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Commit abfcbe62 authored by Antoine Cyril David Hoffmann's avatar Antoine Cyril David Hoffmann
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Interface for Marconi's cluster

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wk/batch_script.sh 0 → 100644
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View file @ abfcbe62
#!/bin/bash
#SBATCH --time=24:00:00
#SBATCH --nodes=1
#SBATCH --cpus-per-task=1
#SBATCH --ntasks-per-node=16
#SBATCH --mem=32GB
#SBATCH --error=../results/Marconi/512x256_L_100_Pe_2_Je_1_Pi_2_Ji_1_nB_0.5_nN_1_nu_1e-01_FC_mu_5e-04/err.txt
#SBATCH --output=../results/Marconi/512x256_L_100_Pe_2_Je_1_Pi_2_Ji_1_nB_0.5_nN_1_nu_1e-01_FC_mu_5e-04/out.txt
#SBATCH --account=FUA34_GBSedge
#SBATCH --partition=skl_fua_prod
module load intel
module load intelmpi
module load autoload hdf5/1.10.4--intelmpi--2018--binary
module load fftw
srun --cpu-bind=cores ./../bin/helaz
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wk/marconi_run.m 0 → 100644
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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
CLUSTER.NODES = '1'; % MPI process
CLUSTER.CPUPT = '1'; % CPU per task
CLUSTER.NTPN = '16'; % 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
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 = 2; % Highest electron Hermite polynomial degree
JMAXE = 1; % Highest '' Laguerre ''
PMAXI = 2; % Highest ion Hermite polynomial degree
JMAXI = 1; % Highest '' Laguerre ''
%% TIME PARAMETERS
TMAX = 100; % Maximal time unit
DT = 5e-3; % Time step
SPS0D = 1/DT/4; % 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 = 0; % To restart from last checkpoint
JOB2LOAD= 0;
%% OPTIONS
SIMID = 'Marconi'; % Name of the simulation
CO = -1; % Collision operator (0 : L.Bernstein, -1 : Full Coulomb, -2 : Dougherty)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% 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;
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
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');
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wk/marconi_scaling.m 0 → 100644
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%clear all;
addpath(genpath('../matlab')) % ... add
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% Set Up parameters
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% CLUSTER PARAMETERS
CLUSTER.TIME = '12:00:00'; % allocation time hh:mm:ss
CLUSTER.NODES = '1'; % MPI process
CLUSTER.CPUPT = '1'; % CPU per task
CLUSTER.NTPN = '20'; % N tasks per node
CLUSTER.PART = 'prod'; % dbg or prod
CLUSTER.MEM = '10GB'; % Memory
%% PHYSICAL PARAMETERS
NU = 1e-1; % Collision frequency
TAU = 1.0; % e/i temperature ratio
ETAB = 0.0; % Magnetic gradient
ETAN = 1.0; % Density gradient
ETAT = 0.0; % Temperature gradient
MU = 0e-4; % Hyper diffusivity coefficient
NOISE0 = 1.0e-5;
%% GRID PARAMETERS
N = 1024; % Frequency gridpoints (Nkr = N/2)
L = 100; % Size of the squared frequency domain
PMAXE = 6; % Highest electron Hermite polynomial degree
JMAXE = 4; % Highest '' Laguerre ''
PMAXI = 6; % Highest ion Hermite polynomial degree
JMAXI = 4; % Highest '' Laguerre ''
%% TIME PARAMETERS
TMAX = 1; % Maximal time unit
DT = 1e-2; % Time step
SPS0D = 0; % Sampling per time unit for profiler
SPS2D = 0; % Sampling per time unit for 2D arrays
SPS5D = 0; % Sampling per time unit for 5D arrays
RESTART = 0; % To restart from last checkpoint
JOB2LOAD= 0;
%% OPTIONS
SIMID = ['Scaling_np',num2str(CLUSTER.NTPN)]; % Name of the simulation
CO = -2; % Collision operator (0 : L.Bernstein, -1 : Full Coulomb, -2 : Dougherty)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% 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;
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
wk/parallel_scaling.m 0 → 100644
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default_plots_options
%% Strong scaling measurement
% Handwritten results for 256x128, P,J=2,1, Tmax = 20
Results_256_21.np = [ 1, 2, 4, 8, 10, 12];
Results_256_21.time = [2450, 1346, 0680, 0389, 0323, 0307];
% Handwritten results for 512x256, P,J=2,1, Tmax = 5
Results_512_21.np = [ 1, 2, 4, 8, 16, 20, 24];
Results_512_21.time = [3429, 1680, 0842, 0443, 0292, 0322, 0362];
% Handwritten results for 512x256, P,J=3,2, Tmax = 2
Results_512_32.np = [ 1, 2, 4, 8, 16, 20];
Results_512_32.time = [4450, 2267, 1136, 0595, 0363, 0323];
% Handwritten results for 1024x512, P,J=1,1, Tmax = 5 dt = 0.05, mu = 0
Results_1024_11.np = [ 1, 2, 4, 6, 8, 12, 16];
Results_1024_11.time = [1568, 1046, 0490, 0347, 0257, 0221, 219];
% Handwritten results for 1024x512, P,J=2,2, Tmax = 2 dt = 0.05, mu = 0
Results_1024_22.np = [ 1, 2, 4, 6, 8, 10, 12, 16, 20];
Results_1024_22.time = [2391, 1373, 0654, 0457, 0343, 0297, 0274, 0219, 0206];
% Handwritten results for 1024x512, P,J=6,4, Tmax = 2 dt = 0.05, mu = 0
Results_1024_22.np = [ 1, 2, 4, 6, 8, 10, 12, 16, 20];
Results_1024_22.time = [2391, 1373, 0654, 0457, 0343, 0297, 0274, 0219, 0206];
%
fig = figure;
plot(1:24,1:24,'--k','DisplayName','Ideal')
hold on
res = Results_256_21;
plot(res.np,res.time(1)./(res.time),'o-','DisplayName','$256\times128$, $P,J=2,1$');
res = Results_512_21;
plot(res.np,res.time(1)./(res.time),'o-','DisplayName','$512\times256$, $P,J=2,1$');
res = Results_512_32;
plot(res.np,res.time(1)./(res.time),'o-','DisplayName','$512\times256$, $P,J=3,2$');
res = Results_1024_11;
plot(res.np,res.time(1)./(res.time),'o-','DisplayName','$1024\times512$, $P,J=1,1$');
res = Results_1024_22;
plot(res.np,res.time(1)./(res.time),'o-','DisplayName','$1024\times512$, $P,J=2,2$');xlim([1,max(res.np)]);
xlabel('$N_p$'); ylabel('speedup')
legend('show')
title('Strong scaling')
grid on
FIGNAME = [SIMDIR,'strong_scaling.png'];
saveas(fig,FIGNAME);
disp(['Figure saved @ : ',FIGNAME])
%% Weak scaling
% Handwritten results for P,J=2,1, Tmax = 5, dt = 0.01, Nz = Nr
Results_1_64.np = [ 1, 2, 4, 8];
Results_1_64.Nr = [ 64, 90, 128, 180];
Results_1_64.time = [0064, 0074, 0082, 0101];
% Handwritten results for P,J=2,1, Tmax = 5, dt = 0.01, Nz = 128
Results_1_128.np = [ 1, 2, 4, 8, 16];
Results_1_128.Nr = [ 32, 64, 128, 256, 512];
Results_1_128.time = [0032, 0037, 0043, 0049, 0070];
% Handwritten results for Tmax = 5, dt = 0.05, mu = 0, etab =0, Pi=Ji=Pe=Je=1
Results_1_128.np = [ 1, 2, 4, 6, 16];
Results_1_128.N = [ 256, 360, 512, 720, 1024];
Results_1_128.time = [0059, 0072, 0000, 0153, 0070];
%
fig = figure;
plot(Results_1_64.np,Results_1_64.time,'ob','DisplayName','$256\times128$');
hold on
plot(Results_1_64.np,Results_1_64.time(1)*ones(numel(Results_1_64.np)),'--b','DisplayName','Ideal')
plot(Results_1_128.np,Results_1_128.time,'or','DisplayName','$256\times128$');
plot(Results_1_128.np,Results_1_128.time(1)*ones(numel(Results_1_128.np)),'--r','DisplayName','Ideal')
xlim([1,max(res.np)]);
xlabel('$N_p$'); ylabel('CPU time [s]')
legend('show')
title('Weak scaling')
grid on
FIGNAME = [SIMDIR,'weak_scaling.png'];
saveas(fig,FIGNAME);
disp(['Figure saved @ : ',FIGNAME])
wk/run_helaz.sh 0 → 100644
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#!/bin/bash
#SBATCH --time=01:00:00
#SBATCH --nodes=1
#SBATCH --cpus-per-task=1
#SBATCH --ntasks-per-node=1
#SBATCH --mem=10GB
#SBATCH --error=../results/Scaling/1024x512_L_100_Pe_1_Je_1_Pi_1_Ji_1_nB_0_nN_1_nu_1e-01_DG_mu_0e+00/err.txt
#SBATCH --output=../results/Scaling/1024x512_L_100_Pe_1_Je_1_Pi_1_Ji_1_nB_0_nN_1_nu_1e-01_DG_mu_0e+00/out.txt
#SBATCH --account=FUA34_GBSedge
#SBATCH --partition=skl_fua_dbg
#SBATCH --job-name=1024x512_L_100_Pe_1_Je_1_Pi_1_Ji_1_nB_0_nN_1_nu_1e-01_DG_mu_0e+00
module load intel
module load intelmpi
module load autoload hdf5/1.10.4--intelmpi--2018--binary
module load fftw
srun --cpu-bind=cores ./../bin/helaz
\ No newline at end of file
wk/setup_and_run.sh 0 → 100644
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#!/bin/bash
mkdir -p $CINECA_SCRATCH/HeLaZ/wk
mkdir -p $CINECA_SCRATCH/HeLaZ/bin
cd $CINECA_SCRATCH/HeLaZ/wk/
cp $HOME/HeLaZ/wk/fort.90 .
cp $HOME/HeLaZ/wk/batch_script.sh .
cp -r $HOME/HeLaZ/iCa ..
mkdir -p ../results/Marconi/512x256_L_100_Pe_2_Je_1_Pi_2_Ji_1_nB_0.5_nN_1_nu_1e-01_FC_mu_5e-04/
sbatch batch_script.sh
echo $CINECA_SCRATCH/HeLaZ/results/Marconi/512x256_L_100_Pe_2_Je_1_Pi_2_Ji_1_nB_0.5_nN_1_nu_1e-01_FC_mu_5e-04/out.txt
\ No newline at end of file
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