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Improve hexa mesh generation (gmsh) #139

Merged
merged 2 commits into from
Sep 20, 2024
Merged

Improve hexa mesh generation (gmsh) #139

merged 2 commits into from
Sep 20, 2024

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bmxam
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@bmxam bmxam commented Sep 20, 2024

Simplified version of hexa mesh generation with gmsh and more control parameters (for instance lc).

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Benchmark Results

main 98b05cb... main/98b05cbfa0ef84...
assemble/basic bilinear/mass matrix 15.7 ± 0.33 ms 16 ± 0.22 ms 0.98
assemble/basic bilinear/stiffness matrix 0.0815 ± 0.00054 s 0.0814 ± 0.00032 s 1
assemble/poisson DG/AffineFESystem 0.0537 ± 0.0063 s 0.0552 ± 0.0063 s 0.974
assemble/poisson DG/a_Γ(u, v) 0.0381 ± 0.004 s 0.0379 ± 0.0048 s 1.01
assemble/poisson DG/a_Γb(u, v) 7.33 ± 0.057 ms 7.73 ± 0.085 ms 0.948
assemble/poisson DG/a_Ω(u, v) 7.82 ± 0.015 ms 7.7 ± 0.055 ms 1.02
assemble/poisson DG/l_Γb(v) 0.117 ± 0.014 ms 0.119 ± 0.013 ms 0.982
assemble/poisson DG/l_Ω(v) 12.8 ± 0.16 μs 12.6 ± 0.19 μs 1.01
covo/Quad/explicit_step 0.0805 ± 0.001 s 0.0828 ± 0.0009 s 0.972
covo/Quad/integral_surface 0.0513 ± 0.00035 s 0.0526 ± 0.00017 s 0.976
covo/Quad/integral_volume 20.4 ± 0.055 ms 20.7 ± 0.049 ms 0.985
covo/TriQuad/explicit_step 0.395 ± 0.028 s 0.4 ± 0.017 s 0.988
covo/TriQuad/integral_surface 0.304 ± 0.0045 s 0.31 ± 0.0031 s 0.983
covo/TriQuad/integral_volume 0.0762 ± 0.0014 s 0.0779 ± 0.0016 s 0.977
entities/edges2nodes 1.55 ± 0.01 ns 1.55 ± 0.01 ns 1
entities/nedges 1.55 ± 0.01 ns 1.55 ± 0.01 ns 1
entities/nnodes 3.41 ± 0.01 ns 3.41 ± 0.01 ns 1
entities/nodes 1.55 ± 0.01 ns 1.56 ± 0.01 ns 0.995
mesh/todo 1.55 ± 0.01 ns 1.55 ± 0.01 ns 1
time_to_load 3.73 ± 0.0094 s 3.69 ± 0.0043 s 1.01

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).

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Benchmark result

Judge result

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

Job Properties

  • Time of benchmarks:
    • Target: 20 Sep 2024 - 07:30
    • Baseline: 20 Sep 2024 - 07:33
  • Package commits:
    • Target: 551d62
    • Baseline: e94b26
  • Julia commits:
    • Target: 6f3fdf
    • Baseline: 6f3fdf
  • 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
["assemble", "poisson DG", "a_Γ(u, v)"] 0.72 (5%) ✅ 1.00 (1%)
["assemble", "poisson DG", "l_Γb(v)"] 0.82 (5%) ✅ 1.00 (1%)
["covo", "TriQuad", "integral_volume"] 0.94 (5%) ✅ 1.00 (1%)
["entities", "nnodes"] 1.22 (5%) ❌ 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 1.10.5
Commit 6f3fdf7b362 (2024-08-27 14:19 UTC)
Build Info:
  Official https://julialang.org/ release
Platform Info:
  OS: Linux (x86_64-linux-gnu)
      Ubuntu 22.04.5 LTS
  uname: Linux 6.8.0-1014-azure #16~22.04.1-Ubuntu SMP Thu Aug 15 21:31:41 UTC 2024 x86_64 x86_64
  CPU: AMD EPYC 7763 64-Core Processor: 
              speed         user         nice          sys         idle          irq
       #1  3245 MHz       1958 s          0 s        202 s       3799 s          0 s
       #2  3257 MHz       2183 s          0 s        241 s       3511 s          0 s
       #3  2445 MHz       1931 s          0 s        212 s       3818 s          0 s
       #4  2626 MHz       2095 s          0 s        276 s       3570 s          0 s
  Memory: 15.615272521972656 GB (12066.02734375 MB free)
  Uptime: 598.81 sec
  Load Avg:  1.09  1.26  0.81
  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 1.10.5
Commit 6f3fdf7b362 (2024-08-27 14:19 UTC)
Build Info:
  Official https://julialang.org/ release
Platform Info:
  OS: Linux (x86_64-linux-gnu)
      Ubuntu 22.04.5 LTS
  uname: Linux 6.8.0-1014-azure #16~22.04.1-Ubuntu SMP Thu Aug 15 21:31:41 UTC 2024 x86_64 x86_64
  CPU: AMD EPYC 7763 64-Core Processor: 
              speed         user         nice          sys         idle          irq
       #1  3111 MHz       2240 s          0 s        243 s       5544 s          0 s
       #2  3302 MHz       2636 s          0 s        299 s       5070 s          0 s
       #3  3242 MHz       2173 s          0 s        250 s       5608 s          0 s
       #4  2625 MHz       3094 s          0 s        339 s       4579 s          0 s
  Memory: 15.615272521972656 GB (12067.3125 MB free)
  Uptime: 806.08 sec
  Load Avg:  1.15  1.17  0.88
  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: 20 Sep 2024 - 7:30
  • Package commit: 551d62
  • Julia commit: 6f3fdf
  • 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"] 16.269 ms (5%) 13.37 MiB (1%) 50
["assemble", "basic bilinear", "stiffness matrix"] 82.804 ms (5%) 13.37 MiB (1%) 50
["assemble", "poisson DG", "AffineFESystem"] 54.314 ms (5%) 71.64 MiB (1%) 17153
["assemble", "poisson DG", "a_Γ(u, v)"] 39.174 ms (5%) 59.32 MiB (1%) 13065
["assemble", "poisson DG", "a_Γb(u, v)"] 7.342 ms (5%) 10.79 MiB (1%) 3163
["assemble", "poisson DG", "a_Ω(u, v)"] 7.744 ms (5%) 304.58 KiB (1%) 27
["assemble", "poisson DG", "l_Γb(v)"] 60.304 μs (5%) 139.38 KiB (1%) 929
["assemble", "poisson DG", "l_Ω(v)"] 12.334 μs (5%) 2.12 KiB (1%) 1
["covo", "Quad", "explicit_step"] 80.577 ms (5%) 29.25 MiB (1%) 4398
["covo", "Quad", "integral_surface"] 51.420 ms (5%)
["covo", "Quad", "integral_volume"] 21.341 ms (5%)
["covo", "TriQuad", "explicit_step"] 384.056 ms (5%) 30.341 ms 341.57 MiB (1%) 1812322
["covo", "TriQuad", "integral_surface"] 275.414 ms (5%) 234.44 MiB (1%) 1424064
["covo", "TriQuad", "integral_volume"] 59.152 ms (5%) 51.71 MiB (1%) 379526
["entities", "edges2nodes"] 1.552 ns (5%)
["entities", "nedges"] 1.552 ns (5%)
["entities", "nnodes"] 3.396 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 1.10.5
Commit 6f3fdf7b362 (2024-08-27 14:19 UTC)
Build Info:
  Official https://julialang.org/ release
Platform Info:
  OS: Linux (x86_64-linux-gnu)
      Ubuntu 22.04.5 LTS
  uname: Linux 6.8.0-1014-azure #16~22.04.1-Ubuntu SMP Thu Aug 15 21:31:41 UTC 2024 x86_64 x86_64
  CPU: AMD EPYC 7763 64-Core Processor: 
              speed         user         nice          sys         idle          irq
       #1  3245 MHz       1958 s          0 s        202 s       3799 s          0 s
       #2  3257 MHz       2183 s          0 s        241 s       3511 s          0 s
       #3  2445 MHz       1931 s          0 s        212 s       3818 s          0 s
       #4  2626 MHz       2095 s          0 s        276 s       3570 s          0 s
  Memory: 15.615272521972656 GB (12066.02734375 MB free)
  Uptime: 598.81 sec
  Load Avg:  1.09  1.26  0.81
  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: 20 Sep 2024 - 7:33
  • Package commit: e94b26
  • Julia commit: 6f3fdf
  • 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"] 15.807 ms (5%) 13.37 MiB (1%) 50
["assemble", "basic bilinear", "stiffness matrix"] 81.288 ms (5%) 13.37 MiB (1%) 50
["assemble", "poisson DG", "AffineFESystem"] 56.499 ms (5%) 71.64 MiB (1%) 17153
["assemble", "poisson DG", "a_Γ(u, v)"] 54.139 ms (5%) 59.32 MiB (1%) 13065
["assemble", "poisson DG", "a_Γb(u, v)"] 7.656 ms (5%) 10.79 MiB (1%) 3163
["assemble", "poisson DG", "a_Ω(u, v)"] 7.746 ms (5%) 304.58 KiB (1%) 27
["assemble", "poisson DG", "l_Γb(v)"] 73.989 μs (5%) 139.38 KiB (1%) 929
["assemble", "poisson DG", "l_Ω(v)"] 12.273 μs (5%) 2.12 KiB (1%) 1
["covo", "Quad", "explicit_step"] 79.830 ms (5%) 29.25 MiB (1%) 4398
["covo", "Quad", "integral_surface"] 50.839 ms (5%)
["covo", "Quad", "integral_volume"] 21.202 ms (5%)
["covo", "TriQuad", "explicit_step"] 387.935 ms (5%) 29.621 ms 341.57 MiB (1%) 1812322
["covo", "TriQuad", "integral_surface"] 285.320 ms (5%) 234.44 MiB (1%) 1424064
["covo", "TriQuad", "integral_volume"] 62.705 ms (5%) 51.71 MiB (1%) 379526
["entities", "edges2nodes"] 1.552 ns (5%)
["entities", "nedges"] 1.552 ns (5%)
["entities", "nnodes"] 2.785 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 1.10.5
Commit 6f3fdf7b362 (2024-08-27 14:19 UTC)
Build Info:
  Official https://julialang.org/ release
Platform Info:
  OS: Linux (x86_64-linux-gnu)
      Ubuntu 22.04.5 LTS
  uname: Linux 6.8.0-1014-azure #16~22.04.1-Ubuntu SMP Thu Aug 15 21:31:41 UTC 2024 x86_64 x86_64
  CPU: AMD EPYC 7763 64-Core Processor: 
              speed         user         nice          sys         idle          irq
       #1  3111 MHz       2240 s          0 s        243 s       5544 s          0 s
       #2  3302 MHz       2636 s          0 s        299 s       5070 s          0 s
       #3  3242 MHz       2173 s          0 s        250 s       5608 s          0 s
       #4  2625 MHz       3094 s          0 s        339 s       4579 s          0 s
  Memory: 15.615272521972656 GB (12067.3125 MB free)
  Uptime: 806.08 sec
  Load Avg:  1.15  1.17  0.88
  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 vmmcall fsgsbase bmi1 avx2 smep bmi2 erms invpcid rdseed adx smap clflushopt clwb sha_ni xsaveopt xsavec xgetbv1 xsaves user_shstk 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 Reg file data sampling: 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; BHI 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

@ghislainb ghislainb merged commit 1754796 into main Sep 20, 2024
10 checks passed
@bmxam bmxam deleted the improve_gen_hexa_mesh branch September 20, 2024 08:27
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@ghislainb ghislainb ghislainb approved these changes

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@bmxam @ghislainb