update scripts

matlab/write_sbash_marconi.m

@@ -39,7 +39,7 @@ fprintf(fid,[...
 'module load intelmpi\n',...
 'module load autoload hdf5/1.10.4--intelmpi--2018--binary\n',...
 'module load fftw\n',...
-'srun --cpu-bind=cores ./../../../bin/helaz']);
+'srun --cpu-bind=cores ./../../../bin/helaz ',num2str(NP_P),' ',num2str(NP_KR)]);
 
 fclose(fid);
 system(['cp batch_script.sh ',BASIC.RESDIR,'/.']);

wk/analysis_2D.m

 %% Load results
 outfile ='';
-if 0
+if 1
     %% Load from Marconi
     outfile ='';
     outfile ='';
-    outfile ='/marconi_scratch/userexternal/ahoffman/HeLaZ/results/Marconi_new_eta_0.6_nu_1e-01/200x100_L_120_P_10_J_5_eta_0.6_nu_1e-01_DGGK_CLOS_0_mu_2e-03/out.txt';
-%     outfile ='/marconi_scratch/userexternal/ahoffman/HeLaZ/results/Marconi_DGGK_eta_0.6_nu_1e-01/250x125_L_120_P_10_J_5_eta_0.6_nu_1e-01_DGGK_CLOS_0_mu_2e-03/out.txt';
-%     outfile ='/marconi_scratch/userexternal/ahoffman/HeLaZ/results/Marconi_DGGK_eta_0.6_nu_1e-01/200x100_L_120_P_14_J_5_eta_0.6_nu_1e-01_DGGK_CLOS_0_mu_2e-03/out.txt';
-%     outfile ='/marconi_scratch/userexternal/ahoffman/HeLaZ/results/Marconi_DGGK_eta_0.6_nu_1e-01/250x125_L_120_P_10_J_5_eta_0.6_nu_1e-01_DGGK_CLOS_0_mu_2e-03/out.txt';
+    outfile ='';
+    outfile ='/marconi_scratch/userexternal/ahoffman/HeLaZ/results/HeLaZ_v2.4_2_12_eta_0.6_nu_1e-01/50x25_L_100_P_10_J_1_eta_0.6_nu_1e-01_DGGK_CLOS_0_mu_3e-01/out.txt';
     BASIC.RESDIR = load_marconi(outfile);
 end
 if 0
@@ -211,7 +209,7 @@ set(gcf, 'Position',  [100, 100, 900, 800])
 save_figure
 end
 
-if 1
+if 0
 %% Particle fluxes
 SCALING = Nkr*dkr * Nkz*dkz;
 fig = figure; FIGNAME = ['gamma',sprintf('_%.2d',JOBNUM),'_',PARAMS];
@@ -227,7 +225,7 @@ set(gcf, 'Position',  [100, 100, 800, 300])
 save_figure
 end
 
-if 1
+if 0
 %% Space time diagramm (fig 11 Ivanov 2020)
 fig = figure; FIGNAME = ['space_time_drphi','_',PARAMS];set(gcf, 'Position',  [100, 100, 1200, 600])
     subplot(311)
@@ -355,7 +353,7 @@ FIELD = real(ni00); X = RR; Y = ZZ; T = Ts2D; FRAMES = FRAMES_2D;
 FIELDNAME = '$n_i$'; XNAME = '$r/\rho_s$'; YNAME = '$z/\rho_s$';
 create_gif
 end
-if 1
+if 0
 %% Phi real space
 GIFNAME = ['phi',sprintf('_%.2d',JOBNUM),'_',PARAMS];INTERP = 1;
 FIELD = real(phi); X = RR; Y = ZZ; T = Ts2D; FRAMES = FRAMES_2D;
@@ -406,7 +404,7 @@ FIELD =plt(Sipj(:,1,:,:,:)); X = kr'; Y = Pi'; T = Ts5D; FRAMES = FRAMES_5D;
 FIELDNAME = '$N_i^{p0}$'; XNAME = '$k_{max}\rho_s$'; YNAME = '$P$';
 create_gif_imagesc
 end
-if 1
+if 0
 %% maxkz, kr vs p, for all Nipj over time
 GIFNAME = ['Nipj_kr',sprintf('_%.2d',JOBNUM),'_',PARAMS]; INTERP = 0;
 plt = @(x) squeeze(max((abs(x)),[],4));

wk/local_run.m

@@ -16,7 +16,7 @@ JMAXE   = 1;     % Highest ''       Laguerre ''
 PMAXI   = 10;     % Highest ion      Hermite polynomial degree
 JMAXI   = 1;     % Highest ''       Laguerre ''
 %% TIME PARAMETERS
-TMAX    = 10;  % Maximal time unit
+TMAX    = 100;  % Maximal time unit
 DT      = 2e-2;   % Time step
 SPS0D   = 1/DT;    % Sampling per time unit for profiler
 SPS2D   = 1/2;      % Sampling per time unit for 2D arrays

wk/marconi_run.m

@@ -4,28 +4,27 @@ addpath(genpath('../matlab')) % ... add
 %% Set Up parameters
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 %% CLUSTER PARAMETERS
-CLUSTER.TIME  = '24:00:00'; % allocation time hh:mm:ss
-CLUSTER.NODES = '1';        % MPI process
-CLUSTER.CPUPT = '1';        % CPU per task
-CLUSTER.NTPN  = '24';       % N tasks per node
-CLUSTER.PART  = 'prod';     % dbg or prod
+CLUSTER.TIME  = '01:00:00'; % allocation time hh:mm:ss
+CLUSTER.PART  = 'dbg';     % dbg or prod
 CLUSTER.MEM   = '16GB';     % Memory
 CLUSTER.JNAME = 'gamma_inf';% Job name
+NP_P          = 2;          % MPI processes along p  
+NP_KR         = 12;         % MPI processes along kr
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 %% PHYSICAL PARAMETERS
 NU      = 0.1;   % Collision frequency
 ETAB    = 0.6;   % Magnetic gradient
 NU_HYP  = 0.1;   % Hyperdiffusivity coefficient
 %% GRID PARAMETERS
-N       = 200;   % Frequency gridpoints (Nkr = N/2)
-L       = 120;   % Size of the squared frequency domain
+N       = 050;   % Frequency gridpoints (Nkr = N/2)
+L       = 100;   % Size of the squared frequency domain
 P       = 10;    % Electron and Ion highest Hermite polynomial degree
-J       = 05;    % Electron and Ion highest Laguerre polynomial degree
+J       = 01;    % Electron and Ion highest Laguerre polynomial degree
 MU_P    = 0;     % Hermite  hyperdiffusivity -mu_p*(d/dvpar)^4 f
 MU_J    = 0;     % Laguerre hyperdiffusivity -mu_j*(d/dvperp)^4 f
 %% TIME PARAMETERS
-TMAX    = 1000;  % Maximal time unit
-DT      = 1e-2;  % Time step
+TMAX    = 50;  % Maximal time unit
+DT      = 2e-2;  % Time step
 SPS0D   = 1;      % Sampling per time unit for profiler
 SPS2D   = 1/2;   % Sampling per time unit for 2D arrays
 SPS5D   = 1/10;  % Sampling per time unit for 5D arrays
@@ -33,13 +32,13 @@ SPSCP   = 0;  % Sampling per time unit for checkpoints
 RESTART = 0;     % To restart from last checkpoint
 JOB2LOAD= 0;
 %% OPTIONS
-SIMID   = ['Marconi_new_eta_',num2str(ETAB),'_nu_%0.0e'];  % Name of the simulation
+SIMID   = ['HeLaZ_v2.4_2_12_eta_',num2str(ETAB),'_nu_%0.0e'];  % Name of the simulation
 % SIMID   = 'Marconi_test';  % Name of the simulation
 SIMID   = sprintf(SIMID,NU);
 CO      = -3;  % Collision operator (0 : L.Bernstein, -1 : Full Coulomb, -2 : Dougherty, -3 : GK Dougherty)
 CLOS    = 0;   % Closure model (0: =0 truncation, 1: semi coll, 2: Copy closure J+1 = J, P+2 = P)
 KERN    = 0;   % Kernel model (0 : GK)
-INIT_PHI= 0;   % Start simulation with a noisy phi and moments
+INIT_PHI= 1;   % Start simulation with a noisy phi and moments
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 %% fixed parameters (for current study)
@@ -59,6 +58,13 @@ NOISE0  = 1.0e-5;
 ETAT    = 0.0;    % Temperature gradient
 ETAN    = 1.0;    % Density gradient
 TAU     = 1.0;    % e/i temperature ratio
+% Compute processes distribution
+Ntot = NP_P * NP_KR;
+Nnodes = ceil(Ntot/24);
+Nppn   = Ntot/Nnodes; 
+CLUSTER.NODES =  num2str(Nnodes);  % MPI process along p
+CLUSTER.NTPN  =  num2str(Nppn); % MPI process along kr
+CLUSTER.CPUPT = '1';        % CPU per task
 %% Run file management scripts
 setup
 write_sbash_marconi