From 4a3e2165642e25e7a95a4797f25f1b954a661cb5 Mon Sep 17 00:00:00 2001
From: Antoine Hoffmann <antoine.hoffmann@epfl.ch>
Date: Mon, 10 Oct 2022 11:17:19 +0200
Subject: [PATCH] Include a folder for saving useful scripts
---
.gitignore | 3 +-
scripts/fort_00.90 | 85 +++++++++++++++++++++++++++++++++++++++++
scripts/job_pipeline.sh | 44 +++++++++++++++++++++
scripts/submit_00.cmd | 13 +++++++
4 files changed, 144 insertions(+), 1 deletion(-)
create mode 100644 scripts/fort_00.90
create mode 100644 scripts/job_pipeline.sh
create mode 100644 scripts/submit_00.cmd
diff --git a/.gitignore b/.gitignore
index cf060981..35b853be 100644
--- a/.gitignore
+++ b/.gitignore
@@ -41,4 +41,5 @@ Gallery/
.vscode/settings.json
*figure*
*results*
-out*
+out*
+!scripts/*
diff --git a/scripts/fort_00.90 b/scripts/fort_00.90
new file mode 100644
index 00000000..ae9b19ba
--- /dev/null
+++ b/scripts/fort_00.90
@@ -0,0 +1,85 @@
+&BASIC
+ nrun = 100000000
+ dt = 0.01
+ tmax = 500
+ maxruntime = 60 ! 1h 14400 !4h
+/
+&GRID
+ pmaxe = 6
+ jmaxe = 3
+ pmaxi = 6
+ jmaxi = 3
+ Nx = 200
+ Lx = 120
+ Ny = 32
+ Ly = 60
+ Nz = 1
+ SG = .f.
+/
+&GEOMETRY
+ geom = 'Z-pinch'
+ q0 = 0
+ shear = 0
+ eps = 0
+/
+&OUTPUT_PAR
+ nsave_0d = 10
+ nsave_1d = -1
+ nsave_2d = -1
+ nsave_3d = 100
+ nsave_5d = 10000
+ write_doubleprecision = .t.
+ write_gamma = .t.
+ write_hf = .t.
+ write_phi = .t.
+ write_Na00 = .t.
+ write_Napj = .t.
+ write_Sapj = .f.
+ write_dens = .t.
+ write_temp = .t.
+ job2load = -1
+/
+&MODEL_PAR
+ ! Collisionality
+ CLOS = 0
+ NL_CLOS = 0
+ LINEARITY = 'nonlinear'
+ KIN_E = .t.
+ mu_x = 1.0
+ mu_y = 1.0
+ N_HD = 4
+ mu_z = 0.0
+ mu_p = 0
+ mu_j = 0
+ nu = 0.01
+ tau_e = 1
+ tau_i = 1
+ sigma_e = 0.023338
+ sigma_i = 1
+ q_e = -1
+ q_i = 1
+ K_Ne = 1.7
+ K_Ni = 1.7
+ K_Te = 0.425
+ K_Ti = 0.425
+ GradB = 1
+ CurvB = 1
+ lambdaD = 0
+/
+&COLLISION_PAR
+ collision_model = 'LD'
+ gyrokin_CO = .true.
+ interspecies = .true.
+ mat_file = 'LDGK_P10_J5_dk_5e-2_km_5_NFLR_30.h5'
+ collision_kcut = 1.8
+/
+&INITIAL_CON
+ INIT_OPT = 'phi'
+ ACT_ON_MODES = 'donothing'
+ init_background = 0
+ init_noiselvl = 0.001
+ iseed = 42
+/
+&TIME_INTEGRATION_PAR
+ numerical_scheme = 'RK4'
+/
diff --git a/scripts/job_pipeline.sh b/scripts/job_pipeline.sh
new file mode 100644
index 00000000..7cf4f334
--- /dev/null
+++ b/scripts/job_pipeline.sh
@@ -0,0 +1,44 @@
+#! /bin/bash
+#This script automatizes the launch of multiple job with chain dependency.
+nu_=0.01
+dnu=0.01
+
+Tm_=2000
+dTm=2000
+
+# First submit
+lastji=$(sbatch submit_00.cmd)
+lastjid=${lastji##* }
+echo $lastji
+#echo $lastjid
+
+for i in {1..1}; do
+ # Setup indices of job id (current and previous one)
+ im1=$(awk "BEGIN {print $i-1}")
+ idm1=$(printf '%02d' $im1)
+ id=$(printf '%02d' $i)
+
+ # Create new submit file from older one
+ awk -v "ID=$id" '{
+ if (NR == 8) print "#SBATCH --error=err_"ID".txt";
+ else if (NR == 9) print "#SBATCH --output=out_"ID".txt";
+ else if (NR == 12) print "srun --cpu-bind=cores ./gyacomo 2 24 1 "ID;
+ else print $0}' submit_$idm1.cmd > submit_$id.cmd
+
+ # Create new fort file from older one
+ awk -v "NU=$nu_" -v "TM=$Tm_" -v "J2L=$im1" '{
+ if (NR == 04) print " tmax = "TM;
+ else if (NR == 40) print " job2load = "J2L;
+ else if (NR == 54) print " nu = "NU;
+ else print $0}' fort_$idm1.90 > fort_$id.90
+
+ # Retrieve last jobid and launch next job with dep
+ lastji=$(sbatch --dependency=afterok:$lastjid submit_0$i.cmd)
+ lastjid=${lastji##* }
+ echo $lastjid
+
+ # Increment variables
+ nu_=$(awk "BEGIN {print $nu_+$dnu}")
+ Tm_=$(awk "BEGIN {print $Tm_+$dTm}")
+done
+
diff --git a/scripts/submit_00.cmd b/scripts/submit_00.cmd
new file mode 100644
index 00000000..a08f8813
--- /dev/null
+++ b/scripts/submit_00.cmd
@@ -0,0 +1,13 @@
+#!/bin/bash
+#SBATCH --job-name=test_pipe
+#SBATCH --time=00:02:00
+#SBATCH --nodes=1
+#SBATCH --cpus-per-task=1
+#SBATCH --ntasks-per-node=48
+#SBATCH --mem=64GB
+#SBATCH --error=err_00.txt
+#SBATCH --output=out_00.txt
+#SBATCH --account=FUA36_TSVVT422
+#SBATCH --partition=skl_fua_dbg
+srun --cpu-bind=cores ./gyacomo 2 24 1 0
+
--
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