xiaowang119
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xiaowang119
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xiaowang119
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1 year ago The function of uploading attachment seems to get wrong. I will post text directly here.
# ----------------------------------------------------------------------------------------
# SIMULATION PARAMETERS FOR THE PIC-CODE SMILEI
# ----------------------------------------------------------------------------------------
import math
# Reference
l0 = 2.0 * math.pi # laser wavelength 800nm/1um (2*pi*lr)
t0 = l0 # optical cicle 2.66851fs/3.333fs
# Simulation parameters for 800nu
# lm = l0 * 5.0 / 4.0 # 1um
# lr = 8e-7 / (2.0 * math.pi) # show the value of unit of length in smilei as SI unit
# tm = 5.0 * math.pi / 2.0 # 3.33fs
# Simulation parameters for 1um
lm = l0 # 1um
lr = 1e-6 / (2.0 * math.pi) # show the value of unit of length in smilei as SI unit
tm = t0 # 3.33fs
Lsim = [4.0 * lm, 2.0 * lm] # length of the simulation 4um × 2um
# Lsim = [5.0 * lm, 15.0 * lm]
# Lcell = [0.01*l0, 0.01*l0]
resx = 128.0 # nb of cells in on a lm
resy = 128.0
Tsim = 200.0 * t0 # duration of the simulation for 10 laser wavelength (about 48 tm)
# rest = 60. # time of timestep in one optical cycle
# Laser
omega = 1.0 # = 2PI/t0
a0 = 5.0 # 8.4 、10 、11.85
# particles in per cell
ppc = 16
def preprocess():
# density = 22.2203 # density of Carbon atom on 800nm
density = 34.6643 # density of Carbon atom on 1um
if smilei_mpi_rank == 0:
import numpy as np
from numpy import linspace, meshgrid, ceil
import h5py
# 输出模拟尺寸 及 网格大小(用作delta)
with open("Box.txt", "w") as f:
f.write(f"{Lsim[0]} {Lsim[1]} {2.0*lm/resx}")
vertices = [
(0.2 * Lsim[0], 0.2 * Lsim[1]), # (0.8 * Lsim[0], 0.1 * Lsim[1]),
(0.2 * Lsim[0], 0.8 * Lsim[1]), # (0.8 * Lsim[0], 0.9 * Lsim[1]),
(0.8 * Lsim[0], 0.8 * Lsim[1]), # (0.9 * Lsim[0], 0.9 * Lsim[1]),
(0.8 * Lsim[0], 0.2 * Lsim[1]), # (0.9 * Lsim[0], 0.1 * Lsim[1]),
] # 多边形顶点数据
with open("vertices.txt", "w") as f:
for vertex in vertices:
f.write(f"{vertex[0]} {vertex[1]}\n")
vertices = np.loadtxt("vertices.txt")
p = linspace(0.0, Lsim[0], int(resx * ceil(Lsim[0] / lm)) + 1)
q = linspace(0.0, Lsim[1], int(resy * ceil(Lsim[1] / lm)) + 1)
xx, yy = meshgrid(p, q)
points = np.vstack((xx.ravel(), yy.ravel())).T
def is_point_in_polygon(point, polygon):
"""
判断一个点是否在多边形内部
Args:
point: tuple, 待判断的点坐标
polygon: ndarray, 多边形的顶点坐标, 形状为(n, 2)
Returns:
bool, True表示在多边形内部, False表示在外部
"""
# 将多边形的顶点按顺时针排序
x, y = polygon[:, 0], polygon[:, 1]
cx, cy = x.mean(), y.mean()
angles = np.arctan2(y - cy, x - cx)
sorted_idx = np.argsort(angles)
polygon = polygon[sorted_idx]
# 计算射线与多边形的交点个数
x, y = polygon[:, 0], polygon[:, 1]
n = len(polygon)
count = 0
for i in range(n):
x1, y1 = x[i], y[i]
x2, y2 = x[(i + 1) % n], y[(i + 1) % n]
if (point[0] == x1 and point[1] == y1) or (
point[0] == x2 and point[1] == y2
):
return True # 点在多边形上
if (y1 > point[1]) != (y2 > point[1]) and point[0] < x1 + (x2 - x1) * (
point[1] - y1
) / (y2 - y1):
count += 1
return count % 2 == 1
is_inside = np.array([is_point_in_polygon(p, vertices) for p in points])
lenx = p.size
leny = q.size
data_C = np.zeros((lenx, leny)) # for Carbon atom
data_D = np.zeros((lenx, leny)) # for Deuterium atom
# data_E = np.zeros((lenx, leny)) # for Electron
for j in range(leny):
for i in range(lenx):
data_C[i, j] = density if (is_inside[j * lenx + i]) else 0.0
data_D[i, j] = density * 2.0 if (is_inside[j * lenx + i]) else 0.0
# data_E[i, j] = density*8. if (is_inside[j*lenx+i]) else 0.0
with h5py.File("CD2-profile.h5", "w") as f:
g = f.create_group("density_group")
g.create_dataset("C_profile", data=data_C)
g.create_dataset("D_profile", data=data_D)
# g.create_dataset("E_profile", data=data_E)
Main(
geometry="2Dcartesian",
interpolation_order=2,
# reference_angular_frequency_SI=2*math.pi*3e8/1.e-6/0.8, # Lr=0.8/2pi
reference_angular_frequency_SI=3e8 / lr, # ωr = c/lr
grid_length=Lsim,
cell_length=[lm / resx, lm / resx], # [l0/resx, l0/resx],
number_of_patches=[8, 8],
# timestep=t0/rest,
timestep_over_CFL=0.9,
simulation_time=Tsim,
EM_boundary_conditions=[
["silver-muller"],
["periodic"],
],
# print_every = 1,
cluster_width=1,
)
LaserPlanar1D(
box_side="xmin",
a0=a0,
omega=omega,
polarization_phi=0.0,
ellipticity=0.0,
# time_envelope=tconstant(),
time_envelope=tgaussian(
start=0.0, duration=33 * t0, fwhm=15.0 * t0, center=15.0 * t0
),
)
# Deuterium
Species(
name="Deuterium",
position_initialization="regular",
momentum_initialization="mj",
ionization_model="tunnel",
ionization_electrons="Electron",
temperature=[5.0e-8],
particles_per_cell=ppc,
# c_part_max=1.0,
mass=3670.03, # 3675.18,
charge=0.0,
atomic_number=1,
number_density="CD2-profile.h5/density_group/D_profile",
# mean_velocity=[0.5, 0., 0.],
# time_frozen=0.0,
boundary_conditions=[
["stop", "stop"],
["periodic", "periodic"],
],
)
# Carbon
Species(
name="Carbon",
position_initialization="regular",
momentum_initialization="mj",
ionization_model="tunnel",
ionization_electrons="Electron",
temperature=[5.0e-8],
particles_per_cell=ppc,
# c_part_max=1.0,
mass=21866.04,
charge=0.0,
atomic_number=6,
number_density="CD2-profile.h5/density_group/C_profile",
# mean_velocity=[-0.5, 0., 0.],
# time_frozen=0.0,
boundary_conditions=[
["stop", "stop"],
["periodic", "periodic"],
],
)
# Helium-3
Species(
name="He3",
position_initialization="regular",
momentum_initialization="cold",
# ionization_model='tunnel',
# ionization_electrons='Electron',
# temperature=[5.0e-8],
particles_per_cell=ppc,
# c_part_max=1.0,
mass=5495.66,
charge=0.0,
atomic_number=2,
number_density=0.0, # 'CD2-profile.h5/density_group/C_profile',
# mean_velocity=[-0.5, 0., 0.],
# time_frozen=0.0,
boundary_conditions=[
["stop", "stop"],
["periodic", "periodic"],
],
)
# Neutron
Species(
name="Neutron",
position_initialization="regular",
momentum_initialization="mj",
temperature=[5.0e-8],
particles_per_cell=ppc,
# c_part_max=1.0,
mass=1822.17,
charge=0.0,
atomic_number=0,
number_density=0.0, # 'CD2-profile.h5/density_group/C_profile',
# mean_velocity=[-0.5, 0., 0.],
# time_frozen=0.0,
boundary_conditions=[
["stop", "stop"],
["periodic", "periodic"],
],
)
# Electron
Species(
name="Electron",
position_initialization="regular",
momentum_initialization="mj",
temperature=[5.0e-8],
particles_per_cell=ppc,
# c_part_max=1.0,
mass=1.0,
charge=-1.0,
number_density=0.0, # 'CD2-profile.h5/density_group/E_profile',
# mean_velocity=[0.5, 0., 0.],
# time_frozen=0.0,
boundary_conditions=[
["stop", "stop"],
["periodic", "periodic"],
],
)
Collisions(
species1=["Deuterium"],
species2=["Deuterium"],
# coulomb_log=0.001,
nuclear_reaction=["He3", "Neutron"],
debug_every=10,
)
every = 400
DiagParticleBinning(
deposited_quantity="weight",
every=every,
flush_every=5 * every,
species=["Neutron"],
axes=[["ekin", 0.0, 2.0, 10000, "edge_inclusive"]], # 0keV-1MeV
# axes=[["ekin", 0.002, 20, 1000, "logscale", "edge_inclusive"]], # 1keV-10MeV
)
DiagParticleBinning(
deposited_quantity="weight",
every=every,
flush_every=5 * every,
species=["Electron"],
axes=[["ekin", 0.0, 2.0, 10000, "edge_inclusive"]], # 0keV-1MeV
# axes=[["ekin", 0.002, 20, 1000, "logscale", "edge_inclusive"]], # 1keV-10MeV
)
DiagParticleBinning(
deposited_quantity="weight",
every=every,
flush_every=5 * every,
species=["Deuterium"],
axes=[["ekin", 0.0, 2.0, 10000, "edge_inclusive"]], # 0keV-1MeV
# axes=[["ekin", 0.002, 20, 1000, "logscale", "edge_inclusive"]], # 1keV-10MeV
)
DiagScalar(
every=every,
vars=["Dens_Neutron", "Ntot_Neutron"],
precision=5,
) _ _
___ _ | | _ \ \ Version : ??-??
/ __| _ __ (_) | | ___ (_) | |
\__ \ | ' \ _ | | / -_) _ | |
|___/ |_|_|_| |_| |_| \___| |_| | |
/_/
Reading the simulation parameters [333/1866]│
--------------------------------------------------------------------------------
HDF5 version 1.12.0
Python version 3.8.10
Code run to here 0
Code run to here 1
Code run to here 2
Parsing pyinit.py
Parsing ??-??
Code run to here 3
Parsing pyprofiles.py
Parsing MyDDfusion.py
Parsing pycontrol.py
Check for function preprocess()
Calling python preprocess
/home/wyj/.local/lib/python3.8/site-packages/h5py/__init__.py:36: UserWarning: h5py is running again[318/1866$
12.0 when it was built against 1.12.2, this may cause problems
_warn(("h5py is running against HDF5 {0} when it was built against {1}, "
Warning! ***HDF5 library version mismatched error***
The HDF5 header files used to compile this application do not match
the version used by the HDF5 library to which this application is linked.
Data corruption or segmentation faults may occur if the application continues.
This can happen when an application was compiled by one version of HDF5 but
linked with a different version of static or shared HDF5 library.
You should recompile the application or check your shared library related
settings such as 'LD_LIBRARY_PATH'.
'HDF5_DISABLE_VERSION_CHECK' environment variable is set to 1, application will
continue at your own risk.
Headers are 1.12.2, library is 1.12.0
SUMMARY OF THE HDF5 CONFIGURATION
=================================
General Information:
------------------- [300/1866]
HDF5 Version: 1.12.0
Configured on: Sat Jun 5 20:40:41 CST 2021
Configured by: fcb@t2
Host system: x86_64-unknown-linux-gnu
Uname information: Linux t2 5.4.0-74-generic #83-Ubuntu SMP Sat May 8 02:35:39 UTC 2021 x86_64 x
86_64 x86_64 GNU/Linux
Byte sex: little-endian
Installation point: /usr/local/hdf5
Compiling Options:
------------------
Build Mode: production
Debugging Symbols: no
Asserts: no
Profiling: no
Optimization Level: high
Linking Options: [282/1866]
----------------
Libraries: static, shared
Statically Linked Executables:
LDFLAGS:
H5_LDFLAGS:
AM_LDFLAGS:
Extra libraries: -lz -ldl -lm
Archiver: ar
AR_FLAGS: cr
Ranlib: ranlib
Languages:
----------
C: yes
C Compiler: /usr/local/openmpi/bin/mpicc ( Configured with: ../src/configure -v --with-pk
gversion='Ubuntu 9.3.0-17ubuntu1~20.04' --with-bugurl=file:///usr/share/doc/gcc-9/README.Bugs --enable-languag
es=c,ada,c++,go,brig,d,fortran,objc,obj-c++,gm2 --prefix=/usr --with-gcc-major-version-only --progra[265/1866$
9 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-
included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx
-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtabl
e-verify --enable-plugin --enable-default-pie --with-system-zlib --with-target-system-zlib=auto --enable-objc-
gc=auto --enable-multiarch --disable-werror --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx
32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none=/build/gcc-9-HskZEa/gcc-9-9.3.0/d
ebian/tmp-nvptx/usr,hsa --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64
-linux-gnu --target=x86_64-linux-gnu built with gcc version 9.3.0 (Ubuntu 9.3.0-17ubuntu1~20.04))
CPPFLAGS:
H5_CPPFLAGS: -D_GNU_SOURCE -D_POSIX_C_SOURCE=200809L -DNDEBUG -UH5_DEBUG_API
AM_CPPFLAGS:
C Flags:
H5 C Flags: -std=c99 -Wall -Wcast-qual -Wconversion -Wextra -Wfloat-equal -Wformat=2 -W
init-self -Winvalid-pch -Wmissing-include-dirs -Wno-c++-compat -Wno-format-nonliteral -Wshadow -Wundef -Wwrite
-strings -pedantic -Wbad-function-cast -Wcast-align -Wdeclaration-after-statement -Wdisabled-optimization -Wmi
ssing-declarations -Wmissing-prototypes -Wnested-externs -Wold-style-definition -Wpacked -Wredundant[249/1866$
trict-prototypes -Wswitch-enum -Wswitch-default -Wunused-macros -Wunsafe-loop-optimizations -Wlogical-op -Wlar
ger-than=2560 -Wsync-nand -Wframe-larger-than=16384 -Wpacked-bitfield-compat -Wstrict-overflow=5 -Wjump-misses
-init -Wunsuffixed-float-constants -Wdouble-promotion -Wtrampolines -Wstack-usage=8192 -Wvector-operation-perf
ormance -Wdate-time -Warray-bounds=2 -Wc99-c11-compat -Wnull-dereference -Wunused-const-variable -Wduplicated-
cond -Whsa -Wnormalized -Walloc-zero -Walloca -Wduplicated-branches -Wformat-overflow=2 -Wformat-truncation=2
-Wimplicit-fallthrough=5 -Wrestrict -Wattribute-alias -Wcast-align=strict -Wshift-overflow=2 -Wattribute-alias
=2 -Wmissing-profile -fstdarg-opt -s -Wno-aggregate-return -Wno-inline -Wno-missing-format-attribute -Wno-miss
ing-noreturn -Wno-suggest-attribute=const -Wno-suggest-attribute=pure -Wno-suggest-attribute=noreturn -Wno-sug
gest-attribute=format -Wno-suggest-attribute=cold -Wno-suggest-attribute=malloc -O3
AM C Flags:
Shared C Library: yes
Static C Library: yes
Fortran: no
C++: no [232/1866]│
Java: no
Features:
---------
Parallel HDF5: yes
Parallel Filtered Dataset Writes: yes
Large Parallel I/O: yes
High-level library: yes
Build HDF5 Tests: yes
Build HDF5 Tools: yes
Threadsafety: no
Default API mapping: v112
With deprecated public symbols: yes
I/O filters (external): deflate(zlib) [216/1866]
MPE:
Map (H5M) API: no
Direct VFD: no
(Read-Only) S3 VFD: no
(Read-Only) HDFS VFD: no
dmalloc: no
Packages w/ extra debug output: none
API tracing: no
Using memory checker: no
Memory allocation sanity checks: no
Function stack tracing: no
Strict file format checks: no
Optimization instrumentation: no
Calling python _smilei_check
Calling python _prepare_checkpoint_dir
Calling python _keep_python_running() :
[WARNING](0) src/Params/Params.cpp:642 (Params) Resources allocated 104 underloaded regarding the total number
of patches 64
[WARNING](0) src/Params/Params.cpp:660 (Params) Patches distribution: hilbertian
[WARNING](0) src/Params/Params.cpp:1052 (compute) simulation_time has been redefined from 1256.637061 to 1256.
620845 to match timestep.
Geometry: 2Dcartesian │
--------------------------------------------------------------------------------
Interpolation order : 2
Maxwell solver : Yee
simulation duration = 1256.620845, total number of iterations = 40226
timestep = 0.031239 = 0.900000 x CFL, time resolution = 32.011247
Grid length: 25.1327, 12.5664
Cell length: 0.0490874, 0.0490874, 0
Number of cells: 512, 256
Spatial resolution: 20.3718, 20.3718
cell sorting: Activated
Electromagnetic boundary conditions
--------------------------------------------------------------------------------
xmin silver-muller, absorbing vector [1, 0]
xmax silver-muller, absorbing vector [-1, -0]
ymin periodic
ymax periodic
Vectorization:
--------------------------------------------------------------------------------
Mode: off
Initializing MPI
--------------------------------------------------------------------------------
2D built-in profile `constant` (value: 16.000000) [160/1866]
2D built-in profile `constant` (value: 16.000000)
2D built-in profile `constant` (value: 16.000000)
2D built-in profile `constant` (value: 16.000000)
applied topology for periodic BCs in y-direction
MPI_THREAD_MULTIPLE enabled
Number of MPI processes: 1
Number of threads per MPI process : 104
Number of patches: 8 x 8
Number of cells in one patch: 64 x 32
Dynamic load balancing: never
Initializing the restart environment
--------------------------------------------------------------------------------
Initializing species │
--------------------------------------------------------------------------------
Creating Species #0: Deuterium
> Pusher: boris
> Boundary conditions: stop stop periodic periodic
> Density profile: 2D from file `CD2-profile.h5/density_group/D_profile`
Creating Species #1: Carbon
> Pusher: boris
> Boundary conditions: stop stop periodic periodic
> Density profile: 2D from file `CD2-profile.h5/density_group/C_profile`
Creating Species #2: He3 [128/1866]
> Pusher: boris
> Boundary conditions: stop stop periodic periodic
> Density profile: 2D built-in profile `constant` (value: 0.000000)
Creating Species #3: Neutron
> Pusher: boris
> Boundary conditions: stop stop periodic periodic
> Density profile: 2D built-in profile `constant` (value: 0.000000)
Creating Species #4: Electron
> Pusher: boris
> Boundary conditions: stop stop periodic periodic
> Density profile: 2D built-in profile `constant` (value: 0.000000)
Initializing laser parameters [112/1866]│
--------------------------------------------------------------------------------
Laser #0: separable profile
omega : 1
chirp_profile : 1D built-in profile `tconstant` (0.000000)
time envelope : 1D built-in profile `tgaussian` (start: 0.000000, duration: 207.3
45115, sigma: 3203.736598, center: 94.247780, order: 2.000000)
space envelope (y) : 1D built-in profile `constant` (value: 0.000000)
space envelope (z) : 1D built-in profile `constant` (value: 5.000000)
phase (y) : 1D built-in profile `constant` (value: 0.000000)
phase (z) : 1D built-in profile `constant` (value: -0.000000)
delay phase (y) : 0
delay phase (z) : 0
Parameters for collisions #0 :
Intra collisions within species (0)
Coulomb logarithm: 0.000000
Debug every 10 timesteps
Collisional nuclear reaction D-D fusion
Initializing Patches
--------------------------------------------------------------------------------
First patch created
Approximately 10% of patches created
Approximately 20% of patches created
Approximately 30% of patches created
Approximately 40% of patches created
Approximately 50% of patches created
Approximately 60% of patches created
Approximately 70% of patches created
Approximately 80% of patches created
Approximately 90% of patches created
All patches created
Creating Diagnostics, antennas, and external fields │
--------------------------------------------------------------------------------
Created ParticleBinning #0: species Neutron
Axis ekin from 0 to 2 in 10000 steps [EDGE INCLUSIVE]
Created ParticleBinning #1: species Electron
Axis ekin from 0 to 2 in 10000 steps [EDGE INCLUSIVE]
Created ParticleBinning #2: species Deuterium
Axis ekin from 0 to 2 in 10000 steps [EDGE INCLUSIVE]
finalize MPI
--------------------------------------------------------------------------------
Done creating diagnostics, antennas, and external fields
Minimum memory consumption (does not include all temporary buffers)
--------------------------------------------------------------------------------
Particles: Master 143 MB; Max 143 MB; Global 0.14 GB
Fields: Master 16 MB; Max 16 MB; Global 0.0158 GB
scalars.txt: Master 0 MB; Max 0 MB; Global 0 GB
ParticleBinning0.h5: Master 0 MB; Max 0 MB; Global 7.45e-05 GB
ParticleBinning1.h5: Master 0 MB; Max 0 MB; Global 7.45e-05 GB
ParticleBinning2.h5: Master 0 MB; Max 0 MB; Global 7.45e-05 GB
Initial fields setup
--------------------------------------------------------------------------------
Applying external fields at time t = 0
Applying prescribed fields at time t = 0
Applying antennas at time t = 0
│
Open files & initialize diagnostics
--------------------------------------------------------------------------------
Running diags at time t = 0
--------------------------------------------------------------------------------
Species creation summary
--------------------------------------------------------------------------------
Species 0 (Deuterium) created with 751536 particles
Species 1 (Carbon) created with 751536 particles
Species 2 (He3) created with 0 particles
Species 3 (Neutron) created with 0 particles [32/1866]
Species 4 (Electron) created with 0 particles
Expected disk usage (approximate)
--------------------------------------------------------------------------------
WARNING: disk usage by non-uniform particles maybe strongly underestimated,
especially when particles are created at runtime (ionization, pair generation, etc.)
Expected disk usage for diagnostics:
File scalars.txt: 4.51 K
File ParticleBinning0.h5: 7.77 M
File ParticleBinning1.h5: 7.77 M
File ParticleBinning2.h5: 7.77 M
Total disk usage for diagnostics: 23.31 M
[16/1866]│
Keeping or closing the python runtime environment
--------------------------------------------------------------------------------
Checking for cleanup() function:
python cleanup function does not exist
Closing Python
Time-Loop started: number of time-steps n_time = 40226
--------------------------------------------------------------------------------
[WARNING](0) src/Params/Params.cpp:1385 (print_timestep_headers) The following `push time` assumes a global nu
mber of 104 cores (hyperthreading is unknown)
timestep sim time cpu time [s] ( diff [s] ) push time [ns]
4022/40226 1.2566e+02 1.0048e+03 ( 1.0048e+03 ) 4920
8044/40226 2.5130e+02 2.0287e+03 ( 1.0239e+03 ) 4961
12066/40226 3.7695e+02 3.0853e+03 ( 1.0566e+03 ) 5051
Stack trace (most recent call last) in thread 2180634:
#7 Object "[0xffffffffffffffff]", at 0xffffffffffffffff, in
#6 Object "/lib/x86_64-linux-gnu/libc.so.6", at 0x7f567063b132, in clone
#5 Object "/lib/x86_64-linux-gnu/libpthread.so.0", at 0x7f5670bd4608, in
#4 Object "/usr/lib/x86_64-linux-gnu/libgomp.so.1", at 0x7f567074378d, in
#3 Object "../build/smilei", at 0x5603fb36320d, in
#2 Object "../build/smilei", at 0x5603fb2b712f, in VectorPatch::dynamics(Params&, SmileiMPI*, SimWindow*, R
adiationTables&, MultiphotonBreitWheelerTables&, double, Timers&, int)
#1 Object "../build/smilei", at 0x5603fb3762d5, in SpeciesV::dynamics(double, unsigned int, ElectroMagn*, P
arams&, bool, PartWalls*, Patch*, SmileiMPI*, RadiationTables&, MultiphotonBreitWheelerTables&, std::vector<Di
agnostic*, std::allocator<Diagnostic*> >&)
#0 Object "../build/smilei", at 0x5603fb375896, in SpeciesV::computeParticleCellKeys(Params&, Particles*, i
nt*, int*, unsigned int, unsigned int)
Segmentation fault (Address not mapped to object [0x5601fdb15110])
Segmentation fault (core dumped)
mccoys
commented
1 year ago Are you able to reproduce the bug with a smaller simulation?
mccoys
commented
1 year ago Please also provide an input that does not rely on external resources (Box.txt, etc.)
xiaowang119
commented
1 year ago Here is a new inputfile which has smaller scale and don't rely on any external resources. But the same error still occurs!
mccoys
commented
1 year ago ``` # ---------------------------------------------------------------------------------------- # SIMULATION PARAMETERS FOR THE PIC-CODE SMILEI # ---------------------------------------------------------------------------------------- import math # Reference l0 = 2.0 * math.pi # laser wavelength 800nm/1um (2*pi*lr) t0 = l0 # optical cicle 2.66851fs/3.333fs # Simulation parameters for 800nu # lm = l0 * 5.0 / 4.0 # 1um # lr = 8e-7 / (2.0 * math.pi) # show the value of unit of length in smilei as SI unit # tm = 5.0 * math.pi / 2.0 # 3.33fs # Simulation parameters for 1um lm = l0 # 1um lr = 1e-6 / (2.0 * math.pi) # show the value of unit of length in smilei as SI unit tm = t0 # 3.33fs Lsim = [1.0 * lm, 1.0 * lm] # length of the simulation 4um × 2um # Lsim = [5.0 * lm, 15.0 * lm] # Lcell = [0.01*l0, 0.01*l0] resx = 120.0 # nb of cells in on a lm resy = 120.0 Tsim = 200.0 * t0 # duration of the simulation for 10 laser wavelength (about 48 tm) # rest = 60. # time of timestep in one optical cycle # Laser omega = 1.0 # = 2PI/t0 a0 = 5.0 # 8.4 、10 、11.85 # particles in per cell ppc = 16 def densityCarbon(x, y): density = 34.6643 if (x >= 0.2 * Lsim[0] and x <= 0.8 * Lsim[0]) and ( y >= 0.2 * Lsim[1] and y <= 0.8 * Lsim[1] ): return density else: return 0.0 def densityDeuterium(x, y): density = 34.6643 * 2.0 if (x >= 0.2 * Lsim[0] and x <= 0.8 * Lsim[0]) and ( y >= 0.2 * Lsim[1] and y <= 0.8 * Lsim[1] ): return density else: return 0.0 Main( geometry="2Dcartesian", interpolation_order=2, # reference_angular_frequency_SI=2*math.pi*3e8/1.e-6/0.8, # Lr=0.8/2pi reference_angular_frequency_SI=3e8 / lr, # ωr = c/lr grid_length=Lsim, cell_length=[lm / resx, lm / resx], # [l0/resx, l0/resx], number_of_patches=[8, 8], # timestep=t0/rest, # timestep_over_CFL=0.6, timestep_over_CFL=0.9, simulation_time=Tsim, EM_boundary_conditions=[ ["silver-muller"], ["periodic"], ], # print_every = 1, cluster_width=1, ) LaserPlanar1D( box_side="xmin", a0=a0, omega=omega, polarization_phi=0.0, ellipticity=0.0, # time_envelope=tconstant(), time_envelope=tgaussian( start=0.0, duration=33 * t0, fwhm=15.0 * t0, center=15.0 * t0 ), ) # LaserGaussian2D( # box_side="xmin", # a0=a0, # 电磁矢势，用于控制激光强度 # omega=omega, # focus=[2.0 * lm, 1.0 * lm], # waist=4.0 * lm, # # focus=[4.0 * lm, 7.5 * lm], # # waist=2 * lm, # 10 * lm, # incidence_angle=0, # polarization_phi=0, # ellipticity=0, # # time_envelope=tconstant(), # time_envelope=tgaussian( # start=0.0, duration=40 * tm, fwhm=15.0 * tm, center=15.0 * tm # ), # ) # LoadBalancing( # initial_balance=True, # every=100, # cell_load=1.0, # frozen_particle_load=0.1, # ) # Deuterium Species( name="Deuterium", position_initialization="regular", momentum_initialization="cold", ionization_model="tunnel", ionization_electrons="Electron", # temperature=[5.0e-8], particles_per_cell=ppc, # c_part_max=1.0, mass=3670.03, # 3675.18, charge=0.0, atomic_number=1, number_density=densityDeuterium, # mean_velocity=[0.5, 0., 0.], # time_frozen=0.0, boundary_conditions=[ ["stop", "stop"], ["periodic", "periodic"], ], ) # Carbon Species( name="Carbon", position_initialization="regular", momentum_initialization="cold", ionization_model="tunnel", ionization_electrons="Electron", # temperature=[5.0e-8], particles_per_cell=ppc, # c_part_max=1.0, mass=21866.04, charge=0.0, atomic_number=6, number_density=densityCarbon, # mean_velocity=[-0.5, 0., 0.], # time_frozen=0.0, boundary_conditions=[ ["stop", "stop"], ["periodic", "periodic"], ], ) # Helium-3 Species( name="He3", position_initialization="regular", momentum_initialization="cold", ionization_model="tunnel", ionization_electrons="Electron", # temperature=[5.0e-8], particles_per_cell=ppc, # c_part_max=1.0, mass=5495.66, charge=0.0, atomic_number=2, number_density=0.0, # 'CD2-profile.h5/density_group/C_profile', # mean_velocity=[-0.5, 0., 0.], # time_frozen=0.0, boundary_conditions=[ ["stop", "stop"], ["periodic", "periodic"], ], ) # Neutron Species( name="Neutron", position_initialization="regular", momentum_initialization="mj", # temperature=[5.0e-8], particles_per_cell=ppc, # c_part_max=1.0, mass=1822.17, charge=0.0, atomic_number=0, number_density=0.0, # 'CD2-profile.h5/density_group/C_profile', # mean_velocity=[-0.5, 0., 0.], # time_frozen=0.0, boundary_conditions=[ ["stop", "stop"], ["periodic", "periodic"], ], ) # Electron Species( name="Electron", position_initialization="regular", momentum_initialization="mj", temperature=[5.0e-8], particles_per_cell=ppc, # c_part_max=1.0, mass=1.0, charge=-1.0, number_density=0.0, # 'CD2-profile.h5/density_group/E_profile', # mean_velocity=[0.5, 0., 0.], # time_frozen=0.0, boundary_conditions=[ ["stop", "stop"], ["periodic", "periodic"], ], ) Collisions( species1=["Deuterium"], species2=["Deuterium"], # coulomb_log=0.001, nuclear_reaction=["He3", "Neutron"], # nuclear_reaction_multiplier=1.0, debug_every=10, ) every = 400 DiagParticleBinning( deposited_quantity="weight", every=every, flush_every=5 * every, species=["Neutron"], axes=[["ekin", 0.0, 2.0, 10000, "edge_inclusive"]], # 0keV-1MeV # axes=[["ekin", 0.002, 20, 1000, "logscale", "edge_inclusive"]], # 1keV-10MeV ) DiagParticleBinning( deposited_quantity="weight", every=every, flush_every=5 * every, species=["Electron"], axes=[["ekin", 0.0, 2.0, 10000, "edge_inclusive"]], # 0keV-1MeV # axes=[["ekin", 0.002, 20, 1000, "logscale", "edge_inclusive"]], # 1keV-10MeV ) DiagParticleBinning( deposited_quantity="weight", every=every, flush_every=5 * every, species=["Deuterium"], axes=[["ekin", 0.0, 2.0, 10000, "edge_inclusive"]], # 0keV-1MeV # axes=[["ekin", 0.002, 20, 1000, "logscale", "edge_inclusive"]], # 1keV-10MeV ) # DiagFields( # # name = "my field diag", # every=every, # flush_every=5 * every, # fields=["Ex", "Ey", "Ez", "Bx", "By", "Bz"], # # subgrid = None # ) DiagScalar( every=every, vars=["Dens_Neutron", "Ntot_Neutron"], precision=5, ) ```
mccoys
commented
1 year ago At which timestep do you see the error occur? Is this reproducible?
mccoys
commented
1 year ago I was able to run your reduced simulation without error. Please specify your version of smilei (and where you got it) and of MPI (mpirun --version). Is your output log for the reduced simulation identical?
xiaowang119
commented
1 year ago After simplifying the code overhead, I ran it again and encountered the same error as before when it reached 30%. Strangely, now when I run it again, it seems to be working properly again. I have been using Smilei-4.7.tar.gz downloaded from GitHub, and the version of MPI is mpirun (Open MPI) 4.1.1.
I will make further attempts.
xiaowang119
commented
1 year ago I have carried out simulations of two sizes and repeated each three times. The same error occurred each time, but the timing of the error was not consistent. Attached are my namelist and outlog files.
mccoys
commented
1 year ago Can you try using less threads? Like 16? You are using way too many compared to the number of patches.
Your pushtime is catastrophic because of this, and I wonder whether it could cause memory issues.
mccoys
commented
1 year ago Additionally, I don't think you have provided the exact same input file as that you have used because the basic data I obtain at the start of the log is different from yours
xiaowang119
commented
1 year ago I have tried repeatedly to run the program using mpirun -n 4 smilei namelist.py and set OMP_NUM_THREADS to 4 or 8; however, sometimes it reports an error and other times it runs normally.
I'm sorry, but I have also been puzzled by this bug. I am no longer sure if it is caused by the fusion part, as this error can occur with changes in simulation scale, grid division, and even density distribution. The most lethal thing is that even without any changes, you can repeatedly run it and get different results.
xiaowang119
commented
1 year ago The only thing that remains unchanged is the error message.
Stack trace (most recent call last) in thread 78755:#7 Object "[0xffffffffffffffff]", at 0xffffffffffffffff, in #6 Object "/usr/lib/x86_64-linux-gnu/libc.so.6", at 0x7f04f9567132, in clone
5 Object "/usr/lib/x86_64-linux-gnu/libpthread.so.0", at 0x7f04f9b15608, in #4 Object "/usr/lib/x86_64-linux-gnu/libgomp.so.1", at 0x7f04f966f78d, in
3 Object "/home/Data/wyj/Smilei-4.7/build/smilei", at 0x55e3aee6e1ed, in
2 Object "/home/Data/wyj/Smilei-4.7/build/smilei", at 0x55e3aed8ba0f, in VectorPatch::dynamics(Params&, SmileiMPI, SimWindow, RadiationTables&, MultiphotonBreitWheelerTables&, double, Timers&, int)
1 Object "/home/Data/wyj/Smilei-4.7/build/smilei", at 0x55e3aee8fd25, in SpeciesV::dynamics(double, unsigned int, ElectroMagn, Params&, bool, PartWalls, Patch, SmileiMPI, RadiationTables&, MultiphotonBreitWheelerTables&, std::vector<Diagnostic, std::allocator<Diagnostic> >&)
0 Object "/home/Data/wyj/Smilei-4.7/build/smilei", at 0x55e3aee8f2e6, in SpeciesV::computeParticleCellKeys(Params&, Particles, int, int*, unsigned int, unsigned int)
Segmentation fault (Address not mapped to object [0x55e1b12ec7a0])
mccoys
commented
1 year ago Could you try with pure MPI (no openmp), using OMP_NUM_THREADS set to 1?
If it works, try to recompile with the no_mpi_tm option:
make clean
make config=no_mpi_tmThen run again with openmp activated
xiaowang119
commented
1 year ago Thank you a lot! According to your previous advice, I carried out the operation (let OMP_NUM_THREADS=1) and the previous error magically disappeared. I repeatedly ran it in a loop and modified the initial conditions, and now I am confident that it can run normally. So what caused this?
mccoys
commented
1 year ago Have you tried what I indicated above? no_mpi_tm
If it works again then the problem is that mpi was not compiled with the THREAD_MULTIPLE option
xiaowang119
commented
1 year ago I just tried with pure MPI, then it worked well. So I will continue to push forward with my work in this way for now. After I'm done with this busy period, I will come back and test the recompile option.
mccoys
commented
1 year ago Let me close the issue. Please reopen if the solution did not work in the end
xiaowang119
commented
1 year ago Recently, I have try make config=no_mpi_tm and run again with openmp activated. I set the environment variable export OMP_NUM_THREADS=25 before running mpirun -n 4 smilei namelist.py. But each MPI process calls far fewer than 25 openMP threads.
Worst of all, the error mentioned above will still occur. It seems to work well only with pure MPI.
mccoys
commented
1 year ago Is this still happening with the same previous input files?
And did you make clean before compiling?
xiaowang119
commented
1 year ago Yes, I did make clean, and uesed the previous namelist.
Description
Hi, friends! Some error occur when I use SMILEI for D-D fusion. Code will be Interrupted with "Segmentation fault (core dumped)" for some cell number(eg. resx=resy=128), but run well for others(eg. resx=resy=64). And it also run well while I removed the fusion section. Any suggestion for me? Thanks a lot!
Parameters
g++ --version) g++ (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0mpic++ --version,mpic++ -show) g++ (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0 g++ -I/usr/local/openmpi/include -pthread -Wl,-rpath -Wl,/usr/local/openmpi/lib -Wl,--enable-new-dtags -L/usr/local/openmpi/lib -lmpih5cc --version) g++ (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0python --version) Python 3.8.10Namelist and outlog are attached.