ood_core 0.11.4 → 0.12.0

checksums.yaml

@@ -1,7 +1,7 @@
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-  data.tar.gz: f30a99239692b568b30453a0c519cbf8adb977589c4dfa35132bd4a0f6019c17
+  metadata.gz: bb944d43beb0aced99e13efb2ef10bf33f9666c705c50ca5ae1727751de43073
+  data.tar.gz: 6e3cd66160be3bbd63124d6f2ddc794bce4ae64e385977828faba5dfd28ff838
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+  data.tar.gz: 15481101ad3120d3e8457612f2b8a8be4f1e268b38538b18b710f27887836f7a47eac3bf2e89d8f73745ae96ae78e21cd5ba5afefb4161cf95f435d6f2fdf001

data/CHANGELOG.md

@@ -6,6 +6,16 @@ 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]
+## [0.12.0] - 2020-08-05
+### Added
+- qos option to Slurm and Torque [#205](https://github.com/OSC/ood_core/pull/205)
+- native hash returned in qstat for SGE adapter [#198](https://github.com/OSC/ood_core/pull/198)
+- option for specifying `submit_host` to submit jobs via ssh on other host [#204](https://github.com/OSC/ood_core/pull/204)
+
+### Fixed
+- SGE handle milliseconds instead of seconds when milliseconds used [#206](https://github.com/OSC/ood_core/issues/206)
+- Torque's native "hash" for job submission now handles env vars values with spaces [#202](https://github.com/OSC/ood_core/pull/202)
+
 ## [0.11.4] - 2020-05-27
 ### Fixed
 - Environment exports in SLURM while implementing [#158](https://github.com/OSC/ood_core/issues/158)
@@ -233,7 +243,8 @@ 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/v0.11.4...HEAD
+[Unreleased]: https://github.com/OSC/ood_core/compare/v0.12.0...HEAD
+[0.12.0]: https://github.com/OSC/ood_core/compare/v0.11.4...v0.12.0
 [0.11.4]: https://github.com/OSC/ood_core/compare/v0.11.3...v0.11.4
 [0.11.3]: https://github.com/OSC/ood_core/compare/v0.11.2...v0.11.3
 [0.11.2]: https://github.com/OSC/ood_core/compare/v0.11.1...v0.11.2

data/README.md

@@ -4,12 +4,13 @@
 ![GitHub Release](https://img.shields.io/github/release/osc/ood_core.svg)
 ![GitHub License](https://img.shields.io/github/license/osc/ood_core.svg)
 
-Welcome to your new gem! In this directory, you'll find the files you need to
-be able to package up your Ruby library into a gem. Put your Ruby code in the
-file `lib/ood_core`. To experiment with that code, run `bin/console` for an
-interactive prompt.
+- Website: http://openondemand.org/
+- Website repo with JOSS publication: https://github.com/OSC/Open-OnDemand
+- Documentation: https://osc.github.io/ood-documentation/master/
+- Main code repo: https://github.com/OSC/ondemand
+- Core library repo: https://github.com/OSC/ood_core
 
-TODO: Delete this and the text above, and describe your gem
+OnDemand core library with adapters for each batch scheduler.
 
 ## Installation
 

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

@@ -12,7 +12,26 @@ module OodCore
         def self.bin_path(cmd, bin_default, bin_overrides)
           bin_overrides.fetch(cmd.to_s) { Pathname.new(bin_default.to_s).join(cmd.to_s).to_s }
         end
+        
+        # Gets a command that submits command on another host via ssh
+        # @param submit_host [String] where to submit the command
+        # @param cmd [String] the desired command to execute on another host
+        # @param cmd_args [Array] arguments to the command specified above
+        # @param strict_host_checking [Bool] whether to use strict_host_checking
+        # @param env [Hash] env variables to be set w/ssh
+        #
+        # @return cmd [String] command wrapped in ssh if submit_host is present
+        # @return args [Array] command arguments including ssh_flags and original command
+        def self.ssh_wrap(submit_host, cmd, cmd_args, strict_host_checking = true, env = {})
+          return cmd, cmd_args if submit_host.to_s.empty?
+
+          check_host = strict_host_checking ? "yes" : "no"
+          args = ['-o', 'BatchMode=yes', '-o', 'UserKnownHostsFile=/dev/null', '-o', "StrictHostKeyChecking=#{check_host}", "#{submit_host}"]
+          env.each{|key, value| args.push("export #{key}=#{value};")}
+
+          return 'ssh', args + [cmd] + cmd_args
+        end
       end
     end
   end
-end
+end

data/lib/ood_core/job/adapters/linux_host/launcher.rb

@@ -174,6 +174,7 @@ class OodCore::Job::Adapters::LinuxHost::Launcher
         'session_name' => session_name,
         'singularity_bin' => singularity_bin,
         'singularity_image' => singularity_image(script.native),
+        'ssh_hosts' => ssh_hosts,
         'tmux_bin' => tmux_bin,
       }.each{
         |key, value| bnd.local_variable_set(key, value)

data/lib/ood_core/job/adapters/linux_host/templates/script_wrapper.erb.sh

@@ -1,5 +1,19 @@
 #!/bin/bash
-hostname
+SSH_HOSTS=(<%= ssh_hosts.join(' ').to_s %>)
+hostnames=`hostname -A`
+for host in ${SSH_HOSTS[@]}
+do
+    if [[ " ${hostnames[@]} " =~ " ${host} " ]]; then
+        hostname=$host
+    fi
+done
+
+if [ -z "$hostname" ]; then
+    printf >&2 "ERROR: Can't start job on [${hostnames[@]}] because it does not match any hostname configured \nin ssh_hosts [${SSH_HOSTS[@]}]. The output of 'hostname -A' must match an entry in ssh_hosts \nfrom the cluster configuration."
+    exit 1
+fi
+
+echo $hostname
 
 # Put the script into a temp file on localhost
 <% if debug %>

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

@@ -14,6 +14,7 @@ module OodCore
       # @option config [#to_s] :serverdir ('') Path to lsf client etc dir
       # @option config [#to_s] :cluster ('') name of cluster, if in multi-cluster mode
       # @option config [#to_h] :bin_overrides ({}) Optional overrides to LSF client executables
+      # @option config [#to_s] :submit_host ('') Host to submit commands to
       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

@@ -2,21 +2,22 @@
 #
 # @api private
 class OodCore::Job::Adapters::Lsf::Batch
-  attr_reader :bindir, :libdir, :envdir, :serverdir, :cluster, :bin_overrides
+  attr_reader :bindir, :libdir, :envdir, :serverdir, :cluster, :bin_overrides, :submit_host, :strict_host_checking
 
   # 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: "", cluster: "", bin_overrides: {}, **_)
+  def initialize(bindir: "", envdir: "", libdir: "", serverdir: "", cluster: "", bin_overrides: {}, submit_host: "", strict_host_checking: true, **_)
     @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
     @bin_overrides = bin_overrides
+    @submit_host = submit_host.to_s
+    @strict_host_checking = strict_host_checking
   end
 
   def default_env
@@ -143,6 +144,7 @@ class OodCore::Job::Adapters::Lsf::Batch
       cmd = OodCore::Job::Adapters::Helper.bin_path(cmd, bindir, bin_overrides)
       args = cluster_args + args
       env = default_env.merge(env.to_h)
+      cmd, args = OodCore::Job::Adapters::Helper.ssh_wrap(submit_host, cmd, args, strict_host_checking, env)
       o, e, s = Open3.capture3(env, cmd, *(args.map(&:to_s)), stdin_data: stdin.to_s)
       s.success? ? o : raise(Error, e)
     end

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

@@ -78,40 +78,40 @@ class OodCore::Job::Adapters::Lsf::Helper
   def batch_submit_args(script, after: [], afterok: [], afternotok: [], afterany: [])
     args = []
 
-    args += ["-P", script.accounting_id] unless script.accounting_id.nil?
-    args += ["-cwd", script.workdir.to_s] unless script.workdir.nil?
-    args += ["-J", script.job_name] unless script.job_name.nil?
-    args[-1] += "[#{script.job_array_request}]" unless script.job_array_request.nil?
-
-    args += ["-q", script.queue_name] unless script.queue_name.nil?
-    args += ["-U", script.reservation_id] unless script.reservation_id.nil?
-    args += ["-sp", script.priority] unless script.priority.nil?
-    args += ["-H"] if script.submit_as_hold
-    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?
+    args.concat ["-P", script.accounting_id] unless script.accounting_id.nil?
+    args.concat ["-cwd", script.workdir.to_s] unless script.workdir.nil?
+    args.concat ["-J", script.job_name] unless script.job_name.nil?
+    args[-1].concat "[#{script.job_array_request}]" unless script.job_array_request.nil?
+
+    args.concat ["-q", script.queue_name] unless script.queue_name.nil?
+    args.concat ["-U", script.reservation_id] unless script.reservation_id.nil?
+    args.concat ["-sp", script.priority] unless script.priority.nil?
+    args.concat ["-H"] if script.submit_as_hold
+    args.concat (script.rerunnable ? ["-r"] : ["-rn"]) unless script.rerunnable.nil?
+    args.concat ["-b", script.start_time.localtime.strftime("%Y:%m:%d:%H:%M")] unless script.start_time.nil?
+    args.concat ["-W", (script.wall_time / 60).to_i] unless script.wall_time.nil?
+    args.concat ["-L", script.shell_path.to_s] unless script.shell_path.nil?
 
     # environment
     env = script.job_environment || {}
     # To preserve pre-existing behavior we only act when true or false, when nil we do nothing
     if script.copy_environment?
-      args += ["-env", (["all"] + env.keys).join(",")]
+      args.concat ["-env", (["all"] + env.keys).join(",")]
     elsif script.copy_environment? == false
-      args += ["-env", (["none"] + env.keys).join(",")]
+      args.concat ["-env", (["none"] + env.keys).join(",")]
     end
 
     # input and output files
-    args += ["-i", script.input_path] unless script.input_path.nil?
-    args += ["-o", script.output_path] unless script.output_path.nil?
-    args += ["-e", script.error_path] unless script.error_path.nil?
+    args.concat ["-i", script.input_path] unless script.input_path.nil?
+    args.concat ["-o", script.output_path] unless script.output_path.nil?
+    args.concat ["-e", script.error_path] unless script.error_path.nil?
 
     # email
-    args += ["-B"] if script.email_on_started
-    args += ["-N"] if script.email_on_terminated
-    args += ["-u", script.email.join(",")] unless script.email.nil? || script.email.empty?
+    args.concat ["-B"] if script.email_on_started
+    args.concat ["-N"] if script.email_on_terminated
+    args.concat ["-u", script.email.join(",")] unless script.email.nil? || script.email.empty?
 
-    args += script.native unless script.native.nil?
+    args.concat script.native unless script.native.nil?
 
     {args: args, env: env}
   end

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

@@ -10,17 +10,21 @@ module OodCore
       # Build the PBS Pro adapter from a configuration
       # @param config [#to_h] the configuration for job adapter
       # @option config [Object] :host (nil) The batch server host
+      # @option config [Object] :submit_host ("") The login node where the job is submitted
+      # @option config [Object] :strict_host_checking (true) Whether to use strict host checking when ssh to submit_host
       # @option config [Object] :exec (nil) Path to PBS Pro executables
       # @option config [Object] :qstat_factor (nil) Deciding factor on how to
       #   call qstat for a user
       # @option config [#to_h] :bin_overrides ({}) Optional overrides to PBS Pro client executables
       def self.build_pbspro(config)
         c = config.to_h.compact.symbolize_keys
-        host = c.fetch(:host, nil)
-        pbs_exec = c.fetch(:exec, nil)
-        qstat_factor = c.fetch(:qstat_factor, nil)
-        bin_overrides = c.fetch(:bin_overrides, {})
-        pbspro = Adapters::PBSPro::Batch.new(host: host, pbs_exec: pbs_exec, bin_overrides: bin_overrides)
+        host                 = c.fetch(:host, nil)
+        submit_host          = c.fetch(:submit_host, "")
+        strict_host_checking = c.fetch(:strict_host_checking, true)
+        pbs_exec             = c.fetch(:exec, nil)
+        qstat_factor         = c.fetch(:qstat_factor, nil)
+        bin_overrides         = c.fetch(:bin_overrides, {})
+        pbspro = Adapters::PBSPro::Batch.new(host: host, submit_host: submit_host, strict_host_checking: strict_host_checking, pbs_exec: pbs_exec, bin_overrides: bin_overrides)
         Adapters::PBSPro.new(pbspro: pbspro, qstat_factor: qstat_factor)
       end
     end
@@ -41,6 +45,18 @@ module OodCore
           # @return [String, nil] the batch server host
           attr_reader :host
 
+          # The login node to submit the job via ssh
+          # @example
+          #   my_batch.submit_host #=> "my_batch.server.edu"
+          # @return [String, nil] the login node
+          attr_reader :submit_host
+
+          # Whether to use strict host checking when ssh to submit_host
+          # @example
+          #   my_batch.strict_host_checking #=> "false"
+          # @return [Bool, true] the login node; true if not present
+          attr_reader :strict_host_checking
+
           # The path containing the PBS executables
           # @example
           #   my_batch.pbs_exec.to_s #=> "/usr/local/pbspro/10.0.0
@@ -58,11 +74,15 @@ module OodCore
           class Error < StandardError; end
 
           # @param host [#to_s, nil] the batch server host
+          # @param submit_host [#to_s, nil] the login node to ssh to
+          # @param strict_host_checking [bool, true] wheter to use strict host checking when ssh to submit_host
           # @param exec [#to_s, nil] path to pbs executables
-          def initialize(host: nil, pbs_exec: nil, bin_overrides: {})
-            @host = host && host.to_s
-            @pbs_exec = pbs_exec && Pathname.new(pbs_exec.to_s)
-            @bin_overrides = bin_overrides
+          def initialize(host: nil, submit_host: "", strict_host_checking: true, pbs_exec: nil, bin_overrides: {})
+            @host                 = host && host.to_s
+            @submit_host          = submit_host && submit_host.to_s
+            @strict_host_checking = strict_host_checking
+            @pbs_exec             = pbs_exec && Pathname.new(pbs_exec.to_s)
+            @bin_overrides        = bin_overrides
           end
 
           # Get a list of hashes detailing each of the jobs on the batch server
@@ -87,7 +107,7 @@ module OodCore
           # @return [Array<Hash>] list of details for jobs
           def get_jobs(id: "")
             args = ["-f", "-t"]   # display all information
-            args += [id.to_s] unless id.to_s.empty?
+            args.concat [id.to_s] unless id.to_s.empty?
             lines = call("qstat", *args).gsub("\n\t", "").split("\n").map(&:strip)
 
             jobs = []
@@ -159,12 +179,12 @@ module OodCore
               cmd = cmd.to_s
               bindir = (!!pbs_exec) ? pbs_exec.join("bin").to_s : ''
               cmd = OodCore::Job::Adapters::Helper.bin_path(cmd, bindir, bin_overrides)
-              args = args.map(&:to_s)
               env = env.to_h.each_with_object({}) { |(k, v), h| h[k.to_s] = v.to_s }
               env["PBS_DEFAULT"] = host.to_s if host
               env["PBS_EXEC"]    = pbs_exec.to_s if pbs_exec
+              cmd, args = OodCore::Job::Adapters::Helper.ssh_wrap(submit_host, cmd, args, strict_host_checking)
               chdir ||= "."
-              o, e, s = Open3.capture3(env, cmd, *args, stdin_data: stdin.to_s, chdir: chdir.to_s)
+              o, e, s = Open3.capture3(env, cmd, *(args.map(&:to_s)), stdin_data: stdin.to_s, chdir: chdir.to_s)
               s.success? ? o : raise(Error, e)
             end
         end
@@ -227,28 +247,28 @@ module OodCore
           # Set qsub options
           args = []
           # ignore args, can't use these if submitting from STDIN
-          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.concat ["-h"] if script.submit_as_hold
+          args.concat ["-r", script.rerunnable ? "y" : "n"] unless script.rerunnable.nil?
+          args.concat ["-M", script.email.join(",")] unless script.email.nil?
           if script.email_on_started && script.email_on_terminated
-            args += ["-m", "be"]
+            args.concat ["-m", "be"]
           elsif script.email_on_started
-            args += ["-m", "b"]
+            args.concat ["-m", "b"]
           elsif script.email_on_terminated
-            args += ["-m", "e"]
+            args.concat ["-m", "e"]
           end
-          args += ["-N", script.job_name] unless script.job_name.nil?
-          args += ["-S", script.shell_path] unless script.shell_path.nil?
+          args.concat ["-N", script.job_name] unless script.job_name.nil?
+          args.concat ["-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?
+          args.concat ["-o", script.output_path] unless script.output_path.nil?
+          args.concat ["-e", script.error_path] unless script.error_path.nil?
           # Reservations are actually just queues in PBS Pro
-          args += ["-q", script.reservation_id] if !script.reservation_id.nil? && script.queue_name.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 += ["-l", "walltime=#{seconds_to_duration(script.wall_time)}"] unless script.wall_time.nil?
+          args.concat ["-q", script.reservation_id] if !script.reservation_id.nil? && script.queue_name.nil?
+          args.concat ["-q", script.queue_name] unless script.queue_name.nil?
+          args.concat ["-p", script.priority] unless script.priority.nil?
+          args.concat ["-a", script.start_time.localtime.strftime("%C%y%m%d%H%M.%S")] unless script.start_time.nil?
+          args.concat ["-A", script.accounting_id] unless script.accounting_id.nil?
+          args.concat ["-l", "walltime=#{seconds_to_duration(script.wall_time)}"] unless script.wall_time.nil?
 
           # Set dependencies
           depend = []
@@ -256,21 +276,21 @@ module OodCore
           depend << "afterok:#{afterok.join(":")}"       unless afterok.empty?
           depend << "afternotok:#{afternotok.join(":")}" unless afternotok.empty?
           depend << "afterany:#{afterany.join(":")}"     unless afterany.empty?
-          args += ["-W", "depend=#{depend.join(",")}"]   unless depend.empty?
+          args.concat ["-W", "depend=#{depend.join(",")}"]   unless depend.empty?
 
           # Set environment variables
           envvars = script.job_environment.to_h
-          args += ["-v", envvars.map{|k,v| "#{k}=#{v}"}.join(",")] unless envvars.empty?
-          args += ["-V"] if script.copy_environment?
+          args.concat ["-v", envvars.map{|k,v| "#{k}=#{v}"}.join(",")] unless envvars.empty?
+          args.concat ["-V"] if script.copy_environment?
 
           # 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?
+          args.concat ["-j", "oe"] if script.error_path.nil?
 
-          args += ["-J", script.job_array_request] unless script.job_array_request.nil?
+          args.concat ["-J", script.job_array_request] unless script.job_array_request.nil?
 
           # Set native options
-          args += script.native if script.native
+          args.concat script.native if script.native
 
           # Submit job
           @pbspro.submit_string(script.content, args: args, chdir: script.workdir)

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

@@ -15,7 +15,7 @@ end
 class OodCore::Job::Adapters::Sge::Batch
   using OodCore::Refinements::HashExtensions
 
-  attr_reader :bin, :bin_overrides, :conf, :cluster, :helper
+  attr_reader :bin, :bin_overrides, :conf, :cluster, :helper, :submit_host, :strict_host_checking
   
   require "ood_core/job/adapters/sge/qstat_xml_j_r_listener"
   require "ood_core/job/adapters/sge/qstat_xml_r_listener"
@@ -36,6 +36,8 @@ class OodCore::Job::Adapters::Sge::Batch
     @bin              = Pathname.new(config.fetch(:bin, nil).to_s)
     @sge_root         = Pathname.new(config[:sge_root] || ENV['SGE_ROOT'] || "/var/lib/gridengine")
     @bin_overrides    = config.fetch(:bin_overrides, {})
+    @submit_host      = config.fetch(:submit_host, "")
+    @strict_host_checking = config.fetch(:strict_host_checking, true)
 
     # FIXME: hack as this affects env of the process!
     ENV['SGE_ROOT'] = @sge_root.to_s
@@ -62,7 +64,7 @@ class OodCore::Job::Adapters::Sge::Batch
   def get_all(owner: nil)
     listener = QstatXmlRListener.new
     argv = ['qstat', '-r', '-xml']
-    argv += ['-u', owner] unless owner.nil?
+    argv.concat ['-u', owner] unless owner.nil?
     REXML::Parsers::StreamParser.new(call(*argv), listener).parse
 
     listener.parsed_jobs.map{
@@ -166,11 +168,10 @@ class OodCore::Job::Adapters::Sge::Batch
   # Call a forked SGE command for a given batch server
   def call(cmd, *args, env: {}, stdin: "", chdir: nil)
     cmd = OodCore::Job::Adapters::Helper.bin_path(cmd, bin, bin_overrides)
-    args = args.map(&:to_s)
-
     env = env.to_h.each_with_object({}) { |(k, v), h| h[k.to_s] = v.to_s }
+    cmd, args = OodCore::Job::Adapters::Helper.ssh_wrap(submit_host, cmd, args, strict_host_checking, env)
     chdir ||= "."
-    o, e, s = Open3.capture3(env, cmd, *args, stdin_data: stdin.to_s, chdir: chdir.to_s)
+    o, e, s = Open3.capture3(env, cmd, *(args.map(&:to_s)), stdin_data: stdin.to_s, chdir: chdir.to_s)
     s.success? ? o : raise(Error, e)
   end
 

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

@@ -17,38 +17,38 @@ class OodCore::Job::Adapters::Sge::Helper
     raise_error_on_unsupported_args(script, after: after, afterok: afterok, afternotok: afternotok, afterany: afterany)
 
     args = []
-    args += ['-h'] if script.submit_as_hold
-    args += ['-r', 'yes'] if script.rerunnable
-    script.job_environment.each_pair {|k, v| args += ['-v', "#{k.to_s}=#{v.to_s}"]} unless script.job_environment.nil?
-    args += ["-V"] if script.copy_environment?
+    args.concat ['-h'] if script.submit_as_hold
+    args.concat ['-r', 'yes'] if script.rerunnable
+    script.job_environment.each_pair {|k, v| args.concat ['-v', "#{k.to_s}=#{v.to_s}"]} unless script.job_environment.nil?
+    args.concat ["-V"] if script.copy_environment?
 
     if script.workdir
-      args += ['-wd', script.workdir]
+      args.concat ['-wd', script.workdir]
     elsif ! script_contains_wd_directive?(script.content)
-      args += ['-cwd']
+      args.concat ['-cwd']
     end
 
     on_event_email = []
     on_event_email << 'b' if script.email_on_started  # beginning
     on_event_email << 'ea' if script.email_on_terminated  # end, aborted
 
-    args += ['-M', script.email.first, '-m', on_event_email.join] if script.email && ! on_event_email.empty?
+    args.concat ['-M', script.email.first, '-m', on_event_email.join] if script.email && ! on_event_email.empty?
 
     afterok  = Array(afterok).map(&:to_s)
-    args += ['-hold_jid_ad', afterok.join(',')] unless afterok.empty?
+    args.concat ['-hold_jid_ad', afterok.join(',')] unless afterok.empty?
 
     # ignoring email_on_started
-    args += ['-N', script.job_name] unless script.job_name.nil?
-    args += ['-e', script.error_path] unless script.error_path.nil?
-    args += ['-o', script.output_path] unless script.output_path.nil?
-    args += ['-ar', 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.strftime('%C%y%m%d%H%M.%S')] unless script.start_time.nil?
-    args += ['-l', "h_rt=" + seconds_to_duration(script.wall_time)] unless script.wall_time.nil?
-    args += ['-P', script.accounting_id] unless script.accounting_id.nil?
-    args += ['-t', script.job_array_request] unless script.job_array_request.nil?
-    args += Array.wrap(script.native) if script.native
+    args.concat ['-N', script.job_name] unless script.job_name.nil?
+    args.concat ['-e', script.error_path] unless script.error_path.nil?
+    args.concat ['-o', script.output_path] unless script.output_path.nil?
+    args.concat ['-ar', script.reservation_id] unless script.reservation_id.nil?
+    args.concat ['-q', script.queue_name] unless script.queue_name.nil?
+    args.concat ['-p', script.priority] unless script.priority.nil?
+    args.concat ['-a', script.start_time.strftime('%C%y%m%d%H%M.%S')] unless script.start_time.nil?
+    args.concat ['-l', "h_rt=" + seconds_to_duration(script.wall_time)] unless script.wall_time.nil?
+    args.concat ['-P', script.accounting_id] unless script.accounting_id.nil?
+    args.concat ['-t', script.job_array_request] unless script.job_array_request.nil?
+    args.concat Array.wrap(script.native) if script.native
 
     args
   end

data/lib/ood_core/job/adapters/sge/qstat_xml_j_r_listener.rb

@@ -28,10 +28,13 @@ class QstatXmlJRListener
       :tasks => [],
       :status => :queued,
       :procs => 1,
-      :native => {}  # TODO: improve native attribute reporting
+      :native => {
+        :ST_name => ''
+      } 
     }
     @current_text = nil
     @current_request = nil
+    @processing_JB_stdout_path_list = false
 
     @processing_job_array_spec = false
     @adding_slots = false
@@ -42,6 +45,7 @@ class QstatXmlJRListener
       step: 1,  # Step can have a default of 1
     }
     @running_tasks = []
+    @native_tags = ['JB_job_number', 'JB_job_name', 'JB_version', 'JB_project', 'JB_exec_file', 'JB_script_file', 'JB_script_size', 'JB_submission_time', 'JB_execution_time', 'JB_deadline', 'JB_owner', 'JB_uid', 'JB_group', 'JB_gid', 'JB_account', 'JB_cwd', 'JB_notify', 'JB_type', 'JB_reserve', 'JB_priority', 'JB_jobshare', 'JB_verify', 'JB_checkpoint_attr', 'JB_checkpoint_interval', 'JB_restart']
   end
 
   def tag_start(name, attrs)
@@ -50,10 +54,17 @@ class QstatXmlJRListener
       toggle_processing_array_spec
     when 'JB_pe_range'
       toggle_adding_slots
+    when 'JB_stdout_path_list'
+      @processing_JB_stdout_path_list = true
     end
   end
 
   def tag_end(name)
+    #Add to native hash if in native_tags
+    if (@native_tags.include?(name))
+      @parsed_job[:native][:"#{name}"] = @current_text
+    end
+
     case name
     when 'JB_ja_tasks'
       end_JB_ja_tasks
@@ -92,6 +103,10 @@ class QstatXmlJRListener
       toggle_processing_array_spec
     when 'JB_pe_range'
       toggle_adding_slots
+    when 'PN_path' 
+      end_PN_path
+    when 'ST_name'
+      end_ST_name
     end
   end
 
@@ -118,7 +133,7 @@ class QstatXmlJRListener
   end
 
   def end_JB_submission_time
-    @parsed_job[:submission_time] = @current_text.to_i
+    @parsed_job[:submission_time] = ms_to_seconds(@current_text.to_i)
   end
 
   def end_JB_ja_tasks
@@ -127,7 +142,7 @@ class QstatXmlJRListener
 
   def end_JAT_start_time
     @parsed_job[:status] = :running
-    @parsed_job[:dispatch_time] = @current_text.to_i
+    @parsed_job[:dispatch_time] = ms_to_seconds(@current_text.to_i)
     @parsed_job[:wallclock_time] = Time.now.to_i - @parsed_job[:dispatch_time]
   end
 
@@ -153,6 +168,15 @@ class QstatXmlJRListener
     @running_tasks << @current_text
   end
 
+  def end_PN_path
+    @parsed_job[:native][:PN_path] = @current_text if @processing_JB_stdout_path_list
+    @processing_JB_stdout_path_list = false
+  end
+
+  def end_ST_name
+    @parsed_job[:native][:ST_name] = @parsed_job[:native][:ST_name] + @current_text + ' '
+  end
+
   def set_job_array_piece(key)
     @job_array_spec[key] = @current_text if @processing_job_array_spec
   end
@@ -201,5 +225,12 @@ class QstatXmlJRListener
   def set_slots
     @parsed_job[:procs] = @current_text.to_i
   end
-end
 
+  private
+
+  # Some Grid Engines (like UGE) use milliseconds were others use
+  # seconds past the epoch.
+  def ms_to_seconds(raw)
+    raw.digits.length >= 13 ? raw / 1000 : raw
+  end
+end

data/lib/ood_core/job/adapters/sge/qstat_xml_r_listener.rb

@@ -24,21 +24,32 @@ class QstatXmlRListener
     @parsed_jobs = []
     @current_job = {
       :tasks => [],
-      :native => {}  # TODO: improve native reporting
+      :native => {
+        :ST_name => ''
+      } 
     }
     @current_text = nil
+    @processing_JB_stdout_path_list = false
 
     @current_request = nil
+    @native_tags = ['JB_job_number', 'JB_job_name', 'JB_version', 'JB_project', 'JB_exec_file', 'JB_script_file', 'JB_script_size', 'JB_submission_time', 'JB_execution_time', 'JB_deadline', 'JB_owner', 'JB_uid', 'JB_group', 'JB_gid', 'JB_account', 'JB_cwd', 'JB_notify', 'JB_type', 'JB_reserve', 'JB_priority', 'JB_jobshare', 'JB_verify', 'JB_checkpoint_attr', 'JB_checkpoint_interval', 'JB_restart']
   end
 
   def tag_start(name, attributes)
     case name
     when 'hard_request'
       start_hard_request(attributes)
+    when "JB_stdout_path_list"
+      @processing_JB_stdout_path_list = true
     end
   end
 
   def tag_end(name)
+    #Add text if in native_tags
+    if (@native_tags.include?(name))
+      @current_job[:native][:"#{name}"] = @current_text
+    end
+    
     case name
     when 'job_list'
       end_job_list
@@ -64,6 +75,10 @@ class QstatXmlRListener
       end_hard_request
     when 'tasks'
       add_child_tasks
+    when 'PN_path'
+      end_PN_path
+    when 'ST_name'
+      end_ST_name
     end
   end
 
@@ -130,6 +145,15 @@ class QstatXmlRListener
     end
   end
 
+  def end_PN_path
+    @current_job[:native][:PN_path] = @current_text if @processing_JB_stdout_path_list
+    @processing_JB_stdout_path_list = false
+  end
+
+  def end_ST_name
+    @current_job[:native][:ST_name] = @current_job[:native][:ST_name] + @current_text + ' '
+  end
+
   # Store a completed job and reset current_job for the next pass
   def end_job_list
     @parsed_jobs << @current_job
@@ -145,4 +169,3 @@ class QstatXmlRListener
     }
   end
 end
-

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

@@ -14,13 +14,17 @@ module OodCore
       # @option config [Object] :conf (nil) Path to the slurm conf
       # @option config [Object] :bin (nil) Path to slurm client binaries
       # @option config [#to_h] :bin_overrides ({}) Optional overrides to Slurm client executables
+      # @option config [Object] :submit_host ("") Submit job on login node via ssh
+      # @option config [Object] :strict_host_checking (true) Whether to use strict host checking when ssh to submit_host
       def self.build_slurm(config)
         c = config.to_h.symbolize_keys
-        cluster = c.fetch(:cluster, nil)
-        conf    = c.fetch(:conf, nil)
-        bin     = c.fetch(:bin, nil)
-        bin_overrides = c.fetch(:bin_overrides, {})
-        slurm = Adapters::Slurm::Batch.new(cluster: cluster, conf: conf, bin: bin, bin_overrides: bin_overrides)
+        cluster              = c.fetch(:cluster, nil)
+        conf                 = c.fetch(:conf, nil)
+        bin                  = c.fetch(:bin, nil)
+        bin_overrides        = c.fetch(:bin_overrides, {})
+        submit_host          = c.fetch(:submit_host, "")
+        strict_host_checking = c.fetch(:strict_host_checking, true)
+        slurm = Adapters::Slurm::Batch.new(cluster: cluster, conf: conf, bin: bin, bin_overrides: bin_overrides, submit_host: submit_host, strict_host_checking: strict_host_checking)
         Adapters::Slurm.new(slurm: slurm)
       end
     end
@@ -62,6 +66,16 @@ module OodCore
           # @return Hash<String, String>
           attr_reader :bin_overrides
 
+          # The login node where the job is submitted via ssh
+          # @example owens.osc.edu
+          # @return [String] The login node
+          attr_reader :submit_host
+
+          # Wheter to use strict host checking when ssh to submit_host
+          # @example false
+          # @return [Bool]; true if empty
+          attr_reader :strict_host_checking
+
           # The root exception class that all Slurm-specific exceptions inherit
           # from
           class Error < StandardError; end
@@ -69,11 +83,16 @@ module OodCore
           # @param cluster [#to_s, nil] the cluster name
           # @param conf [#to_s, nil] path to the slurm conf
           # @param bin [#to_s] path to slurm installation binaries
-          def initialize(cluster: nil, bin: nil, conf: nil, bin_overrides: {})
-            @cluster = cluster && cluster.to_s
-            @conf    = conf    && Pathname.new(conf.to_s)
-            @bin     = Pathname.new(bin.to_s)
-            @bin_overrides = bin_overrides
+          # @param bin_overrides [#to_h] a hash of bin ovverides to be used in job
+          # @param submit_host [#to_s] Submits the job on a login node via ssh
+          # @param strict_host_checking [Bool] Whether to use strict host checking when ssh to submit_host
+          def initialize(cluster: nil, bin: nil, conf: nil, bin_overrides: {}, submit_host: "", strict_host_checking: true)
+            @cluster              = cluster && cluster.to_s
+            @conf                 = conf    && Pathname.new(conf.to_s)
+            @bin                  = Pathname.new(bin.to_s)
+            @bin_overrides        = bin_overrides
+            @submit_host          = submit_host.to_s
+            @strict_host_checking = strict_host_checking
           end
 
           # Get a list of hashes detailing each of the jobs on the batch server
@@ -148,9 +167,9 @@ module OodCore
           #TODO: write some barebones test for this? like 2 options and id or no id
           def squeue_args(id: "", owner: nil, options: [])
             args  = ["--all", "--states=all", "--noconvert"]
-            args += ["-o", "#{RECORD_SEPARATOR}#{options.join(UNIT_SEPARATOR)}"]
-            args += ["-u", owner.to_s] unless owner.to_s.empty?
-            args += ["-j", id.to_s] unless id.to_s.empty?
+            args.concat ["-o", "#{RECORD_SEPARATOR}#{options.join(UNIT_SEPARATOR)}"]
+            args.concat ["-u", owner.to_s] unless owner.to_s.empty?
+            args.concat ["-j", id.to_s] unless id.to_s.empty?
             args
           end
 
@@ -275,11 +294,15 @@ module OodCore
             # Call a forked Slurm command for a given cluster
             def call(cmd, *args, env: {}, stdin: "")
               cmd = OodCore::Job::Adapters::Helper.bin_path(cmd, bin, bin_overrides)
+
               args  = args.map(&:to_s)
-              args += ["-M", cluster] if cluster
+              args.concat ["-M", cluster] if cluster
+
               env = env.to_h
               env["SLURM_CONF"] = conf.to_s if conf
-              o, e, s = Open3.capture3(env, cmd, *args, stdin_data: stdin.to_s)
+
+              cmd, args = OodCore::Job::Adapters::Helper.ssh_wrap(submit_host, cmd, args, strict_host_checking)
+              o, e, s = Open3.capture3(env, cmd, *(args.map(&:to_s)), stdin_data: stdin.to_s)
               s.success? ? o : raise(Error, e)
             end
 
@@ -358,30 +381,31 @@ module OodCore
           # Set sbatch options
           args = []
           # ignore args, don't know how to do this for slurm
-          args += ["-H"] if script.submit_as_hold
-          args += (script.rerunnable ? ["--requeue"] : ["--no-requeue"]) unless script.rerunnable.nil?
-          args += ["-D", script.workdir.to_s] unless script.workdir.nil?
-          args += ["--mail-user", script.email.join(",")] unless script.email.nil?
+          args.concat ["-H"] if script.submit_as_hold
+          args.concat (script.rerunnable ? ["--requeue"] : ["--no-requeue"]) unless script.rerunnable.nil?
+          args.concat ["-D", script.workdir.to_s] unless script.workdir.nil?
+          args.concat ["--mail-user", script.email.join(",")] unless script.email.nil?
           if script.email_on_started && script.email_on_terminated
-            args += ["--mail-type", "ALL"]
+            args.concat ["--mail-type", "ALL"]
           elsif script.email_on_started
-            args += ["--mail-type", "BEGIN"]
+            args.concat ["--mail-type", "BEGIN"]
           elsif script.email_on_terminated
-            args += ["--mail-type", "END"]
+            args.concat ["--mail-type", "END"]
           elsif script.email_on_started == false && script.email_on_terminated == false
-            args += ["--mail-type", "NONE"]
+            args.concat ["--mail-type", "NONE"]
           end
-          args += ["-J", script.job_name] unless script.job_name.nil?
-          args += ["-i", script.input_path] unless script.input_path.nil?
-          args += ["-o", script.output_path] unless script.output_path.nil?
-          args += ["-e", script.error_path] unless script.error_path.nil?
-          args += ["--reservation", script.reservation_id] unless script.reservation_id.nil?
-          args += ["-p", script.queue_name] unless script.queue_name.nil?
-          args += ["--priority", script.priority] unless script.priority.nil?
-          args += ["--begin", script.start_time.localtime.strftime("%C%y-%m-%dT%H:%M:%S")] unless script.start_time.nil?
-          args += ["-A", script.accounting_id] unless script.accounting_id.nil?
-          args += ["-t", seconds_to_duration(script.wall_time)] unless script.wall_time.nil?
-          args += ['-a', script.job_array_request] unless script.job_array_request.nil?
+          args.concat ["-J", script.job_name] unless script.job_name.nil?
+          args.concat ["-i", script.input_path] unless script.input_path.nil?
+          args.concat ["-o", script.output_path] unless script.output_path.nil?
+          args.concat ["-e", script.error_path] unless script.error_path.nil?
+          args.concat ["--reservation", script.reservation_id] unless script.reservation_id.nil?
+          args.concat ["-p", script.queue_name] unless script.queue_name.nil?
+          args.concat ["--priority", script.priority] unless script.priority.nil?
+          args.concat ["--begin", script.start_time.localtime.strftime("%C%y-%m-%dT%H:%M:%S")] unless script.start_time.nil?
+          args.concat ["-A", script.accounting_id] unless script.accounting_id.nil?
+          args.concat ["-t", seconds_to_duration(script.wall_time)] unless script.wall_time.nil?
+          args.concat ['-a', script.job_array_request] unless script.job_array_request.nil?
+          args.concat ['--qos', script.qos] unless script.qos.nil?
           # ignore nodes, don't know how to do this for slurm
 
           # Set dependencies
@@ -390,14 +414,14 @@ module OodCore
           depend << "afterok:#{afterok.join(":")}"       unless afterok.empty?
           depend << "afternotok:#{afternotok.join(":")}" unless afternotok.empty?
           depend << "afterany:#{afterany.join(":")}"     unless afterany.empty?
-          args += ["-d", depend.join(",")]               unless depend.empty?
+          args.concat ["-d", depend.join(",")]               unless depend.empty?
 
           # Set environment variables
           env = script.job_environment || {}
-          args += ["--export", export_arg(env, script.copy_environment?)]
+          args.concat ["--export", export_arg(env, script.copy_environment?)]
 
           # Set native options
-          args += script.native if script.native
+          args.concat script.native if script.native
 
           # Set content
           content = if script.shell_path.nil?

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

@@ -1,5 +1,6 @@
 require "ood_core/refinements/hash_extensions"
 require "ood_core/job/adapters/helper"
+require 'shellwords'
 
 module OodCore
   module Job
@@ -9,16 +10,18 @@ module OodCore
       # Build the Torque adapter from a configuration
       # @param config [#to_h] the configuration for job adapter
       # @option config [#to_s] :host The batch server host
+      # @option config [#to_s] :submit_host The login node to submit the job via ssh
       # @option config [#to_s] :lib ('') Path to torque client libraries
       # @option config [#to_s] :bin ('') Path to torque client binaries
       # @option config [#to_h] :custom_bin ({}) Optional overrides to Torque client executables
       def self.build_torque(config)
         c = config.to_h.symbolize_keys
         host = c.fetch(:host) { raise ArgumentError, "No host specified. Missing argument: host" }.to_s
+        submit_host = c.fetch(:submit_host, "").to_s
         lib  = c.fetch(:lib, "").to_s
         bin  = c.fetch(:bin, "").to_s
         custom_bin = c.fetch(:custom_bin, {})
-        pbs  = Adapters::Torque::Batch.new(host: host, lib: lib, bin: bin, custom_bin: custom_bin)
+        pbs  = Adapters::Torque::Batch.new(host: host, submit_host: submit_host, lib: lib, bin: bin, custom_bin: custom_bin)
         Adapters::Torque.new(pbs: pbs)
       end
     end
@@ -85,7 +88,7 @@ module OodCore
           depend << "afterany:#{afterany.join(':')}"     unless afterany.empty?
 
           # Set mailing options
-          mail_points  = ""
+          mail_points = ""
           mail_points += "b" if script.email_on_started
           mail_points += "e" if script.email_on_terminated
 
@@ -129,40 +132,44 @@ module OodCore
               envvars.merge!   script.native.fetch(:envvars, {})
             end
 
+            # Destructively change envvars to shellescape values
+            envvars.transform_values! { |v| Shellwords.escape(v) }
+
             # 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?
+            args.concat ["-F", script.args.join(" ")] unless script.args.nil?
+            args.concat ["-h"] if script.submit_as_hold
+            args.concat ["-r", script.rerunnable ? "y" : "n"] unless script.rerunnable.nil?
+            args.concat ["-M", script.email.join(",")] unless script.email.nil?
+            args.concat ["-m", mail_points] unless mail_points.empty?
+            args.concat ["-N", script.job_name] unless script.job_name.nil?
+            args.concat ["-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?
-            args += ['-t', script.job_array_request] unless script.job_array_request.nil?
+            args.concat ["-o", script.output_path] unless script.output_path.nil?
+            args.concat ["-e", script.error_path] unless script.error_path.nil?
+            args.concat ["-W", "x=advres:#{script.reservation_id}"] unless script.reservation_id.nil?
+            args.concat ["-q", script.queue_name] unless script.queue_name.nil?
+            args.concat ["-p", script.priority] unless script.priority.nil?
+            args.concat ["-a", script.start_time.localtime.strftime("%C%y%m%d%H%M.%S")] unless script.start_time.nil?
+            args.concat ["-A", script.accounting_id] unless script.accounting_id.nil?
+            args.concat ["-W", "depend=#{depend.join(",")}"] unless depend.empty?
+            args.concat ["-l", "walltime=#{seconds_to_duration(script.wall_time)}"] unless script.wall_time.nil?
+            args.concat ['-t', script.job_array_request] unless script.job_array_request.nil?
+            args.concat ['-l', "qos=#{script.qos}"] unless script.qos.nil?
             # Set environment variables
             env = script.job_environment.to_h
-            args += ["-v", env.keys.join(",")] unless env.empty?
-            args += ["-V"] if script.copy_environment?
+            args.concat ["-v", env.keys.join(",")] unless env.empty?
+            args.concat ["-V"] if script.copy_environment?
 
             # 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?
+            args.concat ["-j", "oe"] if script.error_path.nil?
 
             # Set native options
-            args += script.native if script.native
+            args.concat script.native if script.native
 
             # Submit job
             @pbs.submit(script.content, args: args, env: env, chdir: script.workdir)

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

@@ -9,6 +9,18 @@ class OodCore::Job::Adapters::Torque
     # @return [String] the batch server host
     attr_reader :host
 
+    # The login node where job is submitted via ssh
+    # @example OSC's owens login node
+    #   my_conn.submit_host #=> "owens.osc.edu"
+    # @return [String] the login node
+    attr_reader :submit_host
+
+    # Determines whether to use strict_host_checking for ssh
+    # @example 
+    #   my_conn.strict_host_checking.to_s #=> "owens.osc.edu"
+    # @return [Bool] 
+    attr_reader :strict_host_checking
+
     # The path to the Torque client installation libraries
     # @example For Torque 5.0.0
     #   my_conn.lib.to_s #=> "/usr/local/Torque/5.0.0/lib"
@@ -32,19 +44,23 @@ class OodCore::Job::Adapters::Torque
     class Error < StandardError; end
 
     # @param host [#to_s] the batch server host
+    # @param submit_host [#to_s] the login node
+    # @param strict_host_checking [bool] use strict host checking when ssh to submit_host
     # @param lib [#to_s] path to FFI installation libraries
     # @param bin [#to_s] path to FFI installation binaries
-    def initialize(host:, lib: "", bin: "", bin_overrides: {}, **_)
-      @host    = host.to_s
-      @lib     = Pathname.new(lib.to_s)
-      @bin     = Pathname.new(bin.to_s)
-      @bin_overrides = bin_overrides
+    def initialize(host:, submit_host: "", strict_host_checking: true, lib: "", bin: "", bin_overrides: {}, **_)
+      @host                 = host.to_s
+      @submit_host          = submit_host.to_s
+      @strict_host_checking = strict_host_checking
+      @lib                  = Pathname.new(lib.to_s)
+      @bin                  = Pathname.new(bin.to_s)
+      @bin_overrides        = bin_overrides
     end
 
     # Convert object to hash
     # @return [Hash] the hash describing this object
     def to_h
-      {host: host, lib: lib, bin: bin}
+      {host: host, submit_host: submit_host, strict_host_checking: strict_host_checking, lib: lib, bin: bin}
     end
 
     # The comparison operator
@@ -437,10 +453,10 @@ class OodCore::Job::Adapters::Torque
       # NB: The binary includes many useful filters and is preferred
       def qsub_submit(script, queue, headers, resources, envvars)
         params  = []
-        params += ["-q", "#{queue}"] unless queue.empty?
-        params += headers.map {|k,v| qsub_arg(k,v)}.flatten
-        params += resources.map{|k,v| ["-l", "#{k}=#{v}"]}.flatten
-        params += ["-v", envvars.map{|k,v| "#{k}=#{v}"}.join(",")] unless envvars.empty?
+        params.concat ["-q", "#{queue}"] unless queue.empty?
+        params.concat headers.map {|k,v| qsub_arg(k,v)}.flatten
+        params.concat resources.map{|k,v| ["-l", "#{k}=#{v}"]}.flatten
+        params.concat ["-v", envvars.map{|k,v| "#{k}=#{v}"}.join(",")] unless envvars.empty?
         params << script
 
         env = {
@@ -448,6 +464,7 @@ class OodCore::Job::Adapters::Torque
           "LD_LIBRARY_PATH" => "#{lib}:#{ENV['LD_LIBRARY_PATH']}"
         }
         cmd = OodCore::Job::Adapters::Helper.bin_path('qsub', bin, bin_overrides)
+        cmd, params = OodCore::Job::Adapters::Helper.ssh_wrap(submit_host, cmd, params, strict_host_checking, env)
         o, e, s = Open3.capture3(env, cmd, *params)
         raise Error, e unless s.success?
         o.chomp
@@ -456,14 +473,14 @@ class OodCore::Job::Adapters::Torque
       # Call a forked PBS command for a given host
       def call(cmd, *args, env: {}, stdin: "", chdir: nil)
         cmd = OodCore::Job::Adapters::Helper.bin_path(cmd, bin, bin_overrides)
-        args = args.map(&:to_s)
         env  = env.to_h.each_with_object({}) {|(k,v), h| h[k.to_s] = v.to_s}.merge({
           "PBS_DEFAULT"     => host,
           "LD_LIBRARY_PATH" => %{#{lib}:#{ENV["LD_LIBRARY_PATH"]}}
         })
+        cmd, args = OodCore::Job::Adapters::Helper.ssh_wrap(submit_host, cmd, args, strict_host_checking, env)
         stdin = stdin.to_s
         chdir ||= "."
-        o, e, s = Open3.capture3(env, cmd, *args, stdin_data: stdin, chdir: chdir.to_s)
+        o, e, s = Open3.capture3(env, cmd, *(args.map(&:to_s)), stdin_data: stdin, chdir: chdir.to_s)
         s.success? ? o : raise(Error, e)
       end
   end

data/lib/ood_core/job/script.rb

@@ -99,6 +99,10 @@ module OodCore
       # @return [String, nil] job array request
       attr_reader :job_array_request
 
+      # The qos selected for the job
+      # @return [String, nil] qos
+      attr_reader :qos
+
       # Object detailing any native specifications that are implementation specific
       # @note Should not be used at all costs.
       # @return [Object, nil] native specifications
@@ -130,6 +134,8 @@ module OodCore
       # @param start_time [#to_i, nil] eligible start time
       # @param wall_time [#to_i, nil] max real time
       # @param accounting_id [#to_s, nil] accounting id
+      # @param job_array_request [#to_s, nil] job array request
+      # @param qos [#to_s, nil] qos
       # @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,
@@ -139,7 +145,7 @@ module OodCore
                      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, copy_environment: nil, **_)
+                     qos: nil, native: nil, copy_environment: nil, **_)
         @content = content.to_s
 
         @submit_as_hold      = submit_as_hold
@@ -163,6 +169,7 @@ module OodCore
         @wall_time          = wall_time         && wall_time.to_i
         @accounting_id      = accounting_id     && accounting_id.to_s
         @job_array_request  = job_array_request && job_array_request.to_s
+        @qos                = qos               && qos.to_s
         @native             = native
         @copy_environment   = (copy_environment.nil?) ? nil : !! copy_environment
       end
@@ -192,6 +199,7 @@ module OodCore
           wall_time:           wall_time,
           accounting_id:       accounting_id,
           job_array_request:   job_array_request,
+          qos:                 qos,
           native:              native,
           copy_environment:    copy_environment
         }

data/lib/ood_core/version.rb

@@ -1,4 +1,4 @@
 module OodCore
   # The current version of {OodCore}
-  VERSION = "0.11.4"
+  VERSION = "0.12.0"
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: ood_core
 version: !ruby/object:Gem::Version
-  version: 0.11.4
+  version: 0.12.0
 platform: ruby
 authors:
 - Eric Franz
@@ -10,7 +10,7 @@ authors:
 autorequire: 
 bindir: exe
 cert_chain: []
-date: 2020-05-27 00:00:00.000000000 Z
+date: 2020-08-05 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: ood_support