gryfxcrmod 0.1.10 → 0.1.11

checksums.yaml

@@ -1,7 +1,7 @@
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-  data.tar.gz: 36ac4d1d5e4224efc7af68ac191b5f91836ed67c
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data/VERSION

@@ -1 +1 @@
-0.1.10
+0.1.11

data/gryfxcrmod.gemspec

@@ -2,16 +2,16 @@
 # DO NOT EDIT THIS FILE DIRECTLY
 # Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
 # -*- encoding: utf-8 -*-
-# stub: gryfxcrmod 0.1.10 ruby lib
+# stub: gryfxcrmod 0.1.11 ruby lib
 
 Gem::Specification.new do |s|
   s.name = "gryfxcrmod"
-  s.version = "0.1.10"
+  s.version = "0.1.11"
 
   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 = "2015-07-27"
+  s.date = "2016-09-23"
   s.description = "This is a customised subclass of the CodeRunner::Run  class which allows CodeRunner to run and analyse the gyrofluid GPU turbulent transport solver Gryfx."
   s.email = "edmundhighcock@users.sourceforge.net"
   s.extra_rdoc_files = [
@@ -42,7 +42,7 @@ Gem::Specification.new do |s|
   ]
   s.homepage = "http://github.com/edmundhighcock/gryfxcrmod"
   s.licenses = ["MIT"]
-  s.rubygems_version = "2.4.8"
+  s.rubygems_version = "2.2.0"
   s.summary = "CodeRunner module for the Gryfx Gyrofluid Transport Solver"
 
   if s.respond_to? :specification_version then

data/lib/gryfxcrmod/gryfx.rb

@@ -3,13 +3,18 @@ class CodeRunner
 	#
 	#  It  generates the Gryfx input file, and both analyses the results and allows easy plotting of them. 
 	CodeRunner.setup_run_class('gs2')
+  class Gs2
+    # This is necessary because the restart
+    # parameter overrwrites this function in Gryfx
+    alias :set_restart :restart
+  end
 	class Gryfx < Gs2
 		#include CodeRunner::SYSTEM_MODULE
 
 
 
 		# Where this file is
-		@code_module_folder = folder = File.dirname(File.expand_path(__FILE__)) # i.e. the directory this file is in
+		@code_module_folder = File.dirname(File.expand_path(__FILE__)) # i.e. the directory this file is in
 
 		# Use the Run::FortranNamelist tools to process the variable database
 		setup_namelists(@code_module_folder)
@@ -64,11 +69,44 @@ class CodeRunner
 			beginning
 		end
 
+    def set_restart(new_run)
+      eputs 'Restarting ' + @run_name
+      #(rcp.variables).each{|v| new_run.set(v, send(v)) if send(v)}
+      #@naming_pars.delete(:preamble)
+      #SUBMIT_OPTIONS.each{|v| new_run.set(v, self.send(v)) unless new_run.send(v)}
+      #new_run.is_a_restart = true
+      #new_run.restart_id = @id
+      #new_run.restart_run_name = @run_name
+      #@runner.nprocs = @nprocs if @runner.nprocs == "1" # 1 is the default
+      #new_run.run_name = nil
+      #new_run.naming_pars = @naming_pars
+      #new_run.update_submission_parameters(new_run.parameter_hash_string, false) if new_run.parameter_hash
+      #new_run.naming_pars.delete(:restart_id)
+      #new_run.generate_run_name
+      #copy_restart_files(new_run)
+      super(new_run)
+      new_run.restart = "on"
+      # Gryfx automatically configures GS2 for restart so here we set the GS2
+      # parameters to default
+      new_run.delt_option = "default"
+      new_run.ginit_option = "noise"
+      new_run
+    end
+
+    def copy_restart_files(new_run)
+      eputs 'Copying gryfx restart file...', ''
+      FileUtils.cp(
+        @directory + '/' + @run_name + '.restart.cdf', 
+        new_run.directory + '/' + new_run.run_name + '.restart.cdf'
+      )
+      super(new_run)
+    end
+
 
 		#  This is a hook which gets called just before submitting a simulation. It sets up the folder and generates any necessary input files.
 		def generate_input_file
       if @restart_id and (not @is_a_restart or @resubmit_id)   
-        @runner.run_list[@restart_id].restart(self)
+        @runner.run_list[@restart_id].set_restart(self)
       elsif ((@save_for_restart and @save_for_restart.fortran_true?) or
              (@save_for_restart_new and @save_for_restart_new.fortran_true?)) and 
         (not @is_a_restart or @resubmit_id)
@@ -76,6 +114,7 @@ class CodeRunner
         FileUtils.makedirs @restart_dir
         @restart_file = "#@run_name.nc"
       end
+      @avail_cpu_time = (@wall_mins - 1.0) * 60.0 if @wall_mins
 				write_input_file
 		end
 
@@ -99,7 +138,7 @@ class CodeRunner
 		#
 		def process_directory_code_specific
 			@grid_option = "box" # For compatibility with the GS2 routines
-			@write_phi_over_time  = "true" # For compatibility with the GS2 routines
+			@write_phi_over_time  = ".true." # For compatibility with the GS2 routines
 			get_status
 			#p ['id is', id, 'ctd is ', ctd]
 			if ctd
@@ -132,7 +171,16 @@ class CodeRunner
 
 		def get_completed_timesteps
 			if FileTest.exist?(@run_name  + '.cdf')
-				@completed_timesteps = netcdf_file.var('t').get.size #gsl_vector('t').size
+        count = 0
+        begin
+          @completed_timesteps = netcdf_file.var('t').get.size #gsl_vector('t').size
+        rescue NetcdfError => err 
+          eputs err
+          count += 1
+          eputs "Retrying: #{count} attempt(s) out of 4"
+          sleep 1
+          count < 5 ?  retry : raise(err)
+        end
 			else
 				@completed_timesteps = 0
 			end

data/lib/gryfxcrmod/namelists.rb

@@ -2113,6 +2113,16 @@
           :explanation=>"This variable must be an integer."}],
        :type=>:Integer,
        :autoscanned_defaults=>[1]},
+     :write_netcdf=>
+      {:should_include=>"true",
+       :description=>"Set true to write to netcdf file.",
+       :help=>"",
+       :code_name=>:write_netcdf,
+       :must_pass=>
+        [{:test=>"kind_of? String and FORTRAN_BOOLS.include? self",
+          :explanation=>
+           "This variable must be a fortran boolean. (In Ruby this is represented as a string: e.g. '.true.')"}],
+       :type=>:Fortran_Bool},
      :hyper=>
       {:should_include=>"true",
        :description=>"",

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: gryfxcrmod
 version: !ruby/object:Gem::Version
-  version: 0.1.10
+  version: 0.1.11
 platform: ruby
 authors:
 - Edmund Highcock
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2015-07-27 00:00:00.000000000 Z
+date: 2016-09-23 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: coderunner
@@ -143,7 +143,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.4.8
+rubygems_version: 2.2.0
 signing_key: 
 specification_version: 4
 summary: CodeRunner module for the Gryfx Gyrofluid Transport Solver