diff --git a/wk/analysis_2D.m b/wk/analysis_2D.m
index 1d2f1bb101ba5f4fe1b3283a9db73b1d8044fe60..dc5198904d5581f68e0b5ac458cb358db1a61010 100644
--- a/wk/analysis_2D.m
+++ b/wk/analysis_2D.m
@@ -1,12 +1,12 @@
%% Load results
-if LOAD_MARCONI
+if LOAD_MARCONI==1
hostfolder = ['/marconi_scratch/userexternal/ahoffman/HeLaZ/results/',BASIC.SIMID,'/',BASIC.PARAMS];
localfolder= [BASIC.RESDIR,'..'];
system(['scp -r ahoffman@login.marconi.cineca.it:',hostfolder,' ',localfolder])
end
-JOBNUM = 0; load_results;
+% JOBNUM = 0; load_results;
% JOBNUM = 1; load_results;
-% compile_results
+compile_results
%% Retrieving max polynomial degree and sampling info
Npe = numel(Pe); Nje = numel(Je); [JE,PE] = meshgrid(Je,Pe);
@@ -106,6 +106,7 @@ end
%% Compute growth rate
+if NON_LIN == 0
disp('- growth rate')
tend = Ts2D(end); tstart = 0.6*tend;
g_ = zeros(Nkr,Nkz);
@@ -117,7 +118,7 @@ for ikr = 1:Nkr
end
% gkr0kz_Ni00 = max(real(g_(:,:)),[],1);
gkr0kz_Ni00 = real(g_(ikr0KH,:));
-
+end
%% PLOTS %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
default_plots_options
disp('Plots')
@@ -203,33 +204,35 @@ suptitle(['$\nu_{',CONAME,'}=$', num2str(NU), ', $\eta_B=$',num2str(ETAB), sprin
save_figure
end
-if 1
+if 0
%% Photomaton : real space
-% FIELD = ni00; FNAME = 'ni';
-FIELD = phi; FNAME = 'phi';
-tf = 60; [~,it1] = min(abs(Ts2D-tf));
-tf = 65; [~,it2] = min(abs(Ts2D-tf));
-tf = 200; [~,it3] = min(abs(Ts2D-tf));
-tf = 400; [~,it4] = min(abs(Ts2D-tf));
+FIELD = ni00; FNAME = 'ni';
+% FIELD = ne00; FNAME = 'ne';
+% FIELD = phi; FNAME = 'phi';
+tf = 19; [~,it1] = min(abs(Ts2D-tf));
+tf = 20; [~,it2] = min(abs(Ts2D-tf));
+tf = 21; [~,it3] = min(abs(Ts2D-tf));
+tf = 22; [~,it4] = min(abs(Ts2D-tf));
fig = figure; FIGNAME = [FNAME,'_snaps']; set(gcf, 'Position', [100, 100, 1500, 400])
- subplot(141); plt = @(x) ((x));
+plt = @(x) x;%./max(max(x));
+ subplot(141)
DATA = plt(FIELD(:,:,it1));
- pclr = pcolor((RR),(ZZ),DATA./max(max(DATA))); set(pclr, 'edgecolor','none');pbaspect([1 1 1])
+ pclr = pcolor((RR),(ZZ),DATA); set(pclr, 'edgecolor','none');pbaspect([1 1 1])
xlabel('$r/\rho_s$'); ylabel('$z/\rho_s$');set(gca,'ytick',[]);
title(sprintf('$t c_s/R=%.0f$',Ts2D(it1)));
- subplot(142); plt = @(x) ((x));
+ subplot(142)
DATA = plt(FIELD(:,:,it2));
- pclr = pcolor((RR),(ZZ),DATA./max(max(DATA))); set(pclr, 'edgecolor','none');pbaspect([1 1 1])
+ pclr = pcolor((RR),(ZZ),DATA); set(pclr, 'edgecolor','none');pbaspect([1 1 1])
xlabel('$r/\rho_s$');ylabel('$z/\rho_s$'); set(gca,'ytick',[]);
title(sprintf('$t c_s/R=%.0f$',Ts2D(it2)));
- subplot(143); plt = @(x) ((x));
+ subplot(143)
DATA = plt(FIELD(:,:,it3));
- pclr = pcolor((RR),(ZZ),DATA./max(max(DATA))); set(pclr, 'edgecolor','none');pbaspect([1 1 1])
+ pclr = pcolor((RR),(ZZ),DATA); set(pclr, 'edgecolor','none');pbaspect([1 1 1])
xlabel('$r/\rho_s$');ylabel('$z/\rho_s$');set(gca,'ytick',[]);
title(sprintf('$t c_s/R=%.0f$',Ts2D(it3)));
- subplot(144); plt = @(x) ((x));
+ subplot(144)
DATA = plt(FIELD(:,:,it4));
- pclr = pcolor((RR),(ZZ),DATA./max(max(DATA))); set(pclr, 'edgecolor','none');pbaspect([1 1 1])
+ pclr = pcolor((RR),(ZZ),DATA); set(pclr, 'edgecolor','none');pbaspect([1 1 1])
xlabel('$r/\rho_s$');ylabel('$z/\rho_s$'); set(gca,'ytick',[]);
title(sprintf('$t c_s/R=%.0f$',Ts2D(it4)));
% suptitle(['$\',FNAME,'$, $\nu_{',CONAME,'}=$', num2str(NU), ', $\eta_B=$',num2str(ETAB),...
@@ -363,7 +366,7 @@ end
%%
if 0
%% Show frame in kspace
-tf = 200; [~,it2] = min(abs(Ts2D-tf)); [~,it5] = min(abs(Ts5D-tf));
+tf = 100; [~,it2] = min(abs(Ts2D-tf)); [~,it5] = min(abs(Ts5D-tf));
fig = figure; FIGNAME = ['krkz_frame',sprintf('t=%.0f',Ts2D(it2))];set(gcf, 'Position', [100, 100, 700, 600])
subplot(221); plt = @(x) fftshift((abs(x)),2);
pclr = pcolor(fftshift(KR,2),fftshift(KZ,2),plt(PHI(:,:,it2))); set(pclr, 'edgecolor','none'); colorbar;
diff --git a/wk/linear_study.m b/wk/linear_study.m
index b84475b511ad811c5466de0c08110e5ee22f485d..60e8ce23d5cb5f390198e0fe5243da512ec77120 100644
--- a/wk/linear_study.m
+++ b/wk/linear_study.m
@@ -11,17 +11,17 @@ ETAB = 0.5;
ETAN = 1.0; % Density gradient
ETAT = 0.0; % Temperature gradient
MU = 0e-4; % Hyper diffusivity coefficient
-LAMBDAD = 0.0;
+LAMBDAD = 0.0;
NOISE0 = 1.0e-5;
%% GRID PARAMETERS
N = 50; % Frequency gridpoints (Nkr = N/2)
L = 100; % Size of the squared frequency domain
PMAXE = 12;
-JMAXE = 6;
+JMAXE = 6;
PMAXI = 12;
JMAXI = 6;
KREQ0 = 1; % put kr = 0
-%% TIME PARAMETERS
+%% TIME PARAMETERS
TMAX = 300; % Maximal time unit
DT = 1e-3; % Time step
SPS0D = 0.5; % Sampling per time unit for 2D arrays
@@ -36,12 +36,10 @@ CO = -1; % Collision operator (0 : L.Bernstein, -1 : Full Coulomb, -2 : Do
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% unused
-KR0KH = 0; A0KH = 0; % Background phi mode to drive Ray-Tay inst.
NO_E = 0; % Remove electrons dynamic
% DK = 0; % Drift kinetic model (put every kernel_n to 0 except n=0 to 1)
JOBNUM = 00;
-CANCEL_ODD_P = 0;% Cancels the odd polynomials degree
-KPAR = 0.0 * (1-CANCEL_ODD_P); % Parellel wave vector component
+KPAR = 0.0; % Parellel wave vector component
%% PARAMETER SCANS
if 1
@@ -70,7 +68,7 @@ for i = 1:Nparam
system('./../bin/helaz');
% Load and process results
load_results
- tend = Ts2D(end); tstart = 0.4*tend;
+ tend = Ts2D(end); tstart = 0.4*tend;
for ikz = 1:N
gamma_Ni(i,ikz) = LinearFit_s(Ts2D,squeeze(abs(Ni00(1,ikz,:))),tstart,tend);
Ni00_ST(i,ikz,1:numel(Ts2D)) = squeeze((Ni00(1,ikz,:)));
@@ -83,7 +81,7 @@ end
% %% Plot
% fig = figure; FIGNAME = 'space_time_Ni00';
% i = 1;
-%
+%
% [YY, XX] = meshgrid(Ts2D,kz);
% plt = @(x) squeeze(log(abs(x)))
% pclr = pcolor(XX,YY,plt(Ni00_ST(i,:,:)));set(pclr, 'edgecolor','none');
@@ -149,7 +147,7 @@ for i = 1:Nparam
run
% Load and process results
load_results
- tend = Ts2D(end); tstart = 0.6*tend;
+ tend = Ts2D(end); tstart = 0.6*tend;
for ikz = 1:N
gamma_Ni(i,ikz) = LinearFit_s(Ts2D,squeeze(abs(Ni00(1,ikz,:))),tstart,tend);
end
@@ -177,4 +175,4 @@ title(['$P_e=',num2str(PMAXE),'$',', $J_e=',num2str(JMAXE),'$',...
legend('show')
saveas(fig,[SIMDIR,'gamma_Ni_vs_',param_name,'_',PARAMS,'.fig']);
end
-end
\ No newline at end of file
+end
diff --git a/wk/marconi_run.m b/wk/marconi_run.m
index 0c709cbe32818b159abebd5d4fc45a736c8b9512..4a2ae9df68cd32a7b06d353f2738715857497c4b 100644
--- a/wk/marconi_run.m
+++ b/wk/marconi_run.m
@@ -7,31 +7,32 @@ addpath(genpath('../matlab')) % ... add
CLUSTER.TIME = '24:00:00'; % allocation time hh:mm:ss
CLUSTER.NODES = '1'; % MPI process
CLUSTER.CPUPT = '1'; % CPU per task
-CLUSTER.NTPN = '16'; % N tasks per node
+CLUSTER.NTPN = '20'; % N tasks per node
CLUSTER.PART = 'prod'; % dbg or prod
CLUSTER.MEM = '32GB'; % Memory
%% PHYSICAL PARAMETERS
NU = 1e-1; % Collision frequency
TAU = 1.0; % e/i temperature ratio
-ETAB = 0.5; % Magnetic gradient
+ETAB = 0.4; % Magnetic gradient
ETAN = 1.0; % Density gradient
ETAT = 0.0; % Temperature gradient
MU = 5e-4; % Hyper diffusivity coefficient
NOISE0 = 1.0e-5;
%% GRID PARAMETERS
N = 512; % Frequency gridpoints (Nkr = N/2)
-L = 100; % Size of the squared frequency domain
-PMAXE = 4; % Highest electron Hermite polynomial degree
-JMAXE = 2; % Highest '' Laguerre ''
-PMAXI = 4; % Highest ion Hermite polynomial degree
-JMAXI = 2; % Highest '' Laguerre ''
-%% TIME PARAMETERS
-TMAX = 250; % Maximal time unit
+L = 150; % Size of the squared frequency domain
+PMAXE = 2; % Highest electron Hermite polynomial degree
+JMAXE = 1; % Highest '' Laguerre ''
+PMAXI = 2; % Highest ion Hermite polynomial degree
+JMAXI = 1; % Highest '' Laguerre ''
+%% TIME PARAMETERS
+TMAX = 200; % Maximal time unit
DT = 5e-3; % Time step
-SPS0D = 1/DT/4; % Sampling per time unit for profiler
+SPS0D = 10; % Sampling per time unit for profiler
SPS2D = 1; % Sampling per time unit for 2D arrays
-SPS5D = 0.1; % Sampling per time unit for 5D arrays
-RESTART = 1; % To restart from last checkpoint
+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 = 'Marconi'; % Name of the simulation
@@ -44,9 +45,8 @@ NO_E = 0; % Remove electrons dynamic
% DK = 0; % Drift kinetic model (put every kernel_n to 0 except n=0 to 1)
KREQ0 = 0; % put kr = 0
KPAR = 0.0; % Parellel wave vector component
-LAMBDAD = 0.0;
+LAMBDAD = 0.0;
NON_LIN = 1 *(1-KREQ0); % activate non-linearity (is cancelled if KREQ0 = 1)
-CANCEL_ODD_P = 0;% Cancels the odd polynomials degree
%% Run following scripts
setup
@@ -56,4 +56,4 @@ write_sbash
system(['scp {fort.90,batch_script.sh,setup_and_run.sh}',...
' ahoffman@login.marconi.cineca.it:/marconi/home/userexternal/ahoffman/HeLaZ/wk']);
LOAD_MARCONI = 1;
-disp('done');
\ No newline at end of file
+disp('done');
diff --git a/wk/marconi_scaling.m b/wk/marconi_scaling.m
index 1aecc4a58613d4d1e06ef878ed9a2bb99c9a9dba..ec5aa14864f524b8884c99c606ac1b46fd82c1a7 100644
--- a/wk/marconi_scaling.m
+++ b/wk/marconi_scaling.m
@@ -4,11 +4,11 @@ addpath(genpath('../matlab')) % ... add
%% Set Up parameters
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% CLUSTER PARAMETERS
-CLUSTER.TIME = '01:30:00'; % allocation time hh:mm:ss
-CLUSTER.NODES = '1'; % MPI process
-CLUSTER.CPUPT = '1'; % CPU per task
-CLUSTER.NTPN = '4'; % N tasks per node
-CLUSTER.PART = 'prod'; % dbg or prod
+CLUSTER.TIME = '01:00:00'; % allocation time hh:mm:ss
+CLUSTER.NODES = '01'; % MPI process
+CLUSTER.CPUPT = '01'; % CPU per task
+CLUSTER.NTPN = '01'; % N tasks per node (openMP)
+CLUSTER.PART = 'dbg'; % dbg or prod
CLUSTER.MEM = '16GB'; % Memory
%% PHYSICAL PARAMETERS
NU = 1e-1; % Collision frequency
@@ -19,22 +19,23 @@ ETAT = 0.0; % Temperature gradient
MU = 0e-4; % Hyper diffusivity coefficient
NOISE0 = 1.0e-5;
%% GRID PARAMETERS
-N = 1024; % Frequency gridpoints (Nkr = N/2)
+N = 512; % Frequency gridpoints (Nkr = N/2)
L = 100; % Size of the squared frequency domain
PMAXE = 2; % Highest electron Hermite polynomial degree
JMAXE = 1; % Highest '' Laguerre ''
PMAXI = 2; % Highest ion Hermite polynomial degree
JMAXI = 1; % Highest '' Laguerre ''
-%% TIME PARAMETERS
-TMAX = 10; % Maximal time unit
+%% TIME PARAMETERS
+TMAX = 5; % Maximal time unit
DT = 5e-2; % Time step
SPS0D = 1/DT; % Sampling per time unit for profiler
-SPS2D = 1; % Sampling per time unit for 2D arrays
-SPS5D = 0; % Sampling per time unit for 5D arrays
+SPS2D = 0; % Sampling per time unit for 2D arrays
+SPS5D = 0; % Sampling per time unit for 5D arrays
+SPSCP = 0; % Sampling per time unit for checkpoints
RESTART = 0; % To restart from last checkpoint
JOB2LOAD= 0;
%% OPTIONS
-SIMID = ['Scaling_np',num2str(CLUSTER.NTPN)]; % Name of the simulation
+SIMID = ['Scaling__np',num2str(CLUSTER.NTPN)]; % Name of the simulation
CO = -2; % Collision operator (0 : L.Bernstein, -1 : Full Coulomb, -2 : Dougherty)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
@@ -44,13 +45,12 @@ NO_E = 0; % Remove electrons dynamic
% DK = 0; % Drift kinetic model (put every kernel_n to 0 except n=0 to 1)
KREQ0 = 0; % put kr = 0
KPAR = 0.0; % Parellel wave vector component
-LAMBDAD = 0.0;
+LAMBDAD = 0.0;
NON_LIN = 1 *(1-KREQ0); % activate non-linearity (is cancelled if KREQ0 = 1)
-CANCEL_ODD_P = 0;% Cancels the odd polynomials degree
%% Run following scripts
setup
write_sbash
-MARCONI = 1;
\ No newline at end of file
+MARCONI = 1;
diff --git a/wk/parallel_scaling_new.m b/wk/parallel_scaling_new.m
index 4526a5dbc9439d7b59ecbcb23a32dd7dec01c425..c9608265e7ed5bdc343f27a279464439d2bce4cb 100644
--- a/wk/parallel_scaling_new.m
+++ b/wk/parallel_scaling_new.m
@@ -7,33 +7,34 @@ if 0
i_ = 1;
for np = NPS
SIM_NAME = sprintf('Scaling_np%02d',np);
- hostfile = ['/marconi_scratch/userexternal/ahoffman/HeLaZ/results/',SIM_NAME,'/',BASIC.PARAMS,'/outputs_00.h5'];
- localfile= ['../results/',SIM_NAME,'/',BASIC.PARAMS,'/.'];
- system(['scp -p ahoffman@login.marconi.cineca.it:',hostfile,' ',localfile]);
+ hostfile = ['/marconi_scratch/userexternal/ahoffman/HeLaZ/results/',SIM_NAME,'/',BASIC.PARAMS];
+ localfile= ['../results/',SIM_NAME,'/'];
+ system(['scp -r ahoffman@login.marconi.cineca.it:',hostfile,' ',localfile]);
filename = ['../results/',SIM_NAME,'/',BASIC.PARAMS,'/outputs_00.h5'];
TIMES(i_) = h5readatt(filename,'/data/input','cpu_time');
i_ = i_ + 1;
end
+TIMES
end
-%% Strong scaling measurement
+%% Strong scaling measurement (no diagnostics)
% Handwritten results for 512x256, P,J=2,1, Tmax = 10, mu=0, dt = 5e-2
Results_512_21.np = NPS;
-Results_512_21.time = [789 422 206 106 81 72 66 82]; %tmax 10
+Results_512_21.time = [799 422 206 106 81 72 66 82]; %tmax 10
% Results_512_21.time = [0162, 0108, 0055, 0032, 0030, 0045, 0061, 0084]; %tmax 2
-% Handwritten results for 512x256, P,J=3,2, Tmax = 5, mu=0, dt 5e-2
+% Handwritten results for 512x256, P,J=3,2, Tmax = 10, mu=0, dt 5e-2
Results_512_32.np = [ 1, 2, 4, 8, 12, 16, 20, 24];
-Results_512_32.time = [1221, 0608, 0307, 0163, 0130, 0127, 0194, 0260];
+Results_512_32.time = [2421 1241 0598 0309 0221 0188 0159 0148];
% Handwritten results for 1024x512, P,J=2,1, Tmax = 5 dt = 0.05, mu = 0
Results_1024_21.np = [ 1, 2, 4, 8, 12, 16, 20, 24];
% Results_1024_21.time = [1920, 0000, 0563, 0306, 0247, 0240, 0000, 0000];
-Results_1024_21.time = [3808, 0000, 1108, 0586, 0465, 0443, 0483, 0496];
+Results_1024_21.time = [1920, 1260, 0556, 0289, 0219, 0189, 0172, 0167];
% Handwritten results for 1024x512, P,J=3,2, Tmax = 2 dt = 0.05, mu = 0
Results_1024_32.np = [ 1, 2, 4, 8, 12, 16, 20, 24];
-Results_1024_32.time = [0000, 0000, 0000, 0000, 0000, 0000, 0000, 0000];
+Results_1024_32.time = [2199, 1424, 0623, 0324, 0243, 0208, 0188, 0180];
% Handwritten results for 1024x512, P,J=6,4, Tmax = 2 dt = 0.05, mu = 0
Results_1024_64.np = [ 1, 2, 4, 8, 12, 16, 20, 24];
diff --git a/wk/parameters_ZP.m b/wk/parameters_ZP.m
index 7991aa72404769f3f19cec2765246e24b6d214dc..41d2dd46a59ef0dd9d6f38bc31ed8f03f5cdf44b 100644
--- a/wk/parameters_ZP.m
+++ b/wk/parameters_ZP.m
@@ -12,19 +12,19 @@ ETAT = 0.0; % Temperature gradient
MU = 5e-4; % Hyper diffusivity coefficient
NOISE0 = 1.0e-5;
%% GRID PARAMETERS
-N = 256; % Frequency gridpoints (Nkr = N/2)
-L = 66; % Size of the squared frequency domain
-PMAXE = 2; % Highest electron Hermite polynomial degree
-JMAXE = 1; % Highest '' Laguerre ''
-PMAXI = 2; % Highest ion Hermite polynomial degree
-JMAXI = 1; % Highest '' Laguerre ''
-%% TIME PARAMETERS
-TMAX = 400; % Maximal time unit
+N = 128; % Frequency gridpoints (Nkr = N/2)
+L = 33; % Size of the squared frequency domain
+PMAXE = 0; % Highest electron Hermite polynomial degree
+JMAXE = 0; % Highest '' Laguerre ''
+PMAXI = 0; % Highest ion Hermite polynomial degree
+JMAXI = 0; % Highest '' Laguerre ''
+%% TIME PARAMETERS
+TMAX = 10; % Maximal time unit
DT = 1e-2; % Time step
SPS0D = 1; % Sampling per time unit for 2D arrays
SPS2D = 1; % Sampling per time unit for 2D arrays
SPS5D = 0.1; % Sampling per time unit for 5D arrays
-RESTART = 1; % To restart from last checkpoint
+RESTART = 0; % To restart from last checkpoint
JOB2LOAD= 1;
%% OPTIONS
SIMID = 'ZP'; % Name of the simulation
@@ -32,14 +32,11 @@ CO = -1; % Collision operator (0 : L.Bernstein, -1 : Full Coulomb, -2 : Do
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% unused
-KR0KH = 0; A0KH = 0; % Background phi mode to drive Ray-Tay inst.
-NO_E = 0; % Remove electrons dynamic
% DK = 0; % Drift kinetic model (put every kernel_n to 0 except n=0 to 1)
KREQ0 = 0; % put kr = 0
KPAR = 0.0; % Parellel wave vector component
-LAMBDAD = 0.0;
+LAMBDAD = 0.0;
NON_LIN = 1 *(1-KREQ0); % activate non-linearity (is cancelled if KREQ0 = 1)
LOAD_MARCONI = 0;
-CANCEL_ODD_P = 0;% Cancels the odd polynomials degree
setup
diff --git a/wk/profiler.m b/wk/profiler.m
index 30aa7bfc8e92e29262583d8a19a448de62a1b524..4ca0045721d43681bbfcf726c2b66a7a68338484 100644
--- a/wk/profiler.m
+++ b/wk/profiler.m
@@ -1,7 +1,7 @@
%% load profiling
filename = sprintf([BASIC.RESDIR,'outputs_%.2d.h5'],00);
-CPUTIME = h5readatt(filename,'/data/input','cpu_time');
+CPUTIME = double(h5readatt(filename,'/data/input','cpu_time'));
DT_SIM = h5readatt(filename,'/data/input','dt');
@@ -17,21 +17,41 @@ Ts0D = h5read(filename,'/profiler/time');
missing_Tc = step_Tc - rhs_Tc - adv_field_Tc -...
poisson_Tc - Sapj_Tc -diag_Tc -checkfield_Tc;
total_Tc = step_Tc;
+
+TIME_PER_FCT = [diff(rhs_Tc); diff(adv_field_Tc); diff(poisson_Tc);...
+ diff(Sapj_Tc); diff(checkfield_Tc); diff(diag_Tc); diff(missing_Tc)];
+TIME_PER_FCT = reshape(TIME_PER_FCT,[numel(TIME_PER_FCT)/7,7]);
+
+TIME_PER_STEP = sum(TIME_PER_FCT,2);
+TIME_PER_CPU = trapz(Ts0D(2:end),TIME_PER_STEP);
+
%% Plots
-Y = [diff(rhs_Tc); diff(adv_field_Tc); diff(poisson_Tc);...
+TIME_PER_FCT = [diff(rhs_Tc); diff(adv_field_Tc); diff(poisson_Tc);...
diff(Sapj_Tc); diff(checkfield_Tc); diff(diag_Tc); diff(missing_Tc)];
-Y = reshape(Y,[numel(Y)/7,7]);
+TIME_PER_FCT = reshape(TIME_PER_FCT,[numel(TIME_PER_FCT)/7,7]);
fig = figure;
-p1 = area(Ts0D(2:end),100*Y./diff(total_Tc),'LineStyle','none');
+p1 = area(Ts0D(2:end),TIME_PER_FCT,'LineStyle','none');
legend('Compute RHS','Adv. fields','Poisson','Sapj','Check+Sym','Diag','Missing')
-xlabel('Sim. Time'); ylabel('Step Comp. Time [\%]')
-ylim([0,100]); xlim([Ts0D(2),Ts0D(end)]);
+xlabel('Sim. Time [$\rho_s/c_s$]'); ylabel('Step Comp. Time [s]')
+xlim([Ts0D(2),Ts0D(end)]);
+title(sprintf('Proc. #1, total sim. time ~%.0f [h]',CPUTIME/3600))
hold on
-yyaxis right
-p2 = plot(Ts0D(2:end),diff(total_Tc),'--r','LineWidth',1.0);
-ylabel('Step Comp. Time [s]')
-ylim([0,1.1*max(diff(total_Tc))])
-set(gca,'ycolor','r')
FIGNAME = 'profiler';
-save_figure
\ No newline at end of file
+save_figure
+
+%% Plots
+% fig = figure;
+%
+% p1 = area(Ts0D(2:end),100*TIME_PER_FCT./diff(total_Tc),'LineStyle','none');
+% legend('Compute RHS','Adv. fields','Poisson','Sapj','Check+Sym','Diag','Missing')
+% xlabel('Sim. Time'); ylabel('Step Comp. Time [\%]')
+% ylim([0,100]); xlim([Ts0D(2),Ts0D(end)]);
+% hold on
+% yyaxis right
+% p2 = plot(Ts0D(2:end),diff(total_Tc),'--r','LineWidth',1.0);
+% ylabel('Step Comp. Time [s]')
+% ylim([0,1.1*max(diff(total_Tc))])
+% set(gca,'ycolor','r')
+% FIGNAME = 'profiler';
+% save_figure
\ No newline at end of file
diff --git a/wk/setup.m b/wk/setup.m
index 1d84c183a2a4c43dc59d6a274158ae8722369cfa..0636b57da3df91f5bc76ecf1fc9a4546bff50730 100644
--- a/wk/setup.m
+++ b/wk/setup.m
@@ -2,7 +2,7 @@
SIMDIR = ['../results/',SIMID,'/'];
% Grid parameters
GRID.pmaxe = PMAXE; % Electron Hermite moments
-GRID.jmaxe = JMAXE; % Electron Laguerre moments
+GRID.jmaxe = JMAXE; % Electron Laguerre moments
GRID.pmaxi = PMAXI; % Ion Hermite moments
GRID.jmaxi = JMAXI; % Ion Laguerre moments
GRID.Nr = N * (1-KREQ0) + KREQ0; % r grid resolution
@@ -10,11 +10,7 @@ GRID.Lr = L * (1-KREQ0); % r length
GRID.Nz = N; % z ''
GRID.Lz = L; % z ''
GRID.kpar = KPAR;
-if CANCEL_ODD_P
-GRID.CANCEL_ODD_P = '.true.';
-else
-GRID.CANCEL_ODD_P = '.false.';
-end
+
% Model parameters
MODEL.CO = CO; % Collision operator (0 : L.Bernstein, -1 : Full Coulomb, -2 : Dougherty)
if 0; MODEL.DK = '.true.'; else; MODEL.DK = '.false.';end;
@@ -36,9 +32,6 @@ MODEL.eta_n = ETAN; % source term kappa for HW
MODEL.eta_T = ETAT; % Temperature
MODEL.eta_B = ETAB; % Magnetic
MODEL.lambdaD = LAMBDAD;
-% background phi drive for Kelvin-Helmholtz instability
-MODEL.kr0KH = KR0KH;
-MODEL.A0KH = A0KH;
if A0KH ~= 0; SIMID = [SIMID,'_Nz_',num2str(L/2/pi*KR0KH),'_A_',num2str(A0KH)]; end;
% Time integration and intialization parameters
TIME_INTEGRATION.numerical_scheme = '''RK4''';
@@ -76,8 +69,11 @@ BASIC.RESDIR = [SIMDIR,PARAMS,'/'];
BASIC.PARAMS = PARAMS;
BASIC.SIMID = SIMID;
BASIC.nrun = 1e8;
-BASIC.dt = DT;
+BASIC.dt = DT;
BASIC.tmax = TMAX; %time normalized to 1/omega_pe
+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);
diff --git a/wk/test_parallel.m b/wk/test_parallel.m
index 70eadc474a6c2e72b7ddc8c2c115866cacdc9832..4a6afc8c86dcac22e63dba3a124f16a5b1d3e66a 100644
--- a/wk/test_parallel.m
+++ b/wk/test_parallel.m
@@ -2,6 +2,7 @@ clear all;
addpath(genpath('../matlab')) % ... add
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% Set Up parameters
+CLUSTER.TIME = '00:00:10'; % allocation time hh:mm:ss
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% PHYSICAL PARAMETERS
NU = 1e-1; % Collision frequency
@@ -18,16 +19,17 @@ PMAXE = 2; % Highest electron Hermite polynomial degree
JMAXE = 1; % Highest '' Laguerre ''
PMAXI = 2; % Highest ion Hermite polynomial degree
JMAXI = 1; % Highest '' Laguerre ''
-%% TIME PARAMETERS
-TMAX = 40; % Maximal time unit
+%% TIME PARAMETERS
+TMAX = 20; % Maximal time unit
DT = 2e-2; % Time step
SPS0D = 1/DT; % Sampling per time unit for profiler
SPS2D = 2; % Sampling per time unit for 2D arrays
SPS5D = 2; % Sampling per time unit for 5D arrays
+SPSCP = 1/10; % Sampling per time unit for checkpoints
RESTART = 0; % To restart from last checkpoint
-JOB2LOAD= 1;
+JOB2LOAD= 0;
%% OPTIONS
-SIMID = 'test_sapj_opt'; % Name of the simulation
+SIMID = 'test_runtime'; % Name of the simulation
CO = -1; % Collision operator (0 : L.Bernstein, -1 : Full Coulomb, -2 : Dougherty)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
@@ -37,9 +39,8 @@ NO_E = 0; % Remove electrons dynamic
% DK = 0; % Drift kinetic model (put every kernel_n to 0 except n=0 to 1)
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)
-CANCEL_ODD_P = 0;% Cancels the odd polynomials degree
+LAMBDAD = 0.0;
+NON_LIN = 0 *(1-KREQ0); % activate non-linearity (is cancelled if KREQ0 = 1)
LOAD_MARCONI = 0;
setup