Demo Taylor-Green vortex (snek5000-tgv solver)#
Snek5000 repository contains a simple example solver for the Taylor-Green vortex flow. We are going to show how it can be used on a very small and short simulation.
Run a simulation by executing a script#
We will run the simulation by executing the script docs/examples/scripts/tuto_tgv.py, which contains:
from snek5000_tgv.solver import Simul
params = Simul.create_default_params()
params.output.sub_directory = "examples_snek/tuto"
params.oper.nx = params.oper.ny = params.oper.nz = 8
params.oper.elem.order = params.oper.elem.order_out = 8
params.oper.nproc_min = 2
params.nek.velocity.residual_tol = 1e-07
params.nek.pressure.residual_tol = 1e-05
params.nek.general.end_time = 10
params.nek.general.dt = -1
params.nek.general.target_cfl = 1.4
params.nek.general.extrapolation = "OIFS"
params.nek.general.write_control = "runTime"
params.nek.general.write_interval = 2.0
params.output.spatial_means.write_interval = 0.5
sim = Simul(params)
sim.make.exec("run_fg", nproc=2)
In normal life, we would just execute this script with something like
python tuto_tgv.py.
command = "python3 examples/scripts/tuto_tgv.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_tgv.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_tgv.py... (It can take few minutes.)
Script executed in 64.63 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).
Let us first look at the first lines, until the beginning of the time stepping:
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
INFO: session_id: 0
INFO: Writing params files... /home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/tgv.par, params_simul.xml, info_solver.xml
INFO: sim: <class 'snek5000_tgv.solver.SimulTGV'>
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.spatial_means: <class 'snek5000.output.spatial_means.SpatialMeans'>
sim.output: <class 'snek5000_tgv.output.OutputTGV'>
sim.make: <class 'snek5000.make.Make'>
INFO: Writing box file... /home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/tgv.box
INFO: Writing SIZE file... /home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/SIZE
Changing to shadow directory: /home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53
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_fg 1
total 7
Select jobs to execute...
[Mon Jun 9 09:19:53 2025]
rule internal_generate_box:
input: tgv.box, /home/docs/Nek5000/bin/genbox
output: box.re2
jobid: 2
reason: Missing output files: box.re2
resources: tmpdir=/tmp
input file name:
-3 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 -8 nelx nely nelz
Reading 512 = 8 8 8 elements for box 1.
Reading 2 =
0.0000 6.2832 1.0000 x0 x1 ratio
0.0000 6.2832 1.0000 y0 y1 ratio
0.0000 6.2832 1.0000 z0 z1 ratio
P ,P ,P ,P ,P ,P Velocity BCs
Beginning construction of box.re2
512 elements will be created for 1 boxes.
[Mon Jun 9 09:19:53 2025]
Finished job 2.
1 of 7 steps (14%) done
Select jobs to execute...
[Mon Jun 9 09:19:53 2025]
rule internal_move_box:
input: box.re2
output: tgv.re2
jobid: 1
reason: Missing output files: tgv.re2; Input files updated by another job: box.re2
resources: tmpdir=/tmp
[Mon Jun 9 09:19:53 2025]
Finished job 1.
2 of 7 steps (29%) done
Select jobs to execute...
[Mon Jun 9 09:19:53 2025]
rule internal_generate_map:
input: tgv.re2, /home/docs/Nek5000/bin/genmap
output: tgv.ma2
jobid: 3
reason: Missing output files: tgv.ma2; Input files updated by another job: tgv.re2
resources: tmpdir=/tmp, tolerance=0.01
Input .rea / .re2 name:
reading tgv.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: 8 512 4096 1.0000000000000000E-002
locglob: 1 1 4096
locglob: 2 9 4096
locglob: 3 81 4096
locglob: 1 729 4096
locglob: 2 729 4096
locglob: 3 729 4096
locglob: 1 729 4096
locglob: 2 729 4096
locglob: 3 729 4096
done locglob_lexico: 729 729 4096 8
start periodic vtx: 512 729
1 1 5 3 0.00000000E+00 1 shift
1 3 5 3 0.00000000E+00 2 shift
1 5 5 3 0.00000000E+00 3 shift
done: 93.8%
done: 94.7%
done: 95.7%
done: 96.7%
done: 97.7%
done: 98.6%
done: 99.6%
done rec_bisect
writing tgv.ma2
[Mon Jun 9 09:19:53 2025]
Finished job 3.
3 of 7 steps (43%) done
Select jobs to execute...
[Mon Jun 9 09:19:53 2025]
rule internal_generate_session:
input: tgv.re2, tgv.ma2, tgv.par
output: SESSION.NAME
jobid: 4
reason: Missing output files: SESSION.NAME; Input files updated by another job: tgv.re2, tgv.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...
[Mon Jun 9 09:19:54 2025]
Finished job 4.
4 of 7 steps (57%) done
Select jobs to execute...
[Mon Jun 9 09:19:54 2025]
rule internal_generate_makefile:
input: tgv.re2, tgv.ma2, tgv.usr, /home/docs/Nek5000/bin/nekconfig
output: makefile, .state
jobid: 6
reason: Missing output files: makefile; Input files updated by another job: tgv.re2, tgv.ma2
resources: tmpdir=/tmp
generating makefile ... done
[Mon Jun 9 09:19:55 2025]
Finished job 6.
5 of 7 steps (71%) done
Select jobs to execute...
[Mon Jun 9 09:19:55 2025]
rule compile:
input: SIZE, tgv.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 -DMPI -DUNDERSCORE -DGLOBAL_LONG_LONG -DTIMER -I/home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53 -I/home/docs/Nek5000/core -I./ -I/home/docs/Nek5000/core/experimental -I/home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj /home/docs/Nek5000/core/drive1.f -o /home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj/drive1.o
mpif77 -c -O2 -cpp -fdefault-real-8 -fdefault-double-8 -w -std=legacy -march=native -mcmodel=medium -std=legacy -w -DMPI -DUNDERSCORE -DGLOBAL_LONG_LONG -DTIMER -I/home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53 -I/home/docs/Nek5000/core -I./ -I/home/docs/Nek5000/core/experimental -I/home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj /home/docs/Nek5000/core/drive2.f -o /home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj/drive2.o
mpif77 -c -O2 -cpp -fdefault-real-8 -fdefault-double-8 -w -std=legacy -march=native -mcmodel=medium -std=legacy -w -DMPI -DUNDERSCORE -DGLOBAL_LONG_LONG -DTIMER -I/home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53 -I/home/docs/Nek5000/core -I./ -I/home/docs/Nek5000/core/experimental -I/home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj /home/docs/Nek5000/core/plan5.f -o /home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj/plan5.o
mpif77 -c -O2 -cpp -fdefault-real-8 -fdefault-double-8 -w -std=legacy -march=native -mcmodel=medium -std=legacy -w -DMPI -DUNDERSCORE -DGLOBAL_LONG_LONG -DTIMER -I/home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53 -I/home/docs/Nek5000/core -I./ -I/home/docs/Nek5000/core/experimental -I/home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj /home/docs/Nek5000/core/plan4.f -o /home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj/plan4.o
mpif77 -c -O2 -cpp -fdefault-real-8 -fdefault-double-8 -w -std=legacy -march=native -mcmodel=medium -std=legacy -w -DMPI -DUNDERSCORE -DGLOBAL_LONG_LONG -DTIMER -I/home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53 -I/home/docs/Nek5000/core -I./ -I/home/docs/Nek5000/core/experimental -I/home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj /home/docs/Nek5000/core/bdry.f -o /home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj/bdry.o
mpif77 -c -O2 -cpp -fdefault-real-8 -fdefault-double-8 -w -std=legacy -march=native -mcmodel=medium -std=legacy -w -DMPI -DUNDERSCORE -DGLOBAL_LONG_LONG -DTIMER -I/home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53 -I/home/docs/Nek5000/core -I./ -I/home/docs/Nek5000/core/experimental -I/home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj /home/docs/Nek5000/core/coef.f -o /home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj/coef.o
mpif77 -c -O2 -cpp -fdefault-real-8 -fdefault-double-8 -w -std=legacy -march=native -mcmodel=medium -std=legacy -w -DMPI -DUNDERSCORE -DGLOBAL_LONG_LONG -DTIMER -I/home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53 -I/home/docs/Nek5000/core -I./ -I/home/docs/Nek5000/core/experimental -I/home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj /home/docs/Nek5000/core/conduct.f -o /home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj/conduct.o
mpif77 -c -O2 -cpp -fdefault-real-8 -fdefault-double-8 -w -std=legacy -march=native -mcmodel=medium -std=legacy -w -DMPI -DUNDERSCORE -DGLOBAL_LONG_LONG -DTIMER -I/home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53 -I/home/docs/Nek5000/core -I./ -I/home/docs/Nek5000/core/experimental -I/home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj /home/docs/Nek5000/core/connect1.f -o /home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj/connect1.o
mpif77 -c -O2 -cpp -fdefault-real-8 -fdefault-double-8 -w -std=legacy -march=native -mcmodel=medium -std=legacy -w -DMPI -DUNDERSCORE -DGLOBAL_LONG_LONG -DTIMER -I/home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53 -I/home/docs/Nek5000/core -I./ -I/home/docs/Nek5000/core/experimental -I/home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj /home/docs/Nek5000/core/connect2.f -o /home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj/connect2.o
mpif77 -c -O2 -cpp -fdefault-real-8 -fdefault-double-8 -w -std=legacy -march=native -mcmodel=medium -std=legacy -w -DMPI -DUNDERSCORE -DGLOBAL_LONG_LONG -DTIMER -I/home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53 -I/home/docs/Nek5000/core -I./ -I/home/docs/Nek5000/core/experimental -I/home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj /home/docs/Nek5000/core/dssum.f -o /home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj/dssum.o
mpif77 -c -O2 -cpp -fdefault-real-8 -fdefault-double-8 -w -std=legacy -march=native -mcmodel=medium -std=legacy -w -DMPI -DUNDERSCORE -DGLOBAL_LONG_LONG -DTIMER -I/home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53 -I/home/docs/Nek5000/core -I./ -I/home/docs/Nek5000/core/experimental -I/home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj /home/docs/Nek5000/core/eigsolv.f -o /home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj/eigsolv.o
mpif77 -c -O2 -cpp -fdefault-real-8 -fdefault-double-8 -w -std=legacy -march=native -mcmodel=medium -std=legacy -w -DMPI -DUNDERSCORE -DGLOBAL_LONG_LONG -DTIMER -I/home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53 -I/home/docs/Nek5000/core -I./ -I/home/docs/Nek5000/core/experimental -I/home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj /home/docs/Nek5000/core/gauss.f -o /home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj/gauss.o
mpif77 -c -O2 -cpp -fdefault-real-8 -fdefault-double-8 -w -std=legacy -march=native -mcmodel=medium -std=legacy -w -DMPI -DUNDERSCORE -DGLOBAL_LONG_LONG -DTIMER -I/home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53 -I/home/docs/Nek5000/core -I./ -I/home/docs/Nek5000/core/experimental -I/home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj /home/docs/Nek5000/core/genxyz.f -o /home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj/genxyz.o
mpif77 -c -O2 -cpp -fdefault-real-8 -fdefault-double-8 -w -std=legacy -march=native -mcmodel=medium -std=legacy -w -DMPI -DUNDERSCORE -DGLOBAL_LONG_LONG -DTIMER -I/home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53 -I/home/docs/Nek5000/core -I./ -I/home/docs/Nek5000/core/experimental -I/home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj /home/docs/Nek5000/core/navier1.f -o /home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj/navier1.o
mpif77 -c -O2 -cpp -fdefault-real-8 -fdefault-double-8 -w -std=legacy -march=native -mcmodel=medium -std=legacy -w -DMPI -DUNDERSCORE -DGLOBAL_LONG_LONG -DTIMER -I/home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53 -I/home/docs/Nek5000/core -I./ -I/home/docs/Nek5000/core/experimental -I/home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj /home/docs/Nek5000/core/makeq.f -o /home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj/makeq.o
mpif77 -c -O2 -cpp -fdefault-real-8 -fdefault-double-8 -w -std=legacy -march=native -mcmodel=medium -std=legacy -w -DMPI -DUNDERSCORE -DGLOBAL_LONG_LONG -DTIMER -I/home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53 -I/home/docs/Nek5000/core -I./ -I/home/docs/Nek5000/core/experimental -I/home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj /home/docs/Nek5000/core/navier0.f -o /home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj/navier0.o
mpif77 -c -O2 -cpp -fdefault-real-8 -fdefault-double-8 -w -std=legacy -march=native -mcmodel=medium -std=legacy -w -DMPI -DUNDERSCORE -DGLOBAL_LONG_LONG -DTIMER -I/home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53 -I/home/docs/Nek5000/core -I./ -I/home/docs/Nek5000/core/experimental -I/home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj /home/docs/Nek5000/core/navier2.f -o /home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj/navier2.o
mpif77 -c -O2 -cpp -fdefault-real-8 -fdefault-double-8 -w -std=legacy -march=native -mcmodel=medium -std=legacy -w -DMPI -DUNDERSCORE -DGLOBAL_LONG_LONG -DTIMER -I/home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53 -I/home/docs/Nek5000/core -I./ -I/home/docs/Nek5000/core/experimental -I/home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj /home/docs/Nek5000/core/navier3.f -o /home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj/navier3.o
mpif77 -c -O2 -cpp -fdefault-real-8 -fdefault-double-8 -w -std=legacy -march=native -mcmodel=medium -std=legacy -w -DMPI -DUNDERSCORE -DGLOBAL_LONG_LONG -DTIMER -I/home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53 -I/home/docs/Nek5000/core -I./ -I/home/docs/Nek5000/core/experimental -I/home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj /home/docs/Nek5000/core/navier4.f -o /home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj/navier4.o
mpif77 -c -O2 -cpp -fdefault-real-8 -fdefault-double-8 -w -std=legacy -march=native -mcmodel=medium -std=legacy -w -DMPI -DUNDERSCORE -DGLOBAL_LONG_LONG -DTIMER -I/home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53 -I/home/docs/Nek5000/core -I./ -I/home/docs/Nek5000/core/experimental -I/home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj /home/docs/Nek5000/core/prepost.f -o /home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj/prepost.o
mpif77 -c -O2 -cpp -fdefault-real-8 -fdefault-double-8 -w -std=legacy -march=native -mcmodel=medium -std=legacy -w -DMPI -DUNDERSCORE -DGLOBAL_LONG_LONG -DTIMER -I/home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53 -I/home/docs/Nek5000/core -I./ -I/home/docs/Nek5000/core/experimental -I/home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj /home/docs/Nek5000/core/speclib.f -o /home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj/speclib.o
mpif77 -c -O2 -cpp -fdefault-real-8 -fdefault-double-8 -w -std=legacy -march=native -mcmodel=medium -std=legacy -w -DMPI -DUNDERSCORE -DGLOBAL_LONG_LONG -DTIMER -I/home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53 -I/home/docs/Nek5000/core -I./ -I/home/docs/Nek5000/core/experimental -I/home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj /home/docs/Nek5000/core/map2.f -o /home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj/map2.o
mpif77 -c -O2 -cpp -fdefault-real-8 -fdefault-double-8 -w -std=legacy -march=native -mcmodel=medium -std=legacy -w -DMPI -DUNDERSCORE -DGLOBAL_LONG_LONG -DTIMER -I/home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53 -I/home/docs/Nek5000/core -I./ -I/home/docs/Nek5000/core/experimental -I/home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj /home/docs/Nek5000/core/mvmesh.f -o /home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj/mvmesh.o
mpif77 -c -O2 -cpp -fdefault-real-8 -fdefault-double-8 -w -std=legacy -march=native -mcmodel=medium -std=legacy -w -DMPI -DUNDERSCORE -DGLOBAL_LONG_LONG -DTIMER -I/home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53 -I/home/docs/Nek5000/core -I./ -I/home/docs/Nek5000/core/experimental -I/home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj /home/docs/Nek5000/core/ic.f -o /home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj/ic.o
mpif77 -c -O2 -cpp -fdefault-real-8 -fdefault-double-8 -w -std=legacy -march=native -mcmodel=medium -std=legacy -w -DMPI -DUNDERSCORE -DGLOBAL_LONG_LONG -DTIMER -I/home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53 -I/home/docs/Nek5000/core -I./ -I/home/docs/Nek5000/core/experimental -I/home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj /home/docs/Nek5000/core/gfldr.f -o /home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj/gfldr.o
mpif77 -c -O2 -cpp -fdefault-real-8 -fdefault-double-8 -w -std=legacy -march=native -mcmodel=medium -std=legacy -w -DMPI -DUNDERSCORE -DGLOBAL_LONG_LONG -DTIMER -I/home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53 -I/home/docs/Nek5000/core -I./ -I/home/docs/Nek5000/core/experimental -I/home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj /home/docs/Nek5000/core/ssolv.f -o /home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj/ssolv.o
mpif77 -c -O2 -cpp -fdefault-real-8 -fdefault-double-8 -w -std=legacy -march=native -mcmodel=medium -std=legacy -w -DMPI -DUNDERSCORE -DGLOBAL_LONG_LONG -DTIMER -I/home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53 -I/home/docs/Nek5000/core -I./ -I/home/docs/Nek5000/core/experimental -I/home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj /home/docs/Nek5000/core/planx.f -o /home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj/planx.o
mpif77 -c -O3 -cpp -fdefault-real-8 -fdefault-double-8 -w -std=legacy -march=native -mcmodel=medium -std=legacy -w -DMPI -DUNDERSCORE -DGLOBAL_LONG_LONG -DTIMER -I/home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53 -I/home/docs/Nek5000/core -I./ -I/home/docs/Nek5000/core/experimental -I/home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj /home/docs/Nek5000/core/math.f -o /home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj/math.o
mpif77 -c -O2 -cpp -fdefault-real-8 -fdefault-double-8 -w -std=legacy -march=native -mcmodel=medium -std=legacy -w -DMPI -DUNDERSCORE -DGLOBAL_LONG_LONG -DTIMER -I/home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53 -I/home/docs/Nek5000/core -I./ -I/home/docs/Nek5000/core/experimental -I/home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj /home/docs/Nek5000/core/mxm_wrapper.f -o /home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj/mxm_wrapper.o
mpif77 -c -O2 -cpp -fdefault-real-8 -fdefault-double-8 -w -std=legacy -march=native -mcmodel=medium -std=legacy -w -DMPI -DUNDERSCORE -DGLOBAL_LONG_LONG -DTIMER -I/home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53 -I/home/docs/Nek5000/core -I./ -I/home/docs/Nek5000/core/experimental -I/home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj /home/docs/Nek5000/core/hmholtz.f -o /home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj/hmholtz.o
mpif77 -c -O2 -cpp -fdefault-real-8 -fdefault-double-8 -w -std=legacy -march=native -mcmodel=medium -std=legacy -w -DMPI -DUNDERSCORE -DGLOBAL_LONG_LONG -DTIMER -I/home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53 -I/home/docs/Nek5000/core -I./ -I/home/docs/Nek5000/core/experimental -I/home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj /home/docs/Nek5000/core/subs1.f -o /home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj/subs1.o
mpif77 -c -O2 -cpp -fdefault-real-8 -fdefault-double-8 -w -std=legacy -march=native -mcmodel=medium -std=legacy -w -DMPI -DUNDERSCORE -DGLOBAL_LONG_LONG -DTIMER -I/home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53 -I/home/docs/Nek5000/core -I./ -I/home/docs/Nek5000/core/experimental -I/home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj /home/docs/Nek5000/core/subs2.f -o /home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj/subs2.o
mpif77 -c -O2 -cpp -fdefault-real-8 -fdefault-double-8 -w -std=legacy -march=native -mcmodel=medium -std=legacy -w -DMPI -DUNDERSCORE -DGLOBAL_LONG_LONG -DTIMER -I/home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53 -I/home/docs/Nek5000/core -I./ -I/home/docs/Nek5000/core/experimental -I/home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj /home/docs/Nek5000/core/gmres.f -o /home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj/gmres.o
mpif77 -c -O2 -cpp -fdefault-real-8 -fdefault-double-8 -w -std=legacy -march=native -mcmodel=medium -std=legacy -w -DMPI -DUNDERSCORE -DGLOBAL_LONG_LONG -DTIMER -I/home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53 -I/home/docs/Nek5000/core -I./ -I/home/docs/Nek5000/core/experimental -I/home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj /home/docs/Nek5000/core/hsmg.f -o /home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj/hsmg.o
mpif77 -c -O2 -cpp -fdefault-real-8 -fdefault-double-8 -w -std=legacy -march=native -mcmodel=medium -std=legacy -w -DMPI -DUNDERSCORE -DGLOBAL_LONG_LONG -DTIMER -I/home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53 -I/home/docs/Nek5000/core -I./ -I/home/docs/Nek5000/core/experimental -I/home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj /home/docs/Nek5000/core/convect.f -o /home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj/convect.o
mpif77 -c -O0 -cpp -fdefault-real-8 -fdefault-double-8 -w -std=legacy -march=native -mcmodel=medium -std=legacy -w -DMPI -DUNDERSCORE -DGLOBAL_LONG_LONG -DTIMER -I/home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53 -I/home/docs/Nek5000/core -I./ -I/home/docs/Nek5000/core/experimental -I/home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj /home/docs/Nek5000/core/convect2.f -o /home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj/convect2.o
mpif77 -c -O2 -cpp -fdefault-real-8 -fdefault-double-8 -w -std=legacy -march=native -mcmodel=medium -std=legacy -w -DMPI -DUNDERSCORE -DGLOBAL_LONG_LONG -DTIMER -I/home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53 -I/home/docs/Nek5000/core -I./ -I/home/docs/Nek5000/core/experimental -I/home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj /home/docs/Nek5000/core/induct.f -o /home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj/induct.o
mpif77 -c -O2 -cpp -fdefault-real-8 -fdefault-double-8 -w -std=legacy -march=native -mcmodel=medium -std=legacy -w -DMPI -DUNDERSCORE -DGLOBAL_LONG_LONG -DTIMER -I/home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53 -I/home/docs/Nek5000/core -I./ -I/home/docs/Nek5000/core/experimental -I/home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj /home/docs/Nek5000/core/perturb.f -o /home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj/perturb.o
mpif77 -c -O2 -cpp -fdefault-real-8 -fdefault-double-8 -w -std=legacy -march=native -mcmodel=medium -std=legacy -w -DMPI -DUNDERSCORE -DGLOBAL_LONG_LONG -DTIMER -I/home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53 -I/home/docs/Nek5000/core -I./ -I/home/docs/Nek5000/core/experimental -I/home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj /home/docs/Nek5000/core/navier5.f -o /home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj/navier5.o
mpif77 -c -O2 -cpp -fdefault-real-8 -fdefault-double-8 -w -std=legacy -march=native -mcmodel=medium -std=legacy -w -DMPI -DUNDERSCORE -DGLOBAL_LONG_LONG -DTIMER -I/home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53 -I/home/docs/Nek5000/core -I./ -I/home/docs/Nek5000/core/experimental -I/home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj /home/docs/Nek5000/core/navier6.f -o /home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj/navier6.o
mpif77 -c -O2 -cpp -fdefault-real-8 -fdefault-double-8 -w -std=legacy -march=native -mcmodel=medium -std=legacy -w -DMPI -DUNDERSCORE -DGLOBAL_LONG_LONG -DTIMER -I/home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53 -I/home/docs/Nek5000/core -I./ -I/home/docs/Nek5000/core/experimental -I/home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj /home/docs/Nek5000/core/navier7.f -o /home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj/navier7.o
mpif77 -c -O2 -cpp -fdefault-real-8 -fdefault-double-8 -w -std=legacy -march=native -mcmodel=medium -std=legacy -w -DMPI -DUNDERSCORE -DGLOBAL_LONG_LONG -DTIMER -I/home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53 -I/home/docs/Nek5000/core -I./ -I/home/docs/Nek5000/core/experimental -I/home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj /home/docs/Nek5000/core/navier8.f -o /home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj/navier8.o
mpif77 -c -O2 -cpp -fdefault-real-8 -fdefault-double-8 -w -std=legacy -march=native -mcmodel=medium -std=legacy -w -DMPI -DUNDERSCORE -DGLOBAL_LONG_LONG -DTIMER -I/home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53 -I/home/docs/Nek5000/core -I./ -I/home/docs/Nek5000/core/experimental -I/home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj /home/docs/Nek5000/core/fast3d.f -o /home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj/fast3d.o
mpif77 -c -O2 -cpp -fdefault-real-8 -fdefault-double-8 -w -std=legacy -march=native -mcmodel=medium -std=legacy -w -DMPI -DUNDERSCORE -DGLOBAL_LONG_LONG -DTIMER -I/home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53 -I/home/docs/Nek5000/core -I./ -I/home/docs/Nek5000/core/experimental -I/home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj /home/docs/Nek5000/core/fasts.f -o /home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj/fasts.o
mpif77 -c -O2 -cpp -fdefault-real-8 -fdefault-double-8 -w -std=legacy -march=native -mcmodel=medium -std=legacy -w -DMPI -DUNDERSCORE -DGLOBAL_LONG_LONG -DTIMER -I/home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53 -I/home/docs/Nek5000/core -I./ -I/home/docs/Nek5000/core/experimental -I/home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj /home/docs/Nek5000/core/calcz.f -o /home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj/calcz.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/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj /home/docs/Nek5000/core/byte.c -o /home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj/byte.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/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj /home/docs/Nek5000/core/chelpers.c -o /home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj/chelpers.o
mpif77 -c -O2 -cpp -fdefault-real-8 -fdefault-double-8 -w -std=legacy -march=native -mcmodel=medium -std=legacy -w -DMPI -DUNDERSCORE -DGLOBAL_LONG_LONG -DTIMER -I/home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53 -I/home/docs/Nek5000/core -I./ -I/home/docs/Nek5000/core/experimental -I/home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj /home/docs/Nek5000/core/byte_mpi.f -o /home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj/byte_mpi.o
mpif77 -c -O2 -cpp -fdefault-real-8 -fdefault-double-8 -w -std=legacy -march=native -mcmodel=medium -std=legacy -w -DMPI -DUNDERSCORE -DGLOBAL_LONG_LONG -DTIMER -I/home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53 -I/home/docs/Nek5000/core -I./ -I/home/docs/Nek5000/core/experimental -I/home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj /home/docs/Nek5000/core/postpro.f -o /home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj/postpro.o
mpif77 -c -O2 -cpp -fdefault-real-8 -fdefault-double-8 -w -std=legacy -march=native -mcmodel=medium -std=legacy -w -DMPI -DUNDERSCORE -DGLOBAL_LONG_LONG -DTIMER -I/home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53 -I/home/docs/Nek5000/core -I./ -I/home/docs/Nek5000/core/experimental -I/home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj /home/docs/Nek5000/core/interp.f -o /home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj/interp.o
mpif77 -c -O2 -cpp -fdefault-real-8 -fdefault-double-8 -w -std=legacy -march=native -mcmodel=medium -std=legacy -w -DMPI -DUNDERSCORE -DGLOBAL_LONG_LONG -DTIMER -I/home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53 -I/home/docs/Nek5000/core -I./ -I/home/docs/Nek5000/core/experimental -I/home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj /home/docs/Nek5000/core/cvode_driver.f -o /home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj/cvode_driver.o
mpif77 -c -O2 -cpp -fdefault-real-8 -fdefault-double-8 -w -std=legacy -march=native -mcmodel=medium -std=legacy -w -DMPI -DUNDERSCORE -DGLOBAL_LONG_LONG -DTIMER -I/home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53 -I/home/docs/Nek5000/core -I./ -I/home/docs/Nek5000/core/experimental -I/home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj /home/docs/Nek5000/core/multimesh.f -o /home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj/multimesh.o
mpif77 -c -O2 -cpp -fdefault-real-8 -fdefault-double-8 -w -std=legacy -march=native -mcmodel=medium -std=legacy -w -DMPI -DUNDERSCORE -DGLOBAL_LONG_LONG -DTIMER -I/home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53 -I/home/docs/Nek5000/core -I./ -I/home/docs/Nek5000/core/experimental -I/home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj /home/docs/Nek5000/core/vprops.f -o /home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj/vprops.o
mpif77 -c -O2 -cpp -fdefault-real-8 -fdefault-double-8 -w -std=legacy -march=native -mcmodel=medium -std=legacy -w -DMPI -DUNDERSCORE -DGLOBAL_LONG_LONG -DTIMER -I/home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53 -I/home/docs/Nek5000/core -I./ -I/home/docs/Nek5000/core/experimental -I/home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj /home/docs/Nek5000/core/makeq_aux.f -o /home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj/makeq_aux.o
mpif77 -c -O2 -cpp -fdefault-real-8 -fdefault-double-8 -w -std=legacy -march=native -mcmodel=medium -std=legacy -w -DMPI -DUNDERSCORE -DGLOBAL_LONG_LONG -DTIMER -I/home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53 -I/home/docs/Nek5000/core -I./ -I/home/docs/Nek5000/core/experimental -I/home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj /home/docs/Nek5000/core/papi.f -o /home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj/papi.o
mpif77 -c -O2 -cpp -fdefault-real-8 -fdefault-double-8 -w -std=legacy -march=native -mcmodel=medium -std=legacy -w -DMPI -DUNDERSCORE -DGLOBAL_LONG_LONG -DTIMER -I/home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53 -I/home/docs/Nek5000/core -I./ -I/home/docs/Nek5000/core/experimental -I/home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj /home/docs/Nek5000/core/3rd_party/nek_in_situ.f -o /home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj/nek_in_situ.o
mpif77 -c -O2 -cpp -fdefault-real-8 -fdefault-double-8 -w -std=legacy -march=native -mcmodel=medium -std=legacy -w -DMPI -DUNDERSCORE -DGLOBAL_LONG_LONG -DTIMER -I/home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53 -I/home/docs/Nek5000/core -I./ -I/home/docs/Nek5000/core/experimental -I/home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj /home/docs/Nek5000/core/reader_rea.f -o /home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj/reader_rea.o
mpif77 -c -O2 -cpp -fdefault-real-8 -fdefault-double-8 -w -std=legacy -march=native -mcmodel=medium -std=legacy -w -DMPI -DUNDERSCORE -DGLOBAL_LONG_LONG -DTIMER -I/home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53 -I/home/docs/Nek5000/core -I./ -I/home/docs/Nek5000/core/experimental -I/home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj /home/docs/Nek5000/core/reader_par.f -o /home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj/reader_par.o
mpif77 -c -O2 -cpp -fdefault-real-8 -fdefault-double-8 -w -std=legacy -march=native -mcmodel=medium -std=legacy -w -DMPI -DUNDERSCORE -DGLOBAL_LONG_LONG -DTIMER -I/home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53 -I/home/docs/Nek5000/core -I./ -I/home/docs/Nek5000/core/experimental -I/home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj /home/docs/Nek5000/core/reader_re2.f -o /home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj/reader_re2.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/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj /home/docs/Nek5000/core/3rd_party/finiparser.c -o /home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/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/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj /home/docs/Nek5000/core/3rd_party/iniparser.c -o /home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/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/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj /home/docs/Nek5000/core/3rd_party/dictionary.c -o /home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj/dictionary.o
mpif77 -c -O2 -cpp -fdefault-real-8 -fdefault-double-8 -w -std=legacy -march=native -mcmodel=medium -std=legacy -w -DMPI -DUNDERSCORE -DGLOBAL_LONG_LONG -DTIMER -I/home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53 -I/home/docs/Nek5000/core -I./ -I/home/docs/Nek5000/core/experimental -I/home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj /home/docs/Nek5000/core/hpf.f -o /home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj/hpf.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/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj -I/home/docs/Nek5000/3rd_party/gslib/include /home/docs/Nek5000/core/fcrs.c -o /home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/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/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj -I/home/docs/Nek5000/3rd_party/gslib/include /home/docs/Nek5000/core/crs_xxt.c -o /home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/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/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj -I/home/docs/Nek5000/3rd_party/gslib/include /home/docs/Nek5000/core/crs_amg.c -o /home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/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/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/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/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/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/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/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/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/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/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj -I/home/docs/Nek5000/3rd_party/gslib/include /home/docs/Nek5000/core/partitioner.c -o /home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj/partitioner.o
mpif77 -c -O3 -cpp -fdefault-real-8 -fdefault-double-8 -w -std=legacy -march=native -mcmodel=medium -std=legacy -w -DMPI -DUNDERSCORE -DGLOBAL_LONG_LONG -DTIMER -I/home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53 -I/home/docs/Nek5000/core -I./ -I/home/docs/Nek5000/core/experimental -I/home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj /home/docs/Nek5000/core/mxm_std.f -o /home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj/mxm_std.o
mpif77 -c -O2 -cpp -fdefault-real-8 -fdefault-double-8 -w -std=legacy -march=native -mcmodel=medium -std=legacy -w -DMPI -DUNDERSCORE -DGLOBAL_LONG_LONG -DTIMER -I/home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53 -I/home/docs/Nek5000/core -I./ -I/home/docs/Nek5000/core/experimental -I/home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj /home/docs/Nek5000/core/comm_mpi.f -o /home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj/comm_mpi.o
mpif77 -O2 -cpp -fdefault-real-8 -fdefault-double-8 -w -std=legacy -march=native -mcmodel=medium -std=legacy -w -DMPI -DUNDERSCORE -DGLOBAL_LONG_LONG -DTIMER -I/home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53 -I/home/docs/Nek5000/core -I./ -I/home/docs/Nek5000/core/experimental -I/home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj -c /home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/tgv.f -o /home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj/tgv.o
done
mpif77 -c -O2 -cpp -fdefault-real-8 -fdefault-double-8 -w -std=legacy -march=native -mcmodel=medium -std=legacy -w -DMPI -DUNDERSCORE -DGLOBAL_LONG_LONG -DTIMER -I/home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53 -I/home/docs/Nek5000/core -I./ -I/home/docs/Nek5000/core/experimental -I/home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/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 -DMPI -DUNDERSCORE -DGLOBAL_LONG_LONG -DTIMER -I/home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53 -I/home/docs/Nek5000/core -I./ -I/home/docs/Nek5000/core/experimental -I/home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj -o nek5000 drive.o /home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/obj/tgv.o /home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/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
1814279 38356 727962240 729814875 2b80175b nek5000
[Mon Jun 9 09:20:11 2025]
Finished job 5.
6 of 7 steps (86%) done
Select jobs to execute...
[Mon Jun 9 09:20:11 2025]
rule run_fg:
input: tgv.re2, tgv.ma2, tgv.par, SESSION.NAME, nek5000
output: logs/run_2025-06-09T09-19-53.log
jobid: 0
reason: Missing output files: logs/run_2025-06-09T09-19-53.log; Input files updated by another job: SESSION.NAME, tgv.re2, nek5000, tgv.ma2
resources: tmpdir=/tmp, nproc=2
Log file:
/home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53/logs/run_2025-06-09T09-19-53.log
/----------------------------------------------------------\\
| _ __ ______ __ __ ______ ____ ____ ____ |
| / | / // ____// //_/ / ____/ / __ \\/ __ \\/ __ \\ |
| / |/ // __/ / ,< /___ \\ / / / // / / // / / / |
| / /| // /___ / /| | ____/ / / /_/ // /_/ // /_/ / |
| /_/ |_//_____//_/ |_|/_____/ \\___/ \\___/ \\___/ |
| |
|----------------------------------------------------------|
| |
| 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/tgv.par
general = [(null)]
general:stopat = [endTime]
general:endtime = [10]
general:dt = [-1]
general:timestepper = [bdf2]
general:extrapolation = [OIFS]
general:targetcfl = [1.4]
general:writecontrol = [runTime]
general:writeinterval = [2.0]
general:numsteps = [1]
general:variabledt = [yes]
general:filtering = [none]
general:filtermodes = [2]
general:filtercutoffratio = [0.65]
general:filterweight = [12.0]
general:writedoubleprecision = [yes]
general:dealiasing = [yes]
general:optlevel = [2]
general:loglevel = [2]
general:userparam01 = [6.283185307179586]
general:userparam10 = [100]
general:userparam11 = [0.5]
general:userparam12 = [5.0]
problemtype = [(null)]
problemtype:equation = [incompNS]
problemtype:variableproperties = [no]
problemtype:stressformulation = [no]
pressure = [(null)]
pressure:residualtol = [1e-05]
pressure:residualproj = [yes]
pressure:writetofieldfile = [yes]
pressure:preconditioner = [semg_xxt]
velocity = [(null)]
velocity:residualtol = [1e-07]
velocity:density = [1]
velocity:viscosity = [-1600]
velocity:residualproj = [no]
velocity:writetofieldfile = [yes]
reading ./session_00/tgv.re2
hdr:#v002 512 3 512 hdr
partioning elements to MPI ranks
reading mesh
readp_re2_mesh:pack/cr/unpack : 0.69E-04 0.44E-04 0.81E-05
readp_re2_mesh:byte_read_mpi : 0.43E-04
reading boundary faces 384 for ifield 1
readp_re2_bc:pack/cr/unpack : 0.14E-05 0.51E-05 0.75E-05
readp_re2_bc:byte_read_mpi : 0.12E-04
done :: read .re2 file 0.22E-02 sec
Reading ./session_00/tgv.ma2
done :: partioning 0.23989E-02 sec
reading mesh
readp_re2_mesh:pack/cr/unpack : 0.34E-04 0.96E-04 0.55E-05
readp_re2_mesh:byte_read_mpi : 0.10E-04
reading boundary faces 384 for ifield 1
readp_re2_bc:pack/cr/unpack : 0.13E-05 0.11E-04 0.47E-05
readp_re2_bc:byte_read_mpi : 0.11E-04
done :: read .re2 file 0.62E-03 sec
nelgt/nelgv/lelt: 512 512 256
lx1/lx2/lx3/lxd: 8 8 8 12
RK4 substeps: 1
setup mesh topology
Right-handed check complete for 512 elements. OK.
setvert3d: 8 65024 175616 65024 65024
gs_setup: 6272 unique labels shared
pairwise times (avg, min, max): 5.9031e-06 5.9001e-06 5.9061e-06
crystal router : 6.0201e-06 6.0191e-06 6.0211e-06
all reduce : 1.9787e-05 1.97795e-05 1.97945e-05
used all_to_all method: pairwise
handle bytes (avg, min, max): 968444 968444 968444
buffer bytes (avg, min, max): 100352 100352 100352
setupds time 1.2804E-02 seconds 0 8 65024 512
nElements max/min/bal: 256 256 1.00
nMessages max/min/avg: 1 1 1.00
msgSize max/min/avg: 6272 6272 6272.00
msgSizeSum max/min/avg: 6272 6272 6272.00
max multiplicity 8
done :: setup mesh topology
call usrdat
done :: usrdat
generate geometry data
done :: generate geometry data
call usrdat2
done :: usrdat2
8.8818E-16 8.8818E-16 8.8818E-16 8.8818E-16 8.8818E-16 8.8818E-16 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
0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 0.0000E+00 xyz repair 4
regenerate geometry data 1
done :: regenerate geometry data 1
verify mesh topology
0.0000000000000000 6.2831999999999999 Xrange
0.0000000000000000 6.2831999999999999 Yrange
0.0000000000000000 6.2831999999999999 Zrange
done :: verify mesh topology
mesh metrics:
GLL grid spacing min/max : 5.04E-02 1.64E-01
scaled Jacobian min/max/avg: 1.00E+00 1.00E+00 1.00E+00
aspect ratio min/max/avg: 1.00E+00 1.00E+00 1.00E+00
IFTRAN = T
IFFLOW = T
IFHEAT = F
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
Dealiasing enabled, nxd= 12
Estimated eigenvalues
EIGAA = 0.24999883078660279
EIGGA = 6344.2205330389206
EIGAE = 0.24999883078660282
EIGAS = 8.3333333333333343E-002
EIGGE = 6344.2205330389206
EIGGS = 2.0000000000000000
initialize pressure solver
mg_nx: 1 3 7
mg_ny: 1 3 7
mg_nz: 1 3 7
gs_setup: 128 unique labels shared
pairwise times (avg, min, max): 3.95e-07 3.93e-07 3.97e-07
crystal router : 3.89e-07 3.89e-07 3.89e-07
all reduce : 5.085e-07 5.06e-07 5.11e-07
used all_to_all method: crystal router
handle bytes (avg, min, max): 28564 28564 28564
buffer bytes (avg, min, max): 4096 4096 4096
setupds time 3.9010E-04 seconds 1 2 512 512
setvert3d: 4 9728 13824 9728 9728
gs_setup: 1152 unique labels shared
pairwise times (avg, min, max): 2.9926e-06 2.9871e-06 2.9981e-06
crystal router : 3.0246e-06 3.0221e-06 3.0271e-06
all reduce : 5.0646e-06 5.0131e-06 5.1161e-06
used all_to_all method: pairwise
handle bytes (avg, min, max): 177916 177916 177916
buffer bytes (avg, min, max): 18432 18432 18432
setupds time 3.1376E-03 seconds 2 4 9728 512
setvert3d: 4 9728 13824 9728 9728
gs_setup: 1152 unique labels shared
pairwise times (avg, min, max): 2.9781e-06 2.9761e-06 2.9801e-06
crystal router : 2.9591e-06 2.9551e-06 2.9631e-06
all reduce : 4.9676e-06 4.9261e-06 5.0091e-06
used all_to_all method: crystal router
handle bytes (avg, min, max): 233364 233364 233364
buffer bytes (avg, min, max): 36864 36864 36864
setupds time 2.9621E-03 seconds 3 4 9728 512
setvert3d: 6 31232 64000 31232 31232
gs_setup: 3200 unique labels shared
pairwise times (avg, min, max): 4.2176e-06 4.2021e-06 4.2331e-06
crystal router : 4.3911e-06 4.3871e-06 4.3951e-06
all reduce : 1.14213e-05 1.14193e-05 1.14233e-05
used all_to_all method: pairwise
handle bytes (avg, min, max): 493308 493308 493308
buffer bytes (avg, min, max): 51200 51200 51200
setupds time 5.9864E-03 seconds 4 6 31232 512
regenerate geometry data 1
done :: regenerate geometry data 1
h1_mg_nx: 1 3 7
h1_mg_ny: 1 3 7
h1_mg_nz: 1 3 7
gs_setup: 128 unique labels shared
pairwise times (avg, min, max): 4.11e-07 4.1e-07 4.12e-07
crystal router : 4.095e-07 4.09e-07 4.1e-07
all reduce : 5.265e-07 5.24e-07 5.29e-07
used all_to_all method: crystal router
handle bytes (avg, min, max): 28564 28564 28564
buffer bytes (avg, min, max): 4096 4096 4096
setupds time 2.7857E-04 seconds 5 2 512 512
setvert3d: 4 9728 13824 9728 9728
gs_setup: 1152 unique labels shared
pairwise times (avg, min, max): 2.98e-06 2.976e-06 2.984e-06
crystal router : 2.9536e-06 2.9511e-06 2.9561e-06
all reduce : 5.26965e-06 5.2191e-06 5.3202e-06
used all_to_all method: crystal router
handle bytes (avg, min, max): 233364 233364 233364
buffer bytes (avg, min, max): 36864 36864 36864
setupds time 2.9844E-03 seconds 6 4 9728 512
setvert3d: 4 9728 13824 9728 9728
gs_setup: 1152 unique labels shared
pairwise times (avg, min, max): 2.9425e-06 2.93e-06 2.955e-06
crystal router : 2.9661e-06 2.9661e-06 2.9661e-06
all reduce : 7.1626e-06 7.1111e-06 7.2141e-06
used all_to_all method: pairwise
handle bytes (avg, min, max): 177916 177916 177916
buffer bytes (avg, min, max): 18432 18432 18432
setupds time 2.8780E-03 seconds 7 4 9728 512
setvert3d: 6 31232 64000 31232 31232
gs_setup: 3200 unique labels shared
pairwise times (avg, min, max): 4.1935e-06 4.183e-06 4.204e-06
crystal router : 4.3916e-06 4.3851e-06 4.3981e-06
all reduce : 1.15622e-05 1.15512e-05 1.15732e-05
used all_to_all method: pairwise
handle bytes (avg, min, max): 493308 493308 493308
buffer bytes (avg, min, max): 51200 51200 51200
setupds time 5.5550E-03 seconds 8 6 31232 512
setvert3d: 8 65024 175616 65024 65024
gs_setup: 6272 unique labels shared
pairwise times (avg, min, max): 6.9307e-06 6.9202e-06 6.9412e-06
crystal router : 6.0686e-06 6.0631e-06 6.0741e-06
all reduce : 1.85639e-05 1.85604e-05 1.85674e-05
used all_to_all method: crystal router
handle bytes (avg, min, max): 1.26965e+06 1269652 1269652
buffer bytes (avg, min, max): 200704 200704 200704
setupds time 1.0688E-02 seconds 9 8 65024 512
setvert3d: 10 111104 373248 111104 111104
gs_setup: 10368 unique labels shared
pairwise times (avg, min, max): 8.2252e-06 8.2152e-06 8.2352e-06
crystal router : 8.4122e-06 8.4082e-06 8.4162e-06
all reduce : 2.54296e-05 2.54276e-05 2.54316e-05
used all_to_all method: pairwise
handle bytes (avg, min, max): 1.60332e+06 1603324 1603324
buffer bytes (avg, min, max): 165888 165888 165888
setupds time 1.8533E-02 seconds 10 10 111104 512
setup h1 coarse grid, nx_crs= 2
gs_setup: 128 unique labels shared
pairwise times (avg, min, max): 4.195e-07 4.16e-07 4.23e-07
crystal router : 3.91e-07 3.9e-07 3.92e-07
all reduce : 5.191e-07 5.161e-07 5.221e-07
used all_to_all method: crystal router
handle bytes (avg, min, max): 28564 28564 28564
buffer bytes (avg, min, max): 4096 4096 4096
done :: setup h1 coarse grid 1.8934624999999983E-002 sec
call usrdat3
done :: usrdat3
set initial conditions
nekuic (1) for ifld 1
call nekuic for vel
xyz min 0.0000 0.0000 0.0000
uvwpt min -1.0000 -1.0000 0.0000 0.0000 0.0000
xyz max 6.2832 6.2832 6.2832
uvwpt max 1.0000 1.0000 0.0000 0.0000 0.0000
done :: set initial conditions
call userchk
done :: userchk
gridpoints unique/tot: 175616 262144
dofs vel/pr: 175616 175616
Initialization successfully completed 0.29239 sec
Starting time loop ...
DT/DTCFL/DTFS/DTINIT 0.705E-01 0.705E-01 0.000E+00 0.100E+01
Step 1, t= 7.0514701E-02, DT= 7.0514701E-02, C= 1.400 0.0000E+00 0.0000E+00
Solving for fluid
1 1.00000E-05 2.52360E-02 2.90119E-02 8.69851E-01 1 Divergence
2 1.00000E-05 1.96682E-02 2.90119E-02 6.77936E-01 1 Divergence
3 1.00000E-05 4.90290E-03 2.90119E-02 1.68996E-01 1 Divergence
4 1.00000E-05 9.83124E-04 2.90119E-02 3.38870E-02 1 Divergence
5 1.00000E-05 2.97185E-04 2.90119E-02 1.02436E-02 1 Divergence
6 1.00000E-05 8.08661E-05 2.90119E-02 2.78735E-03 1 Divergence
7 1.00000E-05 1.99279E-05 2.90119E-02 6.86889E-04 1 Divergence
8 1.00000E-05 5.84148E-06 2.90119E-02 2.01348E-04 1 Divergence
1 PRES gmres 8 5.8415E-06 2.9012E-02 1.0000E-05 4.1769E-02 6.9694E-02 F
1 Hmholtz VELX 1 6.2719E-02 6.2500E-04 1.0000E-07 1.4181E+01 F
1 Hmholtz VELX 2 1.4356E-03 6.2500E-04 1.0000E-07 1.4181E+01 F
1 Hmholtz VELX 3 4.5884E-05 6.2500E-04 1.0000E-07 1.4181E+01 F
1 Hmholtz VELX 4 1.9981E-06 6.2500E-04 1.0000E-07 1.4181E+01 F
1 Hmholtz VELX 5 7.6937E-08 6.2500E-04 1.0000E-07 1.4181E+01 F
1 Hmholtz VELX 4 7.6937E-08 6.2719E-02 1.0000E-07
1 Hmholtz VELY 1 6.2719E-02 6.2500E-04 1.0000E-07 1.4181E+01 F
1 Hmholtz VELY 2 1.4356E-03 6.2500E-04 1.0000E-07 1.4181E+01 F
1 Hmholtz VELY 3 4.5884E-05 6.2500E-04 1.0000E-07 1.4181E+01 F
1 Hmholtz VELY 4 1.9981E-06 6.2500E-04 1.0000E-07 1.4181E+01 F
1 Hmholtz VELY 5 7.6937E-08 6.2500E-04 1.0000E-07 1.4181E+01 F
1 Hmholtz VELY 4 7.6937E-08 6.2719E-02 1.0000E-07
1 Hmholtz VELZ 1 8.8340E-02 6.2500E-04 1.0000E-07 1.4181E+01 F
1 Hmholtz VELZ 2 2.0220E-03 6.2500E-04 1.0000E-07 1.4181E+01 F
1 Hmholtz VELZ 3 6.4629E-05 6.2500E-04 1.0000E-07 1.4181E+01 F
1 Hmholtz VELZ 4 2.8144E-06 6.2500E-04 1.0000E-07 1.4181E+01 F
1 Hmholtz VELZ 5 1.0837E-07 6.2500E-04 1.0000E-07 1.4181E+01 F
1 Hmholtz VELZ 6 6.2106E-09 6.2500E-04 1.0000E-07 1.4181E+01 F
1 Hmholtz VELZ 5 6.2106E-09 8.8340E-02 1.0000E-07
L1/L2 DIV(V) 8.2201E-20 1.1544E-05
L1/L2 QTL 0.0000E+00 0.0000E+00
L1/L2 DIV(V)-QTL 8.2201E-20 1.1544E-05
1 Fluid done 7.0515E-02 1.3965E-01
Step 2, t= 1.4102940E-01, DT= 7.0514701E-02, C= 1.398 2.4337E-01 2.4337E-01
Solving for fluid
2 PRES gmres 5 3.1277E-06 3.7775E-04 1.0000E-05 2.7993E-02 4.1827E-02 F
2 Hmholtz VELX 4 2.5189E-08 9.3788E-02 1.0000E-07
2 Hmholtz VELY 4 2.5189E-08 9.3788E-02 1.0000E-07
2 Hmholtz VELZ 4 3.5489E-08 1.3213E-01 1.0000E-07
L1/L2 DIV(V) 1.0992E-18 5.2770E-06
L1/L2 QTL 0.0000E+00 0.0000E+00
L1/L2 DIV(V)-QTL 1.0992E-18 5.2770E-06
2 Fluid done 1.4103E-01 1.0991E-01
Step 3, t= 2.1154410E-01, DT= 7.0514701E-02, C= 1.397 4.9193E-01 2.4856E-01
Solving for fluid
3 PRES gmres 5 4.3838E-06 4.8295E-04 1.0000E-05 2.4103E-02 3.7778E-02 F
3 Hmholtz VELX 4 2.5213E-08 9.3874E-02 1.0000E-07
3 Hmholtz VELY 4 2.5213E-08 9.3874E-02 1.0000E-07
3 Hmholtz VELZ 4 3.5424E-08 1.3187E-01 1.0000E-07
L1/L2 DIV(V) -8.3398E-19 5.8739E-06
L1/L2 QTL 0.0000E+00 0.0000E+00
L1/L2 DIV(V)-QTL -8.3398E-19 5.8739E-06
3 Fluid done 2.1154E-01 1.0218E-01
And then at the last lines, from the end of the time stepping:
index_final_step = 0
for line in lines[::-1]:
if line.startswith(" Final time step ="):
break
index_final_step -= 1
print("\n".join(lines[index_final_step-10:]))
Show code cell output
189 PRES gmres 6 5.1840E-06 2.0008E-02 1.0000E-05 2.9008E-02 4.5313E-02 F
189 Hmholtz VELX 4 4.6718E-08 4.8531E-01 1.0000E-07
189 Hmholtz VELY 4 4.6718E-08 4.8531E-01 1.0000E-07
189 Hmholtz VELZ 4 4.8170E-08 5.2882E-01 1.0000E-07
L1/L2 DIV(V) 5.4596E-17 2.2517E-01
L1/L2 QTL 0.0000E+00 0.0000E+00
L1/L2 DIV(V)-QTL 5.4596E-17 2.2517E-01
WARNING: DIV(V)-QTL too large!
189 Fluid done 9.9932E+00 1.1457E-01
Final time step = 6.7923831016951652E-003
Solving for fluid
190 Project PRES 3.1354E+00 1.1510E+01 3.6709E+00 8 8
190 PRES gmres 8 6.3968E-06 1.9908E-01 1.0000E-05 4.4350E-02 6.7007E-02 F
190 Hmholtz VELX 3 1.5445E-08 3.9761E-01 1.0000E-07
190 Hmholtz VELY 3 1.5445E-08 3.9761E-01 1.0000E-07
190 Hmholtz VELZ 3 1.5898E-08 4.3548E-01 1.0000E-07
L1/L2 DIV(V) 5.3094E-17 1.8640E-01
L1/L2 QTL 0.0000E+00 0.0000E+00
L1/L2 DIV(V)-QTL 5.3094E-17 1.8640E-01
WARNING: DIV(V)-QTL too large!
190 Fluid done 1.0000E+01 1.3404E-01
190 1.0000E+01 Write checkpoint
FILE:./session_00/tgv0.f00005
min/max: 0.0000 6.2832 0.0000 6.2832 0.0000 6.2832
min/max: -0.93992 0.93937 -0.93992 0.93936 -1.2602 1.2630
min/max: -0.59962 0.65044
190 1.0000E+01 done :: Write checkpoint
file size = 147.E-04GB
avg data-throughput = 1.6GB/s
io-nodes = 2
end of time-step loop
runtime statistics:
init time 0.29238685900000000 6.4487089450600797E-003
prep time 5 4.8814692000007653E-002 1.0766275270627059E-003
pres time 190 11.608973013999993 0.25604053607054489
crsl time 821 3.6201313000042035E-002 7.9843441584456028E-004
crsl min 3.5973882999847717E-002
crsl max 3.6201313000042035E-002
crsl avg 3.6087597999944876E-002
hmhz time 570 12.547839073999860 0.27674760197645298
eslv time 0 0.0000000000000000 0.0000000000000000
makf time 22.174886254000018 0.48907597226132421
makq time 0.0000000000000000 0.0000000000000000
proj time 2.1000799660000595 4.6318102353861433E-002
usvp time 192 1.8543515999989268E-002 4.0898465105778059E-004
usfq time 0 0.54202087800001064 1.1954486929824664E-002
usbc time 379 0.28036758900000752 6.1836191451041800E-003
usbc min 0.28036758900000752
usbc max 0.30500129300001666
usb avg 0.29268444100001212
uchk time 5.4674166999994611E-002 1.2058605882714238E-003
mltd time 570 0.58777982299997800 1.2963718736435375E-002
cdtp time 570 0.34994806400004796 7.7182443094118893E-003
axhm time 5625 6.3530661030001054 0.14011941010992823
advc time 190 21.449074347999975 0.47306790080879157
mxmf time 0.0000000000000000 0.0000000000000000
adc3 time 0.0000000000000000 0.0000000000000000
col2 time 0.0000000000000000 0.0000000000000000
col3 time 0.0000000000000000 0.0000000000000000
a2s2 time 0.0000000000000000 0.0000000000000000
add2 time 0.0000000000000000 0.0000000000000000
invc time 0.0000000000000000 0.0000000000000000
tgop time 17009 0.26624867600024538 5.8722208802591408E-003
dadd time 0 0.80731821999984987 1.7805725758772945E-002
vdss time 571 0.23119174900001171 5.0990263546709536E-003
vdss min 0.19559971599993792
vdss max 0.23119174900001171
vdss avg 0.21339573249997482
dsum time 5700 0.91450158499990675 2.0169697679403981E-002
dsum min 0.84869053700008112
dsum max 0.91450158499990675
dsum avg 0.88159606099999399
ddsl time 0 0.0000000000000000 0.0000000000000000
# nid tusbc tdadd tcrsl tvdss tdsum tgop qqq F
0 2.8037E-01 8.0732E-01 3.6201E-02 2.3119E-01 9.1450E-01 2.6625E-01 qqq
1 3.0500E-01 6.4095E-01 3.5974E-02 1.9560E-01 8.4869E-01 2.0605E-01 qqq
run successful: dying ...
total elapsed time : 4.56756E+01 sec
total solver time w/o IO : 4.52916E+01 sec
time/timestep : 2.38377E-01 sec
avg throughput per timestep : 3.68358E+05 gridpts/CPUs
total max memory usage : 6.01883E-01 GB
/home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53
[Mon Jun 9 09:20:57 2025]
Finished job 0.
7 of 7 steps (100%) done
Complete log: .snakemake/log/2025-06-09T091953.777826.snakemake.log
path_run: /home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53
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/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53'
Load the simulation#
We can now load the simulation and process the output.
from snek5000 import load
sim = load(path_run)
path_run: /home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53
INFO: session_id: 0
INFO: sim: <class 'snek5000_tgv.solver.SimulTGV'>
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.spatial_means: <class 'snek5000.output.spatial_means.SpatialMeans'>
sim.output: <class 'snek5000_tgv.output.OutputTGV'>
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.
How long was the run?#
snek5000-tgv saves a file remaining_clock_time.csv during the simulation. It can be
read manually,
!cat {path_run}/remaining_clock_time.csv
it,equation_times,dt,delta_clock_times,remaining_equation_times,remaining_clock_times
0, 0.0000000 , 1.0000000 , 0.0000000 ,nan,nan
1,0.70514701E-01,0.70514701E-01,0.56570400 , 9.9294853 , 79.659269
2,0.14102940 ,0.70514701E-01,0.26525800 , 9.8589706 , 37.086888
39, 2.7500733 ,0.70514701E-01, 8.1914860 , 7.2499267 , 22.762236
62, 4.0924894 ,0.58365917E-01, 5.1976380 , 5.9075106 , 22.873014
121, 7.0235319 ,0.47589975E-01, 14.131328 , 2.9764681 , 14.350337
163, 8.7145937 ,0.38392204E-01, 10.270252 , 1.2854063 , 7.8066027
190, 10.000000 ,0.67923831E-02, 6.8019440 , 0.0000000 , 0.0000000
and there is also an object sim.output.remaining_clock_time to load and plot these
data (which is especially useful during the simulation!):
sim.output.remaining_clock_time.plot()
Mean clock time per time step: 0.288 s
Parse, load and plot information contained in the Nek5000 log#
The object sim.output.print_stdout (see
snek5000.output.print_stdout.PrintStdOut) contains utilities to represent
information contained in the Nek5000 log. For example, one can do:
log_data = sim.output.print_stdout.load()
log_data
| t | dt | CFL | pres_it | pres_div | pres_div0 | pres_tol | pres_etime | pres_etime1 | |
|---|---|---|---|---|---|---|---|---|---|
| it | |||||||||
| 1.0 | 0.070515 | 0.070515 | 1.400 | 8.0 | 0.000006 | 0.029012 | 0.00001 | 0.041769 | 0.069694 |
| 2.0 | 0.141029 | 0.070515 | 1.398 | 5.0 | 0.000003 | 0.000378 | 0.00001 | 0.027993 | 0.041827 |
| 3.0 | 0.211544 | 0.070515 | 1.397 | 5.0 | 0.000004 | 0.000483 | 0.00001 | 0.024103 | 0.037778 |
| 4.0 | 0.282059 | 0.070515 | 1.395 | 5.0 | 0.000005 | 0.000541 | 0.00001 | 0.024533 | 0.038192 |
| 5.0 | 0.352574 | 0.070515 | 1.392 | 5.0 | 0.000005 | 0.000606 | 0.00001 | 0.024087 | 0.037702 |
| ... | ... | ... | ... | ... | ... | ... | ... | ... | ... |
| 185.0 | 9.794182 | 0.055285 | 1.502 | 6.0 | 0.000003 | 0.008834 | 0.00001 | 0.028540 | 0.044733 |
| 186.0 | 9.849467 | 0.055285 | 1.513 | 6.0 | 0.000003 | 0.007422 | 0.00001 | 0.029805 | 0.046206 |
| 187.0 | 9.904752 | 0.055285 | 1.459 | 5.0 | 0.000008 | 0.006278 | 0.00001 | 0.025854 | 0.041588 |
| 188.0 | 9.948980 | 0.044228 | 1.491 | 7.0 | 0.000003 | 0.032300 | 0.00001 | 0.034978 | 0.054312 |
| 189.0 | 9.993208 | 0.044228 | 1.441 | 6.0 | 0.000005 | 0.020008 | 0.00001 | 0.029008 | 0.045313 |
189 rows × 9 columns
and plot useful figures with
sim.output.print_stdout.plot_dt_cfl()
and
sim.output.print_stdout.plot_nb_iterations()
Visualize spatial means data#
In subroutine userchk of tgv.usr.f, the time stamp, kinetic energy and enstrophy are
output in a file spatial_means.csv. The data can be loaded with
df = sim.output.spatial_means.load()
df.head()
| time | energy | enstrophy | |
|---|---|---|---|
| 0 | 0.070515 | 0.124773 | 0.374512 |
| 1 | 0.564118 | 0.124451 | 0.385976 |
| 2 | 1.057721 | 0.124221 | 0.419261 |
| 3 | 1.551323 | 0.123958 | 0.479489 |
| 4 | 2.044926 | 0.123637 | 0.574664 |
Reference data#
import pandas as pd
ref = pd.read_csv(
"examples/snek5000-tgv/ref_data_spectral_code.csv",
sep=" ",
names=("time", "ref:energy", "ref:dE/dt", "ref:enstrophy"),
comment="#"
)
ref.head()
| time | ref:energy | ref:dE/dt | ref:enstrophy | |
|---|---|---|---|---|
| 0 | 0.00 | 0.125000 | 0.000469 | 0.375000 |
| 1 | 0.01 | 0.124995 | 0.000469 | 0.374990 |
| 2 | 0.02 | 0.124991 | 0.000469 | 0.374987 |
| 3 | 0.03 | 0.124986 | 0.000469 | 0.374993 |
| 4 | 0.04 | 0.124981 | 0.000469 | 0.375006 |
Result#
sim.output.spatial_means.plot(logy=True, colormap="Accent")
import matplotlib.pyplot as plt
ax = plt.gca()
ref.plot(
"time",
["ref:energy", "ref:enstrophy"],
ax=ax,
style="--",
logy=True,
colormap="Accent"
)
ax.set(
title=f"Taylor-Green vortex: evolution of K.E. and enstrophy. Re={-sim.params.nek.velocity.viscosity}"
)
ax.figure.tight_layout()
/tmp/ipykernel_3547/149631164.py:17: UserWarning: The figure layout has changed to tight
ax.figure.tight_layout()
Restart to run further#
We see that our first simulation was clearly too short. We can use the command line tool
snek-restart (see the How to page dedicated to restart) to
continue the simulation from the last saved file (--use-start-from -1):
print("Running the restart command...")
t_start = perf_counter()
lines = !snek-restart {sim.path_run} --use-start-from -1 --add-to-end-time 4
print(f"Command executed in {perf_counter() - t_start:.2f} s")
Running the restart command...
Command executed in 19.17 s
Let’s look at the end of the output of this command:
print("\n".join(lines[-120:]))
Show code cell output
61 PRES gmres 4 9.0073E-06 2.0465E-03 1.0000E-05 2.2678E-02 3.1821E-02 F
61 Hmholtz VELX 5 7.9906E-09 2.0020E-01 1.0000E-07
61 Hmholtz VELY 5 7.9906E-09 2.0020E-01 1.0000E-07
61 Hmholtz VELZ 5 9.7927E-09 1.9874E-01 1.0000E-07
L1/L2 DIV(V) -5.1157E-18 1.6627E-01
L1/L2 QTL 0.0000E+00 0.0000E+00
L1/L2 DIV(V)-QTL -5.1157E-18 1.6627E-01
WARNING: DIV(V)-QTL too large!
61 Fluid done 1.3864E+01 1.0986E-01
Step 62, t= 1.3965261E+01, DT= 1.0147541E-01, C= 1.300 1.5806E+01 2.4605E-01
Solving for fluid
62 Project PRES 1.4125E-01 6.1215E-01 4.3339E+00 8 8
62 PRES gmres 5 8.7856E-06 8.9682E-03 1.0000E-05 2.8717E-02 3.9545E-02 F
62 Hmholtz VELX 5 1.5474E-08 2.0425E-01 1.0000E-07
62 Hmholtz VELY 5 1.5474E-08 2.0425E-01 1.0000E-07
62 Hmholtz VELZ 5 1.9796E-08 2.0334E-01 1.0000E-07
L1/L2 DIV(V) -1.3137E-17 1.6877E-01
L1/L2 QTL 0.0000E+00 0.0000E+00
L1/L2 DIV(V)-QTL -1.3137E-17 1.6877E-01
WARNING: DIV(V)-QTL too large!
62 Fluid done 1.3965E+01 1.1828E-01
Final time step = 3.4738634141188385E-002
Solving for fluid
63 Project PRES 3.1862E-01 1.4639E+00 4.5943E+00 8 8
63 PRES gmres 6 7.3972E-06 2.0230E-02 1.0000E-05 3.4977E-02 5.0389E-02 F
63 Hmholtz VELX 4 1.0404E-08 1.6432E-01 1.0000E-07
63 Hmholtz VELY 4 1.0404E-08 1.6432E-01 1.0000E-07
63 Hmholtz VELZ 4 1.2799E-08 1.6366E-01 1.0000E-07
L1/L2 DIV(V) -1.5436E-17 1.5004E-01
L1/L2 QTL 0.0000E+00 0.0000E+00
L1/L2 DIV(V)-QTL -1.5436E-17 1.5004E-01
WARNING: DIV(V)-QTL too large!
63 Fluid done 1.4000E+01 1.2496E-01
63 1.4000E+01 Write checkpoint
FILE:./session_01/tgv0.f00002
min/max: 0.0000 6.2832 0.0000 6.2832 0.0000 6.2832
min/max: -0.71934 0.71884 -0.71965 0.71915 -0.69198 0.68791
min/max: -0.99884E-01 0.20793
63 1.4000E+01 done :: Write checkpoint
file size = 147.E-04GB
avg data-throughput = 0.4GB/s
io-nodes = 4
end of time-step loop
runtime statistics:
init time 0.39815722400000003 2.4343273487517744E-002
prep time 2 6.8770725000000255E-002 4.2046319034258683E-003
pres time 63 4.4986284189999903 0.27504547279653607
crsl time 336 3.3299467000006189E-002 2.0359244622665004E-003
crsl min 3.3299467000006189E-002
crsl max 9.3229952000005056E-002
crsl avg 6.4345992749998082E-002
hmhz time 189 5.1117385340000023 0.31253093408609123
eslv time 0 0.0000000000000000 0.0000000000000000
makf time 7.5589747930000044 0.46215459516879676
makq time 0.0000000000000000 0.0000000000000000
proj time 0.63547605900000548 3.8852911780917716E-002
usvp time 65 3.9231759999999172E-003 2.3986239744243316E-004
usfq time 0 0.10993288100000009 6.7212800023282891E-003
usbc time 125 0.24093224300000282 1.4730561521370641E-002
usbc min 0.19463937999999903
usbc max 0.24093224300000282
usb avg 0.22261690675000026
uchk time 2.5147816000004042E-002 1.5375337319055472E-003
mltd time 189 0.10451156100000103 6.3898213034316777E-003
cdtp time 189 6.0872742999998120E-002 3.7217504580158902E-003
axhm time 2055 1.1603582130000150 7.0944128650411553E-002
advc time 63 7.4158564400000060 0.45340436034155657
mxmf time 0.0000000000000000 0.0000000000000000
adc3 time 0.0000000000000000 0.0000000000000000
col2 time 0.0000000000000000 0.0000000000000000
col3 time 0.0000000000000000 0.0000000000000000
a2s2 time 0.0000000000000000 0.0000000000000000
add2 time 0.0000000000000000 0.0000000000000000
invc time 0.0000000000000000 0.0000000000000000
tgop time 6137 2.1224170259999640 0.12976426146290687
dadd time 0 0.90410342800002752 5.5276749188925868E-002
vdss time 190 0.30913814899998771 1.8900660475098426E-002
vdss min 0.30913814899998771
vdss max 0.32600714800000297
vdss avg 0.31954339075000027
dsum time 2154 1.0213741339999878 6.2446662720951403E-002
dsum min 1.0213741339999878
dsum max 1.3385237219999917
dsum avg 1.1864073209999884
ddsl time 0 0.0000000000000000 0.0000000000000000
# nid tusbc tdadd tcrsl tvdss tdsum tgop qqq F
0 2.4093E-01 9.0410E-01 3.3299E-02 3.0914E-01 1.0214E+00 2.1224E+00 qqq
1 2.2314E-01 9.3645E-01 5.8432E-02 3.2359E-01 1.3385E+00 2.0266E+00 qqq
2 2.3175E-01 9.2924E-01 7.2422E-02 3.2601E-01 1.0524E+00 2.2794E+00 qqq
3 1.9464E-01 9.1558E-01 9.3230E-02 3.1944E-01 1.3333E+00 1.8787E+00 qqq
run successful: dying ...
total elapsed time : 1.67989E+01 sec
total solver time w/o IO : 1.62872E+01 sec
time/timestep : 2.58527E-01 sec
avg throughput per timestep : 1.69824E+05 gridpts/CPUs
total max memory usage : 6.99716E-01 GB
/home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53
[Mon Jun 9 09:21:19 2025]
Finished job 0.
2 of 2 steps (100%) done
Complete log: .snakemake/log/2025-06-09T092100.737244.snakemake.log
Namespace(add_to_end_time=4.0, end_time=None, modify_params=None, nb_mpi_procs=4, new_dir_results=False, num_steps=None, only_check=False, only_init=False, path='/home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53', session_id=None, skip_verify_contents=False, use_checkpoint=None, use_start_from='-1')
path_run: /home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53
# To visualize with IPython:
cd /home/docs/Sim_data/examples_snek/tuto/tgv_run_8x8x8_V2pix2pix2pi_2025-06-09_09-19-53; snek-ipy-load
The results of the new simulation were saved in a directory session_01
sorted(p.name for p in sim.path_run.iterdir())
['.snakemake',
'.state',
'SESSION.NAME',
'SIZE',
'Snakefile',
'build.log',
'config_simul.yml',
'info_solver.xml',
'logs',
'makefile',
'makefile_usr.inc',
'map_user_params.json',
'nek5000',
'obj',
'params_simul.xml',
'remaining_clock_time.csv',
'session_00',
'session_01',
'spatial_means.csv',
'tgv.box',
'tgv.log',
'tgv.ma2',
'tgv.nek5000',
'tgv.par',
'tgv.re2',
'tgv.usr']
which contains:
sorted(p.name for p in (sim.path_run / "session_01").iterdir())
['init_state.restart',
'tgv.ma2',
'tgv.par',
'tgv.re2',
'tgv0.f00001',
'tgv0.f00002']
The log files of the simulations are saved in logs:
paths_log = sorted(sim.path_run.glob("logs/*"))
[p.name for p in paths_log]
['run_2025-06-09T09-19-53.log', 'run_2025-06-09T09-21-00.log']
Let’s get the spatial means data from the second simulation:
df_new = sim.output.spatial_means.load()
df_new = df_new[df_new.time > df.time.max()]
We finally plot the new points!
df_new.plot("time", ["energy", "enstrophy"], ax=ax, logy=True, colormap="Accent", style=".-")
ax.figure
Note that we use for this tutorial very small and coarse simulations, which explain the differences between our results and the reference!
Let us see what gives the remaining_clock_time plot after the second simulation:
sim.output.remaining_clock_time.plot()
Mean clock time per time step: 0.266 s
