rbbt-util 5.30.8 → 5.30.9
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- checksums.yaml +4 -4
- data/lib/rbbt/hpc/orchestrate.rb +13 -2
- data/share/rbbt_commands/workflow/server +1 -0
- metadata +1 -1
checksums.yaml
CHANGED
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@@ -1,7 +1,7 @@
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|
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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: 8985df2e0e2353224b5b075acb1bb04243d12351b8d904441009b93ccf490288
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4
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+
data.tar.gz: 3a1e7d8561fcc72a83c2b0006c49cf50f35a87cfa037c0186bdc3563435a0e8f
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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: baae9121f3d757bcda2add9f666c740e5647f38d4bbc511d3456e36d466fc443c8a04b0ae12431bbf226e4e0c75eec5700b28720c117954005fe836ad74b76e8
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|
7
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+
data.tar.gz: ea61b36cec82f6634546aecf5de356d7d3b3c9d28eccfad52282f309e5ad6e1e28c2bfb627a100970d6a553fdc90b3900a4247101210cfbaae461c35d8e0399a
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data/lib/rbbt/hpc/orchestrate.rb
CHANGED
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@@ -140,21 +140,30 @@ module HPC
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140
140
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job_rules.delete :tasks
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141
141
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job_rules.delete :workflow
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|
142
142
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143
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-
config_keys = job_rules.delete(:config_keys)
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|
144
143
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145
144
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job_options = IndiferentHash.setup(options.merge(job_rules).merge(:slurm_dependencies => dep_ids))
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146
145
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job_options.delete :orchestration_rules
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|
146
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+
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147
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+
config_keys = job_rules.delete(:config_keys)
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|
147
148
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if config_keys
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|
148
149
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config_keys.gsub!(/,\s+/,',')
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|
149
150
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job_options[:config_keys] = job_options[:config_keys] ? config_keys + "," + job_options[:config_keys] : config_keys
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|
150
151
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end
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|
151
152
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|
|
152
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-
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|
153
153
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if options[:piggyback]
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|
154
154
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manifest = options[:piggyback].uniq
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|
155
155
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manifest += [job]
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|
156
156
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manifest.concat chain if chain
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|
157
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+
|
|
157
158
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job = options[:piggyback].first
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|
159
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+
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|
160
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+
job_rules = self.job_rules(rules, job)
|
|
161
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+
new_config_keys = self.job_rules(rules, job)[:config_keys]
|
|
162
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+
if new_config_keys
|
|
163
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+
new_config_keys = new_config_keys.gsub(/,\s+/,',')
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|
164
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+
job_options[:config_keys] = job_options[:config_keys] ? new_config_keys + "," + job_options[:config_keys] : new_config_keys
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|
165
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+
end
|
|
166
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+
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|
158
167
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job_options.delete :piggyback
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|
159
168
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else
|
|
160
169
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manifest = [job]
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@@ -165,6 +174,8 @@ module HPC
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|
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165
174
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|
|
166
175
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job_options[:manifest] = manifest.collect{|j| j.workflow_short_path }
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|
167
176
|
|
|
177
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+
job_options[:config_keys] = job_options[:config_keys].split(",").uniq * "," if job_options[:config_keys]
|
|
178
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+
|
|
168
179
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if options[:dry_run]
|
|
169
180
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puts Log.color(:magenta, "Manifest: ") + Log.color(:blue, job_options[:manifest] * ", ") + " - tasks: #{job_options[:task_cpus] || 1} - time: #{job_options[:time]} - config: #{job_options[:config_keys]}"
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|
170
181
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puts Log.color(:yellow, "Deps: ") + Log.color(:blue, job_options[:slurm_dependencies]*", ")
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@@ -16,6 +16,7 @@ $ rbbt workflow server [options] <Workflow>
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16
16
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-B--Bind* Bind IP
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|
17
17
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-p--port* TCP port
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|
18
18
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-s--server* Server type: thin, webrick, unicorn, etc
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|
19
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+
-w--workers* Number of workers for cluster mode (puma)
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19
20
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-so--server_options* Additional options for server (e.g. option1=value1;option2=value2)
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20
21
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-f--finder Start server with finder functionality
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21
22
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-RS--Rserve_session* Rserve session to use, otherwise start new one
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