Demo sidewall convection (snek5000-cbox solver)#
A more advanced script adapted for a particular instability#
This example is based on the study From onset of unsteadiness to chaos in a differentially heated square cavity by Le Quéré & Behnia (1998).
The configuration is convection in a 2D square cavity heated and cooled at two opposite sides. The control parameters are the Prandtl number \(Pr= 0.71\) and the Rayleigh number \(Ra = 2 \times 10^{8}\). The mesh size is \(64 \times 64\) (8 elements in each direction).
The simulation will be carried out with the script docs/examples/scripts/tuto_cbox.py (code shown just below). Note that this script is more complicated than for the previous tutorials. Here, we want to demonstrate that it is possible to check what happen in the simulation from Python and to stop the simulation depending on its outputs. We know that for some moderate Rayleigh number values, the side wall convection in a box first reach a quasi-steady state from which emerges an oscillatory instability. Here, we want to stop the simulation as soon as the linear instability starts to saturate, i.e. as soon as the growth of the unstable mode becomes slower than exponential.
We want to have \(25\) probes (using Nek5000 history points feature) to record the signals of the different physical variables and to use these probe signals to monitor and postprocess the simulation.
import builtins
import os
import signal
from time import perf_counter, sleep
import numpy as np
from scipy.signal import argrelmax
from snek5000_cbox.solver import Simul
from fluiddyn.util import time_as_str
params = Simul.create_default_params()
aspect_ratio = 1.0
params.prandtl = 0.71
# The onset of oscillatory flow for aspect ratio 1.0 is at Ra_c = 1.825e8
params.Ra_side = 2e8
params.output.sub_directory = "examples_snek/tuto"
params.oper.dim = 2
params.oper.nproc_min = 2
nb_elements = ny = 8
params.oper.ny = nb_elements
nx = params.oper.nx = int(nb_elements / aspect_ratio)
Ly = params.oper.Ly
Lx = params.oper.Lx = Ly / aspect_ratio
order = params.oper.elem.order = params.oper.elem.order_out = 8
params.oper.mesh_stretch_factor = 0.1 # zero means regular
params.short_name_type_run = f"Ra{params.Ra_side:.3e}_{nx*order}x{ny*order}"
# creation of the coordinates of the points saved by history points
n1d = 5
small = Lx / 10
xs = np.linspace(0, Lx, n1d)
xs[0] = small
xs[-1] = Lx - small
ys = np.linspace(0, Ly, n1d)
ys[0] = small
ys[-1] = Ly - small
coords = [(x, y) for x in xs for y in ys]
params.output.history_points.coords = coords
params.oper.max.hist = len(coords) + 1
params.nek.velocity.residual_tol = 1e-08
params.nek.pressure.residual_tol = 1e-05
params.nek.general.end_time = 1000
params.nek.general.stop_at = "endTime"
params.nek.general.target_cfl = 2.0
params.nek.general.time_stepper = "BDF3"
params.nek.general.extrapolation = "OIFS"
params.nek.general.write_control = "runTime"
params.nek.general.write_interval = 50
params.output.history_points.write_interval = 10
if __name__ == "__main__":
sim = Simul(params)
# to save the PID of the simulation (a number associated with the process)
sim.output.write_snakemake_config(
custom_env_vars={"MPIEXEC_FLAGS": "--report-pid PID.txt --oversubscribe"}
)
# run the simulation in the background (non blocking call)
sim.make.exec("run", nproc=2)
pid_file = sim.path_run / "PID.txt"
# we wait for the simulation to be started and the PID file to be created
n = 0
while not pid_file.exists():
sleep(1)
n += 1
if n > 60:
raise RuntimeError(f"{pid_file} does not exist.")
with open(pid_file) as file:
pid = int(file.read().strip())
# we know the PID of the simulation so we can control it!
# a simple way to print in stdout and in a file
path_log_py = sim.path_run / f"log_py_{time_as_str()}.txt"
def print(*args, sep=" ", end="\n", **kwargs):
builtins.print(*args, **kwargs)
with open(path_log_py, "a") as file:
file.write(sep.join(str(arg) for arg in args) + end)
print(f"{pid = }")
def check_running():
"""Check for the existence of a running process"""
try:
os.kill(pid, 0)
except OSError:
return False
else:
return True
while check_running():
sleep(2)
t0 = perf_counter()
coords, df = sim.output.history_points.load_1point(
index_point=12, key="temperature"
)
t_last = df.time.max()
print(
f"{time_as_str()}, {t_last = :.2f}: "
f"history_points loaded in {perf_counter() - t0:.2f} s"
)
if t_last < 500:
continue
temperature = df.temperature.to_numpy()
times = df.time.to_numpy()
temperature = temperature[times > 500]
times = times[times > 500]
# we know that there are oscillations growing exponentially
# we look for the positive maxima of the signal
indices_maxima = argrelmax(temperature)
temp_maxima = temperature[indices_maxima]
temp_maxima = temp_maxima[temp_maxima > 0]
# similar to a second order derivative
diff_maxima = np.diff(np.diff(temp_maxima))
if any(diff_maxima < 0):
# as soon as the growth starts to saturate
print(
f"Saturation of the instability detected at t = {t_last}\n"
"Terminate simulation."
)
os.kill(pid, signal.SIGTERM)
break
In normal life, we would just execute this script with something like
python tuto_cbox.py.
command = "python3 examples/scripts/tuto_cbox.py"
However, in this notebook, we need a bit more code. How we execute this command is very specific to these tutorials written as notebooks so you can just look at the output of this cell.
Show code cell source
from subprocess import run, PIPE, STDOUT
from time import perf_counter
print("Running the script tuto_cbox.py... (It can take few minutes.)")
t_start = perf_counter()
process = run(
command.split(), check=True, text=True, stdout=PIPE, stderr=STDOUT
)
print(f"Script executed in {perf_counter() - t_start:.2f} s")
lines = process.stdout.split("\n")
Running the script tuto_cbox.py... (It can take few minutes.)
Script executed in 161.83 s
The simulation is done! We are going to look at its output (which is now in a variable
lines). However, be prepared to get something long because Nek5000 is very verbose.
For readability of this tutorial, the output is hidden by default (click to show it):
print("\n".join(lines))
Show code cell output
INFO: session_id: 0
INFO: Writing params files... /home/docs/Sim_data/examples_snek/tuto/cbox_Ra2.000e+08_64x64_8x8_V1.x1._2023-08-24_07-52-10/cbox.par, params_simul.xml, info_solver.xml
INFO: sim: <class 'snek5000_cbox.solver.SimulCbox'>
sim.oper: <class 'snek5000.operators.Operators'>
sim.output.print_stdout: <class 'snek5000.output.print_stdout.PrintStdOut'>
sim.output.phys_fields: <class 'snek5000.output.phys_fields.PhysFields'>
sim.output.history_points: <class 'snek5000.output.history_points.HistoryPoints'>
sim.output.remaining_clock_time: <class 'snek5000.output.remaining_clock_time.RemainingClockTime'>
sim.output: <class 'snek5000_cbox.output.OutputCbox'>
sim.make: <class 'snek5000.make.Make'>
INFO: Writing box file... /home/docs/Sim_data/examples_snek/tuto/cbox_Ra2.000e+08_64x64_8x8_V1.x1._2023-08-24_07-52-10/cbox.box
INFO: Writing SIZE file... /home/docs/Sim_data/examples_snek/tuto/cbox_Ra2.000e+08_64x64_8x8_V1.x1._2023-08-24_07-52-10/SIZE
Changing to shadow directory: /home/docs/Sim_data/examples_snek/tuto/cbox_Ra2.000e+08_64x64_8x8_V1.x1._2023-08-24_07-52-10
Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cores: 1 (use --cores to define parallelism)
Rules claiming more threads will be scaled down.
Job stats:
job count
-------------------------- -------
compile 1
internal_generate_box 1
internal_generate_makefile 1
internal_generate_map 1
internal_generate_session 1
internal_move_box 1
run 1
total 7
Select jobs to execute...
[Thu Aug 24 07:52:11 2023]
rule internal_generate_box:
input: cbox.box, /home/docs/Nek5000/bin/genbox
output: box.re2
jobid: 2
reason: Missing output files: box.re2
resources: tmpdir=/tmp
input file name:
-2 spatial dimension (dim<0 will create box.re2)
2 number of fields
T T F 2 2.0000000000000000
1 i1#
1 i1#
1 i1#
1 i1#
1 i1#
1 i1#
1 i1#
1 i1#
1 i1#
1 i1#
1 i1#
1 i1#
1 i1#
1 i1#
1 i1#
1 i1#
1 i1#
1 i1#
Box
-8 -8 nelx nely nelz
Reading 64 = 8 8 8 elements for box 1.
Reading 2 =
0.0000 1.0000 1.0000 x0 x1 ratio
0.0000 1.0000 1.0000 y0 y1 ratio
W ,W ,W ,W Velocity BCs
t ,t ,I ,I Temperature / scalar BCs
Beginning construction of box.re2
64 elements will be created for 1 boxes.
[Thu Aug 24 07:52:11 2023]
Finished job 2.
1 of 7 steps (14%) done
Select jobs to execute...
[Thu Aug 24 07:52:11 2023]
rule internal_move_box:
input: box.re2
output: cbox.re2
jobid: 1
reason: Missing output files: cbox.re2; Input files updated by another job: box.re2
resources: tmpdir=/tmp
[Thu Aug 24 07:52:11 2023]
Finished job 1.
2 of 7 steps (29%) done
Select jobs to execute...
[Thu Aug 24 07:52:11 2023]
rule internal_generate_map:
input: cbox.re2, /home/docs/Nek5000/bin/genmap
output: cbox.ma2
jobid: 3
reason: Missing output files: cbox.ma2; Input files updated by another job: cbox.re2
resources: tmpdir=/tmp, tolerance=0.01
Input .rea / .re2 name:
reading cbox.re2
Input mesh tolerance (default 0.2):
NOTE: smaller is better, but generous is more forgiving for bad meshes.
reading mesh data ...
start locglob_lexico: 4 64 256 1.0000000000000000E-002
locglob: 1 1 256
locglob: 2 9 256
locglob: 1 81 256
locglob: 2 81 256
done locglob_lexico: 81 81 256 4
start periodic vtx: 64 81
done periodic vtx
start rec_bisect: 64
done: 1.6%
done: 3.1%
done: 4.7%
done: 6.2%
done: 7.8%
done: 9.4%
done: 90.6%
done: 92.2%
done: 93.8%
done: 95.3%
done: 96.9%
done: 98.4%
done: 100.0%
done rec_bisect
writing cbox.ma2
[Thu Aug 24 07:52:11 2023]
Finished job 3.
3 of 7 steps (43%) done
Select jobs to execute...
[Thu Aug 24 07:52:11 2023]
rule internal_generate_session:
input: cbox.re2, cbox.ma2, cbox.par
output: SESSION.NAME
jobid: 4
reason: Missing output files: SESSION.NAME; Input files updated by another job: cbox.re2, cbox.ma2
resources: tmpdir=/tmp
Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cores: 1 (use --cores to define parallelism)
Rules claiming more threads will be scaled down.
Select jobs to execute...
[Thu Aug 24 07:52:12 2023]
Finished job 4.
4 of 7 steps (57%) done
Select jobs to execute...
[Thu Aug 24 07:52:12 2023]
rule internal_generate_makefile:
input: cbox.re2, cbox.ma2, cbox.usr, /home/docs/Nek5000/bin/nekconfig
output: makefile, .state
jobid: 6
reason: Missing output files: makefile; Input files updated by another job: cbox.re2, cbox.ma2
resources: tmpdir=/tmp
generating makefile ... done
[Thu Aug 24 07:52:12 2023]
Finished job 6.
5 of 7 steps (71%) done
Select jobs to execute...
[Thu Aug 24 07:52:12 2023]
rule compile:
input: SIZE, cbox.usr, makefile_usr.inc, makefile, /home/docs/Nek5000/3rd_party/gslib/lib/libgs.a, /home/docs/Nek5000/3rd_party/blasLapack/libblasLapack.a
output: nek5000
jobid: 5
reason: Missing output files: nek5000; Input files updated by another job: makefile
resources: tmpdir=/tmp
mpif77 -c -O2 -cpp -fdefault-real-8 -fdefault-double-8 -w -std=legacy -march=native -mcmodel=medium -std=legacy -w -Itoolbox -DMPI -DUNDERSCORE -DGLOBAL_LONG_LONG -DTIMER -I/home/docs/Sim_data/examples_snek/tuto/cbox_Ra2.000e+08_64x64_8x8_V1.x1._2023-08-24_07-52-10 -I/home/docs/Nek5000/core -I./ -I/home/docs/Nek5000/core/experimental -I/home/docs/Sim_data/examples_snek/tuto/cbox_Ra2.000e+08_64x64_8x8_V1.x1._2023-08-24_07-52-10/obj /home/docs/Nek5000/core/drive1.f -o /home/docs/Sim_data/examples_snek/tuto/cbox_Ra2.000e+08_64x64_8x8_V1.x1._2023-08-24_07-52-10/obj/drive1.o
mpif77 -c -O2 -cpp -fdefault-real-8 -fdefault-double-8 -w -std=legacy -march=native -mcmodel=medium -std=legacy -w -Itoolbox -DMPI -DUNDERSCORE -DGLOBAL_LONG_LONG -DTIMER -I/home/docs/Sim_data/examples_snek/tuto/cbox_Ra2.000e+08_64x64_8x8_V1.x1._2023-08-24_07-52-10 -I/home/docs/Nek5000/core -I./ -I/home/docs/Nek5000/core/experimental -I/home/docs/Sim_data/examples_snek/tuto/cbox_Ra2.000e+08_64x64_8x8_V1.x1._2023-08-24_07-52-10/obj /home/docs/Nek5000/core/drive2.f -o /home/docs/Sim_data/examples_snek/tuto/cbox_Ra2.000e+08_64x64_8x8_V1.x1._2023-08-24_07-52-10/obj/drive2.o
mpif77 -c -O2 -cpp -fdefault-real-8 -fdefault-double-8 -w -std=legacy -march=native -mcmodel=medium -std=legacy -w -Itoolbox -DMPI -DUNDERSCORE -DGLOBAL_LONG_LONG -DTIMER -I/home/docs/Sim_data/examples_snek/tuto/cbox_Ra2.000e+08_64x64_8x8_V1.x1._2023-08-24_07-52-10 -I/home/docs/Nek5000/core -I./ -I/home/docs/Nek5000/core/experimental -I/home/docs/Sim_data/examples_snek/tuto/cbox_Ra2.000e+08_64x64_8x8_V1.x1._2023-08-24_07-52-10/obj /home/docs/Nek5000/core/plan5.f -o /home/docs/Sim_data/examples_snek/tuto/cbox_Ra2.000e+08_64x64_8x8_V1.x1._2023-08-24_07-52-10/obj/plan5.o
mpif77 -c -O2 -cpp -fdefault-real-8 -fdefault-double-8 -w -std=legacy -march=native -mcmodel=medium -std=legacy -w -Itoolbox -DMPI -DUNDERSCORE -DGLOBAL_LONG_LONG -DTIMER -I/home/docs/Sim_data/examples_snek/tuto/cbox_Ra2.000e+08_64x64_8x8_V1.x1._2023-08-24_07-52-10 -I/home/docs/Nek5000/core -I./ -I/home/docs/Nek5000/core/experimental -I/home/docs/Sim_data/examples_snek/tuto/cbox_Ra2.000e+08_64x64_8x8_V1.x1._2023-08-24_07-52-10/obj /home/docs/Nek5000/core/plan4.f -o /home/docs/Sim_data/examples_snek/tuto/cbox_Ra2.000e+08_64x64_8x8_V1.x1._2023-08-24_07-52-10/obj/plan4.o
mpif77 -c -O2 -cpp -fdefault-real-8 -fdefault-double-8 -w -std=legacy -march=native -mcmodel=medium -std=legacy -w -Itoolbox -DMPI -DUNDERSCORE -DGLOBAL_LONG_LONG -DTIMER -I/home/docs/Sim_data/examples_snek/tuto/cbox_Ra2.000e+08_64x64_8x8_V1.x1._2023-08-24_07-52-10 -I/home/docs/Nek5000/core -I./ -I/home/docs/Nek5000/core/experimental -I/home/docs/Sim_data/examples_snek/tuto/cbox_Ra2.000e+08_64x64_8x8_V1.x1._2023-08-24_07-52-10/obj /home/docs/Nek5000/core/bdry.f -o /home/docs/Sim_data/examples_snek/tuto/cbox_Ra2.000e+08_64x64_8x8_V1.x1._2023-08-24_07-52-10/obj/bdry.o
mpif77 -c -O2 -cpp -fdefault-real-8 -fdefault-double-8 -w -std=legacy -march=native -mcmodel=medium -std=legacy -w -Itoolbox -DMPI -DUNDERSCORE -DGLOBAL_LONG_LONG -DTIMER -I/home/docs/Sim_data/examples_snek/tuto/cbox_Ra2.000e+08_64x64_8x8_V1.x1._2023-08-24_07-52-10 -I/home/docs/Nek5000/core -I./ -I/home/docs/Nek5000/core/experimental -I/home/docs/Sim_data/examples_snek/tuto/cbox_Ra2.000e+08_64x64_8x8_V1.x1._2023-08-24_07-52-10/obj /home/docs/Nek5000/core/coef.f -o /home/docs/Sim_data/examples_snek/tuto/cbox_Ra2.000e+08_64x64_8x8_V1.x1._2023-08-24_07-52-10/obj/coef.o
mpif77 -c -O2 -cpp -fdefault-real-8 -fdefault-double-8 -w -std=legacy -march=native -mcmodel=medium -std=legacy -w -Itoolbox -DMPI -DUNDERSCORE -DGLOBAL_LONG_LONG -DTIMER -I/home/docs/Sim_data/examples_snek/tuto/cbox_Ra2.000e+08_64x64_8x8_V1.x1._2023-08-24_07-52-10 -I/home/docs/Nek5000/core -I./ -I/home/docs/Nek5000/core/experimental -I/home/docs/Sim_data/examples_snek/tuto/cbox_Ra2.000e+08_64x64_8x8_V1.x1._2023-08-24_07-52-10/obj /home/docs/Nek5000/core/conduct.f -o /home/docs/Sim_data/examples_snek/tuto/cbox_Ra2.000e+08_64x64_8x8_V1.x1._2023-08-24_07-52-10/obj/conduct.o
mpif77 -c -O2 -cpp -fdefault-real-8 -fdefault-double-8 -w -std=legacy -march=native -mcmodel=medium -std=legacy -w -Itoolbox -DMPI -DUNDERSCORE -DGLOBAL_LONG_LONG -DTIMER -I/home/docs/Sim_data/examples_snek/tuto/cbox_Ra2.000e+08_64x64_8x8_V1.x1._2023-08-24_07-52-10 -I/home/docs/Nek5000/core -I./ -I/home/docs/Nek5000/core/experimental -I/home/docs/Sim_data/examples_snek/tuto/cbox_Ra2.000e+08_64x64_8x8_V1.x1._2023-08-24_07-52-10/obj /home/docs/Nek5000/core/connect1.f -o /home/docs/Sim_data/examples_snek/tuto/cbox_Ra2.000e+08_64x64_8x8_V1.x1._2023-08-24_07-52-10/obj/connect1.o
mpif77 -c -O2 -cpp -fdefault-real-8 -fdefault-double-8 -w -std=legacy -march=native -mcmodel=medium -std=legacy -w -Itoolbox -DMPI -DUNDERSCORE -DGLOBAL_LONG_LONG -DTIMER -I/home/docs/Sim_data/examples_snek/tuto/cbox_Ra2.000e+08_64x64_8x8_V1.x1._2023-08-24_07-52-10 -I/home/docs/Nek5000/core -I./ -I/home/docs/Nek5000/core/experimental -I/home/docs/Sim_data/examples_snek/tuto/cbox_Ra2.000e+08_64x64_8x8_V1.x1._2023-08-24_07-52-10/obj /home/docs/Nek5000/core/connect2.f -o /home/docs/Sim_data/examples_snek/tuto/cbox_Ra2.000e+08_64x64_8x8_V1.x1._2023-08-24_07-52-10/obj/connect2.o
mpif77 -c -O2 -cpp -fdefault-real-8 -fdefault-double-8 -w -std=legacy -march=native -mcmodel=medium -std=legacy -w -Itoolbox -DMPI -DUNDERSCORE -DGLOBAL_LONG_LONG -DTIMER -I/home/docs/Sim_data/examples_snek/tuto/cbox_Ra2.000e+08_64x64_8x8_V1.x1._2023-08-24_07-52-10 -I/home/docs/Nek5000/core -I./ -I/home/docs/Nek5000/core/experimental -I/home/docs/Sim_data/examples_snek/tuto/cbox_Ra2.000e+08_64x64_8x8_V1.x1._2023-08-24_07-52-10/obj /home/docs/Nek5000/core/dssum.f -o /home/docs/Sim_data/examples_snek/tuto/cbox_Ra2.000e+08_64x64_8x8_V1.x1._2023-08-24_07-52-10/obj/dssum.o
mpif77 -c -O2 -cpp -fdefault-real-8 -fdefault-double-8 -w -std=legacy -march=native -mcmodel=medium -std=legacy -w -Itoolbox -DMPI -DUNDERSCORE -DGLOBAL_LONG_LONG -DTIMER -I/home/docs/Sim_data/examples_snek/tuto/cbox_Ra2.000e+08_64x64_8x8_V1.x1._2023-08-24_07-52-10 -I/home/docs/Nek5000/core -I./ -I/home/docs/Nek5000/core/experimental -I/home/docs/Sim_data/examples_snek/tuto/cbox_Ra2.000e+08_64x64_8x8_V1.x1._2023-08-24_07-52-10/obj /home/docs/Nek5000/core/eigsolv.f -o /home/docs/Sim_data/examples_snek/tuto/cbox_Ra2.000e+08_64x64_8x8_V1.x1._2023-08-24_07-52-10/obj/eigsolv.o
mpif77 -c -O2 -cpp -fdefault-real-8 -fdefault-double-8 -w -std=legacy -march=native -mcmodel=medium -std=legacy -w -Itoolbox -DMPI -DUNDERSCORE -DGLOBAL_LONG_LONG -DTIMER -I/home/docs/Sim_data/examples_snek/tuto/cbox_Ra2.000e+08_64x64_8x8_V1.x1._2023-08-24_07-52-10 -I/home/docs/Nek5000/core -I./ -I/home/docs/Nek5000/core/experimental -I/home/docs/Sim_data/examples_snek/tuto/cbox_Ra2.000e+08_64x64_8x8_V1.x1._2023-08-24_07-52-10/obj /home/docs/Nek5000/core/gauss.f -o /home/docs/Sim_data/examples_snek/tuto/cbox_Ra2.000e+08_64x64_8x8_V1.x1._2023-08-24_07-52-10/obj/gauss.o
mpif77 -c -O2 -cpp -fdefault-real-8 -fdefault-double-8 -w -std=legacy -march=native -mcmodel=medium -std=legacy -w -Itoolbox -DMPI -DUNDERSCORE -DGLOBAL_LONG_LONG -DTIMER -I/home/docs/Sim_data/examples_snek/tuto/cbox_Ra2.000e+08_64x64_8x8_V1.x1._2023-08-24_07-52-10 -I/home/docs/Nek5000/core -I./ -I/home/docs/Nek5000/core/experimental -I/home/docs/Sim_data/examples_snek/tuto/cbox_Ra2.000e+08_64x64_8x8_V1.x1._2023-08-24_07-52-10/obj /home/docs/Nek5000/core/genxyz.f -o /home/docs/Sim_data/examples_snek/tuto/cbox_Ra2.000e+08_64x64_8x8_V1.x1._2023-08-24_07-52-10/obj/genxyz.o
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mpicc -c -O2 -march=native -w -DMPI -DUNDERSCORE -DGLOBAL_LONG_LONG -DTIMER -I/home/docs/Nek5000/core -I./ -I/home/docs/Nek5000/core/experimental -I/home/docs/Sim_data/examples_snek/tuto/cbox_Ra2.000e+08_64x64_8x8_V1.x1._2023-08-24_07-52-10/obj /home/docs/Nek5000/core/chelpers.c -o /home/docs/Sim_data/examples_snek/tuto/cbox_Ra2.000e+08_64x64_8x8_V1.x1._2023-08-24_07-52-10/obj/chelpers.o
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mpicc -c -O2 -march=native -w -DMPI -DUNDERSCORE -DGLOBAL_LONG_LONG -DTIMER -I/home/docs/Nek5000/core -I./ -I/home/docs/Nek5000/core/experimental -I/home/docs/Sim_data/examples_snek/tuto/cbox_Ra2.000e+08_64x64_8x8_V1.x1._2023-08-24_07-52-10/obj /home/docs/Nek5000/core/3rd_party/finiparser.c -o /home/docs/Sim_data/examples_snek/tuto/cbox_Ra2.000e+08_64x64_8x8_V1.x1._2023-08-24_07-52-10/obj/finiparser.o
mpicc -c -O2 -march=native -w -DMPI -DUNDERSCORE -DGLOBAL_LONG_LONG -DTIMER -I/home/docs/Nek5000/core -I./ -I/home/docs/Nek5000/core/experimental -I/home/docs/Sim_data/examples_snek/tuto/cbox_Ra2.000e+08_64x64_8x8_V1.x1._2023-08-24_07-52-10/obj /home/docs/Nek5000/core/3rd_party/iniparser.c -o /home/docs/Sim_data/examples_snek/tuto/cbox_Ra2.000e+08_64x64_8x8_V1.x1._2023-08-24_07-52-10/obj/iniparser.o
mpicc -c -O2 -march=native -w -DMPI -DUNDERSCORE -DGLOBAL_LONG_LONG -DTIMER -I/home/docs/Nek5000/core -I./ -I/home/docs/Nek5000/core/experimental -I/home/docs/Sim_data/examples_snek/tuto/cbox_Ra2.000e+08_64x64_8x8_V1.x1._2023-08-24_07-52-10/obj /home/docs/Nek5000/core/3rd_party/dictionary.c -o /home/docs/Sim_data/examples_snek/tuto/cbox_Ra2.000e+08_64x64_8x8_V1.x1._2023-08-24_07-52-10/obj/dictionary.o
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mpicc -c -O2 -march=native -w -DMPI -DUNDERSCORE -DGLOBAL_LONG_LONG -DTIMER -I/home/docs/Nek5000/core -I./ -I/home/docs/Nek5000/core/experimental -I/home/docs/Sim_data/examples_snek/tuto/cbox_Ra2.000e+08_64x64_8x8_V1.x1._2023-08-24_07-52-10/obj -I/home/docs/Nek5000/3rd_party/gslib/include /home/docs/Nek5000/core/fcrs.c -o /home/docs/Sim_data/examples_snek/tuto/cbox_Ra2.000e+08_64x64_8x8_V1.x1._2023-08-24_07-52-10/obj/fcrs.o
mpicc -c -O2 -march=native -w -DMPI -DUNDERSCORE -DGLOBAL_LONG_LONG -DTIMER -I/home/docs/Nek5000/core -I./ -I/home/docs/Nek5000/core/experimental -I/home/docs/Sim_data/examples_snek/tuto/cbox_Ra2.000e+08_64x64_8x8_V1.x1._2023-08-24_07-52-10/obj -I/home/docs/Nek5000/3rd_party/gslib/include /home/docs/Nek5000/core/crs_xxt.c -o /home/docs/Sim_data/examples_snek/tuto/cbox_Ra2.000e+08_64x64_8x8_V1.x1._2023-08-24_07-52-10/obj/crs_xxt.o
mpicc -c -O2 -march=native -w -DMPI -DUNDERSCORE -DGLOBAL_LONG_LONG -DTIMER -I/home/docs/Nek5000/core -I./ -I/home/docs/Nek5000/core/experimental -I/home/docs/Sim_data/examples_snek/tuto/cbox_Ra2.000e+08_64x64_8x8_V1.x1._2023-08-24_07-52-10/obj -I/home/docs/Nek5000/3rd_party/gslib/include /home/docs/Nek5000/core/crs_amg.c -o /home/docs/Sim_data/examples_snek/tuto/cbox_Ra2.000e+08_64x64_8x8_V1.x1._2023-08-24_07-52-10/obj/crs_amg.o
mpicc -c -O2 -march=native -w -DMPI -DUNDERSCORE -DGLOBAL_LONG_LONG -DTIMER -I/home/docs/Nek5000/core -I./ -I/home/docs/Nek5000/core/experimental -I/home/docs/Sim_data/examples_snek/tuto/cbox_Ra2.000e+08_64x64_8x8_V1.x1._2023-08-24_07-52-10/obj -I/home/docs/Nek5000/3rd_party/gslib/include /home/docs/Nek5000/core/experimental/fem_amg_preco.c -o /home/docs/Sim_data/examples_snek/tuto/cbox_Ra2.000e+08_64x64_8x8_V1.x1._2023-08-24_07-52-10/obj/fem_amg_preco.o
mpicc -c -O2 -march=native -w -DMPI -DUNDERSCORE -DGLOBAL_LONG_LONG -DTIMER -I/home/docs/Nek5000/core -I./ -I/home/docs/Nek5000/core/experimental -I/home/docs/Sim_data/examples_snek/tuto/cbox_Ra2.000e+08_64x64_8x8_V1.x1._2023-08-24_07-52-10/obj -I/home/docs/Nek5000/3rd_party/gslib/include /home/docs/Nek5000/core/experimental/crs_hypre.c -o /home/docs/Sim_data/examples_snek/tuto/cbox_Ra2.000e+08_64x64_8x8_V1.x1._2023-08-24_07-52-10/obj/crs_hypre.o
mpicc -c -O2 -march=native -w -DMPI -DUNDERSCORE -DGLOBAL_LONG_LONG -DTIMER -I/home/docs/Nek5000/core -I./ -I/home/docs/Nek5000/core/experimental -I/home/docs/Sim_data/examples_snek/tuto/cbox_Ra2.000e+08_64x64_8x8_V1.x1._2023-08-24_07-52-10/obj -I/home/docs/Nek5000/3rd_party/gslib/include /home/docs/Nek5000/core/partitioner.c -o /home/docs/Sim_data/examples_snek/tuto/cbox_Ra2.000e+08_64x64_8x8_V1.x1._2023-08-24_07-52-10/obj/partitioner.o
mpif77 -c -O3 -cpp -fdefault-real-8 -fdefault-double-8 -w -std=legacy -march=native -mcmodel=medium -std=legacy -w -Itoolbox -DMPI -DUNDERSCORE -DGLOBAL_LONG_LONG -DTIMER -I/home/docs/Sim_data/examples_snek/tuto/cbox_Ra2.000e+08_64x64_8x8_V1.x1._2023-08-24_07-52-10 -I/home/docs/Nek5000/core -I./ -I/home/docs/Nek5000/core/experimental -I/home/docs/Sim_data/examples_snek/tuto/cbox_Ra2.000e+08_64x64_8x8_V1.x1._2023-08-24_07-52-10/obj /home/docs/Nek5000/core/mxm_std.f -o /home/docs/Sim_data/examples_snek/tuto/cbox_Ra2.000e+08_64x64_8x8_V1.x1._2023-08-24_07-52-10/obj/mxm_std.o
mpif77 -c -O2 -cpp -fdefault-real-8 -fdefault-double-8 -w -std=legacy -march=native -mcmodel=medium -std=legacy -w -Itoolbox -DMPI -DUNDERSCORE -DGLOBAL_LONG_LONG -DTIMER -I/home/docs/Sim_data/examples_snek/tuto/cbox_Ra2.000e+08_64x64_8x8_V1.x1._2023-08-24_07-52-10 -I/home/docs/Nek5000/core -I./ -I/home/docs/Nek5000/core/experimental -I/home/docs/Sim_data/examples_snek/tuto/cbox_Ra2.000e+08_64x64_8x8_V1.x1._2023-08-24_07-52-10/obj -I./ toolbox/frame.f -o /home/docs/Sim_data/examples_snek/tuto/cbox_Ra2.000e+08_64x64_8x8_V1.x1._2023-08-24_07-52-10/obj/frame.o
mpif77 -c -O2 -cpp -fdefault-real-8 -fdefault-double-8 -w -std=legacy -march=native -mcmodel=medium -std=legacy -w -Itoolbox -DMPI -DUNDERSCORE -DGLOBAL_LONG_LONG -DTIMER -I/home/docs/Sim_data/examples_snek/tuto/cbox_Ra2.000e+08_64x64_8x8_V1.x1._2023-08-24_07-52-10 -I/home/docs/Nek5000/core -I./ -I/home/docs/Nek5000/core/experimental -I/home/docs/Sim_data/examples_snek/tuto/cbox_Ra2.000e+08_64x64_8x8_V1.x1._2023-08-24_07-52-10/obj -I./ toolbox/mntrlog_block.f -o /home/docs/Sim_data/examples_snek/tuto/cbox_Ra2.000e+08_64x64_8x8_V1.x1._2023-08-24_07-52-10/obj/mntrlog_block.o
mpif77 -c -O2 -cpp -fdefault-real-8 -fdefault-double-8 -w -std=legacy -march=native -mcmodel=medium -std=legacy -w -Itoolbox -DMPI -DUNDERSCORE -DGLOBAL_LONG_LONG -DTIMER -I/home/docs/Sim_data/examples_snek/tuto/cbox_Ra2.000e+08_64x64_8x8_V1.x1._2023-08-24_07-52-10 -I/home/docs/Nek5000/core -I./ -I/home/docs/Nek5000/core/experimental -I/home/docs/Sim_data/examples_snek/tuto/cbox_Ra2.000e+08_64x64_8x8_V1.x1._2023-08-24_07-52-10/obj -I./ toolbox/mntrlog.f -o /home/docs/Sim_data/examples_snek/tuto/cbox_Ra2.000e+08_64x64_8x8_V1.x1._2023-08-24_07-52-10/obj/mntrlog.o
mpif77 -c -O2 -cpp -fdefault-real-8 -fdefault-double-8 -w -std=legacy -march=native -mcmodel=medium -std=legacy -w -Itoolbox -DMPI -DUNDERSCORE -DGLOBAL_LONG_LONG -DTIMER -I/home/docs/Sim_data/examples_snek/tuto/cbox_Ra2.000e+08_64x64_8x8_V1.x1._2023-08-24_07-52-10 -I/home/docs/Nek5000/core -I./ -I/home/docs/Nek5000/core/experimental -I/home/docs/Sim_data/examples_snek/tuto/cbox_Ra2.000e+08_64x64_8x8_V1.x1._2023-08-24_07-52-10/obj -I./ toolbox/mntrtmr_block.f -o /home/docs/Sim_data/examples_snek/tuto/cbox_Ra2.000e+08_64x64_8x8_V1.x1._2023-08-24_07-52-10/obj/mntrtmr_block.o
mpif77 -c -O2 -cpp -fdefault-real-8 -fdefault-double-8 -w -std=legacy -march=native -mcmodel=medium -std=legacy -w -Itoolbox -DMPI -DUNDERSCORE -DGLOBAL_LONG_LONG -DTIMER -I/home/docs/Sim_data/examples_snek/tuto/cbox_Ra2.000e+08_64x64_8x8_V1.x1._2023-08-24_07-52-10 -I/home/docs/Nek5000/core -I./ -I/home/docs/Nek5000/core/experimental -I/home/docs/Sim_data/examples_snek/tuto/cbox_Ra2.000e+08_64x64_8x8_V1.x1._2023-08-24_07-52-10/obj -I./ toolbox/mntrtmr.f -o /home/docs/Sim_data/examples_snek/tuto/cbox_Ra2.000e+08_64x64_8x8_V1.x1._2023-08-24_07-52-10/obj/mntrtmr.o
mpif77 -c -O2 -cpp -fdefault-real-8 -fdefault-double-8 -w -std=legacy -march=native -mcmodel=medium -std=legacy -w -Itoolbox -DMPI -DUNDERSCORE -DGLOBAL_LONG_LONG -DTIMER -I/home/docs/Sim_data/examples_snek/tuto/cbox_Ra2.000e+08_64x64_8x8_V1.x1._2023-08-24_07-52-10 -I/home/docs/Nek5000/core -I./ -I/home/docs/Nek5000/core/experimental -I/home/docs/Sim_data/examples_snek/tuto/cbox_Ra2.000e+08_64x64_8x8_V1.x1._2023-08-24_07-52-10/obj -I./ toolbox/rprm_block.f -o /home/docs/Sim_data/examples_snek/tuto/cbox_Ra2.000e+08_64x64_8x8_V1.x1._2023-08-24_07-52-10/obj/rprm_block.o
mpif77 -c -O2 -cpp -fdefault-real-8 -fdefault-double-8 -w -std=legacy -march=native -mcmodel=medium -std=legacy -w -Itoolbox -DMPI -DUNDERSCORE -DGLOBAL_LONG_LONG -DTIMER -I/home/docs/Sim_data/examples_snek/tuto/cbox_Ra2.000e+08_64x64_8x8_V1.x1._2023-08-24_07-52-10 -I/home/docs/Nek5000/core -I./ -I/home/docs/Nek5000/core/experimental -I/home/docs/Sim_data/examples_snek/tuto/cbox_Ra2.000e+08_64x64_8x8_V1.x1._2023-08-24_07-52-10/obj -I./ toolbox/rprm.f -o /home/docs/Sim_data/examples_snek/tuto/cbox_Ra2.000e+08_64x64_8x8_V1.x1._2023-08-24_07-52-10/obj/rprm.o
mpif77 -c -O2 -cpp -fdefault-real-8 -fdefault-double-8 -w -std=legacy -march=native -mcmodel=medium -std=legacy -w -Itoolbox -DMPI -DUNDERSCORE -DGLOBAL_LONG_LONG -DTIMER -I/home/docs/Sim_data/examples_snek/tuto/cbox_Ra2.000e+08_64x64_8x8_V1.x1._2023-08-24_07-52-10 -I/home/docs/Nek5000/core -I./ -I/home/docs/Nek5000/core/experimental -I/home/docs/Sim_data/examples_snek/tuto/cbox_Ra2.000e+08_64x64_8x8_V1.x1._2023-08-24_07-52-10/obj -I./ toolbox/io_tools_block.f -o /home/docs/Sim_data/examples_snek/tuto/cbox_Ra2.000e+08_64x64_8x8_V1.x1._2023-08-24_07-52-10/obj/io_tools_block.o
mpif77 -c -O2 -cpp -fdefault-real-8 -fdefault-double-8 -w -std=legacy -march=native -mcmodel=medium -std=legacy -w -Itoolbox -DMPI -DUNDERSCORE -DGLOBAL_LONG_LONG -DTIMER -I/home/docs/Sim_data/examples_snek/tuto/cbox_Ra2.000e+08_64x64_8x8_V1.x1._2023-08-24_07-52-10 -I/home/docs/Nek5000/core -I./ -I/home/docs/Nek5000/core/experimental -I/home/docs/Sim_data/examples_snek/tuto/cbox_Ra2.000e+08_64x64_8x8_V1.x1._2023-08-24_07-52-10/obj -I./ toolbox/io_tools.f -o /home/docs/Sim_data/examples_snek/tuto/cbox_Ra2.000e+08_64x64_8x8_V1.x1._2023-08-24_07-52-10/obj/io_tools.o
mpif77 -c -O2 -cpp -fdefault-real-8 -fdefault-double-8 -w -std=legacy -march=native -mcmodel=medium -std=legacy -w -Itoolbox -DMPI -DUNDERSCORE -DGLOBAL_LONG_LONG -DTIMER -I/home/docs/Sim_data/examples_snek/tuto/cbox_Ra2.000e+08_64x64_8x8_V1.x1._2023-08-24_07-52-10 -I/home/docs/Nek5000/core -I./ -I/home/docs/Nek5000/core/experimental -I/home/docs/Sim_data/examples_snek/tuto/cbox_Ra2.000e+08_64x64_8x8_V1.x1._2023-08-24_07-52-10/obj -I./ toolbox/chkpoint.f -o /home/docs/Sim_data/examples_snek/tuto/cbox_Ra2.000e+08_64x64_8x8_V1.x1._2023-08-24_07-52-10/obj/chkpoint.o
mpif77 -c -O2 -cpp -fdefault-real-8 -fdefault-double-8 -w -std=legacy -march=native -mcmodel=medium -std=legacy -w -Itoolbox -DMPI -DUNDERSCORE -DGLOBAL_LONG_LONG -DTIMER -I/home/docs/Sim_data/examples_snek/tuto/cbox_Ra2.000e+08_64x64_8x8_V1.x1._2023-08-24_07-52-10 -I/home/docs/Nek5000/core -I./ -I/home/docs/Nek5000/core/experimental -I/home/docs/Sim_data/examples_snek/tuto/cbox_Ra2.000e+08_64x64_8x8_V1.x1._2023-08-24_07-52-10/obj -I./ toolbox/chkpt_mstp.f -o /home/docs/Sim_data/examples_snek/tuto/cbox_Ra2.000e+08_64x64_8x8_V1.x1._2023-08-24_07-52-10/obj/chkpt_mstp.o
mpif77 -c -O2 -cpp -fdefault-real-8 -fdefault-double-8 -w -std=legacy -march=native -mcmodel=medium -std=legacy -w -Itoolbox -DMPI -DUNDERSCORE -DGLOBAL_LONG_LONG -DTIMER -I/home/docs/Sim_data/examples_snek/tuto/cbox_Ra2.000e+08_64x64_8x8_V1.x1._2023-08-24_07-52-10 -I/home/docs/Nek5000/core -I./ -I/home/docs/Nek5000/core/experimental -I/home/docs/Sim_data/examples_snek/tuto/cbox_Ra2.000e+08_64x64_8x8_V1.x1._2023-08-24_07-52-10/obj -I./ toolbox/map2D.f -o /home/docs/Sim_data/examples_snek/tuto/cbox_Ra2.000e+08_64x64_8x8_V1.x1._2023-08-24_07-52-10/obj/map2D.o
mpif77 -c -O2 -cpp -fdefault-real-8 -fdefault-double-8 -w -std=legacy -march=native -mcmodel=medium -std=legacy -w -Itoolbox -DMPI -DUNDERSCORE -DGLOBAL_LONG_LONG -DTIMER -I/home/docs/Sim_data/examples_snek/tuto/cbox_Ra2.000e+08_64x64_8x8_V1.x1._2023-08-24_07-52-10 -I/home/docs/Nek5000/core -I./ -I/home/docs/Nek5000/core/experimental -I/home/docs/Sim_data/examples_snek/tuto/cbox_Ra2.000e+08_64x64_8x8_V1.x1._2023-08-24_07-52-10/obj -I./ toolbox/stat.f -o /home/docs/Sim_data/examples_snek/tuto/cbox_Ra2.000e+08_64x64_8x8_V1.x1._2023-08-24_07-52-10/obj/stat.o
mpif77 -c -O2 -cpp -fdefault-real-8 -fdefault-double-8 -w -std=legacy -march=native -mcmodel=medium -std=legacy -w -Itoolbox -DMPI -DUNDERSCORE -DGLOBAL_LONG_LONG -DTIMER -I/home/docs/Sim_data/examples_snek/tuto/cbox_Ra2.000e+08_64x64_8x8_V1.x1._2023-08-24_07-52-10 -I/home/docs/Nek5000/core -I./ -I/home/docs/Nek5000/core/experimental -I/home/docs/Sim_data/examples_snek/tuto/cbox_Ra2.000e+08_64x64_8x8_V1.x1._2023-08-24_07-52-10/obj -I./ toolbox/stat_IO.f -o /home/docs/Sim_data/examples_snek/tuto/cbox_Ra2.000e+08_64x64_8x8_V1.x1._2023-08-24_07-52-10/obj/stat_IO.o
mpif77 -c -O2 -cpp -fdefault-real-8 -fdefault-double-8 -w -std=legacy -march=native -mcmodel=medium -std=legacy -w -Itoolbox -DMPI -DUNDERSCORE -DGLOBAL_LONG_LONG -DTIMER -I/home/docs/Sim_data/examples_snek/tuto/cbox_Ra2.000e+08_64x64_8x8_V1.x1._2023-08-24_07-52-10 -I/home/docs/Nek5000/core -I./ -I/home/docs/Nek5000/core/experimental -I/home/docs/Sim_data/examples_snek/tuto/cbox_Ra2.000e+08_64x64_8x8_V1.x1._2023-08-24_07-52-10/obj -I./ toolbox/sfd.f -o /home/docs/Sim_data/examples_snek/tuto/cbox_Ra2.000e+08_64x64_8x8_V1.x1._2023-08-24_07-52-10/obj/sfd.o
mpif77 -c -O2 -cpp -fdefault-real-8 -fdefault-double-8 -w -std=legacy -march=native -mcmodel=medium -std=legacy -w -Itoolbox -DMPI -DUNDERSCORE -DGLOBAL_LONG_LONG -DTIMER -I/home/docs/Sim_data/examples_snek/tuto/cbox_Ra2.000e+08_64x64_8x8_V1.x1._2023-08-24_07-52-10 -I/home/docs/Nek5000/core -I./ -I/home/docs/Nek5000/core/experimental -I/home/docs/Sim_data/examples_snek/tuto/cbox_Ra2.000e+08_64x64_8x8_V1.x1._2023-08-24_07-52-10/obj -I./ toolbox/math_tools.f -o /home/docs/Sim_data/examples_snek/tuto/cbox_Ra2.000e+08_64x64_8x8_V1.x1._2023-08-24_07-52-10/obj/math_tools.o
mpif77 -c -O2 -cpp -fdefault-real-8 -fdefault-double-8 -w -std=legacy -march=native -mcmodel=medium -std=legacy -w -Itoolbox -DMPI -DUNDERSCORE -DGLOBAL_LONG_LONG -DTIMER -I/home/docs/Sim_data/examples_snek/tuto/cbox_Ra2.000e+08_64x64_8x8_V1.x1._2023-08-24_07-52-10 -I/home/docs/Nek5000/core -I./ -I/home/docs/Nek5000/core/experimental -I/home/docs/Sim_data/examples_snek/tuto/cbox_Ra2.000e+08_64x64_8x8_V1.x1._2023-08-24_07-52-10/obj /home/docs/Nek5000/core/comm_mpi.f -o /home/docs/Sim_data/examples_snek/tuto/cbox_Ra2.000e+08_64x64_8x8_V1.x1._2023-08-24_07-52-10/obj/comm_mpi.o
mpif77 -O2 -cpp -fdefault-real-8 -fdefault-double-8 -w -std=legacy -march=native -mcmodel=medium -std=legacy -w -Itoolbox -DMPI -DUNDERSCORE -DGLOBAL_LONG_LONG -DTIMER -I/home/docs/Sim_data/examples_snek/tuto/cbox_Ra2.000e+08_64x64_8x8_V1.x1._2023-08-24_07-52-10 -I/home/docs/Nek5000/core -I./ -I/home/docs/Nek5000/core/experimental -I/home/docs/Sim_data/examples_snek/tuto/cbox_Ra2.000e+08_64x64_8x8_V1.x1._2023-08-24_07-52-10/obj -c /home/docs/Sim_data/examples_snek/tuto/cbox_Ra2.000e+08_64x64_8x8_V1.x1._2023-08-24_07-52-10/cbox.f -o /home/docs/Sim_data/examples_snek/tuto/cbox_Ra2.000e+08_64x64_8x8_V1.x1._2023-08-24_07-52-10/obj/cbox.o
done
mpif77 -c -O2 -cpp -fdefault-real-8 -fdefault-double-8 -w -std=legacy -march=native -mcmodel=medium -std=legacy -w -Itoolbox -DMPI -DUNDERSCORE -DGLOBAL_LONG_LONG -DTIMER -I/home/docs/Sim_data/examples_snek/tuto/cbox_Ra2.000e+08_64x64_8x8_V1.x1._2023-08-24_07-52-10 -I/home/docs/Nek5000/core -I./ -I/home/docs/Nek5000/core/experimental -I/home/docs/Sim_data/examples_snek/tuto/cbox_Ra2.000e+08_64x64_8x8_V1.x1._2023-08-24_07-52-10/obj /home/docs/Nek5000/core/drive.f
mpif77 -O2 -cpp -fdefault-real-8 -fdefault-double-8 -w -std=legacy -march=native -mcmodel=medium -std=legacy -w -Itoolbox -DMPI -DUNDERSCORE -DGLOBAL_LONG_LONG -DTIMER -I/home/docs/Sim_data/examples_snek/tuto/cbox_Ra2.000e+08_64x64_8x8_V1.x1._2023-08-24_07-52-10 -I/home/docs/Nek5000/core -I./ -I/home/docs/Nek5000/core/experimental -I/home/docs/Sim_data/examples_snek/tuto/cbox_Ra2.000e+08_64x64_8x8_V1.x1._2023-08-24_07-52-10/obj -o nek5000 drive.o /home/docs/Sim_data/examples_snek/tuto/cbox_Ra2.000e+08_64x64_8x8_V1.x1._2023-08-24_07-52-10/obj/cbox.o /home/docs/Sim_data/examples_snek/tuto/cbox_Ra2.000e+08_64x64_8x8_V1.x1._2023-08-24_07-52-10/obj/libnek5000.a -L/home/docs/Nek5000/3rd_party/blasLapack -lblasLapack -L/home/docs/Nek5000/3rd_party/gslib/lib -lgs -Wl,--allow-multiple-definition
#############################################################
# Compilation successful! #
#############################################################
text data bss dec hex filename
1818355 200084 12784576 14803015 e1e047 nek5000
[Thu Aug 24 07:52:53 2023]
Finished job 5.
6 of 7 steps (86%) done
Select jobs to execute...
[Thu Aug 24 07:52:53 2023]
rule run:
input: cbox.re2, cbox.ma2, cbox.par, SESSION.NAME, nek5000
output: logs/run_2023-08-24T07-52-11.log
jobid: 0
reason: Missing output files: logs/run_2023-08-24T07-52-11.log; Input files updated by another job: cbox.re2, SESSION.NAME, nek5000, cbox.ma2
resources: tmpdir=/tmp, nproc=2
Log file:
/home/docs/Sim_data/examples_snek/tuto/cbox_Ra2.000e+08_64x64_8x8_V1.x1._2023-08-24_07-52-10/logs/run_2023-08-24T07-52-11.log
/home/docs/Sim_data/examples_snek/tuto/cbox_Ra2.000e+08_64x64_8x8_V1.x1._2023-08-24_07-52-10
[Thu Aug 24 07:52:53 2023]
Finished job 0.
7 of 7 steps (100%) done
Complete log: .snakemake/log/2023-08-24T075211.008433.snakemake.log
path_run: /home/docs/Sim_data/examples_snek/tuto/cbox_Ra2.000e+08_64x64_8x8_V1.x1._2023-08-24_07-52-10
pid = 3476
2023-08-24_07-52-56, t_last = 6.61: history_points loaded in 0.05 s
2023-08-24_07-52-58, t_last = 11.62: history_points loaded in 0.03 s
2023-08-24_07-53-00, t_last = 17.44: history_points loaded in 0.03 s
2023-08-24_07-53-02, t_last = 25.33: history_points loaded in 0.03 s
2023-08-24_07-53-04, t_last = 33.25: history_points loaded in 0.03 s
2023-08-24_07-53-06, t_last = 42.00: history_points loaded in 0.04 s
2023-08-24_07-53-08, t_last = 49.79: history_points loaded in 0.03 s
2023-08-24_07-53-10, t_last = 58.59: history_points loaded in 0.03 s
2023-08-24_07-53-12, t_last = 68.85: history_points loaded in 0.03 s
2023-08-24_07-53-14, t_last = 78.63: history_points loaded in 0.03 s
2023-08-24_07-53-16, t_last = 87.92: history_points loaded in 0.03 s
2023-08-24_07-53-18, t_last = 98.67: history_points loaded in 0.03 s
2023-08-24_07-53-20, t_last = 107.96: history_points loaded in 0.03 s
2023-08-24_07-53-22, t_last = 119.19: history_points loaded in 0.03 s
2023-08-24_07-53-24, t_last = 131.51: history_points loaded in 0.03 s
2023-08-24_07-53-26, t_last = 143.24: history_points loaded in 0.04 s
2023-08-24_07-53-28, t_last = 155.56: history_points loaded in 0.03 s
2023-08-24_07-53-30, t_last = 168.46: history_points loaded in 0.03 s
2023-08-24_07-53-32, t_last = 179.61: history_points loaded in 0.03 s
2023-08-24_07-53-34, t_last = 192.52: history_points loaded in 0.04 s
2023-08-24_07-53-36, t_last = 205.42: history_points loaded in 0.03 s
2023-08-24_07-53-38, t_last = 218.91: history_points loaded in 0.03 s
2023-08-24_07-53-41, t_last = 231.82: history_points loaded in 0.03 s
2023-08-24_07-53-43, t_last = 244.73: history_points loaded in 0.04 s
2023-08-24_07-53-45, t_last = 257.04: history_points loaded in 0.03 s
2023-08-24_07-53-47, t_last = 269.95: history_points loaded in 0.03 s
2023-08-24_07-53-49, t_last = 282.27: history_points loaded in 0.03 s
2023-08-24_07-53-51, t_last = 295.18: history_points loaded in 0.03 s
2023-08-24_07-53-53, t_last = 308.08: history_points loaded in 0.04 s
2023-08-24_07-53-55, t_last = 321.57: history_points loaded in 0.03 s
2023-08-24_07-53-57, t_last = 334.48: history_points loaded in 0.04 s
2023-08-24_07-53-59, t_last = 347.39: history_points loaded in 0.04 s
2023-08-24_07-54-01, t_last = 359.70: history_points loaded in 0.03 s
2023-08-24_07-54-03, t_last = 372.61: history_points loaded in 0.03 s
2023-08-24_07-54-05, t_last = 386.10: history_points loaded in 0.04 s
2023-08-24_07-54-07, t_last = 399.01: history_points loaded in 0.04 s
2023-08-24_07-54-09, t_last = 411.91: history_points loaded in 0.03 s
2023-08-24_07-54-11, t_last = 425.41: history_points loaded in 0.04 s
2023-08-24_07-54-13, t_last = 438.31: history_points loaded in 0.03 s
2023-08-24_07-54-15, t_last = 451.22: history_points loaded in 0.04 s
2023-08-24_07-54-17, t_last = 464.71: history_points loaded in 0.04 s
2023-08-24_07-54-19, t_last = 476.44: history_points loaded in 0.04 s
2023-08-24_07-54-21, t_last = 488.76: history_points loaded in 0.03 s
2023-08-24_07-54-23, t_last = 501.67: history_points loaded in 0.04 s
2023-08-24_07-54-25, t_last = 514.57: history_points loaded in 0.04 s
2023-08-24_07-54-27, t_last = 526.89: history_points loaded in 0.04 s
2023-08-24_07-54-29, t_last = 539.80: history_points loaded in 0.04 s
2023-08-24_07-54-31, t_last = 552.12: history_points loaded in 0.03 s
2023-08-24_07-54-33, t_last = 565.02: history_points loaded in 0.04 s
2023-08-24_07-54-36, t_last = 577.93: history_points loaded in 0.04 s
2023-08-24_07-54-38, t_last = 590.25: history_points loaded in 0.04 s
2023-08-24_07-54-40, t_last = 603.15: history_points loaded in 0.04 s
2023-08-24_07-54-42, t_last = 615.47: history_points loaded in 0.03 s
2023-08-24_07-54-44, t_last = 628.38: history_points loaded in 0.04 s
2023-08-24_07-54-46, t_last = 641.29: history_points loaded in 0.04 s
2023-08-24_07-54-48, t_last = 653.60: history_points loaded in 0.04 s
2023-08-24_07-54-50, t_last = 666.51: history_points loaded in 0.04 s
Saturation of the instability detected at t = 666.51056
Terminate simulation.
The last lines of the output should be related to the checks done in our script:
print("\n".join(lines[-6:]))
2023-08-24_07-54-46, t_last = 641.29: history_points loaded in 0.04 s
2023-08-24_07-54-48, t_last = 653.60: history_points loaded in 0.04 s
2023-08-24_07-54-50, t_last = 666.51: history_points loaded in 0.04 s
Saturation of the instability detected at t = 666.51056
Terminate simulation.
To “load the simulation”, i.e. to recreate a simulation object, we now need to extract from the output the path of the directory of the simulation. This is also very specific to these tutorials, so you don’t need to focus on this code. In real life, we can just read the log to know where the data has been saved.
Show code cell source
path_run = None
for line in lines:
if "path_run: " in line:
path_run = line.split("path_run: ")[1].split(" ", 1)[0]
break
if path_run is None:
raise RuntimeError
path_run
'/home/docs/Sim_data/examples_snek/tuto/cbox_Ra2.000e+08_64x64_8x8_V1.x1._2023-08-24_07-52-10'
We can now read the Nek5000 log file. First the first lines:
from pathlib import Path
path_log = Path(path_run) / "cbox.log"
lines = path_log.read_text().split("\n")
index_step2 = 0
for line in lines:
if line.startswith("Step 2, t= "):
break
index_step2 += 1
print("\n".join(lines[:index_step2+20]))
Show code cell output
/----------------------------------------------------------\\
| _ __ ______ __ __ ______ ____ ____ ____ |
| / | / // ____// //_/ / ____/ / __ \\/ __ \\/ __ \\ |
| / |/ // __/ / ,< /___ \\ / / / // / / // / / / |
| / /| // /___ / /| | ____/ / / /_/ // /_/ // /_/ / |
| /_/ |_//_____//_/ |_|/_____/ \\___/ \\___/ \\___/ |
| |
|----------------------------------------------------------|
| |
| COPYRIGHT (c) 2008-2020 UCHICAGO ARGONNE, LLC |
| Version: 20.0-dev |
| Web: https://nek5000.mcs.anl.gov |
| |
\\----------------------------------------------------------/
Number of MPI ranks : 2
Reading ./session_00/cbox.par
general = [(null)]
general:stopat = [endTime]
general:endtime = [1000]
general:numsteps = [1]
general:variabledt = [yes]
general:targetcfl = [2.0]
general:writecontrol = [runTime]
general:writeinterval = [50]
general:filtering = [none]
general:filtermodes = [2]
general:filtercutoffratio = [0.65]
general:filterweight = [12.0]
general:writedoubleprecision = [yes]
general:dealiasing = [yes]
general:timestepper = [BDF3]
general:extrapolation = [OIFS]
general:optlevel = [2]
general:loglevel = [2]
general:userparam01 = [0.71]
general:userparam02 = [200000000.0]
general:userparam03 = [0.0]
general:userparam04 = [0.1]
general:userparam05 = [1.0]
general:userparam06 = [0.0]
general:userparam07 = [0.0]
general:userparam09 = [1000]
general:userparam10 = [10]
general:userparam12 = [5.0]
problemtype = [(null)]
problemtype:equation = [incompNS]
problemtype:variableproperties = [no]
problemtype:stressformulation = [no]
problemtype:solvebaseflow = [no]
problemtype:numberofperturbations = [1]
velocity = [(null)]
velocity:residualtol = [1e-08]
velocity:residualproj = [no]
velocity:writetofieldfile = [yes]
velocity:viscosity = [5.020458146424487e-05]
velocity:density = [1.0]
pressure = [(null)]
pressure:residualtol = [1e-05]
pressure:residualproj = [no]
pressure:writetofieldfile = [yes]
pressure:preconditioner = [semg_xxt]
temperature = [(null)]
temperature:residualtol = [1e-08]
temperature:residualproj = [no]
temperature:writetofieldfile = [yes]
temperature:solver = [helm]
temperature:advection = [yes]
temperature:absolutetol = [1e-08]
temperature:conjugateheattransfer = [no]
temperature:conductivity = [7.071067811865475e-05]
temperature:rhocp = [1.0]
_runpar = [(null)]
_runpar:parfwrite = [no]
_runpar:parfname = [outparfile]
_monitor = [(null)]
_monitor:loglevel = [4]
_monitor:walltime = [23:45]
_chkpoint = [(null)]
_chkpoint:readchkpt = [no]
_chkpoint:chkpfnumber = [1]
_chkpoint:chkpinterval = [250]
_stat = [(null)]
_stat:avstep = [4]
_stat:iostep = [50]
_sfd = [(null)]
_sfd:filterwdth = [1.05]
_sfd:controlcff = [0.5]
_sfd:residualtol = [1e-08]
_sfd:loginterval = [50]
_sfd:sfdreadchpnt = [no]
reading ./session_00/cbox.re2
hdr:#v002 64 2 64 hdr
partioning elements to MPI ranks
reading mesh
readp_re2_mesh:pack/cr/unpack : 0.74E-05 0.17E-04 0.22E-05
readp_re2_mesh:byte_read_mpi : 0.23E-04
reading boundary faces 32 for ifield 1
readp_re2_bc:pack/cr/unpack : 0.11E-05 0.59E-05 0.26E-05
readp_re2_bc:byte_read_mpi : 0.42E-05
reading boundary faces 32 for ifield 2
readp_re2_bc:pack/cr/unpack : 0.99E-06 0.45E-05 0.25E-05
readp_re2_bc:byte_read_mpi : 0.37E-05
done :: read .re2 file 0.43E-02 sec
Reading ./session_00/cbox.ma2
done :: partioning 0.47378E-02 sec
reading mesh
readp_re2_mesh:pack/cr/unpack : 0.24E-05 0.28E-04 0.31E-05
readp_re2_mesh:byte_read_mpi : 0.80E-05
reading boundary faces 32 for ifield 1
readp_re2_bc:pack/cr/unpack : 0.21E-05 0.64E-05 0.24E-05
readp_re2_bc:byte_read_mpi : 0.53E-05
reading boundary faces 32 for ifield 2
readp_re2_bc:pack/cr/unpack : 0.11E-05 0.42E-05 0.25E-05
readp_re2_bc:byte_read_mpi : 0.10E-04
done :: read .re2 file 0.98E-03 sec
nelgt/nelgv/lelt: 64 64 32
lx1/lx2/lx3/lxd: 8 8 8 12
RK4 substeps: 1
setup mesh topology
Right-handed check complete for 64 elements. OK.
setvert2d: 8 945 3249 945 945
gs_setup: 57 unique labels shared
pairwise times (avg, min, max): 2.01475e-06 2.0044e-06 2.0251e-06
crystal router : 2.1845e-06 2.1709e-06 2.1981e-06
all reduce : 1.96065e-06 1.867e-06 2.0543e-06
used all_to_all method: pairwise
handle bytes (avg, min, max): 10428 10428 10428
buffer bytes (avg, min, max): 912 912 912
setupds time 1.0498E-03 seconds 0 8 945 64
nElements max/min/bal: 32 32 1.00
nMessages max/min/avg: 1 1 1.00
msgSize max/min/avg: 57 57 57.00
msgSizeSum max/min/avg: 57 57 57.00
max multiplicity 4
done :: setup mesh topology
call usrdat
done :: usrdat
generate geometry data
done :: generate geometry data
call usrdat2
done :: usrdat2
0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 xyz repair 1
0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 xyz repair 2
0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 xyz repair 3
regenerate geometry data 1
done :: regenerate geometry data 1
verify mesh topology
0.0000000000000000 1.0000000000000000 Xrange
0.0000000000000000 1.0000000000000000 Yrange
0.0000000000000000 0.0000000000000000 Zrange
done :: verify mesh topology
mesh metrics:
GLL grid spacing min/max : 2.98E-03 4.13E-02
scaled Jacobian min/max/avg: 3.09E-01 7.87E-01 4.91E-01
aspect ratio min/max/avg: 1.00E+00 3.60E+00 1.89E+00
IFTRAN = T
IFFLOW = T
IFHEAT = T
IFSPLIT = T
IFLOMACH = F
IFUSERVP = F
IFUSERMV = F
IFPERT = F
IFADJ = F
IFSTRS = F
IFCHAR = T
IFCYCLIC = F
IFAXIS = F
IFMVBD = F
IFMELT = F
IFNEKNEK = F
IFNEKNEKC = F
IFSYNC = F
IFVCOR = T
IFINTQ = F
IFGEOM = F
IFSURT = F
IFWCNO = F
IFTMSH for field 1 = F
IFADVC for field 1 = T
IFNONL for field 1 = F
IFTMSH for field 2 = F
IFADVC for field 2 = T
IFNONL for field 2 = F
Dealiasing enabled, nxd= 12
Estimated eigenvalues
EIGAA = 9.8696044010893580
EIGGA = 543865.78071959876
EIGAE = 9.8696044010893580
EIGAS = 0.12500000000000000
EIGGE = 543865.78071959876
EIGGS = 2.0000000000000000
initialize pressure solver
mg_nx: 1 3 7
mg_ny: 1 3 7
mg_nz: 0 0 0
gs_setup: 9 unique labels shared
pairwise times (avg, min, max): 1.3141e-06 1.3084e-06 1.3198e-06
crystal router : 1.21725e-06 1.1449e-06 1.2896e-06
all reduce : 1.2932e-06 1.2892e-06 1.2972e-06
used all_to_all method: crystal router
handle bytes (avg, min, max): 2372 2372 2372
buffer bytes (avg, min, max): 288 288 288
setupds time 4.7999E-04 seconds 1 2 81 64
setvert2d: 4 369 625 369 369
gs_setup: 25 unique labels shared
pairwise times (avg, min, max): 1.80265e-06 1.776e-06 1.8293e-06
crystal router : 1.31545e-06 1.2829e-06 1.348e-06
all reduce : 1.30555e-06 1.3001e-06 1.311e-06
used all_to_all method: allreduce
handle bytes (avg, min, max): 5196 5196 5196
buffer bytes (avg, min, max): 400 400 400
setupds time 6.9989E-04 seconds 2 4 369 64
setvert2d: 4 369 625 369 369
gs_setup: 25 unique labels shared
pairwise times (avg, min, max): 1.32555e-06 1.3143e-06 1.3368e-06
crystal router : 1.5334e-06 1.5131e-06 1.5537e-06
all reduce : 1.93175e-06 1.891e-06 1.9725e-06
used all_to_all method: pairwise
handle bytes (avg, min, max): 4668 4668 4668
buffer bytes (avg, min, max): 400 400 400
setupds time 6.7301E-04 seconds 3 4 369 64
setvert2d: 6 657 1681 657 657
gs_setup: 41 unique labels shared
pairwise times (avg, min, max): 1.76305e-06 1.7503e-06 1.7758e-06
crystal router : 1.7743e-06 1.6865e-06 1.8621e-06
all reduce : 2.2199e-06 2.2071e-06 2.2327e-06
used all_to_all method: pairwise
handle bytes (avg, min, max): 7548 7548 7548
buffer bytes (avg, min, max): 656 656 656
setupds time 7.2154E-04 seconds 4 6 657 64
regenerate geometry data 1
done :: regenerate geometry data 1
h1_mg_nx: 1 3 7
h1_mg_ny: 1 3 7
h1_mg_nz: 0 0 0
gs_setup: 9 unique labels shared
pairwise times (avg, min, max): 1.4878e-06 1.4781e-06 1.4975e-06
crystal router : 1.21395e-06 1.1574e-06 1.2705e-06
all reduce : 1.4439e-06 1.4396e-06 1.4482e-06
used all_to_all method: crystal router
handle bytes (avg, min, max): 2372 2372 2372
buffer bytes (avg, min, max): 288 288 288
setupds time 5.2473E-04 seconds 5 2 81 64
setvert2d: 4 369 625 369 369
gs_setup: 25 unique labels shared
pairwise times (avg, min, max): 1.3542e-06 1.3053e-06 1.4031e-06
crystal router : 1.54895e-06 1.5488e-06 1.5491e-06
all reduce : 1.9118e-06 1.8677e-06 1.9559e-06
used all_to_all method: pairwise
handle bytes (avg, min, max): 4668 4668 4668
buffer bytes (avg, min, max): 400 400 400
setupds time 6.5813E-04 seconds 6 4 369 64
setvert2d: 4 369 625 369 369
gs_setup: 25 unique labels shared
pairwise times (avg, min, max): 1.4894e-06 1.4816e-06 1.4972e-06
crystal router : 1.55595e-06 1.5457e-06 1.5662e-06
all reduce : 1.5546e-06 1.5444e-06 1.5648e-06
used all_to_all method: pairwise
handle bytes (avg, min, max): 4668 4668 4668
buffer bytes (avg, min, max): 400 400 400
setupds time 6.6358E-04 seconds 7 4 369 64
setvert2d: 6 657 1681 657 657
gs_setup: 41 unique labels shared
pairwise times (avg, min, max): 2.0902e-06 2.0721e-06 2.1083e-06
crystal router : 2.0381e-06 1.9906e-06 2.0856e-06
all reduce : 2.2513e-06 2.2315e-06 2.2711e-06
used all_to_all method: crystal router
handle bytes (avg, min, max): 9668 9668 9668
buffer bytes (avg, min, max): 1312 1312 1312
setupds time 7.4400E-04 seconds 8 6 657 64
setvert2d: 8 945 3249 945 945
gs_setup: 57 unique labels shared
pairwise times (avg, min, max): 2.1126e-06 2.102e-06 2.1232e-06
crystal router : 2.1253e-06 2.0581e-06 2.1925e-06
all reduce : 2.2958e-06 2.2946e-06 2.297e-06
used all_to_all method: pairwise
handle bytes (avg, min, max): 10428 10428 10428
buffer bytes (avg, min, max): 912 912 912
setupds time 8.3897E-04 seconds 9 8 945 64
setvert2d: 10 1233 5329 1233 1233
gs_setup: 73 unique labels shared
pairwise times (avg, min, max): 1.98445e-06 1.9804e-06 1.9885e-06
crystal router : 1.73215e-06 1.7151e-06 1.7492e-06
all reduce : 2.2492e-06 2.2214e-06 2.277e-06
used all_to_all method: crystal router
handle bytes (avg, min, max): 16964 16964 16964
buffer bytes (avg, min, max): 2336 2336 2336
setupds time 9.4811E-04 seconds 10 10 1233 64
setup h1 coarse grid, nx_crs= 2
gs_setup: 9 unique labels shared
pairwise times (avg, min, max): 1.3196e-06 1.3104e-06 1.3288e-06
crystal router : 1.28985e-06 1.2886e-06 1.2911e-06
all reduce : 1.7317e-06 1.692e-06 1.7714e-06
used all_to_all method: crystal router
handle bytes (avg, min, max): 2372 2372 2372
buffer bytes (avg, min, max): 288 288 288
done :: setup h1 coarse grid 1.2001920000000027E-003 sec
call usrdat3
done :: usrdat3
set initial conditions
nekuic (1) for ifld 1
nekuic (1) for ifld 2
call nekuic for ifld 2
call nekuic for vel
xyz min 0.0000 0.0000 0.0000
uvwpt min 0.0000 0.0000 0.0000 0.0000 -0.50000
xyz max 1.0000 1.0000 0.0000
uvwpt max 0.0000 0.0000 0.0000 0.0000 0.50001
done :: set initial conditions
call userchk
[MONITOR] Registered module [FRAME]: Framework backbone
[MONITOR] Registered module [MONITOR]: Monitoring module
[MONITOR] Registered timer [FRM_TOT]: Total elapsed framework time
[MONITOR] Initial log threshold set to: 4
[MONITOR] Module [RUNPAR] not registered
[MONITOR] Registered module [RUNPAR]: Runtime parameters
[RUNPAR] Module [RUNPAR] registered section _RUNPAR: Runtime parameter section for rprm module
[RUNPAR] Section _RUNPAR registered parameter PARFWRITE: Do we write runtime parameter file
[RUNPAR] Section _RUNPAR registered parameter PARFNAME: Runtime parameter file name for output (without .par)
[RUNPAR] Module [MONITOR] registered section _MONITOR: Runtime parameter section for monitor module
[RUNPAR] Section _MONITOR registered parameter LOGLEVEL: Logging threshold for toolboxes
[RUNPAR] Section _MONITOR registered parameter IFTIMDSCR: Write timer description in the summary
[RUNPAR] Section _MONITOR registered parameter WALLTIME: Simulation wall time
[MONITOR] Module [IOTOOL] not registered
[MONITOR] Registered module [IOTOOL]: I/O TOOLS
[MONITOR] Module [CHKPOINT] not registered
[MONITOR] Registered module [CHKPOINT]: Checkpointing I/O
[MONITOR] Registered timer [CHP_TOT]: Checkpointing total time
[MONITOR] Registered timer [CHP_INI]: Checkpointing initialisation time
[RUNPAR] Module [CHKPOINT] registered section _CHKPOINT: Runtime paramere section for checkpoint module
[RUNPAR] Section _CHKPOINT registered parameter READCHKPT: Restat from checkpoint
[RUNPAR] Section _CHKPOINT registered parameter CHKPFNUMBER: Restart file number
[RUNPAR] Section _CHKPOINT registered parameter CHKPINTERVAL: Checkpiont saving frequency (number of time steps)
[MONITOR] Module [MSTEP] not registered
[MONITOR] Registered module [MSTEP]: Multi-file checkpointing
[MONITOR] Registered timer [CHP_READ]: Checkpointing reading time
[MONITOR] Registered timer [CHP_WRITE]: Checkpointing writing time
[MONITOR] Reseting log threshold to: 4
[MONITOR] Summary of registered modules
[FRAME ] : Framework backbone
[MONITOR ] : Monitoring module
[RUNPAR ] : Runtime parameters
[IOTOOL ] : I/O TOOLS
[CHKPOINT ] : Checkpointing I/O
[MSTEP ] : Multi-file checkpointing
[RUNPAR] Summary of registered runtime parameters for active sections
#
[_RUNPAR] # Runtime parameter section for rprm module
PARFWRITE = no # Do we write runtime parameter file
PARFNAME = outparfile # Runtime parameter file name for output (without .par)
#
[_MONITOR] # Runtime parameter section for monitor module
LOGLEVEL = 4 # Logging threshold for toolboxes
IFTIMDSCR = no # Write timer description in the summary
WALLTIME = 23:45 # Simulation wall time
#
[_CHKPOINT] # Runtime paramere section for checkpoint module
READCHKPT = no # Restat from checkpoint
CHKPFNUMBER = 1 # Restart file number
CHKPINTERVAL = 250 # Checkpiont saving frequency (number of time steps)
0 0.0000E+00 Write checkpoint
FILE:./session_00/cbox0.f00001
min/max: 0.0000 1.0000 0.0000 1.0000 0.0000 0.0000
min/max: 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000
min/max: 0.0000 0.0000
min/max: -0.50000 0.50001
0 0.0000E+00 done :: Write checkpoint
file size = 197.E-06GB
avg data-throughput = 0.2GB/s
io-nodes = 2
dump history points
reading history points
found 25 points
done :: userchk
gridpoints unique/tot: 3249 4096
dofs vel/pr: 3025 3249
Initialization successfully completed 0.42206E-01 sec
Starting time loop ...
WARNING: CFL-condition & surface tension
are not applicable
WARNING: Set DT=0.001 (arbitrarily)
DT/DTCFL/DTFS/DTINIT 0.100E-02 0.000E+00 0.000E+00 0.000E+00
Step 1, t= 1.0000000E-03, DT= 1.0000000E-03, C= 0.000 0.0000E+00 0.0000E+00
Solving for Hmholtz scalars
Temperature/Passive scalar solution
1 Hmholtz TEMP 1 1.2135E-05 7.0711E-05 1.0000E-07 1.0000E+03 F
1 Hmholtz TEMP 2 9.4476E-08 7.0711E-05 1.0000E-07 1.0000E+03 F
1 Hmholtz TEMP 1 9.4476E-08 1.2135E-05 1.0000E-07
1 Scalars done 1.0000E-03 1.0557E-03
Solving for fluid
1 1.00000E-05 2.66590E-02 3.83786E-02 6.94632E-01 1 Divergence
2 1.00000E-05 2.65944E-02 3.83786E-02 6.92948E-01 1 Divergence
3 1.00000E-05 1.35544E-02 3.83786E-02 3.53175E-01 1 Divergence
4 1.00000E-05 7.15514E-03 3.83786E-02 1.86436E-01 1 Divergence
5 1.00000E-05 2.74580E-03 3.83786E-02 7.15451E-02 1 Divergence
6 1.00000E-05 1.07267E-03 3.83786E-02 2.79497E-02 1 Divergence
7 1.00000E-05 3.93637E-04 3.83786E-02 1.02567E-02 1 Divergence
8 1.00000E-05 1.53015E-04 3.83786E-02 3.98699E-03 1 Divergence
9 1.00000E-05 6.38645E-05 3.83786E-02 1.66407E-03 1 Divergence
10 1.00000E-05 2.25613E-05 3.83786E-02 5.87863E-04 1 Divergence
11 1.00000E-05 8.70959E-06 3.83786E-02 2.26939E-04 1 Divergence
1 PRES gmres 11 8.7096E-06 3.8379E-02 1.0000E-05 2.1385E-03 3.9946E-03 F
New CG1-tolerance (RINIT*epsm) = 9.3802751400672878E-015 0.0000000000000000
1 Hmholtz VELX 1 9.3803E-02 5.0205E-05 1.0000E-08 1.0000E+03 F
1 Hmholtz VELX 2 1.4891E-04 5.0205E-05 1.0000E-08 1.0000E+03 F
1 Hmholtz VELX 3 4.1708E-07 5.0205E-05 1.0000E-08 1.0000E+03 F
1 Hmholtz VELX 4 1.8322E-09 5.0205E-05 1.0000E-08 1.0000E+03 F
1 Hmholtz VELX 3 1.8322E-09 9.3803E-02 1.0000E-08
New CG1-tolerance (RINIT*epsm) = 9.3806696654145940E-015 0.0000000000000000
1 Hmholtz VELY 1 9.3807E-02 5.0205E-05 1.0000E-08 1.0000E+03 F
1 Hmholtz VELY 2 1.4891E-04 5.0205E-05 1.0000E-08 1.0000E+03 F
1 Hmholtz VELY 3 4.1709E-07 5.0205E-05 1.0000E-08 1.0000E+03 F
1 Hmholtz VELY 4 1.8322E-09 5.0205E-05 1.0000E-08 1.0000E+03 F
1 Hmholtz VELY 3 1.8322E-09 9.3807E-02 1.0000E-08
L1/L2 DIV(V) 5.4833E-21 3.7375E-05
L1/L2 QTL 0.0000E+00 0.0000E+00
L1/L2 DIV(V)-QTL 5.4833E-21 3.7375E-05
1 Fluid done 1.0000E-03 6.2169E-03
DT/DTCFL/DTFS/DTINIT 0.500E-02 0.500E-02 0.000E+00 0.000E+00
Step 2, t= 2.2000000E-03, DT= 1.2000000E-03, C= 0.000 1.1409E-02 1.1408E-02
Solving for Hmholtz scalars
2 Hmholtz TEMP 2 5.7252E-09 2.0707E-04 1.0000E-07
2 Scalars done 2.2000E-03 5.3960E-04
Solving for fluid
2 PRES gmres 6 3.6028E-06 2.3462E-04 1.0000E-05 1.0502E-03 1.5017E-03 F
2 Hmholtz VELX 3 1.3271E-09 1.4495E-01 1.0000E-08
2 Hmholtz VELY 3 1.3270E-09 1.4494E-01 1.0000E-08
L1/L2 DIV(V) 1.3682E-20 5.7334E-05
L1/L2 QTL 0.0000E+00 0.0000E+00
L1/L2 DIV(V)-QTL 1.3682E-20 5.7334E-05
2 Fluid done 2.2000E-03 3.1508E-03
Step 3, t= 3.6400000E-03, DT= 1.4400000E-03, C= 0.000 1.9286E-02 7.8771E-03
Solving for Hmholtz scalars
3 Hmholtz TEMP 2 1.2347E-08 5.3061E-04 1.0000E-07
3 Scalars done 3.6400E-03 5.5089E-04
Solving for fluid
3 PRES gmres 5 8.6896E-06 3.3852E-04 1.0000E-05 8.7736E-04 1.8986E-03 F
3 Hmholtz VELX 3 1.4553E-09 1.8202E-01 1.0000E-08
3 Hmholtz VELY 3 1.4553E-09 1.8202E-01 1.0000E-08
And then the last lines:
index_final_step = 0
for line in lines[::-1]:
if line.startswith("Step") and ", t= " in line:
break
index_final_step -= 1
print("\n".join(lines[index_final_step-10:]))
Show code cell output
12076 Scalars done 6.6862E+02 1.1850E-03
Solving for fluid
12076 PRES gmres 4 5.1023E-06 7.7136E-05 1.0000E-05 1.5861E-03 2.1490E-03 F
12076 Hmholtz VELX 5 2.7375E-09 1.3692E-03 1.0000E-08
12076 Hmholtz VELY 5 6.5529E-09 1.6571E-03 1.0000E-08
L1/L2 DIV(V) 5.4939E-17 1.3902E-02
L1/L2 QTL 0.0000E+00 0.0000E+00
L1/L2 DIV(V)-QTL 5.4939E-17 1.3902E-02
12076 Fluid done 6.6862E+02 4.9612E-03
Step 12077, t= 6.6868108E+02, DT= 5.8662762E-02, C= 1.702 1.1718E+02 1.6843E-02
Solving for Hmholtz scalars
12077 Hmholtz TEMP 6 1.1404E-08 1.9579E-03 1.0000E-07
12077 Scalars done 6.6868E+02 9.1234E-03
Solving for fluid
12077 PRES gmres 4 5.1041E-06 7.7299E-05 1.0000E-05 7.2340E-04 1.0553E-03 F
12077 Hmholtz VELX 5 2.7140E-09 1.3700E-03 1.0000E-08
12077 Hmholtz VELY 5 6.5262E-09 1.6649E-03 1.0000E-08
L1/L2 DIV(V) 5.3329E-17 1.3909E-02
L1/L2 QTL 0.0000E+00 0.0000E+00
L1/L2 DIV(V)-QTL 5.3329E-17 1.3909E-02
12077 Fluid done 6.6868E+02 2.5126E-03
Load the simulation#
One can recreate a simulation object from the simulation directory.
from snek5000 import load
sim = load(path_run)
path_run: /home/docs/Sim_data/examples_snek/tuto/cbox_Ra2.000e+08_64x64_8x8_V1.x1._2023-08-24_07-52-10
INFO: session_id: 0
INFO: sim: <class 'snek5000_cbox.solver.SimulCbox'>
sim.oper: <class 'snek5000.operators.Operators'>
sim.output.print_stdout: <class 'snek5000.output.print_stdout.PrintStdOut'>
sim.output.phys_fields: <class 'snek5000.output.phys_fields.PhysFields'>
sim.output.history_points: <class 'snek5000.output.history_points.HistoryPoints'>
sim.output.remaining_clock_time: <class 'snek5000.output.remaining_clock_time.RemainingClockTime'>
sim.output: <class 'snek5000_cbox.output.OutputCbox'>
sim.make: <class 'snek5000.make.Make'>
Quickly start IPython and load a simulation
The command snek-ipy-load can be used to start a IPython session and load the
simulation saved in the current directory.
Load and plot history points data#
Then we are able to plot all the history points for one variable (here the temperature),
sim.output.history_points.plot(key='temperature');
ax = sim.output.history_points.plot(key='temperature')
ax.set_xlim(left=300)
ax.set_ylim([0.2, 0.36]);
or just one history point:
ax = sim.output.history_points.plot_1point(
index_point=12, key='temperature', tmin=300, tmax=800
)
coords, df = sim.output.history_points.load()
import numpy as np
from scipy import stats
from scipy.signal import argrelmax
df_point = df[df.index_points == 12]
times = df_point["time"].to_numpy()
signal = df_point["temperature"].to_numpy()
cond = times > 400
times = times[cond]
signal = signal[cond]
indices_maxima = argrelmax(signal)
times_maxima = times[indices_maxima]
signal_maxima = signal[indices_maxima]
cond = signal_maxima > 0
times_maxima = times_maxima[cond]
signal_maxima = signal_maxima[cond]
ax.plot(times_maxima, signal_maxima, "xr");
Moreover, we can also compute an approximation of the growth rate:
try:
slope, intercept, r_value, p_value, std_err = stats.linregress(
times_maxima, np.log(abs(signal_maxima))
)
except ValueError:
pass
else:
growth_rate = slope
print(f"The growth rate is {growth_rate:.2e}")
The growth rate is 3.79e-03
Load the flow field as xarray dataset#
There is also the possibility to load to whole field file in xarray dataset
field = sim.output.phys_fields.load()
field.temperature.plot();
which makes postprocessing of data easier:
x_new = np.linspace(field.x[0], field.x[-1], field.x.size)
y_new = np.linspace(field.y[0], field.y[-1], field.y.size)
field = field.drop_duplicates(["x", "y"])
field = field.interp(x=x_new, y=y_new)
field.temperature.mean('x').plot();
