ood_core 0.9.3 → 0.11.4

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

@@ -192,7 +192,7 @@ module OodCore
           # @return [String] the id of the job that was created
           def submit_string(str, args: [], env: {})
             args = args.map(&:to_s) + ["--parsable"]
-            env = {"SBATCH_EXPORT" => "NONE"}.merge env.each_with_object({}) { |(k, v), h| h[k.to_s] = v.to_s }
+            env = env.to_h.each_with_object({}) { |(k, v), h| h[k.to_s] = v.to_s }
             call("sbatch", *args, env: env, stdin: str.to_s).strip.split(";").first
           end
 
@@ -394,7 +394,7 @@ module OodCore
 
           # Set environment variables
           env = script.job_environment || {}
-          args += ["--export", script.job_environment.keys.join(",")] unless script.job_environment.nil? || script.job_environment.empty?
+          args += ["--export", export_arg(env, script.copy_environment?)]
 
           # Set native options
           args += script.native if script.native
@@ -530,6 +530,10 @@ module OodCore
           raise JobAdapterError, e.message unless /Invalid job id specified/ =~ e.message
         end
 
+        def directive_prefix
+          '#SBATCH'
+        end
+
         private
           # Convert duration to seconds
           def duration_in_seconds(time)
@@ -623,6 +627,25 @@ module OodCore
 
             Info.new(**parent_task_hash)
           end
+
+
+          # we default to export NONE, but SLURM defaults to ALL.
+          # we do this bc SLURM setups a new environment, loading /etc/profile
+          # and all giving 'module' function (among other things shells give),
+          # where the PUN did not.
+          # --export=ALL export the PUN's environment.
+          def export_arg(env, copy_environment)
+            if !env.empty? && !copy_environment
+              env.keys.join(",")
+            elsif !env.empty? && copy_environment
+              "ALL," + env.keys.join(",")
+            elsif env.empty? && copy_environment
+              # only this option changes behaivor dramatically
+              "ALL"
+            else
+              "NONE"
+            end
+          end
       end
     end
   end

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

@@ -155,6 +155,7 @@ module OodCore
             # Set environment variables
             env = script.job_environment.to_h
             args += ["-v", env.keys.join(",")] unless env.empty?
+            args += ["-V"] if script.copy_environment?
 
             # If error_path is not specified we join stdout & stderr (as this
             # mimics what the other resource managers do)
@@ -288,6 +289,10 @@ module OodCore
           raise JobAdapterError, e.message
         end
 
+        def directive_prefix
+          '#QSUB'
+        end
+
         private
           # Convert duration to seconds
           def duration_in_seconds(time)

data/lib/ood_core/job/array_ids.rb

@@ -10,68 +10,33 @@
 module OodCore
   module Job
     class ArrayIds
-      class Error < StandardError ; end
+      attr_reader :spec_string
 
-      attr_reader :ids
       def initialize(spec_string)
-        @ids = []
-        begin
-          parse_spec_string(spec_string) if spec_string
-        rescue Error
-        end
-      end
-
-      protected
-      def parse_spec_string(spec_string)
-        @ids = get_components(spec_string).map{
-          |component| process_component(component)
-        }.reduce(:+).sort
+        @spec_string = spec_string
       end
 
-      def get_components(spec_string)
-        base = discard_percent_modifier(spec_string)
-        raise Error unless base
-        base.split(',')
+      def ids
+        @ids ||= parse_spec_string(spec_string)
       end
 
-      # A few adapters use percent to define an arrays maximum number of
-      # simultaneous tasks. The percent is expected to come at the end.
-      def discard_percent_modifier(spec_string)
-        spec_string.split('%').first
-      end
+      protected
 
-      def process_component(component)
-        if is_range?(component)
-          get_range(component)
-        elsif numbers_valid?([component])
-          [ component.to_i ]
-        else
-          raise Error
+      def parse_spec_string(spec_string)
+        return [] unless spec_string
+
+        rx = /^(\d+)-?(\d+)?:?(\d+)?%?\d*$/
+        spec_string.split(',').reduce([]) do |ids, spec|
+          if rx =~ spec
+            start = ($1 || 1).to_i
+            finish = ($2 || start).to_i
+            step = ($3 || 1).to_i
+            ids.concat (start..finish).step(step).to_a
+          end
+
+          ids
         end
       end
-
-      def get_range(component)
-        raw_range, raw_step = component.split(':')
-        start, stop = raw_range.split('-')
-        raise Error unless numbers_valid?(
-          # Only include Step if it is not nil
-          [start, stop].tap { |a| a << raw_step if raw_step }
-        )
-        range = Range.new(start.to_i, stop.to_i)
-        step = raw_step.to_i
-        step = 1 if step == 0
-
-        range.step(step).to_a
-      end
-
-      def is_range?(component)
-        component.include?('-')
-      end
-
-      # Protect against Ruby's String#to_i returning 0 for arbitrary strings
-      def numbers_valid?(numbers)
-        numbers.all? { |str| /^[0-9]+$/ =~ str }
-      end
     end
   end
 end

data/lib/ood_core/job/script.rb

@@ -104,6 +104,11 @@ module OodCore
       # @return [Object, nil] native specifications
       attr_reader :native
 
+      # Flag whether the job should contain a copy of its calling environment
+      # @return [Boolean] copy environment
+      attr_reader :copy_environment
+      alias_method :copy_environment?, :copy_environment
+
       # @param content [#to_s] the script content
       # @param args [Array<#to_s>, nil] arguments supplied to script
       # @param submit_as_hold [Boolean, nil] whether job is held after submit
@@ -126,13 +131,15 @@ module OodCore
       # @param wall_time [#to_i, nil] max real time
       # @param accounting_id [#to_s, nil] accounting id
       # @param native [Object, nil] native specifications
+      # @param copy_environment [Boolean, nil] copy the environment
       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, 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, job_array_request: nil, native: nil, **_)
+                     wall_time: nil, accounting_id: nil, job_array_request: nil,
+                     native: nil, copy_environment: nil, **_)
         @content = content.to_s
 
         @submit_as_hold      = submit_as_hold
@@ -157,6 +164,7 @@ module OodCore
         @accounting_id      = accounting_id     && accounting_id.to_s
         @job_array_request  = job_array_request && job_array_request.to_s
         @native             = native
+        @copy_environment   = (copy_environment.nil?) ? nil : !! copy_environment
       end
 
       # Convert object to hash
@@ -184,7 +192,8 @@ module OodCore
           wall_time:           wall_time,
           accounting_id:       accounting_id,
           job_array_request:   job_array_request,
-          native:              native
+          native:              native,
+          copy_environment:    copy_environment
         }
       end
 

data/lib/ood_core/version.rb

@@ -1,4 +1,4 @@
 module OodCore
   # The current version of {OodCore}
-  VERSION = "0.9.3"
+  VERSION = "0.11.4"
 end

data/ood_core.gemspec

@@ -25,8 +25,9 @@ Gem::Specification.new do |spec|
   spec.add_runtime_dependency "ood_support", "~> 0.0.2"
   spec.add_runtime_dependency "ffi", "~> 1.9", ">= 1.9.6"
   spec.add_development_dependency "bundler", "~> 1.7"
-  spec.add_development_dependency "rake", "~> 10.0"
+  spec.add_development_dependency "rake", "~> 13.0.1"
   spec.add_development_dependency "rspec", "~> 3.0"
   spec.add_development_dependency "pry", "~> 0.10"
   spec.add_development_dependency "timecop", "~> 0.8"
+  spec.add_development_dependency "climate_control", "~> 0.2.0"
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: ood_core
 version: !ruby/object:Gem::Version
-  version: 0.9.3
+  version: 0.11.4
 platform: ruby
 authors:
 - Eric Franz
@@ -10,7 +10,7 @@ authors:
 autorequire: 
 bindir: exe
 cert_chain: []
-date: 2019-05-09 00:00:00.000000000 Z
+date: 2020-05-27 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: ood_support
@@ -66,14 +66,14 @@ dependencies:
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '10.0'
+        version: 13.0.1
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '10.0'
+        version: 13.0.1
 - !ruby/object:Gem::Dependency
   name: rspec
   requirement: !ruby/object:Gem::Requirement
@@ -116,6 +116,20 @@ dependencies:
     - - "~>"
       - !ruby/object:Gem::Version
         version: '0.8'
+- !ruby/object:Gem::Dependency
+  name: climate_control
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 0.2.0
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 0.2.0
 description: Open OnDemand core library that provides support for an HPC Center to
   globally define HPC services that web applications can then take advantage of.
 email:
@@ -147,9 +161,14 @@ files:
 - lib/ood_core/cluster.rb
 - lib/ood_core/clusters.rb
 - lib/ood_core/errors.rb
+- lib/ood_core/invalid_cluster.rb
 - lib/ood_core/job/adapter.rb
 - lib/ood_core/job/adapters/drmaa.rb
 - lib/ood_core/job/adapters/helper.rb
+- lib/ood_core/job/adapters/linux_host.rb
+- lib/ood_core/job/adapters/linux_host/launcher.rb
+- lib/ood_core/job/adapters/linux_host/templates/email.erb.sh
+- lib/ood_core/job/adapters/linux_host/templates/script_wrapper.erb.sh
 - lib/ood_core/job/adapters/lsf.rb
 - lib/ood_core/job/adapters/lsf/batch.rb
 - lib/ood_core/job/adapters/lsf/helper.rb
@@ -196,8 +215,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubyforge_project: 
-rubygems_version: 2.6.14
+rubygems_version: 3.0.3
 signing_key: 
 specification_version: 4
 summary: Open OnDemand core library