class_methods.rb in coderunner-0.17.2

- old
+ new

@@ -16,11 +16,10 @@
       set(var, CLASS_OPTIONS[var])
     end
   end
 
   # List the available modlets for the given code (copts[:C] or -C on the command line).
-
   def self.available_modlets(copts={})
     process_command_options(copts)
     puts "\nAvailable modlets for #{copts[:C]}:"
     entries = []
     begin
@@ -35,11 +34,10 @@
       puts "\t" + File.basename(modlet, '.rb') unless ['.', '..', '.svn', '.directory'].include? modlet or modlet=~ /defaults/
     end
   end
 
     # List the available defaults files for the given code (copts[:C] or -C on the command line).
-
   def self.available_defaults_files(copts={})
     process_command_options(copts)
     entries = []
     #begin
       ##entries += Dir.entries(SCRIPT_FOLDER + "/code_modules/#{copts[:C]}/my_defaults_files")
@@ -59,12 +57,13 @@
       #puts "\t" + File.basename(defaults_file, '.rb').sub(/_defaults/, '') unless ['.', '..', '.svn', '.directory'].include? defaults_file
       puts "\t" + File.basename(defaults_file, '.rb').sub(/_defaults/, '')
     end
   end
 
-  # Cancel the job with the given id. The user is asked interactively for confirmation and whether they would like to delete the folder for that job as well.
-
+  # Cancel the job with the given id. The user is asked interactively for 
+  # confirmation and whether they would like to delete the folder for that job 
+  # as well.
   def self.cancel(id, copts={})
     runner = fetch_runner(copts)
     runner.cancel_job(id.to_i)
   end
 
@@ -76,10 +75,33 @@
     end
 
     runner.continue_in_new_folder(folder, options)
   end
 
+  # Method which concatenates NetCDF output files 
+  def self.concat(name, copts={})
+    begin
+      require "numru/netcdf"
+    rescue LoadError
+      eputs "Error: No Ruby NetCDF library (was it installed correctly?): "\
+            "concatenation for netcdf files not possible."
+      return
+    end
+
+    runner = fetch_runner(copts)
+    runs = runner.filtered_ids.map{|id| runner.combined_run_list[id]}
+
+    concat_string = 'ncrcat '
+    runs.each do |r|
+      concat_string += r.directory + '/' + r.run_name + '.out.nc '
+    end
+
+    concat_string += runner.root_folder + '/' + name
+
+    exec "#{concat_string}"
+  end
+
   # This section defines the report report writing function in. The latex header is defined in run.rb. It is a run method and can be redefined in a particular CRMOD.
   # The function is simply called as follows:
   #
   #   interactively: wr j:<run no.>
   #   command line: coderunner write_report -j <run no>
@@ -108,15 +130,17 @@
             file.puts r.latex_report_header
             file.puts <<-EOF.gsub(/^ {14}/, "")
               \\begin{itemize}
             EOF
 
-            #Need to call some methods here which reads the graphs we want from gs2crmod, generates the graphs
-            #then generates the latex code to display graphs.
+            # Need to call some methods here which reads the graphs we want 
+            # from gs2crmod, generates the graphs then generates the latex code 
+            # to display graphs.
             latex_code = r.latex_graphs.inject("") do |tmp_latex_code, (kit, latexstring)|
               kit.gnuplot_write(kit.file_name) #write the graph
-              tmp_latex_code += "\\item " + latexstring + " \n\n\\newfig{#{kit.file_name}}"
+              tmp_latex_code += "\\item " + latexstring + 
+                                " \n\n\\newfig{#{kit.file_name}}"
               tmp_latex_code += "\n\n"
               tmp_latex_code
             end
 
             file.puts <<-EOF.gsub(/^ {14}/, "")
@@ -133,10 +157,11 @@
 
   def self.delete(copts={})
     runner = fetch_runner(copts)
     runner.destroy
   end
+
   def self.differences_between(copts = {})
     runner = fetch_runner(copts)
     runs = runner.filtered_ids.map{|id| runner.combined_run_list[id]}
     rcp_fetcher = (runs[0] || runner.run_class).rcp
     vars = rcp_fetcher.variables.dup + rcp_fetcher.run_info.dup
@@ -178,18 +203,12 @@
       kit = runner.graphkit_from_lists(copts[:G], copts[:g], index_name => index)
       kit.gp.term =  term
       kit.gnuplot(eval: string_to_eval)
       sleep(copts[:F][:fr] ? 1.0/copts[:F][:fr] :  0.1)
     end
-  end
-#   def self.executable_name # :nodoc:
-#     ""
-#   end
-#
-#   def self.rcp # :nodoc:
-#     @rcp ||= KitHash.new
-#   end
+  end 
+
   def self.netcdf_plot(netcdf_file, vars, indices, copts={})
     process_command_options(copts)
     begin
       require "numru/netcdf"
     rescue LoadError
@@ -212,12 +231,10 @@
     kit.gnuplot
     STDIN.gets
     kit.close
   end
 
-
-
   def self.print_queue_status(copts={})
     begin
       eputs queue_status
     rescue => _err
       eputs "General queue status doesn't work on this system; showing queue status for this folder"
@@ -225,14 +242,10 @@
       runner = fetch_runner(copts)
       eputs runner.queue_status
     end
   end
 
-
-
-
-
   def self.reference(class_or_method, copts={})
     code_folders = Dir.recursive_entries(SCRIPT_FOLDER + '/code_modules').grep(/\/ri$/).map{|fold| ['-d', fold]}.flatten
 #     ep code_folders
 
 #     require 'rdoc/ri/driver'
@@ -249,15 +262,15 @@
       eputs "Unknown class or method or no help available: #{err}"
     end
 #     trap(1){}
   end
 
-
   def self.directory(id, copts={})
     runner = fetch_runner(copts)
     puts runner.run_list[id.to_i].directory
   end
+
   def self.film(copts={})
     runner = fetch_runner(copts)
     copts[:F][:graphkit_modify] = copts[:w]
     runner.make_film_from_lists(copts[:G], copts[:g], copts[:F])
   end
@@ -307,11 +320,10 @@
     puts string
     exec string
 
   end
 
-
   def self.generate_cubecalc(copts={})
     #return
     File.open('cubecalc.cc', 'w') do |file|
     file.puts <<EOF
 #include <stdio.h>
@@ -370,13 +382,15 @@
 
 EOF
 
     end
   end
+
   def self.launcher_directory
     ENV['HOME'] + "/.coderunner/to_launch/#{ENV['CODE_RUNNER_LAUNCHER']}"
   end
+  
   def self.start_launcher(refresh, max_queue, copts={})
     #eputs "Starting launcher!"
     raise "Raise refresh is #{refresh}: it must be >= 0.1" if refresh.to_f < 0.1
     raise "Raise max_queue is #{max_queue}: it must be >= 5" if max_queue.to_i < 5
     #raise "Launcher already running" if %x[ps -e -o cmd].split("\n").grep(/coderunner\s+launch/).size > 0
@@ -475,19 +489,20 @@
       end
     end
 
   end
 
-
   def self.code_runner_execute(ruby_fragment, copts={})
     #eval(ruby_fragment, GLOBAL_BINDING)
     eval(ruby_fragment)
   end
+
   def self.execute(ruby_fragment, copts={})
     eval(ruby_fragment, GLOBAL_BINDING)
     #eval(ruby_fragment)
   end
+  
   def self.load_file(files, copts={})
     process_command_options(copts)
 #     begin
       files.split(/\s*,\s*/).each do |file|
 #         p file
@@ -517,10 +532,11 @@
         end
     end
     @@psppipe.finish
     @@psppipe = nil
   end
+
   def self.plot_graph(copts = {})
 #     process_copts(copts)
     runner = fetch_runner(copts)
     string_to_eval = copts[:w]
     #options = (options and options =~ /\S/) ? eval(options): {}
@@ -528,21 +544,22 @@
     kit = runner.graphkit_from_lists(copts[:G], copts[:g])
     kit.gnuplot(eval: string_to_eval)
     gets
     kit.close
   end
+
   def self.readout(copts={})
-#     process_copts(copts)
     runner = fetch_runner(copts)
     puts runner.readout
   end
+  
   def self.recheck(id, copts={})
-#     process_copts(copts)
     runner = fetch_runner(copts)
     runner.run_list[copts[:R]].recheck
     runner.respond_to_requests
   end
+
   def self.run_class(copts={})
     process_command_options(copts)
     copts[:no_update] = true
     unless copts[:C]
       if FileTest.exist? file=Dir.pwd + '/.code_runner_script_defaults.rb'
@@ -555,16 +572,18 @@
     end
     #ep ['code', 'modlet is', copts[:C], copts[:m]]
 
     return setup_run_class(copts[:C], modlet: copts[:m])
   end
+
   def self.code_command(string, copts = {})
     run_class(copts).class_eval(string)
 
 #      runner = fetch_runner(copts)
 #      runner.run_class.class_eval(string)
   end
+  
   def self.run_command(string, copts={})
 #       process_copts(copts)
     runner = fetch_runner(copts)
 
     eputs "Calling run_commmand..."
@@ -604,10 +623,11 @@
     end
 
 #     Process.waitall
     runner.respond_to_requests
   end
+
   def self.runner_eval(string, copts = {})
 #      process_copts(copts)
      runner = fetch_runner(copts)
 
      #ep ['server string is', string]
@@ -619,15 +639,17 @@
      else
        return return_val
      end
 
   end
+  
   def self.scan(scan_string, copts={})
 #       process_copts(copts)
     runner = fetch_runner(copts)
       runner.simple_scan(scan_string, nprocs: copts[:n], version: copts[:v], skip: copts[:k], parameters: copts[:p][0])
   end
+
   def self.submit(copts = {})
 #     process_copts(copts)
     runner = get_submit_runner(copts)
 #     raise "something is already submitting" if FileTest.exist? "submitting"
     runs = []
@@ -646,10 +668,11 @@
 #       exit
     end
     runner.submit(runs, nprocs: copts[:n], version: copts[:v], skip: copts[:k], job_chain: copts[:J], no_update_before_submit: copts[:no_update_before_submit])
     #exit(0)
   end
+
   # Fetch a runner appropriate for submitting simulations. In 
   # all usual cases this is just the default runner for the command
   # but where several folders have been specified and we are dealing
   # with a merged runner, a single runner is chosen from the merged
   # runners using submit_runner_index
@@ -663,14 +686,13 @@
       else
         return runner.runners[copts[:submit_runner_index]]
       end
     end
   end
+
   def self.resubmit(copts = {})
     runner = get_submit_runner(copts)
-#     process_copts(copts)
-#     raise "something is already submitting" if FileTest.exist? "submitting"
     runs = []
     raise "Parameters must be an array of inspected hashes" unless copts[:p].kind_of? Array
     Dir.chdir(runner.root_folder) do
       runs = runner.filtered_ids.map do |id|
         eputs id
@@ -686,16 +708,16 @@
         run.update_submission_parameters(copts[:p][0], false)
         run.run_name = nil unless copts[:rerun]
         run
       end
     end
-    #throw(:here)
 
     runner.submit(runs, nprocs: copts[:n], version: copts[:v], skip: copts[:k], job_chain: copts[:J], no_update_before_submit: copts[:no_update_before_submit], replace_existing: copts[:replace_existing], smart_resubmit_name: copts[:smart_resubmit_name], rerun: copts[:rerun])
   end
 
-  # This method allows the straightforward submission of a single command using the batch queue on any system.
+  # This method allows the straightforward submission of a single command using 
+  # the batch queue on any system.
   def self.submit_command(jid, comm, copts={})
     process_command_options(copts)
     submitter = Object.new
     submitter.instance_variable_set(:@command, comm)
     submitter.instance_variable_set(:@jid, jid)
@@ -715,29 +737,31 @@
       end
     end
     submitter.execute
   end
 
-
-
   def self.readout(copts={})
     runner = fetch_runner(copts)
     runner.readout
   end
+
   def self.show_values_of(expression, copts={})
     runner = fetch_runner(copts)
     p runner.filtered_ids.map{|id| runner.combined_run_list[id].instance_eval(expression)}.uniq.sort
   end
+  
   def self.status_with_comments(copts={})
     copts[:with_comments] = true
     status(copts)
   end
+  
   def self.status(copts={})
 #     process_copts(copts)
     runner = fetch_runner(copts)
     runner.print_out(0, with_comments: copts[:with_comments]) unless copts[:interactive_start] or copts[:Z] or copts[:no_print_out]
   end
+  
   def self.status_loop(copts={})
 #     process_copts(copts)
     runner = fetch_runner(copts)
     runner.print_out(0, with_comments: copts[:with_comments]) unless copts[:interactive_start] or copts[:Z] or copts[:no_print_out]
     break_out = false
@@ -756,18 +780,20 @@
       #ep "sleep"
       sleep 3
       #ep "end sleep"
     end
   end
+
   def self.status_loop_running(copts={})
     copts[:f] = "@running"
     runner = fetch_runner(copts)
     ids = runner.filtered_ids
     copts[:f] = "#{ids.inspect}.include? id"
     copts[:j] = nil
     status_loop(copts)
   end
+  
   def self.status_loop(copts={})
 #     process_copts(copts)
     runner = fetch_runner(copts)
     runner.print_out(0, with_comments: copts[:with_comments]) unless copts[:interactive_start] or copts[:Z] or copts[:no_print_out]
     break_out = false
@@ -786,10 +812,11 @@
       #ep "sleep"
       sleep 3
       #ep "end sleep"
     end
   end
+
   def self.write_graph(name, copts={})
 #     process_copts(copts)
     runner = fetch_runner(copts)
     eputs 'Starting Graph'
     kit = runner.graphkit_from_lists(copts[:G], copts[:g])
@@ -806,15 +833,17 @@
       name = name.sub(/%d/, (max + 1).to_s)
     end
     raise "kit doesn't have a file_name and no filename specified; can't write graph" unless name or (kit.file_name.class == String and kit.file_name =~ /\S/)
     Dir.chdir(COMMAND_FOLDER){kit.gnuplot_write((name or kit.file_name), {eval: copts[:w]})}
   end
+
   def self.read_default_command_options(copts)
     DEFAULT_COMMAND_OPTIONS.each do |key, value|
       copts[key] ||= value
     end
   end
+  
   def self.process_command_options(copts)
     if copts[:true]
       copts[:true].to_s.split(//).each do |letter|
         copts[letter.to_sym] = true
       end
@@ -867,12 +896,12 @@
     end
 
 
   end
 
-  # Analyse copts[:Y], the choice of the root folder for the runner, and make appropriate
-  # modifications to the command options for running remotely, etc.
+  # Analyse copts[:Y], the choice of the root folder for the runner, and make 
+  # appropriate modifications to the command options for running remotely, etc.
   def self.process_root_folder(copts)
     copts[:Y] ||= DEFAULT_COMMAND_OPTIONS[:Y] if DEFAULT_COMMAND_OPTIONS[:Y]
     if copts[:Y] and copts[:Y].kind_of? Array
       eputs "Warning: ignoring additional folders... selecting folder: #{copts[:Y]=copts[:Y][0]}"
     end
@@ -888,12 +917,12 @@
     end
   end
 
   CODE_OPTIONS={}
 
-  # Retrieve the runner with the folder (and possibly server) given in copts[:Y]. If no runner has been loaded for that folder, load one.
-
+  # Retrieve the runner with the folder (and possibly server) given in 
+  # copts[:Y]. If no runner has been loaded for that folder, load one.
   def self.fetch_runner(copts={})
 #     ep copts
     #read_default_command_options(copts)
     process_command_options(copts)
     # If copts(:Y) is an array of locations, return a merged runner of those locations
@@ -941,26 +970,25 @@
     end
 #     ep copts
     return runner
 #     @r.read_defaults
   end
+
   def self.update_runners
     @runners ||= {}
     @runners.each{|runner| runner.update}
   end
 
-
   def self.runner
     @runners ||={}
     @runners.values[0]
   end
 
+  def self.manual(copts={})
+    help = <<EOF
 
-    def self.manual(copts={})
-      help = <<EOF
 
-
 -------------CodeRunner Manual---------------
 
   Written by Edmund Highcock (2009)
 
 NAME
@@ -1016,14 +1044,6 @@
 EOF
      #help.gsub(/(.{63,73} |.{73})/){"#$1\n\t"}.paginate
      help.paginate
     end
 
-
-
-
-
 end
-
-
-
-