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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

Compute cocycles for infinite intervals #109

Closed mtsch closed 4 years ago

codecov[bot] commented 4 years ago

Codecov Report

Merging #109 into master will increase coverage by 0.00%. The diff coverage is 100.00%.

Impacted file tree graph

@@           Coverage Diff           @@
##           master     #109   +/-   ##
=======================================
  Coverage   95.81%   95.81%           
=======================================
  Files          18       18           
  Lines        1146     1148    +2     
=======================================
+ Hits         1098     1100    +2     
  Misses         48       48
Impacted Files Coverage Δ
src/computation/coboundarymatrices.jl 97.64% <100.00%> (ø)
src/computation/reducedmatrix.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: 6 Oct 2020 - 02:21 - Baseline: 6 Oct 2020 - 02:26 * Package commits: - Target: 723a11 - Baseline: 02b5f5 * 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", "bonsai64.dipha"]` | 0.93 (5%) :white_check_mark: | 1.00 (1%) | | `["cubical", "lena1024.dipha"]` | 0.92 (5%) :white_check_mark: | 1.00 (1%) | | `["homology", "klein200.pts"]` | 0.99 (5%) | 0.93 (1%) :white_check_mark: | ## 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 5.4.0-1025-azure #25~18.04.1-Ubuntu SMP Sat Sep 5 15:28:57 UTC 2020 x86_64 x86_64 CPU: Intel(R) Xeon(R) CPU E5-2673 v3 @ 2.40GHz: speed user nice sys idle irq #1 2397 MHz 10039 s 0 s 1772 s 98512 s 0 s #2 2397 MHz 33650 s 0 s 2542 s 74683 s 0 s Memory: 6.791393280029297 GB (2747.98046875 MB free) Uptime: 1121.0 sec Load Avg: 1.05712890625 0.82470703125 0.44384765625 WORD_SIZE: 64 LIBM: libopenlibm LLVM: libLLVM-9.0.1 (ORCJIT, haswell) ``` ### 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 5.4.0-1025-azure #25~18.04.1-Ubuntu SMP Sat Sep 5 15:28:57 UTC 2020 x86_64 x86_64 CPU: Intel(R) Xeon(R) CPU E5-2673 v3 @ 2.40GHz: speed user nice sys idle irq #1 2397 MHz 19121 s 0 s 2191 s 118622 s 0 s #2 2397 MHz 53550 s 0 s 3045 s 83930 s 0 s Memory: 6.791393280029297 GB (2703.4609375 MB free) Uptime: 1418.0 sec Load Avg: 1.013671875 0.97607421875 0.62548828125 WORD_SIZE: 64 LIBM: libopenlibm LLVM: libLLVM-9.0.1 (ORCJIT, haswell) ``` --- # Target result # Benchmark Report for */home/runner/work/Ripserer.jl/Ripserer.jl* ## Job Properties * Time of benchmark: 6 Oct 2020 - 2:21 * Package commit: 723a11 * 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"]` | 32.892 s (5%) | 895.262 ms | 4.13 GiB (1%) | 53514848 | | `["cubical", "bonsai64.dipha"]` | 3.103 s (5%) | 65.424 ms | 582.26 MiB (1%) | 7104718 | | `["cubical", "lena1024.dipha"]` | 2.522 s (5%) | 137.115 ms | 952.84 MiB (1%) | 14470858 | | `["cubical", "lena2048.dipha"]` | 9.484 s (5%) | 669.992 ms | 2.68 GiB (1%) | 33880732 | | `["homology", "bonsai64.dipha"]` | 10.159 s (5%) | 254.291 ms | 911.66 MiB (1%) | 11464708 | | `["homology", "klein200.pts"]` | 3.020 s (5%) | 17.375 ms | 102.44 MiB (1%) | 1896590 | | `["homology", "lena1024.dipha"]` | 8.467 s (5%) | 305.005 ms | 1.11 GiB (1%) | 16809016 | | `["homology", "sphere100.pts"]` | 1.927 s (5%) | 14.601 ms | 119.16 MiB (1%) | 1589656 | | `["rips", "dense", "dragon2000.pts"]` | 3.360 s (5%) | 38.089 ms | 301.15 MiB (1%) | 227714 | | `["rips", "dense", "fract-r.dist"]` | 21.841 s (5%) | 326.930 ms | 1.79 GiB (1%) | 186542 | | `["rips", "dense", "o3_1024.pts"]` | 6.679 s (5%) | 74.266 ms | 448.92 MiB (1%) | 2375176 | | `["rips", "sparse", "alpha_3_sphere_3000.spdist"]` | 3.156 s (5%) | 14.902 ms | 168.91 MiB (1%) | 2376642 | | `["rips", "sparse", "alpha_4_sphere_2000.spdist"]` | 8.024 s (5%) | 28.126 ms | 546.56 MiB (1%) | 3184564 | | `["rips", "sparse", "alpha_5_sphere_1000.spdist"]` | 51.175 s (5%) | 498.454 ms | 3.40 GiB (1%) | 3015424 | | `["rips", "sparse", "dragon2000.pts"]` | 3.586 s (5%) | 39.109 ms | 331.51 MiB (1%) | 223713 | | `["rips", "sparse", "fract-r.dist"]` | 24.983 s (5%) | 345.141 ms | 1.80 GiB (1%) | 185517 | | `["rips", "sparse", "o3_1024.pts"]` | 3.187 s (5%) | 43.941 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 5.4.0-1025-azure #25~18.04.1-Ubuntu SMP Sat Sep 5 15:28:57 UTC 2020 x86_64 x86_64 CPU: Intel(R) Xeon(R) CPU E5-2673 v3 @ 2.40GHz: speed user nice sys idle irq #1 2397 MHz 10039 s 0 s 1772 s 98512 s 0 s #2 2397 MHz 33650 s 0 s 2542 s 74683 s 0 s Memory: 6.791393280029297 GB (2747.98046875 MB free) Uptime: 1121.0 sec Load Avg: 1.05712890625 0.82470703125 0.44384765625 WORD_SIZE: 64 LIBM: libopenlibm LLVM: libLLVM-9.0.1 (ORCJIT, haswell) ``` --- # Baseline result # Benchmark Report for */home/runner/work/Ripserer.jl/Ripserer.jl* ## Job Properties * Time of benchmark: 6 Oct 2020 - 2:26 * Package commit: 02b5f5 * 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"]` | 34.154 s (5%) | 949.019 ms | 4.13 GiB (1%) | 53518975 | | `["cubical", "bonsai64.dipha"]` | 3.352 s (5%) | 65.492 ms | 582.26 MiB (1%) | 7104718 | | `["cubical", "lena1024.dipha"]` | 2.754 s (5%) | 269.649 ms | 952.84 MiB (1%) | 14470858 | | `["cubical", "lena2048.dipha"]` | 9.977 s (5%) | 690.185 ms | 2.68 GiB (1%) | 33883102 | | `["homology", "bonsai64.dipha"]` | 10.336 s (5%) | 254.657 ms | 911.60 MiB (1%) | 11462683 | | `["homology", "klein200.pts"]` | 3.053 s (5%) | 16.565 ms | 110.61 MiB (1%) | 2060686 | | `["homology", "lena1024.dipha"]` | 8.715 s (5%) | 312.477 ms | 1.11 GiB (1%) | 16807719 | | `["homology", "sphere100.pts"]` | 1.990 s (5%) | | 119.17 MiB (1%) | 1589943 | | `["rips", "dense", "dragon2000.pts"]` | 3.346 s (5%) | 41.610 ms | 301.15 MiB (1%) | 227714 | | `["rips", "dense", "fract-r.dist"]` | 22.618 s (5%) | 359.421 ms | 1.79 GiB (1%) | 186542 | | `["rips", "dense", "o3_1024.pts"]` | 6.837 s (5%) | 77.076 ms | 449.01 MiB (1%) | 2377102 | | `["rips", "sparse", "alpha_3_sphere_3000.spdist"]` | 3.167 s (5%) | 16.015 ms | 169.07 MiB (1%) | 2379106 | | `["rips", "sparse", "alpha_4_sphere_2000.spdist"]` | 8.197 s (5%) | 46.056 ms | 546.59 MiB (1%) | 3185364 | | `["rips", "sparse", "alpha_5_sphere_1000.spdist"]` | 52.502 s (5%) | 509.808 ms | 3.40 GiB (1%) | 3016226 | | `["rips", "sparse", "dragon2000.pts"]` | 3.544 s (5%) | 38.005 ms | 331.51 MiB (1%) | 223713 | | `["rips", "sparse", "fract-r.dist"]` | 24.556 s (5%) | 345.659 ms | 1.80 GiB (1%) | 185517 | | `["rips", "sparse", "o3_1024.pts"]` | 3.256 s (5%) | 47.756 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 5.4.0-1025-azure #25~18.04.1-Ubuntu SMP Sat Sep 5 15:28:57 UTC 2020 x86_64 x86_64 CPU: Intel(R) Xeon(R) CPU E5-2673 v3 @ 2.40GHz: speed user nice sys idle irq #1 2397 MHz 19121 s 0 s 2191 s 118622 s 0 s #2 2397 MHz 53550 s 0 s 3045 s 83930 s 0 s Memory: 6.791393280029297 GB (2703.4609375 MB free) Uptime: 1418.0 sec Load Avg: 1.013671875 0.97607421875 0.62548828125 WORD_SIZE: 64 LIBM: libopenlibm LLVM: libLLVM-9.0.1 (ORCJIT, haswell) ``` --- # 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: 63 Model name: Intel(R) Xeon(R) CPU E5-2673 v3 @ 2.40GHz Stepping: 2 CPU MHz: 2397.223 BogoMIPS: 4794.44 Hypervisor vendor: Microsoft Virtualization type: full L1d cache: 32K L1i cache: 32K L2 cache: 256K L3 cache: 30720K 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 invpcid_single pti fsgsbase bmi1 avx2 smep bmi2 erms invpcid xsaveopt md_clear | Cpu Property | Value | |:------------------ |:------------------------------------------------------- | | Brand | Intel(R) Xeon(R) CPU E5-2673 v3 @ 2.40GHz | | Vendor | :Intel | | Architecture | :Haswell | | Model | Family: 0x06, Model: 0x3f, Stepping: 0x02, 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, 30720) kbytes | | | 64 byte cache line size | | Address Size | 48 bits virtual, 46 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 |