coderunner 0.12.13 → 0.12.14

data/VERSION

@@ -1 +1 @@
-0.12.13
+0.12.14

data/coderunner.gemspec

@@ -5,11 +5,11 @@
 
 Gem::Specification.new do |s|
   s.name = "coderunner"
-  s.version = "0.12.13"
+  s.version = "0.12.14"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Edmund Highcock"]
-  s.date = "2013-07-16"
+  s.date = "2013-07-26"
   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"]
@@ -61,6 +61,7 @@ Gem::Specification.new do |s|
     "lib/coderunner/system_modules/moab.rb",
     "lib/coderunner/system_modules/new_hydra.rb",
     "lib/coderunner/system_modules/slurm.rb",
+    "lib/coderunner/system_modules/stampede.rb",
     "lib/coderunner/test.rb",
     "lib/coderunner/version.rb",
     "lib/cubecalccrmod.rb",
@@ -71,6 +72,7 @@ Gem::Specification.new do |s|
     "lib/cubecalccrmod/empty.rb",
     "lib/cubecalccrmod/sleep.rb",
     "test/cubecalc.cc",
+    "test/fortran_namelist.in",
     "test/helper.rb",
     "test/old_test.rb",
     "test/test_coderunner.rb"

data/lib/coderunner/class_methods.rb

@@ -668,8 +668,9 @@ EOF
 			copts_r[:Y] = nil
 			copts[:Y] = nil
 			unless @runners[[host, folder]]
+				copts[:cache] ||= :auto
 				runner = @runners[[host, folder]] = RemoteCodeRunner.new(host, folder, copts)
-				(eputs 'Updating remote...'; runner.update) unless (copts[:g] and (copts[:g].kind_of? String or copts[:g].size > 0)) or copts[:no_update] or copts[:cache] 
+				#(eputs 'Updating remote...'; runner.update) unless (copts[:g] and (copts[:g].kind_of? String or copts[:g].size > 0)) or copts[:no_update] or copts[:cache] 
 			else 
 				runner = @runners[[host, folder]]
 			end

data/lib/coderunner/system_modules/stampede.rb

@@ -0,0 +1,21 @@
+class CodeRunner
+	require SCRIPT_FOLDER + '/system_modules/slurm.rb'
+	module Stampede
+		include Slurm
+		#def batch_script
+			#raise "Please specify project" unless @project
+			#super
+		#end
+		def max_ppn
+			16
+		end
+		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}]
+			else
+				"ibrun #{executable_location}/#{executable_name} #{parameter_string}"
+			end
+		end
+	end
+end

data/test/fortran_namelist.in

@@ -0,0 +1,255 @@
+!==============================================================================
+!  		GS2 INPUT FILE automatically generated by CodeRunner 
+!==============================================================================
+!
+!  GS2 is a gyrokinetic flux tube initial value turbulence code 
+!  which can be used for fusion or astrophysical plasmas.
+!  
+!  	See http://gyrokinetics.sourceforge.net
+!
+!  CodeRunner is a framework for the automated running and analysis 
+!  of large simulations. 
+!
+!  	See http://coderunner.sourceforge.net
+!      by CodeRunner version 0.12.6.0
+!
+!==============================================================================
+
+!==============================
+!GENERAL PARAMETERS  
+!==============================
+&parameters
+ beta = 0.0 ! Ratio of particle to magnetic pressure (reference Beta, not total beta):  beta=n_0 T_0 /( B^2 / (8 pi))
+ zeff = 1.0 ! Effective ionic charge.
+/
+
+&kt_grids_knobs
+ grid_option = "single" ! The general layout of the perpendicular grid.
+/
+
+!==============================
+!  
+!==============================
+&kt_grids_single_parameters
+  aky = 1.0
+  akx = 0.0
+/
+
+!==============================
+!  
+!==============================
+&theta_grid_parameters
+ ntheta = 24 ! Number of points along field line (theta) per 2 pi segment
+ nperiod = 1 ! Number of 2 pi segments along equilibrium magnetic field.
+ eps = 0.18 ! eps=r/R
+ epsl = 2.0 ! epsl=2 a/R
+ shat = 0.8 ! 
+ pk = 1.44 ! pk = 2 a / q R
+ shift = 0.0 ! shift = -R q**2 dbeta/drho (>0)
+/
+
+!==============================
+!  
+!==============================
+&theta_grid_knobs
+ equilibrium_option = "s-alpha" ! Controls which geometric assumptions are used in the run.
+/
+
+!==============================
+!  
+!==============================
+&theta_grid_salpha_knobs
+ model_option = "default" 
+/
+
+!==============================
+!PITCH ANGLE/ENERGY GRID SETUP  
+!==============================
+&le_grids_knobs
+ ngauss = 5 ! Number of untrapped pitch-angles moving in one direction along field line.
+ negrid = 8 ! Total number of energy grid points
+/
+
+!==============================
+!BOUNDARY CONDITIONS  
+!==============================
+&dist_fn_knobs
+ gridfac = 1.0 ! Affects boundary condition at end of theta grid.
+ omprimfac = 1.0 
+ boundary_option = "linked" ! Sets the boundary condition along the field line (i.e. the boundary conditions at theta = +- pi).
+ adiabatic_option = "iphi00=2" ! The form of the adiabatic response (if a species is being modeled as adiabatic).
+ g_exb = 0.0 
+ nonad_zero = .true. ! If true switches on new parallel boundary condition where h=0 at incoming boundary instead of g=0.
+/
+
+!==============================
+!ALGORITHMIC CHOICES  
+!==============================
+&fields_knobs
+ field_option = "implicit" ! Controls which time-advance algorithm is used for the linear terms.
+/
+
+!==============================
+!  
+!==============================
+&knobs
+ wstar_units = .false. ! For linear runs only. Evolves each k_y with a different timestep.
+ fphi = 1.0 ! Multiplies Phi (electrostatic potential).
+ fapar = 0.0 ! Multiplies A_par. Use 1 for finite beta (electromagnetic), 0 otherwise (electrostatic)
+ faperp = 0.0 ! Multiplies A_perp. Use 1 for high beta, 0 otherwise. Deprecated: use fbpar instead
+ delt = 0.05 ! Time step
+ nstep = 1000 ! Maximum number of timesteps
+/
+
+!==============================
+!  
+!==============================
+&reinit_knobs
+ delt_adj = 2.0 ! When the time step needs to be changed, it is adjusted 
+ delt_minimum = 1.0e-06 ! The minimum time step is delt_minimum.
+/
+
+!==============================
+!  
+!==============================
+&layouts_knobs
+ layout = "lexys" ! 'yxles', 'lxyes', 'lyxes', 'lexys' Determines the way the grids are laid out in memory.
+/
+
+!==============================
+!COLLISIONS  
+!==============================
+&collisions_knobs
+ collision_model = "default" ! Collision model used in the simulation. Options: 'default', 'none', 'lorentz', 'ediffuse'
+/
+
+!==============================
+!NONLINEARITY  
+!==============================
+&nonlinear_terms_knobs
+ nonlinear_mode = "off" ! Include nonlinear terms? ('on','off')
+ flow_mode = "off" 
+ cfl = 0.5 ! The maximum delt < cfl * min(Delta_perp/v_perp)
+/
+
+!==============================
+!EVOLVED SPECIES  
+!==============================
+&species_knobs
+ nspec = 1 ! Number of kinetic species evolved.
+/
+
+!==============================
+!SPECIES PARAMETERS 1 
+!==============================
+&species_parameters_1
+ z = 1.0 ! Charge
+ mass = 1.0 ! Mass
+ dens = 1.0 ! Density	
+ temp = 1.0 ! Temperature
+ tprim = 6.9 ! -1/T (dT/drho)
+ fprim = 2.2 ! -1/n (dn/drho)
+ uprim = 0.0 ! ?
+ vnewk = 0.01 ! collisionality parameter
+ type = "ion" ! Type of species, e.g. 'ion', 'electron', 'beam'
+/
+
+!==============================
+! 1 
+!==============================
+&dist_fn_species_knobs_1
+ fexpr = 0.45 ! Temporal implicitness parameter. Recommended value: 0.48
+ bakdif = 0.05 ! Spatial implicitness parameter. Recommended value: 0.05
+/
+
+!==============================
+!SPECIES PARAMETERS 2 
+!==============================
+&species_parameters_2
+ z = 1.0 ! Charge
+ mass = 1.0 ! Mass
+ dens = 0.0 ! Density	
+ temp = 3.5e2 ! Temperature
+ sprim = 0.0 ! ?
+ type = "alpha" ! Type of species, e.g. 'ion', 'electron', 'beam'
+/
+
+!==============================
+! 1 
+!==============================
+&dist_fn_species_knobs_2
+ fexpr = 0.45 ! Temporal implicitness parameter. Recommended value: 0.48
+ bakdif = 0.05 ! Spatial implicitness parameter. Recommended value: 0.05
+/
+
+!==============================
+!INITIAL CONDITIONS  
+!==============================
+&init_g_knobs
+ chop_side = .false. ! Rarely needed. Forces asymmetry into initial condition.
+ phiinit = 0.001 ! Average amplitude of initial perturbation of each Fourier mode.
+ ginit_option = "noise" ! Sets the way that the distribution function is initialized.
+/
+
+!==============================
+!DIAGNOSTICS  
+!==============================
+&gs2_diagnostics_knobs
+ print_flux_line = .F. ! Instantaneous fluxes output to screen
+ write_nl_flux = .true. ! Write nonlinear fluxes as a function of time.
+ print_line = .false. ! Estimated frequencies and growth rates to the screen/stdout
+ write_verr = .true. ! Write velocity space diagnostics to '.lpc' and '.verr' files
+  ! write_g not specified --- Write the distribution function to the '.dist' (NetCDF?)
+ write_line = .false. ! If (write_ascii = T) write estimated frequencies and growth rates to the output file
+  ! write_gyx not specified --- Write dist fn at a given physical spacial point to a file
+ write_hrate = .false. ! Write heating rate, collisonal entropy generation etc to '.heat'
+  ! write_final_epar not specified --- If (write_ascii = T) E_parallel(theta) written to runname.eigenfunc
+ write_avg_moments = .F. ! Write flux surface averaged low-order moments of g to runname.out.nc and runname.moments (if write_ascii = T)
+  ! write_lorentzian not specified --- Frequency Sweep Data
+ write_omega = .false. ! If (write_ascii = T) instantaneous omega to output file. Very heavy output
+ write_omavg = .false. ! If (write_ascii = T) time-averaged growth rate and frequency to the output file.
+ write_eigenfunc = .true. ! If (write_ascii = T) Normalized phi written to runname.eigenfunc
+ write_final_fields = .true. ! If (write_ascii = T) Phi(theta) written to '.fields'
+ write_final_moments = .true. ! write final n, T
+  ! write_parity not specified --- Writes parities in dist fn and particle fluxes
+ nsave = 100 ! Write restart files every nsave timesteps
+ nwrite = 1 ! Output diagnostic data every nwrite
+ navg = 10 ! Any time averages performed over navg
+ omegatol = -0.001 ! The convergence has to be better than one part in 1/omegatol
+ omegatinst = 500.0 ! Recommended value: 500.
+ save_for_restart = .true. ! Write restart files.
+  ! write_flux_line not specified --- 
+  ! write_ascii not specified --- 
+  ! write_kpar not specified --- 
+  ! write_gs not specified --- 
+  ! write_gg not specified --- 
+  ! write_lpoly not specified --- 
+  ! write_fields not specified --- 
+  ! write_final_antot not specified --- 
+  ! write_cerr not specified --- 
+  ! write_max_verr not specified --- 
+  ! nmovie not specified --- 
+  ! igomega not specified --- 
+  ! exit_when_converged not specified --- 
+  ! write_full_moments_notgc not specified --- 
+  ! write_cross_phase not specified --- 
+  ! dump_check1 not specified --- 
+  ! dump_check2 not specified --- 
+  ! dump_fields_periodically not specified --- 
+  ! make_movie not specified --- 
+ write_phi_over_time = .false. ! Write entire Phi field to NetCDF file every nwrite.
+  ! write_apar_over_time not specified --- Write entire A_parallel field to NetCDF file every nwrite.
+  ! write_bpar_over_time not specified --- Write entire B_parallel field to NetCDF file every nwrite.
+  ! write_symmetry not specified --- Test the symmetry properties of the GK eqn.
+  ! save_distfn not specified --- Save dist_fn with lots of detail.
+  ! write_correlation_extend not specified --- Extend domain of correlation function calculation.
+  ! nwrite_mult not specified --- Large datasets written every nwrite_mult * nwrite timesteps.
+  ! write_correlation not specified --- Write parallel correlation.
+  ! write_moments not specified --- 
+  ! write_final_db not specified --- Write final delta B.
+/
+
+&general_f0_parameters
+  alpha_f0 = 'analytic'
+  energy_0 = 0.01
+/

data/test/test_coderunner.rb

@@ -332,3 +332,12 @@ EOF
 		
 end # class TestCodeRunner
 
+#class TestFortranNamelist < Test::Unit::TestCase
+	##require 'gs2crmod'
+	#def test_make_defaults
+		#Dir.chdir('test') do
+			#CodeRunner.code_command('make_new_defaults_file("fortran_namelist", "fortran_namelist.in")', C: 'gs2')
+			#assert(File.read('fortran_namelist_defaults.rb')=~/tprim_1/)
+		#end
+	#end
+#end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: coderunner
 version: !ruby/object:Gem::Version
-  version: 0.12.13
+  version: 0.12.14
   prerelease: 
 platform: ruby
 authors:
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-07-16 00:00:00.000000000 Z
+date: 2013-07-26 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: graphkit
@@ -228,6 +228,7 @@ files:
 - lib/coderunner/system_modules/moab.rb
 - lib/coderunner/system_modules/new_hydra.rb
 - lib/coderunner/system_modules/slurm.rb
+- lib/coderunner/system_modules/stampede.rb
 - lib/coderunner/test.rb
 - lib/coderunner/version.rb
 - lib/cubecalccrmod.rb
@@ -238,6 +239,7 @@ files:
 - lib/cubecalccrmod/empty.rb
 - lib/cubecalccrmod/sleep.rb
 - test/cubecalc.cc
+- test/fortran_namelist.in
 - test/helper.rb
 - test/old_test.rb
 - test/test_coderunner.rb