory and sync jobs
|
16
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+
-e--exclusive Make exclusive use of the node
|
17
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+
-hm--highmem Make use of highmem cores
|
18
|
+
-wc--wipe_container* Wipe the jobs from the contain directory
|
19
|
+
-CS--contain_and_sync Contain and sync to default locations
|
20
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+
-ci--copy_image When using a container directory, copy image there
|
21
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+
-t--tail Tail the logs
|
22
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+
-q--queue* Queue
|
23
|
+
-t--task_cpus* Tasks
|
24
|
+
-tm--time* Time
|
25
|
+
-S--server* SLURM login node
|
26
|
+
EOF
|
27
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+
|
28
|
+
class Step
|
29
|
+
def run(*args)
|
30
|
+
if done?
|
31
|
+
self.load
|
32
|
+
else
|
33
|
+
Marenostrum::SLURM.run_job(self, SOPT::GOT_OPTIONS.merge($slurm_options))
|
34
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+
end
|
35
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+
end
|
36
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+
end
|
37
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+
|
38
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+
load Rbbt.share.rbbt_commands.workflow.task.find
|
metadata
CHANGED
@@ -1,14 +1,14 @@
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|
1
1
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--- !ruby/object:Gem::Specification
|
2
2
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name: rbbt-util
|
3
3
|
version: !ruby/object:Gem::Version
|
4
|
-
version: 5.26.
|
4
|
+
version: 5.26.91
|
5
5
|
platform: ruby
|
6
6
|
authors:
|
7
7
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- Miguel Vazquez
|
8
8
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autorequire:
|
9
9
|
bindir: bin
|
10
10
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cert_chain: []
|
11
|
-
date: 2019-11-
|
11
|
+
date: 2019-11-28 00:00:00.000000000 Z
|
12
12
|
dependencies:
|
13
13
|
- !ruby/object:Gem::Dependency
|
14
14
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name: rake
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@@ -426,6 +426,7 @@ files:
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|
426
426
|
- share/rbbt_commands/workflow/remote/list
|
427
427
|
- share/rbbt_commands/workflow/remote/remove
|
428
428
|
- share/rbbt_commands/workflow/server
|
429
|
+
- share/rbbt_commands/workflow/slurm
|
429
430
|
- share/rbbt_commands/workflow/task
|
430
431
|
- share/rbbt_commands/workflow/trace
|
431
432
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- share/unicorn.rb
|