rbbt-util 5.25.10 → 5.25.12
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- checksums.yaml +4 -4
- data/lib/rbbt/hpc.rb +11 -5
- data/lib/rbbt/rest/client/step.rb +3 -1
- data/lib/rbbt/util/concurrency/processes.rb +1 -1
- metadata +2 -2
checksums.yaml
CHANGED
@@ -1,7 +1,7 @@
|
|
1
1
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---
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2
2
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SHA1:
|
3
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-
metadata.gz:
|
4
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-
data.tar.gz:
|
3
|
+
metadata.gz: 6ae58162f37a549950ca17612244b5dc6e557369
|
4
|
+
data.tar.gz: d87001e2b5313efe465e6f55a6d7a38a631dab15
|
5
5
|
SHA512:
|
6
|
-
metadata.gz:
|
7
|
-
data.tar.gz:
|
6
|
+
metadata.gz: dbd7d9e31a15cc49014c5539247188dd036fbee214c67068a9c398c72fa4b4999b575d4fd7751b90ff5dfa40c29b513400e4148a11f43f5f1ce8c44c1a4b54f4
|
7
|
+
data.tar.gz: 6538afe285d095537e301a5a749b3aa80543da58b5fc73f523986215c7b3c2602555d38d6c6b8cbccba4056ecf2b8e1636e5ebc56410d43855a2ba364f0bafca
|
data/lib/rbbt/hpc.rb
CHANGED
@@ -7,7 +7,6 @@ module Marenostrum
|
|
7
7
|
|
8
8
|
def self.template(args, options = {})
|
9
9
|
|
10
|
-
dry_run = options.delete :dry_run
|
11
10
|
development = options.delete :drbbt
|
12
11
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contain = options.delete :contain
|
13
12
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sync = options.delete :sync
|
@@ -228,12 +227,15 @@ EOF
|
|
228
227
|
|
229
228
|
workdir = options[:workdir]
|
230
229
|
Open.mkdir workdir
|
231
|
-
|
232
|
-
|
233
|
-
|
230
|
+
|
231
|
+
dry_run = options.delete :dry_run
|
232
|
+
|
233
|
+
fout = File.join(workdir, 'std.out')
|
234
|
+
ferr = File.join(workdir, 'std.err')
|
235
|
+
fjob = File.join(workdir, 'job.id')
|
234
236
|
fexit = File.join(workdir, 'exit.status')
|
235
237
|
fsync = File.join(workdir, 'sync.log')
|
236
|
-
fcmd
|
238
|
+
fcmd = File.join(workdir, 'command.slurm')
|
237
239
|
|
238
240
|
job = nil
|
239
241
|
if options[:clean_job]
|
@@ -253,6 +255,10 @@ EOF
|
|
253
255
|
else
|
254
256
|
if File.exists?(fout)
|
255
257
|
return
|
258
|
+
elsif dry_run
|
259
|
+
STDERR.puts Log.color(:magenta, "Prepared work directory: ")
|
260
|
+
puts workdir
|
261
|
+
STDERR.puts Log.color(:magenta, "To execute run: sbatch '#{workdir}/command.slurm'")
|
256
262
|
else
|
257
263
|
Open.rm fsync
|
258
264
|
Open.rm fexit
|
@@ -207,7 +207,9 @@ class WorkflowRESTClient
|
|
207
207
|
@done = false
|
208
208
|
get_streams
|
209
209
|
@name ||= Persist.memory("RemoteSteps", :workflow => self, :task => task, :jobname => @name, :inputs => inputs, :cache_type => cache_type) do
|
210
|
-
|
210
|
+
Misc.insist do
|
211
|
+
WorkflowRESTClient.post_jobname(File.join(base_url, task.to_s), inputs.merge(other_params).merge(:jobname => @name||@base_name, :_cache_type => cache_type))
|
212
|
+
end
|
211
213
|
end
|
212
214
|
if Open.remote? @name
|
213
215
|
@url = @name
|
@@ -146,7 +146,7 @@ class RbbtProcessQueue
|
|
146
146
|
|
147
147
|
@callback_queue.close_read if @callback_queue
|
148
148
|
|
149
|
-
num_processes.times do |i|
|
149
|
+
num_processes.to_i.times do |i|
|
150
150
|
@total += 1
|
151
151
|
process_mutex.synchronize do
|
152
152
|
processes << RbbtProcessQueueWorker.new(@queue, @callback_queue, @cleanup, @respawn, (@offset ? @total : false), &@init_block)
|
metadata
CHANGED
@@ -1,14 +1,14 @@
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
2
2
|
name: rbbt-util
|
3
3
|
version: !ruby/object:Gem::Version
|
4
|
-
version: 5.25.
|
4
|
+
version: 5.25.12
|
5
5
|
platform: ruby
|
6
6
|
authors:
|
7
7
|
- Miguel Vazquez
|
8
8
|
autorequire:
|
9
9
|
bindir: bin
|
10
10
|
cert_chain: []
|
11
|
-
date:
|
11
|
+
date: 2019-01-08 00:00:00.000000000 Z
|
12
12
|
dependencies:
|
13
13
|
- !ruby/object:Gem::Dependency
|
14
14
|
name: rake
|