ood_core 0.2.1 → 0.3.0

checksums.yaml

@@ -1,7 +1,7 @@
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-  data.tar.gz: b51795a22118a9d364ab46da9c10008fb79a79e5
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+  data.tar.gz: cfaa8e4bad41f728f6bf08e6db0bea634dca9e4b
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data/CHANGELOG.md

@@ -7,6 +7,19 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 
 ## [Unreleased]
 
+## [0.3.0] - 2018-04-05
+### Added
+- Basic multi-cluster support for LSF by specifying name of cluster for -m
+  argument. [#24](https://github.com/OSC/ood_core/issues/24)
+- Added `OodCore::Job::Script#shell_path` as an option to all adapters.
+  [#82](https://github.com/OSC/ood_core/issues/82)
+- Added `header` and `footer` options to a Batch Connect template.
+  [#64](https://github.com/OSC/ood_core/issues/64)
+
+### Fixed
+- Replaced `Fixnum` code comments with `Integer`.
+  [#67](https://github.com/OSC/ood_core/issues/67)
+
 ## [0.2.1] - 2018-01-26
 ### Changed
 - Updated the date in the `LICENSE.txt` file.
@@ -99,7 +112,8 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 ### Added
 - Initial release!
 
-[Unreleased]: https://github.com/OSC/ood_core/compare/v0.2.1...HEAD
+[Unreleased]: https://github.com/OSC/ood_core/compare/v0.3.0...HEAD
+[0.3.0]: https://github.com/OSC/ood_core/compare/v0.2.1...v0.3.0
 [0.2.1]: https://github.com/OSC/ood_core/compare/v0.2.0...v0.2.1
 [0.2.0]: https://github.com/OSC/ood_core/compare/v0.1.1...v0.2.0
 [0.1.1]: https://github.com/OSC/ood_core/compare/v0.1.0...v0.1.1

data/lib/ood_core/batch_connect/template.rb

@@ -26,6 +26,10 @@ module OodCore
       #   looking for available port
       # @option context [#to_i] :passwd_size (32) Length of randomly generated
       #   password
+      # @option context [#to_s] :header ("") Shell code prepended at the top of
+      #   the script body
+      # @option context [#to_s] :footer ("") Shell code appended at the bottom
+      #   of the script body
       # @option context [#to_s] :script_wrapper ("%s") Bash code that wraps
       #   around the body of the template script (use `%s` to interpolate the
       #   body)
@@ -58,9 +62,9 @@ module OodCore
       # @return [String] rendered template
       def to_s
         <<-EOT.gsub(/^ {10}/, '')
-          #!/bin/bash
-
+          #{header}
           #{script_wrapper}
+          #{footer}
         EOT
       end
 
@@ -148,6 +152,16 @@ module OodCore
           end.to_s
         end
 
+        # Shell code that is prepended at the top of the script body
+        def header
+          context.fetch(:header, "").to_s
+        end
+
+        # Shell code that is appended at the bottom of the script body
+        def footer
+          context.fetch(:footer, "").to_s
+        end
+
         # Bash code that wraps around the body of the template script (use `%s`
         # to interpolate the body)
         def script_wrapper

data/lib/ood_core/job/adapters/lsf.rb

@@ -11,6 +11,7 @@ module OodCore
       # @option config [#to_s] :libdir ('') Path to lsf client lib dir
       # @option config [#to_s] :envdir ('') Path to lsf client conf dir
       # @option config [#to_s] :serverdir ('') Path to lsf client etc dir
+      # @option config [#to_s] :cluster ('') name of cluster, if in multi-cluster mode
       def self.build_lsf(config)
         batch = Adapters::Lsf::Batch.new(config.to_h.symbolize_keys)
         Adapters::Lsf.new(batch: batch)

data/lib/ood_core/job/adapters/lsf/batch.rb

@@ -2,19 +2,20 @@
 #
 # @api private
 class OodCore::Job::Adapters::Lsf::Batch
-  attr_reader :bindir, :libdir, :envdir, :serverdir
+  attr_reader :bindir, :libdir, :envdir, :serverdir, :cluster
 
   # The root exception class that all LSF-specific exceptions inherit
   # from
   class Error < StandardError; end
 
   # @param bin [#to_s] path to LSF installation binaries
-  def initialize(bindir: "", envdir: "", libdir: "", serverdir: "", **_)
+  def initialize(bindir: "", envdir: "", libdir: "", serverdir: "", cluster: "", **_)
     @bindir = Pathname.new(bindir.to_s)
 
     @envdir = Pathname.new(envdir.to_s)
     @libdir = Pathname.new(libdir.to_s)
     @serverdir = Pathname.new(serverdir.to_s)
+    @cluster = cluster.to_s
   end
 
   def default_env
@@ -127,11 +128,19 @@ class OodCore::Job::Adapters::Lsf::Batch
     end
   end
 
+  def cluster_args
+    if cluster.nil? || cluster.strip.empty?
+      []
+    else
+      ["-m", cluster]
+    end
+  end
+
   private
     # Call a forked Lsf command for a given cluster
     def call(cmd, *args, env: {}, stdin: "")
       cmd = bindir.join(cmd.to_s).to_s
-      #TODO: args = ["-m", cluster] + args.map(&:to_s)
+      args = cluster_args + args
       env = default_env.merge(env.to_h)
       o, e, s = Open3.capture3(env, cmd, *(args.map(&:to_s)), stdin_data: stdin.to_s)
       s.success? ? o : raise(Error, e)

data/lib/ood_core/job/adapters/lsf/helper.rb

@@ -68,7 +68,7 @@ class OodCore::Job::Adapters::Lsf::Helper
   #
   # my guess is: hours:minutes:seconds.????
   #
-  # @return [Fixnum, nil] cpu used as seconds
+  # @return [Integer, nil] cpu used as seconds
   def parse_cpu_used(cpu_used)
     if cpu_used =~ /^(\d+):(\d+):(\d+)\..*$/
       $1.to_i*3600 + $2.to_i*60 + $3.to_i
@@ -88,6 +88,7 @@ class OodCore::Job::Adapters::Lsf::Helper
     args += (script.rerunnable ? ["-r"] : ["-rn"]) unless script.rerunnable.nil?
     args += ["-b", script.start_time.localtime.strftime("%Y:%m:%d:%H:%M")] unless script.start_time.nil?
     args += ["-W", (script.wall_time / 60).to_i] unless script.wall_time.nil?
+    args += ["-L", script.shell_path.to_s] unless script.shell_path.nil?
 
     # input and output files
     args += ["-i", script.input_path] unless script.input_path.nil?

data/lib/ood_core/job/adapters/pbspro.rb

@@ -227,6 +227,7 @@ module OodCore
             args += ["-m", "e"]
           end
           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 PBS Pro)
           args += ["-o", script.output_path] unless script.output_path.nil?
           args += ["-e", script.error_path] unless script.error_path.nil?

data/lib/ood_core/job/adapters/slurm.rb

@@ -298,8 +298,15 @@ module OodCore
           # Set native options
           args += script.native if script.native
 
+          # Set content
+          content = if script.shell_path.nil?
+                      script.content
+                    else
+                      "#!#{script.shell_path}\n#{script.content}"
+                    end
+
           # Submit job
-          @slurm.submit_string(script.content, args: args, env: env)
+          @slurm.submit_string(content, args: args, env: env)
         rescue Batch::Error => e
           raise JobAdapterError, e.message
         end

data/lib/ood_core/job/adapters/torque.rb

@@ -83,6 +83,7 @@ module OodCore
           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?

data/lib/ood_core/job/info.rb

@@ -33,7 +33,7 @@ module OodCore
       attr_reader :accounting_id
 
       # Number of procs allocated for job
-      # @return [Fixnum, nil] allocated total number of procs
+      # @return [Integer, nil] allocated total number of procs
       attr_reader :procs
 
       # Name of the queue in which the job was queued or started
@@ -41,15 +41,15 @@ module OodCore
       attr_reader :queue_name
 
       # The accumulated wall clock time in seconds
-      # @return [Fixnum, nil] wallclock time
+      # @return [Integer, nil] wallclock time
       attr_reader :wallclock_time
 
       # The total wall clock time limit in seconds
-      # @return [Fixnum, nil] wallclock time limit
+      # @return [Integer, nil] wallclock time limit
       attr_reader :wallclock_limit
 
       # The accumulated CPU time in seconds
-      # @return [Fixnum, nil] cpu time
+      # @return [Integer, nil] cpu time
       attr_reader :cpu_time
 
       # The time at which the job was submitted
@@ -139,7 +139,7 @@ module OodCore
       end
 
       # Generate a hash value for this object
-      # @return [Fixnum] hash value of object
+      # @return [Integer] hash value of object
       def hash
         [self.class, to_h].hash
       end

data/lib/ood_core/job/node_info.rb

@@ -7,7 +7,7 @@ module OodCore
       attr_reader :name
 
       # The number of procs reserved on the given machine
-      # @return [Fixnum, nil] number of procs
+      # @return [Integer, nil] number of procs
       attr_reader :procs
 
       # @param name [#to_s] node name
@@ -38,7 +38,7 @@ module OodCore
       end
 
       # Generate a hash value for this object
-      # @return [Fixnum] hash value of object
+      # @return [Integer] hash value of object
       def hash
         [self.class, to_h].hash
       end

data/lib/ood_core/job/script.rb

@@ -54,6 +54,10 @@ module OodCore
       # @return [String, nil] name of job
       attr_reader :job_name
 
+      # Path to file specifying the login shell of the job
+      # @return [Pathname, nil] file path specifying login shell
+      attr_reader :shell_path
+
       # Path to file specifying the input stream of the job
       # @return [Pathname, nil] file path specifying input stream
       attr_reader :input_path
@@ -75,7 +79,7 @@ module OodCore
       attr_reader :queue_name
 
       # The scheduling priority for the job
-      # @return [Fixnum, nil] scheduling priority
+      # @return [Integer, nil] scheduling priority
       attr_reader :priority
 
       # The earliest time when the job may be eligible to run
@@ -84,7 +88,7 @@ module OodCore
 
       # The maximum amount of real time during which the job can be running in
       # seconds
-      # @return [Fixnum, nil] max real time
+      # @return [Integer, nil] max real time
       attr_reader :wall_time
 
       # The attribute used for job accounting purposes
@@ -106,6 +110,8 @@ module OodCore
       # @param email_on_started [Boolean, nil] whether email when job starts
       # @param email_on_terminated [Boolean, nil] whether email when job ends
       # @param job_name [#to_s, nil] name of job
+      # @param shell_path [#to_s, nil] file path specifying login shell
+      # @param error_path [#to_s, nil] file path specifying error stream
       # @param input_path [#to_s, nil] file path specifying input stream
       # @param output_path [#to_s, nil] file path specifying output stream
       # @param error_path [#to_s, nil] file path specifying error stream
@@ -119,10 +125,10 @@ module OodCore
       def initialize(content:, args: nil, submit_as_hold: nil, rerunnable: nil,
                      job_environment: nil, workdir: nil, email: nil,
                      email_on_started: nil, email_on_terminated: nil,
-                     job_name: nil, input_path: nil, output_path: nil,
-                     error_path: nil, reservation_id: nil, queue_name: nil,
-                     priority: nil, start_time: nil, wall_time: nil,
-                     accounting_id: nil, native: nil, **_)
+                     job_name: nil, shell_path: nil, input_path: nil,
+                     output_path: nil, error_path: nil, reservation_id: nil,
+                     queue_name: nil, priority: nil, start_time: nil,
+                     wall_time: nil, accounting_id: nil, native: nil, **_)
         @content = content.to_s
 
         @submit_as_hold      = submit_as_hold
@@ -135,6 +141,7 @@ module OodCore
         @workdir          = workdir         && Pathname.new(workdir.to_s)
         @email            = email           && Array.wrap(email).map(&:to_s)
         @job_name         = job_name        && job_name.to_s
+        @shell_path       = shell_path      && Pathname.new(shell_path.to_s)
         @input_path       = input_path      && Pathname.new(input_path.to_s)
         @output_path      = output_path     && Pathname.new(output_path.to_s)
         @error_path       = error_path      && Pathname.new(error_path.to_s)
@@ -161,6 +168,7 @@ module OodCore
           email_on_started:    email_on_started,
           email_on_terminated: email_on_terminated,
           job_name:            job_name,
+          shell_path:          shell_path,
           input_path:          input_path,
           output_path:         output_path,
           error_path:          error_path,
@@ -189,7 +197,7 @@ module OodCore
       end
 
       # Generate a hash value for this object
-      # @return [Fixnum] hash value of object
+      # @return [Integer] hash value of object
       def hash
         [self.class, to_h].hash
       end

data/lib/ood_core/job/status.rb

@@ -72,7 +72,7 @@ module OodCore
       end
 
       # Generate a hash value for this object
-      # @return [Fixnum] hash value of object
+      # @return [Integer] hash value of object
       def hash
         [self.class, to_sym].hash
       end

data/lib/ood_core/version.rb

@@ -1,4 +1,4 @@
 module OodCore
   # The current version of {OodCore}
-  VERSION = "0.2.1"
+  VERSION = "0.3.0"
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: ood_core
 version: !ruby/object:Gem::Version
-  version: 0.2.1
+  version: 0.3.0
 platform: ruby
 authors:
 - Jeremy Nicklas
 autorequire: 
 bindir: exe
 cert_chain: []
-date: 2018-01-26 00:00:00.000000000 Z
+date: 2018-04-05 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: ood_support
@@ -179,7 +179,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.4.5
+rubygems_version: 2.4.5.4
 signing_key: 
 specification_version: 4
 summary: Open OnDemand core library