rbbt-util 5.30.0 → 5.30.1
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- checksums.yaml +4 -4
- data/lib/rbbt/hpc/orchestrate.rb +1 -1
- data/lib/rbbt/hpc/slurm.rb +7 -7
- data/lib/rbbt/persist/tsv/adapter.rb +1 -5
- data/lib/rbbt/tsv.rb +6 -2
- data/share/rbbt_commands/slurm/list +1 -1
- data/share/rbbt_commands/workflow/task +12 -2
- metadata +2 -2
checksums.yaml
CHANGED
@@ -1,7 +1,7 @@
|
|
1
1
|
---
|
2
2
|
SHA256:
|
3
|
-
metadata.gz:
|
4
|
-
data.tar.gz:
|
3
|
+
metadata.gz: 0275d0f8a0922abe3e0abee0f02935fb6e393452a68c0cad86de075b153a8457
|
4
|
+
data.tar.gz: 8a182bd87be2e1b4c538d0faaf8a16848e8f077c9f61f96f6df67ca07dd222f6
|
5
5
|
SHA512:
|
6
|
-
metadata.gz:
|
7
|
-
data.tar.gz:
|
6
|
+
metadata.gz: 02fd852c70355b89d187db04c52f27207012a2fe00f1fd7f414b95bea86bf47c3d19b0b766fa12d8520ee7c9270dfde369ce2a0c1dc60595e7a9b8062a176b92
|
7
|
+
data.tar.gz: 69591fffbf60d68a57dc319692adff4f4f28bb46d9b378fa23a0b01c55303b780d058f1e4ab1f41be52c43abb48ac8db7962e96f77fb2765f6f8f74587ee8825
|
data/lib/rbbt/hpc/orchestrate.rb
CHANGED
@@ -83,7 +83,7 @@ module HPC
|
|
83
83
|
|
84
84
|
deps = seen[dep.path] ||= self.orchestrate_job(dep, options, skip_dep, seen)
|
85
85
|
if job.canfail_paths.include? dep.path
|
86
|
-
[deps].flatten.collect{|id| ['canfail', id] * ":"}
|
86
|
+
[deps].flatten.compact.collect{|id| ['canfail', id] * ":"}
|
87
87
|
else
|
88
88
|
deps
|
89
89
|
end
|
data/lib/rbbt/hpc/slurm.rb
CHANGED
@@ -525,7 +525,10 @@ EOF
|
|
525
525
|
tail = options.delete :tail
|
526
526
|
dependencies = options.delete :slurm_dependencies
|
527
527
|
procpath = options.delete :SLURM_procpath
|
528
|
+
|
528
529
|
options[:jobname] = job.clean_name
|
530
|
+
log_level = options.delete :log
|
531
|
+
log_level ||= Log.severity
|
529
532
|
|
530
533
|
workflow = job.workflow
|
531
534
|
|
@@ -550,16 +553,13 @@ EOF
|
|
550
553
|
inputs_dir = File.join(tmp_directory, 'inputs_dir')
|
551
554
|
saved = Step.save_job_inputs(job, inputs_dir)
|
552
555
|
|
553
|
-
|
554
|
-
|
555
|
-
|
556
|
-
else
|
557
|
-
cmd = ['workflow', 'task', workflow.to_s, task.to_s, '--printpath', '--log', (options[:log] || Log.severity).to_s]
|
558
|
-
end
|
556
|
+
cmd = ['workflow', 'task', workflow.to_s, task.to_s, '--printpath', '--log', log_level.to_s]
|
557
|
+
|
558
|
+
cmd << "--procpath_performance='#{tmp_directory}/procpath##{procpath.gsub(',', '#')}'" if procpath
|
559
559
|
|
560
560
|
cmd << "--override_deps='#{override_deps.gsub("'", '\'')}'" if override_deps and not override_deps.empty?
|
561
561
|
|
562
|
-
cmd << "--
|
562
|
+
cmd << "--load_inputs='#{inputs_dir}'" if saved && saved.any?
|
563
563
|
|
564
564
|
template = self.template(cmd, options)
|
565
565
|
jobid = self.issue_template(template, options.merge(:slurm_basedir => slurm_basedir, :dry_run => dry_run, :slurm_dependencies => dependencies))
|
data/lib/rbbt/tsv.rb
CHANGED
@@ -113,8 +113,8 @@ module TSV
|
|
113
113
|
|
114
114
|
data.entity_options = entity_options
|
115
115
|
|
116
|
-
if Path === source
|
117
|
-
|
116
|
+
if Path === source && data.identifiers
|
117
|
+
Path.setup(data.identifiers, source.pkgdir, source.resource)
|
118
118
|
end
|
119
119
|
|
120
120
|
if data.respond_to? :persistence_path
|
@@ -124,6 +124,10 @@ module TSV
|
|
124
124
|
data.clear
|
125
125
|
data.annotate h
|
126
126
|
end
|
127
|
+
|
128
|
+
data.read
|
129
|
+
|
130
|
+
data
|
127
131
|
end
|
128
132
|
|
129
133
|
def self.parse_header(stream, options = {})
|
@@ -410,10 +410,20 @@ begin
|
|
410
410
|
|
411
411
|
if options[:procpath_performance]
|
412
412
|
require 'rbbt/util/procpath'
|
413
|
+
current_pid = job.info[:pid]
|
413
414
|
job.fork
|
414
415
|
job.soft_grace
|
415
|
-
|
416
|
-
|
416
|
+
sleep 2 if job.info[:pid] == current_pid
|
417
|
+
if job.info[:pid] != current_pid
|
418
|
+
pid = job.info[:pid]
|
419
|
+
begin
|
420
|
+
ProcPath.monitor(pid, options[:procpath_performance])
|
421
|
+
rescue Errno::ECHILD
|
422
|
+
Log.warn "Procpath didn't find process #{pid} to monitor. Maybe it finished already"
|
423
|
+
rescue
|
424
|
+
Log.warn "Procpath failed: #{$!.message}"
|
425
|
+
end
|
426
|
+
end
|
417
427
|
end
|
418
428
|
|
419
429
|
if do_fork
|
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: 5.30.
|
4
|
+
version: 5.30.1
|
5
5
|
platform: ruby
|
6
6
|
authors:
|
7
7
|
- Miguel Vazquez
|
8
8
|
autorequire:
|
9
9
|
bindir: bin
|
10
10
|
cert_chain: []
|
11
|
-
date: 2021-02-
|
11
|
+
date: 2021-02-02 00:00:00.000000000 Z
|
12
12
|
dependencies:
|
13
13
|
- !ruby/object:Gem::Dependency
|
14
14
|
name: rake
|