ood_core 0.0.4 → 0.0.5

checksums.yaml

@@ -1,7 +1,7 @@
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data/CHANGELOG.md

@@ -1,33 +1,76 @@
-## Unreleased
+# Changelog
 
-## 0.0.4 (2017-05-17)
+All notable changes to this project will be documented in this file.
 
-Features:
+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).
 
-  - removed `OodCore::Job::Script#min_phys_memory` due to lack of commonality
-    across resource managers
-  - removed `OodCore::Job::Script#join_files` due to lack of support in
-    resource managers
-  - by default all PBS jobs output stdout & stderr to output path unless an
-    error path is specified (mimics behavior of Slurm and LSF)
+## [Unreleased]
 
-## 0.0.3 (2017-04-28)
+## [0.0.5] - 2017-07-05
 
-Features:
+### Added
 
-  - provide support for slurm conf file
+- Add wallclock time limit to `OodCore::Job::Info` object.
+- Add further support for the LSF adapter.
+- Add a new Batch Connect template feature that builds batch scripts to launch
+  web servers.
+- Add support for the PBS Professional resource manager.
+- Add method to filter list of batch jobs for a given owner or owners.
 
-Bugfixes:
+### Changed
 
-  - correct code documentation for `Script#min_phys_memory`
-  - fix for login feature being allowed on all clusters even if not defined
+- Torque adapter provides nodes/procs info if available for non-running jobs.
+- Slurm adapter provides node info if available for non-running jobs.
+- Changed the `CHANGELOG.md` formatting.
 
-## 0.0.2 (2017-04-27)
+### Removed
 
-Features:
+- Remove deprecated tests for the Slurm adapter.
 
-  - removed the `OodCore::Job::NodeRequest` object
+### Fixed
 
-## 0.0.1 (2017-04-17)
+- Fix parsing bjobs output for LSF 9.1, which has extra SLOTS column.
 
-Initial release!
+## [0.0.4] - 2017-05-17
+
+### Changed
+
+- By default all PBS jobs output stdout & stderr to output path unless an error
+  path is specified (mimics behavior of Slurm and LSF)
+
+### Removed
+
+- Remove `OodCore::Job::Script#min_phys_memory` due to lack of commonality
+  across resource managers.
+- Remove `OodCore::Job::Script#join_files` due to lack of support in resource
+  managers.
+
+## [0.0.3] - 2017-04-28
+
+### Added
+
+- Provide support for Slurm conf file.
+
+### Fixed
+
+- Correct code documentation for `Script#min_phys_memory`.
+- Add fix for login feature being allowed on all clusters even if not defined.
+
+## [0.0.2] - 2017-04-27
+
+### Removed
+
+- Remove the `OodCore::Job::NodeRequest` object.
+
+## 0.0.1 - 2017-04-17
+
+### Added
+
+- Initial release!
+
+[Unreleased]: https://github.com/OSC/ood_core/compare/v0.0.5...HEAD
+[0.0.5]: https://github.com/OSC/ood_core/compare/v0.0.4...v0.0.5
+[0.0.4]: https://github.com/OSC/ood_core/compare/v0.0.3...v0.0.4
+[0.0.3]: https://github.com/OSC/ood_core/compare/v0.0.2...v0.0.3
+[0.0.2]: https://github.com/OSC/ood_core/compare/v0.0.1...v0.0.2

data/lib/ood_core.rb

@@ -30,4 +30,10 @@ module OodCore
     module Adapters
     end
   end
+
+  # A namespace for batch connect code
+  module BatchConnect
+    require "ood_core/batch_connect/template"
+    require "ood_core/batch_connect/factory"
+  end
 end

data/lib/ood_core/batch_connect/factory.rb

@@ -0,0 +1,42 @@
+require "ood_core/refinements/hash_extensions"
+
+module OodCore
+  module BatchConnect
+    # A factory that builds a batch connect template object from a
+    # configuration.
+    class Factory
+      using Refinements::HashExtensions
+
+      class << self
+        # Build a batch connect template from a configuration
+        # @param config [#to_h] configuration describing batch connect template
+        # @option config [#to_s] :template The batch connect template to use
+        # @raise [TemplateNotSpecified] if no template is specified
+        # @raise [TemplateNotFound] if the specified template does not exist
+        # @return [Template] the batch connect template object
+        def build(config)
+          c = config.to_h.symbolize_keys
+
+          template = c.fetch(:template) { raise TemplateNotSpecified, "batch connect configuration does not specify template" }.to_s
+
+          path_to_template = "ood_core/batch_connect/templates/#{template}"
+          begin
+            require path_to_template
+          rescue Gem::LoadError => e
+            raise Gem::LoadError, "Specified '#{template}' for batch connect template, but the gem is not loaded."
+          rescue LoadError => e
+            raise LoadError, "Could not load '#{template}'. Make sure that that batch connect template in the configuration file is valid."
+          end
+
+          template_method = "build_#{template}"
+
+          unless respond_to?(template_method)
+            raise TemplateNotFound, "batch connect configuration specifies nonexistent #{template} template"
+          end
+
+          send(template_method, c)
+        end
+      end
+    end
+  end
+end

data/lib/ood_core/batch_connect/template.rb

@@ -0,0 +1,207 @@
+require "ood_core/refinements/hash_extensions"
+
+module OodCore
+  module BatchConnect
+    # A template class that renders a batch script designed to facilitate
+    # external connections to the running job
+    class Template
+      using Refinements::HashExtensions
+      using Refinements::ArrayExtensions
+
+      # The context used to render this template
+      # @return [Hash] context hash
+      attr_reader :context
+
+      # @param context [#to_h] the context used to render the template
+      # @option context [#to_s] :work_dir Working directory for batch script
+      # @option context [#to_s] :conn_file ("connection.yml") The file that
+      #   holds connection information
+      # @option context [#to_sym, Array<#to_sym>] :conn_params ([]) A list of
+      #   connection parameters added to the connection file (`:host`, `:port`,
+      #   and `:password` will always exist)
+      # @option context [#to_s] :bash_helpers ("...") Bash helper methods
+      # @option context [#to_i] :min_port (2000) Minimum port used when looking
+      #   for available port
+      # @option context [#to_i] :max_port (65535) Maximum port used when
+      #   looking for available port
+      # @option context [#to_i] :passwd_size (32) Length of randomly generated
+      #   password
+      # @option context [#to_s] :script_wrapper ("%s") Bash code that wraps
+      #   around the body of the template script (use `%s` to interpolate the
+      #   body)
+      # @option context [#to_s] :before_script ("...") Bash code run before the
+      #   main script is forked off
+      # @option context [#to_s] :before_file ("before.sh") Path to script that
+      #   is sourced before main script is forked (assumes you don't modify
+      #   `:before_script`)
+      # @option context [#to_s] :run_script ("...") Bash code that is forked
+      #   off and treated as the main script
+      # @option context [#to_s] :script_file ("./script.sh") Path to script
+      #   that is forked as the main scripta (assumes you don't modify
+      #   `:run_script`)
+      # @option context [#to_s] :timeout ("") Timeout the main script in
+      #   seconds, if empty then let script run for full walltime (assumes you
+      #   don't modify `:run_script`)
+      # @option context [#to_s] :clean_script ("...") Bash code run during
+      #   clean up after job finishes
+      # @option context [#to_s] :clean_file ("clean.sh") Path to script that is
+      #   sourced during clean up (assumes you don't modify `:clean_script`)
+      def initialize(context = {})
+        @context = context.to_h.compact.symbolize_keys
+        raise ArgumentError, "No work_dir specified. Missing argument: work_dir" unless context.include?(:work_dir)
+      end
+
+      # Render this template as string
+      # @return [String] rendered template
+      def to_s
+        <<-EOT.gsub(/^ {10}/, '')
+          #!/bin/bash
+
+          #{script_wrapper}
+        EOT
+      end
+
+      private
+        # Working directory that batch script runs in
+        def work_dir
+          context.fetch(:work_dir).to_s
+        end
+
+        # The file that holds the connection information in yaml format
+        def conn_file
+          context.fetch(:conn_file, "connection.yml").to_s
+        end
+
+        # The parameters to include in the connection file
+        def conn_params
+          conn_params = Array.wrap(context.fetch(:conn_params, [])).map(&:to_sym)
+          (conn_params + [:host, :port, :password]).uniq
+        end
+
+        # Helper methods used in the bash scripts
+        def bash_helpers
+          context.fetch(:bash_helpers) do
+            min_port    = context.fetch(:min_port, 2000).to_i
+            max_port    = context.fetch(:max_port, 65535).to_i
+            passwd_size = context.fetch(:passwd_size, 32).to_i
+
+            <<-EOT.gsub(/^ {14}/, '')
+              # Generate random integer in range [$1..$2]
+              function random () {
+                shuf -i ${1}-${2} -n 1
+              }
+
+              # Check if port $1 is in use
+              function used_port () {
+                local PORT=${1}
+                nc -z localhost ${PORT} &>/dev/null
+              }
+
+              # Find available port in range [$1..$2]
+              # Default: [#{min_port}..#{max_port}]
+              function find_port () {
+                local PORT=$(random ${1:-#{min_port}} ${2:-#{max_port}})
+                while $(used_port ${PORT}); do
+                  PORT=$(random ${1:-#{min_port}} ${2:-#{max_port}})
+                done
+                echo ${PORT}
+              }
+
+              # Generate random alphanumeric password with $1 (default: #{passwd_size}) characters
+              function create_passwd () {
+                tr -cd '[:alnum:]' < /dev/urandom 2>/dev/null | head -c${1:-#{passwd_size}}
+              }
+            EOT
+          end.to_s
+        end
+
+        # Bash code that wraps around the body of the template script (use `%s`
+        # to interpolate the body)
+        def script_wrapper
+          context.fetch(:script_wrapper, "%s").to_s % base_script
+        end
+
+        # Source in a developer defined script before running the main script
+        def before_script
+          context.fetch(:before_script) do
+            before_file = context.fetch(:before_file, "before.sh").to_s
+
+            "host=$(hostname)\n[[ -e \"#{before_file}\" ]] && source \"#{before_file}\""
+          end.to_s
+        end
+
+        # Fork off a developer defined main script and possibly time it out after
+        # a period of time
+        def run_script
+          context.fetch(:run_script) do
+            script_file = context.fetch(:script_file,  "./script.sh").to_s
+            timeout     = context.fetch(:timeout, "").to_s
+
+            timeout.empty? ? "\"#{script_file}\"" : "timeout #{timeout} \"#{script_file}\""
+          end.to_s
+        end
+
+        # Source in a developer defined script after running the main script
+        def after_script
+          context.fetch(:after_script) do
+            after_file = context.fetch(:after_file, "after.sh").to_s
+
+            "[[ -e \"#{after_file}\" ]] && source \"#{after_file}\""
+          end.to_s
+        end
+
+        # Source in a developer defined clean up script that is run during the
+        # clean up stage
+        def clean_script
+          context.fetch(:clean_script) do
+            clean_file = context.fetch(:clean_file, "clean.sh").to_s
+
+            "[[ -e \"#{clean_file}\" ]] && source \"#{clean_file}\""
+          end.to_s
+        end
+
+        # The base script template
+        def base_script
+          <<-EOT.gsub(/^ {12}/, '')
+            cd #{work_dir}
+
+            # Generate a connection yaml file with given parameters
+            function create_yml () {
+              echo "Generating connection YAML file..."
+              (
+                umask 077
+                echo -e "#{conn_params.map { |p| "#{p}: $#{p}" }.join('\n')}" > "#{conn_file}"
+              )
+            }
+
+            # Cleanliness is next to Godliness
+            function clean_up () {
+              echo "Cleaning up..."
+              #{clean_script.gsub(/\n(?=[^\s])/, "\n  ")}
+              pkill -P $$
+              exit ${1:-0}
+            }
+
+            #{bash_helpers}
+
+            #{before_script}
+
+            echo "Script starting..."
+            #{run_script} &
+            SCRIPT_PID=$!
+
+            #{after_script}
+
+            # Create the connection yaml file
+            create_yml
+
+            # Wait for script process to finish
+            wait ${SCRIPT_PID} || clean_up 1
+
+            # Exit cleanly
+            clean_up
+          EOT
+        end
+    end
+  end
+end

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

@@ -0,0 +1,23 @@
+require "ood_core/refinements/hash_extensions"
+
+module OodCore
+  module BatchConnect
+    class Factory
+      using Refinements::HashExtensions
+
+      # Build the basic template from a configuration
+      # @param config [#to_h] the configuration for the batch connect template
+      def self.build_basic(config)
+        context = config.to_h.symbolize_keys.reject { |k, _| k == :template }
+        Templates::Basic.new(context)
+      end
+    end
+
+    module Templates
+      # A batch connect template that expects to start up a basic web server
+      # within a batch job
+      class Basic < Template
+      end
+    end
+  end
+end

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

@@ -0,0 +1,201 @@
+require "ood_core/refinements/hash_extensions"
+
+module OodCore
+  module BatchConnect
+    class Factory
+      using Refinements::HashExtensions
+
+      # Build the VNC template from a configuration
+      # @param config [#to_h] the configuration for the batch connect template
+      def self.build_vnc(config)
+        context = config.to_h.symbolize_keys.reject { |k, _| k == :template }
+        Templates::VNC.new(context)
+      end
+    end
+
+    module Templates
+      # A batch connect template that starts up a VNC server within a batch job
+      class VNC < Template
+        # @param context [#to_h] the context used to render the template
+        # @option context [#to_sym, Array<#to_sym>] :conn_params ([]) A list of
+        #   connection parameters added to the connection file (`:host`,
+        #   `:port`, `:password`, `:spassword`, `:display` and `:websocket`
+        #   will always exist)
+        # @option context [#to_s] :websockify_cmd
+        #   ("${WEBSOCKIFY_CMD:-/opt/websockify/run}") the path to the
+        #   websockify script (assumes you don't modify `:after_script`)
+        # @option context [#to_s] :vnc_log ("vnc.log") path to vnc server log
+        #   file (assumes you don't modify `:before_script` or `:after_script`)
+        # @option context [#to_s] :vnc_passwd ("vnc.passwd") path to the file
+        #   generated that contains the encrypted vnc password (assumes you
+        #   don't modify `:before_script`)
+        # @option context [#to_s] :vnc_args arguments used when starting up the
+        #   vnc server (overrides any specific vnc argument) (assumes you don't
+        #   modify `:before_script`)
+        # @option context [#to_s] :name ("") name of the vnc server session
+        #   (not set if blank or `:vnc_args` is set) (assumes you don't modify
+        #   `:before_script`)
+        # @option context [#to_s] :geometry ("") resolution of vnc display (not
+        #   set if blank or `:vnc_args` is set) (assumes you don't modify
+        #   `:before_script`)
+        # @option context [#to_s] :dpi ("") dpi of vnc display (not set if
+        #   blank or `:vnc_args` is set) (assumes you don't modify
+        #   `:before_script`)
+        # @option context [#to_s] :fonts ("") command delimited list of fonts
+        #   available in vnc display (not set if blank or `:vnc_args` is set)
+        #   (assumes you don't modify `:before_script`)
+        # @option context [#to_s] :idle ("") timeout vnc server if no
+        #   connection in this amount of time in seconds (not set if blank or
+        #   `:vnc_args` is set) (assumes you don't modify `:before_script`)
+        # @option context [#to_s] :extra_args ("") any extra arguments used
+        #   when initializing the vnc server process (not set if blank or
+        #   `:vnc_args` is set) (assumes you don't modify `:before_script`)
+        # @option context [#to_s] :vnc_clean ("...") script used to clean up
+        #   any active vnc sessions (assumes you don't modify `:before_script`
+        #   or `:clean_script`)
+        # @see Template
+        def initialize(context = {})
+          super
+        end
+
+        private
+          # We need to know the VNC and websockify connection information
+          def conn_params
+            (super + [:display, :websocket, :spassword]).uniq
+          end
+
+          # Before running the main script, start up a VNC server and record
+          # the connection information
+          def before_script
+            <<-EOT.gsub(/^ {14}/, "")
+              # Setup one-time use passwords and initialize the VNC password
+              function change_passwd () {
+                echo "Setting VNC password..."
+                password=$(create_passwd 8)
+                spassword=${spassword:-$(create_passwd 8)}
+                (
+                  umask 077
+                  echo -ne "${password}\\n${spassword}" | vncpasswd -f > "#{vnc_passwd}"
+                )
+              }
+              change_passwd
+
+              # Start up vnc server (if at first you don't succeed, try, try again)
+              echo "Starting VNC server..."
+              for i in $(seq 1 10); do
+                # Clean up any old VNC sessions that weren't cleaned before
+                #{vnc_clean}
+
+                # Attempt to start VNC server
+                VNC_OUT=$(vncserver -log "#{vnc_log}" -rfbauth "#{vnc_passwd}" -nohttpd -noxstartup #{vnc_args} 2>&1)
+                VNC_PID=$(pgrep -s 0 Xvnc) # the script above will daemonize the Xvnc process
+                echo "${VNC_OUT}"
+
+                # Sometimes Xvnc hangs if it fails to find working disaply, we
+                # should kill it and try again
+                kill -0 ${VNC_PID} 2>/dev/null && [[ "${VNC_OUT}" =~ "Fatal server error" ]] && kill -TERM ${VNC_PID}
+
+                # Check that Xvnc process is running, if not assume it died and
+                # wait some random period of time before restarting
+                kill -0 ${VNC_PID} 2>/dev/null || sleep 0.$(random 1 9)s
+
+                # If running, then all is well and break out of loop
+                kill -0 ${VNC_PID} 2>/dev/null && break
+              done
+
+              # If we fail to start it after so many tries, then just give up
+              kill -0 ${VNC_PID} 2>/dev/null || clean_up 1
+
+              # Parse output for ports used
+              display=$(echo "${VNC_OUT}" | awk -F':' '/^Desktop/{print $NF}')
+              port=$((5900+display))
+
+              echo "Successfully started VNC server on ${host}:${port}..."
+
+              #{super}
+            EOT
+          end
+
+          # Run the script under the VNC server's display
+          def run_script
+            %(DISPLAY=:${display} #{super})
+          end
+
+          # After startup the main script, scan the VNC server log file for
+          # successful connections so that the password can be reset
+          def after_script
+            websockify_cmd = context.fetch(:websockify_cmd, "${WEBSOCKIFY_CMD:-/opt/websockify/run}").to_s
+
+            <<-EOT.gsub(/^ {14}/, "")
+              #{super}
+
+              # Launch websockify websocket server
+              echo "Starting websocket server..."
+              websocket=$(find_port)
+              #{websockify_cmd} -D ${websocket} localhost:${port}
+
+              # Set up background process that scans the log file for successful
+              # connections by users, and change the password after every
+              # connection
+              echo "Scanning VNC log file for user authentications..."
+              while read -r line; do
+                if [[ ${line} =~ "Full-control authentication enabled for" ]]; then
+                  change_passwd
+                  create_yml
+                fi
+              done < <(tail -f --pid=${SCRIPT_PID} "#{vnc_log}") &
+            EOT
+          end
+
+          # Clean up the running VNC server and any other stale VNC servers
+          def clean_script
+            <<-EOT.gsub(/^ {14}/, "")
+              #{super}
+
+              #{vnc_clean}
+              [[ -n ${display} ]] && vncserver -kill :${display}
+            EOT
+          end
+
+          # Log file for VNC server
+          def vnc_log
+            context.fetch(:vnc_log, "vnc.log").to_s
+          end
+
+          # Password file for VNC server
+          def vnc_passwd
+            context.fetch(:vnc_passwd, "vnc.passwd").to_s
+          end
+
+          # Arguments sent to `vncserver` command
+          def vnc_args
+            context.fetch(:vnc_args) do
+              name       = context.fetch(:name, "").to_s
+              geometry   = context.fetch(:geometry, "").to_s
+              dpi        = context.fetch(:dpi, "").to_s
+              fonts      = context.fetch(:fonts, "").to_s
+              idle       = context.fetch(:idle, "").to_s
+              extra_args = context.fetch(:extra_args, "").to_s
+
+              args = []
+              args << "-name #{name}" unless name.empty?
+              args << "-geometry #{geometry}" unless geometry.empty?
+              args << "-dpi #{dpi}" unless dpi.empty?
+              args << "-fp #{fonts}" unless fonts.empty?
+              args << "-idletimeout #{idle}" unless idle.empty?
+              args << extra_args
+
+              args.join(" ")
+            end.to_s
+          end
+
+          # Clean up any stale VNC sessions
+          def vnc_clean
+            context.fetch(:vnc_clean) do
+              %(vncserver -list | awk '/^:/{system("kill -0 "$2" 2>/dev/null || vncserver -kill "$1)}')
+            end.to_s
+          end
+      end
+    end
+  end
+end