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gyacomo/wk/ppb110_run.m
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ppb110_run.m
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%clear all;
addpath(genpath('../matlab')) % ... add
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% Set Up parameters
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% CLUSTER PARAMETERS
CLUSTER.TIME = '01:00:00'; % allocation time hh:mm:ss
CLUSTER.NODES = '8'; % MPI process
CLUSTER.MEM = '2000'; % Memory
CLUSTER.JNAME = 'test_HeLaZ'; % Job name
USERNAME = 'ahoffman'; % username at ppb110 for folder naming
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% PHYSICAL PARAMETERS
NU = 1.0; % Collision frequency
ETAB = 0.5; % 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 = 2; % Electron and Ion highest Hermite polynomial degree
J = 1; % 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 = 150; % 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
SPSCP = 1/10; % Sampling per time unit for checkpoints
RESTART = 0; % To restart from last checkpoint
JOB2LOAD= 0;
%% OPTIONS
SIMID = '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)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% fixed parameters (for current study)
KR0KH = 0; A0KH = 0; % Background phi mode to drive Ray-Tay inst. (not implemented)
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 -n ', CLUSTER.NODES,'\n',...
'#SBATCH --mem-per-cpu=', CLUSTER.MEM,'\n',...
'#SBATCH --error=err.txt\n',...
'#SBATCH --output=out.txt\n',...
'module load intel_comp/17.0 impi/17.0 hdf5/1.8.12_intel13.1\n',...
'srun ./../../../bin/helaz']);
fclose(fid);
system(['cp batch_script.sh ',BASIC.RESDIR,'/.']);
disp('done');
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