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bcube-project / Bcube.jl

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Better support for `MeshCellData` with `write_vtk_lagrange` #90

Closed ghislainb closed 5 months ago

ghislainb commented 6 months ago

Better support for writting MeshCellData with write_vtk_lagrange and add a nodal averaging step for DG variable written on a continuous FESpace

github-actions[bot] commented 6 months ago
Benchmark result # Judge result # Benchmark Report for */home/runner/work/Bcube.jl/Bcube.jl* ## Job Properties * Time of benchmarks: - Target: 9 May 2024 - 13:35 - Baseline: 9 May 2024 - 13:38 * Package commits: - Target: 80ffec - Baseline: 1b27aa * Julia commits: - Target: 0b4590 - Baseline: 0b4590 * 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 | |------------------------------------------------------|------------------------------|--------------| | `["assemble", "poisson DG", "l_Γb(v)"]` | 0.94 (5%) :white_check_mark: | 1.00 (1%) | | `["assemble", "poisson DG", "l_Ω(v)"]` | 1.10 (5%) :x: | 1.00 (1%) | | `["covo", "TriQuad", "integral_volume"]` | 1.06 (5%) :x: | 1.00 (1%) | ## Benchmark Group List Here's a list of all the benchmark groups executed by this job: - `["assemble", "basic bilinear"]` - `["assemble", "poisson DG"]` - `["covo", "Quad"]` - `["covo", "TriQuad"]` - `["entities"]` - `["mesh"]` ## Julia versioninfo ### Target ``` Julia Version 1.10.3 Commit 0b4590a5507 (2024-04-30 10:59 UTC) Build Info: Official https://julialang.org/ release Platform Info: OS: Linux (x86_64-linux-gnu) Ubuntu 22.04.4 LTS uname: Linux 6.5.0-1018-azure #19~22.04.2-Ubuntu SMP Thu Mar 21 16:45:46 UTC 2024 x86_64 x86_64 CPU: AMD EPYC 7763 64-Core Processor: speed user nice sys idle irq #1 2445 MHz 1666 s 0 s 194 s 5098 s 0 s #2 3243 MHz 2294 s 0 s 239 s 4424 s 0 s #3 2445 MHz 1710 s 0 s 216 s 5033 s 0 s #4 2595 MHz 2231 s 0 s 254 s 4468 s 0 s Memory: 15.606494903564453 GB (12360.75 MB free) Uptime: 700.2 sec Load Avg: 1.01 1.2 0.77 WORD_SIZE: 64 LIBM: libopenlibm LLVM: libLLVM-15.0.7 (ORCJIT, znver3) Threads: 1 default, 0 interactive, 1 GC (on 4 virtual cores) ``` ### Baseline ``` Julia Version 1.10.3 Commit 0b4590a5507 (2024-04-30 10:59 UTC) Build Info: Official https://julialang.org/ release Platform Info: OS: Linux (x86_64-linux-gnu) Ubuntu 22.04.4 LTS uname: Linux 6.5.0-1018-azure #19~22.04.2-Ubuntu SMP Thu Mar 21 16:45:46 UTC 2024 x86_64 x86_64 CPU: AMD EPYC 7763 64-Core Processor: speed user nice sys idle irq #1 2581 MHz 2090 s 0 s 239 s 6663 s 0 s #2 2445 MHz 3065 s 0 s 288 s 5639 s 0 s #3 3241 MHz 2078 s 0 s 267 s 6649 s 0 s #4 3144 MHz 2613 s 0 s 290 s 6082 s 0 s Memory: 15.606494903564453 GB (12262.203125 MB free) Uptime: 903.96 sec Load Avg: 1.09 1.12 0.83 WORD_SIZE: 64 LIBM: libopenlibm LLVM: libLLVM-15.0.7 (ORCJIT, znver3) Threads: 1 default, 0 interactive, 1 GC (on 4 virtual cores) ``` --- # Target result # Benchmark Report for */home/runner/work/Bcube.jl/Bcube.jl* ## Job Properties * Time of benchmark: 9 May 2024 - 13:35 * Package commit: 80ffec * Julia commit: 0b4590 * 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 | |------------------------------------------------------|----------------:|----------:|----------------:|------------:| | `["assemble", "basic bilinear", "mass matrix"]` | 16.534 ms (5%) | | 13.82 MiB (1%) | 117 | | `["assemble", "basic bilinear", "stiffness matrix"]` | 100.295 ms (5%) | | 13.82 MiB (1%) | 117 | | `["assemble", "poisson DG", "AffineFESystem"]` | 53.337 ms (5%) | | 71.70 MiB (1%) | 17213 | | `["assemble", "poisson DG", "a_Γ(u, v)"]` | 37.019 ms (5%) | | 59.36 MiB (1%) | 13105 | | `["assemble", "poisson DG", "a_Γb(u, v)"]` | 7.256 ms (5%) | | 10.83 MiB (1%) | 3203 | | `["assemble", "poisson DG", "a_Ω(u, v)"]` | 7.692 ms (5%) | | 349.81 KiB (1%) | 69 | | `["assemble", "poisson DG", "l_Γb(v)"]` | 72.205 μs (5%) | | 159.66 KiB (1%) | 949 | | `["assemble", "poisson DG", "l_Ω(v)"]` | 20.147 μs (5%) | | 22.61 KiB (1%) | 21 | | `["covo", "Quad", "explicit_step"]` | 101.794 ms (5%) | | 69.43 MiB (1%) | 5263 | | `["covo", "Quad", "integral_surface"]` | 52.573 ms (5%) | | | | | `["covo", "Quad", "integral_volume"]` | 21.038 ms (5%) | | | | | `["covo", "TriQuad", "explicit_step"]` | 402.106 ms (5%) | 20.494 ms | 382.36 MiB (1%) | 1813713 | | `["covo", "TriQuad", "integral_surface"]` | 285.077 ms (5%) | | 227.64 MiB (1%) | 1424064 | | `["covo", "TriQuad", "integral_volume"]` | 64.837 ms (5%) | | 48.39 MiB (1%) | 379526 | | `["entities", "edges2nodes"]` | 1.552 ns (5%) | | | | | `["entities", "nedges"]` | 1.552 ns (5%) | | | | | `["entities", "nnodes"]` | 3.095 ns (5%) | | | | | `["entities", "nodes"]` | 1.552 ns (5%) | | | | | `["mesh", "todo"]` | 1.552 ns (5%) | | | | ## Benchmark Group List Here's a list of all the benchmark groups executed by this job: - `["assemble", "basic bilinear"]` - `["assemble", "poisson DG"]` - `["covo", "Quad"]` - `["covo", "TriQuad"]` - `["entities"]` - `["mesh"]` ## Julia versioninfo ``` Julia Version 1.10.3 Commit 0b4590a5507 (2024-04-30 10:59 UTC) Build Info: Official https://julialang.org/ release Platform Info: OS: Linux (x86_64-linux-gnu) Ubuntu 22.04.4 LTS uname: Linux 6.5.0-1018-azure #19~22.04.2-Ubuntu SMP Thu Mar 21 16:45:46 UTC 2024 x86_64 x86_64 CPU: AMD EPYC 7763 64-Core Processor: speed user nice sys idle irq #1 2445 MHz 1666 s 0 s 194 s 5098 s 0 s #2 3243 MHz 2294 s 0 s 239 s 4424 s 0 s #3 2445 MHz 1710 s 0 s 216 s 5033 s 0 s #4 2595 MHz 2231 s 0 s 254 s 4468 s 0 s Memory: 15.606494903564453 GB (12360.75 MB free) Uptime: 700.2 sec Load Avg: 1.01 1.2 0.77 WORD_SIZE: 64 LIBM: libopenlibm LLVM: libLLVM-15.0.7 (ORCJIT, znver3) Threads: 1 default, 0 interactive, 1 GC (on 4 virtual cores) ``` --- # Baseline result # Benchmark Report for */home/runner/work/Bcube.jl/Bcube.jl* ## Job Properties * Time of benchmark: 9 May 2024 - 13:38 * Package commit: 1b27aa * Julia commit: 0b4590 * 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 | |------------------------------------------------------|----------------:|----------:|----------------:|------------:| | `["assemble", "basic bilinear", "mass matrix"]` | 16.698 ms (5%) | | 13.82 MiB (1%) | 117 | | `["assemble", "basic bilinear", "stiffness matrix"]` | 100.162 ms (5%) | | 13.82 MiB (1%) | 117 | | `["assemble", "poisson DG", "AffineFESystem"]` | 55.289 ms (5%) | | 71.70 MiB (1%) | 17213 | | `["assemble", "poisson DG", "a_Γ(u, v)"]` | 38.183 ms (5%) | | 59.36 MiB (1%) | 13105 | | `["assemble", "poisson DG", "a_Γb(u, v)"]` | 7.591 ms (5%) | | 10.83 MiB (1%) | 3203 | | `["assemble", "poisson DG", "a_Ω(u, v)"]` | 7.813 ms (5%) | | 349.81 KiB (1%) | 69 | | `["assemble", "poisson DG", "l_Γb(v)"]` | 76.503 μs (5%) | | 159.66 KiB (1%) | 949 | | `["assemble", "poisson DG", "l_Ω(v)"]` | 18.374 μs (5%) | | 22.61 KiB (1%) | 21 | | `["covo", "Quad", "explicit_step"]` | 100.084 ms (5%) | | 69.43 MiB (1%) | 5263 | | `["covo", "Quad", "integral_surface"]` | 51.534 ms (5%) | | | | | `["covo", "Quad", "integral_volume"]` | 20.075 ms (5%) | | | | | `["covo", "TriQuad", "explicit_step"]` | 388.149 ms (5%) | 20.549 ms | 382.36 MiB (1%) | 1813713 | | `["covo", "TriQuad", "integral_surface"]` | 273.989 ms (5%) | | 227.64 MiB (1%) | 1424064 | | `["covo", "TriQuad", "integral_volume"]` | 61.140 ms (5%) | | 48.39 MiB (1%) | 379526 | | `["entities", "edges2nodes"]` | 1.552 ns (5%) | | | | | `["entities", "nedges"]` | 1.552 ns (5%) | | | | | `["entities", "nnodes"]` | 3.095 ns (5%) | | | | | `["entities", "nodes"]` | 1.552 ns (5%) | | | | | `["mesh", "todo"]` | 1.552 ns (5%) | | | | ## Benchmark Group List Here's a list of all the benchmark groups executed by this job: - `["assemble", "basic bilinear"]` - `["assemble", "poisson DG"]` - `["covo", "Quad"]` - `["covo", "TriQuad"]` - `["entities"]` - `["mesh"]` ## Julia versioninfo ``` Julia Version 1.10.3 Commit 0b4590a5507 (2024-04-30 10:59 UTC) Build Info: Official https://julialang.org/ release Platform Info: OS: Linux (x86_64-linux-gnu) Ubuntu 22.04.4 LTS uname: Linux 6.5.0-1018-azure #19~22.04.2-Ubuntu SMP Thu Mar 21 16:45:46 UTC 2024 x86_64 x86_64 CPU: AMD EPYC 7763 64-Core Processor: speed user nice sys idle irq #1 2581 MHz 2090 s 0 s 239 s 6663 s 0 s #2 2445 MHz 3065 s 0 s 288 s 5639 s 0 s #3 3241 MHz 2078 s 0 s 267 s 6649 s 0 s #4 3144 MHz 2613 s 0 s 290 s 6082 s 0 s Memory: 15.606494903564453 GB (12262.203125 MB free) Uptime: 903.96 sec Load Avg: 1.09 1.12 0.83 WORD_SIZE: 64 LIBM: libopenlibm LLVM: libLLVM-15.0.7 (ORCJIT, znver3) Threads: 1 default, 0 interactive, 1 GC (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: Vulnerable: 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 |
github-actions[bot] commented 6 months ago

Benchmark Results

main d709127f8309ba... main/d709127f8309ba...
assemble/basic bilinear/mass matrix 16.5 ± 0.13 ms 16.5 ± 0.23 ms 1
assemble/basic bilinear/stiffness matrix 0.0812 ± 0.00019 s 0.0999 ± 0.0019 s 0.813
assemble/poisson DG/AffineFESystem 0.0547 ± 0.0066 s 0.0547 ± 0.0065 s 1
assemble/poisson DG/a_Γ(u, v) 0.0388 ± 0.0063 s 0.0386 ± 0.0061 s 1.01
assemble/poisson DG/a_Γb(u, v) 7.54 ± 0.16 ms 7.4 ± 0.11 ms 1.02
assemble/poisson DG/a_Ω(u, v) 7.74 ± 0.021 ms 7.82 ± 0.02 ms 0.99
assemble/poisson DG/l_Γb(v) 0.125 ± 0.051 ms 0.124 ± 0.052 ms 1
assemble/poisson DG/l_Ω(v) 20.9 ± 2.6 μs 20.9 ± 2.5 μs 0.999
covo/Quad/explicit_step 0.103 ± 0.0012 s 0.102 ± 0.0011 s 1
covo/Quad/integral_surface 0.0501 ± 0.00014 s 0.0522 ± 0.00014 s 0.959
covo/Quad/integral_volume 20.2 ± 0.13 ms 20.3 ± 0.041 ms 0.993
covo/TriQuad/explicit_step 0.433 ± 0.019 s 0.431 ± 0.024 s 1.01
covo/TriQuad/integral_surface 0.313 ± 0.0025 s 0.308 ± 0.0017 s 1.01
covo/TriQuad/integral_volume 0.0747 ± 0.0037 s 0.0742 ± 0.0047 s 1.01
entities/edges2nodes 1.56 ± 0.01 ns 1.55 ± 0.01 ns 1.01
entities/nedges 1.55 ± 0.01 ns 1.55 ± 0.01 ns 1
entities/nnodes 3.11 ± 0.001 ns 3.11 ± 0.01 ns 1
entities/nodes 1.56 ± 0.01 ns 1.56 ± 0.01 ns 1
mesh/todo 1.56 ± 0.01 ns 1.56 ± 0.01 ns 0.999
time_to_load 3.21 ± 0.01 s 3.2 ± 0.029 s 1

Benchmark Plots

A plot of the benchmark results have been uploaded as an artifact to the workflow run for this PR. Go to "Actions"->"Benchmark a pull request"->[the most recent run]->"Artifacts" (at the bottom).