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mtsch / Ripserer.jl

Flexible and efficient persistent homology computation.
https://mtsch.github.io/Ripserer.jl/dev/
MIT License
66 stars 8 forks source link

Packed element fix #81

Closed mtsch closed 4 years ago

codecov[bot] commented 4 years ago

Codecov Report

Merging #81 into master will not change coverage. The diff coverage is 100.00%.

Impacted file tree graph

@@           Coverage Diff           @@
##           master      #81   +/-   ##
=======================================
  Coverage   95.41%   95.41%           
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  Files          11       11           
  Lines         764      764           
=======================================
  Hits          729      729           
  Misses         35       35
Impacted Files Coverage Δ
src/chainelement.jl 100.00% <100.00%> (ø)

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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: 14 Aug 2020 - 10:34 - Baseline: 14 Aug 2020 - 10:38 * Package commits: - Target: df7843 - Baseline: 07c3f9 * 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", "sparse, 50% full"]` | 1.07 (5%) :x: | 1.00 (1%) | | `["sparse", "20 tori with 50 points, dim_max=3, modulus=2"]` | 1.09 (5%) :x: | 1.00 (1%) | | `["sparse", "30 tori with 200 points, dim_max=1, modulus=2"]` | 1.06 (5%) :x: | 1.00 (1%) | | `["torus", "n=1024, dim_max=1, modulus=2, threshold=1"]` | 1.07 (5%) :x: | 1.00 (1%) | | `["torus", "n=1024, dim_max=1, modulus=7, threshold=nothing"]` | 1.06 (5%) :x: | 1.00 (1%) | | `["torus", "n=81, dim_max=4, modulus=3, threshold=1"]` | 0.94 (5%) :white_check_mark: | 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 5.3.0-1034-azure #35~18.04.1-Ubuntu SMP Mon Jul 13 12:54:45 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 9070 s 0 s 1675 s 48574 s 0 s #2 2294 MHz 30994 s 0 s 3448 s 25562 s 0 s Memory: 6.764881134033203 GB (1930.28515625 MB free) Uptime: 615.0 sec Load Avg: 1.0 0.8759765625 0.4951171875 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 5.3.0-1034-azure #35~18.04.1-Ubuntu SMP Mon Jul 13 12:54:45 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 29674 s 0 s 3290 s 51360 s 0 s #2 2294 MHz 33680 s 0 s 3647 s 47745 s 0 s Memory: 6.764881134033203 GB (2205.421875 MB free) Uptime: 867.0 sec Load Avg: 1.0615234375 0.97119140625 0.6337890625 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: 14 Aug 2020 - 10:34 * Package commit: df7843 * 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"]` | 6.175 s (5%) | | 3.05 MiB (1%) | 50000 | | `["coboundary", "full, threshold=1"]` | 3.877 s (5%) | | 3.05 MiB (1%) | 50000 | | `["coboundary", "sparse, 25% full"]` | 192.040 ms (5%) | | 4.27 MiB (1%) | 40000 | | `["coboundary", "sparse, 50% full"]` | 1.062 s (5%) | | 2.14 MiB (1%) | 20000 | | `["coboundary", "sparse, 75% full"]` | 1.332 s (5%) | | 1.07 MiB (1%) | 10000 | | `["image", "bonsai"]` | 2.424 s (5%) | 70.409 ms | 311.45 MiB (1%) | 4091791 | | `["image", "hubble"]` | 6.595 s (5%) | 275.816 ms | 1.74 GiB (1%) | 33913637 | | `["sparse", "20 tori with 100 points, dim_max=2, modulus=3"]` | 5.953 s (5%) | 96.111 ms | 1.07 GiB (1%) | 7796522 | | `["sparse", "20 tori with 300 points, dim_max=1, modulus=3"]` | 7.987 s (5%) | | 443.02 MiB (1%) | 4821645 | | `["sparse", "20 tori with 50 points, dim_max=3, modulus=2"]` | 8.132 s (5%) | 107.927 ms | 1.46 GiB (1%) | 11303988 | | `["sparse", "30 tori with 200 points, dim_max=1, modulus=2"]` | 3.035 s (5%) | 52.626 ms | 256.16 MiB (1%) | 3243097 | | `["torus", "n=1024, dim_max=1, modulus=2, threshold=1"]` | 10.980 s (5%) | | 463.39 MiB (1%) | 1084846 | | `["torus", "n=1024, dim_max=1, modulus=7, threshold=nothing"]` | 36.906 s (5%) | 33.397 ms | 1.54 GiB (1%) | 2385160 | | `["torus", "n=256, dim_max=2, modulus=2, threshold=nothing"]` | 3.381 s (5%) | 34.434 ms | 594.86 MiB (1%) | 5233142 | | `["torus", "n=256, dim_max=2, modulus=7, threshold=1"]` | 2.290 s (5%) | 37.087 ms | 336.16 MiB (1%) | 2819142 | | `["torus", "n=64, dim_max=4, modulus=2, threshold=nothing"]` | 6.608 s (5%) | 123.131 ms | 1.17 GiB (1%) | 10873666 | | `["torus", "n=81, dim_max=4, modulus=3, threshold=1"]` | 9.849 s (5%) | 143.889 ms | 1.34 GiB (1%) | 14425542 | ## 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 5.3.0-1034-azure #35~18.04.1-Ubuntu SMP Mon Jul 13 12:54:45 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 9070 s 0 s 1675 s 48574 s 0 s #2 2294 MHz 30994 s 0 s 3448 s 25562 s 0 s Memory: 6.764881134033203 GB (1930.28515625 MB free) Uptime: 615.0 sec Load Avg: 1.0 0.8759765625 0.4951171875 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: 14 Aug 2020 - 10:38 * Package commit: 07c3f9 * 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"]` | 6.219 s (5%) | | 3.05 MiB (1%) | 50000 | | `["coboundary", "full, threshold=1"]` | 3.858 s (5%) | | 3.05 MiB (1%) | 50000 | | `["coboundary", "sparse, 25% full"]` | 197.615 ms (5%) | | 4.27 MiB (1%) | 40000 | | `["coboundary", "sparse, 50% full"]` | 993.653 ms (5%) | | 2.14 MiB (1%) | 20000 | | `["coboundary", "sparse, 75% full"]` | 1.301 s (5%) | | 1.07 MiB (1%) | 10000 | | `["image", "bonsai"]` | 2.445 s (5%) | 64.359 ms | 311.45 MiB (1%) | 4091791 | | `["image", "hubble"]` | 6.728 s (5%) | 275.226 ms | 1.74 GiB (1%) | 33913632 | | `["sparse", "20 tori with 100 points, dim_max=2, modulus=3"]` | 5.836 s (5%) | 96.335 ms | 1.07 GiB (1%) | 7796522 | | `["sparse", "20 tori with 300 points, dim_max=1, modulus=3"]` | 7.759 s (5%) | | 443.02 MiB (1%) | 4821645 | | `["sparse", "20 tori with 50 points, dim_max=3, modulus=2"]` | 7.448 s (5%) | 97.963 ms | 1.46 GiB (1%) | 11298905 | | `["sparse", "30 tori with 200 points, dim_max=1, modulus=2"]` | 2.874 s (5%) | 53.719 ms | 256.16 MiB (1%) | 3243097 | | `["torus", "n=1024, dim_max=1, modulus=2, threshold=1"]` | 10.249 s (5%) | | 463.38 MiB (1%) | 1084823 | | `["torus", "n=1024, dim_max=1, modulus=7, threshold=nothing"]` | 34.981 s (5%) | 37.013 ms | 1.54 GiB (1%) | 2383700 | | `["torus", "n=256, dim_max=2, modulus=2, threshold=nothing"]` | 3.390 s (5%) | 35.541 ms | 594.86 MiB (1%) | 5233142 | | `["torus", "n=256, dim_max=2, modulus=7, threshold=1"]` | 2.250 s (5%) | 39.145 ms | 336.16 MiB (1%) | 2819142 | | `["torus", "n=64, dim_max=4, modulus=2, threshold=nothing"]` | 6.822 s (5%) | 124.538 ms | 1.17 GiB (1%) | 10830260 | | `["torus", "n=81, dim_max=4, modulus=3, threshold=1"]` | 10.447 s (5%) | 140.057 ms | 1.34 GiB (1%) | 14421877 | ## 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 5.3.0-1034-azure #35~18.04.1-Ubuntu SMP Mon Jul 13 12:54:45 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 29674 s 0 s 3290 s 51360 s 0 s #2 2294 MHz 33680 s 0 s 3647 s 47745 s 0 s Memory: 6.764881134033203 GB (2205.421875 MB free) Uptime: 867.0 sec Load Avg: 1.0615234375 0.97119140625 0.6337890625 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: 2294.689 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 |