From d118c2b79c10d90e73b38c77c94437caedbe5f89 Mon Sep 17 00:00:00 2001
From: Antoine Cyril David Hoffmann <ahoffman@spcpc606.epfl.ch>
Date: Mon, 4 Oct 2021 15:47:40 +0200
Subject: [PATCH] scripts and typos
---
.gitignore | 4 +-
matlab/continue_run.m | 92 ++++++++++++++++++++++++++++++++++++
matlab/load_marconi.m | 5 +-
matlab/setup.m | 4 +-
matlab/write_fort90.m | 15 +++---
matlab/write_sbash_daint.m | 4 +-
matlab/write_sbash_marconi.m | 14 +++---
src/tesend.F90 | 2 +-
wk/analysis_3D.m | 6 +--
wk/local_run.m | 28 +++++------
wk/marconi_run.m | 49 +++++++++++--------
11 files changed, 160 insertions(+), 63 deletions(-)
create mode 100644 matlab/continue_run.m
diff --git a/.gitignore b/.gitignore
index 201e2f75..963a466a 100644
--- a/.gitignore
+++ b/.gitignore
@@ -26,7 +26,7 @@ results_old/
mod/
obj/
bin/
-wk/fort.90
+wk/fort*.90
.directory
checkpoint/
FM/
@@ -34,7 +34,7 @@ iCa/
*.out
src/srcinfo.h
src/srcinfo/srcinfo.h
-fort.90
+fort*.90
local/
*.sh
Gallery/
diff --git a/matlab/continue_run.m b/matlab/continue_run.m
new file mode 100644
index 00000000..bf3c6a53
--- /dev/null
+++ b/matlab/continue_run.m
@@ -0,0 +1,92 @@
+%% Functions to modify preexisting fort.90 input file and launch on marconi
+function [] = continue_run(outfilename)
+ EXECNAME = 'helaz_3.8';
+ %% CLUSTER PARAMETERS
+ CLUSTER.PART = 'prod'; % dbg or prod
+ CLUSTER.TIME = '24:00:00'; % allocation time hh:mm:ss
+ if(strcmp(CLUSTER.PART,'dbg')); CLUSTER.TIME = '00:30:00'; end;
+ CLUSTER.MEM = '64GB'; % Memory
+ CLUSTER.JNAME = 'HeLaZ';% Job name
+ NP_P = 2; % MPI processes along p
+ NP_KX = 24; % MPI processes along kx
+ % 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
+ %%
+ RESDIR = ['../',outfilename(46:end-8),'/'];
+ BASIC.RESDIR = RESDIR;
+ FORT90 = [RESDIR,'fort.90'];
+
+ % Read txt into cell A
+ fid = fopen(FORT90,'r');
+ i = 1;
+ tline = fgetl(fid);
+ A{i} = tline;
+ while ischar(tline)
+ i = i+1;
+ tline = fgetl(fid);
+ A{i} = tline;
+ end
+ fclose(fid);
+
+ % Find previous job2load
+ if( numel(A{5}) == numel(' RESTART = .false.') )
+ A{5} = sprintf(' RESTART = .true.');
+ J2L = 0;
+ else
+ line = A{39};
+ line = line(end-2:end);
+ if(line(1) == '='); line = line(end); end;
+ J2L = str2num(line)+1;
+ end
+ % Change job 2 load in fort.90
+ A{39} = [' job2load = ',num2str(J2L)];
+ disp(A{39})
+ % Change time step
+ line_= A{3};
+ dt_old = str2num(line_(13:end));
+ A{3} = [' dt = ',num2str(dt_old)];
+ % Increase endtime
+ A{4} = [' tmax = 20000'];
+ % Change collision operator
+ line_= A{43};
+ CO_old = str2num(line_(13:end));
+ A{43} = [' CO = ',num2str(2)];
+ % Put non linear term back
+ A{45} = [' NL_CLOS = -1'];
+ % change HD
+ line_= A{47};
+ mu_old = str2num(line_(13:end));
+ A{47} = [' mu = ',num2str(0)];
+ % change L
+ line_= A{14};
+ L_old = str2num(line_(12:end));
+ A{14} = [' Lx = ',num2str(L_old)];
+ A{16} = [' Ly = ',num2str(L_old)];
+ % change eta N
+ line_= A{57};
+ etan_old = str2num(line_(13:end));
+ A{57} = [' eta_n = ',num2str(etan_old)];
+ % change eta B
+ line_= A{59};
+ etab_old = str2num(line_(13:end));
+ A{59} = [' eta_B = ',num2str(etab_old)];
+ % Rewrite fort.90
+ fid = fopen('fort.90', 'w');
+ for i = 1:numel(A)
+ if A{i+1} == -1
+ fprintf(fid,'%s', A{i});
+ break
+ else
+ fprintf(fid,'%s\n', A{i});
+ end
+ end
+ % Copy fort.90 into marconi
+ write_sbash_marconi
+ % Launch the job
+ system('ssh ahoffman@login.marconi.cineca.it sh HeLaZ/wk/setup_and_run.sh');
+end
diff --git a/matlab/load_marconi.m b/matlab/load_marconi.m
index 05c03182..10406e8d 100644
--- a/matlab/load_marconi.m
+++ b/matlab/load_marconi.m
@@ -14,12 +14,11 @@ function [ RESDIR ] = load_marconi( outfilename )
disp(CMD);
system(CMD);
% Load the fort.90 as well in misc folder
- CMD = ['scp -r ahoffman@login.marconi.cineca.it:',hostfolder,'/fort.90',' ',miscfolder];
+ CMD = ['scp -r ahoffman@login.marconi.cineca.it:',hostfolder,'/fort*.90',' ',miscfolder];
disp(CMD);
system(CMD);
% Put it also in the result directory
- CMD = ['scp -r ahoffman@login.marconi.cineca.it:',hostfolder,'/fort.90',' ',resultfolder];
+ CMD = ['scp -r ahoffman@login.marconi.cineca.it:',hostfolder,'/fort*.90',' ',resultfolder];
disp(CMD);
system(CMD);
end
-
diff --git a/matlab/setup.m b/matlab/setup.m
index 168c965a..6452ccea 100644
--- a/matlab/setup.m
+++ b/matlab/setup.m
@@ -111,7 +111,6 @@ BASIC.maxruntime = str2num(CLUSTER.TIME(1:2))*3600 ...
+ str2num(CLUSTER.TIME(4:5))*60 ...
+ str2num(CLUSTER.TIME(7:8));
% Outputs parameters
-if RESTART; BASIC.RESTART = '.true.'; else; BASIC.RESTART = '.false.';end;
OUTPUTS.nsave_0d = floor(1.0/SPS0D/DT);
OUTPUTS.nsave_1d = -1;
OUTPUTS.nsave_2d = floor(1.0/SPS2D/DT);
@@ -120,6 +119,7 @@ OUTPUTS.nsave_5d = floor(1.0/SPS5D/DT);
OUTPUTS.nsave_cp = floor(1.0/SPSCP/DT);
if W_DOUBLE; OUTPUTS.write_doubleprecision = '.true.'; else; OUTPUTS.write_doubleprecision = '.false.';end;
if W_GAMMA; OUTPUTS.write_gamma = '.true.'; else; OUTPUTS.write_gamma = '.false.';end;
+if W_HF; OUTPUTS.write_hf = '.true.'; else; OUTPUTS.write_hf = '.false.';end;
if W_PHI; OUTPUTS.write_phi = '.true.'; else; OUTPUTS.write_phi = '.false.';end;
if W_NA00; OUTPUTS.write_Na00 = '.true.'; else; OUTPUTS.write_Na00 = '.false.';end;
if W_NAPJ; OUTPUTS.write_Napj = '.true.'; else; OUTPUTS.write_Napj = '.false.';end;
@@ -147,7 +147,7 @@ system(MAKE);
%%
disp(['Set up ',SIMID]);
disp([resolution,gridname,degngrad]);
-if RESTART
+if JOB2LOAD>=0
disp(['- restarting from JOBNUM = ',num2str(JOB2LOAD)]); else
disp(['- starting from T = 0']);
end
diff --git a/matlab/write_fort90.m b/matlab/write_fort90.m
index d23fdec6..b4bf4f0b 100644
--- a/matlab/write_fort90.m
+++ b/matlab/write_fort90.m
@@ -1,18 +1,17 @@
function [INPUT] = write_fort90(OUTPUTS,GRID,MODEL,INITIAL,TIME_INTEGRATION,BASIC)
% Write the input script "fort.90" with desired parameters
-INPUT = 'fort.90';
+INPUT = ['fort_',sprintf('%2.2d',OUTPUTS.job2load+1),'.90'];
fid = fopen(INPUT,'wt');
fprintf(fid,'&BASIC\n');
fprintf(fid,[' nrun = ', num2str(BASIC.nrun),'\n']);
fprintf(fid,[' dt = ', num2str(BASIC.dt),'\n']);
fprintf(fid,[' tmax = ', num2str(BASIC.tmax),'\n']);
-fprintf(fid,[' RESTART = ', BASIC.RESTART,'\n']);
fprintf(fid,[' maxruntime = ', num2str(BASIC.maxruntime),'\n']);
fprintf(fid,'/\n');
fprintf(fid,'&GRID\n');
-fprintf(fid,[' pmaxe =', num2str(GRID.pmaxe),'\n']);
+fprintf(fid,[' pmaxe = ', num2str(GRID.pmaxe),'\n']);
fprintf(fid,[' jmaxe = ', num2str(GRID.jmaxe),'\n']);
fprintf(fid,[' pmaxi = ', num2str(GRID.pmaxi),'\n']);
fprintf(fid,[' jmaxi = ', num2str(GRID.jmaxi),'\n']);
@@ -32,18 +31,18 @@ fprintf(fid,[' nsave_1d = ', num2str(OUTPUTS.nsave_1d),'\n']);
fprintf(fid,[' nsave_2d = ', num2str(OUTPUTS.nsave_2d),'\n']);
fprintf(fid,[' nsave_3d = ', num2str(OUTPUTS.nsave_3d),'\n']);
fprintf(fid,[' nsave_5d = ', num2str(OUTPUTS.nsave_5d),'\n']);
-fprintf(fid,[' nsave_cp = ', num2str(OUTPUTS.nsave_cp),'\n']);
fprintf(fid,[' write_doubleprecision = ', OUTPUTS.write_doubleprecision,'\n']);
fprintf(fid,[' write_gamma = ', OUTPUTS.write_gamma,'\n']);
+fprintf(fid,[' write_hf = ', OUTPUTS.write_hf,'\n']);
fprintf(fid,[' write_phi = ', OUTPUTS.write_phi,'\n']);
fprintf(fid,[' write_Na00 = ', OUTPUTS.write_Na00,'\n']);
fprintf(fid,[' write_Napj = ', OUTPUTS.write_Napj,'\n']);
fprintf(fid,[' write_Sapj = ', OUTPUTS.write_Sapj,'\n']);
fprintf(fid,[' write_dens = ', OUTPUTS.write_dens,'\n']);
fprintf(fid,[' write_temp = ', OUTPUTS.write_temp,'\n']);
-fprintf(fid,[' resfile0 = ', OUTPUTS.resfile0,'\n']);
-fprintf(fid,[' rstfile0 = ', OUTPUTS.rstfile0,'\n']);
-fprintf(fid,[' job2load = ', num2str(OUTPUTS.job2load),'\n']);
+fprintf(fid,[' resfile0 = ', OUTPUTS.resfile0,'\n']);
+fprintf(fid,[' rstfile0 = ', OUTPUTS.rstfile0,'\n']);
+fprintf(fid,[' job2load = ', num2str(OUTPUTS.job2load),'\n']);
fprintf(fid,'/\n');
fprintf(fid,'&MODEL_PAR\n');
@@ -85,5 +84,5 @@ fprintf(fid,[' numerical_scheme = ', TIME_INTEGRATION.numerical_scheme,'\n']);
fprintf(fid,'/');
fclose(fid);
-system(['cp fort.90 ',BASIC.RESDIR,'/.']);
+system(['cp fort*.90 ',BASIC.RESDIR,'/.']);
end
diff --git a/matlab/write_sbash_daint.m b/matlab/write_sbash_daint.m
index 62a48ac2..536ff2f7 100644
--- a/matlab/write_sbash_daint.m
+++ b/matlab/write_sbash_daint.m
@@ -10,7 +10,7 @@ fprintf(fid,[...
...
'mkdir -p ', BASIC.RESDIR,'\n',...
'cd ',BASIC.RESDIR,'\n',...
-'cp $HOME/HeLaZ/wk/fort.90 .\n',...
+'cp $HOME/HeLaZ/wk/fort*.90 .\n',...
'cp $HOME/HeLaZ/wk/batch_script.sh .\n',...
...
'jid=$(sbatch batch_script.sh)\n',...
@@ -54,4 +54,4 @@ fprintf(fid,[...
fclose(fid);
system(['cp batch_script.sh ',BASIC.RESDIR,'/.']);
-system('scp {fort.90,setup_and_run.sh,batch_script.sh} ahoffman@ela.cscs.ch:HeLaZ/wk');
\ No newline at end of file
+system('scp {fort*.90,setup_and_run.sh,batch_script.sh} ahoffman@ela.cscs.ch:HeLaZ/wk');
diff --git a/matlab/write_sbash_marconi.m b/matlab/write_sbash_marconi.m
index d4fde784..461b0c53 100644
--- a/matlab/write_sbash_marconi.m
+++ b/matlab/write_sbash_marconi.m
@@ -10,11 +10,11 @@ fprintf(fid,[...
...
'mkdir -p ', BASIC.RESDIR,'\n',...
'cd ',BASIC.RESDIR,'\n',...
-'cp $HOME/HeLaZ/wk/fort.90 .\n',...
+'cp $HOME/HeLaZ/wk/fort*.90 .\n',...
'cp $HOME/HeLaZ/wk/batch_script.sh .\n',...
...
-'sbatch batch_script.sh\n',...
-'echo tail -f $CINECA_SCRATCH/HeLaZ',BASIC.RESDIR(3:end),'out.txt']);
+SBATCH_CMD,...
+'echo tail -f $CINECA_SCRATCH/HeLaZ',BASIC.RESDIR(3:end),'out']);
fclose(fid);
system(['cp setup_and_run.sh ',BASIC.RESDIR,'/.']);
@@ -31,15 +31,15 @@ fprintf(fid,[...
'#SBATCH --cpus-per-task=', CLUSTER.CPUPT,'\n',...
'#SBATCH --ntasks-per-node=', CLUSTER.NTPN,'\n',...
'#SBATCH --mem=', CLUSTER.MEM,'\n',...
-'#SBATCH --error=err.txt\n',...
-'#SBATCH --output=out.txt\n',...
+'#SBATCH --error=err',num2str(JOB2LOAD+1),'.txt\n',...
+'#SBATCH --output=out_',num2str(JOB2LOAD+1),'.txt\n',...
'#SBATCH --account=FUA35_TSVVT421\n',...
'#SBATCH --partition=skl_fua_',CLUSTER.PART,'\n',...
'module load autoload hdf5 fftw\n',...
-'srun --cpu-bind=cores ./../../../bin/',EXECNAME,' ',num2str(NP_P),' ',num2str(NP_KX)]);
+'srun --cpu-bind=cores ./../../../bin/',EXECNAME,' ',num2str(NP_P),' ',num2str(NP_KX),' ',num2str(JOB2LOAD+1)]);
fclose(fid);
system(['cp batch_script.sh ',BASIC.RESDIR,'/.']);
-system('scp {fort.90,setup_and_run.sh,batch_script.sh} ahoffman@login.marconi.cineca.it:/marconi/home/userexternal/ahoffman/HeLaZ/wk > trash.txt');
+system('scp {fort*.90,setup_and_run.sh,batch_script.sh} ahoffman@login.marconi.cineca.it:/marconi/home/userexternal/ahoffman/HeLaZ/wk > trash.txt');
system('rm trash.txt');
\ No newline at end of file
diff --git a/src/tesend.F90 b/src/tesend.F90
index 16ef0764..7e356e9f 100644
--- a/src/tesend.F90
+++ b/src/tesend.F90
@@ -52,7 +52,7 @@ SUBROUTINE tesend
RETURN
END IF
!________________________________________________________________________________
- ! 5. NRUN modified throught "stop file"
+ ! 5. NRUN modified through "stop file"
!
IF( (my_id .EQ. 0) .AND. (MOD(cstep, ncheck_stop) == 0) ) THEN
INQUIRE(file=stop_file, exist=mlexist)
diff --git a/wk/analysis_3D.m b/wk/analysis_3D.m
index 0bdc0cff..dc2ba46b 100644
--- a/wk/analysis_3D.m
+++ b/wk/analysis_3D.m
@@ -2,15 +2,15 @@ addpath(genpath('../matlab')) % ... add
addpath(genpath('../matlab/plots')) % ... add
outfile ='';
%% Directory of the simulation
-if 0% Local results
+if 1% Local results
outfile ='';
outfile ='';
% outfile ='artificial_ZF_freeze/sim_A';
% outfile ='simulation_B/cw_FCGK_kp_3.0';
-% outfile ='nonlin_FCGK/150x75_L_200_P_4_J_2_eta_0.6_nu_1e-01_FCGK_mu_0e+00';
+outfile ='nonlin_FCGK/150x75_L_200_P_4_J_2_eta_0.6_nu_1e-01_FCGK_mu_0e+00';
% outfile ='nonlin_PAGK/100x50_L_200_P_4_J_2_eta_0.6_nu_1e-01_PAGK_mu_0e+00';
% outfile ='nonlin_FCGK/100x50_L_200_P_4_J_2_eta_0.6_nu_1e-01_FCGK_mu_0e+00';
-outfile ='simulation_A';
+% outfile ='simulation_A';
% outfile ='simulation_B/cw_SGGK_like_species';
% outfile ='simulation_A/CO_damping_SGGK';
% outfile ='simulation_A/cw_DGGK_eta_0.5';
diff --git a/wk/local_run.m b/wk/local_run.m
index 7de7329d..06bcd403 100644
--- a/wk/local_run.m
+++ b/wk/local_run.m
@@ -24,30 +24,26 @@ SPS2D = 1; % Sampling per time unit for 2D arrays
SPS3D = 1; % Sampling per time unit for 3D arrays
SPS5D = 1/20; % Sampling per time unit for 5D arrays
SPSCP = 0; % Sampling per time unit for checkpoints/10
-RESTART = 0; % To restart from last checkpoint
-JOB2LOAD= 0;
+JOB2LOAD= -1;
%% OPTIONS AND NAMING
% Collision operator
% (0 : L.Bernstein, 1 : Dougherty, 2: Sugama, 3 : Pitch angle ; 4 : Coulomb; +/- for GK/DK)
-CO = 4;
+CO = 1;
CLOS = 0; % Closure model (0: =0 truncation)
NL_CLOS = -1; % nonlinear closure model (-2: nmax = jmax, -1: nmax = jmax-j, >=0 : nmax = NL_CLOS)
-SIMID = 'nonlin_FCGK'; % Name of the simulation
-% SIMID = 'test_3D'; % Name of the simulation
+% SIMID = 'nonlin_FCGK'; % Name of the simulation
+SIMID = 'test'; % Name of the simulation
% SIMID = ['v3.0_P_',num2str(P),'_J_',num2str(J)]; % Name of the simulation
NON_LIN = 1; % activate non-linearity (is cancelled if KXEQ0 = 1)
% INIT options
INIT_ZF = 0; ZF_AMP = 0.0;
INIT_BLOB = 0; WIPE_TURB = 0; WIPE_ZF = 0;
%% OUTPUTS
-W_DOUBLE = 0;
-W_GAMMA = 1;
-W_PHI = 1;
-W_NA00 = 1;
-W_NAPJ = 1;
-W_SAPJ = 0;
-W_DENS = 1;
-W_TEMP = 1;
+W_DOUBLE = 1;
+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
@@ -62,9 +58,9 @@ KPAR = 0.0; % Parellel wave vector component
LAMBDAD = 0.0;
kmax = N*pi/L;% Highest fourier mode
HD_CO = 0.5; % Hyper diffusivity cutoff ratio
-% kmaxcut = 2.5;
-MU = NU_HYP/(HD_CO*kmax)^4 % Hyperdiffusivity coefficient
+MU = NU_HYP/(HD_CO*kmax)^4; % Hyperdiffusivity coefficient
NOISE0 = 1.0e-5;
+BCKGD0 = 0.0; % Init background
TAU = 1.0; % e/i temperature ratio
ETAT = 0.0; % Temperature gradient
ETAB = 1.0; % Magnetic gradient (1.0 to set R=LB)
@@ -73,6 +69,6 @@ MU_P = 0.0; % Hermite hyperdiffusivity -mu_p*(d/dvpar)^4 f
MU_J = 0.0; % Laguerre hyperdiffusivity -mu_j*(d/dvperp)^4 f
%% Setup and file management
setup
-system('rm fort.90');
+system('rm fort*.90');
outfile = [BASIC.RESDIR,'out.txt'];
disp(outfile);
diff --git a/wk/marconi_run.m b/wk/marconi_run.m
index 577e6b5a..9c2b2b67 100644
--- a/wk/marconi_run.m
+++ b/wk/marconi_run.m
@@ -1,8 +1,9 @@
clear all;
addpath(genpath('../matlab')) % ... add
SUBMIT = 1; % To submit the job automatically
+CHAIN = 1; % To chain jobs (CHAIN = n will launch n jobs in chain)
% EXECNAME = 'helaz_dbg';
- EXECNAME = 'helaz_3.8';
+ EXECNAME = 'helaz_3.81';
for ETAN = [1/0.6]
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% Set Up parameters
@@ -10,15 +11,15 @@ for ETAN = [1/0.6]
%% CLUSTER PARAMETERS
CLUSTER.PART = 'prod'; % dbg or prod
% CLUSTER.PART = 'dbg';
-CLUSTER.TIME = '24:00:00'; % allocation time hh:mm:ss
+CLUSTER.TIME = '20:00:00'; % allocation time hh:mm:ss
if(strcmp(CLUSTER.PART,'dbg')); CLUSTER.TIME = '00:30:00'; end;
CLUSTER.MEM = '128GB'; % Memory
CLUSTER.JNAME = 'HeLaZ';% Job name
NP_P = 2; % MPI processes along p
-NP_KX = 24; % MPI processes along kx
+NP_KX = 48; % MPI processes along kx
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% PHYSICAL PARAMETERS
-NU = 0.5; % Collision frequency
+NU = 0.1; % Collision frequency
ETAN = 1.0/0.6; % Density gradient drive (R/Ln)
NU_HYP = 0.0;
%% GRID PARAMETERS
@@ -32,22 +33,21 @@ P = 8;
J = 4;
%% TIME PARAMETERS
TMAX = 10000; % Maximal time unit
-DT = 5e-3; % Time step
+DT = 8e-3; % Time step
SPS0D = 1; % Sampling per time unit for profiler
SPS2D = 1; % Sampling per time unit for 2D arrays
SPS3D = 1/2; % Sampling per time unit for 3D arrays
SPS5D = 1/100; % Sampling per time unit for 5D arrays
SPSCP = 0; % Sampling per time unit for checkpoints/10
-RESTART = 1; % To restart from last checkpoint
-JOB2LOAD= 0;
+JOB2LOAD= -1; % start from t=0 if <0, else restart from outputs_$job2load
%% OPTIONS AND NAMING
% Collision operator
% (0 : L.Bernstein, 1 : Dougherty, 2: Sugama, 3 : Pitch angle ; +/- for GK/DK)
-CO = 2;
+CO = 3;
CLOS = 0; % Closure model (0: =0 truncation)
NL_CLOS = -1; % nonlinear closure model (-2: nmax = jmax, -1: nmax = jmax-j, >=0 : nmax = NL_CLOS)
-% SIMID = 'test_3D_marconi'; % Name of the simulation
-SIMID = 'simulation_B'; % Name of the simulation
+% SIMID = 'test_chained_job'; % Name of the simulation
+SIMID = 'simulation_A'; % Name of the simulation
% SIMID = ['v3.0_P_',num2str(P),'_J_',num2str(J)]; % Name of the simulation
NON_LIN = 1; % activate non-linearity (is cancelled if KXEQ0 = 1)
% INIT options
@@ -55,13 +55,10 @@ INIT_ZF = 0; ZF_AMP = 0.0;
INIT_BLOB = 0; WIPE_TURB = 0; WIPE_ZF = 0;
%% OUTPUTS
W_DOUBLE = 1;
-W_GAMMA = 1;
-W_PHI = 1;
-W_NA00 = 1;
-W_NAPJ = 1;
-W_SAPJ = 0;
-W_DENS = 1;
-W_TEMP = 1;
+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
@@ -95,13 +92,27 @@ 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
-system('rm fort.90 setup_and_run.sh batch_script.sh');
+system('rm fort*.90 setup_and_run.sh batch_script.sh');
if(mod(NP_P*NP_KX,48)~= 0)
disp('WARNING : unused cores (ntot cores must be a 48 multiple)');
end
if(SUBMIT)
- system('ssh ahoffman@login.marconi.cineca.it sh HeLaZ/wk/setup_and_run.sh');
+ [~,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;
+ 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
disp('done');
end
--
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