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gyacomo/wk/daint_run.m
f9d3e79b033bgather_output

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daint_run.m
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%clear all;
addpath(genpath('../matlab')) % ... add
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% Set Up parameters
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% CLUSTER PARAMETERS
CLUSTER.TIME = '24:00:00'; % allocation time hh:mm:ss
NP_P = 2; % MPI processes along p
NP_KR = 18; % MPI processes along kr
CLUSTER.PART = 'normal'; % debug or normal
if(strcmp(CLUSTER.PART,'debug')); CLUSTER.TIME = '00:30:00'; end;
CLUSTER.MEM = '12GB'; % Memory
CLUSTER.JNAME = 'gamma_inf';% Job name
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% PHYSICAL PARAMETERS
NU = 0.1; % Collision frequency
ETAB = 0.6; % Magnetic gradient
NU_HYP = 1.0; % Hyperdiffusivity coefficient
%% GRID PARAMETERS
N = 200; % Frequency gridpoints (Nkr = N/2)
L = 120; % Size of the squared frequency domain
P = 12; % Electron and Ion highest Hermite polynomial degree
J = 06; % 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
SPS0D = 1; % Sampling per time unit for profiler
SPS2D = 1; % Sampling per time unit for 2D arrays
SPS5D = 1/40; % Sampling per time unit for 5D arrays
SPSCP = 0; % Sampling per time unit for checkpoints
RESTART = 1; % To restart from last checkpoint
JOB2LOAD= 2;
%% OPTIONS
SIMID = ['HeLaZ_v2.5_eta_',num2str(ETAB),'_nu_%0.0e']; % Name of the simulation
% SIMID = 'test_marconi_sugama'; % Name of the simulation
SIMID = sprintf(SIMID,NU);
PREFIX =[];
% PREFIX = sprintf('%d_%d_',NP_P, NP_KR);
% (0 : L.Bernstein, 1 : Dougherty, 2: Sugama, 3 : Full Couloumb ; +/- for GK/DK)
CO = 1;
CLOS = 0; % Closure model (0: =0 truncation, 1: semi coll, 2: Copy closure J+1 = J, P+2 = P)
NL_CLOS = 1; % nonlinear closure model (0: =0 nmax = jmax, 1: nmax = jmax-j, >1 : nmax = NL_CLOS)
KERN = 0; % Kernel model (0 : GK)
INIT_PHI= 1; % Start simulation with a noisy phi and moments
%% OUTPUTS
W_DOUBLE = 1;
W_GAMMA = 1;
W_PHI = 1;
W_NA00 = 1;
W_NAPJ = 1;
W_SAPJ = 0;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% 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
% Compute processes distribution
Ntot = NP_P * NP_KR;
Nnodes = ceil(Ntot/36);
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
CLUSTER.NTPC = '1'; % N tasks per core (openmp threads)
%% Run file management scripts
setup
write_sbash_daint
system('rm fort.90 setup_and_run.sh batch_script.sh');
disp('done');
if(mod(NP_P*NP_KR,36)~= 0)
disp('WARNING : unused cores (ntot cores must be a 36 multiple)');
end
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