ood_core 0.20.0 → 0.21.0

checksums.yaml

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data/CHANGELOG.md

@@ -7,6 +7,21 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 
 ## [Unreleased]
 
+## [0.21.0] - 08-01-2022
+
+### Added
+
+- Added the `fujitsu_tcs` adapter in [766](https://github.com/OSC/ood_core/pull/766).
+
+## [0.20.2] - 07-28-2022
+
+- Fixed an issue with Slurm's `cluster_info` in [762](https://github.com/OSC/ood_core/pull/762).
+- Relaxed Ruby requirement down to 2.5 in [771](https://github.com/OSC/ood_core/pull/771).
+
+## [0.20.1] - 07-21-2022
+
+- Fixed turbovnc compatability issue with the -nohttpd flag in [767](https://github.com/OSC/ood_core/pull/767).
+
 ## [0.20.0] - 06-03-2022
 
 - Adapters can now respond to `cluster_info` in [752](https://github.com/OSC/ood_core/pull/752). This returns information about the cluster like how many nodes are available and so on. Only Slurm support in this release.
@@ -428,7 +443,11 @@ Functionally the same as [0.17.3] but with some CI updates.
 ### Added
 - Initial release!
 
-[Unreleased]: https://github.com/OSC/ood_core/compare/v0.19.0...HEAD
+[Unreleased]: https://github.com/OSC/ood_core/compare/v0.21.0...HEAD
+[0.21.0]: https://github.com/OSC/ood_core/compare/v0.20.2...v0.21.0
+[0.20.2]: https://github.com/OSC/ood_core/compare/v0.20.1...v0.20.2
+[0.20.1]: https://github.com/OSC/ood_core/compare/v0.20.0...v0.20.1
+[0.20.0]: https://github.com/OSC/ood_core/compare/v0.19.0...v0.20.0
 [0.19.0]: https://github.com/OSC/ood_core/compare/v0.18.1...v0.19.0
 [0.18.1]: https://github.com/OSC/ood_core/compare/v0.18.0...v0.18.1
 [0.18.0]: https://github.com/OSC/ood_core/compare/v0.17.8...v0.18.0

data/lib/ood_core/batch_connect/templates/vnc.rb

@@ -86,8 +86,13 @@ module OodCore
                 # Clean up any old VNC sessions that weren't cleaned before
                 #{vnc_clean}
 
+                # for turbovnc 3.0 compatability.
+                if timeout 2 vncserver --help 2>&1 | grep 'nohttpd' >/dev/null 2>&1; then
+                  HTTPD_OPT='-nohttpd'
+                fi
+
                 # Attempt to start VNC server
-                VNC_OUT=$(vncserver -log "#{vnc_log}" -rfbauth "#{vnc_passwd}" -nohttpd -noxstartup #{vnc_args} 2>&1)
+                VNC_OUT=$(vncserver -log "#{vnc_log}" -rfbauth "#{vnc_passwd}" $HTTPD_OPT -noxstartup #{vnc_args} 2>&1)
                 VNC_PID=$(pgrep -s 0 Xvnc) # the script above will daemonize the Xvnc process
                 echo "${VNC_OUT}"
 

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

@@ -0,0 +1,403 @@
+require "time"
+require "ood_core/refinements/hash_extensions"
+require "ood_core/refinements/array_extensions"
+require "ood_core/job/adapters/helper"
+
+module OodCore
+  module Job
+    class Factory
+      using Refinements::HashExtensions
+      
+      # Build the Fujitsu TCS (Technical Computing Suite) adapter from a configuration
+      # @param config [#to_h] the configuration for job adapter
+      # @option config [Object] :bin (nil) Path to Fujitsu TCS resource manager binaries
+      # @option config [#to_h]  :bin_overrides ({}) Optional overrides to Fujitsu TCS resource manager executables
+      def self.build_fujitsu_tcs(config)
+        c = config.to_h.symbolize_keys
+        bin           = c.fetch(:bin, nil)
+        bin_overrides = c.fetch(:bin_overrides, {})
+        fujitsu_tcs   = Adapters::Fujitsu_TCS::Batch.new(bin: bin, bin_overrides: bin_overrides)
+        Adapters::Fujitsu_TCS.new(fujitsu_tcs: fujitsu_tcs)
+      end
+    end
+    
+    module Adapters
+      # An adapter object that describes the communication with a Fujitsu TCS
+      # resource manager for job management.
+      class Fujitsu_TCS < Adapter
+        using Refinements::HashExtensions
+        using Refinements::ArrayExtensions
+        
+        # Object used for simplified communication with a Fujitsu TCS batch server
+        # @api private
+        class Batch
+          # The path to the Fujitsu TCS binaries
+          # @example 
+          #   my_batch.bin.to_s #=> "/usr/local/fujitsu_tcs/10.0.0/bin"
+          # @return [Pathname] path to Fujitsu TCS binaries
+          attr_reader :bin
+
+          # Optional overrides for Fujitsu TCS executables
+          # @example
+          #  {'pjsub' => '/usr/local/bin/pjsub'}
+          # @return Hash<String, String>
+          attr_reader :bin_overrides
+
+          # The root exception class that all Fujitsu TCS specific exceptions inherit
+          # from
+          class Error < StandardError; end
+
+          # An error indicating the Fujitsu TCS command timed out
+          class Fujitsu_TCS_TimeoutError < Error; end
+
+          # @param bin [#to_s] path to Fujitsu TCS installation binaries
+          # @param bin_overrides [#to_h] a hash of bin ovverides to be used in job
+          def initialize(bin: nil, bin_overrides: {})
+            @bin           = Pathname.new(bin.to_s)
+            @bin_overrides = bin_overrides
+          end
+
+          # Get a list of hashes detailing each of the jobs on the batch server
+          # @example Status info for all jobs
+          #   my_batch.get_jobs
+          #   #=>
+          #   #[
+          #   #  {
+          #   #    :JOB_ID => "123",
+          #   #    :JOB_NAME => "my_job",
+          #   #    ...
+          #   #  },
+          #   #  {
+          #   #    :JOB_ID => "125",
+          #   #    :JOB_NAME => "my_other_job",
+          #   #    ...
+          #   #  },
+          #   #  ...
+          #   #]
+          # @param id [#to_s] the id of the job
+          # @param owner [String] the owner(s) of the job
+          # @raise [Error] if `pjstat` command exited unsuccessfully
+          # @return [Array<Hash>] list of details for jobs
+          def get_jobs(id: "", owner: nil)
+            args = ["-s", "--data", "--choose=jid,jnam,rscg,st,std,stde,adt,sdt,nnumr,usr,elpl,elp"]
+            args.concat ["--filter jid=" + id.to_s] unless id.to_s.empty?
+            args.concat ["--filter usr=" + owner.to_s] unless owner.to_s.empty?
+            
+            StringIO.open(call("pjstat", *args)) do |output|
+              output.gets() # Skip header
+              jobs = []
+              output.each_line do |line|
+                l = line.split(",")
+                jobs << {:JOB_ID => l[1],  :JOB_NAME   => l[2],  :RSC_GRP    => l[3].split(" ")[0],
+                         :ST     => l[4],  :STD        => l[5],  :STDE       => l[6],
+                         :ACCEPT => l[7],  :START_DATE => l[8],  :NODES      => l[9].split(":")[0],
+                         :USER   => l[10], :ELAPSE_LIM => l[11], :ELAPSE_TIM => l[12].split(" ")[0] }
+              end
+              jobs
+            end
+          rescue Fujitsu_TCS_TimeoutError
+            return [{ JOB_ID: id, ST: 'undetermined' }]
+          end
+
+          # Put a specified job on hold
+          # @example Put job "1234" on hold
+          #   my_batch.hold_job("1234")
+          # @param id [#to_s] the id of the job
+          # @raise [Error] if `pjhold` command exited unsuccessfully
+          # @return [void]
+          def hold_job(id)
+            call("pjhold", id.to_s)
+          end
+
+          # Release a specified job that is on hold
+          # @example Release job "1234" from on hold
+          #   my_batch.release_job("1234")
+          # @param id [#to_s] the id of the job
+          # @raise [Error] if `pjrls` command exited unsuccessfully
+          # @return [void]
+          def release_job(id)
+            call("pjrls", id.to_s)
+          end
+
+          # Delete a specified job from batch server
+          # @example Delete job "1234"
+          #   my_batch.delete_job("1234")
+          # @param id [#to_s] the id of the job
+          # @raise [Error] if `pjdel` command exited unsuccessfully
+          # @return [void]
+          def delete_job(id)
+            call("pjdel", id.to_s)
+          end
+
+          # Submit a script expanded as a string to the batch server
+          # @param str [#to_s] script as a string
+          # @param args [Array<#to_s>] arguments passed to `pjsub` command
+          # @raise [Error] if `pjsub` command exited unsuccessfully
+          # @return [String] the id of the job that was created
+          def submit_string(str, args: [])
+            args = args.map(&:to_s)
+            call("pjsub", *args, stdin: str.to_s).split(" ")[5]
+          end
+          
+          private
+            # Call a forked Fujitsu TCS command
+            def call(cmd, *args, stdin: "")
+              cmd = OodCore::Job::Adapters::Helper.bin_path(cmd, bin, bin_overrides)
+              args  = args.map(&:to_s)
+              o, e, s = Open3.capture3(cmd, *(args.map(&:to_s)), stdin_data: stdin.to_s)
+              s.success? ? o : raise(Error, e)
+            end
+        end
+
+        # Mapping of state codes for Fujitsu TCS resource manager
+        STATE_MAP = {
+          'ACC' => :queued,    # Accepted job submission
+          'RJT' => :completed, # Rejected job submission
+          'QUE' => :queued,    # Waiting for job execution
+          'RNA' => :queued,    # Acquiring resources required for job execution
+          'RNP' => :running,   # Executing prologue
+          'RUN' => :running,   # Executing job
+          'RNE' => :running,   # Executing epilogue
+          'RNO' => :running,   # Waiting for completion of job termination processing
+          'SPP' => :suspended, # Suspend in progress
+          'SPD' => :suspended, # Suspended
+          'RSM' => :running,   # Resume in progress
+          'EXT' => :completed, # Exited job end execution
+          'CCL' => :completed, # Exited job execution by interruption
+          'HLD' => :suspended, # In fixed state due to users
+          'ERR' => :completed, # In fixed state due to an error
+        }
+
+        # @api private
+        # @param opts [#to_h] the options defining this adapter
+        # @option opts [Batch] :the Fujitsu TCS batch object
+        # @see Factory.build_fujitsu_tcs
+        def initialize(opts = {})
+          o = opts.to_h.symbolize_keys
+
+          @fujitsu_tcs = o.fetch(:fujitsu_tcs) { raise ArgumentError, "No Fujitsu TCS object specified. Missing argument: fujitsu_tcs" }
+        end
+
+        # Submit a job with the attributes defined in the job template instance
+        # @param script [Script] script object that describes the script and
+        #   attributes for the submitted job
+        # @param after [#to_s, Array<#to_s>] this job may be scheduled for
+        #   execution at any point after dependent jobs have started execution
+        # @param afterok [#to_s, Array<#to_s>] this job may be scheduled for
+        #   execution only after dependent jobs have terminated with no errors
+        # @param afternotok [#to_s, Array<#to_s>] this job may be scheduled for
+        #   execution only after dependent jobs have terminated with errors
+        # @param afterany [#to_s, Array<#to_s>] this job may be scheduled for
+        #   execution after dependent jobs have terminated
+        # @raise [JobAdapterError] if something goes wrong submitting a job
+        # @return [String] the job id returned after successfully submitting a
+        #   job
+        # @see Adapter#submit
+        def submit(script, after: [], afterok: [], afternotok: [], afterany: [])
+          #after      = Array(after).map(&:to_s)
+          #afterok    = Array(afterok).map(&:to_s)
+          #afternotok = Array(afternotok).map(&:to_s)
+          #afterany   = Array(afterany).map(&:to_s)
+          if !after.empty? || !afterok.empty? || !afternotok.empty? || !afterany.empty?
+            raise JobAdapterError, "Dependency between jobs has not implemented yet."
+          end
+          
+          # Set pjsub options
+          args = []
+          args.concat (script.rerunnable ? ["--restart"] : ["--norestart"]) unless script.rerunnable.nil?
+          args.concat ["--mail-list", script.email.join(",")] unless script.email.nil?
+          if script.email_on_started && script.email_on_terminated
+            args.concat ["-m", "b,e"]
+          elsif script.email_on_started
+            args.concat ["-m", "b"]
+          elsif script.email_on_terminated
+            args.concat ["-m", "e"]
+          end
+
+          args.concat ["-N", script.job_name] unless script.job_name.nil?
+          args.concat ["-o", script.output_path] unless script.output_path.nil?
+          if script.error_path.nil?
+            args.concat ["-j"]
+          else
+            args.concat ["-e", script.error_path]
+          end
+          args.concat ["--rscgrp", script.queue_name] unless script.queue_name.nil?
+          args.concat ["-p", script.priority] unless script.priority.nil?
+          args.concat ["--at", script.start_time.localtime.strftime("%C%y-%m-%dT%H:%M:%S")] unless script.start_time.nil?
+          args.concat ["-L \"elapse=" + seconds_to_duration(script.wall_time) + "\""] unless script.wall_time.nil?
+          args.concat ["--bulk", "--sparam", script.job_array_request] unless script.job_array_request.nil?
+
+          # Set environment variables
+          envvars = script.job_environment.to_h
+          args.concat ["-x", envvars.map{|k,v| "#{k}=#{v}"}.join(",")] unless envvars.empty?
+          args.concat ["-X"] if script.copy_environment?
+
+          # Set native options
+          args.concat 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
+          @fujitsu_tcs.submit_string(content, args: args)
+        rescue Batch::Error => e
+          raise JobAdapterError, e.message
+        end
+
+        # Retrieve info for all jobs from the resource manager
+        # @raise [JobAdapterError] if something goes wrong getting job info
+        # @return [Array<Info>] information describing submitted jobs
+        # @see Adapter#info_all
+        def info_all(attrs: nil)
+          @fujitsu_tcs.get_jobs().map do |v|
+            parse_job_info(v)
+          end
+        rescue Batch::Error => e
+          raise JobAdapterError, e.message
+        end
+
+        # Retrieve job info from the resource manager
+        # @param id [#to_s] the id of the job
+        # @raise [JobAdapterError] if something goes wrong getting job info
+        # @return [Info] information describing submitted job
+        # @see Adapter#info
+        def info(id)
+          id = id.to_s
+          info_ary = @fujitsu_tcs.get_jobs(id: id).map do |v|
+            parse_job_info(v)
+          end
+
+          # If no job was found we assume that it has completed
+          info_ary.empty? ? Info.new(id: id, status: :completed) : info_ary.first # @fujitsu_tcs.get_jobs() must return only one element.
+        rescue Batch::Error => e
+          # set completed status if can't find job id
+          if /\[ERR\.\] PJM .+ Job .+ does not exist/ =~ e.message
+            Info.new(
+              id: id,
+              status: :completed
+            )
+          else
+            raise JobAdapterError, e.message
+          end
+        end
+
+        # Retrieve info for all jobs for a given owner or owners from the
+        # resource manager
+        # @param owner [#to_s, Array<#to_s>] the owner(s) of the jobs
+        # @raise [JobAdapterError] if something goes wrong getting job info
+        # @return [Array<Info>] information describing submitted jobs
+        def info_where_owner(owner, attrs: nil)
+          owner = Array.wrap(owner).map(&:to_s).join('+')
+          @fujitsu_tcs.get_jobs(owner: owner).map do |v|
+            parse_job_info(v)
+          end
+        rescue Batch::Error => e
+          raise JobAdapterError, e.message
+        end
+
+        # Retrieve job status from resource manager
+        # @param id [#to_s] the id of the job
+        # @raise [JobAdapterError] if something goes wrong getting job status
+        # @return [Status] status of job
+        # @see Adapter#status
+        def status(id)
+          id = id.to_s
+          jobs = @fujitsu_tcs.get_jobs(id: id)
+
+          if job = jobs.detect { |j| j[:JOB_ID] == id }
+            Status.new(state: get_state(job[:ST]))
+          else
+            # set completed status if can't find job id
+            Status.new(state: :completed)
+          end
+        rescue Batch::Error => e
+          # set completed status if can't find job id
+          if /\[ERR\.\] PJM .+ Job .+ does not exist/ =~ e.message
+            Status.new(state: :completed)
+          else
+            raise JobAdapterError, e.message
+          end
+        end
+
+        # Put the submitted job on hold
+        # @param id [#to_s] the id of the job
+        # @raise [JobAdapterError] if something goes wrong holding a job
+        # @return [void]
+        # @see Adapter#hold
+        def hold(id)
+          @fujitsu_tcs.hold_job(id.to_s)
+        rescue Batch::Error => e
+          # assume successful job hold if can't find job id
+          raise JobAdapterError, e.message unless /\[ERR\.\] PJM .+ Job .+ does not exist/ =~ e.message
+        end
+
+        # Release the job that is on hold
+        # @param id [#to_s] the id of the job
+        # @raise [JobAdapterError] if something goes wrong releasing a job
+        # @return [void]
+        # @see Adapter#release
+        def release(id)
+          @fujitsu_tcs.release_job(id.to_s)
+        rescue Batch::Error => e
+          # assume successful job release if can't find job id
+          raise JobAdapterError, e.message unless /\[ERR\.\] PJM .+ Job .+ does not exist/ =~ e.message
+        end
+
+        # Delete the submitted job
+        # @param id [#to_s] the id of the job
+        # @raise [JobAdapterError] if something goes wrong deleting a job
+        # @return [void]
+        # @see Adapter#delete
+        def delete(id)
+          @fujitsu_tcs.delete_job(id.to_s)
+        rescue Batch::Error => e
+          # assume successful job deletion if can't find job id
+          raise JobAdapterError, e.message unless /\[ERR\.\] PJM .+ Job .+ does not exist/ =~ e.message
+        end
+
+        def directive_prefix
+          '#PJM'
+        end
+
+        private
+          # Convert duration to seconds
+          def duration_in_seconds(time)
+            return 0 if time.nil?
+            time, days = time.split("-").reverse
+            days.to_i * 24 * 3600 +
+              time.split(':').map { |v| v.to_i }.inject(0) { |total, v| total * 60 + v }
+          end
+
+          # Convert seconds to duration
+          def seconds_to_duration(time)
+            "%02d:%02d:%02d" % [time/3600, time/60%60, time%60]
+          end
+
+          # Determine state from Fujitsu TCS state code
+          def get_state(st)
+            STATE_MAP.fetch(st, :undetermined)
+          end
+
+          # Parse hash describing Fujitsu TCS job status
+          def parse_job_info(v)
+            Info.new(
+              id: v[:JOB_ID],
+              job_name: v[:JOB_NAME],
+              status: get_state(v[:ST]),
+              job_owner: v[:USER],
+              dispatch_time: v[:START_DATE],
+              wallclock_time: duration_in_seconds(v[:ELAPSE_TIM]),
+              wallclock_limit: duration_in_seconds(v[:ELAPSE_LIM]),
+              submission_time: v[:ACCEPT],
+              queue_name: v[:RSC_GRP],
+              native: v
+            )
+          end
+      end
+    end
+  end
+end

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

@@ -39,7 +39,7 @@ module OodCore
         # Get integer representing the number of gpus used by a node or job,
         # calculated from gres string
         # @return [Integer] the number of gpus in gres
-        def gpus_from_gres(gres)
+        def self.gpus_from_gres(gres)
           gres.to_s.scan(/gpu:[^,]*(\d+)/).flatten.map(&:to_i).sum
         end
 
@@ -116,8 +116,8 @@ module OodCore
                             total_nodes: node_cpu_info[2].to_i,
                             active_processors: node_cpu_info[3].to_i,
                             total_processors: node_cpu_info[6].to_i,
-                            active_gpus: gres_lines.sum { |line| gpus_from_gres(line[2]) },
-                            total_gpus: gres_lines.sum { |line| gpus_from_gres(line[1]) }
+                            active_gpus: gres_lines.sum { |line| Slurm.gpus_from_gres(line[2]) },
+                            total_gpus: gres_lines.sum { |line| Slurm.gpus_from_gres(line[1]) }
             )
           end
 
@@ -673,7 +673,7 @@ module OodCore
               submission_time: v[:submit_time] ? Time.parse(v[:submit_time]) : nil,
               dispatch_time: (v[:start_time].nil? || v[:start_time] == "N/A") ? nil : Time.parse(v[:start_time]),
               native: v,
-              gpus: gpus_from_gres(v[:gres])
+              gpus: self.class.gpus_from_gres(v[:gres])
             )
           end
 

data/lib/ood_core/version.rb

@@ -1,4 +1,4 @@
 module OodCore
   # The current version of {OodCore}
-  VERSION = "0.20.0"
+  VERSION = "0.21.0"
 end

data/ood_core.gemspec

@@ -20,7 +20,7 @@ Gem::Specification.new do |spec|
   spec.bindir        = "exe"
   spec.executables   = spec.files.grep(%r{^exe/}) { |f| File.basename(f) }
   spec.require_paths = ["lib"]
-  spec.required_ruby_version = ">= 2.7.0"
+  spec.required_ruby_version = ">= 2.5.0"
 
   spec.add_runtime_dependency "ood_support", "~> 0.0.2"
   spec.add_runtime_dependency "ffi", "~> 1.9", ">= 1.9.6"
@@ -30,5 +30,5 @@ Gem::Specification.new do |spec|
   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", "~> 1.0.0"
+  spec.add_development_dependency "climate_control", "~> 1.1.1"
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: ood_core
 version: !ruby/object:Gem::Version
-  version: 0.20.0
+  version: 0.21.0
 platform: ruby
 authors:
 - Eric Franz
@@ -10,7 +10,7 @@ authors:
 autorequire: 
 bindir: exe
 cert_chain: []
-date: 2022-06-03 00:00:00.000000000 Z
+date: 2022-08-01 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: ood_support
@@ -136,14 +136,14 @@ dependencies:
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 1.0.0
+        version: 1.1.1
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 1.0.0
+        version: 1.1.1
 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:
@@ -179,6 +179,7 @@ files:
 - lib/ood_core/job/adapter.rb
 - lib/ood_core/job/adapters/ccq.rb
 - lib/ood_core/job/adapters/drmaa.rb
+- lib/ood_core/job/adapters/fujitsu_tcs.rb
 - lib/ood_core/job/adapters/helper.rb
 - lib/ood_core/job/adapters/kubernetes.rb
 - lib/ood_core/job/adapters/kubernetes/batch.rb
@@ -234,7 +235,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
   requirements:
   - - ">="
     - !ruby/object:Gem::Version
-      version: 2.7.0
+      version: 2.5.0
 required_rubygems_version: !ruby/object:Gem::Requirement
   requirements:
   - - ">="