coderunner 0.15.8 → 0.15.9

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 3b40b38fcea184d29203d2d101ceb480eacf1d6b
-  data.tar.gz: 0e0f3a66735a746b44b3973f494496e4f25fe2f3
+  metadata.gz: b2cb05494a17b78bd708cdfb36475697bc777df5
+  data.tar.gz: e3226dda219e54cfd0428fa994e32e24e228ece4
 SHA512:
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+  metadata.gz: 2351cad7c1d4af1b9a873a9bc71e1c657b0e79caefc11729cde60cc989a9b47aba0f10d828457a89bd392430598e3fb65b6fcf6907c7cc5419abb39ae4f0285a
+  data.tar.gz: d50941367780b23c9c7429ae29277a52cb0f914bf4cd943f635686482c52f2f86629d8c12369d29dbb097cfbd11c8b1a64a50b20c88d6fa70f6f6e82172bb0f6

data/VERSION

@@ -1 +1 @@
-0.15.8
+0.15.9

data/coderunner.gemspec

@@ -2,17 +2,17 @@
 # DO NOT EDIT THIS FILE DIRECTLY
 # Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
 # -*- encoding: utf-8 -*-
-# stub: coderunner 0.15.8 ruby lib
+# stub: coderunner 0.15.9 ruby lib
 # stub: ext/extconf.rb
 
 Gem::Specification.new do |s|
   s.name = "coderunner"
-  s.version = "0.15.8"
+  s.version = "0.15.9"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.require_paths = ["lib"]
   s.authors = ["Edmund Highcock"]
-  s.date = "2015-04-02"
+  s.date = "2015-04-08"
   s.description = "CodeRunner is a framework for the automated running and analysis of simulations. It automatically generates any necessary input files, organises the output data and analyses it. Because it is a modular system, it can easily be customised to work with any system and any simulation code. One of its greatest strengths is that it is independent of any one simulation code; thus it can easily plot and compare the data from different codes."
   s.email = "edmundhighcock@sourceforge.net"
   s.executables = ["coderunner"]
@@ -63,6 +63,7 @@ Gem::Specification.new do |s|
     "lib/coderunner/system_modules/hopper.rb",
     "lib/coderunner/system_modules/iridis.rb",
     "lib/coderunner/system_modules/juropa.rb",
+    "lib/coderunner/system_modules/launcher.rb",
     "lib/coderunner/system_modules/load_leveler.rb",
     "lib/coderunner/system_modules/loki.rb",
     "lib/coderunner/system_modules/macosx.rb",

data/lib/coderunner/system_modules/launcher.rb

@@ -0,0 +1,31 @@
+class CodeRunner
+
+  # A module containing methods for submitting runs using the CodeRunner
+  # launcher. Typically this would be used on a home Linux system or in
+  # an interactive session on a supercomputer.
+  module Launcher
+    def launcher_prefix
+		  ENV['CODE_RUNNER_LAUNCHER']
+    end
+    def use_launcher
+      launcher_prefix and launcher_prefix.size > 0
+    end
+    def queue_status_launcher
+			%x[cat #{ENV['HOME']}/.coderunner_to_launch_#{prefix}/queue_status.txt]  +
+			%x[cat #{ENV['HOME']}/.coderunner_to_launch_#{prefix}/queue_status2.txt] 
+    end 
+    def execute_launcher
+      launch_id = "#{Time.now.to_i}#{$$}"
+      fname = ENV['HOME'] + "/.coderunner_to_launch_#{prefix}/#{launch_id}"
+      File.open(fname + '.start', 'w'){|file| file.puts "cd #{Dir.pwd};#{run_command}"}
+      sleep 1 until FileTest.exist? fname + '.pid'
+      pid = File.read(fname + '.pid').to_i
+      FileUtils.rm fname + '.pid'
+      return pid
+    end
+    def cancel_job_launcher
+      fname = ENV['HOME'] + "/.coderunner_to_launch_#{prefix}/#{$$}.stop"
+      File.open(fname, 'w'){|file| file.puts "\n"}
+    end
+  end
+end

data/lib/coderunner/system_modules/slurm.rb

@@ -1,20 +1,22 @@
 class CodeRunner
-	# A module to let CodeRunner run using the SLURM queue system,
-	# used on certain HPC systems.
+require SCRIPT_FOLDER + '/system_modules/launcher.rb'
+# A module to let CodeRunner run using the SLURM queue system,
+# used on certain HPC systems.
 module Slurm
+  include Launcher
 				
 	def queue_status
-		if ((prefix = ENV['CODE_RUNNER_LAUNCHER']).size > 0 rescue false)
-			%x[cat #{ENV['HOME']}/.coderunner_to_launch_#{prefix}/queue_status.txt]  +
-			%x[cat #{ENV['HOME']}/.coderunner_to_launch_#{prefix}/queue_status2.txt] 
+		if use_launcher
+      queue_status_launcher
 		else
-			%x[squeue | grep #{ENV['USER'][0..7]}]
+			#%x[squeue | grep #{ENV['USER'][0..7]}]
+			%x[squeue -u $USER]
 		end
 	end
 
 	def run_command
 # 		"qsub #{batch_script_file}"
-		if (ENV['CODE_RUNNER_LAUNCHER'].size > 0 rescue false)
+		if use_launcher
 			return %[mpiexec -np #{@nprocs} #{executable_location}/#{executable_name} #{parameter_string} > #{output_file} 2> #{error_file}]
 		else
 			"#@preamble #{mpi_prog}  #{executable_location}/#{executable_name} #{parameter_string}"
@@ -27,17 +29,11 @@ module Slurm
   end 
 
 	def execute
-		if ((prefix = ENV['CODE_RUNNER_LAUNCHER']).size > 0 rescue false)
-			launch_id = "#{Time.now.to_i}#{$$}"
-			fname = ENV['HOME'] + "/.coderunner_to_launch_#{prefix}/#{launch_id}"
-			File.open(fname + '.start', 'w'){|file| file.puts "cd #{Dir.pwd};#{run_command}"}
-			sleep 1 until FileTest.exist? fname + '.pid'
-			pid = File.read(fname + '.pid').to_i
-			FileUtils.rm fname + '.pid'
-			return pid
+		if use_launcher
+      return execute_launcher
 		else
 			File.open(batch_script_file, 'w'){|file| file.puts batch_script + run_command + "\n"}
-			pid = %x[sbatch #{batch_script_file}].to_i
+			_pid = %x[sbatch #{batch_script_file}].to_i
 			return nil
 		end
 	end
@@ -87,9 +83,8 @@ EOF
 	end
 
 	def cancel_job
-		if ((prefix = ENV['CODE_RUNNER_LAUNCHER']).size > 0 rescue false)
-			 fname = ENV['HOME'] + "/.coderunner_to_launch_#{prefix}/#{$$}.stop"
-			 File.open(fname, 'w'){|file| file.puts "\n"}
+		if use_launcher
+      cancel_job_launcher
 		else
 			`scancel #{@job_no}`
 		end
@@ -104,7 +99,7 @@ EOF
 	end
 
 def get_run_status(job_no, current_status)
-	if ((prefix = ENV['CODE_RUNNER_LAUNCHER']).size > 0 rescue false)
+	if use_launcher
 		return :Unknown
 	end
 	line = current_status.split(/\n/).grep(Regexp.new(job_no.to_s))[0]
@@ -126,5 +121,5 @@ def get_run_status(job_no, current_status)
 	end
 end
 
-	end
+end
 end

data/lib/coderunner/system_modules/stampede.rb

@@ -12,7 +12,7 @@ class CodeRunner
 		def run_command
 	# 		"qsub #{batch_script_file}"
 			if (ENV['CODE_RUNNER_LAUNCHER'].size > 0 rescue false)
-				return %[mpiexec -np #{@nprocs} #{executable_location}/#{executable_name} #{parameter_string} > #{output_file} 2> #{error_file}]
+				return %[ibrun -n #{@nprocs} -o 0 #{executable_location}/#{executable_name} #{parameter_string} > #{output_file} 2> #{error_file}]
 			else
 				"ibrun #{executable_location}/#{executable_name} #{parameter_string}"
 			end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: coderunner
 version: !ruby/object:Gem::Version
-  version: 0.15.8
+  version: 0.15.9
 platform: ruby
 authors:
 - Edmund Highcock
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2015-04-02 00:00:00.000000000 Z
+date: 2015-04-08 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: graphkit
@@ -206,6 +206,7 @@ files:
 - lib/coderunner/system_modules/hopper.rb
 - lib/coderunner/system_modules/iridis.rb
 - lib/coderunner/system_modules/juropa.rb
+- lib/coderunner/system_modules/launcher.rb
 - lib/coderunner/system_modules/load_leveler.rb
 - lib/coderunner/system_modules/loki.rb
 - lib/coderunner/system_modules/macosx.rb