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Minor optimizations and simd #108

Merged
merged 2 commits into from
Sep 29, 2024
Merged

Minor optimizations and simd #108

merged 2 commits into from
Sep 29, 2024

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gdalle
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@gdalle gdalle commented Sep 29, 2024

  • Add @simd to some linear algebra subroutines
  • Replace some arr .= val with fill!(arr, val)

@gdalle gdalle added the run benchmark Benchmarks are run by CI label Sep 29, 2024
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Benchmark result

Judge result

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

Job Properties

  • Time of benchmarks:
    • Target: 29 Sep 2024 - 06:51
    • Baseline: 29 Sep 2024 - 06:55
  • Package commits:
    • Target: d8fda0
    • Baseline: a8b048
  • Julia commits:
    • Target: 6f3fdf
    • Baseline: 6f3fdf
  • Julia command flags:
    • Target: None
    • Baseline: None
  • Environment variables:
    • Target: OPENBLAS_NUM_THREADS => 1 JULIA_NUM_THREADS => auto
    • Baseline: OPENBLAS_NUM_THREADS => 1 JULIA_NUM_THREADS => auto

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
["HiddenMarkovModels.jl", "nb_states 32 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0", "baum_welch"] 0.72 (5%) ✅ 1.00 (1%)
["HiddenMarkovModels.jl", "nb_states 4 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0", "viterbi"] 1.88 (5%) ❌ 1.00 (1%)
["HiddenMarkovModels.jl", "nb_states 4 obs_dim 10 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0", "baum_welch"] 0.75 (5%) ✅ 1.00 (1%)
["HiddenMarkovModels.jl", "nb_states 4 obs_dim 10 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0", "forward"] 1.30 (5%) ❌ 1.00 (1%)
["HiddenMarkovModels.jl", "nb_states 4 obs_dim 10 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 1", "forward"] 1.15 (5%) ❌ 1.00 (1%)
["HiddenMarkovModels.jl", "nb_states 64 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 1 custom_dist 0", "viterbi"] 1.17 (5%) ❌ 1.00 (1%)
["HiddenMarkovModels.jl", "nb_states 8 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0", "baum_welch"] 1.16 (5%) ❌ 1.00 (1%)

Benchmark Group List

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

  • ["HiddenMarkovModels.jl", "nb_states 16 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0"]
  • ["HiddenMarkovModels.jl", "nb_states 32 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0"]
  • ["HiddenMarkovModels.jl", "nb_states 4 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0"]
  • ["HiddenMarkovModels.jl", "nb_states 4 obs_dim 10 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0"]
  • ["HiddenMarkovModels.jl", "nb_states 4 obs_dim 10 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 1"]
  • ["HiddenMarkovModels.jl", "nb_states 64 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0"]
  • ["HiddenMarkovModels.jl", "nb_states 64 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 1 custom_dist 0"]
  • ["HiddenMarkovModels.jl", "nb_states 8 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0"]

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  3243 MHz       1142 s          0 s        108 s       2520 s          0 s
       #2  2699 MHz       1047 s          0 s        101 s       2635 s          0 s
       #3  2445 MHz       1252 s          0 s         93 s       2448 s          0 s
       #4  3239 MHz       1210 s          0 s        106 s       2484 s          0 s
  Memory: 15.615272521972656 GB (13287.74609375 MB free)
  Uptime: 382.49 sec
  Load Avg:  2.04  1.21  0.53
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-15.0.7 (ORCJIT, znver3)
Threads: 4 default, 0 interactive, 2 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  3243 MHz       1835 s          0 s        142 s       3822 s          0 s
       #2  3258 MHz       1698 s          0 s        133 s       3981 s          0 s
       #3  2610 MHz       2065 s          0 s        128 s       3630 s          0 s
       #4  2445 MHz       1862 s          0 s        142 s       3827 s          0 s
  Memory: 15.615272521972656 GB (13495.140625 MB free)
  Uptime: 585.76 sec
  Load Avg:  1.77  1.36  0.73
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-15.0.7 (ORCJIT, znver3)
Threads: 4 default, 0 interactive, 2 GC (on 4 virtual cores)

Target result

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

Job Properties

  • Time of benchmark: 29 Sep 2024 - 6:51
  • Package commit: d8fda0
  • Julia commit: 6f3fdf
  • Julia command flags: None
  • Environment variables: OPENBLAS_NUM_THREADS => 1 JULIA_NUM_THREADS => auto

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
["HiddenMarkovModels.jl", "nb_states 16 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0", "baum_welch"] 2.364 ms (5%) 5.41 MiB (1%) 2068
["HiddenMarkovModels.jl", "nb_states 16 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0", "forward"] 316.280 μs (5%) 518.52 KiB (1%) 27
["HiddenMarkovModels.jl", "nb_states 16 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0", "forward_backward"] 418.150 μs (5%) 1.26 MiB (1%) 35
["HiddenMarkovModels.jl", "nb_states 16 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0", "viterbi"] 431.035 μs (5%) 768.62 KiB (1%) 29
["HiddenMarkovModels.jl", "nb_states 32 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0", "baum_welch"] 3.909 ms (5%) 18.37 MiB (1%) 2068
["HiddenMarkovModels.jl", "nb_states 32 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0", "forward"] 699.237 μs (5%) 1018.52 KiB (1%) 27
["HiddenMarkovModels.jl", "nb_states 32 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0", "forward_backward"] 777.242 μs (5%) 2.48 MiB (1%) 35
["HiddenMarkovModels.jl", "nb_states 32 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0", "viterbi"] 1.286 ms (5%) 1.48 MiB (1%) 29
["HiddenMarkovModels.jl", "nb_states 4 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0", "baum_welch"] 398.063 μs (5%) 725.77 KiB (1%) 2068
["HiddenMarkovModels.jl", "nb_states 4 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0", "forward"] 136.715 μs (5%) 143.52 KiB (1%) 27
["HiddenMarkovModels.jl", "nb_states 4 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0", "forward_backward"] 211.294 μs (5%) 347.28 KiB (1%) 35
["HiddenMarkovModels.jl", "nb_states 4 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0", "viterbi"] 197.238 μs (5%) 206.12 KiB (1%) 29
["HiddenMarkovModels.jl", "nb_states 4 obs_dim 10 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0", "baum_welch"] 947.272 μs (5%) 2.42 MiB (1%) 10117
["HiddenMarkovModels.jl", "nb_states 4 obs_dim 10 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0", "forward"] 680.611 μs (5%) 1.24 MiB (1%) 8028
["HiddenMarkovModels.jl", "nb_states 4 obs_dim 10 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0", "forward_backward"] 594.450 μs (5%) 1.44 MiB (1%) 8036
["HiddenMarkovModels.jl", "nb_states 4 obs_dim 10 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0", "viterbi"] 628.965 μs (5%) 1.30 MiB (1%) 8030
["HiddenMarkovModels.jl", "nb_states 4 obs_dim 10 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 1", "baum_welch"] 563.773 μs (5%) 728.61 KiB (1%) 2093
["HiddenMarkovModels.jl", "nb_states 4 obs_dim 10 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 1", "forward"] 203.109 μs (5%) 143.52 KiB (1%) 27
["HiddenMarkovModels.jl", "nb_states 4 obs_dim 10 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 1", "forward_backward"] 251.590 μs (5%) 347.28 KiB (1%) 35
["HiddenMarkovModels.jl", "nb_states 4 obs_dim 10 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 1", "viterbi"] 144.160 μs (5%) 206.12 KiB (1%) 29
["HiddenMarkovModels.jl", "nb_states 64 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0", "baum_welch"] 6.455 ms (5%) 67.61 MiB (1%) 4071
["HiddenMarkovModels.jl", "nb_states 64 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0", "forward"] 1.167 ms (5%) 1.97 MiB (1%) 27
["HiddenMarkovModels.jl", "nb_states 64 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0", "forward_backward"] 1.682 ms (5%) 4.95 MiB (1%) 36
["HiddenMarkovModels.jl", "nb_states 64 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0", "viterbi"] 4.117 ms (5%) 2.95 MiB (1%) 29
["HiddenMarkovModels.jl", "nb_states 64 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 1 custom_dist 0", "baum_welch"] 4.769 ms (5%) 15.67 MiB (1%) 16039
["HiddenMarkovModels.jl", "nb_states 64 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 1 custom_dist 0", "forward"] 992.695 μs (5%) 2.06 MiB (1%) 2007
["HiddenMarkovModels.jl", "nb_states 64 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 1 custom_dist 0", "forward_backward"] 1.289 ms (5%) 5.16 MiB (1%) 3998
["HiddenMarkovModels.jl", "nb_states 64 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 1 custom_dist 0", "viterbi"] 1.213 ms (5%) 2.95 MiB (1%) 29
["HiddenMarkovModels.jl", "nb_states 8 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0", "baum_welch"] 629.035 μs (5%) 1.75 MiB (1%) 2068
["HiddenMarkovModels.jl", "nb_states 8 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0", "forward"] 195.605 μs (5%) 268.52 KiB (1%) 27
["HiddenMarkovModels.jl", "nb_states 8 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0", "forward_backward"] 278.611 μs (5%) 660.16 KiB (1%) 35
["HiddenMarkovModels.jl", "nb_states 8 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0", "viterbi"] 188.993 μs (5%) 393.62 KiB (1%) 29

Benchmark Group List

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

  • ["HiddenMarkovModels.jl", "nb_states 16 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0"]
  • ["HiddenMarkovModels.jl", "nb_states 32 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0"]
  • ["HiddenMarkovModels.jl", "nb_states 4 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0"]
  • ["HiddenMarkovModels.jl", "nb_states 4 obs_dim 10 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0"]
  • ["HiddenMarkovModels.jl", "nb_states 4 obs_dim 10 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 1"]
  • ["HiddenMarkovModels.jl", "nb_states 64 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0"]
  • ["HiddenMarkovModels.jl", "nb_states 64 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 1 custom_dist 0"]
  • ["HiddenMarkovModels.jl", "nb_states 8 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0"]

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  3243 MHz       1142 s          0 s        108 s       2520 s          0 s
       #2  2699 MHz       1047 s          0 s        101 s       2635 s          0 s
       #3  2445 MHz       1252 s          0 s         93 s       2448 s          0 s
       #4  3239 MHz       1210 s          0 s        106 s       2484 s          0 s
  Memory: 15.615272521972656 GB (13287.74609375 MB free)
  Uptime: 382.49 sec
  Load Avg:  2.04  1.21  0.53
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-15.0.7 (ORCJIT, znver3)
Threads: 4 default, 0 interactive, 2 GC (on 4 virtual cores)

Baseline result

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

Job Properties

  • Time of benchmark: 29 Sep 2024 - 6:55
  • Package commit: a8b048
  • Julia commit: 6f3fdf
  • Julia command flags: None
  • Environment variables: OPENBLAS_NUM_THREADS => 1 JULIA_NUM_THREADS => auto

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
["HiddenMarkovModels.jl", "nb_states 16 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0", "baum_welch"] 2.348 ms (5%) 5.41 MiB (1%) 2068
["HiddenMarkovModels.jl", "nb_states 16 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0", "forward"] 320.388 μs (5%) 518.52 KiB (1%) 27
["HiddenMarkovModels.jl", "nb_states 16 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0", "forward_backward"] 421.126 μs (5%) 1.26 MiB (1%) 35
["HiddenMarkovModels.jl", "nb_states 16 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0", "viterbi"] 446.624 μs (5%) 768.62 KiB (1%) 29
["HiddenMarkovModels.jl", "nb_states 32 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0", "baum_welch"] 5.416 ms (5%) 18.37 MiB (1%) 2068
["HiddenMarkovModels.jl", "nb_states 32 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0", "forward"] 707.651 μs (5%) 1018.52 KiB (1%) 27
["HiddenMarkovModels.jl", "nb_states 32 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0", "forward_backward"] 767.472 μs (5%) 2.48 MiB (1%) 35
["HiddenMarkovModels.jl", "nb_states 32 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0", "viterbi"] 1.308 ms (5%) 1.48 MiB (1%) 29
["HiddenMarkovModels.jl", "nb_states 4 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0", "baum_welch"] 392.653 μs (5%) 725.77 KiB (1%) 2068
["HiddenMarkovModels.jl", "nb_states 4 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0", "forward"] 137.497 μs (5%) 143.52 KiB (1%) 27
["HiddenMarkovModels.jl", "nb_states 4 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0", "forward_backward"] 212.938 μs (5%) 347.28 KiB (1%) 35
["HiddenMarkovModels.jl", "nb_states 4 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0", "viterbi"] 105.076 μs (5%) 206.12 KiB (1%) 29
["HiddenMarkovModels.jl", "nb_states 4 obs_dim 10 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0", "baum_welch"] 1.259 ms (5%) 2.42 MiB (1%) 10117
["HiddenMarkovModels.jl", "nb_states 4 obs_dim 10 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0", "forward"] 523.297 μs (5%) 1.24 MiB (1%) 8028
["HiddenMarkovModels.jl", "nb_states 4 obs_dim 10 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0", "forward_backward"] 595.742 μs (5%) 1.44 MiB (1%) 8036
["HiddenMarkovModels.jl", "nb_states 4 obs_dim 10 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0", "viterbi"] 637.820 μs (5%) 1.30 MiB (1%) 8030
["HiddenMarkovModels.jl", "nb_states 4 obs_dim 10 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 1", "baum_welch"] 541.992 μs (5%) 728.61 KiB (1%) 2093
["HiddenMarkovModels.jl", "nb_states 4 obs_dim 10 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 1", "forward"] 176.109 μs (5%) 143.52 KiB (1%) 27
["HiddenMarkovModels.jl", "nb_states 4 obs_dim 10 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 1", "forward_backward"] 249.125 μs (5%) 347.28 KiB (1%) 35
["HiddenMarkovModels.jl", "nb_states 4 obs_dim 10 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 1", "viterbi"] 142.907 μs (5%) 206.12 KiB (1%) 29
["HiddenMarkovModels.jl", "nb_states 64 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0", "baum_welch"] 6.656 ms (5%) 67.61 MiB (1%) 4071
["HiddenMarkovModels.jl", "nb_states 64 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0", "forward"] 1.172 ms (5%) 1.97 MiB (1%) 27
["HiddenMarkovModels.jl", "nb_states 64 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0", "forward_backward"] 1.709 ms (5%) 4.95 MiB (1%) 36
["HiddenMarkovModels.jl", "nb_states 64 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0", "viterbi"] 4.177 ms (5%) 2.95 MiB (1%) 29
["HiddenMarkovModels.jl", "nb_states 64 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 1 custom_dist 0", "baum_welch"] 4.659 ms (5%) 15.67 MiB (1%) 16039
["HiddenMarkovModels.jl", "nb_states 64 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 1 custom_dist 0", "forward"] 1.005 ms (5%) 2.06 MiB (1%) 2007
["HiddenMarkovModels.jl", "nb_states 64 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 1 custom_dist 0", "forward_backward"] 1.309 ms (5%) 5.16 MiB (1%) 3998
["HiddenMarkovModels.jl", "nb_states 64 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 1 custom_dist 0", "viterbi"] 1.040 ms (5%) 2.95 MiB (1%) 29
["HiddenMarkovModels.jl", "nb_states 8 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0", "baum_welch"] 541.341 μs (5%) 1.75 MiB (1%) 2068
["HiddenMarkovModels.jl", "nb_states 8 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0", "forward"] 197.639 μs (5%) 268.52 KiB (1%) 27
["HiddenMarkovModels.jl", "nb_states 8 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0", "forward_backward"] 280.424 μs (5%) 660.16 KiB (1%) 35
["HiddenMarkovModels.jl", "nb_states 8 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0", "viterbi"] 192.449 μs (5%) 393.62 KiB (1%) 29

Benchmark Group List

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

  • ["HiddenMarkovModels.jl", "nb_states 16 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0"]
  • ["HiddenMarkovModels.jl", "nb_states 32 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0"]
  • ["HiddenMarkovModels.jl", "nb_states 4 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0"]
  • ["HiddenMarkovModels.jl", "nb_states 4 obs_dim 10 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0"]
  • ["HiddenMarkovModels.jl", "nb_states 4 obs_dim 10 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 1"]
  • ["HiddenMarkovModels.jl", "nb_states 64 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0"]
  • ["HiddenMarkovModels.jl", "nb_states 64 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 1 custom_dist 0"]
  • ["HiddenMarkovModels.jl", "nb_states 8 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0"]

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  3243 MHz       1835 s          0 s        142 s       3822 s          0 s
       #2  3258 MHz       1698 s          0 s        133 s       3981 s          0 s
       #3  2610 MHz       2065 s          0 s        128 s       3630 s          0 s
       #4  2445 MHz       1862 s          0 s        142 s       3827 s          0 s
  Memory: 15.615272521972656 GB (13495.140625 MB free)
  Uptime: 585.76 sec
  Load Avg:  1.77  1.36  0.73
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-15.0.7 (ORCJIT, znver3)
Threads: 4 default, 0 interactive, 2 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

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codecov bot commented Sep 29, 2024 •
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Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 89.77%. Comparing base (a8b048a) to head (b02da17).
Report is 1 commits behind head on main.

Additional details and impacted files 
@@            Coverage Diff             @@
##             main     #108      +/-   ##
==========================================
- Coverage   91.00%   89.77%   -1.23%     
==========================================
  Files          17       17              
  Lines         489      489              
==========================================
- Hits          445      439       -6     
- Misses         44       50       +6

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@gdalle gdalle removed the run benchmark Benchmarks are run by CI label Sep 29, 2024
@gdalle gdalle added the run benchmark Benchmarks are run by CI label Sep 29, 2024
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Benchmark result

Judge result

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

Job Properties

  • Time of benchmarks:
    • Target: 29 Sep 2024 - 07:13
    • Baseline: 29 Sep 2024 - 07:17
  • Package commits:
    • Target: 344dad
    • Baseline: a8b048
  • Julia commits:
    • Target: 6f3fdf
    • Baseline: 6f3fdf
  • Julia command flags:
    • Target: None
    • Baseline: None
  • Environment variables:
    • Target: OPENBLAS_NUM_THREADS => 1 JULIA_NUM_THREADS => auto
    • Baseline: OPENBLAS_NUM_THREADS => 1 JULIA_NUM_THREADS => auto

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
["HiddenMarkovModels.jl", "nb_states 32 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0", "baum_welch"] 0.88 (5%) ✅ 1.00 (1%)
["HiddenMarkovModels.jl", "nb_states 4 obs_dim 10 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0", "baum_welch"] 1.33 (5%) ❌ 1.00 (1%)
["HiddenMarkovModels.jl", "nb_states 4 obs_dim 10 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0", "forward"] 1.32 (5%) ❌ 1.00 (1%)
["HiddenMarkovModels.jl", "nb_states 4 obs_dim 10 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0", "viterbi"] 1.33 (5%) ❌ 1.00 (1%)
["HiddenMarkovModels.jl", "nb_states 64 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0", "baum_welch"] 1.07 (5%) ❌ 1.00 (1%)
["HiddenMarkovModels.jl", "nb_states 64 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0", "viterbi"] 1.06 (5%) ❌ 1.00 (1%)
["HiddenMarkovModels.jl", "nb_states 64 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 1 custom_dist 0", "viterbi"] 1.16 (5%) ❌ 1.00 (1%)

Benchmark Group List

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

  • ["HiddenMarkovModels.jl", "nb_states 16 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0"]
  • ["HiddenMarkovModels.jl", "nb_states 32 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0"]
  • ["HiddenMarkovModels.jl", "nb_states 4 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0"]
  • ["HiddenMarkovModels.jl", "nb_states 4 obs_dim 10 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0"]
  • ["HiddenMarkovModels.jl", "nb_states 4 obs_dim 10 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 1"]
  • ["HiddenMarkovModels.jl", "nb_states 64 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0"]
  • ["HiddenMarkovModels.jl", "nb_states 64 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 1 custom_dist 0"]
  • ["HiddenMarkovModels.jl", "nb_states 8 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0"]

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  2445 MHz        948 s          0 s        103 s       1944 s          0 s
       #2  2743 MHz       1377 s          0 s        120 s       1491 s          0 s
       #3  3240 MHz       1128 s          0 s        100 s       1770 s          0 s
       #4  3236 MHz       1220 s          0 s         89 s       1679 s          0 s
  Memory: 15.615272521972656 GB (13437.15625 MB free)
  Uptime: 301.67 sec
  Load Avg:  2.01  1.24  0.54
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-15.0.7 (ORCJIT, znver3)
Threads: 4 default, 0 interactive, 2 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  2445 MHz       1615 s          0 s        139 s       3288 s          0 s
       #2  3240 MHz       2006 s          0 s        154 s       2876 s          0 s
       #3  2719 MHz       1926 s          0 s        135 s       2986 s          0 s
       #4  2913 MHz       1966 s          0 s        123 s       2947 s          0 s
  Memory: 15.615272521972656 GB (13462.8984375 MB free)
  Uptime: 506.89 sec
  Load Avg:  1.84  1.4  0.74
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-15.0.7 (ORCJIT, znver3)
Threads: 4 default, 0 interactive, 2 GC (on 4 virtual cores)

Target result

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

Job Properties

  • Time of benchmark: 29 Sep 2024 - 7:13
  • Package commit: 344dad
  • Julia commit: 6f3fdf
  • Julia command flags: None
  • Environment variables: OPENBLAS_NUM_THREADS => 1 JULIA_NUM_THREADS => auto

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
["HiddenMarkovModels.jl", "nb_states 16 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0", "baum_welch"] 2.401 ms (5%) 5.41 MiB (1%) 2068
["HiddenMarkovModels.jl", "nb_states 16 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0", "forward"] 316.560 μs (5%) 518.52 KiB (1%) 27
["HiddenMarkovModels.jl", "nb_states 16 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0", "forward_backward"] 421.835 μs (5%) 1.26 MiB (1%) 35
["HiddenMarkovModels.jl", "nb_states 16 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0", "viterbi"] 453.986 μs (5%) 768.62 KiB (1%) 29
["HiddenMarkovModels.jl", "nb_states 32 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0", "baum_welch"] 4.321 ms (5%) 18.37 MiB (1%) 2068
["HiddenMarkovModels.jl", "nb_states 32 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0", "forward"] 701.136 μs (5%) 1018.52 KiB (1%) 27
["HiddenMarkovModels.jl", "nb_states 32 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0", "forward_backward"] 764.654 μs (5%) 2.48 MiB (1%) 35
["HiddenMarkovModels.jl", "nb_states 32 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0", "viterbi"] 1.359 ms (5%) 1.48 MiB (1%) 29
["HiddenMarkovModels.jl", "nb_states 4 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0", "baum_welch"] 392.170 μs (5%) 725.77 KiB (1%) 2068
["HiddenMarkovModels.jl", "nb_states 4 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0", "forward"] 137.867 μs (5%) 143.52 KiB (1%) 27
["HiddenMarkovModels.jl", "nb_states 4 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0", "forward_backward"] 211.424 μs (5%) 347.28 KiB (1%) 35
["HiddenMarkovModels.jl", "nb_states 4 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0", "viterbi"] 101.659 μs (5%) 206.12 KiB (1%) 29
["HiddenMarkovModels.jl", "nb_states 4 obs_dim 10 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0", "baum_welch"] 1.255 ms (5%) 2.42 MiB (1%) 10117
["HiddenMarkovModels.jl", "nb_states 4 obs_dim 10 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0", "forward"] 672.531 μs (5%) 1.24 MiB (1%) 8028
["HiddenMarkovModels.jl", "nb_states 4 obs_dim 10 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0", "forward_backward"] 596.130 μs (5%) 1.44 MiB (1%) 8036
["HiddenMarkovModels.jl", "nb_states 4 obs_dim 10 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0", "viterbi"] 626.957 μs (5%) 1.30 MiB (1%) 8030
["HiddenMarkovModels.jl", "nb_states 4 obs_dim 10 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 1", "baum_welch"] 563.639 μs (5%) 728.61 KiB (1%) 2093
["HiddenMarkovModels.jl", "nb_states 4 obs_dim 10 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 1", "forward"] 177.079 μs (5%) 143.52 KiB (1%) 27
["HiddenMarkovModels.jl", "nb_states 4 obs_dim 10 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 1", "forward_backward"] 253.532 μs (5%) 347.28 KiB (1%) 35
["HiddenMarkovModels.jl", "nb_states 4 obs_dim 10 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 1", "viterbi"] 140.542 μs (5%) 206.12 KiB (1%) 29
["HiddenMarkovModels.jl", "nb_states 64 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0", "baum_welch"] 6.785 ms (5%) 67.61 MiB (1%) 4071
["HiddenMarkovModels.jl", "nb_states 64 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0", "forward"] 1.159 ms (5%) 1.97 MiB (1%) 27
["HiddenMarkovModels.jl", "nb_states 64 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0", "forward_backward"] 1.696 ms (5%) 4.95 MiB (1%) 36
["HiddenMarkovModels.jl", "nb_states 64 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0", "viterbi"] 4.406 ms (5%) 2.95 MiB (1%) 29
["HiddenMarkovModels.jl", "nb_states 64 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 1 custom_dist 0", "baum_welch"] 4.900 ms (5%) 15.67 MiB (1%) 16039
["HiddenMarkovModels.jl", "nb_states 64 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 1 custom_dist 0", "forward"] 1.016 ms (5%) 2.06 MiB (1%) 2007
["HiddenMarkovModels.jl", "nb_states 64 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 1 custom_dist 0", "forward_backward"] 1.291 ms (5%) 5.16 MiB (1%) 3998
["HiddenMarkovModels.jl", "nb_states 64 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 1 custom_dist 0", "viterbi"] 1.212 ms (5%) 2.95 MiB (1%) 29
["HiddenMarkovModels.jl", "nb_states 8 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0", "baum_welch"] 536.298 μs (5%) 1.75 MiB (1%) 2068
["HiddenMarkovModels.jl", "nb_states 8 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0", "forward"] 195.775 μs (5%) 268.52 KiB (1%) 27
["HiddenMarkovModels.jl", "nb_states 8 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0", "forward_backward"] 281.274 μs (5%) 660.16 KiB (1%) 35
["HiddenMarkovModels.jl", "nb_states 8 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0", "viterbi"] 193.490 μs (5%) 393.62 KiB (1%) 29

Benchmark Group List

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

  • ["HiddenMarkovModels.jl", "nb_states 16 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0"]
  • ["HiddenMarkovModels.jl", "nb_states 32 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0"]
  • ["HiddenMarkovModels.jl", "nb_states 4 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0"]
  • ["HiddenMarkovModels.jl", "nb_states 4 obs_dim 10 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0"]
  • ["HiddenMarkovModels.jl", "nb_states 4 obs_dim 10 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 1"]
  • ["HiddenMarkovModels.jl", "nb_states 64 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0"]
  • ["HiddenMarkovModels.jl", "nb_states 64 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 1 custom_dist 0"]
  • ["HiddenMarkovModels.jl", "nb_states 8 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0"]

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  2445 MHz        948 s          0 s        103 s       1944 s          0 s
       #2  2743 MHz       1377 s          0 s        120 s       1491 s          0 s
       #3  3240 MHz       1128 s          0 s        100 s       1770 s          0 s
       #4  3236 MHz       1220 s          0 s         89 s       1679 s          0 s
  Memory: 15.615272521972656 GB (13437.15625 MB free)
  Uptime: 301.67 sec
  Load Avg:  2.01  1.24  0.54
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-15.0.7 (ORCJIT, znver3)
Threads: 4 default, 0 interactive, 2 GC (on 4 virtual cores)

Baseline result

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

Job Properties

  • Time of benchmark: 29 Sep 2024 - 7:17
  • Package commit: a8b048
  • Julia commit: 6f3fdf
  • Julia command flags: None
  • Environment variables: OPENBLAS_NUM_THREADS => 1 JULIA_NUM_THREADS => auto

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
["HiddenMarkovModels.jl", "nb_states 16 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0", "baum_welch"] 2.292 ms (5%) 5.41 MiB (1%) 2068
["HiddenMarkovModels.jl", "nb_states 16 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0", "forward"] 318.773 μs (5%) 518.52 KiB (1%) 27
["HiddenMarkovModels.jl", "nb_states 16 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0", "forward_backward"] 421.404 μs (5%) 1.26 MiB (1%) 35
["HiddenMarkovModels.jl", "nb_states 16 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0", "viterbi"] 444.467 μs (5%) 768.62 KiB (1%) 29
["HiddenMarkovModels.jl", "nb_states 32 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0", "baum_welch"] 4.908 ms (5%) 18.37 MiB (1%) 2068
["HiddenMarkovModels.jl", "nb_states 32 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0", "forward"] 704.641 μs (5%) 1018.52 KiB (1%) 27
["HiddenMarkovModels.jl", "nb_states 32 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0", "forward_backward"] 768.811 μs (5%) 2.48 MiB (1%) 35
["HiddenMarkovModels.jl", "nb_states 32 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0", "viterbi"] 1.310 ms (5%) 1.48 MiB (1%) 29
["HiddenMarkovModels.jl", "nb_states 4 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0", "baum_welch"] 397.389 μs (5%) 725.77 KiB (1%) 2068
["HiddenMarkovModels.jl", "nb_states 4 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0", "forward"] 136.915 μs (5%) 143.52 KiB (1%) 27
["HiddenMarkovModels.jl", "nb_states 4 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0", "forward_backward"] 211.464 μs (5%) 347.28 KiB (1%) 35
["HiddenMarkovModels.jl", "nb_states 4 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0", "viterbi"] 105.647 μs (5%) 206.12 KiB (1%) 29
["HiddenMarkovModels.jl", "nb_states 4 obs_dim 10 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0", "baum_welch"] 940.030 μs (5%) 2.42 MiB (1%) 10117
["HiddenMarkovModels.jl", "nb_states 4 obs_dim 10 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0", "forward"] 510.511 μs (5%) 1.24 MiB (1%) 8028
["HiddenMarkovModels.jl", "nb_states 4 obs_dim 10 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0", "forward_backward"] 586.002 μs (5%) 1.44 MiB (1%) 8036
["HiddenMarkovModels.jl", "nb_states 4 obs_dim 10 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0", "viterbi"] 472.841 μs (5%) 1.30 MiB (1%) 8030
["HiddenMarkovModels.jl", "nb_states 4 obs_dim 10 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 1", "baum_welch"] 541.389 μs (5%) 728.61 KiB (1%) 2093
["HiddenMarkovModels.jl", "nb_states 4 obs_dim 10 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 1", "forward"] 176.018 μs (5%) 143.52 KiB (1%) 27
["HiddenMarkovModels.jl", "nb_states 4 obs_dim 10 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 1", "forward_backward"] 249.615 μs (5%) 347.28 KiB (1%) 35
["HiddenMarkovModels.jl", "nb_states 4 obs_dim 10 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 1", "viterbi"] 143.167 μs (5%) 206.12 KiB (1%) 29
["HiddenMarkovModels.jl", "nb_states 64 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0", "baum_welch"] 6.345 ms (5%) 67.61 MiB (1%) 4071
["HiddenMarkovModels.jl", "nb_states 64 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0", "forward"] 1.177 ms (5%) 1.97 MiB (1%) 27
["HiddenMarkovModels.jl", "nb_states 64 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0", "forward_backward"] 1.711 ms (5%) 4.95 MiB (1%) 36
["HiddenMarkovModels.jl", "nb_states 64 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0", "viterbi"] 4.173 ms (5%) 2.95 MiB (1%) 29
["HiddenMarkovModels.jl", "nb_states 64 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 1 custom_dist 0", "baum_welch"] 4.697 ms (5%) 15.67 MiB (1%) 16039
["HiddenMarkovModels.jl", "nb_states 64 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 1 custom_dist 0", "forward"] 986.598 μs (5%) 2.06 MiB (1%) 2007
["HiddenMarkovModels.jl", "nb_states 64 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 1 custom_dist 0", "forward_backward"] 1.313 ms (5%) 5.16 MiB (1%) 3998
["HiddenMarkovModels.jl", "nb_states 64 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 1 custom_dist 0", "viterbi"] 1.042 ms (5%) 2.95 MiB (1%) 29
["HiddenMarkovModels.jl", "nb_states 8 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0", "baum_welch"] 524.276 μs (5%) 1.75 MiB (1%) 2068
["HiddenMarkovModels.jl", "nb_states 8 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0", "forward"] 195.494 μs (5%) 268.52 KiB (1%) 27
["HiddenMarkovModels.jl", "nb_states 8 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0", "forward_backward"] 280.442 μs (5%) 660.16 KiB (1%) 35
["HiddenMarkovModels.jl", "nb_states 8 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0", "viterbi"] 193.240 μs (5%) 393.62 KiB (1%) 29

Benchmark Group List

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

  • ["HiddenMarkovModels.jl", "nb_states 16 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0"]
  • ["HiddenMarkovModels.jl", "nb_states 32 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0"]
  • ["HiddenMarkovModels.jl", "nb_states 4 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0"]
  • ["HiddenMarkovModels.jl", "nb_states 4 obs_dim 10 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0"]
  • ["HiddenMarkovModels.jl", "nb_states 4 obs_dim 10 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 1"]
  • ["HiddenMarkovModels.jl", "nb_states 64 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0"]
  • ["HiddenMarkovModels.jl", "nb_states 64 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 1 custom_dist 0"]
  • ["HiddenMarkovModels.jl", "nb_states 8 obs_dim 1 seq_length 100 nb_seqs 20 bw_iter 1 sparse 0 custom_dist 0"]

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  2445 MHz       1615 s          0 s        139 s       3288 s          0 s
       #2  3240 MHz       2006 s          0 s        154 s       2876 s          0 s
       #3  2719 MHz       1926 s          0 s        135 s       2986 s          0 s
       #4  2913 MHz       1966 s          0 s        123 s       2947 s          0 s
  Memory: 15.615272521972656 GB (13462.8984375 MB free)
  Uptime: 506.89 sec
  Load Avg:  1.84  1.4  0.74
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-15.0.7 (ORCJIT, znver3)
Threads: 4 default, 0 interactive, 2 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:                             4890.84
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

@gdalle gdalle merged commit d9e4a5d into main Sep 29, 2024
6 of 7 checks passed
@gdalle gdalle deleted the gd/optim branch September 29, 2024 08:48
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