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Torque adapter takes native arrays
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Fixes #65
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Jeremy Nicklas committed Apr 20, 2018
1 parent 597e996 commit 1ad6dec
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Showing 4 changed files with 328 additions and 84 deletions.
3 changes: 3 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -6,6 +6,9 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/)
and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html).

## [Unreleased]
### Changed
- Updated Torque adapter to take into account the new `Script#native` format
allowing for arrays. [#65](https://github.com/OSC/ood_core/issues/65)

## [0.3.0] - 2018-04-05
### Added
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116 changes: 78 additions & 38 deletions lib/ood_core/job/adapters/torque.rb
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Expand Up @@ -71,54 +71,94 @@ def submit(script, after: [], afterok: [], afternotok: [], afterany: [])
afternotok = Array(afternotok).map(&:to_s)
afterany = Array(afterany).map(&:to_s)

# Set headers
headers = {}
headers.merge!(job_arguments: script.args.join(' ')) unless script.args.nil?
headers.merge!(Hold_Types: :u) if script.submit_as_hold
headers.merge!(Rerunable: script.rerunnable ? 'y' : 'n') unless script.rerunnable.nil?
headers.merge!(init_work_dir: script.workdir) unless script.workdir.nil?
headers.merge!(Mail_Users: script.email.join(',')) unless script.email.nil?
mail_points = ''
mail_points += 'b' if script.email_on_started
mail_points += 'e' if script.email_on_terminated
headers.merge!(Mail_Points: mail_points) unless mail_points.empty?
headers.merge!(Job_Name: script.job_name) unless script.job_name.nil?
headers.merge!(Shell_Path_List: script.shell_path) unless script.shell_path.nil?
# ignore input_path (not defined in Torque)
headers.merge!(Output_Path: script.output_path) unless script.output_path.nil?
headers.merge!(Error_Path: script.error_path) unless script.error_path.nil?
# If error_path is not specified we join stdout & stderr (as this
# mimics what the other resource managers do)
headers.merge!(Join_Path: 'oe') if script.error_path.nil?
headers.merge!(reservation_id: script.reservation_id) unless script.reservation_id.nil?
headers.merge!(Priority: script.priority) unless script.priority.nil?
headers.merge!(Execution_Time: script.start_time.localtime.strftime("%C%y%m%d%H%M.%S")) unless script.start_time.nil?
headers.merge!(Account_Name: script.accounting_id) unless script.accounting_id.nil?

# Set dependencies
depend = []
depend << "after:#{after.join(':')}" unless after.empty?
depend << "afterok:#{afterok.join(':')}" unless afterok.empty?
depend << "afternotok:#{afternotok.join(':')}" unless afternotok.empty?
depend << "afterany:#{afterany.join(':')}" unless afterany.empty?
headers.merge!(depend: depend.join(',')) unless depend.empty?

# Set resources
resources = {}
resources.merge!(walltime: seconds_to_duration(script.wall_time)) unless script.wall_time.nil?
# Set mailing options
mail_points = ""
mail_points += "b" if script.email_on_started
mail_points += "e" if script.email_on_terminated

# Set environment variables
envvars = script.job_environment || {}
# FIXME: Remove the Hash option once all Interactive Apps are
# converted to Array format
if script.native.is_a?(Hash)
# Set headers
headers = {}
headers.merge!(job_arguments: script.args.join(' ')) unless script.args.nil?
headers.merge!(Hold_Types: :u) if script.submit_as_hold
headers.merge!(Rerunable: script.rerunnable ? 'y' : 'n') unless script.rerunnable.nil?
headers.merge!(init_work_dir: script.workdir) unless script.workdir.nil?
headers.merge!(Mail_Users: script.email.join(',')) unless script.email.nil?
headers.merge!(Mail_Points: mail_points) unless mail_points.empty?
headers.merge!(Job_Name: script.job_name) unless script.job_name.nil?
headers.merge!(Shell_Path_List: script.shell_path) unless script.shell_path.nil?
# ignore input_path (not defined in Torque)
headers.merge!(Output_Path: script.output_path) unless script.output_path.nil?
headers.merge!(Error_Path: script.error_path) unless script.error_path.nil?
# If error_path is not specified we join stdout & stderr (as this
# mimics what the other resource managers do)
headers.merge!(Join_Path: 'oe') if script.error_path.nil?
headers.merge!(reservation_id: script.reservation_id) unless script.reservation_id.nil?
headers.merge!(Priority: script.priority) unless script.priority.nil?
headers.merge!(Execution_Time: script.start_time.localtime.strftime("%C%y%m%d%H%M.%S")) unless script.start_time.nil?
headers.merge!(Account_Name: script.accounting_id) unless script.accounting_id.nil?
headers.merge!(depend: depend.join(',')) unless depend.empty?

# Set native options
if script.native
headers.merge! script.native.fetch(:headers, {})
resources.merge! script.native.fetch(:resources, {})
envvars.merge! script.native.fetch(:envvars, {})
end
# Set resources
resources = {}
resources.merge!(walltime: seconds_to_duration(script.wall_time)) unless script.wall_time.nil?

# Set environment variables
envvars = script.job_environment || {}

# Set native options
if script.native
headers.merge! script.native.fetch(:headers, {})
resources.merge! script.native.fetch(:resources, {})
envvars.merge! script.native.fetch(:envvars, {})
end

# Submit job
@pbs.submit_string(script.content, queue: script.queue_name, headers: headers, resources: resources, envvars: envvars)
# Submit job
@pbs.submit_string(script.content, queue: script.queue_name, headers: headers, resources: resources, envvars: envvars)
else
# Set qsub arguments
args = []
args += ["-F", script.args.join(" ")] unless script.args.nil?
args += ["-h"] if script.submit_as_hold
args += ["-r", script.rerunnable ? "y" : "n"] unless script.rerunnable.nil?
args += ["-M", script.email.join(",")] unless script.email.nil?
args += ["-m", mail_points] unless mail_points.empty?
args += ["-N", script.job_name] unless script.job_name.nil?
args += ["-S", script.shell_path] unless script.shell_path.nil?
# ignore input_path (not defined in Torque)
args += ["-o", script.output_path] unless script.output_path.nil?
args += ["-e", script.error_path] unless script.error_path.nil?
args += ["-W", "x=advres:#{script.reservation_id}"] unless script.reservation_id.nil?
args += ["-q", script.queue_name] unless script.queue_name.nil?
args += ["-p", script.priority] unless script.priority.nil?
args += ["-a", script.start_time.localtime.strftime("%C%y%m%d%H%M.%S")] unless script.start_time.nil?
args += ["-A", script.accounting_id] unless script.accounting_id.nil?
args += ["-W", "depend=#{depend.join(",")}"] unless depend.empty?
args += ["-l", "walltime=#{seconds_to_duration(script.wall_time)}"] unless script.wall_time.nil?

# Set environment variables
env = script.job_environment.to_h
args += ["-v", env.keys.join(",")] unless env.empty?

# If error_path is not specified we join stdout & stderr (as this
# mimics what the other resource managers do)
args += ["-j", "oe"] if script.error_path.nil?

# Set native options
args += script.native if script.native

# Submit job
@pbs.submit(script.content, args: args, env: env, chdir: script.workdir)
end
rescue PBS::Error => e
raise JobAdapterError, e.message
end
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2 changes: 1 addition & 1 deletion ood_core.gemspec
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Expand Up @@ -23,7 +23,7 @@ Gem::Specification.new do |spec|
spec.required_ruby_version = ">= 2.2.0"

spec.add_runtime_dependency "ood_support", "~> 0.0.2"
spec.add_development_dependency "pbs", "~> 2.1", ">= 2.1.0"
spec.add_development_dependency "pbs", "~> 2.1", ">= 2.2.0"
spec.add_development_dependency "bundler", "~> 1.7"
spec.add_development_dependency "rake", "~> 10.0"
spec.add_development_dependency "rspec", "~> 3.0"
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