search

mtsch / Ripserer.jl

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

Fix type instability in zeroth interval generation #116

Closed mtsch closed 4 years ago

codecov[bot] commented 4 years ago

Codecov Report

Merging #116 into master will decrease coverage by 0.07%. The diff coverage is 87.50%.

Impacted file tree graph

@@            Coverage Diff             @@
##           master     #116      +/-   ##
==========================================
- Coverage   95.81%   95.74%   -0.08%     
==========================================
  Files          18       18              
  Lines        1148     1151       +3     
==========================================
+ Hits         1100     1102       +2     
- Misses         48       49       +1
Impacted Files Coverage Δ
src/filtrations/cubical.jl 99.22% <0.00%> (-0.78%) :arrow_down:
src/abstractfiltration.jl 90.32% <100.00%> (+0.66%) :arrow_up:
src/computation/zerodimensional.jl 100.00% <100.00%> (ø)

Continue to review full report at Codecov.

Legend - Click here to learn more Δ = absolute <relative> (impact), ø = not affected, ? = missing data Powered by Codecov. Last update bb91b8d...8d23372. Read the comment docs.

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: 17 Oct 2020 - 03:07 - Baseline: 17 Oct 2020 - 03:11 * Package commits: - Target: e3c956 - Baseline: bb91b8 * 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 | |----------------------------------------------------|------------------------------|--------------| | `["cubical", "lena2048.dipha"]` | 0.92 (5%) :white_check_mark: | 1.00 (1%) | | `["homology", "bonsai64.dipha"]` | 1.18 (5%) :x: | 1.00 (1%) | | `["homology", "klein200.pts"]` | 0.86 (5%) :white_check_mark: | 1.00 (1%) | | `["homology", "lena1024.dipha"]` | 1.05 (5%) :x: | 1.00 (1%) | | `["homology", "sphere100.pts"]` | 1.22 (5%) :x: | 1.00 (1%) | | `["rips", "dense", "dragon2000.pts"]` | 0.92 (5%) :white_check_mark: | 1.00 (1%) | | `["rips", "dense", "o3_1024.pts"]` | 1.11 (5%) :x: | 1.00 (1%) | | `["rips", "sparse", "alpha_3_sphere_3000.spdist"]` | 0.95 (5%) :white_check_mark: | 1.00 (1%) | | `["rips", "sparse", "alpha_5_sphere_1000.spdist"]` | 0.93 (5%) :white_check_mark: | 1.00 (1%) | | `["rips", "sparse", "fract-r.dist"]` | 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: - `["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) CPU E5-2673 v4 @ 2.30GHz: speed user nice sys idle irq #1 2294 MHz 21537 s 0 s 1962 s 38114 s 0 s #2 2294 MHz 18520 s 0 s 2116 s 41115 s 0 s Memory: 6.764892578125 GB (2307.8046875 MB free) Uptime: 635.0 sec Load Avg: 1.08203125 0.9150390625 0.48974609375 WORD_SIZE: 64 LIBM: libopenlibm LLVM: libLLVM-9.0.1 (ORCJIT, broadwell) ``` ### 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) CPU E5-2673 v4 @ 2.30GHz: speed user nice sys idle irq #1 2294 MHz 31773 s 0 s 2353 s 53202 s 0 s #2 2294 MHz 33269 s 0 s 2653 s 51534 s 0 s Memory: 6.764892578125 GB (2365.86328125 MB free) Uptime: 893.0 sec Load Avg: 1.00244140625 0.98095703125 0.630859375 WORD_SIZE: 64 LIBM: libopenlibm LLVM: libLLVM-9.0.1 (ORCJIT, broadwell) ``` --- # Target result # Benchmark Report for */home/runner/work/Ripserer.jl/Ripserer.jl* ## Job Properties * Time of benchmark: 17 Oct 2020 - 3:7 * Package commit: e3c956 * 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"]` | 28.401 s (5%) | 734.623 ms | 4.12 GiB (1%) | 53490226 | | `["cubical", "bonsai64.dipha"]` | 2.528 s (5%) | 53.481 ms | 582.02 MiB (1%) | 7098674 | | `["cubical", "lena1024.dipha"]` | 2.146 s (5%) | 114.412 ms | 950.02 MiB (1%) | 14391659 | | `["cubical", "lena2048.dipha"]` | 8.441 s (5%) | 556.196 ms | 2.67 GiB (1%) | 33801553 | | `["homology", "bonsai64.dipha"]` | 10.006 s (5%) | 67.580 ms | 911.24 MiB (1%) | 11455561 | | `["homology", "klein200.pts"]` | 2.600 s (5%) | 15.571 ms | 102.41 MiB (1%) | 1896208 | | `["homology", "lena1024.dipha"]` | 8.464 s (5%) | 241.974 ms | 1.10 GiB (1%) | 16726780 | | `["homology", "sphere100.pts"]` | 1.991 s (5%) | 13.883 ms | 119.16 MiB (1%) | 1589592 | | `["rips", "dense", "dragon2000.pts"]` | 2.789 s (5%) | 40.326 ms | 301.15 MiB (1%) | 227714 | | `["rips", "dense", "fract-r.dist"]` | 20.365 s (5%) | 345.176 ms | 1.79 GiB (1%) | 186542 | | `["rips", "dense", "o3_1024.pts"]` | 6.484 s (5%) | 73.900 ms | 448.92 MiB (1%) | 2375057 | | `["rips", "sparse", "alpha_3_sphere_3000.spdist"]` | 2.507 s (5%) | 14.353 ms | 168.90 MiB (1%) | 2376508 | | `["rips", "sparse", "alpha_4_sphere_2000.spdist"]` | 6.578 s (5%) | 36.089 ms | 546.55 MiB (1%) | 3184487 | | `["rips", "sparse", "alpha_5_sphere_1000.spdist"]` | 44.495 s (5%) | 465.746 ms | 3.40 GiB (1%) | 3015348 | | `["rips", "sparse", "dragon2000.pts"]` | 3.130 s (5%) | 45.840 ms | 331.51 MiB (1%) | 223713 | | `["rips", "sparse", "fract-r.dist"]` | 22.119 s (5%) | 324.845 ms | 1.80 GiB (1%) | 185517 | | `["rips", "sparse", "o3_1024.pts"]` | 2.737 s (5%) | 50.280 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) CPU E5-2673 v4 @ 2.30GHz: speed user nice sys idle irq #1 2294 MHz 21537 s 0 s 1962 s 38114 s 0 s #2 2294 MHz 18520 s 0 s 2116 s 41115 s 0 s Memory: 6.764892578125 GB (2307.8046875 MB free) Uptime: 635.0 sec Load Avg: 1.08203125 0.9150390625 0.48974609375 WORD_SIZE: 64 LIBM: libopenlibm LLVM: libLLVM-9.0.1 (ORCJIT, broadwell) ``` --- # Baseline result # Benchmark Report for */home/runner/work/Ripserer.jl/Ripserer.jl* ## Job Properties * Time of benchmark: 17 Oct 2020 - 3:11 * Package commit: bb91b8 * 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"]` | 28.507 s (5%) | 736.965 ms | 4.13 GiB (1%) | 53514848 | | `["cubical", "bonsai64.dipha"]` | 2.518 s (5%) | 52.803 ms | 582.26 MiB (1%) | 7104718 | | `["cubical", "lena1024.dipha"]` | 2.113 s (5%) | 114.319 ms | 952.84 MiB (1%) | 14470858 | | `["cubical", "lena2048.dipha"]` | 9.143 s (5%) | 579.387 ms | 2.68 GiB (1%) | 33880749 | | `["homology", "bonsai64.dipha"]` | 8.503 s (5%) | 61.213 ms | 911.66 MiB (1%) | 11464625 | | `["homology", "klein200.pts"]` | 3.023 s (5%) | 15.478 ms | 102.41 MiB (1%) | 1896206 | | `["homology", "lena1024.dipha"]` | 8.045 s (5%) | 234.716 ms | 1.11 GiB (1%) | 16808998 | | `["homology", "sphere100.pts"]` | 1.631 s (5%) | 13.886 ms | 119.16 MiB (1%) | 1589594 | | `["rips", "dense", "dragon2000.pts"]` | 3.040 s (5%) | 41.774 ms | 301.15 MiB (1%) | 227714 | | `["rips", "dense", "fract-r.dist"]` | 19.729 s (5%) | 319.032 ms | 1.79 GiB (1%) | 186542 | | `["rips", "dense", "o3_1024.pts"]` | 5.833 s (5%) | 74.158 ms | 448.90 MiB (1%) | 2375060 | | `["rips", "sparse", "alpha_3_sphere_3000.spdist"]` | 2.646 s (5%) | 13.817 ms | 168.90 MiB (1%) | 2376504 | | `["rips", "sparse", "alpha_4_sphere_2000.spdist"]` | 6.849 s (5%) | 34.280 ms | 546.55 MiB (1%) | 3184498 | | `["rips", "sparse", "alpha_5_sphere_1000.spdist"]` | 47.780 s (5%) | 474.050 ms | 3.40 GiB (1%) | 3015350 | | `["rips", "sparse", "dragon2000.pts"]` | 3.088 s (5%) | 43.126 ms | 331.51 MiB (1%) | 223713 | | `["rips", "sparse", "fract-r.dist"]` | 23.595 s (5%) | 362.288 ms | 1.80 GiB (1%) | 185517 | | `["rips", "sparse", "o3_1024.pts"]` | 2.681 s (5%) | 45.019 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) CPU E5-2673 v4 @ 2.30GHz: speed user nice sys idle irq #1 2294 MHz 31773 s 0 s 2353 s 53202 s 0 s #2 2294 MHz 33269 s 0 s 2653 s 51534 s 0 s Memory: 6.764892578125 GB (2365.86328125 MB free) Uptime: 893.0 sec Load Avg: 1.00244140625 0.98095703125 0.630859375 WORD_SIZE: 64 LIBM: libopenlibm LLVM: libLLVM-9.0.1 (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: 2294.684 BogoMIPS: 4589.36 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 |
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: 17 Oct 2020 - 03:08 - Baseline: 17 Oct 2020 - 03:12 * Package commits: - Target: 55fc23 - Baseline: bb91b8 * 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 | |----------------------------------------------------|------------|--------------| ## 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) CPU E5-2673 v4 @ 2.30GHz: speed user nice sys idle irq #1 2294 MHz 11300 s 0 s 1617 s 30803 s 0 s #2 2294 MHz 24913 s 0 s 2442 s 16496 s 0 s Memory: 6.764892578125 GB (2455.37109375 MB free) Uptime: 457.0 sec Load Avg: 1.103515625 0.96630859375 0.5205078125 WORD_SIZE: 64 LIBM: libopenlibm LLVM: libLLVM-9.0.1 (ORCJIT, broadwell) ``` ### 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) CPU E5-2673 v4 @ 2.30GHz: speed user nice sys idle irq #1 2294 MHz 30100 s 0 s 2219 s 35252 s 0 s #2 2294 MHz 29347 s 0 s 2740 s 35648 s 0 s Memory: 6.764892578125 GB (2453.05859375 MB free) Uptime: 697.0 sec Load Avg: 1.00439453125 1.0 0.6455078125 WORD_SIZE: 64 LIBM: libopenlibm LLVM: libLLVM-9.0.1 (ORCJIT, broadwell) ``` --- # Target result # Benchmark Report for */home/runner/work/Ripserer.jl/Ripserer.jl* ## Job Properties * Time of benchmark: 17 Oct 2020 - 3:8 * Package commit: 55fc23 * 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"]` | 25.920 s (5%) | 753.042 ms | 4.12 GiB (1%) | 53490230 | | `["cubical", "bonsai64.dipha"]` | 2.369 s (5%) | 54.191 ms | 582.02 MiB (1%) | 7098674 | | `["cubical", "lena1024.dipha"]` | 2.050 s (5%) | 117.514 ms | 950.02 MiB (1%) | 14391659 | | `["cubical", "lena2048.dipha"]` | 7.979 s (5%) | 570.807 ms | 2.67 GiB (1%) | 33801555 | | `["homology", "bonsai64.dipha"]` | 8.017 s (5%) | 217.414 ms | 911.25 MiB (1%) | 11455565 | | `["homology", "klein200.pts"]` | 2.380 s (5%) | 16.824 ms | 102.42 MiB (1%) | 1896223 | | `["homology", "lena1024.dipha"]` | 6.755 s (5%) | 221.140 ms | 1.10 GiB (1%) | 16726786 | | `["homology", "sphere100.pts"]` | 1.552 s (5%) | 13.095 ms | 119.16 MiB (1%) | 1589587 | | `["rips", "dense", "dragon2000.pts"]` | 2.639 s (5%) | 38.379 ms | 301.15 MiB (1%) | 227714 | | `["rips", "dense", "fract-r.dist"]` | 19.646 s (5%) | 310.155 ms | 1.79 GiB (1%) | 186542 | | `["rips", "dense", "o3_1024.pts"]` | 5.371 s (5%) | 69.532 ms | 448.90 MiB (1%) | 2375061 | | `["rips", "sparse", "alpha_3_sphere_3000.spdist"]` | 2.454 s (5%) | 13.233 ms | 168.90 MiB (1%) | 2376517 | | `["rips", "sparse", "alpha_4_sphere_2000.spdist"]` | 6.384 s (5%) | 37.461 ms | 546.55 MiB (1%) | 3184490 | | `["rips", "sparse", "alpha_5_sphere_1000.spdist"]` | 42.322 s (5%) | 450.060 ms | 3.40 GiB (1%) | 3015341 | | `["rips", "sparse", "dragon2000.pts"]` | 2.832 s (5%) | 40.794 ms | 331.51 MiB (1%) | 223713 | | `["rips", "sparse", "fract-r.dist"]` | 21.145 s (5%) | 315.603 ms | 1.80 GiB (1%) | 185517 | | `["rips", "sparse", "o3_1024.pts"]` | 2.598 s (5%) | 43.888 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) CPU E5-2673 v4 @ 2.30GHz: speed user nice sys idle irq #1 2294 MHz 11300 s 0 s 1617 s 30803 s 0 s #2 2294 MHz 24913 s 0 s 2442 s 16496 s 0 s Memory: 6.764892578125 GB (2455.37109375 MB free) Uptime: 457.0 sec Load Avg: 1.103515625 0.96630859375 0.5205078125 WORD_SIZE: 64 LIBM: libopenlibm LLVM: libLLVM-9.0.1 (ORCJIT, broadwell) ``` --- # Baseline result # Benchmark Report for */home/runner/work/Ripserer.jl/Ripserer.jl* ## Job Properties * Time of benchmark: 17 Oct 2020 - 3:12 * Package commit: bb91b8 * 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"]` | 25.820 s (5%) | 717.019 ms | 4.13 GiB (1%) | 53514853 | | `["cubical", "bonsai64.dipha"]` | 2.373 s (5%) | 55.554 ms | 582.26 MiB (1%) | 7104718 | | `["cubical", "lena1024.dipha"]` | 2.033 s (5%) | 111.490 ms | 952.84 MiB (1%) | 14470858 | | `["cubical", "lena2048.dipha"]` | 7.943 s (5%) | 538.972 ms | 2.68 GiB (1%) | 33880755 | | `["homology", "bonsai64.dipha"]` | 7.999 s (5%) | 222.372 ms | 911.64 MiB (1%) | 11464624 | | `["homology", "klein200.pts"]` | 2.348 s (5%) | 14.937 ms | 102.41 MiB (1%) | 1896220 | | `["homology", "lena1024.dipha"]` | 6.743 s (5%) | 225.179 ms | 1.11 GiB (1%) | 16809003 | | `["homology", "sphere100.pts"]` | 1.562 s (5%) | 12.853 ms | 119.16 MiB (1%) | 1589589 | | `["rips", "dense", "dragon2000.pts"]` | 2.639 s (5%) | 35.315 ms | 301.15 MiB (1%) | 227714 | | `["rips", "dense", "fract-r.dist"]` | 19.860 s (5%) | 301.075 ms | 1.79 GiB (1%) | 186542 | | `["rips", "dense", "o3_1024.pts"]` | 5.305 s (5%) | 65.509 ms | 448.90 MiB (1%) | 2375063 | | `["rips", "sparse", "alpha_3_sphere_3000.spdist"]` | 2.409 s (5%) | 13.274 ms | 168.90 MiB (1%) | 2376514 | | `["rips", "sparse", "alpha_4_sphere_2000.spdist"]` | 6.328 s (5%) | 39.096 ms | 546.55 MiB (1%) | 3184489 | | `["rips", "sparse", "alpha_5_sphere_1000.spdist"]` | 42.553 s (5%) | 436.519 ms | 3.40 GiB (1%) | 3015346 | | `["rips", "sparse", "dragon2000.pts"]` | 2.895 s (5%) | 35.030 ms | 331.51 MiB (1%) | 223713 | | `["rips", "sparse", "fract-r.dist"]` | 21.037 s (5%) | 302.722 ms | 1.80 GiB (1%) | 185517 | | `["rips", "sparse", "o3_1024.pts"]` | 2.545 s (5%) | 40.814 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) CPU E5-2673 v4 @ 2.30GHz: speed user nice sys idle irq #1 2294 MHz 30100 s 0 s 2219 s 35252 s 0 s #2 2294 MHz 29347 s 0 s 2740 s 35648 s 0 s Memory: 6.764892578125 GB (2453.05859375 MB free) Uptime: 697.0 sec Load Avg: 1.00439453125 1.0 0.6455078125 WORD_SIZE: 64 LIBM: libopenlibm LLVM: libLLVM-9.0.1 (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 |
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: 17 Oct 2020 - 04:00 - Baseline: 17 Oct 2020 - 04:04 * Package commits: - Target: 168c8f - Baseline: bb91b8 * 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 | |----------------------------------------------------|------------|--------------| ## 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 30800 s 0 s 2235 s 16548 s 0 s #2 2095 MHz 9851 s 0 s 1948 s 37719 s 0 s Memory: 6.791393280029297 GB (2674.38671875 MB free) Uptime: 510.0 sec Load Avg: 1.00341796875 0.90234375 0.49853515625 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 56222 s 0 s 2999 s 17161 s 0 s #2 2095 MHz 10584 s 0 s 2053 s 63608 s 0 s Memory: 6.791393280029297 GB (2619.15625 MB free) Uptime: 778.0 sec Load Avg: 1.0654296875 1.02685546875 0.6669921875 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: 17 Oct 2020 - 4:0 * Package commit: 168c8f * 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"]` | 31.699 s (5%) | 737.273 ms | 4.13 GiB (1%) | 53490211 | | `["cubical", "bonsai64.dipha"]` | 2.987 s (5%) | 53.858 ms | 582.02 MiB (1%) | 7098674 | | `["cubical", "lena1024.dipha"]` | 2.347 s (5%) | 110.679 ms | 950.02 MiB (1%) | 14391659 | | `["cubical", "lena2048.dipha"]` | 8.877 s (5%) | 555.639 ms | 2.67 GiB (1%) | 33801544 | | `["homology", "bonsai64.dipha"]` | 9.036 s (5%) | 214.784 ms | 911.23 MiB (1%) | 11455488 | | `["homology", "klein200.pts"]` | 2.557 s (5%) | 13.995 ms | 102.34 MiB (1%) | 1895638 | | `["homology", "lena1024.dipha"]` | 7.446 s (5%) | 221.949 ms | 1.10 GiB (1%) | 16726738 | | `["homology", "sphere100.pts"]` | 1.704 s (5%) | 13.524 ms | 119.11 MiB (1%) | 1589152 | | `["rips", "dense", "dragon2000.pts"]` | 3.119 s (5%) | 32.846 ms | 300.24 MiB (1%) | 219710 | | `["rips", "dense", "fract-r.dist"]` | 21.208 s (5%) | 300.903 ms | 1.79 GiB (1%) | 184490 | | `["rips", "dense", "o3_1024.pts"]` | 6.139 s (5%) | 64.369 ms | 448.43 MiB (1%) | 2370893 | | `["rips", "sparse", "alpha_3_sphere_3000.spdist"]` | 2.742 s (5%) | 13.150 ms | 167.53 MiB (1%) | 2364542 | | `["rips", "sparse", "alpha_4_sphere_2000.spdist"]` | 7.662 s (5%) | 35.004 ms | 545.63 MiB (1%) | 3176455 | | `["rips", "sparse", "alpha_5_sphere_1000.spdist"]` | 51.657 s (5%) | 449.338 ms | 3.40 GiB (1%) | 3011299 | | `["rips", "sparse", "dragon2000.pts"]` | 3.318 s (5%) | 33.815 ms | 330.60 MiB (1%) | 215709 | | `["rips", "sparse", "fract-r.dist"]` | 22.950 s (5%) | 301.281 ms | 1.80 GiB (1%) | 183465 | | `["rips", "sparse", "o3_1024.pts"]` | 3.026 s (5%) | 37.588 ms | 341.29 MiB (1%) | 162219 | ## 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 30800 s 0 s 2235 s 16548 s 0 s #2 2095 MHz 9851 s 0 s 1948 s 37719 s 0 s Memory: 6.791393280029297 GB (2674.38671875 MB free) Uptime: 510.0 sec Load Avg: 1.00341796875 0.90234375 0.49853515625 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: 17 Oct 2020 - 4:4 * Package commit: bb91b8 * 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"]` | 32.409 s (5%) | 729.885 ms | 4.13 GiB (1%) | 53514830 | | `["cubical", "bonsai64.dipha"]` | 3.062 s (5%) | 51.605 ms | 582.26 MiB (1%) | 7104718 | | `["cubical", "lena1024.dipha"]` | 2.388 s (5%) | 108.952 ms | 952.84 MiB (1%) | 14470858 | | `["cubical", "lena2048.dipha"]` | 8.908 s (5%) | 552.100 ms | 2.68 GiB (1%) | 33880740 | | `["homology", "bonsai64.dipha"]` | 9.183 s (5%) | 215.220 ms | 911.65 MiB (1%) | 11464551 | | `["homology", "klein200.pts"]` | 2.530 s (5%) | | 102.41 MiB (1%) | 1896200 | | `["homology", "lena1024.dipha"]` | 7.412 s (5%) | 220.166 ms | 1.11 GiB (1%) | 16808955 | | `["homology", "sphere100.pts"]` | 1.678 s (5%) | 13.393 ms | 119.16 MiB (1%) | 1589559 | | `["rips", "dense", "dragon2000.pts"]` | 3.138 s (5%) | 33.053 ms | 301.15 MiB (1%) | 227714 | | `["rips", "dense", "fract-r.dist"]` | 21.040 s (5%) | 301.077 ms | 1.79 GiB (1%) | 186542 | | `["rips", "dense", "o3_1024.pts"]` | 6.291 s (5%) | 33.755 ms | 448.90 MiB (1%) | 2374995 | | `["rips", "sparse", "alpha_3_sphere_3000.spdist"]` | 2.749 s (5%) | 13.234 ms | 168.90 MiB (1%) | 2376529 | | `["rips", "sparse", "alpha_4_sphere_2000.spdist"]` | 7.589 s (5%) | 36.013 ms | 546.55 MiB (1%) | 3184466 | | `["rips", "sparse", "alpha_5_sphere_1000.spdist"]` | 51.273 s (5%) | 442.923 ms | 3.40 GiB (1%) | 3015304 | | `["rips", "sparse", "dragon2000.pts"]` | 3.339 s (5%) | 32.436 ms | 331.51 MiB (1%) | 223713 | | `["rips", "sparse", "fract-r.dist"]` | 22.772 s (5%) | 302.657 ms | 1.80 GiB (1%) | 185517 | | `["rips", "sparse", "o3_1024.pts"]` | 3.028 s (5%) | 37.773 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 56222 s 0 s 2999 s 17161 s 0 s #2 2095 MHz 10584 s 0 s 2053 s 63608 s 0 s Memory: 6.791393280029297 GB (2619.15625 MB free) Uptime: 778.0 sec Load Avg: 1.0654296875 1.02685546875 0.6669921875 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: 2095.077 BogoMIPS: 4190.15 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 |