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gyacomo/wk/marconi_run.m
69a45f839ac5shear_version

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marconi_run.m
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clear all;
addpath(genpath('../matlab')) % ... add
SUBMIT = 1; % To submit the job automatically
CHAIN = 0; % To chain jobs (CHAIN = n will launch n jobs in chain)
% EXECNAME = 'helaz3_dbg';
EXECNAME = 'helaz3';
SIMID = 'HP_fig2b_conv';
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% Set Up parameters
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% CLUSTER PARAMETERS
CLUSTER.PART = 'prod'; % dbg or prod
% CLUSTER.PART = 'dbg';
CLUSTER.TIME = '24:00:00'; % allocation time hh:mm:ss
if(strcmp(CLUSTER.PART,'dbg')); CLUSTER.TIME = '00:30:00'; end;
CLUSTER.MEM = '16GB'; % Memory
CLUSTER.JNAME = 'nu0_b_conv';% Job name
NP_P = 1; % MPI processes along p
NP_KX = 12; % MPI processes along kx
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% PHYSICAL PARAMETERS
NU = 0.0; % Collision frequency
K_N = 2.5; % Density gradient drive (R/Ln)
K_T = K_N/4; % Temperature gradient
MU = 0.1;
SIGMA_E = 0.0233380; % mass ratio sqrt(m_a/m_i) (correct = 0.0233380)
%% GRID PARAMETERS
NX = 300; % Realspace x-gridpoints
NY = 300; % Realspace y-gridpoints
LX = 120; % Size of the squared frequency domain
LY = 120; % Size of the squared frequency domain
NZ = 1; % number of perpendicular planes (parallel grid)
Q0 = 1.0; % q factor ()
SHEAR = 0.0; % magnetic shear
EPS = 0.0; % inverse aspect ratio
P = 4;
J = 2;
%% TIME PARAMETERS
TMAX = 1000; % Maximal time unit
DT = 1e-2; % Time step
SPS0D = 1/2; % Sampling per time unit for profiler
SPS2D = 1/2; % Sampling per time unit for 2D arrays
SPS3D = 1/2; % Sampling per time unit for 3D arrays
SPS5D = 1/50; % Sampling per time unit for 5D arrays
JOB2LOAD= -1; % start from t=0 if <0, else restart from outputs_$job2load
%% OPTIONS AND NAMING
% Collision operator
% (LB:L.Bernstein, DG:Dougherty, SG:Sugama, LR: Lorentz, LD: Landau)
CO = 'DG';
GKCO = 1; % gyrokinetic operator
ABCO = 1; % interspecies collisions
CLOS = 0; % Closure model (0: =0 truncation)
NL_CLOS = -1; % nonlinear closure model (-2: nmax = jmax, -1: nmax = jmax-j, >=0 : nmax = NL_CLOS)
LINEARITY = 'nonlinear'; % activate non-linearity (is cancelled if KXEQ0 = 1)
% INIT options
INIT_ZF = 0; ZF_AMP = 0.0;
INIT_OPT = 'phi';
ACT_ON_MODES = 'donothing';
%% OUTPUTS
W_DOUBLE = 0;
W_GAMMA = 1; W_HF = 1;
W_PHI = 1; W_NA00 = 1;
W_DENS = 1; W_TEMP = 1;
W_NAPJ = 1; W_SAPJ = 0;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% unused
KIN_E = 1; % Kinetic (1) or adiabatic (2) electron model
GRADB = 1.0; % Magnetic gradient
CURVB = 1.0; % Magnetic curvature
SG = 0; % Staggered z grids option
PMAXE = P; % Highest electron Hermite polynomial degree
JMAXE = J; % Highest '' Laguerre ''
PMAXI = P; % Highest ion Hermite polynomial degree
JMAXI = J; % Highest '' Laguerre ''
KERN = 0; % Kernel model (0 : GK)
KX0KH = 0; A0KH = 0; % Background phi mode to drive Ray-Tay inst.
KXEQ0 = 0; % put kx = 0
KPAR = 0.0; % Parellel wave vector component
LAMBDAD = 0.0;
MU_X = 1e-1; % Hyperdiffusivity coefficient
MU_Y = 1e-1; % Hyperdiffusivity coefficient
NOISE0 = 1.0e-5;
BCKGD0 = 0.0; % Init background
TAU = 1.0; % e/i temperature ratio
K_E = 0.0; % ES '''
MU_P = 0.0; % Hermite hyperdiffusivity -mu_p*(d/dvpar)^4 f
MU_J = 0.0; % Laguerre hyperdiffusivity -mu_j*(d/dvperp)^4 f
% Compute processes distribution
Ntot = NP_P * NP_KX;
Nnodes = ceil(Ntot/48);
Nppn = Ntot/Nnodes;
CLUSTER.NODES = num2str(Nnodes); % MPI process along p
CLUSTER.NTPN = num2str(Nppn); % MPI process along kx
CLUSTER.CPUPT = '1'; % CPU per task
%% Run file management scripts
setup
SBATCH_CMD = 'sbatch batch_script.sh\n';
write_sbash_marconi
if(mod(NP_P*NP_KX,48)~= 0)
disp('WARNING : unused cores (ntot cores must be a 48 multiple)');
end
if(SUBMIT)
[~,job_info_] = system('ssh ahoffman@login.marconi.cineca.it sh HeLaZ/wk/setup_and_run.sh');
disp(job_info_);
jobid_ = job_info_(21:27);
if(CHAIN>0)
for CHAIN_IDX = 1:CHAIN
SBATCH_CMD = ['sbatch --dependency=afterok:',jobid_,' batch_script.sh\n'];
disp(SBATCH_CMD);
JOB2LOAD= JOB2LOAD+1;
% DT = 1e-1;
% NL_CLOS = -1;
setup
write_sbash_marconi
[~,job_info_] = system('ssh ahoffman@login.marconi.cineca.it sh HeLaZ/wk/setup_and_run.sh');
jobid_ = job_info_(21:27);
end
end
end
% system('rm fort*.90');
disp('done');
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