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Add native Boris method #96

Merged
merged 8 commits into from
Nov 14, 2023
Merged

Add native Boris method #96

merged 8 commits into from
Nov 14, 2023

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henry2004y
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@henry2004y henry2004y commented Nov 13, 2023

It's time to add some native particle pushers in the package!

Background

The Boris method is the de facto particle pusher in plasma physics, because of its excellent conservation behavior and relative simplicity. The Boris method is a second order method with discrete phase error related to the choice of fixed time step. If the time step is not fixed, this method can still be used, but the conservation of phase space trajectory will be violated.

Why do we need this?

The Boris method is specifically designed for the expression of Lorentz force. A general ODE solver in OrdinaryDiffEq.jl does not take into account the special form of the Lorentz equation, which is also the reason why the Boris method does not exist in OrdinaryDiffEq.jl. With my recent tests on multiple algorithms from OrdinaryDiffEq.jl, the default Tsit5() has poor conservation properties in many cases, and there are only a few options that display nice energy conservation behaviors #73. The Boris method also requires a fixed timestep for conservation, which makes it a bit harder for investigating a new problem, but we should have a version of our own in this package.

Plan

  • Implementing a first working version of the Boris method with similar APIs to the ODE solver.
  • Cleaning up the code.
  • Testing the accuracy and performance compared with other ODE solvers.
  • Add a demo using the native Boris method.

Repository owner deleted a comment from github-actions bot Nov 13, 2023
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codecov bot commented Nov 13, 2023

Codecov Report

Attention: 4 lines in your changes are missing coverage. Please review.

Comparison is base (fd5d83e) 47.10% compared to head (7731b61) 52.79%.

Files Patch % Lines
src/pusher.jl 94.52% 4 Missing ⚠️
Additional details and impacted files
@@            Coverage Diff             @@
##           master      #96      +/-   ##
==========================================
+ Coverage   47.10%   52.79%   +5.69%     
==========================================
  Files           9       10       +1     
  Lines         535      608      +73     
==========================================
+ Hits          252      321      +69     
- Misses        283      287       +4     

☔ View full report in Codecov by Sentry.
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src/pusher.jl Outdated Show resolved Hide resolved
@TCLiuu
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TCLiuu commented Nov 13, 2023

This is an exciting idea. Do you have a ToDo list? Maybe I can do something.

@henry2004y
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This is an exciting idea. Do you have a ToDo list? Maybe I can do something.

Yes! I've added a ToDo list above. After I clean up the code a bit more, feel free to directly push to this branch!

Adding the Boris method was not in my original plan for this package. I want to try this now because of some performance issue I encountered recently with a large number of test particles (> 1e7). Tsit5() is fast, at a cost of violation of phase space conservation; Vern9() together with a time step limitation based on local gyroperiod has much nicer conservation behavior, but it consumes a lot of memory with extremely high GC time (>70% in Julia 1.9.3 and 1.10.0-rc1). I frequently encounterd OOM errors running the trials on a cluster.

By adding a native particle pusher, the high GC time may be largely avoided.

Repository owner deleted a comment from github-actions bot Nov 13, 2023
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Benchmark result

Judge result

Benchmark Report for /home/runner/work/TestParticle.jl/TestParticle.jl

Job Properties

  • Time of benchmarks:
    • Target: 13 Nov 2023 - 23:01
    • Baseline: 13 Nov 2023 - 23:02
  • Package commits:
    • Target: 118fcb
    • Baseline: fd5d83
  • Julia commits:
    • Target: bed2cd
    • Baseline: bed2cd
  • Julia command flags:
    • Target: None
    • Baseline: None
  • Environment variables:
    • Target: None
    • Baseline: None

Results

A ratio greater than 1.0 denotes a possible regression (marked with ❌), while a ratio less
than 1.0 denotes a possible improvement (marked with ✅). Only significant results - results
that indicate possible regressions or improvements - are shown below (thus, an empty table means that all
benchmark results remained invariant between builds).

ID time ratio memory ratio

Benchmark Group List

Here's a list of all the benchmark groups executed by this job:

  • ["trace", "analytic field"]
  • ["trace", "numerical field"]
  • ["trace", "time-dependent field"]

Julia versioninfo

Target

Julia Version 1.9.3
Commit bed2cd540a1 (2023-08-24 14:43 UTC)
Build Info:
  Official https://julialang.org/ release
Platform Info:
  OS: Linux (x86_64-linux-gnu)
      Ubuntu 22.04.3 LTS
  uname: Linux 6.2.0-1015-azure #15~22.04.1-Ubuntu SMP Fri Oct  6 13:20:44 UTC 2023 x86_64 x86_64
  CPU: AMD EPYC 7763 64-Core Processor: 
              speed         user         nice          sys         idle          irq
       #1  2445 MHz       1692 s          0 s        173 s       4623 s          0 s
       #2  2746 MHz       1905 s          0 s        154 s       4446 s          0 s
       #3  2606 MHz       1770 s          0 s        176 s       4549 s          0 s
       #4  3242 MHz       2021 s          0 s        176 s       4301 s          0 s
  Memory: 15.606910705566406 GB (13814.3125 MB free)
  Uptime: 653.15 sec
  Load Avg:  1.02  1.2  0.72
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-14.0.6 (ORCJIT, znver3)
  Threads: 1 on 4 virtual cores

Baseline

Julia Version 1.9.3
Commit bed2cd540a1 (2023-08-24 14:43 UTC)
Build Info:
  Official https://julialang.org/ release
Platform Info:
  OS: Linux (x86_64-linux-gnu)
      Ubuntu 22.04.3 LTS
  uname: Linux 6.2.0-1015-azure #15~22.04.1-Ubuntu SMP Fri Oct  6 13:20:44 UTC 2023 x86_64 x86_64
  CPU: AMD EPYC 7763 64-Core Processor: 
              speed         user         nice          sys         idle          irq
       #1  3243 MHz       1792 s          0 s        180 s       5430 s          0 s
       #2  2445 MHz       1966 s          0 s        167 s       5286 s          0 s
       #3  2537 MHz       2078 s          0 s        186 s       5147 s          0 s
       #4  2595 MHz       2452 s          0 s        187 s       4774 s          0 s
  Memory: 15.606910705566406 GB (13816.4375 MB free)
  Uptime: 744.8 sec
  Load Avg:  1.0  1.15  0.75
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-14.0.6 (ORCJIT, znver3)
  Threads: 1 on 4 virtual cores

Target result

Benchmark Report for /home/runner/work/TestParticle.jl/TestParticle.jl

Job Properties

  • Time of benchmark: 13 Nov 2023 - 23:1
  • Package commit: 118fcb
  • Julia commit: bed2cd
  • Julia command flags: None
  • Environment variables: None

Results

Below is a table of this job's results, obtained by running the benchmarks.
The values listed in the ID column have the structure [parent_group, child_group, ..., key], and can be used to
index into the BaseBenchmarks suite to retrieve the corresponding benchmarks.
The percentages accompanying time and memory values in the below table are noise tolerances. The "true"
time/memory value for a given benchmark is expected to fall within this percentage of the reported value.
An empty cell means that the value was zero.

ID time GC time memory allocations
["trace", "analytic field", "in place"] 8.336 μs (5%) 14.06 KiB (1%) 158
["trace", "analytic field", "out of place"] 7.466 μs (5%) 12.28 KiB (1%) 133
["trace", "numerical field", "in place"] 21.220 μs (5%) 23.17 KiB (1%) 173
["trace", "numerical field", "out of place"] 17.042 μs (5%) 17.56 KiB (1%) 145
["trace", "time-dependent field", "in place"] 10.049 μs (5%) 15.27 KiB (1%) 173
["trace", "time-dependent field", "out of place"] 8.285 μs (5%) 13.48 KiB (1%) 148

Benchmark Group List

Here's a list of all the benchmark groups executed by this job:

  • ["trace", "analytic field"]
  • ["trace", "numerical field"]
  • ["trace", "time-dependent field"]

Julia versioninfo

Julia Version 1.9.3
Commit bed2cd540a1 (2023-08-24 14:43 UTC)
Build Info:
  Official https://julialang.org/ release
Platform Info:
  OS: Linux (x86_64-linux-gnu)
      Ubuntu 22.04.3 LTS
  uname: Linux 6.2.0-1015-azure #15~22.04.1-Ubuntu SMP Fri Oct  6 13:20:44 UTC 2023 x86_64 x86_64
  CPU: AMD EPYC 7763 64-Core Processor: 
              speed         user         nice          sys         idle          irq
       #1  2445 MHz       1692 s          0 s        173 s       4623 s          0 s
       #2  2746 MHz       1905 s          0 s        154 s       4446 s          0 s
       #3  2606 MHz       1770 s          0 s        176 s       4549 s          0 s
       #4  3242 MHz       2021 s          0 s        176 s       4301 s          0 s
  Memory: 15.606910705566406 GB (13814.3125 MB free)
  Uptime: 653.15 sec
  Load Avg:  1.02  1.2  0.72
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-14.0.6 (ORCJIT, znver3)
  Threads: 1 on 4 virtual cores

Baseline result

Benchmark Report for /home/runner/work/TestParticle.jl/TestParticle.jl

Job Properties

  • Time of benchmark: 13 Nov 2023 - 23:2
  • Package commit: fd5d83
  • Julia commit: bed2cd
  • Julia command flags: None
  • Environment variables: None

Results

Below is a table of this job's results, obtained by running the benchmarks.
The values listed in the ID column have the structure [parent_group, child_group, ..., key], and can be used to
index into the BaseBenchmarks suite to retrieve the corresponding benchmarks.
The percentages accompanying time and memory values in the below table are noise tolerances. The "true"
time/memory value for a given benchmark is expected to fall within this percentage of the reported value.
An empty cell means that the value was zero.

ID time GC time memory allocations
["trace", "analytic field", "in place"] 8.406 μs (5%) 14.06 KiB (1%) 158
["trace", "analytic field", "out of place"] 7.144 μs (5%) 12.28 KiB (1%) 133
["trace", "numerical field", "in place"] 20.970 μs (5%) 23.17 KiB (1%) 173
["trace", "numerical field", "out of place"] 16.942 μs (5%) 17.56 KiB (1%) 145
["trace", "time-dependent field", "in place"] 10.248 μs (5%) 15.27 KiB (1%) 173
["trace", "time-dependent field", "out of place"] 8.372 μs (5%) 13.48 KiB (1%) 148

Benchmark Group List

Here's a list of all the benchmark groups executed by this job:

  • ["trace", "analytic field"]
  • ["trace", "numerical field"]
  • ["trace", "time-dependent field"]

Julia versioninfo

Julia Version 1.9.3
Commit bed2cd540a1 (2023-08-24 14:43 UTC)
Build Info:
  Official https://julialang.org/ release
Platform Info:
  OS: Linux (x86_64-linux-gnu)
      Ubuntu 22.04.3 LTS
  uname: Linux 6.2.0-1015-azure #15~22.04.1-Ubuntu SMP Fri Oct  6 13:20:44 UTC 2023 x86_64 x86_64
  CPU: AMD EPYC 7763 64-Core Processor: 
              speed         user         nice          sys         idle          irq
       #1  3243 MHz       1792 s          0 s        180 s       5430 s          0 s
       #2  2445 MHz       1966 s          0 s        167 s       5286 s          0 s
       #3  2537 MHz       2078 s          0 s        186 s       5147 s          0 s
       #4  2595 MHz       2452 s          0 s        187 s       4774 s          0 s
  Memory: 15.606910705566406 GB (13816.4375 MB free)
  Uptime: 744.8 sec
  Load Avg:  1.0  1.15  0.75
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-14.0.6 (ORCJIT, znver3)
  Threads: 1 on 4 virtual cores

Runtime information

Runtime Info
BLAS #threads 2
BLAS.vendor() lbt
Sys.CPU_THREADS 4

lscpu output:

Architecture:                       x86_64
CPU op-mode(s):                     32-bit, 64-bit
Address sizes:                      48 bits physical, 48 bits virtual
Byte Order:                         Little Endian
CPU(s):                             4
On-line CPU(s) list:                0-3
Vendor ID:                          AuthenticAMD
Model name:                         AMD EPYC 7763 64-Core Processor
CPU family:                         25
Model:                              1
Thread(s) per core:                 2
Core(s) per socket:                 2
Socket(s):                          1
Stepping:                           1
BogoMIPS:                           4890.86
Flags:                              fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 ht syscall nx mmxext fxsr_opt pdpe1gb rdtscp lm constant_tsc rep_good nopl tsc_reliable nonstop_tsc cpuid extd_apicid aperfmperf pni pclmulqdq ssse3 fma cx16 pcid sse4_1 sse4_2 movbe popcnt aes xsave avx f16c rdrand hypervisor lahf_lm cmp_legacy svm cr8_legacy abm sse4a misalignsse 3dnowprefetch osvw topoext invpcid_single vmmcall fsgsbase bmi1 avx2 smep bmi2 erms invpcid rdseed adx smap clflushopt clwb sha_ni xsaveopt xsavec xgetbv1 xsaves clzero xsaveerptr rdpru arat npt nrip_save tsc_scale vmcb_clean flushbyasid decodeassists pausefilter pfthreshold v_vmsave_vmload umip vaes vpclmulqdq rdpid fsrm
Virtualization:                     AMD-V
Hypervisor vendor:                  Microsoft
Virtualization type:                full
L1d cache:                          64 KiB (2 instances)
L1i cache:                          64 KiB (2 instances)
L2 cache:                           1 MiB (2 instances)
L3 cache:                           32 MiB (1 instance)
NUMA node(s):                       1
NUMA node0 CPU(s):                  0-3
Vulnerability Gather data sampling: Not affected
Vulnerability Itlb multihit:        Not affected
Vulnerability L1tf:                 Not affected
Vulnerability Mds:                  Not affected
Vulnerability Meltdown:             Not affected
Vulnerability Mmio stale data:      Not affected
Vulnerability Retbleed:             Not affected
Vulnerability Spec rstack overflow: Mitigation; safe RET, no microcode
Vulnerability Spec store bypass:    Vulnerable
Vulnerability Spectre v1:           Mitigation; usercopy/swapgs barriers and __user pointer sanitization
Vulnerability Spectre v2:           Mitigation; Retpolines, STIBP disabled, RSB filling, PBRSB-eIBRS Not affected
Vulnerability Srbds:                Not affected
Vulnerability Tsx async abort:      Not affected
Cpu Property Value
Brand AMD EPYC 7763 64-Core Processor
Vendor :AMD
Architecture :Unknown
Model Family: 0xaf, Model: 0x01, Stepping: 0x01, Type: 0x00
Cores 16 physical cores, 16 logical cores (on executing CPU)
No Hyperthreading hardware capability detected
Clock Frequencies Not supported by CPU
Data Cache Level 1:3 : (32, 512, 32768) kbytes
64 byte cache line size
Address Size 48 bits virtual, 48 bits physical
SIMD 256 bit = 32 byte max. SIMD vector size
Time Stamp Counter TSC is accessible via rdtsc
TSC runs at constant rate (invariant from clock frequency)
Perf. Monitoring Performance Monitoring Counters (PMC) are not supported
Hypervisor Yes, Microsoft

Repository owner deleted a comment from github-actions bot Nov 13, 2023
@henry2004y henry2004y marked this pull request as ready for review November 14, 2023 00:46
@henry2004y
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Owner Author

I'm going to merge this to master in order to test the performance for a specific problem. We can further polish this part afterwards.

@henry2004y henry2004y merged commit 5636d4d into master Nov 14, 2023
7 checks passed
@henry2004y henry2004y deleted the boris branch November 14, 2023 00:49
@TCLiuu
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TCLiuu commented Nov 15, 2023

Have you read this paper?

PS. Perhaps you have also come across this author.

@henry2004y
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I've heard of this paper recently from a senior member of my group. By briefly scanning through the derivations, I got the impression that $|R|=1$ is based on the assumption that $\Delta t = \textrm{const}$. I will confirm this with some numerical experiments.

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2 participants