add shell path as script option

Fixes #82

CHANGELOG.md

@@ -9,6 +9,8 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 ### 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)
 
 ## [0.2.1] - 2018-01-26
 ### Changed

lib/ood_core/batch_connect/template.rb

@@ -58,7 +58,9 @@ def initialize(context = {})
       # @return [String] rendered template
       def to_s
         <<-EOT.gsub(/^ {10}/, '')
-          #!/bin/bash
+          #
+          # Generated with ood_core v#{VERSION}
+          #
 
           #{script_wrapper}
         EOT

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

@@ -88,6 +88,7 @@ def batch_submit_args(script, after: [], afterok: [], afternotok: [], afterany:
     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?

lib/ood_core/job/adapters/pbspro.rb

@@ -227,6 +227,7 @@ def submit(script, after: [], afterok: [], afternotok: [], afterany: [])
             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?

lib/ood_core/job/adapters/slurm.rb

@@ -298,8 +298,15 @@ def submit(script, after: [], afterok: [], afternotok: [], afterany: [])
           # 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

lib/ood_core/job/adapters/torque.rb

@@ -83,6 +83,7 @@ def submit(script, after: [], afterok: [], afternotok: [], afterany: [])
           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?

lib/ood_core/job/script.rb

@@ -54,6 +54,10 @@ class Script
       # @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
@@ -106,6 +110,8 @@ class Script
       # @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 @@ class Script
       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 @@ def initialize(content:, args: nil, submit_as_hold: nil, rerunnable: nil,
         @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 @@ def to_h
           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,

spec/job/adapters/lsf/helper_spec.rb

@@ -146,6 +146,10 @@ def args_for(attrs = {})
       expect(args_for(job_name: "my_job")).to eq({args: ["-J", "my_job"], env: {}})
     end
 
+    it "with :shell_path" do
+      expect(args_for(shell_path: "/path/to/shell")).to eq({args: ["-L", "/path/to/shell"], env: {}})
+    end
+
     it "with :workdir" do
       expect(args_for(workdir: "/path/to/workdir")).to eq({args: ["-cwd", "/path/to/workdir"], env: {}})
     end

spec/job/adapters/pbspro_spec.rb

@@ -151,6 +151,12 @@ def build_script(opts = {})
       it { expect(pbspro).to have_received(:submit_string).with(content, args: ["-N", "my_job", "-j", "oe"], chdir: nil) }
     end
 
+    context "with :shell_path" do
+      before { adapter.submit(build_script(shell_path: "/path/to/shell")) }
+
+      it { expect(pbspro).to have_received(:submit_string).with(content, args: ["-S", Pathname.new("/path/to/shell"), "-j", "oe"], chdir: nil) }
+    end
+
     context "with :input_path" do
       before { adapter.submit(build_script(input_path: "/path/to/input")) }
 

spec/job/adapters/slurm_spec.rb

@@ -149,6 +149,12 @@ def build_script(opts = {})
       it { expect(slurm).to have_received(:submit_string).with(content, args: ["-J", "my_job"], env: {}) }
     end
 
+    context "with :shell_path" do
+      before { adapter.submit(build_script(shell_path: "/path/to/shell")) }
+
+      it { expect(slurm).to have_received(:submit_string).with("#!/path/to/shell\n#{content}", args: [], env: {}) }
+    end
+
     context "with :input_path" do
       before { adapter.submit(build_script(input_path: "/path/to/input")) }
 

spec/job/adapters/torque_spec.rb

@@ -150,6 +150,12 @@ def build_script(opts = {})
       it { expect(pbs).to have_received(:submit_string).with(content, queue: nil, headers: {Join_Path: "oe", Job_Name: "my_job"}, resources: {}, envvars: {}) }
     end
 
+    context "with :shell_path" do
+      before { adapter.submit(build_script(shell_path: "/path/to/shell")) }
+
+      it { expect(pbs).to have_received(:submit_string).with(content, queue: nil, headers: {Join_Path: "oe", Shell_Path_List: Pathname.new("/path/to/shell")}, resources: {}, envvars: {}) }
+    end
+
     context "with :input_path" do
       before { adapter.submit(build_script(input_path: "/path/to/input")) }
 

spec/job/script_spec.rb

@@ -25,6 +25,7 @@ def build_script(opts = {})
   it { is_expected.to respond_to(:email_on_started) }
   it { is_expected.to respond_to(:email_on_terminated) }
   it { is_expected.to respond_to(:job_name) }
+  it { is_expected.to respond_to(:shell_path) }
   it { is_expected.to respond_to(:input_path) }
   it { is_expected.to respond_to(:output_path) }
   it { is_expected.to respond_to(:error_path) }
@@ -115,6 +116,12 @@ def build_script(opts = {})
     it { is_expected.to eq("my_job") }
   end
 
+  describe "#shell_path" do
+    subject { build_script(shell_path: double(to_s: "/path/to/shell")).shell_path }
+
+    it { is_expected.to eq(Pathname.new("/path/to/shell")) }
+  end
+
   describe "#input_path" do
     subject { build_script(input_path: double(to_s: "/path/to/input")).input_path }
 
@@ -189,6 +196,7 @@ def build_script(opts = {})
     it { is_expected.to have_key(:email_on_started) }
     it { is_expected.to have_key(:email_on_terminated) }
     it { is_expected.to have_key(:job_name) }
+    it { is_expected.to have_key(:shell_path) }
     it { is_expected.to have_key(:input_path) }
     it { is_expected.to have_key(:output_path) }
     it { is_expected.to have_key(:error_path) }