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An issue about the example cede ohm_solver_magnetic_reconnection #5552

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Ceeeeeeeeeeeee opened this issue Jan 13, 2025 · 1 comment
Open

An issue about the example cede ohm_solver_magnetic_reconnection #5552

Ceeeeeeeeeeeee opened this issue Jan 13, 2025 · 1 comment
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@roelof-groenewald
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component: fluid-ohm Related to the Ohm's law solver (with fluid electrons) machine / system Machine or system-specific issue question Further information is requested

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@Ceeeeeeeeeeeee
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Ceeeeeeeeeeeee commented Jan 13, 2025 •
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Description

I'm giving the example code ohm_solver_magnetic_reconnection a try, where an input( inputs_test_2d_ohm_solver_magnetic_reconnection_picmi.py)and an analysis python script.
I ran the input.py on HPC, using the sbatch code as belows:

#!/bin/bash
#SBATCH -p amd_256
#SBATCH -N 1
#SBATCH -n 64
#SBATCH -t 60
export OMP_NUM_THREADS=64
export PATH=/public3/home/sc54759/soft/anaconda3/bin:$PATH
source activate
source activate warpx
python -u inputs_test_2d_ohm_solver_magnetic_ reconnection_picmi.py

I got some files (plane.dat, sim_parameters.dpkl, fields_000***.npz, warpx_used_inputs and so on) without completely waiting for it to run, and I could analysis theses datas with analysis.py on my Linux.

Then I want to retry the example with another method, i.e. writing an input txt file rather than a python script. After comparing the generated file _ warpx_used_inputs _ with other input files in other exampls, I thought that this file can serve as the input file.

Then I rewrote a sbatch code:
#!/bin/bash
#SBATCH -p amd_256
#SBATCH -N 1
#SBATCH -n 64
#SBATCH -t 1000

export PATH=/public3/home/sc54759/soft/anaconda3/bin:$PATH
source activate
source activate warpx
srun -n 64 warpx.2d /public3/home/sc54759/clx/nnn/warpx_used_inputs

Howerver, the outputs only contain a folder named 'diags' which only includes a plane.dat file.

I wonder why there is no sim_parameters.dpkl, fields_000***.npz? Maybe I should replenish the input file warpx_used_inputs ?
By the way, the HPC cluster I used is already supported.

log files:
Initializing AMReX (24.10)...
Initializing AMReX (24.10)...
Initializing AMReX (24.10)...
Initializing AMReX (24.10)...
Initializing AMReX (24.10)...
Initializing AMReX (24.10)...
Initializing AMReX (24.10)...
Initializing AMReX (24.10)...
Initializing AMReX (24.10)...
Initializing AMReX (24.10)...
Initializing AMReX (24.10)...
Initializing AMReX (24.10)...
Initializing AMReX (24.10)...
Initializing AMReX (24.10)...
Initializing AMReX (24.10)...
Initializing AMReX (24.10)...
Initializing AMReX (24.10)...
Initializing AMReX (24.10)...
Initializing AMReX (24.10)...
Initializing AMReX (24.10)...
Initializing AMReX (24.10)...
Initializing AMReX (24.10)...
Initializing AMReX (24.10)...
Initializing AMReX (24.10)...
Initializing AMReX (24.10)...
Initializing AMReX (24.10)...
Initializing AMReX (24.10)...
Initializing AMReX (24.10)...
Initializing AMReX (24.10)...
Initializing AMReX (24.10)...
Initializing AMReX (24.10)...
Initializing AMReX (24.10)...
Initializing AMReX (24.10)...
Initializing AMReX (24.10)...
Initializing AMReX (24.10)...
Initializing AMReX (24.10)...
Initializing AMReX (24.10)...
Initializing AMReX (24.10)...
Initializing AMReX (24.10)...
Initializing AMReX (24.10)...
Initializing AMReX (24.10)...
Initializing AMReX (24.10)...
Initializing AMReX (24.10)...
Initializing AMReX (24.10)...
Initializing AMReX (24.10)...
Initializing AMReX (24.10)...
Initializing AMReX (24.10)...
Initializing AMReX (24.10)...
Initializing AMReX (24.10)...
Initializing AMReX (24.10)...
Initializing AMReX (24.10)...
Initializing AMReX (24.10)...
Initializing AMReX (24.10)...
Initializing AMReX (24.10)...
Initializing AMReX (24.10)...
Initializing AMReX (24.10)...
Initializing AMReX (24.10)...
Initializing AMReX (24.10)...
Initializing AMReX (24.10)...
Initializing AMReX (24.10)...
Initializing AMReX (24.10)...
Initializing AMReX (24.10)...
Initializing AMReX (24.10)...
Initializing AMReX (24.10)...
OMP initialized with 64 OMP threads
OMP initialized with 64 OMP threads
OMP initialized with 64 OMP threads
...
OMP initialized with 64 OMP threads
OMP initialized with 64 OMP threads
OMP initialized with 64 OMP threads

libgomp: Thread creation failed: Resource temporarily unavailable
libgomp: Thread creation failed: Resource temporarily unavailable
AMReX (24.10) initialized
AMReX (24.10) initialized
AMReX (24.10) initialized
...
AMReX (24.10) initialized
AMReX (24.10) initialized
AMReX (24.10) initialized
AMReX (24.10) initialized
AMReX (24.10) initialized
srun: error: p2114: tasks 38,42: Exited with exit code 1
PICSAR (24.09)
WarpX (Unknown)

__        __             __  __
\ \      / /_ _ _ __ _ __\ \/ /
 \ \ /\ / / _` | '__| '_ \\  /
  \ V  V / (_| | |  | |_) /  \
   \_/\_/ \__,_|_|  | .__/_/\_\
                    |_|

PICSAR (24.09)
WarpX (Unknown)

__        __             __  __
\ \      / /_ _ _ __ _ __\ \/ /
 \ \ /\ / / _` | '__| '_ \\  /
  \ V  V / (_| | |  | |_) /  \
   \_/\_/ \__,_|_|  | .__/_/\_\
                    |_|

PICSAR (24.09)
WarpX (Unknown)

__        __             __  __
\ \      / /_ _ _ __ _ __\ \/ /
 \ \ /\ / / _` | '__| '_ \\  /
  \ V  V / (_| | |  | |_) /  \
   \_/\_/ \__,_|_|  | .__/_/\_\
                    |_|

......

PICSAR (24.09)
WarpX (Unknown)

__        __             __  __
\ \      / /_ _ _ __ _ __\ \/ /
 \ \ /\ / / _` | '__| '_ \\  /
  \ V  V / (_| | |  | |_) /  \
   \_/\_/ \__,_|_|  | .__/_/\_\
                    |_|

PICSAR (24.09)
WarpX (Unknown)

__        __             __  __
\ \      / /_ _ _ __ _ __\ \/ /
 \ \ /\ / / _` | '__| '_ \\  /
  \ V  V / (_| | |  | |_) /  \
   \_/\_/ \__,_|_|  | .__/_/\_\
                    |_|

Level 0: dt = 1.428954701e-10 ; dx = 0.01331647675 ; dz = 0.006658238375
Level 0: dt = 1.428954701e-10 ; dx = 0.01331647675 ; dz = 0.006658238375
Level 0: dt = 1.428954701e-10 ; dx = 0.01331647675 ; dz = 0.006658238375
Level 0: dt = 1.428954701e-10 ; dx = 0.01331647675 ; dz = 0.006658238375
Level 0: dt = 1.428954701e-10 ; dx = 0.01331647675 ; dz = 0.006658238375
Level 0: dt = 1.428954701e-10 ; dx = 0.01331647675 ; dz = 0.006658238375
Level 0: dt = 1.428954701e-10 ; dx = 0.01331647675 ; dz = 0.006658238375
Level 0: dt = 1.428954701e-10 ; dx = 0.01331647675 ; dz = 0.006658238375
Level 0: dt = 1.428954701e-10 ; dx = 0.01331647675 ; dz = 0.006658238375
Level 0: dt = 1.428954701e-10 ; dx = 0.01331647675 ; dz = 0.006658238375
Level 0: dt = 1.428954701e-10 ; dx = 0.01331647675 ; dz = 0.006658238375
Level 0: dt = 1.428954701e-10 ; dx = 0.01331647675 ; dz = 0.006658238375
Level 0: dt = 1.428954701e-10 ; dx = 0.01331647675 ; dz = 0.006658238375
Level 0: dt = 1.428954701e-10 ; dx = 0.01331647675 ; dz = 0.006658238375
Level 0: dt = 1.428954701e-10 ; dx = 0.01331647675 ; dz = 0.006658238375
Level 0: dt = 1.428954701e-10 ; dx = 0.01331647675 ; dz = 0.006658238375
Level 0: dt = 1.428954701e-10 ; dx = 0.01331647675 ; dz = 0.006658238375
Level 0: dt = 1.428954701e-10 ; dx = 0.01331647675 ; dz = 0.006658238375
Level 0: dt = 1.428954701e-10 ; dx = 0.01331647675 ; dz = 0.006658238375
Level 0: dt = 1.428954701e-10 ; dx = 0.01331647675 ; dz = 0.006658238375
Level 0: dt = 1.428954701e-10 ; dx = 0.01331647675 ; dz = 0.006658238375
Level 0: dt = 1.428954701e-10 ; dx = 0.01331647675 ; dz = 0.006658238375
Level 0: dt = 1.428954701e-10 ; dx = 0.01331647675 ; dz = 0.006658238375
Level 0: dt = 1.428954701e-10 ; dx = 0.01331647675 ; dz = 0.006658238375
Level 0: dt = 1.428954701e-10 ; dx = 0.01331647675 ; dz = 0.006658238375
Level 0: dt = 1.428954701e-10 ; dx = 0.01331647675 ; dz = 0.006658238375
Level 0: dt = 1.428954701e-10 ; dx = 0.01331647675 ; dz = 0.006658238375
Level 0: dt = 1.428954701e-10 ; dx = 0.01331647675 ; dz = 0.006658238375
Level 0: dt = 1.428954701e-10 ; dx = 0.01331647675 ; dz = 0.006658238375
Level 0: dt = 1.428954701e-10 ; dx = 0.01331647675 ; dz = 0.006658238375
Level 0: dt = 1.428954701e-10 ; dx = 0.01331647675 ; dz = 0.006658238375
Level 0: dt = 1.428954701e-10 ; dx = 0.01331647675 ; dz = 0.006658238375
Level 0: dt = 1.428954701e-10 ; dx = 0.01331647675 ; dz = 0.006658238375
Level 0: dt = 1.428954701e-10 ; dx = 0.01331647675 ; dz = 0.006658238375
Level 0: dt = 1.428954701e-10 ; dx = 0.01331647675 ; dz = 0.006658238375
Level 0: dt = 1.428954701e-10 ; dx = 0.01331647675 ; dz = 0.006658238375
Level 0: dt = 1.428954701e-10 ; dx = 0.01331647675 ; dz = 0.006658238375
Level 0: dt = 1.428954701e-10 ; dx = 0.01331647675 ; dz = 0.006658238375
Level 0: dt = 1.428954701e-10 ; dx = 0.01331647675 ; dz = 0.006658238375
Level 0: dt = 1.428954701e-10 ; dx = 0.01331647675 ; dz = 0.006658238375
Level 0: dt = 1.428954701e-10 ; dx = 0.01331647675 ; dz = 0.006658238375
Level 0: dt = 1.428954701e-10 ; dx = 0.01331647675 ; dz = 0.006658238375
Level 0: dt = 1.428954701e-10 ; dx = 0.01331647675 ; dz = 0.006658238375
Level 0: dt = 1.428954701e-10 ; dx = 0.01331647675 ; dz = 0.006658238375
Level 0: dt = 1.428954701e-10 ; dx = 0.01331647675 ; dz = 0.006658238375
Level 0: dt = 1.428954701e-10 ; dx = 0.01331647675 ; dz = 0.006658238375
Level 0: dt = 1.428954701e-10 ; dx = 0.01331647675 ; dz = 0.006658238375
Level 0: dt = 1.428954701e-10 ; dx = 0.01331647675 ; dz = 0.006658238375
Level 0: dt = 1.428954701e-10 ; dx = 0.01331647675 ; dz = 0.006658238375
Level 0: dt = 1.428954701e-10 ; dx = 0.01331647675 ; dz = 0.006658238375
Level 0: dt = 1.428954701e-10 ; dx = 0.01331647675 ; dz = 0.006658238375
Level 0: dt = 1.428954701e-10 ; dx = 0.01331647675 ; dz = 0.006658238375
Level 0: dt = 1.428954701e-10 ; dx = 0.01331647675 ; dz = 0.006658238375
Level 0: dt = 1.428954701e-10 ; dx = 0.01331647675 ; dz = 0.006658238375
Level 0: dt = 1.428954701e-10 ; dx = 0.01331647675 ; dz = 0.006658238375
Level 0: dt = 1.428954701e-10 ; dx = 0.01331647675 ; dz = 0.006658238375
Level 0: dt = 1.428954701e-10 ; dx = 0.01331647675 ; dz = 0.006658238375
Level 0: dt = 1.428954701e-10 ; dx = 0.01331647675 ; dz = 0.006658238375
Level 0: dt = 1.428954701e-10 ; dx = 0.01331647675 ; dz = 0.006658238375
Level 0: dt = 1.428954701e-10 ; dx = 0.01331647675 ; dz = 0.006658238375
Level 0: dt = 1.428954701e-10 ; dx = 0.01331647675 ; dz = 0.006658238375
Level 0: dt = 1.428954701e-10 ; dx = 0.01331647675 ; dz = 0.006658238375
@Ceeeeeeeeeeeee Ceeeeeeeeeeeee added the bug Something isn't working label Jan 13, 2025
@ax3l ax3l added question Further information is requested machine / system Machine or system-specific issue and removed bug Something isn't working labels Jan 14, 2025
@ax3l ax3l added the component: fluid-ohm Related to the Ohm's law solver (with fluid electrons) label Jan 14, 2025
@roelof-groenewald
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Hi. Welcome to WarpX!

I'm glad to hear the example script, as is, worked for you. This specific example is setup in a way that relies on some added Python code. For example, the sim_parameters.dpkl file is written at

WarpX/Examples/Tests/ohm_solver_magnetic_reconnection/inputs_test_2d_ohm_solver_magnetic_reconnection_picmi.py

Line 99 in 555f435

with open("sim_parameters.dpkl", "wb") as f:
and the .npz file is written in this function. Since these parts are relying on extra functionality, supplemented from Python, the example does not run "as is" from the native input.

Do you have a specific reason why you would like to run this example without Python? There are other examples that do not use Python if you want to take a look through some other examples.

Btw, based on the output you show, it looks like mpi is not working as it should in your installation, are you sure you compiled with MPI support? (All those output lines should only appear once).

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@ax3l @roelof-groenewald @Ceeeeeeeeeeeee