Refactor Boris ensemble tracing

[henry2004y]

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 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 :warning:

Additional details and impacted files

```diff @@ 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 :x:), while a ratio less than `1.0` denotes a possible improvement (marked with :white_check_mark:). 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%) :white_check_mark: | 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 |