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mtsch / Ripserer.jl

Flexible and efficient persistent homology computation.
https://mtsch.github.io/Ripserer.jl/dev/
MIT License
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Docs Fixes and Tweaks #76

Closed mtsch closed 4 years ago

github-actions[bot] commented 4 years ago
Benchmark result # Judge result # Benchmark Report for */home/runner/work/Ripserer.jl/Ripserer.jl* ## Job Properties * Time of benchmarks: - Target: 1 Aug 2020 - 23:57 - Baseline: 2 Aug 2020 - 00:01 * Package commits: - Target: 884603 - Baseline: a7c559 * Julia commits: - Target: 44fa15 - Baseline: 44fa15 * 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 | |----------------------------------------------------------------|------------------------------|--------------| | `["coboundary", "full, no threshold"]` | 0.92 (5%) :white_check_mark: | 1.00 (1%) | | `["coboundary", "full, threshold=1"]` | 0.91 (5%) :white_check_mark: | 1.00 (1%) | | `["coboundary", "sparse, 25% full"]` | 0.87 (5%) :white_check_mark: | 1.00 (1%) | | `["coboundary", "sparse, 50% full"]` | 0.86 (5%) :white_check_mark: | 1.00 (1%) | | `["coboundary", "sparse, 75% full"]` | 0.87 (5%) :white_check_mark: | 1.00 (1%) | | `["sparse", "20 tori with 100 points, dim_max=2, modulus=3"]` | 0.90 (5%) :white_check_mark: | 1.00 (1%) | | `["sparse", "20 tori with 300 points, dim_max=1, modulus=3"]` | 0.89 (5%) :white_check_mark: | 1.00 (1%) | | `["sparse", "20 tori with 50 points, dim_max=3, modulus=2"]` | 0.90 (5%) :white_check_mark: | 1.00 (1%) | | `["sparse", "30 tori with 200 points, dim_max=1, modulus=2"]` | 0.91 (5%) :white_check_mark: | 1.00 (1%) | | `["torus", "n=1024, dim_max=1, modulus=7, threshold=nothing"]` | 1.05 (5%) :x: | 1.00 (1%) | ## Benchmark Group List Here's a list of all the benchmark groups executed by this job: - `["coboundary"]` - `["image"]` - `["sparse"]` - `["torus"]` ## Julia versioninfo ### Target ``` Julia Version 1.4.2 Commit 44fa15b150* (2020-05-23 18:35 UTC) Platform Info: OS: Linux (x86_64-pc-linux-gnu) Ubuntu 18.04.4 LTS uname: Linux 5.3.0-1032-azure #33~18.04.1-Ubuntu SMP Fri Jun 26 15:01:15 UTC 2020 x86_64 x86_64 CPU: Intel(R) Xeon(R) CPU E5-2673 v4 @ 2.30GHz: speed user nice sys idle irq #1 2294 MHz 9039 s 0 s 1484 s 29550 s 0 s #2 2294 MHz 26694 s 0 s 3212 s 10664 s 0 s Memory: 6.764884948730469 GB (2022.953125 MB free) Uptime: 420.0 sec Load Avg: 1.08544921875 0.9599609375 0.51708984375 WORD_SIZE: 64 LIBM: libopenlibm LLVM: libLLVM-8.0.1 (ORCJIT, broadwell) ``` ### Baseline ``` Julia Version 1.4.2 Commit 44fa15b150* (2020-05-23 18:35 UTC) Platform Info: OS: Linux (x86_64-pc-linux-gnu) Ubuntu 18.04.4 LTS uname: Linux 5.3.0-1032-azure #33~18.04.1-Ubuntu SMP Fri Jun 26 15:01:15 UTC 2020 x86_64 x86_64 CPU: Intel(R) Xeon(R) CPU E5-2673 v4 @ 2.30GHz: speed user nice sys idle irq #1 2294 MHz 9611 s 0 s 1562 s 51562 s 0 s #2 2294 MHz 47239 s 0 s 4789 s 11200 s 0 s Memory: 6.764884948730469 GB (1955.4140625 MB free) Uptime: 648.0 sec Load Avg: 1.0 0.98779296875 0.63427734375 WORD_SIZE: 64 LIBM: libopenlibm LLVM: libLLVM-8.0.1 (ORCJIT, broadwell) ``` --- # Target result # Benchmark Report for */home/runner/work/Ripserer.jl/Ripserer.jl* ## Job Properties * Time of benchmark: 1 Aug 2020 - 23:57 * Package commit: 884603 * Julia commit: 44fa15 * 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 | |----------------------------------------------------------------|----------------:|-----------:|----------------:|------------:| | `["coboundary", "full, no threshold"]` | 4.945 s (5%) | | 3.05 MiB (1%) | 50000 | | `["coboundary", "full, threshold=1"]` | 3.289 s (5%) | | 3.05 MiB (1%) | 50000 | | `["coboundary", "sparse, 25% full"]` | 179.033 ms (5%) | | 4.27 MiB (1%) | 40000 | | `["coboundary", "sparse, 50% full"]` | 921.279 ms (5%) | | 2.14 MiB (1%) | 20000 | | `["coboundary", "sparse, 75% full"]` | 1.258 s (5%) | | 1.07 MiB (1%) | 10000 | | `["image", "bonsai"]` | 2.045 s (5%) | 47.968 ms | 255.89 MiB (1%) | 3042206 | | `["image", "hubble"]` | 1.694 s (5%) | 48.868 ms | 409.45 MiB (1%) | 4010107 | | `["sparse", "20 tori with 100 points, dim_max=2, modulus=3"]` | 5.094 s (5%) | 89.884 ms | 1.04 GiB (1%) | 7316217 | | `["sparse", "20 tori with 300 points, dim_max=1, modulus=3"]` | 6.864 s (5%) | | 409.85 MiB (1%) | 4121886 | | `["sparse", "20 tori with 50 points, dim_max=3, modulus=2"]` | 6.945 s (5%) | 97.057 ms | 1.45 GiB (1%) | 10962198 | | `["sparse", "30 tori with 200 points, dim_max=1, modulus=2"]` | 2.695 s (5%) | | 222.62 MiB (1%) | 2535055 | | `["torus", "n=1024, dim_max=1, modulus=2, threshold=1"]` | 9.297 s (5%) | | 458.44 MiB (1%) | 981410 | | `["torus", "n=1024, dim_max=1, modulus=7, threshold=nothing"]` | 34.271 s (5%) | 28.618 ms | 1.54 GiB (1%) | 2284962 | | `["torus", "n=256, dim_max=2, modulus=2, threshold=nothing"]` | 2.906 s (5%) | 32.462 ms | 593.42 MiB (1%) | 5202911 | | `["torus", "n=256, dim_max=2, modulus=7, threshold=1"]` | 1.949 s (5%) | 35.484 ms | 334.67 MiB (1%) | 2787735 | | `["torus", "n=64, dim_max=4, modulus=2, threshold=nothing"]` | 6.286 s (5%) | 115.438 ms | 1.17 GiB (1%) | 10776691 | | `["torus", "n=81, dim_max=4, modulus=3, threshold=1"]` | 7.630 s (5%) | 134.170 ms | 1.22 GiB (1%) | 12092896 | ## Benchmark Group List Here's a list of all the benchmark groups executed by this job: - `["coboundary"]` - `["image"]` - `["sparse"]` - `["torus"]` ## Julia versioninfo ``` Julia Version 1.4.2 Commit 44fa15b150* (2020-05-23 18:35 UTC) Platform Info: OS: Linux (x86_64-pc-linux-gnu) Ubuntu 18.04.4 LTS uname: Linux 5.3.0-1032-azure #33~18.04.1-Ubuntu SMP Fri Jun 26 15:01:15 UTC 2020 x86_64 x86_64 CPU: Intel(R) Xeon(R) CPU E5-2673 v4 @ 2.30GHz: speed user nice sys idle irq #1 2294 MHz 9039 s 0 s 1484 s 29550 s 0 s #2 2294 MHz 26694 s 0 s 3212 s 10664 s 0 s Memory: 6.764884948730469 GB (2022.953125 MB free) Uptime: 420.0 sec Load Avg: 1.08544921875 0.9599609375 0.51708984375 WORD_SIZE: 64 LIBM: libopenlibm LLVM: libLLVM-8.0.1 (ORCJIT, broadwell) ``` --- # Baseline result # Benchmark Report for */home/runner/work/Ripserer.jl/Ripserer.jl* ## Job Properties * Time of benchmark: 2 Aug 2020 - 0:1 * Package commit: a7c559 * Julia commit: 44fa15 * 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 | |----------------------------------------------------------------|----------------:|-----------:|----------------:|------------:| | `["coboundary", "full, no threshold"]` | 5.382 s (5%) | | 3.05 MiB (1%) | 50000 | | `["coboundary", "full, threshold=1"]` | 3.619 s (5%) | | 3.05 MiB (1%) | 50000 | | `["coboundary", "sparse, 25% full"]` | 206.087 ms (5%) | | 4.27 MiB (1%) | 40000 | | `["coboundary", "sparse, 50% full"]` | 1.066 s (5%) | | 2.14 MiB (1%) | 20000 | | `["coboundary", "sparse, 75% full"]` | 1.444 s (5%) | | 1.07 MiB (1%) | 10000 | | `["image", "bonsai"]` | 2.041 s (5%) | 49.048 ms | 255.89 MiB (1%) | 3042206 | | `["image", "hubble"]` | 1.652 s (5%) | 46.906 ms | 409.45 MiB (1%) | 4010107 | | `["sparse", "20 tori with 100 points, dim_max=2, modulus=3"]` | 5.667 s (5%) | 105.789 ms | 1.04 GiB (1%) | 7316217 | | `["sparse", "20 tori with 300 points, dim_max=1, modulus=3"]` | 7.746 s (5%) | | 409.85 MiB (1%) | 4121886 | | `["sparse", "20 tori with 50 points, dim_max=3, modulus=2"]` | 7.699 s (5%) | 100.941 ms | 1.45 GiB (1%) | 10962198 | | `["sparse", "30 tori with 200 points, dim_max=1, modulus=2"]` | 2.969 s (5%) | | 222.62 MiB (1%) | 2535055 | | `["torus", "n=1024, dim_max=1, modulus=2, threshold=1"]` | 9.100 s (5%) | | 458.44 MiB (1%) | 981410 | | `["torus", "n=1024, dim_max=1, modulus=7, threshold=nothing"]` | 32.621 s (5%) | 30.357 ms | 1.54 GiB (1%) | 2284962 | | `["torus", "n=256, dim_max=2, modulus=2, threshold=nothing"]` | 3.026 s (5%) | 32.434 ms | 593.42 MiB (1%) | 5202911 | | `["torus", "n=256, dim_max=2, modulus=7, threshold=1"]` | 1.947 s (5%) | 36.436 ms | 334.67 MiB (1%) | 2787735 | | `["torus", "n=64, dim_max=4, modulus=2, threshold=nothing"]` | 6.218 s (5%) | 108.911 ms | 1.17 GiB (1%) | 10776691 | | `["torus", "n=81, dim_max=4, modulus=3, threshold=1"]` | 7.621 s (5%) | 129.604 ms | 1.22 GiB (1%) | 12092896 | ## Benchmark Group List Here's a list of all the benchmark groups executed by this job: - `["coboundary"]` - `["image"]` - `["sparse"]` - `["torus"]` ## Julia versioninfo ``` Julia Version 1.4.2 Commit 44fa15b150* (2020-05-23 18:35 UTC) Platform Info: OS: Linux (x86_64-pc-linux-gnu) Ubuntu 18.04.4 LTS uname: Linux 5.3.0-1032-azure #33~18.04.1-Ubuntu SMP Fri Jun 26 15:01:15 UTC 2020 x86_64 x86_64 CPU: Intel(R) Xeon(R) CPU E5-2673 v4 @ 2.30GHz: speed user nice sys idle irq #1 2294 MHz 9611 s 0 s 1562 s 51562 s 0 s #2 2294 MHz 47239 s 0 s 4789 s 11200 s 0 s Memory: 6.764884948730469 GB (1955.4140625 MB free) Uptime: 648.0 sec Load Avg: 1.0 0.98779296875 0.63427734375 WORD_SIZE: 64 LIBM: libopenlibm LLVM: libLLVM-8.0.1 (ORCJIT, broadwell) ``` --- # Runtime information | Runtime Info | | |:--|:--| | BLAS #threads | 2 | | `BLAS.vendor()` | `openblas64` | | `Sys.CPU_THREADS` | 2 | `lscpu` output: Architecture: x86_64 CPU op-mode(s): 32-bit, 64-bit Byte Order: Little Endian CPU(s): 2 On-line CPU(s) list: 0,1 Thread(s) per core: 1 Core(s) per socket: 2 Socket(s): 1 NUMA node(s): 1 Vendor ID: GenuineIntel CPU family: 6 Model: 79 Model name: Intel(R) Xeon(R) CPU E5-2673 v4 @ 2.30GHz Stepping: 1 CPU MHz: 2294.686 BogoMIPS: 4589.37 Hypervisor vendor: Microsoft Virtualization type: full L1d cache: 32K L1i cache: 32K L2 cache: 256K L3 cache: 51200K NUMA node0 CPU(s): 0,1 Flags: fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 ss ht syscall nx pdpe1gb rdtscp lm constant_tsc rep_good nopl xtopology cpuid pni pclmulqdq ssse3 fma cx16 pcid sse4_1 sse4_2 movbe popcnt aes xsave avx f16c rdrand hypervisor lahf_lm abm 3dnowprefetch invpcid_single pti fsgsbase bmi1 hle avx2 smep bmi2 erms invpcid rtm rdseed adx smap xsaveopt md_clear | Cpu Property | Value | |:------------------ |:------------------------------------------------------- | | Brand | Intel(R) Xeon(R) CPU E5-2673 v4 @ 2.30GHz | | Vendor | :Intel | | Architecture | :Broadwell | | Model | Family: 0x06, Model: 0x4f, Stepping: 0x01, Type: 0x00 | | Cores | 2 physical cores, 2 logical cores (on executing CPU) | | | No Hyperthreading detected | | Clock Frequencies | Not supported by CPU | | Data Cache | Level 1:3 : (32, 256, 51200) kbytes | | | 64 byte cache line size | | Address Size | 48 bits virtual, 44 bits physical | | SIMD | 256 bit = 32 byte max. SIMD vector size | | Time Stamp Counter | TSC is accessible via `rdtsc` | | | TSC increased at every clock cycle (non-invariant TSC) | | Perf. Monitoring | Performance Monitoring Counters (PMC) are not supported | | Hypervisor | Yes, Microsoft |
codecov[bot] commented 4 years ago

Codecov Report

Merging #76 into master will not change coverage. The diff coverage is n/a.

Impacted file tree graph

@@           Coverage Diff           @@
##           master      #76   +/-   ##
=======================================
  Coverage   96.10%   96.10%           
=======================================
  Files          11       11           
  Lines         770      770           
=======================================
  Hits          740      740           
  Misses         30       30
Impacted Files Coverage Δ
src/cubical.jl 99.13% <ø> (ø)
src/simplex.jl 93.93% <ø> (ø)

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