Comments (2)
archermarx
commented on July 18, 2024
Update: I installed AMReX and pyAMReX seperately, so python can find those now, but I still get the following error upon trying to run the 1D benchmark
Traceback (most recent call last):
File "/home/marksta/.local/lib/python3.10/site-packages/pywarpx/_libwarpx.py", line 90, in load_library
from . import warpx_pybind_1d as cxx_1d
ImportError: cannot import name 'warpx_pybind_1d' from 'pywarpx' (/home/marksta/.local/lib/python3.10/site-packages/pywarpx/__init__.py)
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/gpfs/accounts/goroda_root/goroda0/marksta/warpx/benchmark-1d/1d.py", line 399, in <module>
run.run_sim()
File "/gpfs/accounts/goroda_root/goroda0/marksta/warpx/benchmark-1d/1d.py", line 355, in run_sim
self.sim.step(self.max_steps - self.diag_steps)
File "/home/marksta/.local/lib/python3.10/site-packages/pywarpx/picmi.py", line 1924, in step
self.initialize_warpx(mpi_comm)
File "/home/marksta/.local/lib/python3.10/site-packages/pywarpx/picmi.py", line 1916, in initialize_warpx
pywarpx.warpx.init(mpi_comm, max_step=self.max_steps, stop_time=self.max_time)
File "/home/marksta/.local/lib/python3.10/site-packages/pywarpx/WarpX.py", line 98, in init
libwarpx.initialize(argv, mpi_comm=mpi_comm)
File "/home/marksta/.local/lib/python3.10/site-packages/pywarpx/_libwarpx.py", line 128, in initialize
self.amrex_init(argv, mpi_comm)
File "/home/marksta/.local/lib/python3.10/site-packages/pywarpx/_libwarpx.py", line 118, in amrex_init
self.libwarpx_so.amrex_init(argv)
File "/home/marksta/.local/lib/python3.10/site-packages/pywarpx/_libwarpx.py", line 42, in __getattr__
self.load_library()
File "/home/marksta/.local/lib/python3.10/site-packages/pywarpx/_libwarpx.py", line 112, in load_library
raise Exception(f"Dimensionality '{self.geometry_dim}' was not compiled in this Python install. Please recompile with -DWarpX_DIMS={_dims}")
Exception: Dimensionality '1d' was not compiled in this Python install. Please recompile with -DWarpX_DIMS=1
This is pyWarpX installed using the SLURM script in the first post. It seems the environment variables aren't working correctly?
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archermarx
commented on July 18, 2024
Ok, I have gotten it installed and running, but I am encountering issues running with OpenMP and MPI.
First, when running with one MPI rank and only one grid, everything works fine. However, when using two or more grids, the code will run fine for a while and then begin to hang or take a second or more per iteration. This makes it impossible to complete even quite small simulations.
Second, if I run with mpirun -n 2, the code crashes while writing the first openpmd file with the following output:
MPI initialized with 2 MPI processes
MPI initialized with thread support level 3
OMP initialized with 1 OMP threads
AMReX (23.10-14-g7ee29121ed70) initialized
PICSAR (23.09)
WarpX (23.10-19-g8459109a725b)
__ __ __ __
\ \ / /_ _ _ __ _ __\ \/ /
\ \ /\ / / _` | '__| '_ \\ /
\ V V / (_| | | | |_) / \
\_/\_/ \__,_|_| | .__/_/\_\
|_|
Level 0: dt = 1.485333333e-11 ; dz = 7.426666667e-05
Grids Summary:
Level 0 15 grids 600 cells 100 % of domain
smallest grid: 40 biggest grid: 40
-------------------------------------------------------------------------------
--------------------------- MAIN EM PIC PARAMETERS ----------------------------
-------------------------------------------------------------------------------
Precision: | DOUBLE
Particle precision: | DOUBLE
Geometry: | 1D (Z)
Operation mode: | Electrostatic
| - laboratory frame
| - vacuum
-------------------------------------------------------------------------------
Current Deposition: | direct
Particle Pusher: | Boris
Charge Deposition: | standard
Field Gathering: | energy-conserving
Particle Shape Factor:| 3
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
For full input parameters, see the file: warpx_used_inputs
--- INFO : Writing openPMD file diags/openpmd000000
[marksta@gl-login3 ecdi-1d-unbounded]$ cat error.log
terminate called after throwing an instance of 'std::runtime_error'
what(): Unknown file format! Did you specify a file ending?
SIGABRT
terminate called after throwing an instance of 'std::runtime_error'
what(): Unknown file format! Did you specify a file ending?
SIGABRT
See Backtrace.1.0 file for details
See Backtrace.0.0 file for details
Note that I have installed with openpmd support. I've attached the input file I used as well as the backtrace file and slurm script.
As an example of what I mean, here's a profiler output from when it's running well (here 16 grids)
STEP 11477 starts ...
STEP 11477 ends. TIME = 2.992538086e-08 DT = 2.607421875e-12
Evolve time = 90.40318536 s; This step = 0.004930898 s; Avg. per step = 0.007876900354 s
And here's from later in the simulation when it slows to a crawl
STEP 22003 starts ...
STEP 22003 ends. TIME = 5.737110352e-08 DT = 2.607421875e-12
Evolve time = 244.2563833 s; This step = 1.05330376 s; Avg. per step = 0.0111010491 s
Backtrace.0.0.txt
Backtrace.1.0.txt
srun.sh.txt
inputs_1d.txt
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Related Issues (20)
- Reusing Checkpoint folder HOT 2
- Reinstalling dependencies with provided script would delete dependencies of other BLAST codes HOT 1
- Function to get particle cell index.
- PICMI: Macroscopic Maxwell Solver
- using special functions as a user defined inputs for particle fields
- Examples: Thomson Parabola
- Non-conserved total weight of intra-species collision in DSMC module HOT 3
- Id track problem HOT 3
- NERSC Perlmutter Compilation Error HOT 2
- CUDA initialization failed HOT 5
- CMake: Finalize WarpX/ABLASTR Installer HOT 2
- CI: CUDA RZ PSATD
- NERSC Perlmutter Compilation Error (pre-#4986) HOT 3
- Error recompiling on Lassen HOT 3
- Some basic AMR questions`1 HOT 2
- Adios2 using Blosc2 HOT 3
- Poor scaling to multiple GPUs with electrostatic solver HOT 3
- PICMI documentation is gone HOT 4
- Issue with Limiting External Electric Field to Specific Boundary in 3D Simulation HOT 8
- Code clean-up: remove `tmp_particle_data`
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