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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

Bump version, reorder tests #113

Closed mtsch closed 4 years ago

codecov[bot] commented 4 years ago

Codecov Report

Merging #113 into master will not change coverage. The diff coverage is n/a.

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@@           Coverage Diff           @@
##           master     #113   +/-   ##
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  Coverage   95.81%   95.81%           
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  Files          18       18           
  Lines        1148     1148           
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  Hits         1100     1100           
  Misses         48       48

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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: 12 Oct 2020 - 10:02 - Baseline: 12 Oct 2020 - 10:06 * Package commits: - Target: 1ab952 - Baseline: 8db9e3 * Julia commits: - Target: 539f3c - Baseline: 539f3c * 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 | |----------------------------------------------------|---------------|--------------| | `["rips", "sparse", "dragon2000.pts"]` | 1.13 (5%) :x: | 1.00 (1%) | ## Benchmark Group List Here's a list of all the benchmark groups executed by this job: - `["cubical"]` - `["homology"]` - `["rips", "dense"]` - `["rips", "sparse"]` ## Julia versioninfo ### Target ``` Julia Version 1.5.2 Commit 539f3ce943 (2020-09-23 23:17 UTC) Platform Info: OS: Linux (x86_64-pc-linux-gnu) Ubuntu 18.04.5 LTS uname: Linux 5.4.0-1026-azure #26~18.04.1-Ubuntu SMP Thu Sep 10 16:19:25 UTC 2020 x86_64 x86_64 CPU: Intel(R) Xeon(R) Platinum 8171M CPU @ 2.60GHz: speed user nice sys idle irq #1 2095 MHz 6986 s 0 s 1592 s 31222 s 0 s #2 2095 MHz 25518 s 0 s 2196 s 12341 s 0 s Memory: 6.791393280029297 GB (2793.578125 MB free) Uptime: 415.0 sec Load Avg: 1.0029296875 0.88671875 0.4677734375 WORD_SIZE: 64 LIBM: libopenlibm LLVM: libLLVM-9.0.1 (ORCJIT, skylake-avx512) ``` ### Baseline ``` Julia Version 1.5.2 Commit 539f3ce943 (2020-09-23 23:17 UTC) Platform Info: OS: Linux (x86_64-pc-linux-gnu) Ubuntu 18.04.5 LTS uname: Linux 5.4.0-1026-azure #26~18.04.1-Ubuntu SMP Thu Sep 10 16:19:25 UTC 2020 x86_64 x86_64 CPU: Intel(R) Xeon(R) Platinum 8171M CPU @ 2.60GHz: speed user nice sys idle irq #1 2095 MHz 27785 s 0 s 2285 s 31617 s 0 s #2 2095 MHz 26041 s 0 s 2278 s 33550 s 0 s Memory: 6.791393280029297 GB (2659.015625 MB free) Uptime: 634.0 sec Load Avg: 1.015625 0.9794921875 0.60205078125 WORD_SIZE: 64 LIBM: libopenlibm LLVM: libLLVM-9.0.1 (ORCJIT, skylake-avx512) ``` --- # Target result # Benchmark Report for */home/runner/work/Ripserer.jl/Ripserer.jl* ## Job Properties * Time of benchmark: 12 Oct 2020 - 10:2 * Package commit: 1ab952 * Julia commit: 539f3c * 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 | |----------------------------------------------------|--------------:|-----------:|----------------:|------------:| | `["cubical", "bonsai128.dipha"]` | 27.191 s (5%) | 645.682 ms | 4.13 GiB (1%) | 53514806 | | `["cubical", "bonsai64.dipha"]` | 2.519 s (5%) | 45.876 ms | 582.26 MiB (1%) | 7104718 | | `["cubical", "lena1024.dipha"]` | 2.065 s (5%) | 96.015 ms | 952.84 MiB (1%) | 14470858 | | `["cubical", "lena2048.dipha"]` | 7.615 s (5%) | 477.358 ms | 2.68 GiB (1%) | 33880715 | | `["homology", "bonsai64.dipha"]` | 7.533 s (5%) | 198.798 ms | 911.63 MiB (1%) | 11464248 | | `["homology", "klein200.pts"]` | 2.040 s (5%) | 13.443 ms | 102.41 MiB (1%) | 1896095 | | `["homology", "lena1024.dipha"]` | 6.116 s (5%) | 190.555 ms | 1.11 GiB (1%) | 16808662 | | `["homology", "sphere100.pts"]` | 1.378 s (5%) | 12.626 ms | 119.18 MiB (1%) | 1589561 | | `["rips", "dense", "dragon2000.pts"]` | 2.571 s (5%) | 29.494 ms | 301.15 MiB (1%) | 227714 | | `["rips", "dense", "fract-r.dist"]` | 18.054 s (5%) | 279.283 ms | 1.79 GiB (1%) | 186542 | | `["rips", "dense", "o3_1024.pts"]` | 5.113 s (5%) | 57.613 ms | 448.89 MiB (1%) | 2374970 | | `["rips", "sparse", "alpha_3_sphere_3000.spdist"]` | 2.270 s (5%) | 11.605 ms | 168.90 MiB (1%) | 2376411 | | `["rips", "sparse", "alpha_4_sphere_2000.spdist"]` | 6.203 s (5%) | 31.139 ms | 546.54 MiB (1%) | 3184460 | | `["rips", "sparse", "alpha_5_sphere_1000.spdist"]` | 41.947 s (5%) | 403.885 ms | 3.40 GiB (1%) | 3015311 | | `["rips", "sparse", "dragon2000.pts"]` | 3.005 s (5%) | 29.941 ms | 331.51 MiB (1%) | 223713 | | `["rips", "sparse", "fract-r.dist"]` | 19.751 s (5%) | 275.390 ms | 1.80 GiB (1%) | 185517 | | `["rips", "sparse", "o3_1024.pts"]` | 2.474 s (5%) | 32.650 ms | 341.76 MiB (1%) | 166323 | ## Benchmark Group List Here's a list of all the benchmark groups executed by this job: - `["cubical"]` - `["homology"]` - `["rips", "dense"]` - `["rips", "sparse"]` ## Julia versioninfo ``` Julia Version 1.5.2 Commit 539f3ce943 (2020-09-23 23:17 UTC) Platform Info: OS: Linux (x86_64-pc-linux-gnu) Ubuntu 18.04.5 LTS uname: Linux 5.4.0-1026-azure #26~18.04.1-Ubuntu SMP Thu Sep 10 16:19:25 UTC 2020 x86_64 x86_64 CPU: Intel(R) Xeon(R) Platinum 8171M CPU @ 2.60GHz: speed user nice sys idle irq #1 2095 MHz 6986 s 0 s 1592 s 31222 s 0 s #2 2095 MHz 25518 s 0 s 2196 s 12341 s 0 s Memory: 6.791393280029297 GB (2793.578125 MB free) Uptime: 415.0 sec Load Avg: 1.0029296875 0.88671875 0.4677734375 WORD_SIZE: 64 LIBM: libopenlibm LLVM: libLLVM-9.0.1 (ORCJIT, skylake-avx512) ``` --- # Baseline result # Benchmark Report for */home/runner/work/Ripserer.jl/Ripserer.jl* ## Job Properties * Time of benchmark: 12 Oct 2020 - 10:6 * Package commit: 8db9e3 * Julia commit: 539f3c * 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 | |----------------------------------------------------|--------------:|-----------:|----------------:|------------:| | `["cubical", "bonsai128.dipha"]` | 26.097 s (5%) | 651.244 ms | 4.13 GiB (1%) | 53514806 | | `["cubical", "bonsai64.dipha"]` | 2.425 s (5%) | 48.355 ms | 582.26 MiB (1%) | 7104718 | | `["cubical", "lena1024.dipha"]` | 2.046 s (5%) | 99.322 ms | 952.84 MiB (1%) | 14470858 | | `["cubical", "lena2048.dipha"]` | 7.730 s (5%) | 492.926 ms | 2.68 GiB (1%) | 33880715 | | `["homology", "bonsai64.dipha"]` | 7.408 s (5%) | 197.803 ms | 911.64 MiB (1%) | 11464249 | | `["homology", "klein200.pts"]` | 2.096 s (5%) | 14.426 ms | 102.41 MiB (1%) | 1896095 | | `["homology", "lena1024.dipha"]` | 6.262 s (5%) | 200.998 ms | 1.11 GiB (1%) | 16808662 | | `["homology", "sphere100.pts"]` | 1.360 s (5%) | 11.661 ms | 119.18 MiB (1%) | 1589561 | | `["rips", "dense", "dragon2000.pts"]` | 2.522 s (5%) | 31.626 ms | 301.15 MiB (1%) | 227714 | | `["rips", "dense", "fract-r.dist"]` | 18.093 s (5%) | 283.330 ms | 1.79 GiB (1%) | 186542 | | `["rips", "dense", "o3_1024.pts"]` | 5.107 s (5%) | 63.272 ms | 448.89 MiB (1%) | 2374970 | | `["rips", "sparse", "alpha_3_sphere_3000.spdist"]` | 2.270 s (5%) | 12.586 ms | 168.90 MiB (1%) | 2376411 | | `["rips", "sparse", "alpha_4_sphere_2000.spdist"]` | 6.286 s (5%) | 33.149 ms | 546.54 MiB (1%) | 3184460 | | `["rips", "sparse", "alpha_5_sphere_1000.spdist"]` | 42.073 s (5%) | 416.146 ms | 3.40 GiB (1%) | 3015311 | | `["rips", "sparse", "dragon2000.pts"]` | 2.661 s (5%) | 32.673 ms | 331.51 MiB (1%) | 223713 | | `["rips", "sparse", "fract-r.dist"]` | 19.443 s (5%) | 278.868 ms | 1.80 GiB (1%) | 185517 | | `["rips", "sparse", "o3_1024.pts"]` | 2.542 s (5%) | 37.491 ms | 341.76 MiB (1%) | 166323 | ## Benchmark Group List Here's a list of all the benchmark groups executed by this job: - `["cubical"]` - `["homology"]` - `["rips", "dense"]` - `["rips", "sparse"]` ## Julia versioninfo ``` Julia Version 1.5.2 Commit 539f3ce943 (2020-09-23 23:17 UTC) Platform Info: OS: Linux (x86_64-pc-linux-gnu) Ubuntu 18.04.5 LTS uname: Linux 5.4.0-1026-azure #26~18.04.1-Ubuntu SMP Thu Sep 10 16:19:25 UTC 2020 x86_64 x86_64 CPU: Intel(R) Xeon(R) Platinum 8171M CPU @ 2.60GHz: speed user nice sys idle irq #1 2095 MHz 27785 s 0 s 2285 s 31617 s 0 s #2 2095 MHz 26041 s 0 s 2278 s 33550 s 0 s Memory: 6.791393280029297 GB (2659.015625 MB free) Uptime: 634.0 sec Load Avg: 1.015625 0.9794921875 0.60205078125 WORD_SIZE: 64 LIBM: libopenlibm LLVM: libLLVM-9.0.1 (ORCJIT, skylake-avx512) ``` --- # 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: 85 Model name: Intel(R) Xeon(R) Platinum 8171M CPU @ 2.60GHz Stepping: 4 CPU MHz: 2095.125 BogoMIPS: 4190.25 Hypervisor vendor: Microsoft Virtualization type: full L1d cache: 32K L1i cache: 32K L2 cache: 1024K L3 cache: 36608K 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 mpx avx512f avx512dq rdseed adx smap clflushopt avx512cd avx512bw avx512vl xsaveopt xsavec xsaves md_clear | Cpu Property | Value | |:------------------ |:------------------------------------------------------- | | Brand | Intel(R) Xeon(R) Platinum 8171M CPU @ 2.60GHz | | Vendor | :Intel | | Architecture | :Skylake | | Model | Family: 0x06, Model: 0x55, Stepping: 0x04, 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, 1024, 36608) kbytes | | | 64 byte cache line size | | Address Size | 48 bits virtual, 46 bits physical | | SIMD | 512 bit = 64 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 |