ood_core 0.26.1 → 0.27.1

checksums.yaml

@@ -1,7 +1,7 @@
 ---
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-  data.tar.gz: 16a5cf6f03ed2be4c563dafb7eaa9e2a04d465a4d8a3cea5d3bb14b634d65868
+  metadata.gz: c4cf552caaaedcb74de1091d8e9d1503b21f140b961ea8ccc3e53c1a25fa88f9
+  data.tar.gz: e69ec942c413e569d232ed8e88ee9a0abb79d5f3e9c7bf2d17cce7d3fe92b465
 SHA512:
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-  data.tar.gz: dc88b7bc4a28e96725bcd2caf0e40659bca94a40ab1c50432af0eee2b649f4a48356e858a7f9ceca1a8a18f99c823bf9ffc4c7cecefecb9820d8ce7621c7c51b
+  metadata.gz: 72e629a77d117b4c370947e72eddc96ebddf766eff5d0459c5291074ab22033ded29e032563e00112051d0ef122e36bf4beca3e81ff94d9f5e9cd5c6576939a8
+  data.tar.gz: 61a4b4d3208796c7b4e365307fd527b081e5eb1be3fbebe02272883a3b7efafbb45c31234300dbe517f2eadc576b3cb4dc11fd91615f706704396541984c91bd

data/CHANGELOG.md

@@ -7,6 +7,18 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 
 ## [Unreleased]
 
+# [0.26.1] - 07-31-2024
+
+- 0.26.0 didn't publish correctly. There's no meaningful difference between 0.26.1 and 0.26.0.
+
+# [0.26.0] - 07-26-2024
+
+- Adapter class now has `nodes` API in [830](https://github.com/OSC/ood_core/pull/830).
+- QueueInfo objects are GPU aware in [825](https://github.com/OSC/ood_core/pull/825).
+- Systemd adapter bugfix for zsh in [834](https://github.com/OSC/ood_core/pull/834).
+- Websockify timeout is variable in [840](https://github.com/OSC/ood_core/pull/840).
+- Slurm adapter now forces utf-8 encoding in [842](https://github.com/OSC/ood_core/pull/842).
+
 # [0.25.0] - 03-27-2024
 
 - [828](https://github.com/OSC/ood_core/pull/828) and [826](https://github.com/OSC/ood_core/pull/826)
@@ -535,6 +547,9 @@ Functionally the same as [0.17.3] but with some CI updates.
 - Initial release!
 
 [Unreleased]: https://github.com/OSC/ood_core/compare/v0.24.2...HEAD
+[0.26.1]: https://github.com/OSC/ood_core/compare/v0.26.0...v0.26.1
+[0.26.0]: https://github.com/OSC/ood_core/compare/v0.25.0...v0.26.0
+[0.25.0]: https://github.com/OSC/ood_core/compare/v0.24.2...v0.25.0
 [0.24.2]: https://github.com/OSC/ood_core/compare/v0.24.1...v0.24.2
 [0.24.1]: https://github.com/OSC/ood_core/compare/v0.24.0...v0.24.1
 [0.24.0]: https://github.com/OSC/ood_core/compare/v0.23.5...v0.24.0

data/Rakefile

@@ -1,6 +1,17 @@
 require "bundler/gem_tasks"
 require "rspec/core/rake_task"
+require "minitest/test_task"
+
+require_relative 'lib/tasks/slurm'
 
 RSpec::Core::RakeTask.new(:spec)
 
+
+Minitest::TestTask.create(:test) do |t|
+  t.libs << "test"
+  t.libs << "lib"
+  t.warning = false
+  t.test_globs = ["test/**/*_test.rb"]
+end
+
 task :default => :spec

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

@@ -233,6 +233,7 @@ module OodCore
 
           args.concat ["-N", script.job_name] unless script.job_name.nil?
           args.concat ["-o", script.output_path] unless script.output_path.nil?
+          args.concat ['--mpi', "proc=#{script.cores}"] unless script.cores.nil?
           if script.error_path.nil?
             args.concat ["-j"]
           else

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

@@ -239,7 +239,7 @@ class OodCore::Job::Adapters::Kubernetes::Batch
     node_selector = native_data[:node_selector].nil? ? {} : native_data[:node_selector]
     gpu_type = native_data[:gpu_type].nil? ? "nvidia.com/gpu" : native_data[:gpu_type]
 
-    template = ERB.new(File.read(resource_file), nil, '-')
+    template = ERB.new(File.read(resource_file), trim_mode: '-')
 
     [template.result(binding), id]
   end
@@ -271,7 +271,7 @@ class OodCore::Job::Adapters::Kubernetes::Batch
   end
 
   def namespace
-    "#{namespace_prefix}#{username}"
+    "#{namespace_prefix}#{username.gsub(/[.@]/, '-')}"
   end
 
   def formatted_ns_cmd

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

@@ -170,6 +170,7 @@ class OodCore::Job::Adapters::LinuxHost::Launcher
         'script_timeout' => script_timeout(script),
         'session_name' => session_name,
         'singularity_bin' => singularity_bin,
+        'singularity_options' => singularity_options(script.native),
         'singularity_image' => singularity_image(script.native),
         'ssh_hosts' => ssh_hosts,
         'tmux_bin' => tmux_bin,
@@ -205,6 +206,12 @@ class OodCore::Job::Adapters::LinuxHost::Launcher
     native[:singularity_bindpath]
   end
 
+  def singularity_options(native)
+    return '' unless native && native[:singularity_options]
+
+    native[:singularity_options]
+  end
+
   def script_timeout(script)
     wall_time = script.wall_time.to_i
     return site_timeout if wall_time == 0
@@ -294,4 +301,4 @@ class OodCore::Job::Adapters::LinuxHost::Launcher
     end.compact.last.to_s
   end
 
-end
+end

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

@@ -47,7 +47,7 @@ trap exit_script SIGINT SIGTERM
 OUTPUT_PATH=<%= output_path %>
 ERROR_PATH=<%= error_path %>
 ({
-timeout <%= script_timeout %>s <%= singularity_bin %> exec <%= contain %> --pid <%= singularity_image %> /bin/bash --login $singularity_tmp_file <%= arguments %>
+timeout <%= script_timeout %>s <%= singularity_bin %> exec <%= singularity_options %> <%= contain %> --pid <%= singularity_image %> /bin/bash --login $singularity_tmp_file <%= arguments %>
 } | tee "$OUTPUT_PATH") 3>&1 1>&2 2>&3 | tee "$ERROR_PATH"
 
 <%= email_on_terminated %>

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

@@ -91,6 +91,7 @@ class OodCore::Job::Adapters::Lsf::Helper
     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?
+    args.concat ['-n', script.cores] unless script.cores.nil?
 
     # environment
     env = script.job_environment || {}

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

@@ -269,6 +269,7 @@ module OodCore
           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?
+          args.concat ppn(script)
 
           # Set dependencies
           depend = []
@@ -422,6 +423,13 @@ module OodCore
           '#PBS'
         end
 
+        # place holder for when we support both nodes and cpus.
+        def ppn(script)
+          return [] if script.cores.nil?
+
+          ['-l', "ncpus=#{script.cpus}"]
+        end
+
         private
           # Convert duration to seconds
           def duration_in_seconds(time)

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

@@ -372,10 +372,14 @@ module OodCore
                                        hsh[:AllowAccounts].to_s.split(',')
                                      end
 
-
               hsh[:deny_accounts] = hsh[:DenyAccounts].nil? ? [] : hsh[:DenyAccounts].to_s.split(',')
-              hsh[:tres] = hsh[:TRES].nil? ? {} : hsh[:TRES].to_s.split(',').map { |str| str.split('=') }.to_h
 
+              hsh[:tres] = case hsh[:TRES]
+                           when nil, '(null)', ''
+                             {}
+                           else
+                             hsh[:TRES].to_s.split(',').map { |str| str.split('=') }.to_h
+                           end
               OodCore::Job::QueueInfo.new(**hsh)
             end
 
@@ -526,6 +530,7 @@ module OodCore
           args.concat ['-a', script.job_array_request] unless script.job_array_request.nil?
           args.concat ['--qos', script.qos] unless script.qos.nil?
           args.concat ['--gpus-per-node', script.gpus_per_node] unless script.gpus_per_node.nil?
+          args.concat ['-n', script.cores] unless script.cores.nil?
           # ignore nodes, don't know how to do this for slurm
 
           # Set dependencies

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

@@ -10,7 +10,7 @@ require 'time'
 # @api private
 class OodCore::Job::Adapters::LinuxSystemd::Launcher
   attr_reader :debug, :site_timeout, :session_name_label, :ssh_hosts,
-    :strict_host_checking, :username
+    :strict_host_checking, :username, :ssh_keyfile
   # The root exception class that all LinuxSystemd adapter-specific exceptions inherit
   # from
   class Error < StandardError; end
@@ -26,6 +26,7 @@ class OodCore::Job::Adapters::LinuxSystemd::Launcher
     ssh_hosts:,
     strict_host_checking: false,
     submit_host:,
+    ssh_keyfile: "",
     **_
   )
     @debug = !! debug
@@ -35,6 +36,7 @@ class OodCore::Job::Adapters::LinuxSystemd::Launcher
     @strict_host_checking = strict_host_checking
     @submit_host = submit_host
     @username = Etc.getlogin
+    @ssh_keyfile = ssh_keyfile
   end
 
   # @param hostname [#to_s] The hostname to submit the work to
@@ -97,27 +99,27 @@ class OodCore::Job::Adapters::LinuxSystemd::Launcher
   # if ! strict_host_checking
   # -o UserKnownHostsFile=/dev/null (do not update the user's known hosts file)
   # -o StrictHostKeyChecking=no (do no check the user's known hosts file)
+  # if ssh_keyfile
+  # -i ssh_keyfile (Use this keyfile location)
   #
   # @param destination_host [#to_s] the destination host you wish to ssh into
   # @param cmd [Array<#to_s>] the command to be executed on the destination host
   def ssh_cmd(destination_host, cmd)
-    if strict_host_checking
-      [
-        'ssh', '-t',
-        '-p', OodCore::Job::Adapters::Helper.ssh_port,
-        '-o', 'BatchMode=yes',
-        "#{username}@#{destination_host}"
-      ].concat(cmd)
-    else
-      [
-        'ssh', '-t',
-        '-p', OodCore::Job::Adapters::Helper.ssh_port,
-        '-o', 'BatchMode=yes',
-        '-o', 'UserKnownHostsFile=/dev/null',
-        '-o', 'StrictHostKeyChecking=no',
-        "#{username}@#{destination_host}"
-      ].concat(cmd)
-    end
+
+    sshcmd = [
+      'ssh', '-t',
+      '-p', OodCore::Job::Adapters::Helper.ssh_port,
+      '-o', 'Batchmode=yes',
+    ]
+
+    sshcmd.concat([
+      '-o','StrictHostKeyChecking=no',
+      '-o','UserKnownHostsFile=/dev/null',
+    ]) unless strict_host_checking
+
+    sshcmd.concat(['-i',ssh_keyfile.to_s,]) unless ssh_keyfile.to_s.empty?
+
+    sshcmd.concat(["#{username}@#{destination_host}"]).concat(cmd)
   end
 
   def shell

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

@@ -15,6 +15,7 @@ module OodCore
       # @option config [Object] :ssh_hosts (nil) The list of permissable hosts, defaults to :submit_host
       # @option config [Object] :strict_host_checking (true) Set to false to disable strict host checking and updating the known_hosts file
       # @option config [Object] :submit_host The SSH target to connect to, may be the head of a round-robin
+      # @option config [Object] :ssh_keyfile The SSH Key file to use as identity.
       def self.build_systemd(config)
         c = config.to_h.symbolize_keys
         debug = c.fetch(:debug, false)
@@ -22,6 +23,7 @@ module OodCore
         ssh_hosts = c.fetch(:ssh_hosts, [c[:submit_host]])
         strict_host_checking = c.fetch(:strict_host_checking, true)
         submit_host = c[:submit_host]
+        ssh_keyfile = c.fetch(:ssh_keyfile, "")
 
         Adapters::LinuxSystemd.new(
           ssh_hosts: ssh_hosts,
@@ -31,6 +33,7 @@ module OodCore
             ssh_hosts: ssh_hosts,
             strict_host_checking: strict_host_checking,
             submit_host: submit_host,
+            ssh_keyfile: ssh_keyfile,
           )
         )
       end

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

@@ -160,6 +160,7 @@ module OodCore
             args.concat ['-t', script.job_array_request] unless script.job_array_request.nil?
             args.concat ['-l', "qos=#{script.qos}"] unless script.qos.nil?
             args.concat ['-l', "gpus=#{script.gpus_per_node}"] unless script.gpus_per_node.nil?
+            args.concat ppn(script)
 
             # Set environment variables
             env = script.job_environment.to_h
@@ -302,6 +303,13 @@ module OodCore
           '#QSUB'
         end
 
+        # place holder for when we support both nodes and cpus.
+        def ppn(script)
+          return [] if script.cores.nil?
+
+          ['-l', "procs=#{script.cpus}"]
+        end
+
         private
           # Convert duration to seconds
           def duration_in_seconds(time)

data/lib/ood_core/job/script.rb

@@ -108,6 +108,10 @@ module OodCore
       # @return [Integer, nil] gpus per node
       attr_reader :gpus_per_node
 
+      # The core request for this job
+      # @return [Integer, nil] cores
+      attr_reader :cores
+
       # Object detailing any native specifications that are implementation specific
       # @note Should not be used at all costs.
       # @return [Object, nil] native specifications
@@ -151,7 +155,8 @@ 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,
-                     qos: nil, gpus_per_node: nil, native: nil, copy_environment: nil, **_)
+                     qos: nil, gpus_per_node: nil, native: nil, copy_environment: nil,
+                     cores: nil, **_)
         @content = content.to_s
 
         @submit_as_hold      = submit_as_hold
@@ -179,6 +184,7 @@ module OodCore
         @gpus_per_node      = gpus_per_node     && gpus_per_node.to_i
         @native             = native
         @copy_environment   = (copy_environment.nil?) ? nil : !! copy_environment
+        @cores              = cores&.to_i
       end
 
       # Convert object to hash
@@ -209,7 +215,8 @@ module OodCore
           qos:                 qos,
           gpus_per_node:       gpus_per_node,
           native:              native,
-          copy_environment:    copy_environment
+          cores:               cores,
+          copy_environment:    copy_environment,
         }
       end
 

data/lib/ood_core/version.rb

@@ -1,4 +1,4 @@
 module OodCore
   # The current version of {OodCore}
-  VERSION = "0.26.1"
+  VERSION = "0.27.1"
 end

data/lib/tasks/slurm.rb

@@ -0,0 +1,17 @@
+# frozen_string_literal: true
+
+require_relative '../ood_core'
+require_relative '../ood_core/job/adapters/slurm'
+
+namespace :slurm do
+
+  desc 'Get squeue output in the format this gem expects'
+  task :squeue do
+    fields = OodCore::Job::Adapters::Slurm::Batch.new.all_squeue_fields
+    args = OodCore::Job::Adapters::Slurm::Batch.new.squeue_args(options: fields.values)
+
+    single_job = `squeue #{args.join(' ')}`.split("\n")[0...2]
+
+    puts single_job
+  end
+end

data/ood_core.gemspec

@@ -31,4 +31,6 @@ Gem::Specification.new do |spec|
   spec.add_development_dependency "pry", "~> 0.10"
   spec.add_development_dependency "timecop", "~> 0.8"
   spec.add_development_dependency "climate_control", "~> 1.2.0"
+  spec.add_development_dependency "minitest", "~> 5"
+  spec.add_development_dependency "mocha", "~> 2.4"
 end

metadata

@@ -1,16 +1,16 @@
 --- !ruby/object:Gem::Specification
 name: ood_core
 version: !ruby/object:Gem::Version
-  version: 0.26.1
+  version: 0.27.1
 platform: ruby
 authors:
 - Eric Franz
 - Morgan Rodgers
 - Jeremy Nicklas
-autorequire: 
+autorequire:
 bindir: exe
 cert_chain: []
-date: 2024-07-31 00:00:00.000000000 Z
+date: 2025-02-10 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: ood_support
@@ -138,6 +138,34 @@ dependencies:
     - - "~>"
       - !ruby/object:Gem::Version
         version: 1.2.0
+- !ruby/object:Gem::Dependency
+  name: minitest
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '5'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '5'
+- !ruby/object:Gem::Dependency
+  name: mocha
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '2.4'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '2.4'
 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:
@@ -221,12 +249,13 @@ files:
 - lib/ood_core/refinements/drmaa_extensions.rb
 - lib/ood_core/refinements/hash_extensions.rb
 - lib/ood_core/version.rb
+- lib/tasks/slurm.rb
 - ood_core.gemspec
 homepage: https://github.com/OSC/ood_core
 licenses:
 - MIT
 metadata: {}
-post_install_message: 
+post_install_message:
 rdoc_options: []
 require_paths:
 - lib
@@ -242,7 +271,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubygems_version: 3.1.2
-signing_key: 
+signing_key:
 specification_version: 4
 summary: Open OnDemand core library
 test_files: []