Wrote a script to run job on PPB110 slurm manager

wk/ppb110_run.m

+%clear all;
+addpath(genpath('../matlab')) % ... add
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%% Set Up parameters
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%% CLUSTER PARAMETERS
+CLUSTER.TIME  = '12:00:00'; % 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.MEM   = '16GB';     % Memory
+CLUSTER.JNAME = 'gamma_inf';% Job name
+USERNAME      = 'ahoffman'; % username at ppb110 for folder naming
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%% PHYSICAL PARAMETERS
+NU      = 1.0;   % Collision frequency
+ETAB    = 0.6;   % Magnetic gradient
+NU_HYP  = 0.1;   % Hyperdiffusivity coefficient
+%% GRID PARAMETERS
+N       = 150;     % Frequency gridpoints (Nkr = N/2)
+L       = 70;     % Size of the squared frequency domain
+P       = 10;       % Electron and Ion highest Hermite polynomial degree
+J       = 5;       % 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    = 500;  % Maximal time unit
+DT      = 1e-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
+SPSCP   = 1/10;  % Sampling per time unit for checkpoints
+RESTART = 1;     % To restart from last checkpoint
+JOB2LOAD= 0;
+%% OPTIONS
+% SIMID   = 'Marconi_DGGK_nu_%0.0e';  % Name of the simulation
+SIMID   = ['Marconi_DGGK_eta_',num2str(ETAB),'_nu_%0.0e'];  % Name of the simulation
+% SIMID   = 'Marconi_restart';  % 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)
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%% fixed parameters (for current study)
+KR0KH   = 0; A0KH = 0; % Background phi mode to drive Ray-Tay inst.
+KREQ0   = 0;      % put kr = 0
+KPAR    = 0.0;    % Parellel wave vector component
+LAMBDAD = 0.0;
+NON_LIN = 1 *(1-KREQ0);   % activate non-linearity (is cancelled if KREQ0 = 1)
+PMAXE   = P;    % Highest electron Hermite polynomial degree
+JMAXE   = J;     % Highest ''       Laguerre ''
+PMAXI   = P;     % Highest ion      Hermite polynomial degree
+JMAXI   = J;     % Highest ''       Laguerre ''
+kmax    = N*pi/L;% Highest fourier mode
+HD_CO   = 0.5;    % Hyper diffusivity cutoff ratio
+MU      = NU_HYP/(HD_CO*kmax)^4 % Hyperdiffusivity coefficient
+NOISE0  = 1.0e-5;
+ETAT    = 0.0;    % Temperature gradient
+ETAN    = 1.0;    % Density gradient
+TAU     = 1.0;    % e/i temperature ratio
+%% Run file management scripts
+setup % Write the input script "fort.90" with desired parameters
+
+%% Write the sh script to launch the job on slurm for PPB110
+INPUT = 'setup_and_run.sh';
+fid = fopen(INPUT,'wt');
+SCRATCH_SIMDIR = ['/scratch/',USERNAME,'/HeLaZ']; % Path to the simulation directory in the scratch
+% Writing of the script
+fprintf(fid,[...
+'#!/bin/bash\n',...
+'mkdir -p ',SCRATCH_SIMDIR,'/wk\n',...
+...
+'cd ',SCRATCH_SIMDIR,'/wk\n',...
+...
+'mkdir -p ', BASIC.RESDIR,'\n',...
+'cd ',BASIC.RESDIR,'\n',...
+'cp $HOME/HeLaZ/wk/fort.90 .\n',...
+'cp $HOME/HeLaZ/wk/batch_script.sh .\n',...
+...
+'sbatch batch_script.sh\n',...
+'echo $',SCRATCH_SIMDIR,'/results/',BASIC.SIMID,'/',BASIC.PARAMS,'/out.txt']);
+
+fclose(fid);
+system(['cp setup_and_run.sh ',BASIC.RESDIR,'/.']);
+
+%% Write the sbatch script for PPB110
+INPUT = 'batch_script.sh';
+fid = fopen(INPUT,'wt');
+
+fprintf(fid,[...
+'#!/bin/bash\n',...
+'#SBATCH --job-name=',CLUSTER.JNAME,'\n',...
+'#SBATCH --time=', CLUSTER.TIME,'\n',...
+'#SBATCH --nodes=', CLUSTER.NODES,'\n',...
+'#SBATCH --mem=', CLUSTER.MEM,'\n',...
+'#SBATCH --error=err.txt\n',...
+'#SBATCH --output=out.txt\n',...
+...% '#SBATCH --job-name=',PARAMS,'\n\n',...
+'module load intel\n',...
+'module load impi\n',...
+'module load hdf5\n',...
+'srun --cpu-bind=cores ./../../../bin/helaz']);
+
+fclose(fid);
+system(['cp batch_script.sh ',BASIC.RESDIR,'/.']);
+
+disp('done');