ood_core 0.13.0 → 0.16.1

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

@@ -16,7 +16,7 @@ class OodCore::Job::Adapters::LinuxHost::Launcher
   # from
   class Error < StandardError; end
 
-  UNIT_SEPARATOR = "\x1F"
+  UNIT_SEPARATOR = ","
 
   # @param debug Whether the adapter should be used in debug mode
   # @param site_timeout [#to_i] A period after which the job should be killed or nil
@@ -80,12 +80,7 @@ class OodCore::Job::Adapters::LinuxHost::Launcher
 
     call(*cmd, stdin: kill_cmd)
   rescue Error => e
-    raise e unless (
-      # The tmux server not running is not an error
-      e.message.include?('failed to connect to server') ||
-      # The session not being found is not an error
-      e.message.include?("session not found: #{session_name_label}")
-    )
+    interpret_and_raise(e)
   end
 
   def list_remote_sessions(host: nil)
@@ -166,7 +161,7 @@ class OodCore::Job::Adapters::LinuxHost::Launcher
         'email_on_terminated' => script_email_on_event(script, 'terminated'),
         'email_on_start' => script_email_on_event(script, 'started'),
         'environment' => export_env(script),
-        'error_path' => (script.error_path) ? script.error_path.to_s : '/dev/null',
+        'error_path' => error_path(script),
         'job_name' => script.job_name.to_s,
         'output_path' => (script.output_path) ? script.output_path.to_s : '/dev/null',
         'script_content' => content,
@@ -176,6 +171,7 @@ class OodCore::Job::Adapters::LinuxHost::Launcher
         'singularity_image' => singularity_image(script.native),
         'ssh_hosts' => ssh_hosts,
         'tmux_bin' => tmux_bin,
+        'workdir' => (script.workdir) ? script.workdir.to_s : '/tmp',
       }.each{
         |key, value| bnd.local_variable_set(key, value)
       }
@@ -263,8 +259,7 @@ class OodCore::Job::Adapters::LinuxHost::Launcher
       |session_hash| session_hash[:session_name].start_with?(session_name_label)
     }
   rescue Error => e
-    # The tmux server not running is not an error
-    raise e unless e.message.include?('failed to connect to server')
+    interpret_and_raise(e)
     []
   end
 
@@ -272,4 +267,24 @@ class OodCore::Job::Adapters::LinuxHost::Launcher
     return false if script.content.empty?
     script.content.split("\n").first.start_with?('#!/')
   end
+
+  def error_path(script)
+    return script.error_path.to_s if script.error_path
+    return script.output_path.to_s if script.output_path
+
+    '/dev/null'
+  end
+
+  # under some conditions tmux returns status code 1 but it's not an actual
+  # error. These are when the session is not found or there are no sessions
+  # at all.
+  def interpret_and_raise(error)
+    if error.message.include?('failed to connect to server') # no sessions in tmux 1.8
+      nil
+    elsif error.message.include?('no server running on') # no sessions in tmux 2.7+ message
+      nil
+    else
+      raise error
+    end
+  end
 end

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

@@ -16,13 +16,9 @@ fi
 echo $hostname
 
 # Put the script into a temp file on localhost
-<% if debug %>
-singularity_tmp_file=$(mktemp -p "$HOME" --suffix '_sing')
-tmux_tmp_file=$(mktemp -p "$HOME" --suffix "_tmux")
-<% else %>
-singularity_tmp_file=$(mktemp)
-tmux_tmp_file=$(mktemp)
-<% end %>
+singularity_tmp_file=$(mktemp -p "<%= workdir %>" --suffix '_sing')
+tmux_tmp_file=$(mktemp -p "<%= workdir %>" --suffix "_tmux")
+
 
 # Create an executable to run in a tmux session
 # The escaped HEREDOC means that we need to substitute in $singularity_tmp_file ourselves
@@ -69,10 +65,3 @@ SINGULARITY_LAUNCHER
 chmod +x "$singularity_tmp_file"
 chmod +x "$tmux_tmp_file"
 <%= tmux_bin %> new-session -d -s "<%= session_name %>" "$tmux_tmp_file"
-
-# Remove the file
-<% if ! debug %>
-# Wait 1 second to ensure that tmux session has started before the file is removed
-sleep 1
-rm -f "$tmux_tmp_file"; rm -f "$singularity_tmp_file"
-<% end %>

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

@@ -80,6 +80,9 @@ module OodCore
           # from
           class Error < StandardError; end
 
+          # An error indicating the slurm command timed out
+          class SlurmTimeoutError < Error; end
+
           # @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
@@ -147,6 +150,9 @@ module OodCore
               end
               jobs
             end
+          rescue SlurmTimeoutError
+            # TODO: could use a log entry here
+            return [{ id: id, state: 'undetermined' }]
           end
 
           def squeue_fields(attrs)
@@ -303,7 +309,18 @@ module OodCore
 
               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)
+              s.success? ? interpret_and_raise(o, e) : raise(Error, e)
+            end
+
+            # Helper function to raise an error based on the contents of stderr.
+            # Slurm exits 0 even when the command fails, so we need to interpret stderr
+            # to see if the command was actually successful.
+            def interpret_and_raise(stdout, stderr)
+              return stdout if stderr.empty?
+
+              raise SlurmTimeoutError, stderr if /^slurm_load_jobs error: Socket timed out/.match(stderr)
+
+              stdout
             end
 
             def squeue_attrs_for_info_attrs(attrs)

data/lib/ood_core/version.rb

@@ -1,4 +1,4 @@
 module OodCore
   # The current version of {OodCore}
-  VERSION = "0.13.0"
+  VERSION = "0.16.1"
 end

data/ood_core.gemspec

@@ -24,7 +24,8 @@ Gem::Specification.new do |spec|
 
   spec.add_runtime_dependency "ood_support", "~> 0.0.2"
   spec.add_runtime_dependency "ffi", "~> 1.9", ">= 1.9.6"
-  spec.add_development_dependency "bundler", "~> 1.7"
+  spec.add_development_dependency "bundler", "~> 2.1"
+  spec.add_runtime_dependency "activesupport", ">= 5.2", "< 6.0"
   spec.add_development_dependency "rake", "~> 13.0.1"
   spec.add_development_dependency "rspec", "~> 3.0"
   spec.add_development_dependency "pry", "~> 0.10"

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: ood_core
 version: !ruby/object:Gem::Version
-  version: 0.13.0
+  version: 0.16.1
 platform: ruby
 authors:
 - Eric Franz
@@ -10,7 +10,7 @@ authors:
 autorequire: 
 bindir: exe
 cert_chain: []
-date: 2020-08-10 00:00:00.000000000 Z
+date: 2021-04-23 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: ood_support
@@ -52,14 +52,34 @@ dependencies:
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '1.7'
+        version: '2.1'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '1.7'
+        version: '2.1'
+- !ruby/object:Gem::Dependency
+  name: activesupport
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '5.2'
+    - - "<"
+      - !ruby/object:Gem::Version
+        version: '6.0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '5.2'
+    - - "<"
+      - !ruby/object:Gem::Version
+        version: '6.0'
 - !ruby/object:Gem::Dependency
   name: rake
   requirement: !ruby/object:Gem::Requirement
@@ -140,9 +160,9 @@ executables: []
 extensions: []
 extra_rdoc_files: []
 files:
+- ".github/workflows/test.yml"
 - ".gitignore"
 - ".rspec"
-- ".travis.yml"
 - CHANGELOG.md
 - Gemfile
 - LICENSE.txt
@@ -166,6 +186,12 @@ files:
 - lib/ood_core/job/adapters/ccq.rb
 - lib/ood_core/job/adapters/drmaa.rb
 - lib/ood_core/job/adapters/helper.rb
+- lib/ood_core/job/adapters/kubernetes.rb
+- lib/ood_core/job/adapters/kubernetes/batch.rb
+- lib/ood_core/job/adapters/kubernetes/helper.rb
+- lib/ood_core/job/adapters/kubernetes/k8s_job_info.rb
+- lib/ood_core/job/adapters/kubernetes/resources.rb
+- lib/ood_core/job/adapters/kubernetes/templates/pod.yml.erb
 - lib/ood_core/job/adapters/linux_host.rb
 - lib/ood_core/job/adapters/linux_host/launcher.rb
 - lib/ood_core/job/adapters/linux_host/templates/email.erb.sh
@@ -216,7 +242,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.0.3
+rubygems_version: 3.1.2
 signing_key: 
 specification_version: 4
 summary: Open OnDemand core library

data/.travis.yml

@@ -1,9 +0,0 @@
-sudo: false
-language: ruby
-rvm:
-  - 2.5.5
-before_install: gem install bundler -v '~> 1.17'
-notifications:
-  email:
-    on_success: never
-    on_failure: always