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Refactor Boris ensemble tracing #128

Merged
merged 4 commits into from
Jan 29, 2024
Merged

Refactor Boris ensemble tracing #128

merged 4 commits into from
Jan 29, 2024

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henry2004y
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Current implementation of the Boris ensemble pusher triggers quite a lot memory allocations, which in turn triggers GC more frequently when running with multithreading (#127). This PR tries to reduce the allocations a bit by assuming that the timestep, EM fields, and particle properties are constant within one batch tracing.

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codecov bot commented Jan 29, 2024 •
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Codecov Report

Attention: 2 lines in your changes are missing coverage. Please review.

Comparison is base (34ec481) 57.88% compared to head (ae09256) 58.07%.

Files Patch % Lines
src/pusher.jl 83.33% 2 Missing ⚠️
Additional details and impacted files 
@@            Coverage Diff             @@
##           master     #128      +/-   ##
==========================================
+ Coverage   57.88%   58.07%   +0.18%     
==========================================
  Files          10       10              
  Lines         672      675       +3     
==========================================
+ Hits          389      392       +3     
  Misses        283      283

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Benchmark result

Judge result

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

Job Properties

  • Time of benchmarks:
    • Target: 29 Jan 2024 - 17:59
    • Baseline: 29 Jan 2024 - 18:00
  • Package commits:
    • Target: d283a2
    • Baseline: 34ec48
  • Julia commits:
    • Target: 312098
    • Baseline: 312098
  • 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
["trace", "numerical field", "in place"] 0.95 (5%) ✅ 1.00 (1%)

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 1.10.0
Commit 3120989f39b (2023-12-25 18:01 UTC)
Build Info:
  Official https://julialang.org/ release
Platform Info:
  OS: Linux (x86_64-linux-gnu)
      Ubuntu 22.04.3 LTS
  uname: Linux 6.2.0-1018-azure #18~22.04.1-Ubuntu SMP Tue Nov 21 19:25:02 UTC 2023 x86_64 x86_64
  CPU: AMD EPYC 7763 64-Core Processor: 
              speed         user         nice          sys         idle          irq
       #1  3248 MHz       2089 s          0 s        164 s       3784 s          0 s
       #2  3242 MHz       2486 s          0 s        177 s       3385 s          0 s
       #3  3209 MHz       2170 s          0 s        183 s       3689 s          0 s
       #4  2445 MHz       1909 s          0 s        174 s       3961 s          0 s
  Memory: 15.60690689086914 GB (13754.52734375 MB free)
  Uptime: 607.68 sec
  Load Avg:  1.18  1.46  0.83
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-15.0.7 (ORCJIT, znver3)
  Threads: 1 on 4 virtual cores

Baseline

Julia Version 1.10.0
Commit 3120989f39b (2023-12-25 18:01 UTC)
Build Info:
  Official https://julialang.org/ release
Platform Info:
  OS: Linux (x86_64-linux-gnu)
      Ubuntu 22.04.3 LTS
  uname: Linux 6.2.0-1018-azure #18~22.04.1-Ubuntu SMP Tue Nov 21 19:25:02 UTC 2023 x86_64 x86_64
  CPU: AMD EPYC 7763 64-Core Processor: 
              speed         user         nice          sys         idle          irq
       #1  3243 MHz       2186 s          0 s        174 s       4567 s          0 s
       #2  3242 MHz       2585 s          0 s        185 s       4168 s          0 s
       #3  2445 MHz       2382 s          0 s        193 s       4358 s          0 s
       #4  2821 MHz       2401 s          0 s        180 s       4354 s          0 s
  Memory: 15.60690689086914 GB (13669.45703125 MB free)
  Uptime: 696.96 sec
  Load Avg:  1.06  1.35  0.85
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-15.0.7 (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: 29 Jan 2024 - 17:59
  • Package commit: d283a2
  • Julia commit: 312098
  • 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"] 9.077 μs (5%) 10.56 KiB (1%) 114
["trace", "analytic field", "out of place"] 5.815 μs (5%) 8.72 KiB (1%) 88
["trace", "numerical field", "Boris ensemble"] 3.591 μs (5%) 608 bytes (1%) 7
["trace", "numerical field", "Boris"] 1.839 μs (5%) 448 bytes (1%) 5
["trace", "numerical field", "in place"] 24.125 μs (5%) 22.45 KiB (1%) 129
["trace", "numerical field", "out of place"] 16.911 μs (5%) 14.80 KiB (1%) 99
["trace", "time-dependent field", "in place"] 9.908 μs (5%) 11.31 KiB (1%) 123
["trace", "time-dependent field", "out of place"] 7.298 μs (5%) 9.50 KiB (1%) 97

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 1.10.0
Commit 3120989f39b (2023-12-25 18:01 UTC)
Build Info:
  Official https://julialang.org/ release
Platform Info:
  OS: Linux (x86_64-linux-gnu)
      Ubuntu 22.04.3 LTS
  uname: Linux 6.2.0-1018-azure #18~22.04.1-Ubuntu SMP Tue Nov 21 19:25:02 UTC 2023 x86_64 x86_64
  CPU: AMD EPYC 7763 64-Core Processor: 
              speed         user         nice          sys         idle          irq
       #1  3248 MHz       2089 s          0 s        164 s       3784 s          0 s
       #2  3242 MHz       2486 s          0 s        177 s       3385 s          0 s
       #3  3209 MHz       2170 s          0 s        183 s       3689 s          0 s
       #4  2445 MHz       1909 s          0 s        174 s       3961 s          0 s
  Memory: 15.60690689086914 GB (13754.52734375 MB free)
  Uptime: 607.68 sec
  Load Avg:  1.18  1.46  0.83
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-15.0.7 (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: 29 Jan 2024 - 18:0
  • Package commit: 34ec48
  • Julia commit: 312098
  • 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"] 8.896 μs (5%) 10.56 KiB (1%) 114
["trace", "analytic field", "out of place"] 5.949 μs (5%) 8.72 KiB (1%) 88
["trace", "numerical field", "Boris"] 1.836 μs (5%) 448 bytes (1%) 5
["trace", "numerical field", "in place"] 25.518 μs (5%) 22.45 KiB (1%) 129
["trace", "numerical field", "out of place"] 16.711 μs (5%) 14.80 KiB (1%) 99
["trace", "time-dependent field", "in place"] 9.858 μs (5%) 11.31 KiB (1%) 123
["trace", "time-dependent field", "out of place"] 7.409 μs (5%) 9.50 KiB (1%) 97

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 1.10.0
Commit 3120989f39b (2023-12-25 18:01 UTC)
Build Info:
  Official https://julialang.org/ release
Platform Info:
  OS: Linux (x86_64-linux-gnu)
      Ubuntu 22.04.3 LTS
  uname: Linux 6.2.0-1018-azure #18~22.04.1-Ubuntu SMP Tue Nov 21 19:25:02 UTC 2023 x86_64 x86_64
  CPU: AMD EPYC 7763 64-Core Processor: 
              speed         user         nice          sys         idle          irq
       #1  3243 MHz       2186 s          0 s        174 s       4567 s          0 s
       #2  3242 MHz       2585 s          0 s        185 s       4168 s          0 s
       #3  2445 MHz       2382 s          0 s        193 s       4358 s          0 s
       #4  2821 MHz       2401 s          0 s        180 s       4354 s          0 s
  Memory: 15.60690689086914 GB (13669.45703125 MB free)
  Uptime: 696.96 sec
  Load Avg:  1.06  1.35  0.85
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-15.0.7 (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:                           4890.85
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 Jan 29, 2024
@henry2004y henry2004y merged commit 7439142 into master Jan 29, 2024
7 checks passed
@henry2004y henry2004y deleted the boris_refactor branch January 29, 2024 18:47
@henry2004y henry2004y mentioned this pull request Jan 29, 2024
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